Reiss RA, Schwert DP, Ashworth AC. 1995. Field preservation of Coleoptera for molecular genetic analyses. Environmental Entomology 24: 716-719.
These authors tested five preservatives for nuclear and mitochondrial DNA preservation. Carabid beetles collected at Kuujjuarapik, Quebec, from shore-line debris on Hudson Bay were placed into either 95% ethanol, Carnoy fixative (3:1 methanol:acetic acid), DNA isolation buffer (half whole, half homogenized with a pestle), cryotubes immersed in liquid nitrogen followed by storage at -80°C, or glass vials containing tissue paper soaked in ethyl acetate; all treatments except liquid nitrogen were at room temperature. Ethanol is widely used as both a fixative and a preservative, though it does often distort or remove body colouration, and is considered a hazardous material for transport. Ethyl acetate is sometimes used by entomologists to preserve morphology, as it causes less distortion than other techniques such as drying (pinned) or ethanol.
Overall, cryopreservation performed best, producing excellent results when the specimens were subjected to DNA extraction and basic molecular techniques examining both nuclear and mitochondrial DNA. Ethanol also performed well, though specimens maintained in ethanol longer than about 6 weeks showed significant degradation. DNA isolation buffer also performed well, as long as specimens were very thoroughly ground and homogenized; intact specimens did not yield good results.
These authors recommend ethanol for remote field studies where the equipment associated with liquid nitrogen would be very difficult to transport and maintain, and DNA isolation buffer combined with thorough grinding where ethanol cannot be carried due to its hazardous nature.
Wednesday, August 13, 2008
Tuesday, August 12, 2008
Rogers 2001
Rogers DC. 2001. Revision of the nearctic Lepidurus (Notostraca). Journal of Crustacean Biology 21: 991-1006.
This author revised the tadpole shrimp (Crustacea: Branchiopoda: Notostraca) occurring in North America, with particular attention to the Western USA, and the description of a new species from northern California identified with the aid of DNA sequence data. The genus had previously been rather confused, with species descriptions and type locality often unclear or poorly described. Many of the morphological traits used in species identification in this group of crustaceans are known to be highly polymorphic within populations, and some are known to be frequently damaged or destroyed by predators or other factors, with subsequent regeneration if the animal survives.
In addition to describing the new species and providing a list of diagnostic traits for each of the six North American species, this author constructed a dichotomous tree for species identification, and tested the morphological effects of variation in diet and amputation / regeneration, removing some hypervariable traits from the diagnostic criteria. Biogeographic distributions focus on California and adjacent areas, with only a few collections from Canada.
This author revised the tadpole shrimp (Crustacea: Branchiopoda: Notostraca) occurring in North America, with particular attention to the Western USA, and the description of a new species from northern California identified with the aid of DNA sequence data. The genus had previously been rather confused, with species descriptions and type locality often unclear or poorly described. Many of the morphological traits used in species identification in this group of crustaceans are known to be highly polymorphic within populations, and some are known to be frequently damaged or destroyed by predators or other factors, with subsequent regeneration if the animal survives.
In addition to describing the new species and providing a list of diagnostic traits for each of the six North American species, this author constructed a dichotomous tree for species identification, and tested the morphological effects of variation in diet and amputation / regeneration, removing some hypervariable traits from the diagnostic criteria. Biogeographic distributions focus on California and adjacent areas, with only a few collections from Canada.
Michelutti et al. 2007
Michelutti N, Douglas MSV, Smol JP. 2007. Evaluating diatom community composition in the absence of marked limnological gradients in the high Arctic: a surface sediment calibration set from Cornwallis Island (Nunavut, Canada). Polar Biology 30: 1459-1473.
These authors measured a range of water chemistry and climatological variables in a large number of lakes and ponds on and near Cornwallis Island. This island is remarkably boring in its geology, with little in the way of relief or patterns of geological variation, and provides a sort of negative control for studies of Arctic limnology and the variables exerting the strongest control on diatom species assemblages.
Overall, this study supports the hypothesis that climate and water chemistry variables are the major determinants of diatom diversity in Arctic ponds and lakes. Cornwallis’ ponds and lakes varied little in altitude, latitude, temperature, or a large number of water chemistry variables, and varied little in diatom communities, too, when compared to the existing database of Arctic limnology and diatoms.
These authors measured a range of water chemistry and climatological variables in a large number of lakes and ponds on and near Cornwallis Island. This island is remarkably boring in its geology, with little in the way of relief or patterns of geological variation, and provides a sort of negative control for studies of Arctic limnology and the variables exerting the strongest control on diatom species assemblages.
Overall, this study supports the hypothesis that climate and water chemistry variables are the major determinants of diatom diversity in Arctic ponds and lakes. Cornwallis’ ponds and lakes varied little in altitude, latitude, temperature, or a large number of water chemistry variables, and varied little in diatom communities, too, when compared to the existing database of Arctic limnology and diatoms.
Monday, August 11, 2008
Maciorowski et al. 1997
Maciorowski Z, Veilleux C, Gibaud A, Bourgeois CA, Klijanienko J, Boenders J, Vielh P. 1997. Comparison of fixation procedures for fluorescent quantitation of DNA content using image cytometry. Cytometry 28: 123-129.
These authors evaluated four different fixatives for nuclear DNA quantitation of peripheral blood and breast cancer tumour cells, in the context of optimization of procedures for multi-colour, multi-parameter analyses, for example simultaneous DNA quantitation and FISH probe examination. The four treatments were “no fixative” (air-dried only), ethanol, ethanol / acetic acid, and paraformaldehyde / ethanol.
The fixation procedures were performed on cells already isolated from tissues, and already separated from other cells and substrates. Staining was with Propidium iodide, at concentrations comparable to current best practices recommendations, but the temperature and time of incubation seems to have varied for fixed vs. “no fixative” cells, and was never performed on ice.
Histograms of the relative DNA contents of various cells and treatments are presented, and none look completely useless. However, the authors state that the best treatment was with either paraformaldehyde or acetic acid with ethanol, depending on the other cellular parameters of interest.
These authors evaluated four different fixatives for nuclear DNA quantitation of peripheral blood and breast cancer tumour cells, in the context of optimization of procedures for multi-colour, multi-parameter analyses, for example simultaneous DNA quantitation and FISH probe examination. The four treatments were “no fixative” (air-dried only), ethanol, ethanol / acetic acid, and paraformaldehyde / ethanol.
The fixation procedures were performed on cells already isolated from tissues, and already separated from other cells and substrates. Staining was with Propidium iodide, at concentrations comparable to current best practices recommendations, but the temperature and time of incubation seems to have varied for fixed vs. “no fixative” cells, and was never performed on ice.
Histograms of the relative DNA contents of various cells and treatments are presented, and none look completely useless. However, the authors state that the best treatment was with either paraformaldehyde or acetic acid with ethanol, depending on the other cellular parameters of interest.
Carbonari et al. 2008
Carbonari M, Mancaniello D, Tedesco T, Fiorilli M. 2008. Flow acetone-staining technique: a highly efficient procedure for the simultaneous analysis of DNA content, cell morphology, and immunophenotype by flow cytometry. Cytometry Part A 73A: 168-174.
These authors have developed a cell-handling procedure that allows simultaneous examination of nuclear DNA content, cell morphology, and some aspects of membrane-associated immunoproteins in mammalian cells from culture. The foundation of this technique is the use of 80% acetone at 8°C as a fixative during the initial stages of cell processing for flow cytometry.
These authors tested a range of fixative agents and conditions, and found that while previous work had rejected acetone as a useful fixative, careful control of temperature at each stage of fixation and preparation allows the useful properties of acetone to outweigh its negative qualities for this type of work.
The application of this technique to my own work seems very limited, as I am not interested in immunochemistry, only in nuclear DNA content.
These authors have developed a cell-handling procedure that allows simultaneous examination of nuclear DNA content, cell morphology, and some aspects of membrane-associated immunoproteins in mammalian cells from culture. The foundation of this technique is the use of 80% acetone at 8°C as a fixative during the initial stages of cell processing for flow cytometry.
These authors tested a range of fixative agents and conditions, and found that while previous work had rejected acetone as a useful fixative, careful control of temperature at each stage of fixation and preparation allows the useful properties of acetone to outweigh its negative qualities for this type of work.
The application of this technique to my own work seems very limited, as I am not interested in immunochemistry, only in nuclear DNA content.
Rousselle et al. 1998
Rousselle C, Robert-Nicoud M, Ronot X. 1998. Flow cytometric analysis of DNA content of living and fixed cells: a comparative study using various fixatives. Histochemical Journal 30: 773-781.
These authors tested a range of fixatives for their effects on cell parameters measured in flow cytometry. Two different fluorochromes, Hoechst 33342 and Propidium iodide were tested, with a standard fixation procedure that varied little between treatments. Fixatives were derived from the relevant literature, including static rather than flow cytometric experiments.
All fixative treatments were applied after initial cell processing steps, including isolation of individual cells using a series of Phosphate-buffered-saline (PBS) washes and Trypsin. No detergent was used to permeabilize or remove cell membranes, though there is some discussion of the use of saponin as a permeabilizing agent in other studies.
Hoechst 33342 will penetrate living cells and stain the DNA in a stoichiometric fashion, allowing these authors to compare fixatives to living cells with this stain. Under these treatments, 68% or 70% ethanol (the figure disagrees with the text on this detail) provides excellent resolution of nuclear DNA content and cell cycle (G0/1 vs. S vs. G2 phases, ratio of G2 to G0/1). Other fixatives such as 85% methanol and Acetone also provide good results, with poor and inconsistent results from Carnoy and Boehm-Sprenger treatments.
The results for Propidium iodide were similar, though because Propidium iodide does not penetrate living cells, ethanol was used as the standard for comparison.
Cell size and cell granularity were measured under all treatments, using forward scatter for size and orthogonal (presumably equivalent to side-scatter) scatter for granularity. It is not clear in this paper what the precise definition of “granularity” might be, but it seems to be related to membrane permeabilization and DNA staining stoichiometry. In any case, all fixatives except 1% formaldehyde caused significant cell shrinkage, and all fixatives caused increased granularity. Though they do not discuss it, ethanol fixation produced relatively non-variable cell shrinkage compared to the other fixatives, shrinking cells to 0.74 +- 0.03 of living cell volume vs. 0.81 +- 0.05 for methanol.
This study did not find that alcohols increased cell aggregations, in contrast to an earlier study by Schimenti and Jacobberger (1992) in which 67%, 81% and 90% ethanol fixation caused cell clumping and increased debris. Alcohols increase cell membrane permeabilization, presumably allowing greater access to the DNA by stains. In this study, acetone treatment was basically not good compared to other fixatives.
This study did not examine the effects of long-term storage in fixatives such as ethanol. Fixatives were applied for 30 minutes, then washed away by centrifugation of cells to a pellet, removal of fixative supernatant, and resuspension in PBS. PBS seems to be the fluid of choice for many flow cytometry studies, and these authors note that separated cells can be stored for months in cold ethanol before flow cytometry, though they do not describe a procedure to replace ethanol with PBS or other solutions.
These authors tested a range of fixatives for their effects on cell parameters measured in flow cytometry. Two different fluorochromes, Hoechst 33342 and Propidium iodide were tested, with a standard fixation procedure that varied little between treatments. Fixatives were derived from the relevant literature, including static rather than flow cytometric experiments.
All fixative treatments were applied after initial cell processing steps, including isolation of individual cells using a series of Phosphate-buffered-saline (PBS) washes and Trypsin. No detergent was used to permeabilize or remove cell membranes, though there is some discussion of the use of saponin as a permeabilizing agent in other studies.
Hoechst 33342 will penetrate living cells and stain the DNA in a stoichiometric fashion, allowing these authors to compare fixatives to living cells with this stain. Under these treatments, 68% or 70% ethanol (the figure disagrees with the text on this detail) provides excellent resolution of nuclear DNA content and cell cycle (G0/1 vs. S vs. G2 phases, ratio of G2 to G0/1). Other fixatives such as 85% methanol and Acetone also provide good results, with poor and inconsistent results from Carnoy and Boehm-Sprenger treatments.
The results for Propidium iodide were similar, though because Propidium iodide does not penetrate living cells, ethanol was used as the standard for comparison.
Cell size and cell granularity were measured under all treatments, using forward scatter for size and orthogonal (presumably equivalent to side-scatter) scatter for granularity. It is not clear in this paper what the precise definition of “granularity” might be, but it seems to be related to membrane permeabilization and DNA staining stoichiometry. In any case, all fixatives except 1% formaldehyde caused significant cell shrinkage, and all fixatives caused increased granularity. Though they do not discuss it, ethanol fixation produced relatively non-variable cell shrinkage compared to the other fixatives, shrinking cells to 0.74 +- 0.03 of living cell volume vs. 0.81 +- 0.05 for methanol.
This study did not find that alcohols increased cell aggregations, in contrast to an earlier study by Schimenti and Jacobberger (1992) in which 67%, 81% and 90% ethanol fixation caused cell clumping and increased debris. Alcohols increase cell membrane permeabilization, presumably allowing greater access to the DNA by stains. In this study, acetone treatment was basically not good compared to other fixatives.
This study did not examine the effects of long-term storage in fixatives such as ethanol. Fixatives were applied for 30 minutes, then washed away by centrifugation of cells to a pellet, removal of fixative supernatant, and resuspension in PBS. PBS seems to be the fluid of choice for many flow cytometry studies, and these authors note that separated cells can be stored for months in cold ethanol before flow cytometry, though they do not describe a procedure to replace ethanol with PBS or other solutions.
Saturday, August 9, 2008
Martin et al. 2007
Martin GG, Oakes CT, Tousignant HR, Crabtree H, Yamakawa R. 2007. Structure and function of haemocytes in two marine gastropods, Megathura crenulata and Aplysia californica. Journal of Molluscan Studies 73: 355-365.
These authors characterised the blood cells of two species of gastropods chosen for their importance to other areas of research. Other studies have reported either one or two types of cells in mollusc blood, either with or without granules visible as electron-dense patches in electron microscopy.
This paper found only a single, generally granule-lacking type of cell in the blood of each species. These cells show phagocytic and aggregation abilities, but the blood does not clot. These cells appear to be general-purpose circulating amoeboid cells, capable of responding to stress, wounds, shell damage, infection, and other insults to the organism. This contributes to the circumstantial and weak evidence that molluscan haemocytes are probably not endopolyploid, as they apparently must be produced rapidly in large numbers by stem cell lineages to respond to changes to both the external and internal environments.
These authors characterised the blood cells of two species of gastropods chosen for their importance to other areas of research. Other studies have reported either one or two types of cells in mollusc blood, either with or without granules visible as electron-dense patches in electron microscopy.
This paper found only a single, generally granule-lacking type of cell in the blood of each species. These cells show phagocytic and aggregation abilities, but the blood does not clot. These cells appear to be general-purpose circulating amoeboid cells, capable of responding to stress, wounds, shell damage, infection, and other insults to the organism. This contributes to the circumstantial and weak evidence that molluscan haemocytes are probably not endopolyploid, as they apparently must be produced rapidly in large numbers by stem cell lineages to respond to changes to both the external and internal environments.
Erenpreisa et al. 2002
Erenpreisa J, Ivanov A, Cragg M, Selivanova G, Illidge T. 2002. Nuclear envelope-limited chromatin sheets are part of mitotic death. Histochemistry & Cell Biology 117: 243-255.
These authors investigated the structure and formation of nuclear envelope-limited chromatin sheets (ELCS) in two lines of mutant human cells commonly used in cancer studies. ELCS are membranous structures of unknown function; they are flat folds of inner nuclear envelope that project outwards from the nucleus, sometimes as far as the cytoplasm, and enfold chromatin. Larger projections containing chromatin are termed nuclear pockets (NP), and are strongly associated with some types of cancer such as leukaemia in mammals, but are also found less commonly in healthy tissues including spermatogonia.
Cells were treated with irradiation to induce double-stranded breaks and with a microtubule inhibitor to inhibit mitosis. Earlier investigations by these and other authors have developed the concept of “mitotic death”, which is a syndrome of cells including failed mitosis, the uncoupling of mitosis from DNA replication, delayed (but inevitable) apoptosis, and the formation of giant cells with high levels of aneuploidy and often endopolyploidy.
This paper demonstrates that mitotic death can be induced by quite different mechanisms, in this case by the failure of mitosis driven by microtubule depolymerisation and by a large number of double-stranded DNA breaks induced by radiation. In both cases, DNA repair was effected over considerable time, though apparently cells were unable to “repair” their aneuploidy.
Of particular interest to my work in this paper is their investigations of nuclear morphology. Cells were suspended in solution, then treated to prepare them for either nuclear DNA contents measures (by PI-flow cytometry and by Feulgen staining), light microscopy, or electron microscopy. For light microscopy cell- and nuclear-morphology investigation, these authors fixed cells in a 1:1 mixture of ethanol and acetone, hydrolysed the cells (and presumably freed the nuclei) in 0.1N HCl, and washed them in a poorly-described solution that may be either MacIlvain buffer (pH 5) or Toluidene blue stain in MacIlvain buffer. All of this occurred at 4°C. This was followed by a rinse in distilled water, and dehydration of slides carrying mounted cells in “warm tertiary butanol”. I have seen ethanol used as a fixative and preservative agent in histology studies before, but this represents the clearest description I have encountered of the process as applied specifically for investigations of cell nuclear morphology. There are some obvious similarities with our procedure for Feulgen staining, which helps to confirm that ethanol preservation may be reversible for whole-nuclear investigations.
These authors investigated the structure and formation of nuclear envelope-limited chromatin sheets (ELCS) in two lines of mutant human cells commonly used in cancer studies. ELCS are membranous structures of unknown function; they are flat folds of inner nuclear envelope that project outwards from the nucleus, sometimes as far as the cytoplasm, and enfold chromatin. Larger projections containing chromatin are termed nuclear pockets (NP), and are strongly associated with some types of cancer such as leukaemia in mammals, but are also found less commonly in healthy tissues including spermatogonia.
Cells were treated with irradiation to induce double-stranded breaks and with a microtubule inhibitor to inhibit mitosis. Earlier investigations by these and other authors have developed the concept of “mitotic death”, which is a syndrome of cells including failed mitosis, the uncoupling of mitosis from DNA replication, delayed (but inevitable) apoptosis, and the formation of giant cells with high levels of aneuploidy and often endopolyploidy.
This paper demonstrates that mitotic death can be induced by quite different mechanisms, in this case by the failure of mitosis driven by microtubule depolymerisation and by a large number of double-stranded DNA breaks induced by radiation. In both cases, DNA repair was effected over considerable time, though apparently cells were unable to “repair” their aneuploidy.
Of particular interest to my work in this paper is their investigations of nuclear morphology. Cells were suspended in solution, then treated to prepare them for either nuclear DNA contents measures (by PI-flow cytometry and by Feulgen staining), light microscopy, or electron microscopy. For light microscopy cell- and nuclear-morphology investigation, these authors fixed cells in a 1:1 mixture of ethanol and acetone, hydrolysed the cells (and presumably freed the nuclei) in 0.1N HCl, and washed them in a poorly-described solution that may be either MacIlvain buffer (pH 5) or Toluidene blue stain in MacIlvain buffer. All of this occurred at 4°C. This was followed by a rinse in distilled water, and dehydration of slides carrying mounted cells in “warm tertiary butanol”. I have seen ethanol used as a fixative and preservative agent in histology studies before, but this represents the clearest description I have encountered of the process as applied specifically for investigations of cell nuclear morphology. There are some obvious similarities with our procedure for Feulgen staining, which helps to confirm that ethanol preservation may be reversible for whole-nuclear investigations.
Friday, August 8, 2008
Vermeij and Roopnarine 2008
Vermeij GJ, Roopnarine PD. 2008. The coming arctic invasion. Science 321: 780-781.
In this short “perspectives” article, these authors describe the historical biogeography of the North Pacific, near shore Arctic, and North Atlantic oceans, in the context of predicted patterns of climate warming over the next fifty years. In general, the climate of these areas is likely to become similar to that during the mid-Pliocene, about 3.5 million years ago. During the mid-Pliocene, large numbers of Pacific lineages of marine animals, especially molluscs, successfully colonized the Arctic ocean and established populations in the North Atlantic. While cores from the Arctic Ocean seabed suggest permanent ice-cover at the highest latitudes, there is some evidence to suggest the near shore Arctic ocean included regions that were largely ice-free. This probably resulted in much higher productivity at these locations, similar to the high productivity of the Bering Sea, and allowing large-bodied, planktotrophic animals to disperse northwards and eastwards in the generally north-east flowing currents. This pattern is expected to repeat under global warming, and because Pacific lineages are generally ecologically quite distinct from extant Atlantic species, the North Atlantic should see increased biodiversity overall. Colonization in the opposite direction, of Atlantic lineages into the North Pacific, is considered unlikely due to generally unfavourable water currents and the intensely competitive and predatory biotic environment of the Bering Sea.
In this short “perspectives” article, these authors describe the historical biogeography of the North Pacific, near shore Arctic, and North Atlantic oceans, in the context of predicted patterns of climate warming over the next fifty years. In general, the climate of these areas is likely to become similar to that during the mid-Pliocene, about 3.5 million years ago. During the mid-Pliocene, large numbers of Pacific lineages of marine animals, especially molluscs, successfully colonized the Arctic ocean and established populations in the North Atlantic. While cores from the Arctic Ocean seabed suggest permanent ice-cover at the highest latitudes, there is some evidence to suggest the near shore Arctic ocean included regions that were largely ice-free. This probably resulted in much higher productivity at these locations, similar to the high productivity of the Bering Sea, and allowing large-bodied, planktotrophic animals to disperse northwards and eastwards in the generally north-east flowing currents. This pattern is expected to repeat under global warming, and because Pacific lineages are generally ecologically quite distinct from extant Atlantic species, the North Atlantic should see increased biodiversity overall. Colonization in the opposite direction, of Atlantic lineages into the North Pacific, is considered unlikely due to generally unfavourable water currents and the intensely competitive and predatory biotic environment of the Bering Sea.
Friday, June 6, 2008
Dillon 1984
Dillon RT. 1984. Geographic distance, environmental difference, and divergence between isolated populations. Systematic Zoology 33: 69-82.
This author examines the relative contributions to population divergence of selection and gene flow (or the lack thereof) using 25 populations of freshwater snails occurring in extremely stable drainages in the south-eastern USA. The system used here has clear advantages for a study that attempts to disentangle these frequently-confounded variables.
Divergence between populations can be correlated by distance in two non-mutually-exclusive ways. A reduction in gene flow that may be associated with longer dispersal distances means that novel mutations take increasingly long times to reach further populations. Environmental differences tend to be spatially autocorrelated such that distant populations are likely to have more different environments and selection will therefore be different. However, if divergence/distance and divergence/environmental difference can be separated, then gene flow and selection can be examined independently.
The drainages of the southern Appalachians appear to have been highly stable since the Cretaceous. The snail Goniobasis proxima appears to be incapable of dispersal overland, though very rare cases of transport by birds or mammals may be responsible for establishing some populations. It is restricted to smaller streams of intermediate flow rates, many of which are distributed on both sides of the southern Appalachians and on the Piedmont (low plateau of small foothills) east of the mountains. Most of the populations examined in this study are completely isolated from each other, such that snails would have to either pass through the marine environment or over the (often very short) land barriers between populations. Development is direct, with egg masses attached to solid substrates producing crawling juveniles. This author notes that at any time, the majority of individuals are crawling upstream against the current, which apparently allows populations to stay approximately in the same place despite the occasional individual that must lose its grip and be swept downstream.
The analysis of population divergence here included comparisons among eight 25 x 25 symmetric matrices, constructed using a comprehensive range of variables including morphological features (shell height, aperture width, etc.), allozyme alleles for seven loci, and 15 environmental variables (11 components of water chemistry, plus temperature, flow rate, stream gradient, and parasite infections by trematodes) and a further independent assessment of environmental similarity derived from an examination of the diatom species diversity in the diets of each population.
Varying levels of genetic divergence were found throughout the study system, but most differences were relatively high compared to similar studies of other organisms. Allozyme alleles fell primarily into two categories: either they were present in all four study drainages, or they occurred in only a single population or small group of neighbouring populations. This suggests that all alleles arose either during a period when rapid spread across drainages was possible, or during a later period when dispersal was more difficult. The geological evidence strongly indicates extreme drainage stability, indicating that something about either the environment and / or the dispersal capabilities of G. proxima was different, perhaps during the Tertiary, than today.
No cline in morphology or allozymes was observed, which may be the result of a lack of gene flow preventing the spread of beneficial alleles. In other words, while nearby populations (overland) may experience very similar environments, adaptations in one population cannot spread to the other.
This author summarizes with a statement that both selection and gene flow restriction seem to be equally important in promoting morphological divergence in isolated populations. However, time since divergence may be the more important diversifying factor, and may underlie both selection and gene flow in this system. Furthermore, measures of divergence using allozymes indicate that time since isolation or gene flow may be more important than selection in structuring differences between populations.
This author examines the relative contributions to population divergence of selection and gene flow (or the lack thereof) using 25 populations of freshwater snails occurring in extremely stable drainages in the south-eastern USA. The system used here has clear advantages for a study that attempts to disentangle these frequently-confounded variables.
Divergence between populations can be correlated by distance in two non-mutually-exclusive ways. A reduction in gene flow that may be associated with longer dispersal distances means that novel mutations take increasingly long times to reach further populations. Environmental differences tend to be spatially autocorrelated such that distant populations are likely to have more different environments and selection will therefore be different. However, if divergence/distance and divergence/environmental difference can be separated, then gene flow and selection can be examined independently.
The drainages of the southern Appalachians appear to have been highly stable since the Cretaceous. The snail Goniobasis proxima appears to be incapable of dispersal overland, though very rare cases of transport by birds or mammals may be responsible for establishing some populations. It is restricted to smaller streams of intermediate flow rates, many of which are distributed on both sides of the southern Appalachians and on the Piedmont (low plateau of small foothills) east of the mountains. Most of the populations examined in this study are completely isolated from each other, such that snails would have to either pass through the marine environment or over the (often very short) land barriers between populations. Development is direct, with egg masses attached to solid substrates producing crawling juveniles. This author notes that at any time, the majority of individuals are crawling upstream against the current, which apparently allows populations to stay approximately in the same place despite the occasional individual that must lose its grip and be swept downstream.
The analysis of population divergence here included comparisons among eight 25 x 25 symmetric matrices, constructed using a comprehensive range of variables including morphological features (shell height, aperture width, etc.), allozyme alleles for seven loci, and 15 environmental variables (11 components of water chemistry, plus temperature, flow rate, stream gradient, and parasite infections by trematodes) and a further independent assessment of environmental similarity derived from an examination of the diatom species diversity in the diets of each population.
Varying levels of genetic divergence were found throughout the study system, but most differences were relatively high compared to similar studies of other organisms. Allozyme alleles fell primarily into two categories: either they were present in all four study drainages, or they occurred in only a single population or small group of neighbouring populations. This suggests that all alleles arose either during a period when rapid spread across drainages was possible, or during a later period when dispersal was more difficult. The geological evidence strongly indicates extreme drainage stability, indicating that something about either the environment and / or the dispersal capabilities of G. proxima was different, perhaps during the Tertiary, than today.
No cline in morphology or allozymes was observed, which may be the result of a lack of gene flow preventing the spread of beneficial alleles. In other words, while nearby populations (overland) may experience very similar environments, adaptations in one population cannot spread to the other.
This author summarizes with a statement that both selection and gene flow restriction seem to be equally important in promoting morphological divergence in isolated populations. However, time since divergence may be the more important diversifying factor, and may underlie both selection and gene flow in this system. Furthermore, measures of divergence using allozymes indicate that time since isolation or gene flow may be more important than selection in structuring differences between populations.
Wednesday, June 4, 2008
Alvarez-Fuster et al. 1991
Alvarez-Fuster A, Juan C, Petitpierre E. 1991. Genome size in Tribolium flour-beetles: inter- and intraspecific variation. Genetical Research 58: 1-5.
These authors measured genome size in nine species of tenebrionid beetles in the tribe Ulomini; all but one of which are members of the genus Tribolium. Tribolium castaneum was and remains an exceptionally well-studied beetle, but genome size information was lacking, and few studies of insects had sought information about intraspecific variation in a comprehensive manner prior to this study.
Genome size was estimated by Feulgen densitometry measures of spermatids. Twenty spermatid nuclei from each of 10 individuals (five individuals of Alphitobius diaperinus) per species were measured, with spermatids of Dermestes maculatus used as a standard. For reasons not clear to me, detailed comparisons between D. maculatus and T. castaneum were carried out prior to studies of the other species. The procedure for isolation, fixation, and staining nuclei is similar to what we currently use but has some differences. Fixation was carried out for only 10 minutes in 10% formalin, rather than > 12 hours in MFA, hydrolysis lasted only 45 minutes (rather than 120) but used 5N-HCl as we use, and staining was for two hours (like what we do), but details of the chemical preparation of the stain are not given, though the cited Juan & Petitpierre (1989) may provide more information.
Statistical analysis included measures derived from Gold & Amemiya (1987) of within and between taxa comparisons. Nested ANOVA was also used to support an argument about the significance of intraspecific variation.
The discussion section includes an argument that large and uniform sampling as carried here provides a “solid base from which to analyze the pattern of distribution of genome sizes both inter- and intraspecifically.” Later discussion includes an odd argument that one species, T. brevicornis, with the largest genome size measured here, may be ancestral to the other species (including, presumably, the one species in another genus) and that genome evolution has proceeded by reduction and associated specialization of the type proposed by e.g. Hinegardner (1976).
Within each species, two to four significantly different groups of genome sizes were found, with the exception of one species (T. destructor), which did not show such structure. This, plus the nested ANOVA that indicated significant variation due to between-individuals-within-species comparisons, is taken as evidence in favour of (biologically) significant intraspecific variation in these beetles. The authors acknowledge that such intraspecific variation is surprising, but their arguments for evolutionary trends are not well constructed, so I do not know what to make of this intraspecific variation.
These authors measured genome size in nine species of tenebrionid beetles in the tribe Ulomini; all but one of which are members of the genus Tribolium. Tribolium castaneum was and remains an exceptionally well-studied beetle, but genome size information was lacking, and few studies of insects had sought information about intraspecific variation in a comprehensive manner prior to this study.
Genome size was estimated by Feulgen densitometry measures of spermatids. Twenty spermatid nuclei from each of 10 individuals (five individuals of Alphitobius diaperinus) per species were measured, with spermatids of Dermestes maculatus used as a standard. For reasons not clear to me, detailed comparisons between D. maculatus and T. castaneum were carried out prior to studies of the other species. The procedure for isolation, fixation, and staining nuclei is similar to what we currently use but has some differences. Fixation was carried out for only 10 minutes in 10% formalin, rather than > 12 hours in MFA, hydrolysis lasted only 45 minutes (rather than 120) but used 5N-HCl as we use, and staining was for two hours (like what we do), but details of the chemical preparation of the stain are not given, though the cited Juan & Petitpierre (1989) may provide more information.
Statistical analysis included measures derived from Gold & Amemiya (1987) of within and between taxa comparisons. Nested ANOVA was also used to support an argument about the significance of intraspecific variation.
The discussion section includes an argument that large and uniform sampling as carried here provides a “solid base from which to analyze the pattern of distribution of genome sizes both inter- and intraspecifically.” Later discussion includes an odd argument that one species, T. brevicornis, with the largest genome size measured here, may be ancestral to the other species (including, presumably, the one species in another genus) and that genome evolution has proceeded by reduction and associated specialization of the type proposed by e.g. Hinegardner (1976).
Within each species, two to four significantly different groups of genome sizes were found, with the exception of one species (T. destructor), which did not show such structure. This, plus the nested ANOVA that indicated significant variation due to between-individuals-within-species comparisons, is taken as evidence in favour of (biologically) significant intraspecific variation in these beetles. The authors acknowledge that such intraspecific variation is surprising, but their arguments for evolutionary trends are not well constructed, so I do not know what to make of this intraspecific variation.
Bell and Collins 2008
Bell G, Collins S. 2008. Adaptation, extinction and global change. Evolutionary Applications 1: 3-16.
These authors review and synthesize the current theory surrounding evolutionary responses to gradual environmental changes, especially increasing atmospheric carbon dioxide concentrations. In this context, these authors argue that the primary task of evolutionary biologists in the early 21st century is to predict adaptive evolution (or extinction) of populations and species in a gradually changing environment.
Populations are assumed to have high fitness, based on historical events. In a stable environment, beneficial alleles will accumulate, thus environmental changes are likely to be changes to the worse. Additionally, populations that do not adapt will suffer gradually declining mean fitness as pathogens and predators should themselves be selected for the most common target genotype.
Environmental variance increases with increasing time scales, that is, events occurring more distantly in time will be more different from each other. This applies to environmental conditions as much as anything else. The major implication of this in the context of this paper is that lineages surviving over long time periods will experience increasingly variable conditions, which also means generally deteriorating conditions if populations start well-adapted.
Many previous studies have found either strong selection, and / or high heritability. This apparent contradiction can be explained by high variability in the direction and magnitude of selection, suggesting that environmental variability is ubiquitous.
Populations can respond to changing conditions in four ways: phenotypic plasticity, dispersal and migration, adaptation, or extinction. These are arranged in order from short time scales to long.
The current pace of global environmental conditions change is probably higher than in most or all previous episodes. Historical levels of CO2 were about 280 ppm (parts per million); currently they are about 380 ppm, with some projections as high as 1000 ppm within the next 100 years.
These authors analysed the effects of the severity and frequency of environmental change (always change for the worse). They found that frequency is much more important to the probability of adaptation or “evolutionary rescue” than is severity. Frequent changes in conditions is likely to lead to extinction because selection does not have enough time to fix beneficial alleles, such that some fraction of the population is not well adapted to start with when the next change hits. In contrast, rare but severe changes lead to strong selection, and expose a long series of potentially beneficial alleles, increasing the mutation supply rate. The mutation supply rate is the critical parameter in determining adaptation or extinction, specifically the fraction of the supply of mutations that are beneficial and can rescue a declining population, i.e. raise a genotype’s rate of growth from negative to positive. Even rapid environmental change can be adapted to if the (rescue) mutation supply is high enough.
A survey of both simulations and studies of natural and laboratory populations revealed several cases of adaptation to frequent or continuous environmental change, and several cases of failure to adapt, even in species with very large population sizes. This indicates primarily that the rate of rescue mutations is unknown, despite being the single most important variable in predicting the evolutionary fates of populations under global climate change. However, these authors argue that a rescue mutation rate of approximately one per generation, regardless of population size, is probably close to the critical value, but qualify this estimate by stating they intend it as a first guess, and stimulus for more exact research in future.
The current driver of global environmental change is increasing CO2 concentrations in the atmosphere. Unlike most other agents of environmental change, CO2 is not in itself likely to represent a lethal stress to organisms, rather the effects will be either direct and positive (increased photosynthesis), or indirect via either temperature and climate changes or via biotic interactions such as competition.
Experiments and simulations by these and other authors have suggested that the short-term physiological responses of phytoplankton to increased CO2 will be opposite in direction to long-term evolutionary responses; this is at least partly because phytoplankton appear to be not limited by CO2 for growth. More specifically, the CO2-importing pump, which is tightly regulated by CO2 concentrations, will become less efficient, removing much of the productivity gain that would otherwise be predicted. Evidence that this will lead to community-level effects such as succession is currently equivocal, and based on short-term studies or idiosyncratic species compositions.
Our current understanding of evolution and ecology is based on populations subjected to a sudden shift from one stable environment to another, and usually a shift to increased stress or scarcity. In contrast, current global change is gradual and continuous, and is a case of nutrient enrichment.
These authors conclude with three main points. First, rescue mutations are critical to the phenomenon of evolutionary rescue and adaptation, but their rate is almost totally unknown. Second, the evolutionary response to increasing atmospheric CO2 concentrations is likely to be reduced efficiency of photosynthesis, rather than increased productivity. Third, these authors urge a general increase in studies of the evolutionary effects of global change, at rates of environmental change between the very fast rates typical of laboratory experimental evolution, and the very slow rates typical of most of the Earth’s history.
These authors review and synthesize the current theory surrounding evolutionary responses to gradual environmental changes, especially increasing atmospheric carbon dioxide concentrations. In this context, these authors argue that the primary task of evolutionary biologists in the early 21st century is to predict adaptive evolution (or extinction) of populations and species in a gradually changing environment.
Populations are assumed to have high fitness, based on historical events. In a stable environment, beneficial alleles will accumulate, thus environmental changes are likely to be changes to the worse. Additionally, populations that do not adapt will suffer gradually declining mean fitness as pathogens and predators should themselves be selected for the most common target genotype.
Environmental variance increases with increasing time scales, that is, events occurring more distantly in time will be more different from each other. This applies to environmental conditions as much as anything else. The major implication of this in the context of this paper is that lineages surviving over long time periods will experience increasingly variable conditions, which also means generally deteriorating conditions if populations start well-adapted.
Many previous studies have found either strong selection, and / or high heritability. This apparent contradiction can be explained by high variability in the direction and magnitude of selection, suggesting that environmental variability is ubiquitous.
Populations can respond to changing conditions in four ways: phenotypic plasticity, dispersal and migration, adaptation, or extinction. These are arranged in order from short time scales to long.
The current pace of global environmental conditions change is probably higher than in most or all previous episodes. Historical levels of CO2 were about 280 ppm (parts per million); currently they are about 380 ppm, with some projections as high as 1000 ppm within the next 100 years.
These authors analysed the effects of the severity and frequency of environmental change (always change for the worse). They found that frequency is much more important to the probability of adaptation or “evolutionary rescue” than is severity. Frequent changes in conditions is likely to lead to extinction because selection does not have enough time to fix beneficial alleles, such that some fraction of the population is not well adapted to start with when the next change hits. In contrast, rare but severe changes lead to strong selection, and expose a long series of potentially beneficial alleles, increasing the mutation supply rate. The mutation supply rate is the critical parameter in determining adaptation or extinction, specifically the fraction of the supply of mutations that are beneficial and can rescue a declining population, i.e. raise a genotype’s rate of growth from negative to positive. Even rapid environmental change can be adapted to if the (rescue) mutation supply is high enough.
A survey of both simulations and studies of natural and laboratory populations revealed several cases of adaptation to frequent or continuous environmental change, and several cases of failure to adapt, even in species with very large population sizes. This indicates primarily that the rate of rescue mutations is unknown, despite being the single most important variable in predicting the evolutionary fates of populations under global climate change. However, these authors argue that a rescue mutation rate of approximately one per generation, regardless of population size, is probably close to the critical value, but qualify this estimate by stating they intend it as a first guess, and stimulus for more exact research in future.
The current driver of global environmental change is increasing CO2 concentrations in the atmosphere. Unlike most other agents of environmental change, CO2 is not in itself likely to represent a lethal stress to organisms, rather the effects will be either direct and positive (increased photosynthesis), or indirect via either temperature and climate changes or via biotic interactions such as competition.
Experiments and simulations by these and other authors have suggested that the short-term physiological responses of phytoplankton to increased CO2 will be opposite in direction to long-term evolutionary responses; this is at least partly because phytoplankton appear to be not limited by CO2 for growth. More specifically, the CO2-importing pump, which is tightly regulated by CO2 concentrations, will become less efficient, removing much of the productivity gain that would otherwise be predicted. Evidence that this will lead to community-level effects such as succession is currently equivocal, and based on short-term studies or idiosyncratic species compositions.
Our current understanding of evolution and ecology is based on populations subjected to a sudden shift from one stable environment to another, and usually a shift to increased stress or scarcity. In contrast, current global change is gradual and continuous, and is a case of nutrient enrichment.
These authors conclude with three main points. First, rescue mutations are critical to the phenomenon of evolutionary rescue and adaptation, but their rate is almost totally unknown. Second, the evolutionary response to increasing atmospheric CO2 concentrations is likely to be reduced efficiency of photosynthesis, rather than increased productivity. Third, these authors urge a general increase in studies of the evolutionary effects of global change, at rates of environmental change between the very fast rates typical of laboratory experimental evolution, and the very slow rates typical of most of the Earth’s history.
Wednesday, May 28, 2008
Dillon and Frankis 2004
Dillon RT, Frankis RC. 2004. High levels of mitochondrial DNA sequence divergence in isolated populations of freshwater snails of the genus Goniobasis Lea, 1862. American Malacological Bulletin 19: 69-77.
These authors examined sequence divergence within and between populations and species of “prosobranch” freshwater gastropods in the south-eastern USA. These species are relatively well studied, and previous work by other authors had suggested very high levels of mtDNA heterogeneity, between populations and between species.
Part of the justification for this work is as a way of calibrating a new measurement tool: DNA sequences may be useful for systematic assignment, but if levels of sequence divergence are to be used to distinguish species, first the levels of divergence between species well-established by other means (e.g. interspecific hybridization trials) must be determined. These snails had previously been well studied for traits associated with concepts of species such as pre- and post-mating isolation (e.g. Dillon 1986).
The other major reason for this paper was to test the hypothesis that freshwater snail populations may be so old, so large, and so isolated that intrapopulation mtDNA sequence divergence is likely to swamp interpopulation (and interspecies) mtDNA divergence. Under this hypothesis, within-population levels of divergence will overlap with between-population levels. Populations studied here are extremely isolated, with no freshwater connections between them; this area was not inundated nor was it ice-bound by the Pleistocene glaciations, suggesting that some populations may have been isolated for millions of years.
The levels of divergence found in COI and 16S mtDNA sequences were extremely high, especially among populations of one species, Goniobasis proxima. In one population, individual conspecific snails collected from adjacent rocks may have more divergent mtDNA than individual snails collected from populations separated by over 400km of (impassable) land. In that same highly heterogeneous-mtDNA population, morphology and seven nuclear markers (allozymes) were essentially homogeneous.
The authors end with a caution that systematic inference must be made with care when faced with high levels of intrapopulation divergences. This paper appears to provide an example situation in mtDNA phylogeography that does not show the “barcode gap”, i.e. a clear distinction between intra- and interpopulation divergences.
These authors examined sequence divergence within and between populations and species of “prosobranch” freshwater gastropods in the south-eastern USA. These species are relatively well studied, and previous work by other authors had suggested very high levels of mtDNA heterogeneity, between populations and between species.
Part of the justification for this work is as a way of calibrating a new measurement tool: DNA sequences may be useful for systematic assignment, but if levels of sequence divergence are to be used to distinguish species, first the levels of divergence between species well-established by other means (e.g. interspecific hybridization trials) must be determined. These snails had previously been well studied for traits associated with concepts of species such as pre- and post-mating isolation (e.g. Dillon 1986).
The other major reason for this paper was to test the hypothesis that freshwater snail populations may be so old, so large, and so isolated that intrapopulation mtDNA sequence divergence is likely to swamp interpopulation (and interspecies) mtDNA divergence. Under this hypothesis, within-population levels of divergence will overlap with between-population levels. Populations studied here are extremely isolated, with no freshwater connections between them; this area was not inundated nor was it ice-bound by the Pleistocene glaciations, suggesting that some populations may have been isolated for millions of years.
The levels of divergence found in COI and 16S mtDNA sequences were extremely high, especially among populations of one species, Goniobasis proxima. In one population, individual conspecific snails collected from adjacent rocks may have more divergent mtDNA than individual snails collected from populations separated by over 400km of (impassable) land. In that same highly heterogeneous-mtDNA population, morphology and seven nuclear markers (allozymes) were essentially homogeneous.
The authors end with a caution that systematic inference must be made with care when faced with high levels of intrapopulation divergences. This paper appears to provide an example situation in mtDNA phylogeography that does not show the “barcode gap”, i.e. a clear distinction between intra- and interpopulation divergences.
Saturday, May 24, 2008
Richardson and Goff 2001
Richardson MS, Goff ML. 2001. Effects of temperature and intraspecific interaction on the development of Dermestes maculatus Coleoptera: Dermestidae). Journal of Medical Entomology 38: 347-357.
These authors measured survivorship and development rate in Dermestes maculatus from Hawaii, and compared these variables between beetles raised at a range of temperatures between 15°C and 35°C, and larval densities between one and 120 individuals per container, with modifications to prevent cannibalism by larvae of eggs.
Beetles were maintained in large plastic boxes (see also Hefti et al. 1980) lined with paper towels, and fed on Lighthouse brand (60% protein) fish meal in Petri dishes, with distilled water provided in separate Petri dishes. Humidity was not controlled, but varied between 60% and 80% relative.
Development times (egg to adult) varied from about three months at 20°C to a little longer than one month at 35°C. Females are generally slightly larger, and this species (or at least this population) shows a reversed size-temperature rule, with larger adult body sizes at higher temperatures. High density impairs larval survival, though there were few differences between intermediate-density treatments.
The authors suggest that optimal growth and survival is probably close to 30°C, and at intermediate population densities. Fish meal seems to be an appropriate and useful growth medium.
These authors measured survivorship and development rate in Dermestes maculatus from Hawaii, and compared these variables between beetles raised at a range of temperatures between 15°C and 35°C, and larval densities between one and 120 individuals per container, with modifications to prevent cannibalism by larvae of eggs.
Beetles were maintained in large plastic boxes (see also Hefti et al. 1980) lined with paper towels, and fed on Lighthouse brand (60% protein) fish meal in Petri dishes, with distilled water provided in separate Petri dishes. Humidity was not controlled, but varied between 60% and 80% relative.
Development times (egg to adult) varied from about three months at 20°C to a little longer than one month at 35°C. Females are generally slightly larger, and this species (or at least this population) shows a reversed size-temperature rule, with larger adult body sizes at higher temperatures. High density impairs larval survival, though there were few differences between intermediate-density treatments.
The authors suggest that optimal growth and survival is probably close to 30°C, and at intermediate population densities. Fish meal seems to be an appropriate and useful growth medium.
Hefti et al. 1980
Hefti E, Trechsel U, Rufenacht H, Fleisch H. 1980. Use of dermestid beetles for cleaning bones. Calcified Tissue International 31: 45-47.
These authors evaluated the quantitative effects on a range of bone measures of carcass cleaning by Dermestes maculatus vs. manually. Standard Wistar rats, healthy and osteoporetic, were cleaned by either a beetle colony or by hand, a time-consuming and tedious process. Hand-cleaning invariably leaves behind small pieces of soft tissue, while the beetles are more thorough but may consume bone when the food supply of softer tissue is depleted. The beetles did not significantly reduce the measured aspects of the bones compared to manual dissection, as long as the rat carcasses were not exposed to the beetles for too long.
The lab beetle colony was maintained in a metal box, because the larvae can “burn through” some types of plastic. When not engaged in cleaning rat carcasses, the beetles were fed on “greaves”, the remainders of industrial fat production.
These authors evaluated the quantitative effects on a range of bone measures of carcass cleaning by Dermestes maculatus vs. manually. Standard Wistar rats, healthy and osteoporetic, were cleaned by either a beetle colony or by hand, a time-consuming and tedious process. Hand-cleaning invariably leaves behind small pieces of soft tissue, while the beetles are more thorough but may consume bone when the food supply of softer tissue is depleted. The beetles did not significantly reduce the measured aspects of the bones compared to manual dissection, as long as the rat carcasses were not exposed to the beetles for too long.
The lab beetle colony was maintained in a metal box, because the larvae can “burn through” some types of plastic. When not engaged in cleaning rat carcasses, the beetles were fed on “greaves”, the remainders of industrial fat production.
Sunday, May 18, 2008
Gill and Cain 1980
Gill JJB, Cain AJ. 1980. The karyotype of Cepaea sylvatica (Pulmonata: Helicidae) and its relationship to those of C. hortensis and C. nemoralis. Biological Journal of the Linnean Society 14: 293-301.
These authors describe the karyotypes of three species of congeneric land snails found in Europe, and discuss the evolutionary implications of their findings in the context of previous work on the genetics of shell colour patterns, particularly in the relatively well-studied Cepaea nemoralis. This paper is an explicit attempt to unite genetic and cytogenetic studies of these snails.
Previous karyotype examinations in this genus had been performed only on meiotic tissue, which these authors consider unsuitable. Mitotic cells for karyotype analysis are difficult to obtain, however, so these authors used embryos from 5-day-old eggs, following the method of Page (1978). Shell pattern variation had previously been associated with between seven and nine tightly linked loci, calculated by Cook (1969) to be most likely located together (as a “supergene”) on one arm of the largest chromosome pair in C. nemoralis.
Among the three studied species, two (C. nemoralis and C. hortensis) have similar karyotypes, with 2n = 44 and one “conspicuously large” pair of chromosomes, while the third species (C. sylvatica) has 2n = 50 and a large pair of chromosomes. A fourth species (C. vindobonensis), possibly restricted to Russia and not studied by these authors, also has 2n = 50 but probably lacks the conspicuous and large chromosomes (Baltzer 1913).
These authors were not able to apply standard banding and u.v. fluorochrome techniques to the karyotypes, rendering most of the chromomes in all three species indistinguishable. The only chromosomes that could be reliably distinguished were the two largest pairs (by their sizes) and a third pair with a clear constriction on one arm. The other chromosomes showed approximately continuous variation in size and no other morphological characteristics.
The large pair of chromosomes in C. sylvatica do not resemble the large chromosomes in the other two species and are therefore probably not homologous. A scenario of chromosome fusions is briefly discussed, but is dismissed as unlikely to generate the patterns of genetic linkage observed. There is also a rather strange evolutionary path described, in which the karyotypes of extant species are taken as indicative of ancestral states, with gradual evolution of the “derived” karyotype of C. nemoralis and C. hortensis from “ancestral” karyotypes represented by C. vindobonensis and C. sylvatica. The authors end with a statement that other species in the subfamily Helicinae have also shown conspicuous large chromosomes and probable high degrees of karytotype stability, though they do not describe shell colour patterns in those other species, nor do they provide references for these observations.
These authors describe the karyotypes of three species of congeneric land snails found in Europe, and discuss the evolutionary implications of their findings in the context of previous work on the genetics of shell colour patterns, particularly in the relatively well-studied Cepaea nemoralis. This paper is an explicit attempt to unite genetic and cytogenetic studies of these snails.
Previous karyotype examinations in this genus had been performed only on meiotic tissue, which these authors consider unsuitable. Mitotic cells for karyotype analysis are difficult to obtain, however, so these authors used embryos from 5-day-old eggs, following the method of Page (1978). Shell pattern variation had previously been associated with between seven and nine tightly linked loci, calculated by Cook (1969) to be most likely located together (as a “supergene”) on one arm of the largest chromosome pair in C. nemoralis.
Among the three studied species, two (C. nemoralis and C. hortensis) have similar karyotypes, with 2n = 44 and one “conspicuously large” pair of chromosomes, while the third species (C. sylvatica) has 2n = 50 and a large pair of chromosomes. A fourth species (C. vindobonensis), possibly restricted to Russia and not studied by these authors, also has 2n = 50 but probably lacks the conspicuous and large chromosomes (Baltzer 1913).
These authors were not able to apply standard banding and u.v. fluorochrome techniques to the karyotypes, rendering most of the chromomes in all three species indistinguishable. The only chromosomes that could be reliably distinguished were the two largest pairs (by their sizes) and a third pair with a clear constriction on one arm. The other chromosomes showed approximately continuous variation in size and no other morphological characteristics.
The large pair of chromosomes in C. sylvatica do not resemble the large chromosomes in the other two species and are therefore probably not homologous. A scenario of chromosome fusions is briefly discussed, but is dismissed as unlikely to generate the patterns of genetic linkage observed. There is also a rather strange evolutionary path described, in which the karyotypes of extant species are taken as indicative of ancestral states, with gradual evolution of the “derived” karyotype of C. nemoralis and C. hortensis from “ancestral” karyotypes represented by C. vindobonensis and C. sylvatica. The authors end with a statement that other species in the subfamily Helicinae have also shown conspicuous large chromosomes and probable high degrees of karytotype stability, though they do not describe shell colour patterns in those other species, nor do they provide references for these observations.
Baršiene et al. 1996
Baršiene J, Tapia G, Barsyte D. 1996. Chromosomes of molluscs inhabiting some mountain springs of eastern Spain. Journal of Molluscan Studies 62: 539-543.
These authors report karyotypes for four species of molluscs (three gastropods and one bivalve) collected from small, high-altitude freshwater habitats in Spain. These habitats are quite diverse, with some very small springs occupying only 3-4 m^2 of surface area. Previous studies had associated small and isolated populations with polyploidy and its effects on tolerance of environmental stress and avoiding inbreeding depression.
Collected animals were injected with (large body) or immersed in (small body) a colchicine solution before dissection. The authors do not clearly describe what tissues from which species and populations were used, though they do describe “gonal and somatic cells”; presumably the gonadal cells were sperm, and the somatic cells are loosely described as “soft tissues” that were dissociated in 45% acetic acid by pipetting.
The high fraction of “hypodiploid” cells found in some individuals of Lymnaea peregra and some instances of apparent cell degeneration was attributed to “ecological stress”, though no supporting evidence or further discussion appears. They also state that the bivalve in their study, Pisidium casertanum, was almost certainly diploid, despite different populations having chromsome numbers ranging from 150 to 180, and other, uncited studies that found high and idiosyncratic levels of polyploidy in this family (Pisidiidae) and the closely related family Sphaeriidae (e.g. Burch and Huber 1966). As a final negative criticism of this paper, I found the frequent reference of the authors’ own unpublished data in support of presumed trends to be rather annoying.
These authors report karyotypes for four species of molluscs (three gastropods and one bivalve) collected from small, high-altitude freshwater habitats in Spain. These habitats are quite diverse, with some very small springs occupying only 3-4 m^2 of surface area. Previous studies had associated small and isolated populations with polyploidy and its effects on tolerance of environmental stress and avoiding inbreeding depression.
Collected animals were injected with (large body) or immersed in (small body) a colchicine solution before dissection. The authors do not clearly describe what tissues from which species and populations were used, though they do describe “gonal and somatic cells”; presumably the gonadal cells were sperm, and the somatic cells are loosely described as “soft tissues” that were dissociated in 45% acetic acid by pipetting.
The high fraction of “hypodiploid” cells found in some individuals of Lymnaea peregra and some instances of apparent cell degeneration was attributed to “ecological stress”, though no supporting evidence or further discussion appears. They also state that the bivalve in their study, Pisidium casertanum, was almost certainly diploid, despite different populations having chromsome numbers ranging from 150 to 180, and other, uncited studies that found high and idiosyncratic levels of polyploidy in this family (Pisidiidae) and the closely related family Sphaeriidae (e.g. Burch and Huber 1966). As a final negative criticism of this paper, I found the frequent reference of the authors’ own unpublished data in support of presumed trends to be rather annoying.
Dressler 1990
Dressler LG. 1990. Controls, standards, and histogram interpretation in DNA flow cytometry. Methods in Cell Biology 33: 157-171.
This author describes and discusses various procedural components and concerns involved in using flow cytometry to measure nuclear DNA contents, in the context of human cancer research and diagnosis.
Among controls, one important control described by this author is the use of cytologic or histologic examination, for example by staining a subsample of a specimen and examining under a compound microscope. In my work, this can be accomplished through Feulgen image analysis densitometry, though I think this author had in mind a less involved technique with the intention of verifying cell types and cell densities. This author also reiterates that the use of internal (ideally co-prepared) standards is critical for flow cytometry.
This paper is divided into procedures for first, fresh and frozen tissues and second, formalin-fixed, paraffin-embedded tissues. For fresh and frozen tissues, the use of duplicates, where one duplicate is the specimen alone, the other the specimen plus the standard, is urged. This fits well with what we have already been doing in our lab, using the unknown specimen alone to determine the approximate range of the position of the peak in the histogram, and the specimen coprepared with a known standard to actually estimate genome size. For fixed tissue, additional procedures are described for removing nuclei from the paraffin matrix, and the DNA index (Vindelov and Christensen 1990) is clearly defined; it is essentially the same as our calculation of genome size by comparison to a known standard.
This author also includes a recipe for freezing medium for use at -70°C, and advice on clarifying peaks in the histogram.
This author describes and discusses various procedural components and concerns involved in using flow cytometry to measure nuclear DNA contents, in the context of human cancer research and diagnosis.
Among controls, one important control described by this author is the use of cytologic or histologic examination, for example by staining a subsample of a specimen and examining under a compound microscope. In my work, this can be accomplished through Feulgen image analysis densitometry, though I think this author had in mind a less involved technique with the intention of verifying cell types and cell densities. This author also reiterates that the use of internal (ideally co-prepared) standards is critical for flow cytometry.
This paper is divided into procedures for first, fresh and frozen tissues and second, formalin-fixed, paraffin-embedded tissues. For fresh and frozen tissues, the use of duplicates, where one duplicate is the specimen alone, the other the specimen plus the standard, is urged. This fits well with what we have already been doing in our lab, using the unknown specimen alone to determine the approximate range of the position of the peak in the histogram, and the specimen coprepared with a known standard to actually estimate genome size. For fixed tissue, additional procedures are described for removing nuclei from the paraffin matrix, and the DNA index (Vindelov and Christensen 1990) is clearly defined; it is essentially the same as our calculation of genome size by comparison to a known standard.
This author also includes a recipe for freezing medium for use at -70°C, and advice on clarifying peaks in the histogram.
Vindeløv and Christensen 1990
Vindeløv L, Christensen IJ. 1990. An integrated set of methods for routine flow cytometric DNA analysis. Methods in Cell Biology 33: 127-137.
These authors present a set of protocols for standard flow cytometry in a clinical setting. The variables that can be obtained from flow cytometry are the number of subpopulations of cells with different DNA contents in a specimen, the relative sizes of these subpopulations, the “DNA index (DI)”, and the fractions of cells in G1, S, and G2 + M phases. DNA index is used here in a human-cancer context, and is roughly equivalent to nuclear DNA content per nucleus. In running flow cytometry, there are six major problems to overcome. These are sample acquisition, storage, standardization, staining, flow cytometry itself, and statistical analysis, also referred to here as “deconvolution”.
Optimal methods for sample acquisition vary with specimen type; these authors were apparently concerned primarily with the differences between soft and solid tumours from humans, but the point applies across eukaryotes in my opinion. These authors recommend storage of specimens at -80°C with DMSO, but caution that specimens should be frozen and thawed at most once. I am not certain that DMSO is a good idea. Standardization is achieved through the use of internal standards; these authors recommend erythrocytes (blood) from chicken (Gallus gallus domesticus) and trout (Onchorynchus mykiss). These authors describe a staining protocol in three steps, that includes the use of trypsin during cell dissociation and a trypsin inhibitor in a later step to prevent interaction with Propidium iodide (see also Krishan 1990). The chicken blood is described as being mixed with heparin at the time of collection, but no mention is made here of the potential interactions between heparin and Propidium iodide (Krishan 1990).
During flow cytometry, the positions of the peaks in the histogram corresponding to the standards (chicken and trout) are used to determine the DNA index of the measured specimen. These histogram heights can be made equal by mixing the standards together and with the specimen in a manner described by these authors; essentially, cell concentrations are measured and the known fluorescence characteristics of the standards are taken into account. Agitation of specimens will tend to increase the presence of debris and the occurrence of nuclear clumping.
These authors report satisfactory results from these protocols with 17 000 samples for all (human) tissues except sperm.
These authors present a set of protocols for standard flow cytometry in a clinical setting. The variables that can be obtained from flow cytometry are the number of subpopulations of cells with different DNA contents in a specimen, the relative sizes of these subpopulations, the “DNA index (DI)”, and the fractions of cells in G1, S, and G2 + M phases. DNA index is used here in a human-cancer context, and is roughly equivalent to nuclear DNA content per nucleus. In running flow cytometry, there are six major problems to overcome. These are sample acquisition, storage, standardization, staining, flow cytometry itself, and statistical analysis, also referred to here as “deconvolution”.
Optimal methods for sample acquisition vary with specimen type; these authors were apparently concerned primarily with the differences between soft and solid tumours from humans, but the point applies across eukaryotes in my opinion. These authors recommend storage of specimens at -80°C with DMSO, but caution that specimens should be frozen and thawed at most once. I am not certain that DMSO is a good idea. Standardization is achieved through the use of internal standards; these authors recommend erythrocytes (blood) from chicken (Gallus gallus domesticus) and trout (Onchorynchus mykiss). These authors describe a staining protocol in three steps, that includes the use of trypsin during cell dissociation and a trypsin inhibitor in a later step to prevent interaction with Propidium iodide (see also Krishan 1990). The chicken blood is described as being mixed with heparin at the time of collection, but no mention is made here of the potential interactions between heparin and Propidium iodide (Krishan 1990).
During flow cytometry, the positions of the peaks in the histogram corresponding to the standards (chicken and trout) are used to determine the DNA index of the measured specimen. These histogram heights can be made equal by mixing the standards together and with the specimen in a manner described by these authors; essentially, cell concentrations are measured and the known fluorescence characteristics of the standards are taken into account. Agitation of specimens will tend to increase the presence of debris and the occurrence of nuclear clumping.
These authors report satisfactory results from these protocols with 17 000 samples for all (human) tissues except sperm.
Krishan 1990
Krishan A. 1990. Rapid DNA content analysis by the Propidium iodide-hypotonic citrate method. Methods in Cell Biology 33: 121-125.
This author describes a set of protocols for staining nuclear DNA with Propidium iodide for use in flow cytometry. The basic protocol is similar to the methods we use in our lab currently, though this author claims that prepared stain solution can be stored at room temperature in a light-proof bottle in a large volume (e.g. 1 L), and that stained specimens can be stored up to 24 hours on ice without noticeable impact on measurements. Trypsin and heparin, frequently used in cell dissociation or blood storage procedures, will interfere with the binding of Propidium iodide to nuclear DNA.
This author describes a set of protocols for staining nuclear DNA with Propidium iodide for use in flow cytometry. The basic protocol is similar to the methods we use in our lab currently, though this author claims that prepared stain solution can be stored at room temperature in a light-proof bottle in a large volume (e.g. 1 L), and that stained specimens can be stored up to 24 hours on ice without noticeable impact on measurements. Trypsin and heparin, frequently used in cell dissociation or blood storage procedures, will interfere with the binding of Propidium iodide to nuclear DNA.
Cerra et al. 1990
Cerra R, Zarbo RJ, Crissman JD. Dissociation of cells from solid tumours. Methods in Cell Biology 33: 1-12.
These authors describe methods to produce cell suspensions from a range of cancer tumour types collectively described as “solid”. Many tumours are relatively easy to extract individual cells in suspension; this paper describes methods suitable for tumours in which the cells are bound to each other and to extracellular materials. Existing methods for flow cytometry analysis of these tumours have focused on enucleation techniques, which avoid the problems associated with cell membrane bonds to other cells by rupturing cell membranes. This causes the loss of potentially informative cell-membrane-bound and cytoplasmic materials, and these authors state they are not convinced enucleation is the best option.
Dissociating cells can be accomplished by a vast range of mechanical and enzymatic techniques, many of which can be used in combination, such that the optimum technique to use on a given tissue must be determined empirically for each case. Mechanical dissociation techniques typically start with cells in the early stages of cell culture. The authors recommend the use of two scalpel blades rather than scissors to slice tissues because scissors tend to mash the tissue rather than cut. The resulting semi-dissociated tissue should be sieved through something called a “100-mesh cell sieve”, whatever that is. I think this step removes clumps of cells and large pieces of extracellular debris. Other mechanical dissociation methods include the use of tissue attached to a wine cork and vibrated with a mechanical engraver to release cells (Eade et al. 1981).
Enzymatic dissociation methods tend to focus either on the use of proteases to disrupt intercellular desmosomes, or collagenases to disrupt the extracellular matrix. Each category of enzymes may damage or remove cell-membrane features that may be useful in diagnosis during flow cytometry. In all cell dissociation techniques, DNAases are routinely used to remove the very sticky free DNA released by dead cells. Liotta et al. (1982) provide a review of the use of collagenases in cell dissociation.
Enucleation techniques can be applied to a wider range of tissues than can cell dissociation techniques, including fixed and frozen tissues. I get the impression that fixed and / or frozen tissues are routinely used in cancer flow cytometry with a range of human tissues. The authors caution that enucleation typically causes high levels of background debris compared to cell dissociation. Thornthwaite et al. (1980) and Vindeløv et al. (1983) provide protocols for one-step isolation and staining of nuclei; these authors provide a more complicated method for the use of paraffin-embedded tissues.
These authors describe methods to produce cell suspensions from a range of cancer tumour types collectively described as “solid”. Many tumours are relatively easy to extract individual cells in suspension; this paper describes methods suitable for tumours in which the cells are bound to each other and to extracellular materials. Existing methods for flow cytometry analysis of these tumours have focused on enucleation techniques, which avoid the problems associated with cell membrane bonds to other cells by rupturing cell membranes. This causes the loss of potentially informative cell-membrane-bound and cytoplasmic materials, and these authors state they are not convinced enucleation is the best option.
Dissociating cells can be accomplished by a vast range of mechanical and enzymatic techniques, many of which can be used in combination, such that the optimum technique to use on a given tissue must be determined empirically for each case. Mechanical dissociation techniques typically start with cells in the early stages of cell culture. The authors recommend the use of two scalpel blades rather than scissors to slice tissues because scissors tend to mash the tissue rather than cut. The resulting semi-dissociated tissue should be sieved through something called a “100-mesh cell sieve”, whatever that is. I think this step removes clumps of cells and large pieces of extracellular debris. Other mechanical dissociation methods include the use of tissue attached to a wine cork and vibrated with a mechanical engraver to release cells (Eade et al. 1981).
Enzymatic dissociation methods tend to focus either on the use of proteases to disrupt intercellular desmosomes, or collagenases to disrupt the extracellular matrix. Each category of enzymes may damage or remove cell-membrane features that may be useful in diagnosis during flow cytometry. In all cell dissociation techniques, DNAases are routinely used to remove the very sticky free DNA released by dead cells. Liotta et al. (1982) provide a review of the use of collagenases in cell dissociation.
Enucleation techniques can be applied to a wider range of tissues than can cell dissociation techniques, including fixed and frozen tissues. I get the impression that fixed and / or frozen tissues are routinely used in cancer flow cytometry with a range of human tissues. The authors caution that enucleation typically causes high levels of background debris compared to cell dissociation. Thornthwaite et al. (1980) and Vindeløv et al. (1983) provide protocols for one-step isolation and staining of nuclei; these authors provide a more complicated method for the use of paraffin-embedded tissues.
Singh 1998
Singh NP. 1998. A rapid method for the preparation of single-cell suspensions from solid tissues. Cytometry 31: 229-232.
This author evaluated the use of a tissue press (BioSpec Product, Inc.) to produce cell suspensions suitable for examination of DNA double-stranded breaks in rat brain tissue. The use of manual cell dissociation with forceps and scalpels was compared to the device, and the device was found to be highly effective and efficient at producing cell suspensions.
This device is not expensive (approx. $30) and looks like it may be useful for my own work with preparing cell suspensions for flow cytometry.
This author evaluated the use of a tissue press (BioSpec Product, Inc.) to produce cell suspensions suitable for examination of DNA double-stranded breaks in rat brain tissue. The use of manual cell dissociation with forceps and scalpels was compared to the device, and the device was found to be highly effective and efficient at producing cell suspensions.
This device is not expensive (approx. $30) and looks like it may be useful for my own work with preparing cell suspensions for flow cytometry.
Brockhoff et al. 1999
Brockhoff G, Fleischmann S, Meier A, Wachs F-P, Hofstaedter F, Knuechel R. 1999. Use of a mechanical dissociation device to improve standardization of flow cytometric cytokeratin DNA measurements of colon carcinomas. Cytometry (Communications in Clinical Cytometry) 38: 184-191.
These authors evaluated the use of a Medimachine (DAKO Diagnostica GmbH) to dissociate cells from specimens of colon tumours in a large number of patients. They compared flow cytometry results from specimens sliced by the Medimachine’s “little crossed blades” to manual dissociation using scalpels. In general, the Medimachine produced a higher fraction of useable cells in flow cytometry, and was more consistent in an interlaboratory comparison.
These authors evaluated the use of a Medimachine (DAKO Diagnostica GmbH) to dissociate cells from specimens of colon tumours in a large number of patients. They compared flow cytometry results from specimens sliced by the Medimachine’s “little crossed blades” to manual dissociation using scalpels. In general, the Medimachine produced a higher fraction of useable cells in flow cytometry, and was more consistent in an interlaboratory comparison.
Saturday, May 17, 2008
Rodríguez-Juiz et al. 1996
Rodríguez-Juiz AM, Torrado M, Méndez J. 1996. Genome-size variation in bivalve molluscs determined by flow cytometry. Marine Biology 126: 489-497.
These authors measured nuclear DNA contents in 10 species of bivalves of commercial importance. Genome size variation in plants and poikilothermal animals had previously been associated with life-history and ecological traits, suggesting links between genome size variation and speciation events. There had been few previous studies of DNA content in molluscs. Early examples of such studies include Mirsky and Ris (1951), Hinegardner (1973, 1976), and Cavalier-Smith (1978); several earlier papers on molluscs and other poikilotherms related genome size to “specialization”, particularly the work of Hinegardner and colleagues.
Unlike most studies of DNA content, these authors included relatively large samples of each species, using 20 individuals in each species. All individuals were purchased from commercial shellfish sellers, either in Spain (9 species) or the Netherlands (Mytilus edulis), and maintained alive in the laboratory until dissection of gill tissue; the assumption that gill tissue is diploid is never stated explicitly but was used in the calculations of genome sizes. Tissue was placed in filtered, autoclaved seawater and subjected to mechanical shaking for 30 minutes; these authors do not describe in detail this shaking, is there a standard rate and magnitude of mechanical shaking of mollusc tissue? The presence of isolated cells was verified using a microscope, and cell preparations were strained through 15mm mesh and sonicated for two minutes to remove cell membranes. The nuclei were then centrifuged, resuspended in buffer that appears similar to Galbraith’s buffer (Galbraith et al. 1983), and fixed with 0.1% formaldehyde on ice. Finally, aggregations of nuclei were disrupted using a 26-gauge needle, pumped three times.
Two internal standards were employed: Capsicum annuum and chicken red blood cells (CRBCs). Isolated nuclei from these species were added to bivalve nuclei suspensions before staining, thus standards and specimens here were co-stained rather than co-prepared. The CRBCs produced a peak in the flow cytometry histograms overlapping seven of the 10 bivalve species, thus the introduction of the plant nuclei. C. annuum nuclei were employed after checking for consistent measurements with the three species of bivalves that did not overlap in peak area with CRBCs, and comparison between C. annuum and CRBCs to determine a C. annuum diploid nuclear content of 8.4 pg, larger than any bivalve measured in this study. 10 000 nuclei were measured per histogram, presumably this means total events recorded above the debris cut-off, and each specimen was measured three times.
These authors report significant intraspecific genome size variation in all 10 bivalve species. Interspecific (and between higher taxa) was much greater than intraspecific variation, but the intraspecific variation was statistically significant under 2-way ANOVA and “GSD” calculations based on the work of Gold and Amemiya (1987) and Alvarez-Fuster et al. (1991).
The discovered and possibly unexpected intraspecific variation is used to bolster an argument made in the discussion that large samples are necessary for accurate determination of genome size and genome size variation in species. This explains the difference between these results and the no-intraspecific-variation results of some previous authors that did not use large samples per species.
Following this is a discussion of Hinegardner’s (several papers in the 1970s) “specialization” assumption / hypothesis. It is described as one, then the other. These data do not support this hypothesis, which is not surprising considering how vague and taxon-specific the terms “specialized” and “generalized” are, and their underlying assumptions about species and lineage ages and rates of evolution.
These authors measured nuclear DNA contents in 10 species of bivalves of commercial importance. Genome size variation in plants and poikilothermal animals had previously been associated with life-history and ecological traits, suggesting links between genome size variation and speciation events. There had been few previous studies of DNA content in molluscs. Early examples of such studies include Mirsky and Ris (1951), Hinegardner (1973, 1976), and Cavalier-Smith (1978); several earlier papers on molluscs and other poikilotherms related genome size to “specialization”, particularly the work of Hinegardner and colleagues.
Unlike most studies of DNA content, these authors included relatively large samples of each species, using 20 individuals in each species. All individuals were purchased from commercial shellfish sellers, either in Spain (9 species) or the Netherlands (Mytilus edulis), and maintained alive in the laboratory until dissection of gill tissue; the assumption that gill tissue is diploid is never stated explicitly but was used in the calculations of genome sizes. Tissue was placed in filtered, autoclaved seawater and subjected to mechanical shaking for 30 minutes; these authors do not describe in detail this shaking, is there a standard rate and magnitude of mechanical shaking of mollusc tissue? The presence of isolated cells was verified using a microscope, and cell preparations were strained through 15mm mesh and sonicated for two minutes to remove cell membranes. The nuclei were then centrifuged, resuspended in buffer that appears similar to Galbraith’s buffer (Galbraith et al. 1983), and fixed with 0.1% formaldehyde on ice. Finally, aggregations of nuclei were disrupted using a 26-gauge needle, pumped three times.
Two internal standards were employed: Capsicum annuum and chicken red blood cells (CRBCs). Isolated nuclei from these species were added to bivalve nuclei suspensions before staining, thus standards and specimens here were co-stained rather than co-prepared. The CRBCs produced a peak in the flow cytometry histograms overlapping seven of the 10 bivalve species, thus the introduction of the plant nuclei. C. annuum nuclei were employed after checking for consistent measurements with the three species of bivalves that did not overlap in peak area with CRBCs, and comparison between C. annuum and CRBCs to determine a C. annuum diploid nuclear content of 8.4 pg, larger than any bivalve measured in this study. 10 000 nuclei were measured per histogram, presumably this means total events recorded above the debris cut-off, and each specimen was measured three times.
These authors report significant intraspecific genome size variation in all 10 bivalve species. Interspecific (and between higher taxa) was much greater than intraspecific variation, but the intraspecific variation was statistically significant under 2-way ANOVA and “GSD” calculations based on the work of Gold and Amemiya (1987) and Alvarez-Fuster et al. (1991).
The discovered and possibly unexpected intraspecific variation is used to bolster an argument made in the discussion that large samples are necessary for accurate determination of genome size and genome size variation in species. This explains the difference between these results and the no-intraspecific-variation results of some previous authors that did not use large samples per species.
Following this is a discussion of Hinegardner’s (several papers in the 1970s) “specialization” assumption / hypothesis. It is described as one, then the other. These data do not support this hypothesis, which is not surprising considering how vague and taxon-specific the terms “specialized” and “generalized” are, and their underlying assumptions about species and lineage ages and rates of evolution.
Healy and Rota 1992
Healy B, Rota E. 1992. Methods for collecting Enchytraeidae during expeditions. Soil Biology and Biochemistry 24: 1279-1281.
These authors succinctly describe methods for collecting, extracting from soil and other materials, sorting, maintaining alive, and fixing and preserving enchytraeid worms. Enchytraeids are found in all moist soils, and other materials such as tide debris and forest litter. In this study, 0.5 kg soil samples were kept in plastic bags for up to five weeks before extraction of worms.
The methods described here were developed during an expedition by the authors to north Africa; Ireland, their home, does not allow import of soil samples so they were forced to extract worms in the field. The basic extraction method is a modification of O’Connor’s (1957) “wet funnel”, which is much more clearly described and illustrated here than in that older work. Figure 1. of this paper shows a wet funnel. Worms move down away from the source of light and heat (a light bulb) into a funnel full of water connected to a bottle. After an undescribed period, probably at least three hours, the water in the bottle is dumped to Petri dishes and worms sorted. The authors describe sorting using the naked eye, but recommend a magnifying glass with attached light source for smaller specimens. Living enchytraeids can be maintained in culture with soil agar, made from 2% agar and a 1:1 mixture of soil and distilled water. Soil and debris added with the worms will ruin sterility, but provides food for the worms. Water should be added periodically to keep everything moist, about every five days. Worms in this study were narcotized with soda water, and the authors describe dilute beer as an acceptable substitute. Fixation and preservation can use “any of the usual fixatives”, though contraction of specimens can make it difficult to distinguish taxonomically-important internal organs.
These authors succinctly describe methods for collecting, extracting from soil and other materials, sorting, maintaining alive, and fixing and preserving enchytraeid worms. Enchytraeids are found in all moist soils, and other materials such as tide debris and forest litter. In this study, 0.5 kg soil samples were kept in plastic bags for up to five weeks before extraction of worms.
The methods described here were developed during an expedition by the authors to north Africa; Ireland, their home, does not allow import of soil samples so they were forced to extract worms in the field. The basic extraction method is a modification of O’Connor’s (1957) “wet funnel”, which is much more clearly described and illustrated here than in that older work. Figure 1. of this paper shows a wet funnel. Worms move down away from the source of light and heat (a light bulb) into a funnel full of water connected to a bottle. After an undescribed period, probably at least three hours, the water in the bottle is dumped to Petri dishes and worms sorted. The authors describe sorting using the naked eye, but recommend a magnifying glass with attached light source for smaller specimens. Living enchytraeids can be maintained in culture with soil agar, made from 2% agar and a 1:1 mixture of soil and distilled water. Soil and debris added with the worms will ruin sterility, but provides food for the worms. Water should be added periodically to keep everything moist, about every five days. Worms in this study were narcotized with soda water, and the authors describe dilute beer as an acceptable substitute. Fixation and preservation can use “any of the usual fixatives”, though contraction of specimens can make it difficult to distinguish taxonomically-important internal organs.
Briones et al. 2007
Briones MJI, Ineson P, Heinemeyer A. 2007. Predicting potential impacts of climate change on the geographical distribution of enchytraeids: a meta-analysis approach. Global Change Biology 13: 2252-2269.
These authors conducted a meta-analysis of all studies describing population abundances of enchytraeids. This meta-analysis required certain standards of error reporting and sample sizes for the analysis, thus many papers were not included. The authors seem inordinately enthusiastic about their meta-analysis, going to great lengths to describe both meta-analyses in general, and their own approach.
These authors focused on enchytraeids because they are often the dominant-biomass organisms of organic soils. Organic soils are not well defined in this paper, but are apparently those with very high carbon contents, thus these soils are important in the context of global climate change because changes to these systems could result in large changes in these soils’ roles as either carbon sinks or sources. Biomass of enchytraeids in organic soils can exceed 50% of all animal biomass in the soil, often dominated by one or a few species, feeding primarily on bacteria and detritus.
As an additional layer of analysis, these authors focused on one species of enchytraeid, Cognettia sphagnetorum, commonly found in European organic soils such as marshlands. The majority of studies analysed were situated in Europe, principally the UK and other parts of north-western Europe. The authors repeatedly describe this geographic bias, but do not seem otherwise concerned.
In general, high population sizes of enchytraeids were associated with Hungary (one site), alpine meadows, tropical grasslands, tropical rainforests, moorlands, moder and brown-earth soils, slightly acidic soils (pH 4 – 6), temperate rainy climates with moisture all year, and regions with moderate or cold summers. Mean annual temperature (I think that’s what the undefined acronym “MAT” stands for) higher than 16°C was strongly associated with reduced population sizes, and the loss of the focal species C. sphagnetorum. MAT higher than 10°C appears to be an inflection point, with reduced population sizes above that limit. Additionally, small population sizes were associated with warm dry summer climates (e.g. Mediterranean) and cold snowy tundra climates.
The authors present a confusing and possibly meaningless discussion of the results of their geographic analysis. They describe the range of population densities in their studies (more than 500 000 m-2 down to less than 5 000 m-2), then state these differences in mean densities were not significant under the Wilcoxon test. If the means are not different, they’re not different, so why bother to report them, except to describe the error associated with comparing across ecosystems? They ran a regression analysis using these population densities, after stating the data were not normally distributed; I do not recall how sensitive to departures from normality regression analysis may be.
The authors state that there was no association between enchytraeid population density and depth in soil, then go on to rather confusingly describe the most enchytraeid-rich soil depth horizons. Apparently, enchytraeids are generally concentrated in the top 3 to 4 cm, with very few individuals found deeper than 12 cm. Enchytraeids generally seem to require permanent high moisture levels.
The focal species apparently reproduces asexually by fragmentation; many of the studies included in the meta-analysis describe numbers of individuals that are “whole” or “regenerating”. This curious and surprising life-history trait is never referenced in this paper, seemingly treated as common knowledge among enchytraeidologists. I know of few animals that habitually reproduce this way.
Overall, I found this a confusing and disappointing paper, though I admire their attempt to reconcile a highly heterogeneous dataset. The reference list contains probably the majority of available papers on Enchytraeidae, and may be very useful in that context.
These authors conducted a meta-analysis of all studies describing population abundances of enchytraeids. This meta-analysis required certain standards of error reporting and sample sizes for the analysis, thus many papers were not included. The authors seem inordinately enthusiastic about their meta-analysis, going to great lengths to describe both meta-analyses in general, and their own approach.
These authors focused on enchytraeids because they are often the dominant-biomass organisms of organic soils. Organic soils are not well defined in this paper, but are apparently those with very high carbon contents, thus these soils are important in the context of global climate change because changes to these systems could result in large changes in these soils’ roles as either carbon sinks or sources. Biomass of enchytraeids in organic soils can exceed 50% of all animal biomass in the soil, often dominated by one or a few species, feeding primarily on bacteria and detritus.
As an additional layer of analysis, these authors focused on one species of enchytraeid, Cognettia sphagnetorum, commonly found in European organic soils such as marshlands. The majority of studies analysed were situated in Europe, principally the UK and other parts of north-western Europe. The authors repeatedly describe this geographic bias, but do not seem otherwise concerned.
In general, high population sizes of enchytraeids were associated with Hungary (one site), alpine meadows, tropical grasslands, tropical rainforests, moorlands, moder and brown-earth soils, slightly acidic soils (pH 4 – 6), temperate rainy climates with moisture all year, and regions with moderate or cold summers. Mean annual temperature (I think that’s what the undefined acronym “MAT” stands for) higher than 16°C was strongly associated with reduced population sizes, and the loss of the focal species C. sphagnetorum. MAT higher than 10°C appears to be an inflection point, with reduced population sizes above that limit. Additionally, small population sizes were associated with warm dry summer climates (e.g. Mediterranean) and cold snowy tundra climates.
The authors present a confusing and possibly meaningless discussion of the results of their geographic analysis. They describe the range of population densities in their studies (more than 500 000 m-2 down to less than 5 000 m-2), then state these differences in mean densities were not significant under the Wilcoxon test. If the means are not different, they’re not different, so why bother to report them, except to describe the error associated with comparing across ecosystems? They ran a regression analysis using these population densities, after stating the data were not normally distributed; I do not recall how sensitive to departures from normality regression analysis may be.
The authors state that there was no association between enchytraeid population density and depth in soil, then go on to rather confusingly describe the most enchytraeid-rich soil depth horizons. Apparently, enchytraeids are generally concentrated in the top 3 to 4 cm, with very few individuals found deeper than 12 cm. Enchytraeids generally seem to require permanent high moisture levels.
The focal species apparently reproduces asexually by fragmentation; many of the studies included in the meta-analysis describe numbers of individuals that are “whole” or “regenerating”. This curious and surprising life-history trait is never referenced in this paper, seemingly treated as common knowledge among enchytraeidologists. I know of few animals that habitually reproduce this way.
Overall, I found this a confusing and disappointing paper, though I admire their attempt to reconcile a highly heterogeneous dataset. The reference list contains probably the majority of available papers on Enchytraeidae, and may be very useful in that context.
Tuesday, May 13, 2008
Dillon 2006
Dillon RT. 2006. The classification of the Lymnaeidae. Letter to the FWGNA project group, December 2006. http://www.cofc.edu/~fwgna/archive/28Dec06.html.
This article describes the current taxonomic uncertainty of the freshwater gastropod family Lymnaeidae, with reference to the major monographs and taxonomic works of the 20th century.
Baker (1911) describes 113 species and subspecies of Lymnaeidae in North America, including seven genera (one of which is only known from fossils). Later work, including aspects of the Modern Synthesis emphasized the considerable intraspecific morphological variation of this and other families of freshwater snails, leading to a major revision of the family by Hubendick (1951), a monograph that this author refers to as a “masterpiece”.
Hubendick (1951) reduced the family to two genera, with most species placed in Lymnaea; only the “weirdo” limpet-like species of genus Lanx remain separate. Approximately 12 species were recognized for North America, either as endemics or holarctic.
Later work, for example by Burch (1980, 1982), did not adopt Hubendick’s (1951) scheme, resulting in a compromise taxonomic scheme somewhere between that of Hubendick (1951) and Baker (1911). This author proposes a modified scheme for current workers, listing two genera (as Hubendick, 1951), and reducing most of Baker’s (1911) genera to subgenus level, to preserve the utility of such terms as “fossarine” and “stagnicoline” as descriptors of groups of species.
I have assembled a taxonomy of the Lymnaeidae for North America from this letter and from Clarke (1973).
This article describes the current taxonomic uncertainty of the freshwater gastropod family Lymnaeidae, with reference to the major monographs and taxonomic works of the 20th century.
Baker (1911) describes 113 species and subspecies of Lymnaeidae in North America, including seven genera (one of which is only known from fossils). Later work, including aspects of the Modern Synthesis emphasized the considerable intraspecific morphological variation of this and other families of freshwater snails, leading to a major revision of the family by Hubendick (1951), a monograph that this author refers to as a “masterpiece”.
Hubendick (1951) reduced the family to two genera, with most species placed in Lymnaea; only the “weirdo” limpet-like species of genus Lanx remain separate. Approximately 12 species were recognized for North America, either as endemics or holarctic.
Later work, for example by Burch (1980, 1982), did not adopt Hubendick’s (1951) scheme, resulting in a compromise taxonomic scheme somewhere between that of Hubendick (1951) and Baker (1911). This author proposes a modified scheme for current workers, listing two genera (as Hubendick, 1951), and reducing most of Baker’s (1911) genera to subgenus level, to preserve the utility of such terms as “fossarine” and “stagnicoline” as descriptors of groups of species.
I have assembled a taxonomy of the Lymnaeidae for North America from this letter and from Clarke (1973).
Leslie et al. 1997
Leslie AJ, Crisman TL, Prenger JP, Ewel KC. 1997. Benthic macroinvertebrates of small Florida pondcypress swamps and the influence of dry periods. Wetlands 17: 447-455.
These authors examined the faunas of three pondcypress swamps in northeastern Florida, over about 18 months from 1993 to 1995. Pondcypress swamps are wetlands with unpredictably-fluctuating water levels and a canopy formed by pondcypress trees (Taxodium distichum var. nutans). These swamps may remain wet for years or dry repeatedly within a single year, presenting a very challenging abiotic environment to aquatic organisms. Prior to this study, there had been few papers describing the biodiversity of pondcypress swamps, particularly during dry periods referred to as “drawdowns”.
The three ponds differed from each other in area, depth, and most dramatically emergent macrophyte vegetation. All three contained large abundances of Sphagnum mosses, and responded to local weather conditions similarly, tending to be driest at the same time, in June 1994. All ponds were highly acidic, with pH ranging between 3.4 and 4.4, and changing over time.
Benthic macroinvertebrates were collected by cores in a random fashion, to allow calculation of species richness and individual density per unit area, in this case reported as per square meter. Collected animals were identified to genus when possible using a range of identification keys from the literature (e.g. Pennak 1978). The beetle families Dytiscidae and Hydrophilidae and the fly family Chironomidae contributed large numbers of genera, and two genera of chironomids and one amphipod genus (Crangonyx) contributed the majority of individuals. Up to 52% of total individuals collected were specimens of Crangonyx.
Total species richness varied between the three pools, with the pool with least emergent vegetation having the lowest richness. Species richnesses were higher than those reported for other wetland habitats in the same region.
The authors report some surprise at the levels of biodiversity maintained even during dry periods. There is some speculation based on Barlocher et al. (1978) that drawdown periods are accompanied by an increase in bacterial and fungal activity, with a net increase in protein levels and therefore food quality in the detritus that forms the bulk of the food of most of the collected animals. Crangonyx and many of the other species found are generalists, and can cope with unpredictable dry periods by burrowing into wet soil or escaping to other habitats, while many of the species excluded during dry periods are obligate aquatics or have restricted life cycles and require a certain minimum period of wetness to complete one or more stages of the life cycle.
The high species richness of Dytiscidae and high population densities of Crangonyx are good indications for my project, as I expect to visit such habitats during the summer of 2008.
These authors examined the faunas of three pondcypress swamps in northeastern Florida, over about 18 months from 1993 to 1995. Pondcypress swamps are wetlands with unpredictably-fluctuating water levels and a canopy formed by pondcypress trees (Taxodium distichum var. nutans). These swamps may remain wet for years or dry repeatedly within a single year, presenting a very challenging abiotic environment to aquatic organisms. Prior to this study, there had been few papers describing the biodiversity of pondcypress swamps, particularly during dry periods referred to as “drawdowns”.
The three ponds differed from each other in area, depth, and most dramatically emergent macrophyte vegetation. All three contained large abundances of Sphagnum mosses, and responded to local weather conditions similarly, tending to be driest at the same time, in June 1994. All ponds were highly acidic, with pH ranging between 3.4 and 4.4, and changing over time.
Benthic macroinvertebrates were collected by cores in a random fashion, to allow calculation of species richness and individual density per unit area, in this case reported as per square meter. Collected animals were identified to genus when possible using a range of identification keys from the literature (e.g. Pennak 1978). The beetle families Dytiscidae and Hydrophilidae and the fly family Chironomidae contributed large numbers of genera, and two genera of chironomids and one amphipod genus (Crangonyx) contributed the majority of individuals. Up to 52% of total individuals collected were specimens of Crangonyx.
Total species richness varied between the three pools, with the pool with least emergent vegetation having the lowest richness. Species richnesses were higher than those reported for other wetland habitats in the same region.
The authors report some surprise at the levels of biodiversity maintained even during dry periods. There is some speculation based on Barlocher et al. (1978) that drawdown periods are accompanied by an increase in bacterial and fungal activity, with a net increase in protein levels and therefore food quality in the detritus that forms the bulk of the food of most of the collected animals. Crangonyx and many of the other species found are generalists, and can cope with unpredictable dry periods by burrowing into wet soil or escaping to other habitats, while many of the species excluded during dry periods are obligate aquatics or have restricted life cycles and require a certain minimum period of wetness to complete one or more stages of the life cycle.
The high species richness of Dytiscidae and high population densities of Crangonyx are good indications for my project, as I expect to visit such habitats during the summer of 2008.
Sunday, May 11, 2008
Miller et al. 2007
Miller KB, Alarie Y, Whiting MF. 2007. Description of the larva of Notaticus fasciatus (Coleoptera: Dytiscidae) associated with adults using DNA sequence data. Annals of the Entomological Society of America 100: 787-797.
These authors were able to associate some larvae collected in French Guiana to a species widespread in lowland South America that did not previously have described larvae. This represents the first description of larvae of the tribe Aubehydrini, though this tribe contains only one described genus with two possibly synonymous species. This is the last tribe in the subfamily Dytiscinae to be so described.
The general methods closely follow those of Miller et al. (2005), though there is little in the way of phylogenetic discussion because, as stated by the authors, this work forms part of the basis of ongoing and future projects to examine dytiscine phylogeny in detail.
The larvae were clearly identified as belonging to the genus Notaticus, and are most likely members of the species N. fasciatus, with sequence differences well below the usual 2% threshold relative to adults of that species. However, the adults used in the comparison came from geographically distant populations in Bolivia, and the sequences of the larvae are sister to the sequences of the adults, rather than nested within in the cladogram. Thus, it is possible though unlikely that these larvae are actually members of a different species within the genus, either N. confusus or some as-yet-undescribed species. In addition, the adults that have been described of the two species of Notaticus are morphologically very similar, and may actually represent members of one species.
These authors were able to associate some larvae collected in French Guiana to a species widespread in lowland South America that did not previously have described larvae. This represents the first description of larvae of the tribe Aubehydrini, though this tribe contains only one described genus with two possibly synonymous species. This is the last tribe in the subfamily Dytiscinae to be so described.
The general methods closely follow those of Miller et al. (2005), though there is little in the way of phylogenetic discussion because, as stated by the authors, this work forms part of the basis of ongoing and future projects to examine dytiscine phylogeny in detail.
The larvae were clearly identified as belonging to the genus Notaticus, and are most likely members of the species N. fasciatus, with sequence differences well below the usual 2% threshold relative to adults of that species. However, the adults used in the comparison came from geographically distant populations in Bolivia, and the sequences of the larvae are sister to the sequences of the adults, rather than nested within in the cladogram. Thus, it is possible though unlikely that these larvae are actually members of a different species within the genus, either N. confusus or some as-yet-undescribed species. In addition, the adults that have been described of the two species of Notaticus are morphologically very similar, and may actually represent members of one species.
Miller et al. 2005
Miller KB, Alarie Y, Wolfe GW, Whiting MF. 2005. Association of insect life stages using DNA sequences: the larvae of Philodytes umbrinus (Motschulsky) (Coleoptera: Dytsicidae). Systematic Entomology 30: 499-509.
These authors used DNA sequence data in the form of 806 bp of mtCOI, to associate unidentified larvae to a described species. The insects were collected from pools in the desert region of the Skeleton Coast of northern Namibia. The larvae were morphologically associated with one tribe of dytiscids, and were collected with adults and larvae of two other species in the tribe in the genus Laccophilus, but were larger-bodied than known larvae of that genus.
Between species differences in sequence ranged between 1.9 and 19.9%, similar to values reported for other insect species. Within species differences were between 0 and 0.82%, and the differences in sequences between the larvae and the adults of their assigned species was 0 to 0.14%, providing clear evidence of the association.
The authors provide a very detailed list of morphological characters that are diagnostic for larvae of this genus (Philodytes), and a longer and even more detailed list of characters diagnostic for the species (P. umbrinus). They state near the end of the paper that their goal was not to provide molecular diagnostic features, but to use DNA sequence data to work backwards to find diagnostic morphological features which had not previously been described. There is some additional discussion of the uses, abuses, and limits of DNA barcoding in a taxonomic context, with a final point that taxonomy without morphology would not be as interesting.
These authors used DNA sequence data in the form of 806 bp of mtCOI, to associate unidentified larvae to a described species. The insects were collected from pools in the desert region of the Skeleton Coast of northern Namibia. The larvae were morphologically associated with one tribe of dytiscids, and were collected with adults and larvae of two other species in the tribe in the genus Laccophilus, but were larger-bodied than known larvae of that genus.
Between species differences in sequence ranged between 1.9 and 19.9%, similar to values reported for other insect species. Within species differences were between 0 and 0.82%, and the differences in sequences between the larvae and the adults of their assigned species was 0 to 0.14%, providing clear evidence of the association.
The authors provide a very detailed list of morphological characters that are diagnostic for larvae of this genus (Philodytes), and a longer and even more detailed list of characters diagnostic for the species (P. umbrinus). They state near the end of the paper that their goal was not to provide molecular diagnostic features, but to use DNA sequence data to work backwards to find diagnostic morphological features which had not previously been described. There is some additional discussion of the uses, abuses, and limits of DNA barcoding in a taxonomic context, with a final point that taxonomy without morphology would not be as interesting.
Friday, May 9, 2008
Bajer et al. 1961
Bajer A, Hansen-Melander E, Melander Y, Molè-Bajer J. 1961. Meiosis in Cepaea nemoralis studied by microcinematography. Chromosoma (Berl.) 12: 374-381.
These authors studied spermatogenesis in the helicid land snail Cepaea nemoralis, an hermaphrodite with accessible meiotic cells containing 28 bivalents. The stated aim of this paper is to contribute to knowledge of basic meiotic processes in animals, and compare them to meiosis in plants. This was accomplished through the use of an apparently cutting-edge-technology phase-contrast microscope, and for at least this paper, 16mm film.
Most of this paper is a description of the changes in shape and size of the nucleus of meiotic cells, and the movements of the chromosomes in the minutes immediately before and after the disappearance of the nuclear membrane. The nucleus is apparently somewhat unstable during prophase, changing position in the cell in a random fashion and changing shape rapidly. The chromosomes inside the intact nucleus also seem to move randomly, in a manner that does not suggest pulling by microtubules or other cytoskeletal components. Just prior to the disappearance of the nuclear membrane, the nucleus increases in size; this phenomenon is not explained even by speculation in this paper.
Previous work by these authors, using the same microscope, included measurements of nucleus mass by interference microscopy. How mass is measured is not clearly explained, but this paper is the first reference to this measurement I have seen.
These authors studied spermatogenesis in the helicid land snail Cepaea nemoralis, an hermaphrodite with accessible meiotic cells containing 28 bivalents. The stated aim of this paper is to contribute to knowledge of basic meiotic processes in animals, and compare them to meiosis in plants. This was accomplished through the use of an apparently cutting-edge-technology phase-contrast microscope, and for at least this paper, 16mm film.
Most of this paper is a description of the changes in shape and size of the nucleus of meiotic cells, and the movements of the chromosomes in the minutes immediately before and after the disappearance of the nuclear membrane. The nucleus is apparently somewhat unstable during prophase, changing position in the cell in a random fashion and changing shape rapidly. The chromosomes inside the intact nucleus also seem to move randomly, in a manner that does not suggest pulling by microtubules or other cytoskeletal components. Just prior to the disappearance of the nuclear membrane, the nucleus increases in size; this phenomenon is not explained even by speculation in this paper.
Previous work by these authors, using the same microscope, included measurements of nucleus mass by interference microscopy. How mass is measured is not clearly explained, but this paper is the first reference to this measurement I have seen.
Wednesday, April 30, 2008
Olsson 1981
Olsson TI. 1981. Overwintering of benthic macroinvertebrates in ice and frozen sediment in a North Swedish river. Holarctic Ecology 4: 161-166.
This author examined freezing tolerance and freezing resistance in some river-dwelling invertebrates in the Arctic. The study river is one of the few in northern Sweden that has not been dammed for hydroelectric purposes, allowing water levels to fluctuate through a wide range. Ice thickness in winter can exceed 50 cm, and the shallow littoral zone of the river freezes several centimetres into the sediment. Water level is lowest in winter, freezing sediments that are under as much as 4m of flowing water in summer. Spring thaw may occur bottom-to-top in shallow areas, as sunlight penetrates ice and heats underlying sediment, which thaws under a layer of ice; this slow thawing in sediments may be important for winter and spring survival of invertebrates and plants.
Ice and sediment cores taken from the river edge in winter included a range of frozen invertebrates. These animals were returned to the lab and allowed to thaw, to estimate winter survival. Most animals had very high survivorship; one major exception was the isopod Asellus aquaticus, found in a single aggregration of nearly 500 individuals, most of whom were dead upon thawing.
Winter survival was also estimated by freezing some animals in the lab, maintaining them frozen for several months, and thawing. Mechanical damage was inferred to be more severe in the lab than under field conditions as animals without shells or hard cases (e.g. gastropods, trichoptera larvae) such as oligochaetes suffered very high mortalities in the lab, but high survivorship in the field. This author is careful to note that lab freezing conditions included natural sediments and plants, as it has previously been shown that simple freezing of open water (e.g. in a bucket) is lethal to even the most cold-tolerant species, probably due to the mechanical damage incurred by expanding ice crystals that can be avoided by shelter among sediments or plant tissues.
Several cold and freezing putative adaptations were discovered, including the formation of epiphragms in some gastropods, a thin closure of the shell apeture not previously observed in aquatic snails, but common among dessication-resistant land snails. Some trichopteran larvae were found to have blocked their cases, though they were not pupal or prepupal. This blockage may have served to prevent ice formation and associated mechanical damage inside the cases. Some species were found in summer collections but were absent from frozen cores, including gammarid amphipods, suggesting winter migration to unfrozen deeper portions of the river.
This author examined freezing tolerance and freezing resistance in some river-dwelling invertebrates in the Arctic. The study river is one of the few in northern Sweden that has not been dammed for hydroelectric purposes, allowing water levels to fluctuate through a wide range. Ice thickness in winter can exceed 50 cm, and the shallow littoral zone of the river freezes several centimetres into the sediment. Water level is lowest in winter, freezing sediments that are under as much as 4m of flowing water in summer. Spring thaw may occur bottom-to-top in shallow areas, as sunlight penetrates ice and heats underlying sediment, which thaws under a layer of ice; this slow thawing in sediments may be important for winter and spring survival of invertebrates and plants.
Ice and sediment cores taken from the river edge in winter included a range of frozen invertebrates. These animals were returned to the lab and allowed to thaw, to estimate winter survival. Most animals had very high survivorship; one major exception was the isopod Asellus aquaticus, found in a single aggregration of nearly 500 individuals, most of whom were dead upon thawing.
Winter survival was also estimated by freezing some animals in the lab, maintaining them frozen for several months, and thawing. Mechanical damage was inferred to be more severe in the lab than under field conditions as animals without shells or hard cases (e.g. gastropods, trichoptera larvae) such as oligochaetes suffered very high mortalities in the lab, but high survivorship in the field. This author is careful to note that lab freezing conditions included natural sediments and plants, as it has previously been shown that simple freezing of open water (e.g. in a bucket) is lethal to even the most cold-tolerant species, probably due to the mechanical damage incurred by expanding ice crystals that can be avoided by shelter among sediments or plant tissues.
Several cold and freezing putative adaptations were discovered, including the formation of epiphragms in some gastropods, a thin closure of the shell apeture not previously observed in aquatic snails, but common among dessication-resistant land snails. Some trichopteran larvae were found to have blocked their cases, though they were not pupal or prepupal. This blockage may have served to prevent ice formation and associated mechanical damage inside the cases. Some species were found in summer collections but were absent from frozen cores, including gammarid amphipods, suggesting winter migration to unfrozen deeper portions of the river.
Milner 1994
Milner AM. 1994. Colonization and succession of invertebrate communities in a new stream in Glacier Bay National Park, Alaska. Freshwater Biology 32: 387-400.
This author describes long term monitoring of colonization and succession in a stream recently formed from a retreating glacier in south-eastern Alaska. The glacier filled its bay around 1700 AD, and has been retreating since, forming new streams and lakes, and novel habitats similar to what is thought to have occurred across northern North America and Eurasia at the end of the last ice age. There are few previous studies of stream systems that completely lack an upstream source of drift-colonizing organisms; this author describes this work as unique regarding its long time frame (12 years), spatial extent (kilometres), and primary succession characteristics.
Of the possible routes for colonization of the study stream by invertebrates, only aerial oviposition is possible as the other routes rely on suitable habitat upstream or downstream of the study site. The study site is bounded by the ocean below, and a new proglacial lake and associated ice field above. The first organisms present in the stream were chironomids, of species known to be exceptionally tolerant of cold water (~2°C). Species richness increased through the study period, with the addition of one species of Ephemeroptera, one species of Plecoptera, and a turnover in chironomid species and relative abundances.
A portion of the discussion section describes the distinction between fugitive species, good dispersers but poor competitors with habitat refugia in extreme environments, and opportunistic species, good dispersers that are also good competitors in their local microhabitats, maintained by disturbance. The first few chironomid species found in the stream are considered fugitive species because their population abundances were severely reduced in later years as other species, including a predatory stonefly, became established. A later portion discusses deterministic and stochastic processes in succession, arguing that water temperature and flow characteristics have been strong deterministic drivers of this stream system, in contrast to the strong role argued for stochastic processes (‘first come first served’) in other, more temperate streams studied by other authors.
The distinctions between fugitives and opportunists, and between stochastic and deterministic, would not be possible without species-level identification of chironomid larvae. Several species are described as Genus sp. A or similar, but nonetheless the ability to discriminate between closely related species with different ecological characteristics is clearly applied, allowing levels of analysis not normally seen in stream-succession studies.
This paper is part of a special issue of the journal Freshwater Biology, devoted to alpine and polar freshwater environments, and seems to be slightly lower in scientific rigour compared to normal papers in this journal. Many of the citations in this paper are of the author’s own previous unpublished data, and key blocks of data such as particular field collection seasons, have already been described in previous publications; this paper apparently serves primarily to integrate across the long time frame of repeated sampling.
This author describes long term monitoring of colonization and succession in a stream recently formed from a retreating glacier in south-eastern Alaska. The glacier filled its bay around 1700 AD, and has been retreating since, forming new streams and lakes, and novel habitats similar to what is thought to have occurred across northern North America and Eurasia at the end of the last ice age. There are few previous studies of stream systems that completely lack an upstream source of drift-colonizing organisms; this author describes this work as unique regarding its long time frame (12 years), spatial extent (kilometres), and primary succession characteristics.
Of the possible routes for colonization of the study stream by invertebrates, only aerial oviposition is possible as the other routes rely on suitable habitat upstream or downstream of the study site. The study site is bounded by the ocean below, and a new proglacial lake and associated ice field above. The first organisms present in the stream were chironomids, of species known to be exceptionally tolerant of cold water (~2°C). Species richness increased through the study period, with the addition of one species of Ephemeroptera, one species of Plecoptera, and a turnover in chironomid species and relative abundances.
A portion of the discussion section describes the distinction between fugitive species, good dispersers but poor competitors with habitat refugia in extreme environments, and opportunistic species, good dispersers that are also good competitors in their local microhabitats, maintained by disturbance. The first few chironomid species found in the stream are considered fugitive species because their population abundances were severely reduced in later years as other species, including a predatory stonefly, became established. A later portion discusses deterministic and stochastic processes in succession, arguing that water temperature and flow characteristics have been strong deterministic drivers of this stream system, in contrast to the strong role argued for stochastic processes (‘first come first served’) in other, more temperate streams studied by other authors.
The distinctions between fugitives and opportunists, and between stochastic and deterministic, would not be possible without species-level identification of chironomid larvae. Several species are described as Genus sp. A or similar, but nonetheless the ability to discriminate between closely related species with different ecological characteristics is clearly applied, allowing levels of analysis not normally seen in stream-succession studies.
This paper is part of a special issue of the journal Freshwater Biology, devoted to alpine and polar freshwater environments, and seems to be slightly lower in scientific rigour compared to normal papers in this journal. Many of the citations in this paper are of the author’s own previous unpublished data, and key blocks of data such as particular field collection seasons, have already been described in previous publications; this paper apparently serves primarily to integrate across the long time frame of repeated sampling.
Tuesday, April 22, 2008
Murkin et al. 1983
Murkin HR, Abbott PG, Kadlec JA. 1983. A comparison of activity traps and sweep nets for sampling nektonic invertebrates in wetlands. Freshwater Invertebrate Biology 2: 99-106.
These authors compared a specific activity trap design to a specific sweep net technique for sampling nektonic animals in small ponds in a wetland in Manitoba, in the context of evaluating incorporation of these techniques into long-term wetlands ecology monitoring programs. The activity trap consists of a 3.8 L glass bottle with a plast funnel inserted in the opening, held together with wire and elastic bands, and suspended in the water column from a stake driven at an angle into the sediment. The sweep net technique avoids benthic organisms and most benthic debris and vegetation by sweeping vertically upwards from resting flat on the substrate.
The fauna collected by the two methods was correlated when measured across variables of water temperature and water depth, suggesting that for at least total diversity, the two methods are collecting similar samples. Differences emerged when fish and predatory invertebrates were present in the traps, possibly attracted to the traps by the presence of prey species, including Hyalella azteca, which may have been subsequently consummed. Fish and other fast-moving animals were also rarely collected by the sweep nets. Activity traps appeared to select for the most mobile size- and age-classes of gastropods such as lymnaeids, which were absent from most sweep net samples.
The activity traps provide quantitative samples of only some taxa, primarily those that were classified as “herbivore-detritivores” in the absence of predators inside the traps. Predatory taxa were probably overrepresented in the traps, while some apparent prey taxa were underrepresented in traps when predators were present.
The activity traps provided several important advantages compared to sweep nets. There is reduced inter-operator variation, traps were easier to use among vegetation, they collected even fast-moving animals such as fish and large predatory invertebrates, and they integrated the nekton over 24 hours, unlike the time-of-day specific sweep nets.
These authors compared a specific activity trap design to a specific sweep net technique for sampling nektonic animals in small ponds in a wetland in Manitoba, in the context of evaluating incorporation of these techniques into long-term wetlands ecology monitoring programs. The activity trap consists of a 3.8 L glass bottle with a plast funnel inserted in the opening, held together with wire and elastic bands, and suspended in the water column from a stake driven at an angle into the sediment. The sweep net technique avoids benthic organisms and most benthic debris and vegetation by sweeping vertically upwards from resting flat on the substrate.
The fauna collected by the two methods was correlated when measured across variables of water temperature and water depth, suggesting that for at least total diversity, the two methods are collecting similar samples. Differences emerged when fish and predatory invertebrates were present in the traps, possibly attracted to the traps by the presence of prey species, including Hyalella azteca, which may have been subsequently consummed. Fish and other fast-moving animals were also rarely collected by the sweep nets. Activity traps appeared to select for the most mobile size- and age-classes of gastropods such as lymnaeids, which were absent from most sweep net samples.
The activity traps provide quantitative samples of only some taxa, primarily those that were classified as “herbivore-detritivores” in the absence of predators inside the traps. Predatory taxa were probably overrepresented in the traps, while some apparent prey taxa were underrepresented in traps when predators were present.
The activity traps provided several important advantages compared to sweep nets. There is reduced inter-operator variation, traps were easier to use among vegetation, they collected even fast-moving animals such as fish and large predatory invertebrates, and they integrated the nekton over 24 hours, unlike the time-of-day specific sweep nets.
Billington et al. 1989
Billington N, Boileau MG, Hebert PDN. 1989. Range extension of the fairy shrimp Polyartemiella hazeni (Murdoch, 1884) (Crustacea: Anostraca) to the eastern Canadian Arctic, with notes on the distribution of other eastern Arctic Anostraca. The Canadian Field-Naturalist 103: 404-405.
These authors present a short note that describes the capture of several species of Anostracans from the western shore of Hudson Bay, in what was then the Northwest Territories. For Polyartemiella hazeni, collections from Rankin Inlet and Eskimo Point represent a range expansion of about 1300 km eastwards; for the other species records here and from Igloolik provide similar range expansion estimates. The ability of one species, Branchinecta paludosa, to facultatively achieve two generations per year when conditions are good suggests circumstantial evidence in favour of a link between dessication and cold tolerance in freshwater animals.
These authors present a short note that describes the capture of several species of Anostracans from the western shore of Hudson Bay, in what was then the Northwest Territories. For Polyartemiella hazeni, collections from Rankin Inlet and Eskimo Point represent a range expansion of about 1300 km eastwards; for the other species records here and from Igloolik provide similar range expansion estimates. The ability of one species, Branchinecta paludosa, to facultatively achieve two generations per year when conditions are good suggests circumstantial evidence in favour of a link between dessication and cold tolerance in freshwater animals.
Whiteside and Lindegaard 1980
Whiteside MC, Lindegaard C. 1980. Complementary procedures for sampling small benthic invertebrates. Oikos 35: 317-320.
These authors recommend the use of two techniques simultaneously for comprehensive sampling of benthic invertebrates in freshwater, soft-bottom habitats. Cores approximately 20 cm in diameter work well for sampling burrowing and non-swimming taxa such as oligochaetes and gastropods, while a funnel trap worked well for sampling taxa that migrate vertically, especially very small forms that would otherwise be lost in benthic samples during seiving.
The funnel trap consists of a plastic funnel fit into a 300 mL glass jar, placed open-side-down on the substrate, being careful not to accidentally trap any planktonic animals during installation. Only individuals prone to vertical movement were collected in funnel traps; all coleoptera in the traps were adults, while the majority of coleoptera collected in cores were larvae. One major advantage of the funnels is the lack of debris or vegetation to sort through during specimen processing. The difference in sampled taxa suggests that both methods would be useful in any strategy of freshwater-benthos sampling.
Saturday, April 12, 2008
Stevens 1989
Stevens GC. 1989. The latitudinal gradient in geographical range: how so many species coexist in the tropics. The American Naturalist 133: 240-256.
This paper is an essay that provides an overview of the evidence suggesting a relationship between Rapoport’s rule (larger species geographic ranges at higher latitudes) and the global latitude biodiversity gradient. Both phenomena show coincident exceptions of taxa, indicating a common underlying cause. This is also the paper that coins the term “Rapoport’s rule”.
The original explanatory mechanism for Rapoport’s rule invokes the range of temperatures or other climatic conditions experienced by individuals during their lifetimes at different latitudes. High latitude locations have wider annual ranges of temperature, for example a spruce tree in an Alaskan forest may experience lows below -50°C and highs above 30°C in a single year, while no tropical sites below mountain tops experience that range. Within the geographic range of a species in the tropics, such ranges of environmental variation may occur, but few or no individuals would experience the full range. In addition, bands of climate (such as between annual mean temperatures) that lie along mountain slopes are narrower in the tropics, providing less space for meso-habitat adapted populations to establish and persist, such that population sizes are smaller and long term persistence and local adaptation are less likely.
Narrower tolerances for abiotic conditions in the tropics results in smaller geographic ranges and higher diversities because areas of diversity measurement will encompass a larger number of distinct climate zones than comparable measurements made in temperate or polar latitudes. Further increasing diversity estimates is a predicted strong-in-the-tropics “rescue effect” (Brown and Kodric-Brown, 1977) that produces sink populations in areas a species is poorly adapted to, maintained by immigration from nearby populations in more suitable habitats.
I find these arguments convincing, but some of the exceptions described here are problematic. One key exception that Stevens (1989) mentions more than once is the hymenopteran family Ichneumonidae. Ichneumonid species richness peaks at temperate, not tropical latitudes (Owen & Owen, 1974). Stevens (1989) explains this exception to the general latitude-diversity pattern by invoking the summer-only activity pattern of these parasitoid wasps. Stevens (1989) claims that because they are inactive during all but the warmest part of the year, ichneumonids “… in sense, live in the tropics, no matter what latitude they call home.” I see two critical problems with this argument as applied to Ichneumonidae as an informative exception to Rapoport’s rule and the latitude-diversity pattern. First, many other organisms, plants and animals and presumably other kingdoms and phyla, show severely reduced winter activity in temperate regions. Why do they not similarly show exceptional species-richness patterns? Second, “inactive” is not a synonym with “immune to environmental factors”. Overwintering in places that have winter (i.e. distinctly lower temperatures in one season compared to other times of the year) requires adaptations, sometimes extreme adaptations. The large body of literature concerning overwintering strategies of animals, and the various adaptations that constitute “freeze-tolerant” and “freeze-resistant” forms, comes readily to mind. Overwintering ichneumonids must survive the conditions of winter, even if they do not move around or show high metabolic rates during winter. As a further consideration, another section of this paper clarifies that Rapoport’s rule does not describe a pattern of increased species numbers per genus, it describes changes in the geographical distribution of functional groups of organisms, and includes the example of willows. Willows do not have higher diversity in the tropics; they are absent from tropical regions. But, willows are not an exception to either pattern because they are replaced by several other genera of morphologically and ecologically similar plants at lower latitudes. Why does Stevens (1989) not apply this functional-group replacement criterion to the example of the Ichneumonidae? There are other families of parasitoids, surely one or more of those taxa have high tropical diversity.
This paper is an essay that provides an overview of the evidence suggesting a relationship between Rapoport’s rule (larger species geographic ranges at higher latitudes) and the global latitude biodiversity gradient. Both phenomena show coincident exceptions of taxa, indicating a common underlying cause. This is also the paper that coins the term “Rapoport’s rule”.
The original explanatory mechanism for Rapoport’s rule invokes the range of temperatures or other climatic conditions experienced by individuals during their lifetimes at different latitudes. High latitude locations have wider annual ranges of temperature, for example a spruce tree in an Alaskan forest may experience lows below -50°C and highs above 30°C in a single year, while no tropical sites below mountain tops experience that range. Within the geographic range of a species in the tropics, such ranges of environmental variation may occur, but few or no individuals would experience the full range. In addition, bands of climate (such as between annual mean temperatures) that lie along mountain slopes are narrower in the tropics, providing less space for meso-habitat adapted populations to establish and persist, such that population sizes are smaller and long term persistence and local adaptation are less likely.
Narrower tolerances for abiotic conditions in the tropics results in smaller geographic ranges and higher diversities because areas of diversity measurement will encompass a larger number of distinct climate zones than comparable measurements made in temperate or polar latitudes. Further increasing diversity estimates is a predicted strong-in-the-tropics “rescue effect” (Brown and Kodric-Brown, 1977) that produces sink populations in areas a species is poorly adapted to, maintained by immigration from nearby populations in more suitable habitats.
I find these arguments convincing, but some of the exceptions described here are problematic. One key exception that Stevens (1989) mentions more than once is the hymenopteran family Ichneumonidae. Ichneumonid species richness peaks at temperate, not tropical latitudes (Owen & Owen, 1974). Stevens (1989) explains this exception to the general latitude-diversity pattern by invoking the summer-only activity pattern of these parasitoid wasps. Stevens (1989) claims that because they are inactive during all but the warmest part of the year, ichneumonids “… in sense, live in the tropics, no matter what latitude they call home.” I see two critical problems with this argument as applied to Ichneumonidae as an informative exception to Rapoport’s rule and the latitude-diversity pattern. First, many other organisms, plants and animals and presumably other kingdoms and phyla, show severely reduced winter activity in temperate regions. Why do they not similarly show exceptional species-richness patterns? Second, “inactive” is not a synonym with “immune to environmental factors”. Overwintering in places that have winter (i.e. distinctly lower temperatures in one season compared to other times of the year) requires adaptations, sometimes extreme adaptations. The large body of literature concerning overwintering strategies of animals, and the various adaptations that constitute “freeze-tolerant” and “freeze-resistant” forms, comes readily to mind. Overwintering ichneumonids must survive the conditions of winter, even if they do not move around or show high metabolic rates during winter. As a further consideration, another section of this paper clarifies that Rapoport’s rule does not describe a pattern of increased species numbers per genus, it describes changes in the geographical distribution of functional groups of organisms, and includes the example of willows. Willows do not have higher diversity in the tropics; they are absent from tropical regions. But, willows are not an exception to either pattern because they are replaced by several other genera of morphologically and ecologically similar plants at lower latitudes. Why does Stevens (1989) not apply this functional-group replacement criterion to the example of the Ichneumonidae? There are other families of parasitoids, surely one or more of those taxa have high tropical diversity.
Friday, April 11, 2008
Matthews 1979
Matthews JV Jr. 1979. Late Tertiary carabid fossils from Alaska and the Canadian archipelago. In: Carabid Beetles: Their Evolution, Natural History, and Classification (Erwin TL, Ball GE, Whitehead DR, Halpern AL eds.). Dr. W Junk bv Publishers, The Hague, Netherlands.
For this special symposium, this author summarizes recently discovered and analysed beetle fossils dating from the late Tertiary, and compares them with similar fossils from the Pleistocene. Most Tertiary fossils of insects are either casts or impressions, and beetle fossils tend to be crushed and scattered too severely for good identification and analysis. However, fossils dating from the late Miocene and early Pliocene (roughly 5 million years ago) were discovered at several sites across the western islands of the Canadian Archipelago and a site in western Alaska that resemble Pleistocene fossils in their quality of preservation. The western Alaska site is particularly valuable because the fossil-bearing layer is overlain by a layer of basalt flow, possibly from a volcanic eruption, that can be dated without recourse to biological materials. There was apparently a narrow connection between Alaska and Siberia at the time these fossils were produced.
In general, smaller-bodied beetles are better preserved than large, but many specimens of numerous genera were discovered. Matthews (1977) includes a complete list of all fossil Coleoptera found, including the carabids described here. Several examples of species-diagnostic features were found, including highly detailed elytra and parts of male genitalia.
The first part of the discussion of this paper is a critique of the strictly-Hennigian methods of Phylogenetic Systematics, which disallows phyletic evolution, i.e. changes in species phenotypes through time without associated lineage splitting. Later parts of the discussion describe the probable Taiga ecosystem present at very high latitudes in the late Miocene. The author ends the paper with optimism that similar high-quality Tertiary fossils may soon be found in other high latitude areas around the world.
For this special symposium, this author summarizes recently discovered and analysed beetle fossils dating from the late Tertiary, and compares them with similar fossils from the Pleistocene. Most Tertiary fossils of insects are either casts or impressions, and beetle fossils tend to be crushed and scattered too severely for good identification and analysis. However, fossils dating from the late Miocene and early Pliocene (roughly 5 million years ago) were discovered at several sites across the western islands of the Canadian Archipelago and a site in western Alaska that resemble Pleistocene fossils in their quality of preservation. The western Alaska site is particularly valuable because the fossil-bearing layer is overlain by a layer of basalt flow, possibly from a volcanic eruption, that can be dated without recourse to biological materials. There was apparently a narrow connection between Alaska and Siberia at the time these fossils were produced.
In general, smaller-bodied beetles are better preserved than large, but many specimens of numerous genera were discovered. Matthews (1977) includes a complete list of all fossil Coleoptera found, including the carabids described here. Several examples of species-diagnostic features were found, including highly detailed elytra and parts of male genitalia.
The first part of the discussion of this paper is a critique of the strictly-Hennigian methods of Phylogenetic Systematics, which disallows phyletic evolution, i.e. changes in species phenotypes through time without associated lineage splitting. Later parts of the discussion describe the probable Taiga ecosystem present at very high latitudes in the late Miocene. The author ends the paper with optimism that similar high-quality Tertiary fossils may soon be found in other high latitude areas around the world.
DeBruyn & Ring 1999
DeBruyn AMH, Ring RA. 1999. Comparative ecology of two species of Hydroporus (Coleoptera: Dytiscidae) in a high arctic oasis. The Canadian Entomologist 131: 405-420.
These authors examined the beetles living in two ponds in a polar oasis on the east coast of Ellesmere Island, during the summers of 1992 and 1993. The two ponds are different from each other in a number of important respects, including sediment and vegetations characteristics, shoreline structure, temperature profile, and duration. Pond A is smaller than Pond B, has a greater diversity of aquatic plants and benthic sediments, and never dries completely, while Pond B dries up in August and has benthic sediment composed mainly of bare rocks with occasional patches of silt and sand. These features may explain why both species of Hydroporus were found in Pond A but only one species was found in Pond B.
While high arctic conditions are generally considered extreme for organisms, because abiotic conditions approach the physical limits for life (e.g. Downes, 1964), aquatic habitats are considered relatively benign, because the large mass of water and winter ice cover buffer temperature changes compared to adjacent terrestrial habitats. However, other authors such as Danks (2007) have noted that smaller ponds freeze completely in winter and may respond to winter temperature variations in much the same way as terrestrial habitats. Interestingly, Danks (1987) does consider aquatic habitats to be more favourable to organisms, and invokes this effect to explain the higher ratios of species richness of aquatic versus terrestrial insects at high latitudes.
Polar oases are described more fully in a book edited by Svoboda and Freedman (1994); briefly, these are locations of high biodiversity and mild conditions. Alexandra Fiord’s lowland (78°53” N) is such an oasis because of the gentle slope near sea level and the surrounding landscape providing good exposure to summer sunlight while restricting exposure to chilling winds. The two ponds examined in this study had exceptionally high temperature profiles in summer, with some microhabitats rising to 37.5°C on one particularly sunny day in July of 1993.
The discussion of how these species of beetles are able to persist at such a high latitude site is somewhat confusing. Both species overwinter as adults, one in microhabitats that dry to at least some extent in winter while the other in microhabitats that remain wet and consequently probably freeze solid. These authors state that the dry-winter species must resist both desiccation and low temperatures, but do not consider that desiccation is a strategy employed by freeze-resistant insects, especially in terrestrial habitats. This is very confusing considering that the second author has published extensively about cold adaptations in insects.
Low temperatures have been invoked to explain the frequent pattern of longer life cycles among Arctic insects compared temperate conspecifics and congeners (e.g. Danks, 1981). These authors do not dismiss this possibility, but point out that the longer development time of one species may explain its absence from the temporary pond, rather than temperature per se. Other potentially explanatory variables, such as various aspects of water chemistry, are dismissed as unlikely, given the other places these species have been found.
These authors examined the beetles living in two ponds in a polar oasis on the east coast of Ellesmere Island, during the summers of 1992 and 1993. The two ponds are different from each other in a number of important respects, including sediment and vegetations characteristics, shoreline structure, temperature profile, and duration. Pond A is smaller than Pond B, has a greater diversity of aquatic plants and benthic sediments, and never dries completely, while Pond B dries up in August and has benthic sediment composed mainly of bare rocks with occasional patches of silt and sand. These features may explain why both species of Hydroporus were found in Pond A but only one species was found in Pond B.
While high arctic conditions are generally considered extreme for organisms, because abiotic conditions approach the physical limits for life (e.g. Downes, 1964), aquatic habitats are considered relatively benign, because the large mass of water and winter ice cover buffer temperature changes compared to adjacent terrestrial habitats. However, other authors such as Danks (2007) have noted that smaller ponds freeze completely in winter and may respond to winter temperature variations in much the same way as terrestrial habitats. Interestingly, Danks (1987) does consider aquatic habitats to be more favourable to organisms, and invokes this effect to explain the higher ratios of species richness of aquatic versus terrestrial insects at high latitudes.
Polar oases are described more fully in a book edited by Svoboda and Freedman (1994); briefly, these are locations of high biodiversity and mild conditions. Alexandra Fiord’s lowland (78°53” N) is such an oasis because of the gentle slope near sea level and the surrounding landscape providing good exposure to summer sunlight while restricting exposure to chilling winds. The two ponds examined in this study had exceptionally high temperature profiles in summer, with some microhabitats rising to 37.5°C on one particularly sunny day in July of 1993.
The discussion of how these species of beetles are able to persist at such a high latitude site is somewhat confusing. Both species overwinter as adults, one in microhabitats that dry to at least some extent in winter while the other in microhabitats that remain wet and consequently probably freeze solid. These authors state that the dry-winter species must resist both desiccation and low temperatures, but do not consider that desiccation is a strategy employed by freeze-resistant insects, especially in terrestrial habitats. This is very confusing considering that the second author has published extensively about cold adaptations in insects.
Low temperatures have been invoked to explain the frequent pattern of longer life cycles among Arctic insects compared temperate conspecifics and congeners (e.g. Danks, 1981). These authors do not dismiss this possibility, but point out that the longer development time of one species may explain its absence from the temporary pond, rather than temperature per se. Other potentially explanatory variables, such as various aspects of water chemistry, are dismissed as unlikely, given the other places these species have been found.
Wednesday, April 9, 2008
Krasnov et al. 2008
Krasnov BR, Shenbrot GI, Khokhlova IS, Mouillot D, Poulin R. 2008. Latitudinal gradients in niche breadth: empirical evidence from haematophagous ectoparasites. Journal of Biogeography 35: 592-601.
This paper examined Rapoport’s rule in fleas that use small mammals in the Palaearctic as hosts, applying phylogenetic independent contrasts (PIC) to questions of geographic range size, latitude, and niche breadth. These authors consider Rapoport’s rule, of increased geographic range sizes with higher latitudes, to be a special case of a more general pattern of niche-breadth expansion (less specialization) with higher latitudes. Under this explanation, specialized species have narrow tolerances of abiotic conditions, use a small range of resources, and / or tolerant of a very limited set of competitors, predators, parasites, and diseases.
There is controversy in the current biogeographic literature about the extent of application of Rapoport’s rule or Rapoport’s effects. Some authors consider it a global phenomenon, driven by global mechanisms such orbital dynamics (Dynesius & Jansson, 2000) or habitat stability (MacArthur 1955; 1972) differences across the globe. Other authors, most notably Rhode (1996; 1999) consider Rapoport’s effects to be localized to only some latitudes or taxonomic groups.
Recently, Vazquez and Stevens (2004) presented a hypothesis for a mechanism underlying a global Rapoport’s rule. Briefly, they proposed that a positive relationship between niche breadth and latitude will occur if 1) there is a latitudinal gradient in species richness and 2) the species interaction network is an asymmetrically specialized interaction network such that specialists tend to interact with generalists. This hypotheses appears to involve the opposite direction of causality compared to hypotheses relating high tropical species richness to narrow species niches (i.e. high specialization) via character displacement and competitive exclusion.
The measure of niche breadth used in this study includes an estimate of the taxonomic distinctiveness of the fleas’ hosts. A flea species with a broad niche will use hosts that are more distantly related to each other than will a flea species with a narrow niche, even if both flea species use the same number of species of host. The authors describe this as the STD index, in which high values indicate more taxonomically distinct hosts such as hosts in different orders. In their analysis, these authors excluded all extreme specialist flea species, those found in only one geographic site or on only one mammal host species.
Analyses included regressions of two dependent variables (host specificity and geographic range size) against the independent variable (geographic range position) using both conventional statistics and PIC. Geographic range position was taken as the midpoint latitude of a species geographic range, which was computed by constructing minimum surface polygons and other techniques more fully described in their methods section.
Species level phylogenies were constructed for each family of fleas, based on a family-level phylogeny previously produced by Medvedev (1995) and morphological and taxonomic characters. Polytomies were considered “soft” i.e. they assumed no knowledge of hidden branching patterns. The PIC conducted by these authors included a range of sophisticated statistical controls, again more fully detailed in their methods section.
The results of this study demonstrate 1. fleas follow Rapoport’s rule, at least in the Palaearctic and 2. host specificity in fleas declines at higher latitudes. Thus the positive relationship in fleas of niche breadth and latitude holds for both abiotic (geographic range size) and biotic (diversity of hosts) components of their niches. There were some exceptions, but the overall trend is clear. These authors propose a mechanism underlying this trend that is much in line with Vazquez and Stevens (2004), involving interactions between niche breadth and geographic range and latitude and niche breadth.
This paper examined Rapoport’s rule in fleas that use small mammals in the Palaearctic as hosts, applying phylogenetic independent contrasts (PIC) to questions of geographic range size, latitude, and niche breadth. These authors consider Rapoport’s rule, of increased geographic range sizes with higher latitudes, to be a special case of a more general pattern of niche-breadth expansion (less specialization) with higher latitudes. Under this explanation, specialized species have narrow tolerances of abiotic conditions, use a small range of resources, and / or tolerant of a very limited set of competitors, predators, parasites, and diseases.
There is controversy in the current biogeographic literature about the extent of application of Rapoport’s rule or Rapoport’s effects. Some authors consider it a global phenomenon, driven by global mechanisms such orbital dynamics (Dynesius & Jansson, 2000) or habitat stability (MacArthur 1955; 1972) differences across the globe. Other authors, most notably Rhode (1996; 1999) consider Rapoport’s effects to be localized to only some latitudes or taxonomic groups.
Recently, Vazquez and Stevens (2004) presented a hypothesis for a mechanism underlying a global Rapoport’s rule. Briefly, they proposed that a positive relationship between niche breadth and latitude will occur if 1) there is a latitudinal gradient in species richness and 2) the species interaction network is an asymmetrically specialized interaction network such that specialists tend to interact with generalists. This hypotheses appears to involve the opposite direction of causality compared to hypotheses relating high tropical species richness to narrow species niches (i.e. high specialization) via character displacement and competitive exclusion.
The measure of niche breadth used in this study includes an estimate of the taxonomic distinctiveness of the fleas’ hosts. A flea species with a broad niche will use hosts that are more distantly related to each other than will a flea species with a narrow niche, even if both flea species use the same number of species of host. The authors describe this as the STD index, in which high values indicate more taxonomically distinct hosts such as hosts in different orders. In their analysis, these authors excluded all extreme specialist flea species, those found in only one geographic site or on only one mammal host species.
Analyses included regressions of two dependent variables (host specificity and geographic range size) against the independent variable (geographic range position) using both conventional statistics and PIC. Geographic range position was taken as the midpoint latitude of a species geographic range, which was computed by constructing minimum surface polygons and other techniques more fully described in their methods section.
Species level phylogenies were constructed for each family of fleas, based on a family-level phylogeny previously produced by Medvedev (1995) and morphological and taxonomic characters. Polytomies were considered “soft” i.e. they assumed no knowledge of hidden branching patterns. The PIC conducted by these authors included a range of sophisticated statistical controls, again more fully detailed in their methods section.
The results of this study demonstrate 1. fleas follow Rapoport’s rule, at least in the Palaearctic and 2. host specificity in fleas declines at higher latitudes. Thus the positive relationship in fleas of niche breadth and latitude holds for both abiotic (geographic range size) and biotic (diversity of hosts) components of their niches. There were some exceptions, but the overall trend is clear. These authors propose a mechanism underlying this trend that is much in line with Vazquez and Stevens (2004), involving interactions between niche breadth and geographic range and latitude and niche breadth.
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