A Practical Guide to Phylogenetic Paleoecology

Understanding variation in rates of evolution and morphological disparity is a goal of macroevolutionary research. In a phylogenetic comparative methods framework, we present three explicit models for linking the rate of evolution of a trait to the state of another evolving trait. This allows testing hypotheses about causal influences on rates of phenotypic evolution with phylogenetic comparative data. We develop a statistical framework for fitting the models with generalized least-squares regression and use this to discuss issues and limitations in the study of rates of evolution more generally. We show that the power to detect effects on rates of evolution is low in that even strong causal effects are unlikely to explain more than a few percent of observed variance in disparity. We illustrate the models and issues by testing if rates of beak-shape evolution in birds are influenced by brain size, as may be predicted from a Baldwin effect in which presumptively more behaviorally flexible large-brained species generate more novel selection on themselves leading to higher rates of evolution. From an analysis of morphometric data for 645 species, we find evidence that both macro- and microevolution of the beak are faster in birds with larger brains, but with the caveat that there are no consistent effects of relative brain size.[Baldwin effect; beak shape; behavioral drive; bird; brain size; disparity; phylogenetic comparative method; rate of evolution.]

The tempo and mode of morphological evolution are influenced by several factors, among which evolutionary transformations in developmental processes are likely to be important. Comparing the embryos of extant species in an explicit phylogenetic fram work allows the estimation of minimum average rates of evolution in quantitative developmental parameters. It also allows delineation of the maximum time that complex qualitative transformations in developmental mechanism take to evolve. This paper analyzes rates of quantitative and qualitative developmental evolution using examples drawn primarily from echinoderms. The results demonstrate that rates of developmental evolution can be comparable to rates of morphological evolution. There is no indication that rates of evolution in development are lower for earlier stages, contrary to the prediction of “tree” models of epigenetic interactions. In particular, rates of evolution in oogenesis can exceed rates of evolution in adult body size. Rates of developmental evolution can vary by up to two orders of magnitude within a clade. Whether such large scale variation in evolutionary rates of developmental processes is a general phenomenon can only be answered by further study.

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.

Mammaliaform extinctions as a driver of the morphological radiation of Cenozoic mammals

Inconsistent results on the association between evolutionary rates and amino acid composition of proteins have been reported in eukaryotes. However, there are few studies of how amino acid composition can influence evolutionary rates in bacteria. Thus, we constructed linear regression models between composition frequencies of amino acids and evolutionary rates for bacteria. Compositions of all amino acids can on average explain 21.5% of the variation in evolutionary rates among 273 investigated bacterial organisms. In five model organisms, amino acid composition contributes more to variation in evolutionary rates than protein abundance, and frequency of optimal codons. The contribution of individual amino acid composition to evolutionary rate varies among organisms. The closer the GC-content of genome to its maximum or minimum, the better the correlation between the amino acid content and the evolutionary rate of proteins would appear in that genome. The types of amino acids that significantly contribute to evolutionary rates can be grouped into GC-rich and AT-rich amino acids. Besides, the amino acid with high composition also contributes more to evolutionary rates than amino acid with low composition in proteome. In summary, amino acid composition significantly contributes to the rate of evolution in bacterial organisms and this in turn is impacted by GC-content.

Understanding why rates of morphological evolution vary is a major goal in evolutionary biology. Classical work suggests that body size, interspecific competition, geographic range size and specialization may all be important, and each may increase or decrease rates of evolution. Here, we investigate correlates of proportional evolutionary rates in phalangeriform possums, phyllostomid bats, platyrrhine monkeys and marmotine squirrels, using phylogenetic comparative methods. We find that the most important correlate is body size. Large species evolve the fastest in all four clades, and there is a nonlinear relationship in platyrrhines and phalangeriformes, with the slowest evolution in species of intermediate size. We also find significant increases in rate with high environmental temperature in phyllostomids, and low mass-specific metabolic rate in marmotine squirrels. The mechanisms underlying these correlations are uncertain and appear to be size specific. We conclude that there is significant variation in rates of evolution, but that its meaning is not yet clear.

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.

SummaryModern bird diversity spans a striking array of forms, behaviours, and ecological roles. Analyses of molecular evolutionary rates can reveal the links between genomic and phenotypic change, but disentangling the drivers of rate variation has been difficult across large numbers of whole-genomes. Using comprehensive estimates of traits and evolutionary rates across a family-level phylogeny of birds, we show that clutch size, generation length, and beak shape are dominant predictors of genome-wide mutation rates. To identify the major axes of evolutionary rate variation, we employ covariance matrix eigendecomposition from rates estimated for branches of the avian phylogeny and across genomic loci. We find that the majority of rate variation occurs along the terminal branches of the phylogeny associated with extant families of birds. Additionally, we use principal components analyses to show that several axes of variation are linked with rapid evolution in microchromosomes immediately after the Cretaceous–Palaeogene transition. These apparent pulses of evolution are consistent with major changes in evolutionary rates in the machineries for meiosis, heart performance, and RNA splicing, surveillance, and translation. They also correlate with the diversification of ecological niches reflected in increased tarsus length. Collectively, our analyses paint a nuanced picture of avian evolutionary rates through time, revealing that the ancestors of the most diverse lineages of birds underwent major genomic changes related to mutation, gene usage, and niche expansion near the beginning of the Palaeogene period.

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.

SummaryMolecular clock calibration is a crucial step for placing phylogenetic trees in the temporal framework required to test evolutionary hypotheses and estimate evolutionary rates. In general, most authors agree that the best approach is to incorporate multiple calibrations to avoid the risk of bias associated with a single dating source. However, the indiscriminate inclusion of as many calibration points as possible can lead to tree shape distortion and an overestimation of the variation in evolutionary rates among branches due to errors in the geological, paleontological or paleogeographic information used for dating.We present a test of congruence among calibration hypotheses to assist their filtering prior to molecular clock analysis, which we have calledBayesFactorClusterAnalysis (BFCA). This is a heuristic method based on the comparison of pairwise calibrations hypotheses byBayes factors that allows identifying sets of congruent calibrations.We have testedBFCAthrough simulation usingbeastandmcmctree programs and analysed a real case of multiple calibration hypotheses to date the evolution of the genusCarabus(Coleoptera:Carabidae).The analyses of simulated data showed the predictability of change inBayes factors when comparing alternative calibration hypotheses on a particular tree topology, and thus the suitability ofBFCAin identifying unreliable calibrations, especially in cases with limited variation in evolutionary rates among branches. The exclusion of inconsistent calibrations as identified byBFCAproduced significant changes in the estimation of divergence times and evolutionary rates in the genusCarabus, illustrating the importance of filtering calibrations before analyses.The method has been implemented in an open‐sourceRpackage calledbfcato simplify its application.

Decision letter: Complex plumages spur rapid color diversification in kingfishers (Aves: Alcedinidae)

Editor's evaluation: Complex plumages spur rapid color diversification in kingfishers (Aves: Alcedinidae)

Rates of molecular evolution may vary widely between populations, yet the causes of this variation are still incompletely understood. Genetic differences between populations may make an important contribution to variation in rates of evolution, owing to differences in fitness, population size, mutation rates, or in the distribution of fitness effects (DFEs) of available beneficial mutations. By whole genome sequencing of Escherichia coli populations experimentally evolved in the presence of a quinolone antibiotic, we found that rates of substitution varied by genotype, with evidence for a contribution from a genotype's starting fitness. Subsequent targeted sequencing showed that genotypes with high average substitution rates were more likely to undergo the simultaneous fixation of several mutations, consistent with theoretical models of multiple mutation dynamics. Moreover, patterns of substitution were indicative of epistatic relationships between known resistance mutations.

Understanding how and why rates of evolutionary diversification vary is a key issue in evolutionary biology, ecology, and biogeography. Evolutionary rates are the net result of interacting processes summarized under concepts such as adaptive radiation and evolutionary stasis. Here, we review the central concepts in the evolutionary diversification literature and synthesize these into a simple, general framework for studying rates of diversification and quantifying their underlying dynamics, which can be applied across clades and regions, and across spatial and temporal scales. Our framework describes the diversification rate (d) as a function of the abiotic environment (a), the biotic environment (b), and clade‐specific phenotypes or traits (c); thus, d ~ a,b,c. We refer to the four components (a–d) and their interactions collectively as the “Evolutionary Arena.” We outline analytical approaches to this framework and present a case study on conifers, for which we parameterize the general model. We also discuss three conceptual examples: the Lupinus radiation in the Andes in the context of emerging ecological opportunity and fluctuating connectivity due to climatic oscillations; oceanic island radiations in the context of island formation and erosion; and biotically driven radiations of the Mediterranean orchid genus Ophrys. The results of the conifer case study are consistent with the long‐standing scenario that low competition and high rates of niche evolution promote diversification. The conceptual examples illustrate how using the synthetic Evolutionary Arena framework helps to identify and structure future directions for research on evolutionary radiations. In this way, the Evolutionary Arena framework promotes a more general understanding of variation in evolutionary rates by making quantitative results comparable between case studies, thereby allowing new syntheses of evolutionary and ecological processes to emerge.

What causes the variations in evolutionary rates is fundamental to molecular evolution. However, in plants, the causes of within-gene evolutionary rate variations remain underexplored. Here we use the principal component regression to examine the contributions of eleven exon features to the within-gene variations in nonsynonymous substitution rate (dN), synonymous substitution rate (dS), and the dN/dS ratio in Arabidopsis species. We demonstrate that exon features related to protein structural-functional constraints and mRNA splicing account for the largest proportions of within-gene variations in dN/dS and dN. Meanwhile, for dS, a combination of expression level, exon length, and structural-functional features explains the largest proportion of within-gene variances. Our results suggest that the determinants of within-gene variations differ from those of between-gene variations in evolutionary rates. Furthermore, the relative importance of different exon features also differs between plants and animals. Our study thus may shed a new light on the evolution of plant genes.