Energy and the rate of evolution: inferences from plant rDNA substitution rates in the western Pacific

In this study, we compare rDNA substitution rates for a group of closely related plant species in the western Pacific that exist in different biomes. The results of this comparison indicate higher rates of substitution for species living in habitats with greater biologically available energy. We interpret that finding as potentially important in understanding evolution because of its implication that substitution rate may be a function of biologically available energy and its correlate, productivity. The relevance of this research is twofold. First, contrasting closely related species across different biomes allows for a comparison between rates of molecular evolution across different energetic/productivity regimes while controlling for phylogenetically influenced variation. Second, the research indicates some of the design parameters for future studies that are required to explore the importance of this relationship among different groups of related organisms. If higher rates of molecular evolution where there is greater available energy are found to be widespread this might bring an additional dimension to the understanding of macroevolutionary pattern and process.     

Energy and the tempo of evolution in amphibians

Aim The evolutionary speed hypothesis (ESH) attempts to explain global patterns of species richness on the basis that rates of molecular evolution and speciation in warmer climates have led to a greater accumulation of taxa at lower latitudes. A substantial alternative hypothesis to the ESH is the tropical conservatism hypothesis (TCH). However, recent tests of the TCH, using amphibians as the model taxon, have relied on the assumption that rates of molecular evolution are stable across latitudes and elevations. Here, we test for the first time for systematic variation in rates of molecular evolution across latitude and elevation among amphibians. Location The dataset is geographically diverse with samples from all continents except Antarctica and also from many of the earth's major tropical–warm temperate archipelagos. Methods We tested for substitution rate heterogeneity across climatically varying habitats with the mitochondrial RNA genes 12S and 16S. Thus, we report here on our findings for amphibians – a taxon whose phylogenetic and trophic contexts are remote from those previously tested – using genes that have also not been examined before. The study utilized paired contrasts of sister species (188 species across 18 families, including both caudates and anurans) that are spatially separated in either latitudinal or elevational dimensions. Results We found substantially faster substitution rates for species living in warmer habitats (P= 0.001–0.002) at both lower latitudes (P < 0.02) and lower elevations (P < 0.01). Main conclusions The consistency of these results with the previous studies that used quite different organisms – and in this instance also using different genes – suggests that this is a ubiquitous pattern in nature consistent with the predictions of the ESH. Recent tests of the TCH that, in estimating diversification rates, have relied on the assumption that DNA evolution occurs at a constant rate across latitudes and elevations, require reconsideration in light of the findings presented here. Our results indicate that greater caution is required when estimating dates of divergence using DNA sequence data.     

Function-specific accelerations in rates of sequence evolution suggest predictable epistatic responses to reduced effective population size

Changes in effective population size impinge on patterns of molecular evolution. Notably, slightly deleterious mutations are more likely to drift to fixation in smaller populations, which should typically also lead to an overall acceleration in the rates of evolution. This prediction has been validated empirically for several endosymbiont and island taxa. Here, we first show that rate accelerations are also evident in bacterial pathogens whose recent shifts in virulence make them prime candidates for reduced effective population size: Bacillus anthracis, Bordetella parapertussis, Mycobacterium leprae, Salmonella enterica typhi, Shigella spp., and Yersinia pestis. Using closely related genomes to analyze substitution rate dynamics across six phylogenetically independent bacterial clades, we demonstrate that relative rates of coding sequence evolution are biased according to gene functional category. Notably, genes that buffer against slightly deleterious mutations, such as chaperones, experience stronger rate accelerations than other functional classes at both nonsynonymous and synonymous sites. Although theory predicts altered evolutionary dynamics for buffer loci in the face of accumulating deleterious mutations, to observe even stronger rate accelerations is surprising. We suggest that buffer loci experience elevated substitution rates because the accumulation of deleterious mutations in the remainder of the genome favors compensatory substitutions in trans. Critically, the hyper-acceleration is evident across phylogenetically independent clades, supporting the hypothesis that reductions in effective population size predictably induce epistatic responses in genes that buffer against slightly deleterious mutations.     

Ecology and signal structure drive the evolution of synchronous displays*

Animal synchrony is found in phylogenetically distant animal groups, indicating behavioral adaptations to different selective pressures and in different signaling modalities. A notable example of synchronous display is found in fiddler crabs in that males wave their single enlarged claw during courtship. They present species-specific signals, which are composed of distinctive movement signatures. Given that synchronous waving has been reported for several fiddler crab species, the display pattern could influence the ability of a given species to sufficiently adjust wave timing to allow for synchrony. In this study, we quantified the wave displays of fiddler crabs to predict their synchronous behavior. We combined this information with the group's phylogenetic relationships to trace the evolution of display synchrony in an animal taxon. We found no phylogenetic signal in interspecific variation in predicted wave synchrony, which mirrors the general nonphylogenetic pattern of synchrony across animal taxa. Interestingly, our analyses show that the phenomenon of synchronization stems from the peculiarities of display pattern, mating systems, and the complexity of microhabitats. This is the first study to combine mathematical simulations and phylogenetic comparative methods to reveal how ecological factors and the mechanics of animal signals affect the evolution of the synchronous phenomena.     

Energy, Density, and Constraints to Species Richness: Ant Assemblages along a Productivity Gradient

Species richness describes the number of species of a given taxon in a given time and space. The energy limitation hypothesis links the species richness of consumer taxa to net primary productivity (NPP) through two relationships: NPP limits a taxon's density, and taxon density limits species richness. We study both relationships with a survey of 15 ground ant assemblages, along a productivity gradient from deserts to rain forests. Ant density (colonies m-2) was a positive, decelerating function of net aboveground productivity (NAP). A stepwise regression suggests that the efficiency with which NAP is converted to ant colonies increases with maximum summer temperature and decreases with precipitation. Ant species richness was a positive decelerating function of density at three spatial scales. This supports the energy limitation hypothesis' assumption that average population densities are higher in environments that are more productive. These two nonlinear functions (NAP-density and density-species richness) combine to create, at a variety of scales, positive, decelerating, productivity-diversity curves for a common, ecologically dominant taxon across the terrestrial productivity gradient. However, variance in the density and diversity explained by NAP decreases with scale, suggesting that energy limitation of diversity predominates at small spatial scales (<1 ha).     

Seed banks alter the molecular evolutionary dynamics of Bacillus subtilis

Fluctuations in the availability of resources constrain the growth and reproduction of individuals, which subsequently affects the evolution of their respective populations. Many organisms contend with such fluctuations by entering a reversible state of reduced metabolic activity, a phenomenon known as dormancy. This pool of dormant individuals (i.e. a seed bank) does not reproduce and is expected to act as an evolutionary buffer, though it is difficult to observe this effect directly over an extended evolutionary timescale. Through genetic manipulation, we analyze the molecular evolutionary dynamics of Bacillus subtilis populations in the presence and absence of a seed bank over 700 days. The ability of these bacteria to enter a dormant state increased the accumulation of genetic diversity over time and altered the trajectory of mutations, findings that were recapitulated using simulations based on a mathematical model of evolutionary dynamics. While the ability to form a seed bank did not alter the degree of negative selection, we found that it consistently altered the direction of molecular evolution across genes. Together, these results show that the ability to form a seed bank can affect the direction and rate of molecular evolution over an extended evolutionary timescale.     

Physiological performance and mating system in Clarkia (Onagraceae): Does phenotypic selection predict divergence between sister species?

? Premise of the study: The evolution of self-fertilization often occurs in association with other floral, life history, and fitness-related traits. A previous study found that field populations of Clarkia exilis (a predominantly autogamous selfer) and its sister species, Clarkia unguiculata (a facultative outcrosser) differ in mean photosynthetic rates and instantaneous water use efficiency (WUE(i)). Here, we investigate the strength and direction of selection on these traits in multiple populations of each taxon to determine whether natural selection may contribute to the phenotypic differences between them. ? Methods: In spring 2008, we measured instantaneous gas exchange rates in nine populations during vegetative growth (Early) and/or during flowering (Late). We conducted selection gradient analyses and estimated selection differentials within populations and across pooled conspecific populations to evaluate the strength, direction, and consistency of selection on each trait early and late in the season. ? Key results: The direction and relative strength of selection on photosynthetic rates in these taxa corresponds to the phenotypic difference between them; C. exilis has higher photosynthetic rates than C. unguiculata, as well as stronger, more consistent selection favoring rapid photosynthesis throughout the growing season. Patterns of selection on transpiration, WUE(i), and the timing of flowering progression are less consistent with phenotypic differences (or lack thereof) between taxa. ? Conclusions: We detected several examples where selection was consistent with the phenotypic divergence between sister taxa, but there were also numerous instances that were equivocal or in which selection did not predict the realized phenotypic difference between taxa.     

Evidence of taxon cycles in an Indo-Pacific passerine bird radiation (Aves: Pachycephala)

Many insular taxa possess extraordinary abilities to disperse but may differ in their abilities to diversify and compete. While some taxa are widespread across archipelagos, others have disjunct (relictual) populations. These types of taxa, exemplified in the literature by selections of unrelated taxa, have been interpreted as representing a continuum of expansions and contractions (i.e. taxon cycles). Here, we use molecular data of 35 out of 40 species of the avian genus Pachycephala (including 54 out of 66 taxa in Pachycephala pectoralis (sensu lato), to assess the spatio-temporal evolution of the group. We also include data on species distributions, morphology, habitat and elevational ranges to test a number of predictions associated with the taxon-cycle hypothesis. We demonstrate that relictual species persist on the largest and highest islands across the Indo-Pacific, whereas recent archipelago expansions resulted in colonization of all islands in a region. For co-occurring island taxa, the earliest colonists generally inhabit the interior and highest parts of an island, with little spatial overlap with later colonists. Collectively, our data support the idea that taxa continuously pass through phases of expansions and contractions (i.e. taxon cycles).     

Beetle or roach: systematic position of the enigmatic Umenocoleidae based on new material from Zhonggou Formation in Jiuquan,Northwest China,and a morphocladistic analysis

The Umenocoleidae is among the most perplexing fossil insect taxa, widespread at lower and middle latitudes during the Early Cretaceous and probably becoming extinct after the mid-Cretaceous. This problematic taxon was first described from the Lower Cretaceous of China and has been variously assigned to stem-group Coleoptera, Protelytroptera, Blattaria, stem-group Dictyoptera, or Mantodea. The systematic position of the enigmatic family — especially its type species Umenocoleus sinuatus Chen et T’an, 1973 — has remained highly controversial owing to the lack of preserved phylogenetically informative or diagnostic characters. Here, we describe a new specimen of the type species from the type horizon of the type locality (Lower Cretaceous Zhonggou Formation at Jiuquan, Yumen City, China), and additionally two forewings of Ponopterix. We found that the Umenocoleidae is similar to stem-group Coleoptera in its forewing venation but differs in its multi-segmented antennae, orthognathous orientation of the head, subdivision of the pronotum by a transverse furrow, ultrastructure of the forewing punctures, and unfolded hindwings. Our phylogenetic analysis, using an extended matrix of 72 characters and 37 taxa, indicates that the Umenocoleidae is likely a specialized taxon of Dictyoptera, sister to Alienoptera. The beetle-like appearance is interpreted to be a result of convergent evolution.     

Ultrastructural description of Breviata anathema, n. gen., n. sp., the organism previously studied as "Mastigamoeba invertens"

An understanding of large-scale eukaryotic evolution is beginning to crystallise, as molecular and morphological data demonstrate that eukaryotes fall into six major groups. However, there are several taxa of which the affinities are yet to be resolved, and for which there are only either molecular or morphological data. One of these is the amoeboid flagellate Mastigamoeba invertens. This organism was originally misidentified and studied as a pelobiont using molecular data. We present its first light microscopical and ultrastructural characterisation. We demonstrate that it does not show affinities to the amoebozoan pelobionts, because unlike the pelobionts, it has a double basal body and two flagellar roots, a classical Golgi stack, and a large branching double membrane-bound organelle. Phylogenetic analyses of small subunit ribosomal RNA suggest an affinity with the apusomonads, when a covariotide correction for rate heterogeneity is used. We suggest that previous molecular results have been subject to artefacts from an insufficient correction for rate heterogeneity. We propose a new name for the taxon, Breviata anathema; and the unranked, apomorphy-based name "Breviates" for Breviata and its close relatives.     

A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock

Current understanding of the diversification of birds is hindered by their incomplete fossil record and uncertainty in phylogenetic relationships and phylogenetic rates of molecular evolution. Here we performed the first comprehensive analysis of mitogenomic data of 48 vertebrates, including 35 birds, to derive a Bayesian timescale for avian evolution and to estimate rates of DNA evolution. Our approach used multiple fossil time constraints scattered throughout the phylogenetic tree and accounts for uncertainties in time constraints, branch lengths, and heterogeneity of rates of DNA evolution. We estimated that the major vertebrate lineages originated in the Permian; the 95% credible intervals of our estimated ages of the origin of archosaurs (258 MYA), the amniote-amphibian split (356 MYA), and the archosaur-lizard divergence (278 MYA) bracket estimates from the fossil record. The origin of modern orders of birds was estimated to have occurred throughout the Cretaceous beginning about 139 MYA, arguing against a cataclysmic extinction of lineages at the Cretaceous/Tertiary boundary. We identified fossils that are useful as time constraints within vertebrates. Our timescale reveals that rates of molecular evolution vary across genes and among taxa through time, thereby refuting the widely used mitogenomic or cytochrome b molecular clock in birds. Moreover, the 5-Myr divergence time assumed between 2 genera of geese (Branta and Anser) to originally calibrate the standard mitochondrial clock rate of 0.01 substitutions per site per lineage per Myr (s/s/l/Myr) in birds was shown to be underestimated by about 9.5 Myr. Phylogenetic rates in birds vary between 0.0009 and 0.012 s/s/l/Myr, indicating that many phylogenetic splits among avian taxa also have been underestimated and need to be revised. We found no support for the hypothesis that the molecular clock in birds "ticks" according to a constant rate of substitution per unit of mass-specific metabolic energy rather than per unit of time, as recently suggested. Our analysis advances knowledge of rates of DNA evolution across birds and other vertebrates and will, therefore, aid comparative biology studies that seek to infer the origin and timing of major adaptive shifts in vertebrates.     

Comparison of diverse protein sequences of the nuclear-encoded subunits of cytochrome C oxidase suggests conservation of structure underlies evolving functional sites

Interspecific comparisons of protein sequences can reveal regions of evolutionary conservation that are under purifying selection because of functional constraints. Interpreting these constraints requires combining evolutionary information with structural, biochemical, and physiological data to understand the biological function of conserved regions. We take this integrative approach to investigate the evolution and function of the nuclear-encoded subunits of cytochrome c oxidase (COX). We find that the nuclear-encoded subunits evolved subsequent to the origin of mitochondria and the subunit composition of the holoenzyme varies across diverse taxa that include animals, yeasts, and plants. By mapping conserved amino acids onto the crystal structure of bovine COX, we show that conserved residues are structurally organized into functional domains. These domains correspond to some known functional sites as well as to other uncharacterized regions. We find that amino acids that are important for structural stability are conserved at frequencies higher than expected within each taxon, and groups of conserved residues cluster together at distances of less than 5 A more frequently than do randomly selected residues. We, therefore, suggest that selection is acting to maintain the structural foundation of COX across taxa, whereas active sites vary or coevolve within lineages.     

Microbial diversity in arctic freshwaters is structured by inoculation of microbes from soils

Microbes are transported in hydrological networks through many environments, but the nature and dynamics of underlying microbial metacommunities and the impact of downslope inoculation on patterns of microbial diversity across landscapes are unknown. Pyrosequencing of small subunit ribosomal RNA gene hypervariable regions to characterize microbial communities along a hydrological continuum in arctic tundra showed a pattern of decreasing diversity downslope, with highest species richness in soil waters and headwater streams, and lowest richness in lake water. In a downstream lake, 58% and 43% of the bacterial and archaeal taxa, respectively, were also detected in diverse upslope communities, including most of the numerically dominant lake taxa. In contrast, only 18% of microbial eukaryotic taxa in the lake were detected upslope. We suggest that patterns of diversity in surface waters are structured by initial inoculation from microbial reservoirs in soils followed by a species-sorting process during downslope dispersal of both common and rare microbial taxa. Our results suggest that, unlike for metazoans, a substantial portion of bacterial and archaeal diversity in surface freshwaters may originate in complex soil environments.     

Resource tracking in marine parasites: going with the flow?

Understanding how diversity interacts with energy supply is of broad ecological interest. Most studies to date have investigated patterns within trophic levels, reflecting a lack of food webs which include information on energy flow. We added parasites to a published marine energy‐flow food web, to explore whether parasite diversity is correlated with energy flow to host taxa. Parasite diversity was high with 36 parasite taxa affecting 40 of the 51 animal taxa. Adding parasites increased the number of trophic links per species, trophic link strength, connectance, and food chain lengths. There was evidence of an asymptotic relationship between energy flowing through a food chain and parasite diversity, although there were clear outliers. High parasite diversity was associated with host taxa which were highly connected within the food web. This suggests that energy flow through a taxon may favour parasite diversity, up to a maximal value. The evolutionary and energetic basis for that limitation is of key interest in understanding the basis for parasite diversity in natural food webs and thus their role in food web dynamics.     

Composition and similarity of bovine rumen microbiota across individual animals

The bovine rumen houses a complex microbiota which is responsible for cattle's remarkable ability to convert indigestible plant mass into food products. Despite this ecosystem's enormous significance for humans, the composition and similarity of bacterial communities across different animals and the possible presence of some bacterial taxa in all animals' rumens have yet to be determined. We characterized the rumen bacterial populations of 16 individual lactating cows using tag amplicon pyrosequencing. Our data showed 51% similarity in bacterial taxa across samples when abundance and occurrence were analyzed using the Bray-Curtis metric. By adding taxon phylogeny to the analysis using a weighted UniFrac metric, the similarity increased to 82%. We also counted 32 genera that are shared by all samples, exhibiting high variability in abundance across samples. Taken together, our results suggest a core microbiome in the bovine rumen. Furthermore, although the bacterial taxa may vary considerably between cow rumens, they appear to be phylogenetically related. This suggests that the functional requirement imposed by the rumen ecological niche selects taxa that potentially share similar genetic features.     

Phylogenetic signal in the song of crests and kinglets (Aves: Regulus)

Territorial song structures are often the most prominent characters for distinguishing closely related taxa among songbirds. Learning processes may cause convergent evolution of passerine songs, but phylogenetic information of acoustic traits can be investigated with the help of molecular phylogenies, which are not affected by cultural evolutionary processes. We used a phylogeny based on cytochrome b sequences to trace the evolution of territorial song within the genus Regulus. Five discrete song units are defined as basic components of regulid song via sonagraphic measurements. Traits of each unit are traced on a molecular tree and a mean acoustic character difference between taxon pairs is calculated. Acoustic divergence between regulid taxa correlates strongly with genetic distances. Syntax features of complete songs and of single units are most consistent with the molecular data, whereas the abundance of certain element types is not. Whether song characters are innate or learned was interpreted using hand-reared birds in aviary experiments. We found that convergent character evolution seems to be most probable for learned acoustic traits. We conclude that syntax traits of whole verses or subunits of territorial song, especially innate song structures, are the most reliable acoustic traits for phylogenetic reconstructions in Regulus.     

Population size and molecular evolution on islands

The nearly neutral theory predicts that the rate and pattern of molecular evolution will be influenced by effective population size (Ne), because in small populations more slightly deleterious mutations are expected to drift to fixation. This important prediction has not been widely empirically tested, largely because of the difficulty of comparing rates of molecular evolution in sufficient numbers of independent lineages which differ only in Ne. Island endemic species provide an ideal test of the effect of Ne on molecular evolution because species restricted to islands frequently have smaller Ne than closely related mainland species, and island endemics have arisen from mainland lineages many times in a wide range of taxa. We collated a dataset of 70 phylogenetically independent comparisons between island and mainland taxa, including vertebrates, invertebrates and plants, from 19 different island groups. The rate of molecular evolution in these lineages was estimated by maximum likelihood using two measures: overall substitution rate and the ratio of non-synonymous to synonymous substitution rates. We show that island lineages have significantly higher ratios of non-synonymous to synonymous substitution rates than mainland lineages, as predicted by the nearly neutral theory, although overall substitution rates do not differ significantly.