Liptzin D. 2006. A banded vegetation pattern in a High Arctic community on Axel Heiberg Island, Nunavut, Canada. Arctic, Antarctic, and Alpine Research 38: 216-223.
This author attempted to explain the observation of banded vegetation on a slope that lacked the usual factors that generate such patterns. In temperate and tropical locations, banded vegetation, also known as “tiger stripes”, forms on shallow slopes in dry areas with a consistent direction of water flow. Plants at a position on the slope increase water retention and facilitate further colonization by plants. Similarly, some locations experience consistent wind direction carrying sea spray that kills trees at some positions. In cold environments, patterned ground from cryoturbation on shallow slopes can also lead to banded vegetation. However, the study site in this paper lacks all of these features, including cryoturbation despite the presence of permafrost within 50cm at most locations.
Some aspect of soil properties is the obvious explanatory hypothesis, which this author explores after describing the transects measuring plant diversity and the soil pits used to examine soil properties. In general, features that would normally be expected to influence plant diversity and abundance such as soil moisture or exchangeable cation levels, had no significant impact in the various statistical tests employed in this study. However, soil type did have some effect, as a few species of plants were found only on sandy soil, and nitrogen levels were negatively correlated with species richness.
The discussion section of this paper is an excellent example of a chain of logical reasoning working through a series of potential explanations. While this paper is interesting, it’s only relevant to my own studies in a narrow area around potential starting points in looking for explanations for whatever patterns I may find in my biogeography studies in 2010. However, this paper seems remarkably suitable as an introduction to the basics of modern soil science research, and may be relevant to my not-quite-mothballed interest in an undergraduate course about the current state of the scientific literature.
Showing posts with label Biogeography. Show all posts
Showing posts with label Biogeography. Show all posts
Friday, February 19, 2010
Thursday, November 12, 2009
Nemergut et al. 2007
Nemergut DR, Anderson SP, Cleveland CC, Martin AP, Miller AE, Seimon A, Schmidt SK. 2007. Microbial community succession in an unvegetated, recently deglaciated soil. Microbial Ecology 53: 110-122.
These authors describe the partly-predictable patterns of succession among the soil microbes of a glacial foreland in Peru. Primary succession on new terrain, as found in front of a receding glacier, has been studied to some extent, especially regarding the vegetation. Studies of the microbial communities have been rarer, but the few that have been conducted have suggested that these communities also show predictable patterns of community assembly and turnover associated with soil age. Basic ecological theory has led to the nitrogen paradigm of primary succession in soils: nitrogen is absent from new mineral substrate, thus nitrogen fixing organisms have a competitive advantage and are therefore abundant. The presence of nitrogen fixers is tightly linked to the accumulation of soil nitrogen; hence these organisms may facilitate later successional stages.
The study site in this paper is in Peru, at a glacier that seems to be receding quickly. These authors sampled from 3 transects arranged parallel to the front of the glacier, located adjacent to the glacier on soil less than a year old, 100m away on soil about 4 years old, and 500m away on soil about 20 years old. This area receives very high inputs of pollen, leading to the hypothesis that heterotrophic, nitrogen-fixing organisms may be present, using the pollen as a carbon source but drawing nitrogen from the atmosphere because the C:N ratio of pollen is higher than that of microbial biomass. Surface soil samples were collected, kept at 0C, and analyzed in Colorado. Much of the analyses were detailed phylogenetic examination, including the P-test of Martin (2002); note that he is one of the authors of this paper. OTU and a range of sequence-data fine-tuning techniques were also employed.
Over the study area, autotrophic nitrogen fixers were abundant. The bacteria found were extremely diverse at the highest taxonomic levels, and many sequences identified were not closely related to existing sequences in public databases. Diversity increased rapidly from the youngest soils to the 4-year-old, then plateaued.
One very interesting group of bacteria found are the Comamodaceae; sequences reported in other studies were in many cases derived from glacial or ice-sheet ice. The Comamodaceae found in the youngest soils here may have persisted as viable populations in the glacier; differences between the two closely-examined youngest communities suggest physical and genetic isolation for hundreds to thousands of years, allowing speciation events to accumulate differences.
Other patterns among the sequences identified suggest that the earliest colonizers of new terrain may be cosmopolitan – some of the Comamodaceae sequences, for example, are similar to those derived from a glacier in Nunavut. Later colonizers may be more endemic, and displace the earliest colonizers as soils age. The trophic status of the first colonizers is not clear; these authors did not have a test for definite autotrophs or heterotrophs, as Comamodaceae are known to include both modes. At the macrobiological level, the earliest arrivals on new terrain are typically heterotrophs, insects that feed on deposited organic matter such as wind-blown pollen.
This paper is very useful to me, describing as it does a complete set of analytical procedures for my planned biogeographic / phylogenetic studies, as well as providing data in the form of publicly-accessible sequences and analyzed information on patterns of soil microbial community assembly.
These authors describe the partly-predictable patterns of succession among the soil microbes of a glacial foreland in Peru. Primary succession on new terrain, as found in front of a receding glacier, has been studied to some extent, especially regarding the vegetation. Studies of the microbial communities have been rarer, but the few that have been conducted have suggested that these communities also show predictable patterns of community assembly and turnover associated with soil age. Basic ecological theory has led to the nitrogen paradigm of primary succession in soils: nitrogen is absent from new mineral substrate, thus nitrogen fixing organisms have a competitive advantage and are therefore abundant. The presence of nitrogen fixers is tightly linked to the accumulation of soil nitrogen; hence these organisms may facilitate later successional stages.
The study site in this paper is in Peru, at a glacier that seems to be receding quickly. These authors sampled from 3 transects arranged parallel to the front of the glacier, located adjacent to the glacier on soil less than a year old, 100m away on soil about 4 years old, and 500m away on soil about 20 years old. This area receives very high inputs of pollen, leading to the hypothesis that heterotrophic, nitrogen-fixing organisms may be present, using the pollen as a carbon source but drawing nitrogen from the atmosphere because the C:N ratio of pollen is higher than that of microbial biomass. Surface soil samples were collected, kept at 0C, and analyzed in Colorado. Much of the analyses were detailed phylogenetic examination, including the P-test of Martin (2002); note that he is one of the authors of this paper. OTU and a range of sequence-data fine-tuning techniques were also employed.
Over the study area, autotrophic nitrogen fixers were abundant. The bacteria found were extremely diverse at the highest taxonomic levels, and many sequences identified were not closely related to existing sequences in public databases. Diversity increased rapidly from the youngest soils to the 4-year-old, then plateaued.
One very interesting group of bacteria found are the Comamodaceae; sequences reported in other studies were in many cases derived from glacial or ice-sheet ice. The Comamodaceae found in the youngest soils here may have persisted as viable populations in the glacier; differences between the two closely-examined youngest communities suggest physical and genetic isolation for hundreds to thousands of years, allowing speciation events to accumulate differences.
Other patterns among the sequences identified suggest that the earliest colonizers of new terrain may be cosmopolitan – some of the Comamodaceae sequences, for example, are similar to those derived from a glacier in Nunavut. Later colonizers may be more endemic, and displace the earliest colonizers as soils age. The trophic status of the first colonizers is not clear; these authors did not have a test for definite autotrophs or heterotrophs, as Comamodaceae are known to include both modes. At the macrobiological level, the earliest arrivals on new terrain are typically heterotrophs, insects that feed on deposited organic matter such as wind-blown pollen.
This paper is very useful to me, describing as it does a complete set of analytical procedures for my planned biogeographic / phylogenetic studies, as well as providing data in the form of publicly-accessible sequences and analyzed information on patterns of soil microbial community assembly.
Monday, November 2, 2009
Jones and Henry 2003
Jones GA, Henry GHR. 2003. Primary plant succession on recently deglaciated terrain in the Canadian High Arctic. Journal of Biogeography 30: 277-296.
These authors examined five glacial foregrounds on Ellesmere Island, one intensively and the other 4 “extensively”, to determine patterns of succession among plant communities on sterile ground. The ecological literature recognizes several different modes of succession, including a categorization by Henry and Svoboda (1987) based on the relative strengths of biotic and abiotic factors. This model of succession recognizes 3 modes; directional succession with species replacement, directional succession without species replacement, and non-directional succession without replacement. They are arranged in increasing importance of abiotic factors, referred to here as “environmental resistance”, which operates in opposition to “biological driving forces”.
In temperate regions, where much of the relevant ecological theory has been developed, biotic factors are mainly competition. In the High Arctic, a successional pattern consistent with directional-with-replacement was found, demonstrating that this can occur even in environments with obviously severe abiotic factors. However, these authors argue that the biotic factor driving this succession was probably not competition, because total plant cover remains below 10% by area even at the fourth stage recognized here, and species richness is always very low. The polar oasis landscape with 80-100% plant cover was never reached within the approximately 50-year old glacial forelands examined by these authors, though it is likely that competition is important in that “stage 5” level of High Arctic succession.
Other biotic variables suggested playing a role in successional dynamics in the High Arctic included facilitation and life-history characteristics. These factors are not independent; later successional species such as Salix arctica appear not to be able to establish until soil fertility has been improved by mats of very-early-colonizing mosses, and are long-lived, slow-growing species that contribute little to the early seed bank and seed rain. Thus, multiple plant and environmental characteristics appear to interact when structuring early communities.
I read this paper to try to gain some understanding of ecological succession and the role of time-since-deglaciation among the ecosystems of Alexandra Fjord. Rather than being distinct successional stages in sequence as I had previously supposed, it appears the various lowland ecosystems are all of a similar age, and have different vegetation communities as a result of other factors besides simply relative proximity to the Twin Glacier. Dryas integrefolia and Cassiope tetragona were important parts of this study, and both appear in stage 4, after primary-colonizing mosses, and early-colonizing forbs such as Papaver radicatum and early-colonizing deciduous shrubs like Saxifraga spp. Both Dryas and Cassiope form associations with mycorrhyzal fungi, a requirement that may slow their colonization of novel habitats; earlier-spreading plants do not form these associations, and instead may be limited by seed dispersal.
This was helpful in organizing the structure of the manuscript I am currently working on, which will describe some of the soil biotic communities both in the Alexandra Fjord lowlands and in the adjacent polar desert. It is not a simple story of succession from one ecosystem to the next, but succession does play a role.
These authors examined five glacial foregrounds on Ellesmere Island, one intensively and the other 4 “extensively”, to determine patterns of succession among plant communities on sterile ground. The ecological literature recognizes several different modes of succession, including a categorization by Henry and Svoboda (1987) based on the relative strengths of biotic and abiotic factors. This model of succession recognizes 3 modes; directional succession with species replacement, directional succession without species replacement, and non-directional succession without replacement. They are arranged in increasing importance of abiotic factors, referred to here as “environmental resistance”, which operates in opposition to “biological driving forces”.
In temperate regions, where much of the relevant ecological theory has been developed, biotic factors are mainly competition. In the High Arctic, a successional pattern consistent with directional-with-replacement was found, demonstrating that this can occur even in environments with obviously severe abiotic factors. However, these authors argue that the biotic factor driving this succession was probably not competition, because total plant cover remains below 10% by area even at the fourth stage recognized here, and species richness is always very low. The polar oasis landscape with 80-100% plant cover was never reached within the approximately 50-year old glacial forelands examined by these authors, though it is likely that competition is important in that “stage 5” level of High Arctic succession.
Other biotic variables suggested playing a role in successional dynamics in the High Arctic included facilitation and life-history characteristics. These factors are not independent; later successional species such as Salix arctica appear not to be able to establish until soil fertility has been improved by mats of very-early-colonizing mosses, and are long-lived, slow-growing species that contribute little to the early seed bank and seed rain. Thus, multiple plant and environmental characteristics appear to interact when structuring early communities.
I read this paper to try to gain some understanding of ecological succession and the role of time-since-deglaciation among the ecosystems of Alexandra Fjord. Rather than being distinct successional stages in sequence as I had previously supposed, it appears the various lowland ecosystems are all of a similar age, and have different vegetation communities as a result of other factors besides simply relative proximity to the Twin Glacier. Dryas integrefolia and Cassiope tetragona were important parts of this study, and both appear in stage 4, after primary-colonizing mosses, and early-colonizing forbs such as Papaver radicatum and early-colonizing deciduous shrubs like Saxifraga spp. Both Dryas and Cassiope form associations with mycorrhyzal fungi, a requirement that may slow their colonization of novel habitats; earlier-spreading plants do not form these associations, and instead may be limited by seed dispersal.
This was helpful in organizing the structure of the manuscript I am currently working on, which will describe some of the soil biotic communities both in the Alexandra Fjord lowlands and in the adjacent polar desert. It is not a simple story of succession from one ecosystem to the next, but succession does play a role.
Tuesday, October 6, 2009
Bohannan and Hughes 2003
Bohannan BJM, Hughes J. 2003. New approaches to analyzing microbial biodiversity data. Current Opinion in Microbiology. 6: 282-287.
These authors review the use of three broad approaches to studying microbial biodiversity in environments. The three are 1) parametric, 2) nonparametric, and 3) community phylogenetics. Each has advantages and disadvantages, and these authors suggest a combined approach may be most beneficial. Both 1) and 2) are based on Operational Taxonomic Units, to avoid the many problems of bacterial species identification, while 3) is based on molecular phylogenies, typically 16s rDNA.
Parametric approaches make simplifying assumptions and are based on some model of species richness in microbial communities; often this model is log-normal, in which some taxa are rare, some are abundant, and most are intermediate. These approaches extrapolate from patterns in a sample to the total environment. The obvious downside to parametric approaches is the vulnerability of the model to incorrect and difficult to test assumptions.
Nonparametric approaches avoid assuming any model, and instead are typically built on an approach analogous to mark-release-recapture. Sequences encountered more than once in a sample are recaptures, and the frequency of these doubletons is assumed to be related to how many unique sequences are present: more doubletons means fewer total sequences. As a downside, these approaches provide only a lower limit to actual richness, thus generally underestimating total diversity.
Community phylogenetics approaches avoid the OTU concept and thereby preserve useful data in the form of genetic information about sequences and sequence relationships. The downside of community phylogenetics approaches is they sample a clone library derived from the environment, not the environment directly, and can therefore not extrapolate from the sample to the environment.
This paper provides several useful examples of each approach, and supports the utility of Martin’s (2002) combined approach, which is what I would like to apply to my data to be collected in 2010. Figure 3 in this paper, for example, provides a useful overview of what Martin (2002) did, and how to make inferences about observed patterns.
These authors review the use of three broad approaches to studying microbial biodiversity in environments. The three are 1) parametric, 2) nonparametric, and 3) community phylogenetics. Each has advantages and disadvantages, and these authors suggest a combined approach may be most beneficial. Both 1) and 2) are based on Operational Taxonomic Units, to avoid the many problems of bacterial species identification, while 3) is based on molecular phylogenies, typically 16s rDNA.
Parametric approaches make simplifying assumptions and are based on some model of species richness in microbial communities; often this model is log-normal, in which some taxa are rare, some are abundant, and most are intermediate. These approaches extrapolate from patterns in a sample to the total environment. The obvious downside to parametric approaches is the vulnerability of the model to incorrect and difficult to test assumptions.
Nonparametric approaches avoid assuming any model, and instead are typically built on an approach analogous to mark-release-recapture. Sequences encountered more than once in a sample are recaptures, and the frequency of these doubletons is assumed to be related to how many unique sequences are present: more doubletons means fewer total sequences. As a downside, these approaches provide only a lower limit to actual richness, thus generally underestimating total diversity.
Community phylogenetics approaches avoid the OTU concept and thereby preserve useful data in the form of genetic information about sequences and sequence relationships. The downside of community phylogenetics approaches is they sample a clone library derived from the environment, not the environment directly, and can therefore not extrapolate from the sample to the environment.
This paper provides several useful examples of each approach, and supports the utility of Martin’s (2002) combined approach, which is what I would like to apply to my data to be collected in 2010. Figure 3 in this paper, for example, provides a useful overview of what Martin (2002) did, and how to make inferences about observed patterns.
Cockell and Stokes 2004
Cockell CS, Stokes MD. 2004. Widespread colonization by polar hypoliths. Nature 431: 414.
These authors present a short report about the colonization of the undersides of rocks in the polar deserts by cyanobacteria and unicellular green algae. Where rocks have a protected but accessible underside, these organisms colonize, forming a pale green band a few centimetres across, between the part of the rock too exposed and dry, and too dark for photosynthesis. In polygon terrain, where the ground is sorted by frost heave (“periglacial processes”) and even large rocks are periodically jostled, areas of finer texture form in the centers of polygons, with larger rocks around the edges. The edge rocks were 100% colonized, while central areas were 5% colonized.
These authors present a short report about the colonization of the undersides of rocks in the polar deserts by cyanobacteria and unicellular green algae. Where rocks have a protected but accessible underside, these organisms colonize, forming a pale green band a few centimetres across, between the part of the rock too exposed and dry, and too dark for photosynthesis. In polygon terrain, where the ground is sorted by frost heave (“periglacial processes”) and even large rocks are periodically jostled, areas of finer texture form in the centers of polygons, with larger rocks around the edges. The edge rocks were 100% colonized, while central areas were 5% colonized.
Fierer and Jackson 2006
Fierer N, Jackson RB. 2006. The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences of the U.S.A. 103: 626-631.
These authors measured biodiversity of soil bacterial communities from 98 samples across North and South America. Rather than the expected variables that structure macroorganism biodiversity such as climate and latitude, the single most important factor for bacterial community diversity was soil pH. Soils with higher pH had greater biodiversity, regardless of geographic separation between sites or geographic position. Because soils with pH greater than 8.5 are rare, it is impossible to distinguish between a unimodal distribution, and a plateau at near-neutral pH.
Most surprising to me was the lack of correlation between bacterial diversity, as either species richness or Shannon-index diversity (richness and evenness) and plant diversity. While these authors did not assess plant diversity, they did express their own surprise that sites in the Peruvian Amazon, with acidic soils, had very low bacterial diversity despite having one of the highest measured plant biodiversities on Earth, and expanded their soil collecting sites to include other tropical and sub-tropical forests with very high plant diversity. Sites with near-neutral pH provided the highest estimates of bacterial diversity, and were primarily dry-grassland, dry-forest, and humid temperate forest sites, with low-to-intermediate plant diversity.
The method used to estimate diversity of bacterial communities was terminal-restriction fragment length polymorphism analysis, or T-RFLP. This technique relies on PCR to amplify the sequence of interest, in this case 16S rDNA, followed by digestion with restriction endonucleases and generation of “fingerprints” for each community. This is a fairly low-resolution method, with less than 100 bands per community, and no ability to distinguish between species with similar restriction sites. However, it does permit high throughput and costs much less per sample than does cloning and sequencing.
This paper is an excellent example of a recent study supporting the hypothesis that microbial global biodiversity is controlled by factors quite distinct from the factors controlling macroorganism (plant and animal) biodiversity. In this case, soil pH is the master control variable, rather than climate or climate factors.
These authors measured biodiversity of soil bacterial communities from 98 samples across North and South America. Rather than the expected variables that structure macroorganism biodiversity such as climate and latitude, the single most important factor for bacterial community diversity was soil pH. Soils with higher pH had greater biodiversity, regardless of geographic separation between sites or geographic position. Because soils with pH greater than 8.5 are rare, it is impossible to distinguish between a unimodal distribution, and a plateau at near-neutral pH.
Most surprising to me was the lack of correlation between bacterial diversity, as either species richness or Shannon-index diversity (richness and evenness) and plant diversity. While these authors did not assess plant diversity, they did express their own surprise that sites in the Peruvian Amazon, with acidic soils, had very low bacterial diversity despite having one of the highest measured plant biodiversities on Earth, and expanded their soil collecting sites to include other tropical and sub-tropical forests with very high plant diversity. Sites with near-neutral pH provided the highest estimates of bacterial diversity, and were primarily dry-grassland, dry-forest, and humid temperate forest sites, with low-to-intermediate plant diversity.
The method used to estimate diversity of bacterial communities was terminal-restriction fragment length polymorphism analysis, or T-RFLP. This technique relies on PCR to amplify the sequence of interest, in this case 16S rDNA, followed by digestion with restriction endonucleases and generation of “fingerprints” for each community. This is a fairly low-resolution method, with less than 100 bands per community, and no ability to distinguish between species with similar restriction sites. However, it does permit high throughput and costs much less per sample than does cloning and sequencing.
This paper is an excellent example of a recent study supporting the hypothesis that microbial global biodiversity is controlled by factors quite distinct from the factors controlling macroorganism (plant and animal) biodiversity. In this case, soil pH is the master control variable, rather than climate or climate factors.
Tuesday, September 22, 2009
Büdel et al. 2009
Büdel B, Darienko T, Deutschewitz K, Dojani S, Friedl T, Mohr KI, Salisch M, Reisser W, Weber B. 2009. Southern African biological soil crusts are ubiquitous and highly diverse in drylands, being restricted by rainfall frequency. Microbial Ecology 57: 229-247.
These authors examined biological soil crusts (BSCs) along a 2000km transect running roughly north-south through Namibia and South Africa. A number of hypotheses relating to BSC composition, frequency, and succession were proposed and tested, with most hypotheses partly confirmed. In general, BSCs are an important and abundant component of these dryland ecosystems, and show patterns of biodiversity associated with biomass, as measured by chlorophyll-a concentrations and species counts.
The major finding of this study, as implied in the title, is that BSC distribution and composition is primarily controlled by patterns of rainfall, but not total rainfall. Species richness and successional stage of BSCs was highest in the winter rain zone, which has a shorter dry season though less total annual rainfall than the summer rain zone. This implies that most BSC organisms are limited by drought tolerance rather than annual water input.
This study is interesting to me for a number of reasons. First, it includes in the references a number of reviews of BSCs and methods to study them, such as protocols for measuring chlorophyll-a concentrations per square metre, and molecular methods for species richness estimation. Second, because BSCs are expected to be the major photosynthetic organisms in the polar desert, I need to know what patterns of their distribution and diversity I should expect. This paper’s Hypothesis 4, that biomass (and productivity) of BSCs increases with species richness, which was essentially confirmed, is of particular interest in this context, as it provides another layer of background expected pattern in addition to my general expectation of a species-richness gradient associated with latitude, particularly as one crosses Lancaster Sound north of Baffin Island. This paper provides some ideas for ways to measure species richness in BSCs, which (third) contribute strongly to the overall biodiversity of dryland regions and therefore will be interesting in their own right in studies of Arctic Biogeography.
These authors examined biological soil crusts (BSCs) along a 2000km transect running roughly north-south through Namibia and South Africa. A number of hypotheses relating to BSC composition, frequency, and succession were proposed and tested, with most hypotheses partly confirmed. In general, BSCs are an important and abundant component of these dryland ecosystems, and show patterns of biodiversity associated with biomass, as measured by chlorophyll-a concentrations and species counts.
The major finding of this study, as implied in the title, is that BSC distribution and composition is primarily controlled by patterns of rainfall, but not total rainfall. Species richness and successional stage of BSCs was highest in the winter rain zone, which has a shorter dry season though less total annual rainfall than the summer rain zone. This implies that most BSC organisms are limited by drought tolerance rather than annual water input.
This study is interesting to me for a number of reasons. First, it includes in the references a number of reviews of BSCs and methods to study them, such as protocols for measuring chlorophyll-a concentrations per square metre, and molecular methods for species richness estimation. Second, because BSCs are expected to be the major photosynthetic organisms in the polar desert, I need to know what patterns of their distribution and diversity I should expect. This paper’s Hypothesis 4, that biomass (and productivity) of BSCs increases with species richness, which was essentially confirmed, is of particular interest in this context, as it provides another layer of background expected pattern in addition to my general expectation of a species-richness gradient associated with latitude, particularly as one crosses Lancaster Sound north of Baffin Island. This paper provides some ideas for ways to measure species richness in BSCs, which (third) contribute strongly to the overall biodiversity of dryland regions and therefore will be interesting in their own right in studies of Arctic Biogeography.
Monday, September 21, 2009
Pilegaard et al. 2006
Pilegaard K, Skiba U, Ambus P, Beier C, Bruggemann N, Butterbach-Bahl, Dick J, Dorsey J, Duyzer J, Gallagher M, Gasche R, Horvath L, Kitzler B, Leip A, Pihlatie MK, Rosenkranz P, Seufert G, Vesala T, Westrate H, Zechmeister-Boltenstern S. 2006. Factors controlling regional differences in forest soil emission of nitrogen oxides (NO and N2O). Biogeosciences 3: 651-661.
These (abundant) authors present an analysis of a large combined dataset covering NO and N2O emissions from a range of forest systems in Europe. The measurements contributing to this large dataset were continuous measures (at least daily, usually hourly or better) and run at least one year. This provides a high-quality dataset that includes variation induced by seasonality.
One of the most interesting findings in this study is a scale-dependent relationship between soil parameters and N2O emissions. Within-forests, soil temperature and moisture were highly predictive of N2O flux, but not at scales encompassing multiple forests in comparison. At larger spatial scales, stand age and C/N ratio were much better predictors.
These (abundant) authors present an analysis of a large combined dataset covering NO and N2O emissions from a range of forest systems in Europe. The measurements contributing to this large dataset were continuous measures (at least daily, usually hourly or better) and run at least one year. This provides a high-quality dataset that includes variation induced by seasonality.
One of the most interesting findings in this study is a scale-dependent relationship between soil parameters and N2O emissions. Within-forests, soil temperature and moisture were highly predictive of N2O flux, but not at scales encompassing multiple forests in comparison. At larger spatial scales, stand age and C/N ratio were much better predictors.
Friday, September 18, 2009
Barrett et al. 2006
Barrett JE, Virginia RA, Wall DH, Cary SC, Adams BJ, Hacker AL, Aislabie JM. 2006. Co-variation in soil biodiversity and biogeochemistry in northern and southern Victoria Land, Antarctica. Antarctic Science 18: 535-548.
These authors examined soil biota at three sites across about 7 degrees of latitude in the drier part of Antarctica. The latitudinal gradient here covers a range of different ecosystems, from relatively wet, more northern and coastal systems to extremely arid and barren southern systems. Here, latitude is not studied for its effects on ecosystems; its effects on ecosystems are exploited to cover the widest available range of conditions. Within each of the three sites, one wet and one dry location were chosen a priori based on obvious surface features such as meltwater drainage channels and the presence of moss beds. At each location, a set of transects were laid out and samples were collected. To quote them directly:
Soil invertebrates were investigated using both morphological and molecular techniques. There are only four metazoan phyla with any significant presence in Antarctica’s soils (Arthropoda, Nematoda, Rotifera, and Tardigrada), all of which are difficult to identify to species using standard morphological methods. While these authors were able to identify nematodes to species, rotifers, tardigrades, and mites were handled as MOTUs, molecular operational taxonomic units (Floyd et al. 2002). These MOTUs, based on ribosomal DNA sequences, were also used to generate a series of cladograms used to assess biodiversity at the research sites. Unfortunately, while the text descriptions of the methods and results are reasonably clear, the figures relating to the biodiversity and metazoan-molecular work are confusing and poorly described.
The results of the microbial analyses are broadly similar to the metazoan dataset. These authors were able to examine biodiversity at the level of microbes, and compare this diversity to both soil chemical characteristics such as water content and C:N ratio, and to the metazoan diversity. Perhaps surprisingly, they found no evidence to support the hypothesis of top-down control on bacterial populations by metazoan predators, as there was no correlation between DGGE and FAME-derived estimates of bacterial population size and species richness and cladogram and sugar-extract-derived estimates of nematode biodiversity. Bacterial diversity is described as not varying across sites, though community composition does. I take this to mean that while total species richness of bacteria (as measured by DGGE) was constant across sites, species turnover (Beta-diversity) was high. This is interesting to me, though not mentioned in the paper, because it seems to directly contradict the microbial-biogeography hypothesis of “everything is everywhere”. There is a mention in the description of this comparison of the importance of geography in structuring biodiversity, which reads to me like an opportunity to apply explicit geospatial techniques to their dataset.
Overall, while it is true that Antarctic soil ecosystems are extremely simple relative to other systems, there are a great many complex and variable interactions between even the few components of these systems, creating a great deal of complexity. This paper will be very useful to me in structuring some of my own investigations in the Arctic.
These authors examined soil biota at three sites across about 7 degrees of latitude in the drier part of Antarctica. The latitudinal gradient here covers a range of different ecosystems, from relatively wet, more northern and coastal systems to extremely arid and barren southern systems. Here, latitude is not studied for its effects on ecosystems; its effects on ecosystems are exploited to cover the widest available range of conditions. Within each of the three sites, one wet and one dry location were chosen a priori based on obvious surface features such as meltwater drainage channels and the presence of moss beds. At each location, a set of transects were laid out and samples were collected. To quote them directly:
"We investigated the structure (bacterial and metazoan diversity) and functioning (soil respiration) of soil communities and the influence of soil biogeochemical properties (organic matter, inorganic nutrients, physicochemical properties) on habitat suitability."This is quite similar in many respects to my planned investigations in the Arctic polar desert. The list of molecular techniques used in this paper, for example, serves as a useful guide or checklist of the procedures I intend to use.
Soil invertebrates were investigated using both morphological and molecular techniques. There are only four metazoan phyla with any significant presence in Antarctica’s soils (Arthropoda, Nematoda, Rotifera, and Tardigrada), all of which are difficult to identify to species using standard morphological methods. While these authors were able to identify nematodes to species, rotifers, tardigrades, and mites were handled as MOTUs, molecular operational taxonomic units (Floyd et al. 2002). These MOTUs, based on ribosomal DNA sequences, were also used to generate a series of cladograms used to assess biodiversity at the research sites. Unfortunately, while the text descriptions of the methods and results are reasonably clear, the figures relating to the biodiversity and metazoan-molecular work are confusing and poorly described.
The results of the microbial analyses are broadly similar to the metazoan dataset. These authors were able to examine biodiversity at the level of microbes, and compare this diversity to both soil chemical characteristics such as water content and C:N ratio, and to the metazoan diversity. Perhaps surprisingly, they found no evidence to support the hypothesis of top-down control on bacterial populations by metazoan predators, as there was no correlation between DGGE and FAME-derived estimates of bacterial population size and species richness and cladogram and sugar-extract-derived estimates of nematode biodiversity. Bacterial diversity is described as not varying across sites, though community composition does. I take this to mean that while total species richness of bacteria (as measured by DGGE) was constant across sites, species turnover (Beta-diversity) was high. This is interesting to me, though not mentioned in the paper, because it seems to directly contradict the microbial-biogeography hypothesis of “everything is everywhere”. There is a mention in the description of this comparison of the importance of geography in structuring biodiversity, which reads to me like an opportunity to apply explicit geospatial techniques to their dataset.
Overall, while it is true that Antarctic soil ecosystems are extremely simple relative to other systems, there are a great many complex and variable interactions between even the few components of these systems, creating a great deal of complexity. This paper will be very useful to me in structuring some of my own investigations in the Arctic.
Tuesday, September 15, 2009
Ettema & Wardle 2002
Ettema CH, Wardle DA. 2002. Spatial soil ecology. Trends in Ecology & Evolution 17: 177-183.
These authors review the growing use of explicit geospatial analysis techniques in soil biology. As this is a TREE article, there are several helpful boxes that explain fundamentals of geospatial analysis such as the terminology and key case studies. This is also a review article, so there are descriptions of various previous studies that include evidence useful in answering the questions set out in this paper. These questions are 1) What are the scales, patterns and causes of spatial variability in soil organism distributions? 2) What are the implications of spatial variability for the structure and function of soil communities? 3) How do spatial properties of the soil biota influence plant communities?
Regarding question 1, the scales and patterns of spatial variability in soil organisms range from 10s and 100s of metres down to millimetres. Studies of soil microbes including methanogenic Archaea have included soil corers of 1mm diameter (based on a hollow needle) and aggregations of organisms separated by distances of 2 to 4mm.
Soil communities and their influence on plant communities were found to be highly non-uniform, and show predictable though complex spatial patterns. However, while much was made of the role of individual plants (especially trees) to structure the soils around them and create spatial patterns of microbes and invertebrates on the same scale as the trees themselves are distributed, very little was made of the role that small-scale aggregations play in structuring larger patterns. This is surprising, given the highly biased view of soil processes in this paper and more generally in the soil science literature: soil is viewed as something that exists primarily to support plants, rather than a system of its own independent importance. That is the impression I have gotten, at least.
This paper is a very useful overview of geospatial analysis, and the reference list includes a number of similarly useful papers. In particular, further exploration of the statistics of semivariance patterns seems useful.
These authors review the growing use of explicit geospatial analysis techniques in soil biology. As this is a TREE article, there are several helpful boxes that explain fundamentals of geospatial analysis such as the terminology and key case studies. This is also a review article, so there are descriptions of various previous studies that include evidence useful in answering the questions set out in this paper. These questions are 1) What are the scales, patterns and causes of spatial variability in soil organism distributions? 2) What are the implications of spatial variability for the structure and function of soil communities? 3) How do spatial properties of the soil biota influence plant communities?
Regarding question 1, the scales and patterns of spatial variability in soil organisms range from 10s and 100s of metres down to millimetres. Studies of soil microbes including methanogenic Archaea have included soil corers of 1mm diameter (based on a hollow needle) and aggregations of organisms separated by distances of 2 to 4mm.
Soil communities and their influence on plant communities were found to be highly non-uniform, and show predictable though complex spatial patterns. However, while much was made of the role of individual plants (especially trees) to structure the soils around them and create spatial patterns of microbes and invertebrates on the same scale as the trees themselves are distributed, very little was made of the role that small-scale aggregations play in structuring larger patterns. This is surprising, given the highly biased view of soil processes in this paper and more generally in the soil science literature: soil is viewed as something that exists primarily to support plants, rather than a system of its own independent importance. That is the impression I have gotten, at least.
This paper is a very useful overview of geospatial analysis, and the reference list includes a number of similarly useful papers. In particular, further exploration of the statistics of semivariance patterns seems useful.
Monday, September 14, 2009
Garten et al. 2007
Garten CT Jr., Kang S, Brice DJ, Schadt CW, Zhou J. 2007. Variability in soil properties at different spatial scales (1m-1km) in a deciduous forest ecosystem. Soil Biology & Biochemistry 39: 2621-2627.
These authors examined some of the fundamental assumptions of geospatial analysis as applied to soil properties, in a pair of transects that I strongly suspect have been used repeatedly for many studies in Tennessee (see, e.g. Zhou et al. 2008). One of the fundamental assumptions is of spatial autocorrelation, that is, samples in close proximity will be more similar to each other than samples separated by greater distances. In this study, this assumption was stated as the null hypothesis “there are no differences in variance at different spatial scales”; a rejection of this null hypothesis can be interpreted as support for the “common sense” (their wording) principle of spatial autocorrelation, at least among the spatial scales discussed here (i.e. metres to kilometres). This and other important assumptions of geospatial analysis come from a series of papers applying these principles to soils, which I should probably read soon.
The 11 soil variables examined in this paper were distinctly non-orthogonal in their relationships. Many of the variables were calculated directly from other variables, and the majority takes the form of either ratios (such as C-to-N) or fractions (such as silt content). The Principle Components Analysis (PCA) these authors conducted on their final, grand-total dataset indicated that the usual suspects of soil properties were important – soil Carbon, soil Nitrogen, and soil Texture are one way to summarize the first three PC variables.
I looked up and read this paper mainly because of the statistical tests used here and the discussion of them. They conducted 5 main statistical tests.
1. Bartlett’s test for equal variances at different distances.
2. Bartlett’s test is sensitive to non-normal data, so they also used the non-parametric Spearman’s Rank Correlation between coefficients of variation (100 x S.D./mean). The other reason a non-parametric test was used was that the functional relationship (linear vs. non-linear) between variance and sampling distance was unknown.
3. Mantel and Partial Mantel tests. These were the central analysis, I think, and provided most of the key results regarding the tests of the main hypotheses. Apparently, Burrough (1993) recommends semivariogram analysis, but the present data set was not amenable to such.
4. PCA, as mentioned above.
5. Power analysis. How many samples would they need to collect to be more certain of being close to the true mean value in their estimates?
Besides the PCA, which produced utterly unsurprising results, I think the statistical tests deployed here will serve as models for my own analysis of 2009 and putative 2010 datasets from the High Arctic. In particular, the Mantel tests and the Power analysis should be very useful in my own examinations.
Overall, the geospatial assumption of spatial autocorrelation was not very well supported by this study. Many soil properties appear to be highly variable at small spatial scales, such that samples collected within a few metres of each other are as variable as samples collected from up to a kilometre away, at least in a temperate forest ecosystem as studied here. This is particularly surprising in light of the consideration of the structure of such a forest, where individual trees presumably have strong impacts on soil properties within perhaps 5 to 10 metres of their trunks.
These authors examined some of the fundamental assumptions of geospatial analysis as applied to soil properties, in a pair of transects that I strongly suspect have been used repeatedly for many studies in Tennessee (see, e.g. Zhou et al. 2008). One of the fundamental assumptions is of spatial autocorrelation, that is, samples in close proximity will be more similar to each other than samples separated by greater distances. In this study, this assumption was stated as the null hypothesis “there are no differences in variance at different spatial scales”; a rejection of this null hypothesis can be interpreted as support for the “common sense” (their wording) principle of spatial autocorrelation, at least among the spatial scales discussed here (i.e. metres to kilometres). This and other important assumptions of geospatial analysis come from a series of papers applying these principles to soils, which I should probably read soon.
The 11 soil variables examined in this paper were distinctly non-orthogonal in their relationships. Many of the variables were calculated directly from other variables, and the majority takes the form of either ratios (such as C-to-N) or fractions (such as silt content). The Principle Components Analysis (PCA) these authors conducted on their final, grand-total dataset indicated that the usual suspects of soil properties were important – soil Carbon, soil Nitrogen, and soil Texture are one way to summarize the first three PC variables.
I looked up and read this paper mainly because of the statistical tests used here and the discussion of them. They conducted 5 main statistical tests.
1. Bartlett’s test for equal variances at different distances.
2. Bartlett’s test is sensitive to non-normal data, so they also used the non-parametric Spearman’s Rank Correlation between coefficients of variation (100 x S.D./mean). The other reason a non-parametric test was used was that the functional relationship (linear vs. non-linear) between variance and sampling distance was unknown.
3. Mantel and Partial Mantel tests. These were the central analysis, I think, and provided most of the key results regarding the tests of the main hypotheses. Apparently, Burrough (1993) recommends semivariogram analysis, but the present data set was not amenable to such.
4. PCA, as mentioned above.
5. Power analysis. How many samples would they need to collect to be more certain of being close to the true mean value in their estimates?
Besides the PCA, which produced utterly unsurprising results, I think the statistical tests deployed here will serve as models for my own analysis of 2009 and putative 2010 datasets from the High Arctic. In particular, the Mantel tests and the Power analysis should be very useful in my own examinations.
Overall, the geospatial assumption of spatial autocorrelation was not very well supported by this study. Many soil properties appear to be highly variable at small spatial scales, such that samples collected within a few metres of each other are as variable as samples collected from up to a kilometre away, at least in a temperate forest ecosystem as studied here. This is particularly surprising in light of the consideration of the structure of such a forest, where individual trees presumably have strong impacts on soil properties within perhaps 5 to 10 metres of their trunks.
Thursday, September 10, 2009
Zhou et al. 2008
Zhou J, Kang S, Schadt CW, Garten CT Jr. 2008. Spatial scaling of functional gene diversity across various microbial taxa. Proceedings of the National Academy of Sciences of the USA 105: 7768-7773.
These authors used a microarray-based technique to estimate biodiversity of soil microbes across a pair of transects in a forest in Tennessee. Their analysis found rates of species turnover through space much lower than rates for macroorganisms such as “higher” plants and animals.
The species-area relationship, generalized to the Taxa-Area-Relationship (TAR), is S=cA^z, where S is the number of species, A is the area, c is the intercept in log-log space, and z is a measure of the rate of species turnover across space. Values of z for macroorganisms have been estimated close the theoretically derived value of 0.25, while previous estimates for microbes have been often much lower, but occasionally much higher. This study found a range of z-values, all a bit less than 0.1.
The key technique used in this study was the GeoChip, a microarray with nearly 25000 50-mer probes for more than 10000 genes in functional groups such as denitrification or heavy-metal resistance. As such, it represents an excellent tool for such investigations, because it reduces or avoids many of the microbe-diversity sampling artifacts such as undersampling that plague other methods.
A large fraction of the observed variation in sequences across the transects was unexplained. These authors speculate that a fraction of this unexplained variation may be driven by unexamined patterns and processes including biotic interactions (competition, trophic interaction), abiotic interactions (O2 concentrations, labile C pool), and microscale effects below 1m scales.
One interesting suggestion by these authors is to use metagenomic approaches to characterize key sequences of interest in a particular system, and then examine biodiversity using a microarray customized for these sequences. This is in line with what I was thinking in regards to using such techniques in polar desert soils – first, characterize what is there; second, look at biodiversity and patterns within diversity relating to groups of interest.
These authors used a microarray-based technique to estimate biodiversity of soil microbes across a pair of transects in a forest in Tennessee. Their analysis found rates of species turnover through space much lower than rates for macroorganisms such as “higher” plants and animals.
The species-area relationship, generalized to the Taxa-Area-Relationship (TAR), is S=cA^z, where S is the number of species, A is the area, c is the intercept in log-log space, and z is a measure of the rate of species turnover across space. Values of z for macroorganisms have been estimated close the theoretically derived value of 0.25, while previous estimates for microbes have been often much lower, but occasionally much higher. This study found a range of z-values, all a bit less than 0.1.
The key technique used in this study was the GeoChip, a microarray with nearly 25000 50-mer probes for more than 10000 genes in functional groups such as denitrification or heavy-metal resistance. As such, it represents an excellent tool for such investigations, because it reduces or avoids many of the microbe-diversity sampling artifacts such as undersampling that plague other methods.
A large fraction of the observed variation in sequences across the transects was unexplained. These authors speculate that a fraction of this unexplained variation may be driven by unexamined patterns and processes including biotic interactions (competition, trophic interaction), abiotic interactions (O2 concentrations, labile C pool), and microscale effects below 1m scales.
One interesting suggestion by these authors is to use metagenomic approaches to characterize key sequences of interest in a particular system, and then examine biodiversity using a microarray customized for these sequences. This is in line with what I was thinking in regards to using such techniques in polar desert soils – first, characterize what is there; second, look at biodiversity and patterns within diversity relating to groups of interest.
Wednesday, September 2, 2009
Niederberger et al. 2008
Neiderberger TD, McDonald IR, Hacker AL, Soo RM, Barrett JE, Wall DH, Cary SC. 2008. Microbial community composition in soils of Northern Victoria Land, Antarctica. Environmental Microbiology 10: 1713-1724.
These authors present an analysis of a large collection of data regarding both microbial and metazoan biodiversity at relatively small scales in one part of Taylor Valley, Antarctica, one of the famous Dry Valleys. This contributes to both the Latitudinal Gradient Project, an international effort to characterize Antarctica, and to the biogeographical debate regarding the distribution and community assemblages of microbes and soil microfauna.
Biodiversity was higher than expected based on the physical characteristics of this extreme environment, and was much more variable at small (~200m) spatial scales. While the microbes identified by 16s sequences were not particularly surprising, the changes in community composition between study sites was high. This supports the hypothesis that extreme environments “select for” particular microbial physiologies, and that differences in soil physical features such as moisture and temperature are highly important, in distinct contrast to the “everything is everywhere” hypothesis of microbial biogeography.
NB October 1 2009: the “everything is everwhere” hypothesis (Beijerinck 1913) includes the second clause “the environment selects”, which implies my earlier impressions, above, are incorrect. This paper’s demonstration that extreme environments select for particular soil communities, and that local-scale variables such as moisture and temperature, rather than regional-scale variables such as climate factors, actually supports Beijerinck’s (1913) hypothesis, rather than countering it.
These authors present an analysis of a large collection of data regarding both microbial and metazoan biodiversity at relatively small scales in one part of Taylor Valley, Antarctica, one of the famous Dry Valleys. This contributes to both the Latitudinal Gradient Project, an international effort to characterize Antarctica, and to the biogeographical debate regarding the distribution and community assemblages of microbes and soil microfauna.
Biodiversity was higher than expected based on the physical characteristics of this extreme environment, and was much more variable at small (~200m) spatial scales. While the microbes identified by 16s sequences were not particularly surprising, the changes in community composition between study sites was high. This supports the hypothesis that extreme environments “select for” particular microbial physiologies, and that differences in soil physical features such as moisture and temperature are highly important, in distinct contrast to the “everything is everywhere” hypothesis of microbial biogeography.
NB October 1 2009: the “everything is everwhere” hypothesis (Beijerinck 1913) includes the second clause “the environment selects”, which implies my earlier impressions, above, are incorrect. This paper’s demonstration that extreme environments select for particular soil communities, and that local-scale variables such as moisture and temperature, rather than regional-scale variables such as climate factors, actually supports Beijerinck’s (1913) hypothesis, rather than countering it.
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.
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, 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.
Sunday, May 18, 2008
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.
Saturday, May 17, 2008
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.
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