An evolutionary framework for the polar regions

Changes in the composition of local communities through time (i.e. species turnover) is a common phenomenon in insular biology. However, the mechanisms promoting variation in species turnover, both among islands and among species, are poorly understood. In an effort to better understand the causes of variation in species turnover, we evaluated the colonization and extinction dynamics of plant populations on 18 small islands off the west coast of Canada. In 1997, we quantified total population sizes of 10 woody angiosperm species. A decade later, we resampled islands to test whether: 1) species turnover occurred, 2) colonization events were offset by extinction events, 2) variation in extinction rates among islands was associated with population sizes, average plant heights, island area, island isolation or each island's exposure to ocean‐born disturbances, and 3) variation in extinction rates among species was associated with plant life history traits. Results showed that extinction events outnumbered colonization events, suggesting that the metacommunity is in ‘disequilibrium’. Variation in extinction rates among islands was unrelated to island area and isolation. However, extinction rates increased with exposure to ocean‐born disturbances and decreased with both initial population sizes and average plant heights. Species with thicker, tougher leaves (i.e. high leaf mass per area) were less prone to extinction than species with thinner, more papery leaves. Overall results indicate that species turnover is common and that it is generated primarily by extinction. Variation in extinction rates appears to result from an interaction between among‐island effects (exposure, population size and plant stature) and among‐species effects (leaf toughness), suggesting that ocean‐born disturbances play a key role in determining metacommunity structure.

Climate is one of the main factors driving species distributions and global biodiversity patterns. Obtaining accurate predictions of species' range shifts in response to ongoing climate change has thus become a key issue in ecology and conservation. Correlative species distribution models (cSDMs) have become a prominent tool to this aim in the last decade and have demonstrated good predictive abilities with current conditions, irrespective of the studied taxon. However, cSDMs rely on statistical association between species' presence and environmental conditions and have rarely been challenged on their actual capacity to reflect causal relationships between species and climate. In this study, we question whether cSDMs can accurately identify if climate and species distributions are causally linked, a prerequisite for accurate prediction of range shift in relation to climate change. We compared the performance of cSDMs in predicting the distributions of 132 European terrestrial species, chosen randomly within five taxonomic groups (three vertebrate groups and two plant groups), and of 1,320 virtual species whose distribution is causally fully independent from climate. We found that (1) for real species, the performance of cSDMs varied principally with range size, rather than with taxonomic groups and (2) cSDMs did not predict the distributions of real species with a greater accuracy than the virtual ones. Our results unambiguously show that the high predictive power of cSDMs can be driven by spatial autocorrelation in climatic and distributional data and does not necessarily reflect causal relationships between climate and species distributions. Thus, high predictive performance of cSDMs does not ensure that they accurately depict the role of climate in shaping species distributions. Our findings therefore call for strong caution when using cSDMs to provide predictions on future range shifts in response to climate change.

One of the central questions of conservation biology is what life-history traits render a species prone to extinction. We addressed this problem by calculating extinction rates for 35 species of turtles and squamates (lizards and snakes) occurring on 87 land-bridge islands in the Mediterranean Sea. We calculated extinction rates in two ways: first, by incorporating the known sequence of historical island separations and second by ignoring history and assuming that the islands became isolated simultaneously. The second procedure is simpler and more frequently used in the literature and produces estimates of extinction rates that are similar to the first, more complex procedure. We then determined the relationship between extinction rates (calculated using both methods) and body mass, longevity, habitat specialization, and population abundance using two methods: first, by accounting for the phylogenetic relationships among species and, second, by ignoring them. Only population abundance and habitat specialization explained a significant amount of the observed variation in species extinction rates. Body mass itself did not explain variation in extinction rates, although it was strongly correlated with abundance. These conclusions were obtained using both procedures for calculating extinction rates and both procedures for correlating extinction rates with life-history traits.

One of the central questions of conservation biology is what life‐history traits render a species prone to extinction. We addressed this problem by calculating extinction rates for 35 species of turtles and squamates (lizards and snakes) occurring on 87 land‐bridge islands in the Mediterranean Sea. We calculated extinction rates in two ways: first, by incorporating the known sequence of historical island separations and second by ignoring history and assuming that the islands became isolated simultaneously. The second procedure is simpler and more frequently used in the literature and produces estimates of extinction rates that are similar to the first, more complex procedure. We then determined the relationship between extinction rates (calculated using both methods) and body mass, longevity, habitat specialization, and population abundance using two methods: first, by accounting for the phylogenetic relationships among species and, second, by ignoring them. Only population abundance and habitat specialization explained a significant amount of the observed variation in species extinction rates. Body mass itself did not explain variation in extinction rates, although it was strongly correlated with abundance. These conclusions were obtained using both procedures for calculating extinction rates and both procedures for correlating extinction rates with life‐history traits.

BackgroundTranscriptomics in non-model plant systems has recently reached a point where the examination of nuclear genome-wide patterns in understudied groups is an achievable reality. This progress is especially notable in evolutionary studies of ferns, for which molecular resources to date have been derived primarily from the plastid genome. Here, we utilize transcriptome data in the first genome-wide comparative study of molecular evolutionary rate in ferns. We focus on the ecologically diverse family Pteridaceae, which comprises about 10 % of fern diversity and includes the enigmatic vittarioid ferns—an epiphytic, tropical lineage known for dramatically reduced morphologies and radically elongated phylogenetic branch lengths. Using expressed sequence data for 2091 loci, we perform pairwise comparisons of molecular evolutionary rate among 12 species spanning the three largest clades in the family and ask whether previously documented heterogeneity in plastid substitution rates is reflected in their nuclear genomes. We then inquire whether variation in evolutionary rate is being shaped by genes belonging to specific functional categories and test for differential patterns of selection.ResultsWe find significant, genome-wide differences in evolutionary rate for vittarioid ferns relative to all other lineages within the Pteridaceae, but we recover few significant correlations between faster/slower vittarioid loci and known functional gene categories. We demonstrate that the faster rates characteristic of the vittarioid ferns are likely not driven by positive selection, nor are they unique to any particular type of nucleotide substitution.ConclusionsOur results reinforce recently reviewed mechanisms hypothesized to shape molecular evolutionary rates in vittarioid ferns and provide novel insight into substitution rate variation both within and among fern nuclear genomes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3034-2) contains supplementary material, which is available to authorized users.

Analyzing endocrine system conservation and evolution

ABSTRACTDispersal ability is a key factor in determining a species' realized niche. However, it remains unclear whether dispersal ability directly, indirectly, or neutrally affects environmental specialization and species' tolerance ranges. Here, we investigate whether, and how, dispersal ability shapes both the realized and fundamental niches. Focusing on plants, invertebrates, and vertebrates in the topographically complex Atlantic Rainforest—one of the world's top biodiversity hotspots—we also assess how dispersal ability correlates with species' range shifts in response to climate change. Our findings indicate that high‐dispersal species exhibit broader thermal tolerances compared to low‐dispersal taxa, which are often restricted to higher elevations. Projected across geographic space, these data forecast a concerning scenario for species with limited dispersal abilities—particularly low‐dispersal ectotherms—which are expected to face the highest risks of local extinction, even under the milder climate projections for the end of the 21st century. In contrast, species with broader thermal tolerances and higher dispersal capacities are expected to undergo reduced range shifts in response to climate change, particularly under the milder climate projection. Therefore, while the milder projections already indicate high extinction rates in the highlands, the warmest future scenario exacerbates this trend by predicting a substantial influx of high‐dispersal species moving upslope (and southward) that are also expected to be locally affected by climate change. These upward movements are expected to negatively affect native communities closely tied to the forest's mountaintop ecosystems. Given the rapid habitat conversion affecting this and similar landscapes globally, we emphasize the importance of prioritizing low‐dispersal species in biodiversity management. Our results highlight the critical role of dispersal ability in species' resilience to ongoing climate warming, especially in biodiversity‐rich but threatened regions like the Atlantic Rainforest.

According to 5-Myr-old fossil evidence, ground squirrels within the genus Spermophilus had diverged into subgenera Spermophilus and Otospermophilus by late Miocene times. Radiometric dating has also provided a precise time for the sudden onset of a geological event, occurring 0.725 Myr ago, that initiated the complete and permanent reproductive isolation of two subspecies within the subgenus Otospermophilus. Since these two subspecies (S. beecheyi beecheyi and S. b. douglasii) readily hybridize with each other under laboratory conditions, allopatric subspeciation is unlikely to have occurred prior to 0.725 Myr ago. We employed Nei's model for estimating genetic distance in units which are linear in time, calibrated on the 0.725-Myr-ago date for initiation of S. b. subspeciation, to test its ability to generate a time scale for subgeneric divergence in keeping with the minimum estimate provided by the fossil record. This represents the most valid test to date of the utility of Nei's model for estimating genetic distance in units which are linear in time. Nei's model was found to underestimate this minimum time by 1 Myr, but it approximated this date after correcting values of D for variation in rates of evolution among loci.

DNA sequences and chromosomal locations of four Drosophila pseudoobscura opsin genes were compared with those from Drosophila melanogaster, to determine factors that influence the evolution of multigene families. Although the opsin proteins perform the same primary functions, the comparisons reveal a wide range of evolutionary rates. Amino acid identities for the opsins range from 90% for Rh2 to more than 95% for Rh1 and Rh4. Variation in the rate of synonymous site substitution is especially striking: the major opsin, encoded by the Rh1 locus, differs at only 26.1% of synonymous sites between D. pseudoobscura and D. melanogaster, while the other opsin loci differ by as much as 39.2% at synonymous sites. Rh3 and Rh4 have similar levels of synonymous nucleotide substitution but significantly different amounts of amino acid replacement. This decoupling of nucleotide substitution and amino acid replacement suggests that different selective pressures are acting on these similar genes. There is significant heterogeneity in base composition and codon usage bias among the opsin genes in both species, but there are no consistent relationships between these factors and the rate of evolution of the opsins. In addition to exhibiting variation in evolutionary rates, the opsin loci in these species reveal rearrangements of chromosome elements.

Genome sequencing projects have revealed frequent gains and losses of genes between species. Previous versions of our software, Computational Analysis of gene Family Evolution (CAFE), have allowed researchers to estimate parameters of gene gain and loss across a phylogenetic tree. However, the underlying model assumed that all gene families had the same rate of evolution, despite evidence suggesting a large amount of variation in rates among families. Here, we present CAFE 5, a completely re-written software package with numerous performance and user-interface enhancements over previous versions. These include improved support for multithreading, the explicit modeling of rate variation among families using gamma-distributed rate categories, and command-line arguments that preclude the use of accessory scripts. CAFE 5 source code, documentation, test data and a detailed manual with examples are freely available at https://github.com/hahnlab/CAFE5/releases. Supplementary data are available at Bioinformatics online.

A gene's rate of sequence evolution is among the most fundamental evolutionary quantities in common use, but what determines evolutionary rates has remained unclear. Here, we carry out the first combined analysis of seven predictors (gene expression level, dispensability, protein abundance, codon adaptation index, gene length, number of protein-protein interactions, and the gene's centrality in the interaction network) previously reported to have independent influences on protein evolutionary rates. Strikingly, our analysis reveals a single dominant variable linked to the number of translation events which explains 40-fold more variation in evolutionary rate than any other, suggesting that protein evolutionary rate has a single major determinant among the seven predictors. The dominant variable explains nearly half the variation in the rate of synonymous and protein evolution. We show that the two most commonly used methods to disentangle the determinants of evolutionary rate, partial correlation analysis and ordinary multivariate regression, produce misleading or spurious results when applied to noisy biological data. We overcome these difficulties by employing principal component regression, a multivariate regression of evolutionary rate against the principal components of the predictor variables. Our results support the hypothesis that translational selection governs the rate of synonymous and protein sequence evolution in yeast.

BackgroundProbabilistic methods have progressively supplanted the Maximum Parsimony (MP) method for inferring phylogenetic trees. One of the major reasons for this shift was that MP is much more sensitive to the Long Branch Attraction (LBA) artefact than is Maximum Likelihood (ML). However, recent work by Kolaczkowski and Thornton suggested, on the basis of simulations, that MP is less sensitive than ML to tree reconstruction artefacts generated by heterotachy, a phenomenon that corresponds to shifts in site-specific evolutionary rates over time. These results led these authors to recommend that the results of ML and MP analyses should be both reported and interpreted with the same caution. This specific conclusion revived the debate on the choice of the most accurate phylogenetic method for analysing real data in which various types of heterogeneities occur. However, variation of evolutionary rates across species was not explicitly incorporated in the original study of Kolaczkowski and Thornton, and in most of the subsequent heterotachous simulations published to date, where all terminal branch lengths were kept equal, an assumption that is biologically unrealistic.ResultsIn this report, we performed more realistic simulations to evaluate the relative performance of MP and ML methods when two kinds of heterogeneities are considered: (i) within-site rate variation (heterotachy), and (ii) rate variation across lineages. Using a similar protocol as Kolaczkowski and Thornton to generate heterotachous datasets, we found that heterotachy, which constitutes a serious violation of existing models, decreases the accuracy of ML whatever the level of rate variation across lineages. In contrast, the accuracy of MP can either increase or decrease when the level of heterotachy increases, depending on the relative branch lengths. This result demonstrates that MP is not insensitive to heterotachy, contrary to the report of Kolaczkowski and Thornton. Finally, in the case of LBA (i.e. when two non-sister lineages evolved faster than the others), ML outperforms MP over a wide range of conditions, except for unrealistic levels of heterotachy.ConclusionFor realistic combinations of both heterotachy and variation of evolutionary rates across lineages, ML is always more accurate than MP. Therefore, ML should be preferred over MP for analysing real data, all the more so since parametric methods also allow one to handle other types of biological heterogeneities much better, such as among sites rate variation. The confounding effects of heterotachy on tree reconstruction methods do exist, but can be eschewed by the development of mixture models in a probabilistic framework, as proposed by Kolaczkowski and Thornton themselves.

Summary Phylogenetic comparative methods provide a powerful way of addressing classic questions about tempo and mode of phenotypic evolution in the fossil record, such as whether mammals increased in body size diversity after the Cretaceous‐Palaeogene (K‐Pg) extinction. Most often, these kinds of questions are addressed in the context of variation in evolutionary rates. Shifts in the mode of phenotypic evolution provide an alternative and, in some cases, more realistic explanation for patterns of trait diversity in the fossil record, but these kinds of processes are rarely tested for. In this study, I use a time‐calibrated phylogeny of living and fossil Mammaliaformes as a framework to test novel models of body size evolution derived from palaeontological theory. Specifically, I ask whether the K‐Pg extinction resulted in a change in rates of body size evolution or release from a constrained adaptive zone. I found that a model comprising an Ornstein–Uhlenbeck process until the K‐Pg event and a Brownian motion process from the Cenozoic onwards was the best supported model for these data. Surprisingly, results indicate a lower absolute rate of body size evolution during the Cenozoic than during the Mesozoic. This is explained by release from a stationary OU process that constrained realized disparity. Despite a lower absolute rate, body size disparity has in fact been increasing since the K‐Pg event. The use of time‐calibrated phylogenies of living and extinct taxa and realistic, process‐based models provides unparalleled power in testing evolutionary hypotheses. However, researchers should take care to ensure that the models they use are appropriate to the question being tested and that the parameters estimated are interpreted in the context of the best fitting model.

The potential of plant and animal populations to spread over the landscape must be better understood in order to predict biotic responses to Global Change. The fossil record has potential for providing a record of indigenous species as they have shifted ranges in response to past changes of climate (Davis 1976, 1981; Huntley & Birks 1983; Prentice et al. 1991). Our purpose in this paper is to examine whether fossil pollen can provide a clear record of range shifts. We use a model of pollen dispersal to ask how the sizes and locations of lakes affect the way fossil pollen records an approaching population. Can small populations established in advance of the species front be detected? Do changes in pollen deposition give accurate estimates of the intrinsic growth rate of populations of invading species? We are using a simulation model, POLLSCAPE (Sugita 1994), that simulates heterogeneous vegetation on a landscape and calculates pollen dispersal to lakes. The results of the experiments provide guidelines for interpretation of fossil pollen records, and suggest how future studies can be designed to maximize information on past range shifts in response to changing climate.

Variation in evolutionary rates among species is a defining characteristic of the tree of life and may be an important predictor of species' capacities to adapt to rapid environmental change. It is broadly assumed that generation length is an important determinant of microevolutionary rates, and body size is often used as a proxy for generation length. However, body size has myriad biological correlates that could affect evolutionary rates independently from generation length. We leverage two large, independently collected datasets on recent morphological change in birds (52 migratory species breeding in North America and 77 South American resident species) to test how body size and generation length are related to the rates of contemporary morphological change. Both datasets show that birds have declined in body size and increased in wing length over the past 40y. We found, in both systems, a consistent pattern wherein smaller species declined proportionally faster in body size and increased proportionally faster in wing length. By contrast, generation length explained less variation in evolutionary rates than did body size. Although the mechanisms warrant further investigation, our study demonstrates that body size is an important predictor of contemporary variation in morphological rates of change. Given the correlations between body size and a breadth of morphological, physiological, and ecological traits predicted to mediate phenotypic responses to environmental change, the relationship between body size and rates of phenotypic change should be considered when testing hypotheses about variation in adaptive responses to climate change.