Relative Divergence Times Research Articles

Fast Bayesian Inference of Phylogenies from Multiple Continuous Characters.

Time-scaled phylogenetic trees are an ultimate goal of evolutionary biology and a necessary ingredient in comparative studies. The accumulation of genomic data has resolved the tree of life to a great extent, yet timing evolutionary events remain challenging if not impossible without external information such as fossil ages and morphological characters. Methods for incorporating morphology in tree estimation have lagged behind their molecular counterparts, especially in the case of continuous characters. Despite recent advances, such tools are still direly needed as we approach the limits of what molecules can teach us. Here, we implement a suite of state-of-the-art methods for leveraging continuous morphology in phylogenetics, and by conducting extensive simulation studies we thoroughly validate and explore our methods' properties. While retaining model generality and scalability, we make it possible to estimate absolute and relative divergence times from multiple continuous characters while accounting for uncertainty. We compile and analyze one of the most data-type diverse data sets to date, comprised of contemporaneous and ancient molecular sequences, and discrete and continuous morphological characters from living and extinct Carnivora taxa. We conclude by synthesizing lessons about our method's behavior, and suggest future research venues.

P324 Phylogenetic and ecological overview of Onygenales

Poster session 3, September 23, 2022, 12:30 PM - 1:30 PMObjectivesTo evaluate the general taxonomy and phylogeny of the order Onygenales using ecological, morphological, and molecular data, stimulate awareness of correct identification of neglected groups in the order, and contribute to the stabilization of the nomenclature.MethodsIn total 97 genera, 385 species, and 553 strains were analyzed in this study. The ITS, LSU, TUB, TEF3, and RP60S gene regions were amplified and sequenced. Sequences for the RPB1, RPB2, and TEF1 regions were retrieved from the NCBI nucleotide database. Whole genome data for 53 strains were also included in phylogenetic tree analyses. Ecology and ascomata morphology for the type species were retrieved from the literature. Phylogenetic trees were constructed using the maximum likelihood methods implemented in IQ-TREE software and MRBAYES v3.2.7 on the CIPRES portal. Additionally, relative divergence time within Onygenales was estimated based on the RelTime method implemented in MEGA 7.ResultsA total of 1667 sequences for LSU (n = 421), ITS (n = 519), TUB (n = 189), RP60S (n = 123), TEF1 (n = 119), TEF3 (n = 144), RPB1 (n = 71), and RPB2 (n = 97) were examined. The results of the combined data analysis yielded 14 clades with ≥90% support for Bayesian probability and ≥80% support for maximum likelihood analyses. Families, based on their type genera and type species, were resolved as Ajellomycetaceae, Arthrodermataceae, Ascosphaeraceae, Eremascaceae, Gymnoascaceae, Onygenaceae, and Spiromastigoidaceae (Fig. 1). Two families were newly introduced as Malbrancheaceae and Neogymnomycetaceae. The family Nannizziopsidaceae clustered amidst members of Onygenaceae. The ecological preferences were classified as soil/oligotrophic, soil/keratinophilic, dung/agricultural, skin/nail, hair/feather, insect/pollen, osmotic habitats, systemic, plant, and other/unknown (Fig. 2). Almost all families in the order have members that can be found on skin and nails, which can cause asymptomatic or symptomatic infections, or members that are able to grow at 37°C and cause systemic infections. Four main types of ascomata morphology were noted: cleistothecium, gymnothecium, spore cyst, and naked fruitbody. The results of RelTime analysis showed that the diversification of species in Onygenales occurred at 103 Mya. The earliest species of the order were found in Gymnoascaceae, while the most recent species were found close to Arthrodermataceae.ConclusionDetermination of the borderlines in the order can be difficult because of the effects of chosen methods, number of samples, number of genes, and also the choice of outgroups. Taxon sampling and inclusion of both type species and related genera in analyses are particularly essential to minimize changes and stabilize nomenclature for longer periods. Providing molecular data for the isolates and making them publicly available is also important to prevent taxonomic disagreements. Significant ecological traits that determine evolution in Onygenales are osmophily, thermophily, cellulolysis, eutrophism, oligotrophism, keratinolysis, and thermal dimorphism. Morphological and physiological characteristics may be informative for habitat choice and evolutionary processes. Cellulolytic and osmophilic abilities might be ancestral characteristics in Onygenales. Even though most of the species are found in soil and are non-pathogenic, environmental and host alterations can lead to the emergence of new fungal pathogens among soil fungi. Therefore, Onygenales continues to deserve close attention.

A tale about vipers’ tails: phylogeography of black-tailed rattlesnakes

The phylogenetic relationships among black-tailed rattlesnakes remain poorly understood and some authors indicated that the diversity of this group has been underestimated and additional analyses are required to clarify the biogeographic patterns throughout its distribution in Mexico. Therefore, the aim of this study was to elucidate the phylogenetic relationships among black-tailed rattlesnakes across their range, identifying relative divergence times among the main clades and reconstructing the biogeographical history of the group. Three partial mitochondrial genes (ND4, cytb and ATPase6) and one nuclear gene (RAG1) were sequenced to infer the phylogenetic relationships, through the maximum likelihood and Bayesian inference-based methods; demographic history reconstruction was investigated through Bayesian Skyline plot analysis and the ancestral area reconstruction was carried out considering a Bayesian framework. We found strong evidence that the black-tailed rattlesnakes’ group is composed of six clades, which is in agreement with subspecies previously reported. Divergence time estimation indicated that the origin of the C. molossus group could be traced to the middle of the Miocene (~7.71 Mya). Ancestral area reconstruction indicated that early divergence events occurred in Central Mexico, probably related to the geological dynamics of the Trans-Mexican Volcanic Belt. The lineage C. m. oaxacus is the basal member of the C. molossus group. Furthermore, the combination of geological events and changes in Quaternary vegetation may have contributed to the divergence of C. molossus clades. Our results suggest several clades within C. molossus complex could be potentially recognized as separate species.

Accounting for Errors in Data Improves Divergence Time Estimates in Single-cell Cancer Evolution.

Single-cell sequencing provides a new way to explore the evolutionary history of cells. Compared to traditional bulk sequencing, where a population of heterogeneous cells is pooled to form a single observation, single-cell sequencing isolates and amplifies genetic material from individual cells, thereby preserving the information about the origin of the sequences. However, single-cell data are more error-prone than bulk sequencing data due to the limited genomic material available per cell. Here, we present error and mutation models for evolutionary inference of single-cell data within a mature and extensible Bayesian framework, BEAST2. Our framework enables integration with biologically informative models such as relaxed molecular clocks and population dynamic models. Our simulations show that modeling errors increase the accuracy of relative divergence times and substitution parameters. We reconstruct the phylogenetic history of a colorectal cancer patient and a healthy patient from single-cell DNA sequencing data. We find that the estimated times of terminal splitting events are shifted forward in time compared to models which ignore errors. We observed that not accounting for errors can overestimate the phylogenetic diversity in single-cell DNA sequencing data. We estimate that 30–50% of the apparent diversity can be attributed to error. Our work enables a full Bayesian approach capable of accounting for errors in the data within the integrative Bayesian software framework BEAST2.

Relative Time Inference Using Lateral Gene Transfers.

Many organisms are able to incorporate exogenous DNA into their genomes. This process, called lateral gene transfer (LGT), has the potential to benefit the recipient organism by providing useful coding sequences, such as antibiotic resistance genes or enzymes which expand the organism's metabolic niche. For evolutionary biologists, LGTs have often been considered a nuisance because they complicate the reconstruction of the underlying species tree that many analyses aim to recover. However, LGT events between distinct organisms harbor information on the relative divergence time of the donor and recipient lineages. As a result transfers provide a novel and as yet mostly unexplored source of information to determine the order of divergence of clades, with the potential for absolute dating if linked to the fossil record.

Analysis of rDNA reveals a high genetic diversity of Halophila major in the Wallacea region.

The genus Halophila shows the highest species diversity within the seagrass genera. Southeast Asian countries where several boundary lines exist were considered as the origin of seagrasses. We hypothesize that the boundary lines, such as Wallace's and Lydekker's Lines, may act as marine geographic barriers to the population structure of Halophila major. Seagrass samples were collected at three islands in Vietnamese waters and analyzed by the molecular maker ITS. These sequences were compared with published ITS sequences from seagrasses collected in the whole region of interest. In this study, we reveal the haplotype and nucleotide diversity, linking population genetics, phylogeography, phylogenetics and estimation of relative divergence times of H. major and other members of the Halophila genus. The morphological characters show variation. The results of the ITS marker analysis reveal smaller groups of H. major from Myanmar, Shoalwater Bay (Australia) and Okinawa (Japan) with high supporting values. The remaining groups including Sri Lanka, Viet Nam, the Philippines, Thailand, Malaysia, Indonesia, Two Peoples Bay (Australia) and Tokushima (Japan) showed low supporting values. The Wallacea region shows the highest haplotype and also nucleotide diversity. Non-significant differences were found among regions, but significant differences were presented among populations. The relative divergence times between some members of section Halophila were estimated 2.15-6.64 Mya.

A phylogeny for the Drosophila montium species group: A model clade for comparative analyses

The Drosophila montium species group is a clade of 94 named species, closely related to the model species D. melanogaster. The montium species group is distributed over a broad geographic range throughout Asia, Africa, and Australasia. Species of this group possess a wide range of morphologies, mating behaviors, and endosymbiont associations, making this clade useful for comparative analyses. We use genomic data from 42 available species to estimate the phylogeny and relative divergence times within the montium species group, and its relative divergence time from D. melanogaster. To assess the robustness of our phylogenetic inferences, we use 3 non-overlapping sets of 20 single-copy coding sequences and analyze all 60 genes with both Bayesian and maximum likelihood methods. Our analyses support monophyly of the group. Apart from the uncertain placement of a single species, D. baimaii, our analyses also support the monophyly of all seven subgroups proposed within the montium group. Our phylograms and relative chronograms provide a highly resolved species tree, with discordance restricted to estimates of relatively short branches deep in the tree. In contrast, age estimates for the montium crown group, relative to its divergence from D. melanogaster, depend critically on prior assumptions concerning variation in rates of molecular evolution across branches, and hence have not been reliably determined. We discuss methodological issues that limit phylogenetic resolution – even when complete genome sequences are available – as well as the utility of the current phylogeny for understanding the evolutionary and biogeographic history of this clade.

Quaternary land bridges have not been universal conduits of gene flow.

Quaternary climate oscillations are a well-known driver of animal diversification, but their effects are most well studied in areas where glaciations lead to habitat fragmentation. In large areas of the planet, however, glaciations have had the opposite effect, but here their impacts are much less well understood. This is especially true in Southeast Asia, where cyclical changes in land distribution have generated enormous land expansions during glacial periods. In this study, we selected a panel of five songbird species complexes covering a range of ecological specificities to investigate the effects Quaternary land bridges have had on the connectivity of Southeast Asian forest biota. Specifically, we combined morphological and bioacoustic analysis with an arsenal of population genomic and modelling approaches applied to thousands of genome-wide DNA markers across a total of more than 100 individuals. Our analyses show that species dependent on forest understorey exhibit deep differentiation between Borneo and western Sundaland, with no evidence of gene flow during the land bridges accompanying the last 1-2 ice ages. In contrast, dispersive canopy species and habitat generalists have experienced more recent gene flow. Our results argue that there remains much cryptic species-level diversity to be discovered in Southeast Asia even in well-known animal groups such as birds, especially in nondispersive forest understorey inhabitants. We also demonstrate that Quaternary land bridges have not been equally suitable conduits of gene flow for all species complexes and that life history is a major factor in predicting relative population divergence time across Quaternary climate fluctuations.

Independent Evolution of Strychnine Recognition by Bitter Taste Receptor Subtypes.

The 25 human bitter taste receptors (hT2Rs) recognize thousands of structurally and chemically diverse bitter substances. The binding modes of human bitter taste receptors hT2R10 and hT2R46, which are responsible for strychnine recognition, were previously established using site-directed mutagenesis, functional assays, and molecular modeling. Here we construct a phylogenetic tree and reconstruct ancestral sequences of the T2R10 and T2R46 clades. We next analyze the binding sites in view of experimental data to predict their ability to recognize strychnine. This analysis suggests that the common ancestor of hT2R10 and hT2R46 is unlikely to bind strychnine in the same mode as either of its two descendants. Estimation of relative divergence times shows that hT2R10 evolved earlier than hT2R46. Strychnine recognition was likely acquired first by the earliest common ancestor of the T2R10 clade before the separation of primates from other mammals, and was highly conserved within the clade. It was probably independently acquired by the common ancestor of T2R43-47 before the homo-ape speciation, lost in most T2Rs within this clade, but enhanced in the hT2R46 after humans diverged from the rest of primates. Our findings suggest hypothetical strychnine T2R receptors in several species, and serve as an experimental guide for further study. Improved understanding of how bitter taste receptors acquire the ability to be activated by particular ligands is valuable for the development of sensors for bitterness and for potential toxicity.

An Evaluation of Different Partitioning Strategies for Bayesian Estimation of Species Divergence Times.

The explosive growth of molecular sequence data has made it possible to estimate species divergence times under relaxed-clock models using genome-scale data sets with many gene loci. In order to improve both model realism and to best extract information about relative divergence times in the sequence data, it is important to account for the heterogeneity in the evolutionary process across genes or genomic regions. Partitioning is a commonly used approach to achieve those goals. We group sites that have similar evolutionary characteristics into the same partition and those with different characteristics into different partitions, and then use different models or different values of model parameters for different partitions to account for the among-partition heterogeneity. However, how to partition data in practical phylogenetic analysis, and in particular in relaxed-clock dating analysis, is more art than science. Here, we use computer simulation and real data analysis to study the impact of the partition scheme on divergence time estimation. The partition schemes had relatively minor effects on the accuracy of posterior time estimates when the prior assumptions were correct and the clock was not seriously violated, but showed large differences when the clock was seriously violated, when the fossil calibrations were in conflict or incorrect, or when the rate prior was mis-specified. Concatenation produced the widest posterior intervals with the least precision. Use of many partitions increased the precision, as predicted by the infinite-sites theory, but the posterior intervals might fail to include the true ages because of the conflicting fossil calibrations or mis-specified rate priors. We analyzed a data set of 78 plastid genes from 15 plant species with serious clock violation and showed that time estimates differed significantly among partition schemes, irrespective of the rate drift model used. Multiple and precise fossil calibrations reduced the differences among partition schemes and were important to improving the precision of divergence time estimates. While the use of many partitions is an important approach to reducing the uncertainty in posterior time estimates, we do not recommend its general use for the present, given the limitations of current models of rate drift for partitioned data and the challenges of interpreting the fossil evidence to construct accurate and informative calibrations.

Phylogeny and diversity of neotropical monkey lizards (Iguanidae: Polychrus Cuvier, 1817).

Neotropical monkey lizards (Polychrus) are arboreal lizards with compressed bodies, partially fused eyelids and strikingly long, whip-like tails. The eight currently recognized species occur in the lowlands of South and Central America. Based on the largest taxon and character sampling to date, we analyze three mitochondrial and one nuclear gene using Bayesian methods to (1) infer the phylogeny of Polychrus under both concatenated-tree and species-tree methods; (2) identify lineages that could represent putative undescribed species; and (3) estimate divergence times. Our species tree places P. acutirostris as the sister taxon to all other species of Polychrus. While the phylogenetic position of P. gutturosus and P. peruvianus is poorly resolved, P. marmoratus and P. femoralis are strongly supported as sister to P. liogaster and P. jacquelinae, respectively. Recognition of P. auduboni and P. marmoratus sensu stricto as distinct species indicates that the populations of "P. marmoratus" from the Amazon and the Atlantic coast in Brazil represent separate species. Similarly, populations of P. femoralis from the Tumbes region might belong to a cryptic undescribed species. Relative divergence times and published age estimates suggest that the orogeny of the Andes did not play a significant role in the early evolution of Polychrus.

Fast evolutionary rates associated with functional loss in class I glucose transporters of Schistosoma mansoni

BackgroundThe trematode parasite, Schistosoma mansoni, has evolved to switch from oxidative phosphorylation to glycolysis in the presence of glucose immediately after invading the human host. This metabolic switch is dependent on extracellular glucose concentration. Four glucose transporters are encoded in the genome of S. mansoni, however, only two were shown to facilitate glucose diffusion.ResultsBy modeling the phase of human host infection, we showed that transporter transcript expression profiles of recently transformed schistosomula have two opposing responses to increased glucose concentrations. Concurring with the transcription profiles, our phylogenetic analyses revealed that S. mansoni glucose transporters belong to two separate clusters, one associated with class I glucose transporters from vertebrates and insects, and the other specific to parasitic Platyhelminthes. To study the evolutionary paths of both groups and their functional implications, we determined evolutionary rates, relative divergence times, genomic organization and performed structural analyses with the protein sequences. We finally used the modelled structures of the S. mansoni glucose transporters to biophysically (i) analyze the dynamics of key residues during glucose binding, (ii) test glucose stability within the active site, and (iii) demonstrate glucose diffusion. The two S. mansoni Platyhelminthes-specific glucose transporters, which seem to be younger than the other two, exhibit slower rates of molecular evolution, are encoded by intron-poor genes, and transport glucose. Interestingly, our molecular dynamic analyses suggest that S. mansoni class I glucose transporters are not able to transport glucose.ConclusionsThe glucose transporter family in S. mansoni exhibit different evolutionary histories. Our results suggested that S. mansoni class I glucose transporters lost their capacity to transport glucose and that this function evolved independently in the Platyhelminthes-specific glucose transporters. Finally, taking into account the differences in the dynamics of glucose transport of the Platyhelminthes-specific transporters of S. mansoni compared to that of humans, we conclude that S. mansoni glucose transporters may be targets for rationally designed drugs against schistosomiasis.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2144-6) contains supplementary material, which is available to authorized users.

A Protocol for Diagnosing the Effect of Calibration Priors on Posterior Time Estimates: A Case Study for the Cambrian Explosion of Animal Phyla.

We present a procedure to test the effect of calibration priors on estimated times, which applies a recently developed calibration-free approach (RelTime) method that produces relative divergence times for all nodes in the tree. We illustrate this protocol by applying it to a timetree of metazoan diversification (Erwin DH, Laflamme M, Tweedt SM, Sperling EA, Pisani D, Peterson KJ. 2011. The Cambrian conundrum: early divergence and later ecological success in the early history of animals. Science 334:1091-1097.), which placed the divergence of animal phyla close to the time of the Cambrian explosion inferred from the fossil record. These analyses revealed that the two maximum-only calibration priors in the pre-Cambrian are the primary determinants of the young divergence times among animal phyla in this study. In fact, these two maximum-only calibrations produce divergence times that severely violate minimum boundaries of almost all of the other 22 calibration constraints. The use of these 22 calibrations produces dates for metazoan divergences that are hundreds of millions of years earlier in the Proterozoic. Our results encourage the use of calibration-free approaches to identify most influential calibration constraints and to evaluate their impact in order to achieve biologically robust interpretations.

Anciently duplicated genes reduce uncertainty in molecular clock estimates

Deciphering the histories of lineages as they have unfolded over billions of years, and placing them in the context of the known fossil record and Earth’s biogeochemical events, is a challenging task in evolutionary biology. Shortly after discovering the molecular structure of DNA and determining the first amino acid sequences of proteins, it was recognized that the evolutionary distances among lineages could be estimated from the changes observed in nucleotide and amino acid sequences (substitutions). Combined with the hypothesis that steady accumulation of substitutions over time is analogous to the “ticking” of a clock [and hence the moniker “molecular clock” (1)], the relative divergence times among lineages could be estimated from the genetic distances among them. Estimating the times of the major evolutionary events in the history of Earth’s biosphere could be made when the branches of the evolutionary tree are calibrated with available fossil evidence, allowing conversion of the relative divergence times to the absolute estimates (2). Realization that the molecular clock “ticks” unevenly within and across genes, among different lineages and over time, as well as a scarce and often controversial fossil record, ultimately led to a development of a new class of Bayesian “relaxed clock” models (3). These models do not require all lineages to evolve at the same rate and allow incorporation of heterogeneous (as well as vague) prior information from multiple genes, a large number of taxa, and multiple calibration points (3). Despite these methodological advances, dating various past evolutionary events has continued to produce conflicting estimates and wide uncertainty intervals. In PNAS, Shih and Matzke (4) introduce a clever approach to decrease the uncertainty associated with the inferred dates via additional constraints provided by anciently duplicated gene families.

Efficient method for estimating divergence times

Methods for estimating the timing of species divergences are widely used but require a large amount of computational time for even a modest number of genomes. Current methods also rely on calibrations of the molecular clock, including modelling differences in the rate of the molecular clock across lineages, which has many uncertainties. To overcome these difficulties, Tamura et al. present a method called RelTime, which estimates relative divergence times for each branch point on a phylogenetic tree, thus overcoming the need for calibrations. It is much faster than existing Bayesian methods.

Bayesian Selection of Nucleotide Substitution Models and Their Site Assignments

Probabilistic inference of a phylogenetic tree from molecular sequence data is predicated on a substitution model describing the relative rates of change between character states along the tree for each site in the multiple sequence alignment. Commonly, one assumes that the substitution model is homogeneous across sites within large partitions of the alignment, assigns these partitions a priori, and then fixes their underlying substitution model to the best-fitting model from a hierarchy of named models. Here, we introduce an automatic model selection and model averaging approach within a Bayesian framework that simultaneously estimates the number of partitions, the assignment of sites to partitions, the substitution model for each partition, and the uncertainty in these selections. This new approach is implemented as an add-on to the BEAST 2 software platform. We find that this approach dramatically improves the fit of the nucleotide substitution model compared with existing approaches, and we show, using a number of example data sets, that as many as nine partitions are required to explain the heterogeneity in nucleotide substitution process across sites in a single gene analysis. In some instances, this improved modeling of the substitution process can have a measurable effect on downstream inference, including the estimated phylogeny, relative divergence times, and effective population size histories.

Imprints from genetic drift and mutation imply relative divergence times across marine transition zones in a pan-European small pelagic fish (Sprattus sprattus).

Geographic distributions of most temperate marine fishes are affected by postglacial recolonisation events, which have left complex genetic imprints on populations of marine species. This study investigated population structure and demographic history of European sprat (Sprattus sprattus L.) by combining inference from both mtDNA and microsatellite genetic markers throughout the species' distribution. We compared effects from genetic drift and mutation for both genetic markers in shaping genetic differentiation across four transition zones. Microsatellite markers revealed significant isolation by distance and a complex population structure across the species' distribution (overall θ(ST)=0.038, P<0.01). Across transition zones markers indicated larger effects of genetic drift over mutations in the northern distribution of sprat contrasting a stronger relative impact of mutation in the species' southern distribution in the Mediterranean region. These results were interpreted to reflect more recent divergence times between northern populations in accordance with previous findings. This study demonstrates the usefulness of comparing inference from different markers and estimators of divergence for phylogeographic and population genetic studies in species with weak genetic structure, as is the case in many marine species.

Using affinity propagation for identifying subspecies among clonal organisms: lessons from M. tuberculosis

BackgroundClassification and naming is a key step in the analysis, understanding and adequate management of living organisms. However, where to set limits between groups can be puzzling especially in clonal organisms. Within the Mycobacterium tuberculosis complex (MTC), the etiological agent of tuberculosis (TB), experts have first identified several groups according to their pattern at repetitive sequences, especially at the CRISPR locus (spoligotyping), and to their epidemiological relevance. Most groups such as "Beijing" found good support when tested with other loci. However, other groups such as T family and T1 subfamily (belonging to the "Euro-American" lineage) correspond to non-monophyletic groups and still need to be refined. Here, we propose to use a method called Affinity Propagation that has been successfully used in image categorization to identify relevant patterns at the CRISPR locus in MTC.ResultsTo adequately infer the relative divergence time between strains, we used a distance method inspired by the recent evolutionary model by Reyes et al. We first confirm that this method performs better than the Jaccard index commonly used to compare spoligotype patterns. Second, we document the support of each spoligotype family among the previous classification using affinity propagation on the international spoligotyping database SpolDB4. This allowed us to propose a consensus assignation for all SpolDB4 spoligotypes. Third, we propose new signatures to subclassify the T family.ConclusionAltogether, this study shows how the new clustering algorithm Affinity Propagation can help building or refining clonal organims classifications. It also describes well-supported families and subfamilies among M. tuberculosis complex, especially inside the modern "Euro-American" lineage.

More reliable estimates of divergence times inPanusing complete mtDNA sequences and accounting for population structure

Here, we report the sequencing and analysis of eight complete mitochondrial genomes of chimpanzees (Pan troglodytes) from each of the three established subspecies (P. t. troglodytes, P. t. schweinfurthii and P. t. verus) and the proposed fourth subspecies (P. t. ellioti). Our population genetic analyses are consistent with neutral patterns of evolution that have been shaped by demography. The high levels of mtDNA diversity in western chimpanzees are unlike those seen at nuclear loci, which may reflect a demographic history of greater female to male effective population sizes possibly owing to the characteristics of the founding population. By using relaxed-clock methods, we have inferred a timetree of chimpanzee species and subspecies. The absolute divergence times vary based on the methods and calibration used, but relative divergence times show extensive uniformity. Overall, mtDNA produces consistently older times than those known from nuclear markers, a discrepancy that is reduced significantly by explicitly accounting for chimpanzee population structures in time estimation. Assuming the human-chimpanzee split to be between 7 and 5 Ma, chimpanzee time estimates are 2.1-1.5, 1.1-0.76 and 0.25-0.18 Ma for the chimpanzee/bonobo, western/(eastern + central) and eastern/central chimpanzee divergences, respectively.

Repeated and time-correlated morphological convergence in cave-dwelling harvestmen (Opiliones, Laniatores) from Montane Western North America.

BackgroundMany cave-dwelling animal species display similar morphologies (troglomorphism) that have evolved convergent within and among lineages under the similar selective pressures imposed by cave habitats. Here we study such ecomorphological evolution in cave-dwelling Sclerobuninae harvestmen (Opiliones) from the western United States, providing general insights into morphological homoplasy, rates of morphological change, and the temporal context of cave evolution.Methodology/Principal FindingsWe gathered DNA sequence data from three independent gene regions, and combined these data with Bayesian hypothesis testing, morphometrics analysis, study of penis morphology, and relaxed molecular clock analyses. Using multivariate morphometric analysis, we find that phylogenetically unrelated taxa have convergently evolved troglomorphism; alternative phylogenetic hypotheses involving less morphological convergence are not supported by Bayesian hypothesis testing. In one instance, this morphology is found in specimens from a high-elevation stony debris habitat, suggesting that troglomorphism can evolve in non-cave habitats. We discovered a strong positive relationship between troglomorphy index and relative divergence time, making it possible to predict taxon age from morphology. Most of our time estimates for the origin of highly-troglomorphic cave forms predate the Pleistocene.Conclusions/SignificanceWhile several regions in the eastern and central United States are well-known hotspots for cave evolution, few modern phylogenetic studies have addressed the evolution of cave-obligate species in the western United States. Our integrative studies reveal the recurrent evolution of troglomorphism in a perhaps unexpected geographic region, at surprisingly deep time depths, and in sometimes surprising habitats. Because some newly discovered troglomorphic populations represent undescribed species, our findings stress the need for further biological exploration, integrative systematic research, and conservation efforts in western US cave habitats.