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.

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.

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.

Bell and Collins 2008

Bell G, Collins S. 2008. Adaptation, extinction and global change. Evolutionary Applications 1: 3-16.

These authors review and synthesize the current theory surrounding evolutionary responses to gradual environmental changes, especially increasing atmospheric carbon dioxide concentrations. In this context, these authors argue that the primary task of evolutionary biologists in the early 21st century is to predict adaptive evolution (or extinction) of populations and species in a gradually changing environment.

Populations are assumed to have high fitness, based on historical events. In a stable environment, beneficial alleles will accumulate, thus environmental changes are likely to be changes to the worse. Additionally, populations that do not adapt will suffer gradually declining mean fitness as pathogens and predators should themselves be selected for the most common target genotype.

Environmental variance increases with increasing time scales, that is, events occurring more distantly in time will be more different from each other. This applies to environmental conditions as much as anything else. The major implication of this in the context of this paper is that lineages surviving over long time periods will experience increasingly variable conditions, which also means generally deteriorating conditions if populations start well-adapted.

Many previous studies have found either strong selection, and / or high heritability. This apparent contradiction can be explained by high variability in the direction and magnitude of selection, suggesting that environmental variability is ubiquitous.

Populations can respond to changing conditions in four ways: phenotypic plasticity, dispersal and migration, adaptation, or extinction. These are arranged in order from short time scales to long.

The current pace of global environmental conditions change is probably higher than in most or all previous episodes. Historical levels of CO2 were about 280 ppm (parts per million); currently they are about 380 ppm, with some projections as high as 1000 ppm within the next 100 years.

These authors analysed the effects of the severity and frequency of environmental change (always change for the worse). They found that frequency is much more important to the probability of adaptation or “evolutionary rescue” than is severity. Frequent changes in conditions is likely to lead to extinction because selection does not have enough time to fix beneficial alleles, such that some fraction of the population is not well adapted to start with when the next change hits. In contrast, rare but severe changes lead to strong selection, and expose a long series of potentially beneficial alleles, increasing the mutation supply rate. The mutation supply rate is the critical parameter in determining adaptation or extinction, specifically the fraction of the supply of mutations that are beneficial and can rescue a declining population, i.e. raise a genotype’s rate of growth from negative to positive. Even rapid environmental change can be adapted to if the (rescue) mutation supply is high enough.

A survey of both simulations and studies of natural and laboratory populations revealed several cases of adaptation to frequent or continuous environmental change, and several cases of failure to adapt, even in species with very large population sizes. This indicates primarily that the rate of rescue mutations is unknown, despite being the single most important variable in predicting the evolutionary fates of populations under global climate change. However, these authors argue that a rescue mutation rate of approximately one per generation, regardless of population size, is probably close to the critical value, but qualify this estimate by stating they intend it as a first guess, and stimulus for more exact research in future.

The current driver of global environmental change is increasing CO2 concentrations in the atmosphere. Unlike most other agents of environmental change, CO2 is not in itself likely to represent a lethal stress to organisms, rather the effects will be either direct and positive (increased photosynthesis), or indirect via either temperature and climate changes or via biotic interactions such as competition.

Experiments and simulations by these and other authors have suggested that the short-term physiological responses of phytoplankton to increased CO2 will be opposite in direction to long-term evolutionary responses; this is at least partly because phytoplankton appear to be not limited by CO2 for growth. More specifically, the CO2-importing pump, which is tightly regulated by CO2 concentrations, will become less efficient, removing much of the productivity gain that would otherwise be predicted. Evidence that this will lead to community-level effects such as succession is currently equivocal, and based on short-term studies or idiosyncratic species compositions.

Our current understanding of evolution and ecology is based on populations subjected to a sudden shift from one stable environment to another, and usually a shift to increased stress or scarcity. In contrast, current global change is gradual and continuous, and is a case of nutrient enrichment.

These authors conclude with three main points. First, rescue mutations are critical to the phenomenon of evolutionary rescue and adaptation, but their rate is almost totally unknown. Second, the evolutionary response to increasing atmospheric CO2 concentrations is likely to be reduced efficiency of photosynthesis, rather than increased productivity. Third, these authors urge a general increase in studies of the evolutionary effects of global change, at rates of environmental change between the very fast rates typical of laboratory experimental evolution, and the very slow rates typical of most of the Earth’s history.

Rodríguez-Juiz et al. 1996

Rodríguez-Juiz AM, Torrado M, Méndez J. 1996. Genome-size variation in bivalve molluscs determined by flow cytometry. Marine Biology 126: 489-497.

These authors measured nuclear DNA contents in 10 species of bivalves of commercial importance. Genome size variation in plants and poikilothermal animals had previously been associated with life-history and ecological traits, suggesting links between genome size variation and speciation events. There had been few previous studies of DNA content in molluscs. Early examples of such studies include Mirsky and Ris (1951), Hinegardner (1973, 1976), and Cavalier-Smith (1978); several earlier papers on molluscs and other poikilotherms related genome size to “specialization”, particularly the work of Hinegardner and colleagues.

Unlike most studies of DNA content, these authors included relatively large samples of each species, using 20 individuals in each species. All individuals were purchased from commercial shellfish sellers, either in Spain (9 species) or the Netherlands (Mytilus edulis), and maintained alive in the laboratory until dissection of gill tissue; the assumption that gill tissue is diploid is never stated explicitly but was used in the calculations of genome sizes. Tissue was placed in filtered, autoclaved seawater and subjected to mechanical shaking for 30 minutes; these authors do not describe in detail this shaking, is there a standard rate and magnitude of mechanical shaking of mollusc tissue? The presence of isolated cells was verified using a microscope, and cell preparations were strained through 15mm mesh and sonicated for two minutes to remove cell membranes. The nuclei were then centrifuged, resuspended in buffer that appears similar to Galbraith’s buffer (Galbraith et al. 1983), and fixed with 0.1% formaldehyde on ice. Finally, aggregations of nuclei were disrupted using a 26-gauge needle, pumped three times.

Two internal standards were employed: Capsicum annuum and chicken red blood cells (CRBCs). Isolated nuclei from these species were added to bivalve nuclei suspensions before staining, thus standards and specimens here were co-stained rather than co-prepared. The CRBCs produced a peak in the flow cytometry histograms overlapping seven of the 10 bivalve species, thus the introduction of the plant nuclei. C. annuum nuclei were employed after checking for consistent measurements with the three species of bivalves that did not overlap in peak area with CRBCs, and comparison between C. annuum and CRBCs to determine a C. annuum diploid nuclear content of 8.4 pg, larger than any bivalve measured in this study. 10 000 nuclei were measured per histogram, presumably this means total events recorded above the debris cut-off, and each specimen was measured three times.

These authors report significant intraspecific genome size variation in all 10 bivalve species. Interspecific (and between higher taxa) was much greater than intraspecific variation, but the intraspecific variation was statistically significant under 2-way ANOVA and “GSD” calculations based on the work of Gold and Amemiya (1987) and Alvarez-Fuster et al. (1991).

The discovered and possibly unexpected intraspecific variation is used to bolster an argument made in the discussion that large samples are necessary for accurate determination of genome size and genome size variation in species. This explains the difference between these results and the no-intraspecific-variation results of some previous authors that did not use large samples per species.

Following this is a discussion of Hinegardner’s (several papers in the 1970s) “specialization” assumption / hypothesis. It is described as one, then the other. These data do not support this hypothesis, which is not surprising considering how vague and taxon-specific the terms “specialized” and “generalized” are, and their underlying assumptions about species and lineage ages and rates of evolution.

Matthews 1979

Matthews JV Jr. 1979. Late Tertiary carabid fossils from Alaska and the Canadian archipelago. In: Carabid Beetles: Their Evolution, Natural History, and Classification (Erwin TL, Ball GE, Whitehead DR, Halpern AL eds.). Dr. W Junk bv Publishers, The Hague, Netherlands.

For this special symposium, this author summarizes recently discovered and analysed beetle fossils dating from the late Tertiary, and compares them with similar fossils from the Pleistocene. Most Tertiary fossils of insects are either casts or impressions, and beetle fossils tend to be crushed and scattered too severely for good identification and analysis. However, fossils dating from the late Miocene and early Pliocene (roughly 5 million years ago) were discovered at several sites across the western islands of the Canadian Archipelago and a site in western Alaska that resemble Pleistocene fossils in their quality of preservation. The western Alaska site is particularly valuable because the fossil-bearing layer is overlain by a layer of basalt flow, possibly from a volcanic eruption, that can be dated without recourse to biological materials. There was apparently a narrow connection between Alaska and Siberia at the time these fossils were produced.

In general, smaller-bodied beetles are better preserved than large, but many specimens of numerous genera were discovered. Matthews (1977) includes a complete list of all fossil Coleoptera found, including the carabids described here. Several examples of species-diagnostic features were found, including highly detailed elytra and parts of male genitalia.

The first part of the discussion of this paper is a critique of the strictly-Hennigian methods of Phylogenetic Systematics, which disallows phyletic evolution, i.e. changes in species phenotypes through time without associated lineage splitting. Later parts of the discussion describe the probable Taiga ecosystem present at very high latitudes in the late Miocene. The author ends the paper with optimism that similar high-quality Tertiary fossils may soon be found in other high latitude areas around the world.

Chapin and Körner 1994

Chapin FS III, Körner C. 1994. Arctic and alpine biodiversity: patterns, causes and ecosystem consequences. Trends in Ecology and Evolution 9: 45-47.

These authors summarize the major points discussed at a meeting in Norway of researchers studying Arctic and alpine ecosystems, in the context of climate change and 14 major biomes. No published works are cited in this paper, rather several prominent researchers are mentioned as contributing various components of the meeting.

Arctic and alpine ecosystems were grouped together and described as “critical” for five reasons: 1. High latitudes are expected to experience the most change in climate; 2. The ecological consequences of warming will be most severe in cold regions; 3. High altitudes with low atmospheric pressures are expected to be most limiting for CO2 and consequently will respond strongly to changes in CO2 concentrations; 4. Arctic systems include large pools of frozen carbon and methane, and will thus generate important feedback effects during warming; 5. Arctic and alpine ecosystems are relatively simple systems and may show clear effects on species of ecosystem processes. Point 5 is probably most directly applicable to my own work, in that it reinforces the utility of low-species-richness and extreme-climate environments for examinations of interactions between abiotic factors and evolutionary processes.

Much of the discussion centres on the Arctic and alpine flora, which show patterns of diversity strongly associated with historical forces such as the Pleistocene glaciations. Arctic floras tend to be broadly distributed, often holarctic, while most alpine systems are more specific to small areas. In general, stable Arctic and alpine systems show diversity curves that fit the geometric model, suggesting that competitive interactions for limiting resources best explain patterns of diversity, rather than abiotic factors.

In contrast, animal diversity shows a clear latitudinal and altitudinal gradient, with associated patterns of taxonomic replacement. For example, coleopteran species richness declines with latitude while dipteran species richness increases.

The processes that humans are most interested in for economic and other reasons are those most sensitive to species composition, such as pollination and trophic dynamics. Other processes are much less sensitive to species composition within functional groups, for example many biogeochemistry processes.

In summary, the described conference demonstrated that a great deal is known about patterns of biodiversity in Arctic and alpine ecosystems as well as globally. These patterns appear to have important consequences for ecosystem function, and further research is urged in refining knowledge of species diversity patterns to better detect changes due to climate, experimental manipulations simulating changes in climate and CO2, and simulation modelling of long-term and large-scale processes.

D'Amico et al. 2002

D’Amico S, Claverie P, Collins T, Georlette D, Gratia E, Hoyoux A, Meuwis M-A, Feller G, Gerday C. 2002. Molecular basis of cold adaptation. Proceedings of the Royal Society of London B 257: 917-925.

These authors review the relationships between enzyme parameters and temperature. A trade-off exists between enzyme activity at low temperatures and thermal stability. This trade-off is driven by enzyme flexibility: more flexible enzymes are more active (lower activation energy) at low temperatures, but become denatured at lower temperatures than less flexible, more stable enzymes. Enzyme flexibility is related to the strengths and frequencies of bonds that hold enzymes in their three-dimensional shapes; greater flexibility, with weaker and/or fewer such bonds can interact with their substrates more readily, especially at low temperatures, but are denatured easily by increasing temperatures.

The flexible portion of a cold-adapted enzyme has always been found in the domain of the active site. This argues strongly against some proposed explanations for enzymes structures and temperature that rely on relaxed selection pressure and the predominance of drift at low temperatures.

High enzyme flexibility may also allow reversible denaturation, though this point is barely explored by these authors. This suggests to me that some cold-adapted organisms may be able to tolerate temporary high temperatures more readily than “mesothermic” organisms could tolerate an increase of a similar magnitude.
Enzymes that break the trade-off and have high stability, high flexibility, and high low-temperature activity may be possible in the laboratory, especially when using particular types of artificial substrates, but have so far never been found in nature.

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.

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.