Mean Divergence Time Research Articles

Evaluation of Bayesian Models of Substitution Rate Evolution—Parental Guidance versus Mutual Independence

We have evaluated the performance of two classes of probabilistic models for substitution rate variation over phylogenetic trees. In the first class, branch rates are considered to be independent and identically distributed (i.i.d.) stochastic variables. Three versions with respect to the underlying distribution (Gamma, Inverse Gaussian, and LogNormal) are considered. The i.i.d. models are compared with the autocorrelated (AC) model, where rates of adjacent nodes in the tree are AC, so that a node rate is LogNormal distributed around the rate of the parent node. The performance of different models is evaluated using three empirical data sets. For all data sets, it was clear that all tested models extracted substantial knowledge from data when posterior divergence time distributions were compared with the prior distributions and, furthermore, that they clearly outperformed a molecular clock. Moreover, the descriptive power of the i.i.d. models, as evaluated by Bayes factors, was either equal to or clearly better than that of the AC model. The latter effect increased with extended taxon sampling. Likewise, under none of the models could we find compelling evidence, in any of the data sets, for rate correlation between adjacent branches/nodes. These findings challenge previous suggestions of universality of autocorrelation in sequence evolution. We also performed an additional comparison with a divergence time prior including calibration information from fossil evidence. Adding fossil information to the prior had negligible effect on Bayes factors and mainly affected the width of the posterior distribution of the divergence times, whereas the relative position of the mean divergence times were largely unaffected.

MTML-msBayes: Approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity

BackgroundMTML-msBayes uses hierarchical approximate Bayesian computation (HABC) under a coalescent model to infer temporal patterns of divergence and gene flow across codistributed taxon-pairs. Under a model of multiple codistributed taxa that diverge into taxon-pairs with subsequent gene flow or isolation, one can estimate hyper-parameters that quantify the mean and variability in divergence times or test models of migration and isolation. The software uses multi-locus DNA sequence data collected from multiple taxon-pairs and allows variation across taxa in demographic parameters as well as heterogeneity in DNA mutation rates across loci. The method also allows a flexible sampling scheme: different numbers of loci of varying length can be sampled from different taxon-pairs.ResultsSimulation tests reveal increasing power with increasing numbers of loci when attempting to distinguish temporal congruence from incongruence in divergence times across taxon-pairs. These results are robust to DNA mutation rate heterogeneity. Estimating mean divergence times and testing simultaneous divergence was less accurate with migration, but improved if one specified the correct migration model. Simulation validation tests demonstrated that one can detect the correct migration or isolation model with high probability, and that this HABC model testing procedure was greatly improved by incorporating a summary statistic originally developed for this task (Wakeley's ΨW). The method is applied to an empirical data set of three Australian avian taxon-pairs and a result of simultaneous divergence with some subsequent gene flow is inferred.ConclusionsTo retain flexibility and compatibility with existing bioinformatics tools, MTML-msBayes is a pipeline software package consisting of Perl, C and R programs that are executed via the command line. Source code and binaries are available for download at http://msbayes.sourceforge.net/ under an open source license (GNU Public License).

Range-wide mtDNA phylogeography yields insights into the origins of Asian elephants

Range-wide mtDNA phylogeography yields insights into the origins of Asian elephants

Multiple hybridization events between Drosophila simulans and Drosophila mauritiana are supported by mtDNA introgression.

The study of speciation has advanced considerably in the last decades because of the increased application of molecular tools. In particular, the quantification of gene flow between recently diverged species could be addressed. Drosophila simulans and Drosophila mauritiana diverged, probably allopatrically, from a common ancestor approximately 250 000 years ago. However, these species share one mitochondrial DNA (mtDNA) haplotype indicative of a recent episode of introgression. To study the extent of gene flow between these species, we took advantage of a large sample of D. mauritiana and employed a range of different markers, i.e. nuclear and mitochondrial sequences, and microsatellites. This allowed us to detect two new mtDNA haplotypes (MAU3 and MAU4). These haplotypes diverged quite recently from haplotypes of the siII group present in cosmopolitan populations of D. simulans. The mean divergence time of the most diverged haplotype (MAU4) is approximately 127 000 years, which is more than 100 000 years before the assumed speciation time. Interestingly, we also found some evidence for gene flow at the nuclear level because an excess of putatively neutral loci shows significantly reduced differentiation between D. simulans and D. mauritiana. Our results suggest that these species are exchanging genes more frequently than previously thought.

Support for vicariant origins of the New Zealand Onychophora

AbstractAim The distribution of Onychophora across the southern continents has long been considered the result of vicariance events. However, it has recently been hypothesized that New Zealand was completely inundated during the late Oligocene (25–22 Ma) and therefore that the entire biota is the result of long‐distance dispersal. We tested this assumption using phylogenetic and molecular dating of DNA sequence data from Onychophora.Location New Zealand, Australia, South Africa, Chile (South America).Methods We obtained DNA sequence data from the nuclear genes 28S and 18S rRNA to reconstruct relationships among species of Peripatopsidae (Onychophora). We performed molecular dating under a Bayesian relaxed clock model with a range of prior distributions using the rifting of South America and South Africa as a calibration.Results Our phylogenetic trees revealed that the New Zealand genera Ooperipatellus and Peripatoides, together with selected Australian genera (Euperipatoides, Phallocephale and an undescribed genus from Tasmania), form a monophyletic group that is the sister group to genera from Chile (Metaperipatus) and South Africa (Peripatopsis and Opisthopatus). The relaxed clock dating analyses yielded mean divergence times from 71.3 to 78.9 Ma for the split of the New Zealand Peripatoides from their Australian sister taxa. The 0.95 Bayesian posterior intervals were very broad and ranged from 24.5 to 137.6 Ma depending on the prior assumptions. The mean divergence of the New Zealand species of Ooperipatellus from the Australian species Ooperipatellus insignis was estimated at between 39.9 and 46.2 Ma, with posterior intervals ranging from 9.5 to 91.6 Ma.Main conclusions The age of Peripatoides is consistent with long‐term survival in New Zealand and implies that New Zealand was not completely submerged during the Oligocene. Ooperipatellus is less informative on the question of continuous land in the New Zealand region because we cannot exclude a post‐Oligocene divergence. The great age of Peripatoides is consistent with a vicariant origin of this genus resulting from the rifting of New Zealand from the eastern margin of Gondwana and supports the assumptions of previous authors who considered the Onychophora to be a relict component of the New Zealand biota.

Spatio‐temporal relationships of the Macaronesian endemic flora: a relictual series or window of opportunity?

AbstractConvolvulus is represented in Macaronesia by two endemic clades. The first (Clade I) has a predominantly western Mediterranean sister group whilst the second (Clade II) is nested within a predominantly eastern Mediterranean clade. The Relictual Series Hypothesis (RSH) predicts that degree of geographical disjunction between Macaronesian groups and their sister taxa is related to time available for continental extinction to occur and this would provide a possible explanation for the observed pattern in Convolvulus if Clade I is younger than Clade II. To test this hypothesis, mean relative divergence times for the two Macaronesian Convolvulus clades are estimated using a nrITS dataset. The results do not support the age‐disjunction hypothesis and indicate that the mean divergence time for Clade I predates that of Clade II, although the difference between mean divergence times is small and the standard deviations are large. The inconsistency between this result and the RSH might be explained by the stochastic nature of evolution: with continental extinction events occurring during a similar time period, there may have been inadequate time for a clear spatio‐temporal pattern to develop. An alternative explanation, termed the "Colonisation Window Hypothesis" (CWH), is also presented. This hypothesis emphasises island establishment rather than continental extinction as the prime determinant of spatio‐temporal relationships of Macaronesian groups and predicts that opportunities for colonisation into Macaronesia has been temporally constrained to discrete waves of colonisation. Whilst the Convolvulus results are consistent with both RSH and CWH, a framework for establishing the ability of these two hypotheses to explain the spatial relationships of the Macaronesian endemic flora is presented.

A molecular timescale for vertebrate evolution.

A timescale is necessary for estimating rates of molecular and morphological change in organisms and for interpreting patterns of macroevolution and biogeography. Traditionally, these times have been obtained from the fossil record, where the earliest representatives of two lineages establish a minimum time of divergence of these lineages. The clock-like accumulation of sequence differences in some genes provides an alternative method by which the mean divergence time can be estimated. Estimates from single genes may have large statistical errors, but multiple genes can be studied to obtain a more reliable estimate of divergence time. However, until recently, the number of genes available for estimation of divergence time has been limited. Here we present divergence-time estimates for mammalian orders and major lineages of vertebrates, from an analysis of 658 nuclear genes. The molecular times agree with most early (Palaeozoic) and late (Cenozoic) fossil-based times, but indicate major gaps in the Mesozoic fossil record. At least five lineages of placental mammals arose more than 100 million years ago, and most of the modern orders seem to have diversified before the Cretaceous/Tertiary extinction of the dinosaurs.