Relaxed Clock Model Research Articles

Dispersal routes between biodiversity hotspots in Asia: the case of the mountain genus Tripterospermum (Gentianinae, Gentianaceae) and its close relatives

AbstractAimWe investigated the biogeography of the subtropical mountain genus Tripterospermum Blume (Gentianaceae), disjunctly distributed at the southern fringe of the Qinghai–Tibetan Plateau (QTP) and other mountain systems within the biodiversity hotspots of Southeast Asia. This study reveals dispersal routes among these areas.LocationEast China, Indochina, Japan, the Philippines, southeastern fringe of the Qinghai–Tibetan Plateau (southern Himalaya and Hengduanshan), Taiwan, Wallacea.MethodsThe evolutionary history of Tripterospermum was studied using the phylogenetic reconstructions (Maximum Likelihood and Bayesian Inference using ITS, atpB–rbcL and trnL–trnF), molecular dating (using BEAST with a relaxed clock model and fossil constraints), and two approaches of ancestral area reconstructions (DEC, S‐DIVA). Our sampling design included 82% of the extant species of subtropical Gentianinae (Tripterospermum, Metagentiana, Sinogentiana and Crawfurdia) as ingroup, and Kuepferia, Gentiana and other Gentianaceae genera as outgroups.ResultsSubtropical Gentianinae originated at the southeastern fringe of the QTP (the southern Himalaya and Hengduanshan) between 16 and 35 million years ago (Ma). With a crown age estimated to be 2.7–8.8 million years (Myr), Tripterospermum originated at the southeastern fringe of the QTP, from where it dispersed to East China, Indochina, Sundaland, Taiwan, Japan and Wallacea.Main conclusionsFor Tripterospermum, the southern Himalaya and the Hengduanshan have acted as a source area for the colonization of East and Southeast Asia. This study depicts dispersal routes among the biodiversity hotspots neighbouring the QTP and those located on Sundaland and Wallacea. Mountain plants seem to have colonized Wallacea using a northern route via Taiwan rather than a more southern route via Sundaland. The latter route has previously been recorded for many lowland lineages. Because Tripterospermum species‐producing berries have dispersed more often across geographical barriers than those producing capsules, we hypothesize that avian transportation of berry‐like fruits might have facilitated their dispersal.

Molecular epidemiology of coxsackievirus type B1.

Coxsackievirus type B1 (CVB1) has emerged globally as the predominant enterovirus serotype and is associated with epidemics of meningitis and chronic diseases. In this report, the phylogeny of CVB1 was studied based on the VP1 sequences of 11 North African isolates and 81 published sequences. All CVB1 isolates segregated into four distinct genogroups and 10 genotypes. Most of the identified genotypes of circulating CVB1 strains appear to have a strict geographical specificity. The North African strains were of a single genotype and probably evolved distinctly. Using a relaxed molecular clock model and three different population models (constant population, exponential growth and Bayesian skyline demographic models) in coalescent analysis using the BEAST program, the substitution rate in CVB1 varied between 6.95 × 10(-3) and 7.37 × 10(-3) substitutions/site/year in the VP1 region. This study permits better identification of circulating CVB1, which has become one of the most predominant enterovirus serotypes in humans.

Molecular phylogeny of the ‘Cape snow’ genus Syncarpha (Asteraceae: Gnaphalieae) reveals a need for generic re-delimitation

A phylogenetic hypothesis is presented for the charismatic but taxonomically poorly-known Cape daisy genus Syncarpha, based on near-complete ingroup sampling and good coverage of outgroup taxa. A combination of nuclear ribosomal and chloroplast spacer DNA sequence data gives a well-resolved phyogenetic hypothesis, the robustness of which is assessed via both parsimony bootstrap and Bayesian posterior probabilities based on the uncorrelated lognormal relaxed clock model. Syncarpha species fall into two well-supported and distantly-related clades that last shared a common ancestor in the mid-Miocene. The larger Syncarpha 1 grouping contains the type species and corresponds to African ‘Helipterum’; this clade is sister to Edmondia and belongs in a larger clade which also includes the Australian Gnaphalieae. The Syncarpha 2 clade contains the taxa associated with Syncarpha paniculata (formerly Helichrysum paniculatum) and is more closely related to Plecostachys and some species of Gnaphalium. Formal assessment of monophyly lays the groundwork for future revisionary taxonomic work.

A molecular genetic time scale demonstrates Cretaceous origins and multiple diversification rate shifts within the order Galliformes (Aves)

The phylogeny of Galliformes (landfowl) has been studied extensively; however, the associated chronologies have been criticized recently due to misplaced or misidentified fossil calibrations. As a consequence, it is unclear whether any crown-group lineages arose in the Cretaceous and survived the Cretaceous–Paleogene (K–Pg; 65.5Ma) mass extinction. Using Bayesian phylogenetic inference on an alignment spanning 14,539bp of mitochondrial and nuclear DNA sequence data, four fossil calibrations, and a combination of uncorrelated lognormally distributed relaxed-clock and strict-clock models, we inferred a time-calibrated molecular phylogeny for 225 of the 291 extant Galliform taxa. These analyses suggest that crown Galliformes diversified in the Cretaceous and that three-stem lineages survived the K–Pg mass extinction. Ideally, characterizing the tempo and mode of diversification involves a taxonomically complete phylogenetic hypothesis. We used simple constraint structures to incorporate 66 data-deficient taxa and inferred the first taxon-complete phylogenetic hypothesis for the Galliformes. Diversification analyses conducted on 10,000 timetrees sampled from the posterior distribution of candidate trees show that the evolutionary history of the Galliformes is best explained by a rate-shift model including 1–3 clade-specific increases in diversification rate. We further show that the tempo and mode of diversification in the Galliformes conforms to a three-pulse model, with three-stem lineages arising in the Cretaceous and inter and intrafamilial diversification occurring after the K–Pg mass extinction, in the Paleocene–Eocene (65.5–33.9Ma) or in association with the Eocene–Oligocene transition (33.9Ma).

Microbial DNA records historical delivery of anthropogenic mercury.

Mercury (Hg) is an anthropogenic pollutant that is toxic to wildlife and humans, but the response of remote ecosystems to globally distributed Hg is elusive. Here, we use DNA extracted from a dated sediment core to infer the response of microbes to historical Hg delivery. We observe a significant association between the mercuric reductase gene (merA) phylogeny and the timing of Hg deposition. Using relaxed molecular clock models, we show a significant increase in the scaled effective population size of the merA gene beginning ~200 years ago, coinciding with the Industrial Revolution and a coincident strong signal for positive selection acting on residues in the terminal region of the mercuric reductase. This rapid evolutionary response of microbes to changes in the delivery of anthropogenic Hg indicates that microbial genomes record ecosystem response to pollutant deposition in remote regions.

A revised time tree of the asterids: establishing a temporal framework for evolutionary studies of the coffee family (rubiaceae).

Divergence time analyses in the coffee family (Rubiaceae) have all relied on the same Gentianales crown group age estimate, reported by an earlier analysis of the asterids, for defining the upper age bound of the root node in their analyses. However, not only did the asterid analysis suffer from several analytical shortcomings, but the estimate itself has been used in highly inconsistent ways in these Rubiaceae analyses. Based on the original data, we here reanalyze the divergence times of the asterids using relaxed-clock models and 14 fossil-based minimum age constraints. We also expand the data set to include an additional 67 taxa from Rubiaceae sampled across all three subfamilies recognized in the family. Three analyses are conducted: a separate analysis of the asterids, which completely mirrors the original asterid analysis in terms of taxon sample and data; a separate analysis of the Gentianales, where the result from the first analysis is used for defining a secondary root calibration point; and a combined analysis where all taxa are analyzed simultaneously. Results are presented in the form of a time-calibrated phylogeny, and age estimates for asterid groups, Gentianales, and major groups of Rubiaceae are compared and discussed in relation to previously published estimates. Our updated age estimates for major groups of Rubiaceae provide a significant step forward towards the long term goal of establishing a robust temporal framework for the divergence of this biologically diverse and fascinating group of plants.

Phylogenomic analysis reveals deep divergence and recombination in an economically important grapevine virus.

The evolutionary history of the exclusively grapevine (Vitis spp.) infecting, grapevine leafroll-associated virus 3 (GLRaV-3) has not been studied extensively, partly due to limited available sequence data. In this study we trace the evolutionary history of GLRaV-3, focussing on isolate GH24, a newly discovered variant. GH24 was discovered through the use of next-generation sequencing (NGS) and the whole genome sequence determined and validated with Sanger sequencing. We assembled an alignment of all 13 available whole genomes of GLRaV-3 isolates and all other publicly available GLRaV-3 sequence data. Using multiple recombination detection methods we identified a clear signal for recombination in one whole genome sequence and further evidence for recombination in two more, including GH24. We inferred phylogenetic trees and networks and estimated the ages of common ancestors of GLRaV-3 clades by means of relaxed clock models calibrated with asynchronous sampling dates. Our results generally confirm previously identified variant groups as well as two new groups (VII and VIII). Higher order groups were defined as supergroups designated A to D. Supergroup A includes variant groups I-V and supergroup B group VI and its related unclassified isolates. Supergroups C and D are less well known, including the newly identified groups VII (including isolate GH24) and VIII respectively. The inferred node ages suggest that the origins of the major groups of GLRaV-3, including isolate GH24, may have occurred prior to worldwide cultivation of grapevines, whilst the current diversity represents closely related isolates that diverged from common ancestors within the last century.

A sisters’ story: comparative phylogeography and taxonomy of Hierophis viridiflavus and H. gemonensis (Serpentes, Colubridae)

We used a multidisciplinary approach to infer the taxonomy and historical biogeography of Hierophis viridiflavus and H. gemonensis, performing molecular analyses of mitochondrial (16S, Cyt‐b, ND4) and nuclear markers (PRLR), a landmark‐based morphometric study and a cytogenetic analysis. Our data distinguished three main groups in the studied species, corresponding to H. gemonensis and to two monophyletic clades (E and W) within H. viridiflavus. Clades E and W display a significant genetic (about 4% for Cyt‐b and ND4) and morphological divergence and a different morphology of the W sex chromosome (submetacentric in clade E and telocentric in clade W). Taking into account the existing divergence, these clades appear to represent independent phylogenetic units, deserving elevation to species status. Specific names should be H. viridiflavus (Lacépède, 1789) and H. carbonarius (Bonaparte 1833) for clades W and E, respectively. The phylogeography of the studied species is only partially concordant with a general pattern of ‘southern richness and northern purity’ of genetic diversity, whereas H. gemonensis exhibits high genetic diversity at low latitudes (especially in the Peloponnese), H. carbonarius shows a number of different haplotypes both at low (along the southern Italian Apennines and in Sicily) and high latitudes in Italy. Furthermore, a relaxed clock model hypothesizes the differentiation between H. gemonensis and H. viridiflavus sensu lato at about 7 Mya, in the Messinian. Subsequently, the speciation involving H. viridiflavus sensu stricto and H. carbonarius took place in the Quaternary, probably as a result of Pleistocene climatic oscillations. Furthermore, our results are consistent with the existence of several ‘refugia within refugia’ in Italy and in the Balkans and depict the major cladogenesis as allopatric events, mainly driven by paleoclimatic and geographical factors.

Species tree phylogeny and biogeography of the Neotropical genus Pradosia (Sapotaceae, Chrysophylloideae)

Recent phylogenetic studies in Sapotaceae have demonstrated that many genera need to be redefined to better correspond to natural groups. The Neotropical genus Pradosia is believed to be monophyletic and includes 26 recognized species. Here we reconstruct the generic phylogeny by a species-tree approach using ∗BEAST, 21 recognized species (36 accessions), sequence data from three nuclear markers (ITS, ETS, and RPB2), a relaxed lognormal clock model, and a fossil calibration. We explore the evolution of five selected morphological characters, reconstruct the evolution of habitat (white-sand vs. clayish soils) preference, as well as space and time by using a recently developed continuous diffusion model in biogeography. We find Pradosia to be monophyletic in its current circumscription and to have originated in the Amazon basin at ∼47.5Ma. Selected morphological characters are useful to readily distinguish three clades. Preferences to white-sand and/or clay are somewhat important for the majority of species, but speciation has not been powered by habitat shifts. Pradosia brevipes is a relative young species (∼1.3Ma) that has evolved a unique geoxylic life strategy within Pradosia and is restricted to savannahs. Molecular dating and phylogenetic pattern indicate that Pradosia reached the Brazilian Atlantic coast at least three times: at 34.4Ma (P. longipedicellata), at 11.7Ma (P. kuhlmannii), and at 3.9Ma (weakly supported node within the red-flowered clade).

Five major shifts of diversification through the long evolutionary history of Magnoliidae (angiosperms).

BackgroundWith 10,000 species, Magnoliidae are the largest clade of flowering plants outside monocots and eudicots. Despite an ancient and rich fossil history, the tempo and mode of diversification of Magnoliidae remain poorly known. Using a molecular data set of 12 markers and 220 species (representing >75% of genera in Magnoliidae) and six robust, internal fossil age constraints, we estimate divergence times and significant shifts of diversification across the clade. In addition, we test the sensitivity of magnoliid divergence times to the choice of relaxed clock model and various maximum age constraints for the angiosperms.ResultsCompared with previous work, our study tends to push back in time the age of the crown node of Magnoliidae (178.78-126.82 million years, Myr), and of the four orders, Canellales (143.18-125.90 Myr), Piperales (158.11-88.15 Myr), Laurales (165.62-112.05 Myr), and Magnoliales (164.09-114.75 Myr). Although families vary in crown ages, Magnoliidae appear to have diversified into most extant families by the end of the Cretaceous. The strongly imbalanced distribution of extant diversity within Magnoliidae appears to be best explained by models of diversification with 6 to 13 shifts in net diversification rates. Significant increases are inferred within Piperaceae and Annonaceae, while the low species richness of Calycanthaceae, Degeneriaceae, and Himantandraceae appears to be the result of decreases in both speciation and extinction rates.ConclusionsThis study provides a new time scale for the evolutionary history of an important, but underexplored, part of the tree of angiosperms. The ages of the main clades of Magnoliidae (above the family level) are older than previously thought, and in several lineages, there were significant increases and decreases in net diversification rates. This study is a new robust framework for future investigations of trait evolution and of factors influencing diversification in this group as well as angiosperms as a whole.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0320-6) contains supplementary material, which is available to authorized users.

Molecular phylogenetic analysis supports a Gondwanan origin of the Hyriidae (Mollusca: Bivalvia: Unionida) and the paraphyly of Australasian taxa

The freshwater mussel family Hyriidae (Mollusca: Bivalvia: Unionida) has a disjunct trans-Pacific distribution in Australasia and South America. Previous phylogenetic analyses have estimated the evolutionary relationships of the family and the major infra-familial taxa (Velesunioninae and Hyriinae: Hyridellini in Australia; Hyriinae: Hyriini, Castaliini, and Rhipidodontini in South America), but taxon and character sampling have been too incomplete to support a predictive classification or allow testing of biogeographical hypotheses. We sampled 30 freshwater mussel individuals representing the aforementioned hyriid taxa, as well as outgroup species representing the five other freshwater mussel families and their marine sister group (order Trigoniida). Our ingroup included representatives of all Australian genera. Phylogenetic relationships were estimated from three gene fragments (nuclear 28S, COI and 16S mtDNA) using maximum parsimony, maximum likelihood, and Bayesian inference, and we applied a Bayesian relaxed clock model calibrated with fossil dates to estimate node ages. Our analyses found good support for monophyly of the Hyriidae and the subfamilies and tribes, as well as the paraphyly of the Australasian taxa (Velesunioninae, (Hyridellini, (Rhipidodontini, (Castaliini, Hyriini)))). The Hyriidae was recovered as sister to a clade comprised of all other Recent freshwater mussel families. Our molecular date estimation supported Cretaceous origins of the major hyriid clades, pre-dating the Tertiary isolation of South America from Antarctica/Australia. We hypothesize that early diversification of the Hyriidae was driven by terrestrial barriers on Gondwana rather than marine barriers following disintegration of the super-continent.

Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci.

Genetic sequence data provide information about the distances between species or branch lengths in a phylogeny, but not about the absolute divergence times or the evolutionary rates directly. Bayesian methods for dating species divergences estimate times and rates by assigning priors on them. In particular, the prior on times (node ages on the phylogeny) incorporates information in the fossil record to calibrate the molecular tree. Because times and rates are confounded, our posterior time estimates will not approach point values even if an infinite amount of sequence data are used in the analysis. In a previous study we developed a finite-sites theory to characterize the uncertainty in Bayesian divergence time estimation in analysis of large but finite sequence data sets under a strict molecular clock. As most modern clock dating analyses use more than one locus and are conducted under relaxed clock models, here we extend the theory to the case of relaxed clock analysis of data from multiple loci (site partitions). Uncertainty in posterior time estimates is partitioned into three sources: Sampling errors in the estimates of branch lengths in the tree for each locus due to limited sequence length, variation of substitution rates among lineages and among loci, and uncertainty in fossil calibrations. Using a simple but analogous estimation problem involving the multivariate normal distribution, we predict that as the number of loci () goes to infinity, the variance in posterior time estimates decreases and approaches the infinite-data limit at the rate of 1/, and the limit is independent of the number of sites in the sequence alignment. We then confirmed the predictions by using computer simulation on phylogenies of two or three species, and by analyzing a real genomic data set for six primate species. Our results suggest that with the fossil calibrations fixed, analyzing multiple loci or site partitions is the most effective way for improving the precision of posterior time estimation. However, even if a huge amount of sequence data is analyzed, considerable uncertainty will persist in time estimates.

Clock model makes a large difference to age estimates of long-stemmed clades with no internal calibration: a test using Australian grasstrees.

BackgroundEstimating divergence times in phylogenies using a molecular clock depends on accurate modeling of nucleotide substitution rates in DNA sequences. Rate heterogeneity among lineages is likely to affect estimates, especially in lineages with long stems and short crowns (“broom” clades) and no internal calibration. We evaluate the performance of the random local clocks model (RLC) and the more routinely employed uncorrelated lognormal relaxed clock model (UCLN) in situations in which a significant rate shift occurs on the stem branch of a broom clade. We compare the results of simulations to empirical results from analyses of a real rate-heterogeneous taxon – Australian grass trees (Xanthorrhoea) – whose substitution rate is slower than in its sister groups, as determined by relative rate tests.ResultsIn the simulated datasets, the RLC model performed much better than UCLN: RLC correctly estimated the age of the crown node of slow-rate broom clades, whereas UCLN estimates were consistently too young. Similarly, in the Xanthorrhoea dataset, UCLN returned significantly younger crown ages than RLC (mean estimates respectively 3–6 Ma versus 25–35 Ma). In both real and simulated datasets, Bayes Factor tests strongly favored the RLC model over the UCLN model.ConclusionsThe choice of an unsuitable molecular clock model can strongly bias divergence time estimates. In particular, for data predicted to have more rate variation among than within clades, dating with RLC is much more likely to be accurate than with UCLN. The choice of clocks should be informed by the biology of the study group (e.g., life-form) or assessed with relative rate tests and post-hoc model comparisons.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-014-0263-3) contains supplementary material, which is available to authorized users.

Ancient dates or accelerated rates? Morphological clocks and the antiquity of placental mammals.

Analyses of a comprehensive morphological character matrix of mammals using 'relaxed' clock models (which simultaneously estimate topology, divergence dates and evolutionary rates), either alone or in combination with an 8.5 kb nuclear sequence dataset, retrieve implausibly ancient, Late Jurassic-Early Cretaceous estimates for the initial diversification of Placentalia (crown-group Eutheria). These dates are much older than all recent molecular and palaeontological estimates. They are recovered using two very different clock models, and regardless of whether the tree topology is freely estimated or constrained using scaffolds to match the current consensus placental phylogeny. This raises the possibility that divergence dates have been overestimated in previous analyses that have applied such clock models to morphological and total evidence datasets. Enforcing additional age constraints on selected internal divergences results in only a slight reduction of the age of Placentalia. Constraining Placentalia to less than 93.8 Ma, congruent with recent molecular estimates, does not require major changes in morphological or molecular evolutionary rates. Even constraining Placentalia to less than 66 Ma to match the 'explosive' palaeontological model results in only a 10- to 20-fold increase in maximum evolutionary rate for morphology, and fivefold for molecules. The large discrepancies between clock- and fossil-based estimates for divergence dates might therefore be attributable to relatively small changes in evolutionary rates through time, although other explanations (such as overly simplistic models of morphological evolution) need to be investigated. Conversely, dates inferred using relaxed clock models (especially with discrete morphological data and MrBayes) should be treated cautiously, as relatively minor deviations in rate patterns can generate large effects on estimated divergence dates.

Viral diversity and clonal evolution from unphased genomic data.

BackgroundClonal expansion is a process in which a single organism reproduces asexually, giving rise to a diversifying population. It is pervasive in nature, from within-host pathogen evolution to emergent infectious disease outbreaks. Standard phylogenetic tools rely on full-length genomes of individual pathogens or population consensus sequences (phased genotypes).Although high-throughput sequencing technologies are able to sample population diversity, the short sequence reads inherent to them preclude assessing whether two reads originate from the same clone (unphased genotypes). This obstacle severely limits the application of phylogenetic methods and investigation of within-host dynamics of acute infections using this rich data source.MethodsWe introduce two measures of diversity to study the evolution of clonal populations using unphased genomic data, which eliminate the need to construct full-length genomes. Our method follows a maximum likelihood approach to estimate evolutionary rates and times to the most recent common ancestor, based on a relaxed molecular clock model; independent of a growth model. Deviations from neutral evolution indicate the presence of selection and bottleneck events.ResultsWe evaluated our methods in silico and then compared it against existing approaches with the well-characterized 2009 H1N1 influenza pandemic. We then applied our method to high-throughput genomic data from marburgvirus-infected non-human primates and inferred the time of infection and the intra-host evolutionary rate, and identified purifying selection in viral populations.ConclusionsOur method has the power to make use of minor variants present in less than 1% of the population and capture genomic diversification within days of infection, making it an ideal tool for the study of acute RNA viral infection dynamics.

Simulating and detecting autocorrelation of molecular evolutionary rates among lineages.

Evolutionary timescales can be estimated from genetic data using phylogenetic methods based on the molecular clock. To account for molecular rate variation among lineages, a number of relaxed-clock models have been developed. Some of these models assume that rates vary among lineages in an autocorrelated manner, so that closely related species share similar rates. In contrast, uncorrelated relaxed clocks allow all of the branch-specific rates to be drawn from a single distribution, without assuming any correlation between rates along neighbouring branches. There is uncertainty about which of these two classes of relaxed-clock models are more appropriate for biological data. We present an R package, NELSI, that allows the evolution of DNA sequences to be simulated according to a range of clock models. Using data generated by this package, we assessed the ability of two Bayesian phylogenetic methods to distinguish among different relaxed-clock models and to quantify rate variation among lineages. The results of our analyses show that rate autocorrelation is typically difficult to detect, even when there is complete taxon sampling. This provides a potential explanation for past failures to detect rate autocorrelation in a range of data sets.

On the Age of Eukaryotes: Evaluating Evidence from Fossils and Molecular Clocks

Our understanding of the phylogenetic relationships among eukaryotic lineages has improved dramatically over the few past decades thanks to the development of sophisticated phylogenetic methods and models of evolution, in combination with the increasing availability of sequence data for a variety of eukaryotic lineages. Concurrently, efforts have been made to infer the age of major evolutionary events along the tree of eukaryotes using fossil-calibrated molecular clock-based methods. Here, we review the progress and pitfalls in estimating the age of the last eukaryotic common ancestor (LECA) and major lineages. After reviewing previous attempts to date deep eukaryote divergences, we present the results of a Bayesian relaxed-molecular clock analysis of a large dataset (159 proteins, 85 taxa) using 19 fossil calibrations. We show that for major eukaryote groups estimated dates of divergence, as well as their credible intervals, are heavily influenced by the relaxed molecular clock models and methods used, and by the nature and treatment of fossil calibrations. Whereas the estimated age of LECA varied widely, ranging from 1007 (943-1102) Ma to 1898 (1655-2094) Ma, all analyses suggested that the eukaryotic supergroups subsequently diverged rapidly (i.e., within 300 Ma of LECA). The extreme variability of these and previously published analyses preclude definitive conclusions regarding the age of major eukaryote clades at this time. As more reliable fossil data on eukaryotes from the Proterozoic become available and improvements are made in relaxed molecular clock modeling, we may be able to date the age of extant eukaryotes more precisely.

Phylogeny and historical biogeography of gnateaters (Passeriformes, Conopophagidae) in the South America forests

We inferred the phylogenetic relationships, divergence time and biogeography of Conopophagidae (gnateaters) based on sequence data of mitochondrial genes (ND2, ND3 and cytb) and nuclear introns (TGFB2 and G3PDH) from 45 tissue samples (43 Conopophaga and 2 Pittasoma) representing all currently recognized species of the family and the majority of subspecies. Phylogenetic relationships were estimated by maximum likelihood and Bayesian inference. Divergence time estimates were obtained based on a Bayesian relaxed clock model. These chronograms were used to calculate diversification rates and reconstruct ancestral areas of the genus Conopophaga. The phylogenetic analyses support the reciprocal monophyly of the two genera, Conopophaga and Pittasoma. All species were monophyletic with the exception of C. lineata, as C. lineata cearae did not cluster with the other two C. lineata subspecies. Divergence time estimates for Conopophagidae suggested that diversification took place during the Neogene, and that the diversification rate within Conopophaga clade was highest in the late Miocene, followed by a slower diversification rate, suggesting a diversity-dependent pattern. Our analyses of the diversification of family Conopophagidae provided a scenario for evolution in Terra Firme forest across tropical South America. The spatio-temporal pattern suggests that Conopophaga originated in the Brazilian Shield and that a complex sequence of events possibly related to the Andean uplift and infilling of former sedimentation basins and erosion cycles shaped the current distribution and diversity of this genus.

Origin and Outbreak of HIV-1 CRF55_01B Among MSM in Shenzhen, China

Origin and Outbreak of HIV-1 CRF55_01B Among MSM in Shenzhen, China

The impact of calibration and clock-model choice on molecular estimates of divergence times

Phylogenetic estimates of evolutionary timescales can be obtained from nucleotide sequence data using the molecular clock. These estimates are important for our understanding of evolutionary processes across all taxonomic levels. The molecular clock needs to be calibrated with an independent source of information, such as fossil evidence, to allow absolute ages to be inferred. Calibration typically involves fixing or constraining the age of at least one node in the phylogeny, enabling the ages of the remaining nodes to be estimated. We conducted an extensive simulation study to investigate the effects of the position and number of calibrations on the resulting estimate of the timescale. Our analyses focused on Bayesian estimates obtained using relaxed molecular clocks. Our findings suggest that an effective strategy is to include multiple calibrations and to prefer those that are close to the root of the phylogeny. Under these conditions, we found that evolutionary timescales could be estimated accurately even when the relaxed-clock model was misspecified and when the sequence data were relatively uninformative. We tested these findings in a case study of simian foamy virus, where we found that shallow calibrations caused the overall timescale to be underestimated by up to three orders of magnitude. Finally, we provide some recommendations for improving the practice of molecular-clock calibration.