Monday, March 31, 2008

Andrews and Rigler 1985

Andrews D, Rigler FH. 1985. The effects of an Arctic winter on benthic invertebrates in the littoral zone of Char Lake, Northwest Territories. Canadian Journal of Zoology 63: 2825-2834.

These authors examined the benthic invertebrates of Char Lake, near Resolute, Nunavut, during both summer and winter. Char Lake freezes to the bottom around its edge, to approximately 2.5m thickness. Surface ice melts first from the edges of the lake, and when the littoral zone is ice-free water temperatures may reach up to 6°C. Deeper areas do not freeze solid in winter, but may never experience total loss of ice cover in summer.

Animals can be roughly categorized as either freezing tolerant, in which ice crystals form inside the body, or as freezing susceptible, in which ice formation is prevented through supercooling. The surrounding liquid water of aquatic habitats may cause tissue freezing by providing nucleating ice crystals at low temperatures, thus aquatic organisms may not be able to supercool, and must therefore either be freezing tolerant or migrate to nonfrozen areas.

The purpose of this study was fourfold. 1. to determine the temperature conditions of the winter benthos in Char Lake; 2. to determine if animals trapped in the zone of freezing can survive; 3. to determine if emigration to deeper, nonfrozen waters occurs; 4. to determine the effects of subzero temperatures on a focus species of harpacticoid copepod.

This paper provides an excellent description of the physical environment of Char Lake, which is located near the Polar Continental Shelf Project in Resolute, and has been intensively studied by many researchers since approximately 1960.

These authors used two distinct sampling methods in summer and winter. Summer sampling of the benthos was by a vacuum system operated by SCUBA divers. Winter sampling was by retrieval of frozen baskets previously embedded in the substrate during summer dives. Plastic chips may still be present in Char Lake from the marker floats used on these benthic baskets, as retrieval was by drilling into the thick ice until the underwater float was reached, followed by expansion of the hole and chiselling out the frozen basket.

Specimens were thawed and examined for survival, though logistical considerations meant that some samples were not as rigorously controlled. Temperature profiles of the lake indicated that the thick layer of ice and snow provided significant insulation, with frozen benthic temperatures never lower than -7.5°C, even with atmospheric temperatures below -20°C. Waters deeper than about 2.5m did not freeze.

The focus harpacticoid species, Attheyella nordenskioldii, persists in Char Lake as two possibly distinct populations. In deeper waters, this species reproduces throughout the year, though most individuals overwinter as adults. In shallower waters, adults may freeze solid for up to 8 months every year, with much more synchronous development than the deeper-water individuals. Both putative populations show 1-year life cycles. The authors explore some hypotheses that could explain how the winter-inactive individuals are able to maintain the same life cycle timing as the winter-active individuals. These hypotheses primarily rest upon energetic considerations, such that the shallow water populations have a summer advantage of temperature and thus metabolic and development rates that can make up for the winter disadvantage of those rates.

Animals trapped in the frozen zone were able to survive, and special overwintering stages were found only in one species of chironomid; all other examined species did not show obvious morphological characteristics associated with overwinter, though it is possible that physiological modifications such as dehydration were occurring. These authors could not separate induced from natural mortality, but were confident that all examined species were capable of high survivorship each winter. Additionally, no significant emigration to deeper, nonfrozen areas was detected, though some levels of such migration probably do occur.

The final part of the discussion of this paper focuses on the different strategies of A. nordenskioldii, and suggests further research on the energetic ecology of this species, this lake, and other seasonally frozen environments is warranted.

Wednesday, March 19, 2008

Burch and Huber 1966

Burch JB, Huber JM. 1966. Polyploidy in mollusks. Malacologia 5: 41-43.

These authors present a very brief summary of examples of polyploidy discovered to date among molluscs. The conditions promoting or presumed necessary for polyploidy in animals are first presented; of chief importance is the ability to physiologically and developmentally tolerate increased chromosome numbers and the ability to either self-fertilize or reproduce parthenogenically.

Among known selfing-capable hermaphroditic molluscs, the family Lymnaeidae has no examples of polyploids among the 40 species studied. There are unconfirmed reports of polyploidy in other families, including the land snails Succineidae and the freshwater clams Sphaeriidae (see also the much more recent Lee and O Foighil, 2002). The authors suggest that most of the observed variation in molluscan chromosome numbers can be attributed to aneuploidy, an hypothesis I find unlikely in light of more recent understanding of genome organization, especially the role of chromosome fissions, fusions, and translocations in structuring genomes.

Monday, March 17, 2008

Libertini et al. 2008

Libertini A, Trisolini R, Rampin M. 2008. Chromosome number, karyotype morphology, heterochromatin distribution and nuclear DNA content of some talitroidean amphipods (Crustacea: Gammaridea). European Journal of Entomology 105: 53-58.

These authors report genome size and other genomic phenotypes for 10 species of amphipods in the infraorder Talitrida, which includes family Hyalellidae and family Talitridae. Talitridae includes intertidal, supralitoral, and fully terrestrial species. The cytogenetics of this group of amphipods are poorly understood, with few species receiving significant scientifica attention to date.

Genome size and AT-content were measured by flow cytometry. Cell suspensions were prepared as in Libertini et al. (2000), primarily of either late embryos or pooled internal organs of adults. Genome sizes were larger in more terrestial species. Additionally, two species with the largest genomes in their respective families, that inhabit the high intertidal in the Mediterranean, shifted their habitats inland to fully terrestial in northern locations such as Iceland.

These patterns support the hypothesis applied to other amphibious or terrestrial-colonizing groups such as gastropods and sarcopterygian fishes, that large genome size is a pre-adaptation or associated with other pre-adaptations to terrestrial life. Additionally, the authors associate the harsh terrestrial environment, large genomes, and the harsher environments of higher latitudes, citing in particular Rees et al. (2007) and the discovery of very large amphipod genomes in Arctic environments.

Wilhelm et al. 2003

Wilhelm J, Pingoud A, Hahn M. 2003. Real-time PCR-based method for the estimation of genome sizes. Nucleic Acids Research 31: e56.

These authors describe and demonstrate a new method for genome size estimation, based on real-time PCR (RT-PCR). The RT-PCR process is used to count copies of a target sequence in a sample of genomic DNA of unknown genome size, simultaneously with the amplification of the same sequence in a standard DNA present in the same reaction tube. As with other methods of genome size estimation, the known standard is used to calculate the unknown genome size, though the actual calculation is different from that employed in flow cytometry or Feulgen image analysis densitometry.

Estimation by RT-PCR involves calculation of the unknown genome size by dividing the total mass of genomic DNA by the number of copies of the target sequence as detected by fluorescence during the amplification reactions. Typically, a target sequence that is known to exist one-copy-per-genome is used. The co-prepared standard is used to calibrate fluorescence intensity and copy number.

This method only works if two conditions can be met: a) the absolute copy number of the target sequence in the standard is known and b) the absolute mass concentration of the genomic DNA in the sample can be determined accurately. Both conditions can be met using the absorbance of the sample at 260 nm (UV-260 abs). Protein contamination will prevent accurate readings, and can be detected by determining the absorbance properties of the sample at the full range of wavelengths between 260 and 320 nm. RNA will also interfere with measurements, at it absorbs similarly to DNA at UV wavelengths; it should be removed with an exhaustive treatment of RNAase.

The copy-concentration of the standard can be determined from pure samples by dividing the measured mass of standard DNA by the known fragment size. To ensure accurate calibration, the standard’s sequence should be identical to the target sequence amplified from the unknown; thus the ideal standard is a fragment that contains the RT-PCR “inner primer” sites and is of known fragment length. This can be determined by gel electrophoresis if the primer positions are not already reliably known.

These authors conclude that RT-PCR genome size estimation is accurate, precise, and useful in situations where other techniques are impractical. For example, they state that it can be used on samples that cannot be used in flow cytometry. Though they provide no examples of such situations, I can think of at least one widespread condition: that of specimens preserved in ethanol with destroyed or damaged nuclei but undamaged DNA. These authors make no mention of their method’s relative advantages compared to Feulgen-based methods.

Oren 2004

Oren A. 2004. Prokaryote diversity and taxonomy: current status and future challenges. Philosophical Trans. of the Royal Society of London B 359: 623-638.

This author provides an overview of the current understanding of prokaryote diversity and taxonomy, and discusses recent developments and expected future challenges. The prokaryotes include two of the three Domains of life (Bacteria and Archaea), and their importance in global ecosystems includes astronomical numbers of cells and perhaps as much Carbon as all plants.

Species concepts in Prokaryotes are difficult, and tend to be pragmatic rather than based solidly in theory. Current concepts favour the use of DNA-DNA reassociation, with a 70% similarity cut-off for species identification, combined with 16s rDNA sequences and chemo-phenotypic markers. Higher taxonomic levels are based entirely on subjective decisions, as no clear guidelines for delineating genera, families, orders et cetera exist. However, the problem of horizontal gene transmission is mostly ignorable because species concepts are based on whole-genome properties, not the properties of individual genes. Additionally, a kind of taxonomic “do-over” in 1980 erased the problem of synonyms, by publishing a list of 100% of the known described prokaryotic species, with one name each.

Official recognition of a prokaryotic species is based on depositing viable cultures in two countries, which makes it impossible to officially recognize any species that cannot be cultured. The vast majority of predicted “candidatus” species cannot currently be cultured, though some interesting breakthroughs with marine pelagic forms have recently been made.

Prokaryotic diversity can be sampled in nature using mass sequencing of 16s rDNA. This approach leads to the above estimate of huge numbers of uncultured species, but because 16s rDNA is not fully congruent with whole-genome measures of species identification, cannot be used on its own to identify species. The inability of researchers to cultivate more than a few percent of predicted species is known as the “Great Plate Count Anomaly” (Staley and Konopka, 1985). Extreme estimates for total global prokaryotic species diversity run to billions, based on both soil samples and the observation that prokaryote species numbers probably climb steadily over time because they have enormous populations, ready dispersal, rapid reproduction, and excellent survival of adverse conditions. Thus, in prokaryotes speciation is probably easy and extinction is probably hard.

Little is know about prokaryotic biogeography, and questions of endemicity have hardly been asked. However, no species has yet been identified from both the Arctic and Antarctic, suggesting a possibility of endemicity at that scale.

Until recently, it was apparently widely thought that while we knew little about species, we knew a great deal about the contributions of prokaryotes to global nutrient cycles. Recent novel discoveries of widepread and important biogeochemical processes indicates this is not so. It has been suggested that all thermodynamically favourable chemical reactions may be exploited by some organism, somewhere on Earth.

No prokaryote is considered “endangered”, but a few species are on lists for eradiction, such as the causative agent of leprosy. Other species are probably realistically endangered, as they are obligate symbionts of (for example) endangered species of animals and plants.


The author concludes with a call for better understanding of the issues facing microbiologists today, especially the vast, unexplored numbers of species, and the generally poor funding situation for microbiological research. Ongoing developments in molecular technologies suggest great promise for future work.

Lee and Ó Foighil 2002

Lee T, Ó Foighil D. 2002. 6-Phosphogluconate dehydrogenase (PGD) allele phylogeny is incongruent with a recent origin of polyploidization in some North American Sphaeriidae (Mollusca, Bivalvia). Molecular Phylogenetics and Evolution 25: 112-124.

These authors produced a phylogeny for seven species in three genera in the freshwater clam family Sphaeriidae. These clams have high and variable chromosome numbers, with previous studies suggesting a majority of species polyploid up to 13n (e.g. Lee, 1999). The earliest fossils from the family are found in Cretaceous freshwater deposits, with some genera appearing in the Miocene.

Allopolyploids, derived by hybridization between relatively interfertile (segmental allopolyploidy) or nearly intersterile (genomic allopolyploidy) cause reticulations in phylogenies. Phylogenies based on mtDNA (as exist for this family: Cooley and Ó Foighil, 2000) will not capture such reticulations because of the uniparental inheritance of mtDNA. Nuclear markers, on the other hand, may show a wide range of fates after a duplication event, including gene silencing, homogenization, or independent evolution and differentiation. This variation makes some nuclear markers difficult to analyze in the context of ancient polyploidy.

These authors chose to construct a phylogeny based on a single nuclear gene, using c-DNA to examine only expressed alleles. They found many alleles for this gene in two major clades in the three genera examined. Clade A was widespread and common, while Clade B was not found at all in several species and had fewer alleles in fewer individuals where it was found. Why this imbalance should appear is difficult to state with great certainty. The authors suggest the most likely explanation is that more Clade B alleles have been lost through psuedogenization and / or recombination, though they also acknowledge the possibility, considered by them less likely, that their primer set was biased towards amplification of Clade A alleles. This is considered less likely because some B alleles were detected, such that any bias must be considerably less than 100% effective.

Overall, while the family-level tree does provide evidence of an allopolyploidization event predating the divergence of the three genera, at least some of the more recently-derived lineages experienced duplication events not reflected in this phylogeny. Further examination of the alleles of this gene in more members of this ecologically important family are required to elucidate the history of genomic and genetic events.

One outgroup species came from Cuba, and was preserved and shipped in a solution containing “TRI Reagent (Molecular Research Center)”. This reagent was also used in RNA extraction procedures for all species. I am unfamiliar with this reagent, though its possible use as a tissue preservative that appears to preserve chromatin as well as RNA is very interesting.

Shine 2005

Shine R. 2005. Life-history evolution in reptiles. Annual Review of Ecology, Evolution and Systematics 36: 23-46.

This author reviews the diversity of life-history traits in reptiles, focusing on how the ablity of reptiles to behaviourally regulate body temperature combined with their freedom from heat-flow and energy-conserving constraints have shaped reptile evolution.

Large body size, dessication resistance, terrestrial living, and ectothermy allow reptiles to respond to a broad range of environmental variables (especially climate related) at multiple time scales. Changes to clutch size, offspring size, offspring growth rate, body size, body shape, hunting style, fat storage, dietary specialization, and many other traits can be driven rapidly by climate factors in reptiles.

Pip 1992

Pip E. 1992. The ecology of subarctic molluscs in the lower Nelson river system, Manitoba, Canada. Journal of Molluscan Studies 58: 121-126.

This author studied the gastropods found at 18 sites along the Nelson river and its tributaries. Total diversity was 13 species, with maximum species richness at a site 10 species and the mean close to four. The single most common species was an apparent hybrid between Gyraulus parvus and G. circumstriatus, based on shell morphology. An earlier work based on incidental collections also found high abundance of this putative hybrid (Clarke, 1973).

Gastropods were collected by scooping macrophytes into plastic bags. Several species showed significant correlations (positive or negative) with some species of macrophytes. Most species appear to overwinter as subadults, and show a semelparous life history, common among freshwater pulmonates (Hunter, 1975; Calow, 1978). Oviposition and gonad development are influenced by minimum temperature in some species (e.g. Van der Schalie and Berry, 1973), though it is not known if local adaptation of this trait has occurred (i.e. lower minimum temperatures in northern Manitoba than southern Canada). This author does not state how species of either gastropods or macrophytes were identified.

In general, the large hydroelectric dams on the Nelson river had a strong negative effect on the structure of ecosystems. Other studies by this author and coworkers examine the water chemistry and macrophyte assemblages of this river.

Danks 1993

Danks HV. 1993. Patterns of diversity in the Canadian insect fauna. Memoirs of the Entomological Society of Canada 165: 51-74.

This author reviews primarily occurrence data for the insects and a few other arthropods of Canada, with a focus on patterns associated with continent-scale variation, especially climate. There are a few deficiencies in the available dataset, including the absence of full taxonomic treatments for many groups, the inability of collections to distinguish between residents and visitors in regions, and varying levels of collecting effort across regions.

The author analyses geographic patterns of reported species in association with estimates and methods of estimating undescribed species abundance. Collection effort in northern Canada is considered probably adequate, despite the logistical difficulties, primarily due to the Northern Insect Survey (reviewed by Danks, 1981). Overall, Canada’s insect fauna is well enough described to permit analysis of regional variation and comparisons between regions.

At the broadest latitudinal and taxonomic scales, some insect orders are overrepresented in the North, while others are underrepresented. In particular, diversity of Orthoptera, Hemiptera, and Coleoptera are reduced in the North, and diversity of Diptera is increased. There are probably more species of Diptera and of Hymenoptera in Canada than species of Coleoptera. These observations lead to questions about why some groups, at multiple taxonomic levels, are overrepresented in the Arctic.

Biogeographic zones in this paper are based on vegetation types. In the arctic, this includes the presence or absence of prostrate shrubs; High Arctic islands such as Bathurst lack these shrubs. While the majority of insect species show fairly consistent boundaries of their geographic ranges, there are many exceptions, and the lines drawn on a map (e.g. Fig. 2) should not be considered as hard and precise as they may appear. Many factors, both biotic and abiotic, change gradually across the landscape, and the occurrence or absence of a species may be a reflection of where its individual requirements are or are not met; these individual requirements probably vary considerably between species, thus absent sharp boundaries (e.g. ocean) many species distributions probably do not overlap completely.

Some Arctic species of insects do not occur on the mainland, suggesting a role for theories of Island Biogeography in structuring the biotas of Canada’s Arctic archipelago, even against the very strong pattern of decreasing diversity with latitude. Diversity is generally higher in the West of Canada; this is especially true north of 60°N. Local diversity may be strongly driven by small patches of favourable habitat, especially in the polar deserts, where these patches may be represented by rare clumps of vegetation surrounded by bare sediment. Most Arctic and Boreal insect species appear to respond to habitat variation individually, not as communities.

The biota of Canada is strongly influenced by the recent history of Pleistocene glaciations. The retreat of the glaciers was not a simple northward progression (Matthews, 1979). The expansion of populations out of glacial refugia varied, particularly with latitude. While Beringian forms were able to expand Eastward (partly driven by prevailing winds), southern populations appear to have been extirpated as local conditions warmed but the areal extent of the ice sheets did not decrease immediately. Much of the evidence for this pattern comes from fossils and sub-fossils of Pleistocene beetles (Schwert and Ashworth, 1988).

The concept of “distributional equilibrium” was introduced by Clarke (1973) in describing and analysing patterns of freshwater mollusc distributions in the Canadian Interior Basin. In that study, approximately 26% of species had achieved full realization of their estimated geographic range. This author suggests that insufficient data are available for a similar analysis of insects, though there are some interesting patterns in insect diversity.

Northern ecosystems may be incomplete and relatively less integrated compared to more southerly systems. This author defines an incomplete ecosystem as one where “…litter accumulates because it is too cold for complete decomposition, where many plants are not seriously attacked by insect herbivores because herbivores are rare, where many sites have not yet been colonized following disturbance (of various scales and frequencies), where large segments of the year and even of the day are unsuitable for activity, and so on.” (Danks, 1993, pg 71). There is apparently insufficient evidence available to state that any particular region qualifies as “incomplete” under these loose criteria, but several studies are suggestive in this direction. This author does not discuss the possibility of ecological release for (some) Arctic vascular plants, though tables 9 and 10 suggest that Arctic herbivorous insects may be under twin constraints. They seem to be more strongly impacted by climate than their plant hosts (table 9), and under relatively strong pressure from parasitoid hymenoptera (table 10).

There is also an indirect suggestion in this paper in favour of the “exclusion” hypothesis of my PhD thesis: overrepresented groups of insects in the Arctic appear to be exapted for Arctic life by family- or subfamily-level traits. For example, butterflies are relatively more diverse in the Arctic than in temperate zones (esp. superfamily Papilionoidea), and have day-active adults and desiccation resistant large-bodied larvae. Both of these traits are especially valuable in the Arctic because of the absence of suitable night-time conditions (cool nights or 24-hour days), and the large areas of dry polar desert.

The author concludes with recommendations that future surveys of the fauna of Canada focus on example regions such that the hypothesis of incomplete ecosystems may be tested, and that the relative roles of biotic vs. abiotic factors in structuring biodiversity may be examined.

Friday, March 14, 2008

Conlan and Kvitek 2005

Conlan KE, Kvitek RG. 2005. Recolonization of soft-sediment ice scours on an exposed Arctic coast. Marine Ecology Progress Series 286: 21-42.

These authors monitored the occurrence, aging, and biotic recolonization of ice scours in the Barrow Strait near Resolute, Nunavut. Ice structures with deep keels, such as icebergs locked in pack ice, can scour the soft bottom even at depths approaching 100m. Scours can be 10 to 15 meters deep, hundreds of meters wide, and kilometers long, though many are smaller than that. A scour forms a characteristic geomorphology, with a deep trough that may include multiple parallel sub-troughs, bordered by berms that may be 4-5m tall relative to unscoured adjacent seabed. The benthos of Barrow Strait is hard-packed clay armored with cobble, a glacial till that lies about 5m thick above the bedrock.

Ice scours remove the cobble, and the berms are much softer than either the troughs or adjacent unscoured seabed. These authors, and a large crew of assistants, sampled the macroinvertebrates of the seabed by cores collected by SCUBA. The faunal analysis was by seiving the samples, fixing specimens in 4% Formalin and preserving them in 70% Ethanol. Most specimens were identified to family or genus, but a large sample of collected polychaetes were sent to experts in Ottawa for species-level identification. Faunal composition was compared across scours, troughs and berms, unscoured seabed, and scours of various ages, monitored over a 9-year period.

Biotically, the examined portion of the Barrow Strait constitues “urchin barrens”. Sea urchins, primarily Strongelocentrotus droebachiensis and S. pallidus, are present in high density and graze on most other epibenthic and shallow-infaunal invertebrates as well as consuming most of the available algae. The invasion by urchins may be recent, as suggested by the presence of Balanus crenatus only in areas where urchins are absent, but crushed shells of this barnacle in many areas. Other macroinvertebrates found included brittle stars, gastropods, soft corals, anenomes, sea cucumbers, etc, as well as several species of bottom dwelling fishes.

In general, the authors found a pattern of biodiversity consistent with the intermediate-disturbance hypothesis. Total species richness and biomass were both higher in areas of scours compared to unscoured areas. A patch of seabed protected from most scours behind a large berm had lower total diversity. No suite of climax species was found in any undisturbed area. One species of polychaete was found only in relatively young scours, but all other species occurred in all habitats, though relative abundances varied. This pattern suggests that ice scours and their associated habitat variation may be maintaining relatively high biodiversity in this region.

Ice scours occur with a frequency of about 1.1 events per kilometer per year, similar to some other ice-scoured habitats in other polar regions. This rate may either increase or decrease with climate warming. Warmer temperatures may increase the rate of iceberg calving, increasing the supply of deep-keel ice structures. Alternately, warmer temperatures may reduce the thickness, strength, or movements of winter pack ice and associated scouring structures.

Selker 1997

Selker EU. 1997. Epigenetic phenomena in filamentous fung: useful paradigms or repeat-induced confusion? Trends in Genetics 13: 296-301.

This author reviews point mutations, methylation, and other mechanisms of gene silencing in two common model fungi, Neurospora and Ascobolus. Repeat induced point mutation (RIP) acts in Neurospora, and causes GC to AT transitions in both copies of duplicate genes, and a low level of CpG methylation in both copies. Methylation induced meiotically (MIP) acts in Ascobolus, and causes methylation without point mutation, again in both copies of duplicate genes. Both processes detect larger sequences and tandem duplications more reliably.

Methylation reduces gene expression by interfering with transcription elongation, not transcription initiation as previously suggested.

There are two components to methylation: de novo methylation of previously unmethylated sites, and maintenance of methylation through DNA replication. Maintenance may be carried out primarily by a system that preferentially methylates hemimethylated CpG sites, as are generated during DNA replication, but other mechanisms must also occur to account for a set of observations other maintenance patterns. The mechanism of de novo methylation was apparently not understood in 1997; I do not know if that situation has changed.
The author describes the phenomenon termed “quelling”, in which transformed DNA in some fungi causes gene silencing of homologous genes; I suspect this is one of the observations that led to the discovery of RNA interference (RNAi), as the author describes further evidence that quelling is caused by some factor that diffuses from the nucleus to the cytoplasm.


The author also describes transvection, in which loci that do not occur in allelic positions on chromosomes have reduced expression. I do not know how widespread this phenomenon is, or if a mechanism has been proposed since 1997.All of these epigenetic processes are considered to function in cells as defenses against transposable elements, as they all would reduce expression (and, in the case of RIP, inheritance) of actively-transposing sequences. RIP and MIP act on very large duplications, up to the scale of chromosome rearrangements; thus they preserve chromosome structure at a range of scales.

Leitch and Bennett 1997

Leitch IJ, Bennett MD. 1997. Polyploidy in angiosperms. Trends in Plant Science 2: 470-476.

These authors reviewed the occurrence and patterns of polyploidy in angiosperms. The majority of “higher plants” apparently have polyploid ancestry, some quite recently reverted to diploid. Most polyploid plants appear to be allopolyploids, derived by hybridization. Allopolyploidy presents the possibility of multiple origins of hybrid polyploid taxa, which has been identified in a few species.

The evolution of duplicated genes is discussed, with an interesting section on homology-dependent gene silencing. This is a phenomenon possibly mediated by repeat-induced changes to chromatin structure, in which some copies within a gene family are silenced or their expression altered.

Pulido and Berthold 2004

Pulido F, Berthold P. 2004. Microevolutionary response to climatic change. Advances in Ecological Research 35: 151-183.

These authors summarize and examine the available empirical evidence for adaptive responses to climate change in birds. Birds are a well studied group in this context, for a variety of reasons. Previous reviews had focused on theoretical considerations, and the likelyhood and rates of adaptive evolution in response to climate change, primarily because of a general paucity of empirical data on the subject.

A few examples of phenotypic change in bird populations have been found associated with either climate change (e.g. shift in breeding dates) or with rare extreme weather events. The authors caution that a response to selection cannot be inferred simply from a phenotypic change, as more variables must be measured and / or controlled for, particularly regarding the possibility of change driven by phenotypic plasticity. At the other extreme, some studies have suggested a change driven solely by plasticity but did not provide sufficient evidence to justify that claim.In general, short-term adaptive responses may or may not be indicative of longer-term trends, as phenotypic change can occur over multiple ecological and evolutionary time scales. Some instances of very rapid adaptation are unlikely to represent long-term trends, as they are responses to inherently limited environmental changes or to temporary conditions of population genetics.

Monday, March 10, 2008

Hijmans et al. 2005

Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A. 2005. Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology 25: 1965-1978.

These authors describe the release of the WorldClim database, which includes data on several climate variables for a very large number of grid squares on land surfaces on Earth. Each grid square is 30 arc-seconds across, thus at the equator these squares are 0.816 square kilometers, and smaller (finer resolution) at higher latitudes.

Data for this database come primarily from weather stations located worldwide. Altitude was estimated from a Shuttle radar mission, for all latitudes south of 60°N, and excluding Antarctica. Each grid square’s climate was estimated by a complex interpolation algorithm that is analagous to regression: it fits a continuous surface to the points, but does not necessarily go through each point.

The authors describe some of the potential sources of error in the dataset, and urge higher quality data for future updates, for example by confirmation of precise locations for weather stations, and greater standardization in weather station record-keeping and reporting.

The database can be downloaded in a variety of formats from http://www.worldclim.org/. Most files are designed for use with GIS programs. A range of biologically meaningful data (maximum and minimum temperatures per year, seasonality) have been made available as well.

Foote et al. 2007

Foote M, Crampton JS, Beu AG, Marshall BA, Cooper RA, Maxwell PA, Matcham I. 2007. Rise and fall of species occupancy in Cenozoic fossil mollusks. Science 318: 1131-1134.

These authors examined a large dataset of species occurences in marine / shelf fossil molluscs in New Zealand, to infer patterns of geographic range and species occupancy. These data relate to hypotheses about extinction risk associated with the size of a species’ geographic range, and the rate of decline of species in ecological to geological time scales. Occupancy was defined here as the proportion of collections in a given interval in which a given species occurs.

The majority of species studied showed a steady increase in occupancy, followed by a long decrease and eventual extinction. Other possibilities, including rapid expansion and rapid decline (truncation) were not found very often, though some species did show such patterns. These results generally support the hypothesis that large geographic ranges are associated with longer species durations and reduced extinction risk, but do not support the hypothesis that species achieve maximal geographic range shortly after speciation. Additionally, the importance of incumbancy was not supported, under which species or higher taxa survive for long periods in the face of apparently superior competitors.

The authors suggest that different processes may control occupancy over ecological versus geological time scales. Competition and dispersal may be very important over ecological scales, but geological processes such as sea-level change and tectonic activity may be more important over longer time scales.

Monday, March 3, 2008

Arif et al. 2007

Arif S, Adams DC, Wicknick JA. 2007. Bioclimatic modelling, morphology, and behaviour reveal alternative mechanisms regulating the distributions of two parapatric salamander species. Evolutionary Ecology Research 9: 843-854.

These authors examined the factors responsible for shaping the geographic ranges of two species of salamanders in the genus Plethodon. One species is broadly distributed in eastern North America (including Guelph), the other occurs only on a group of mountain peaks in western Virginia. The primary working hypothesis was that the more restricted species is so restricted partly by competitive interactions with its congener, that is it cannot expand to lower elevations because it cannot outcompete the other, and is persists in its home range mainly via the congener’s intolerance of local abiotic conditions.

This hypothesis was tested by collecting data on diet, local distribution, head morphology, agonistic behaviour, and climate factors for both species in the region where the very localized species lives. Diet was examined by stomach contents of previously-collected specimens; no difference was found, suggesting these species are not applying pressure to each other by exploitative competition. Local distribution included measurements of parameters in 18 sites, two where both species occur (sympatry), and eight sites for each species where it occurs alone (allopatry). I suppose that taken together, at a larger spatial scale, this site distribution qualifies as parapatric. Head morphology was measured for each site, and analysed by PCA. The two species differ consistently and significantly in head shape, but the sympatric populations are not more or less divergent from each other than expected by chance, implying no character displacement for these traits. Behaviour was measured by a series of encounter trials, in which individual males from allopatric populations were allowed to interact as either “residents” or “intruders”. The highly-restricted species was found, perhaps surprisingly, to behaviourally dominate the more cosmopolitan species, suggesting any competitive exclusion that may be occurring is driven in the opposite direction to the initial prediction.

Climate data came from the WORLDCLIM data set (Hijmans et al. 2005). There was high congruence between the predicted ranges of these species through modelling and the actual observed ranges, with some exceptions – the models predicted some species occurrences where they do not occur, on the other side of obvious geographic barriers such as rivers.

The main conclusion of this paper is that the very restricted range size of one species is apparently constrained by abiotic climate factors, not by competitive exclusion or similar processes. In contrast, the absence of the more cosmopolitan species from these mountain tops is apparently driven more by interspecific interactions than by abiotic factors, a situation precisely opposite that predicted by the initial hypothesis. Additionally, these authors suggest that the differences in morphology may be indicative of local adaptation, but further refinement of those data will be required to test such hypotheses.