Dating species divergences using rocks and clocks

Enallagma damselflies show complex diversification across North America and Eurasia. Abstract Reconstructing evolutionary patterns of species and populations provides a framework for asking questions about the impacts of climate change. Here we use a multilocus dataset to estimate gene trees under maximum likelihood and Bayesian models to obtain a robust estimate of relationships for a genus of North American damselflies, Enallagma. Using a relaxed molecular clock, we estimate the divergence times for this group. Furthermore, to account for the fact that gene tree analyses can overestimate ages of population divergences, we use a multi-population coalescent model to gain a more accurate estimate of divergence times. We also infer diversification rates using a method that allows for variation in diversification rate through time and among lineages. Our results reveal a complex evolutionary history of Enallagma, in which divergence events both predate and occur during Pleistocene climate fluctuations. There is also evidence of diversification rate heterogeneity across the tree.

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Divergence Time Estimation using BEAST v2.x. Molecular dating using heterochronous data and substitution model averaging. If you found Taming the BEAST helpful in designing your research, please cite the following paper: Joëlle Barido-Sottani, Veronika Bošková, Louis du Plessis, Denise Kühnert, Carsten Magnus, Venelin Mitov, Nicola.

We are constantly evaluating the utility of given probe sets and probe designs, in addition to expanding the number of UCE loci we are targeting. We have several larger probes sets in the works, and we are also working on optimizing probe sets based on their capture success, phylogenetic utility, etc. Please check back for updates. You can now buy each of these probe sets direct from MYcroarray in the form of a capture kit. MYcroarray has even made a discounted “pilot” sized kit available for labs who want to do some test enrichments.

We used these probes for our in-silico analysis of the placental mammal phylogeny, our in vitro analysis of extant bird groups, and our in vitro analysis of the phylogenetic position of turtles. By their deposition in Dryad, all probes are available under a CC0 license , thus freely available for you to use, without restriction. We designed probes from UCEs by including flanking sequence from chickens. Because of the highly conserved nature of UCEs and their flanking sequence, we have found these probes work well across amniotes.

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Crocodylia, Thoracosauridae, Archosauria, Crocodylidae, Gavialis, Tomistoma Abstract Simultaneously analysing morphological, molecular and stratigraphic data suggests a potential resolution to a major remaining inconsistency in crocodylian evolution. The ancient, long-snouted thoracosaurs have always been placed near the Indian gharial Gavialis, but their antiquity ca 72 Ma is highly incongruous with genomic evidence for the young age of the Gavialis lineage ca 40 Ma.

We reconcile this contradiction with an updated morphological dataset and novel analysis, and demonstrate that thoracosaurs are an ancient iteration of long-snouted stem crocodylians unrelated to modern gharials. Phylogenetic methods that ignore stratigraphy parsimony and undated Bayesian methods are unable to tease apart these similarities and invariably unite thoracosaurs and Gavialis. However, tip-dated Bayesian approaches additionally consider the large temporal gap separating ancient thoracosaurs and modern Gavialis iterations of similar long-snouted crocodyliforms.

These analyses robustly favour a phylogeny which places thoracosaurs basal to crocodylians, far removed from modern gharials, which accordingly are a very young radiation.

data, dating analyses were also performed using only the Divergence dates were estimated using the 5-gene (Ta- Downloaded by [] at 08 October protein coding genes.

The tutorial involves co-estimation of a gene phylogeny and associated divergence times in the presence of calibration information from fossil evidence. You will need the following software at your disposal: It is available for download from http: It graphically and quantitively summarizes the distributions of continuous parameters and provides diagnostic information. At the time of writing, the current version is v1. FigTree – this is an application for displaying and printing molecular phylogenies, in particular those obtained using BEAST.

This tutorial will guide you through the analysis of an alignment of sequences sampled from twelve primate species see Figure 1. The goal is to estimate the phylogeny, the rate of evolution on each lineage and the ages of the uncalibrated ancestral divergences. Part of the alignment for primates. This is a user-friendly program for setting the evolutionary model and options for the MCMC analysis.

The final step is to explore the output of BEAST in order to diagnose problems and to summarize the results. Run BEAUti by double clicking on its icon. Once running, BEAUti will look similar irrespective of which computer system it is running on.

HowTo/Divergence Time Estimation

Paleoecology Mammoth bone dwelling, Mezhirich site, Ukraine During the last Ice Age , the most recent peak is known as the Last Glacial Maximum when a vast mammoth steppe stretched from Spain eastwards across Eurasia and over the Bering land bridge into Alaska and the Yukon. The continent of Europe was much colder and drier than it is today, with polar desert in the north and the remainder steppe or tundra.

Forest and woodland were almost non-existent except for isolated pockets in the mountain ranges of southern Europe. There is no evidence of megafaunal extinctions at the height of the Last Glacial Maximum , indicating that increasing cold and glaciation were not factors. Multiple events appear to have caused the rapid replacement of one species by another one within the same genus , or one population by another within the same species, across a broad area.

Provided that the priors and models attribute appropriate relative weights to the morphological and stratigraphic signals—an issue that requires investigation—tip-dating approaches are potentially better able to detect homoplasy and improve inferences about phylogenetic relationships, character evolution and divergence dates.

The phylogenetic hypothesis includes strong support for reciprocal monophyly of Actinopterygii and Sarcopterygii. Among sarcopterygians, coelacanths were the sister group to dipnoans plus tetrapods i. The position of the chondrichthyan outgroup node placed Polypteriformes as the earliest diverging group within Actinopterygii. The next actinopterygian group to diverge was the chondrosteans Acipenseriformes.

We obtained strong support for a monophyletic Holostei, rather than either Lepisosteiformes or Amiiformes alone, as the sister group to teleosts. Elopomorpha was consistently obtained as the earliest diverging teleost lineage. This is counter to the previously conventional view of Osteoglossomorpha as the earliest diverging teleost lineage.

In our analyses, the Osteoglossocephalai clade was particularly well supported in analysis with 3rd codon positions excluded with a bootstrap percentage of Elopomorpha was recovered as monophyletic, with successive branches leading to monophyletic Elopiformes, Albuliformes, Notacanthiformes and Anguilliformes, while within Osteoglossomorpha, Hiodontiformes was sister to monophyletic Osteoglossiformes.

Dating lineage divergences The time tree for bony fishes is shown in Figure 2.

A divergence dating analysis of turtles using fossil calibrations: an example of best practices

Bootstrap percentages are shown for 4 analyses: A The reduced bootstrap consensus after Steropodon is pruned. B The bootstrap consensus for all taxa.

BEAST specializes in estimating divergence times under uncorrelated relaxed clock models, estimating species trees using a model that accounts for the independent coalescent history of each gene tree, and Bayesian skyline analyses that estimate population growth or decline through time.

Divergence time estimates using Beast v1. A tutorial posted May 22, , 4: Its applications range from the dynamics of viral disease transmissions e. In this post I will start by provinding a brief history on phylogenetic dating estimation followed by an application on how to use the program Beast v1. The main assumption in their method was that the rate of molecular change was constant through time, and envisioned a molecular clock which could provide non-fossil independent estimates of speciation events.

In essence they proposed a single, global rate of substitution. Later studies however have found that the rate of sequence evolution was not constant through time, and that new methods were needed to incorporate the fact that molecular lineages vary through time and across lineages. The first generation of methods to overcome this issue were known as local and relaxed clocks, where different clocks were included in the phylogeny to account for different rates of molecular evolution.

In , Sanderson proposed a method that minimized the degree of change along branches using a rate-smoothing algorithm within a Maximum likelihood framework that become popular. An alternative approach also in a maximum-likelihood framework was subsequently developed by the same author Sanderson, It has become clear these days that divergence time estimates based on molecular sequences can only provide a relative time scale to a phylogeny and that fossil data are a necessary component in the divergence dating methodology for time calibration in order to convert it to absolute divergence time.

In fact it is argued now by many that multiple fossil calibration points are a requirement for accurate divergence time estimations.

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Dating of each gene tree was conducted with BEAST (v) using the original alignments and gene trees published by Jiao et al. (5) and the original calibrations on the same nodes as extracted from the r8s output file (unless indicated otherwise, see below) (5).

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Phylogenetics: BEAST Lab

Comparisons of node times in RelTime y axis and MC2T x axis for the tree of placental mammals, where marsupials were used to root the tree. Nodes in major clades are color coded by following Meredith et al. Inset shows the distribution of relative evolutionary rates produced by RelTime, where the negative values indicate slower and positive values indicate faster rate than the ancestral average rate of 1. The skewness and kurtosis for the distribution of logarithmically transformed data 0.

The dataset analyzed consisted of an alignment of 11, amino acid positions 4.

Third, the current molecular dating approaches also require reliable knowledge of some a priori divergence times, their minimum-maximum boundaries, and uncertainty distributions, all of which are seldom available or universally agreed on (17 ⇓ –19).

Hide All Anderson, J. Fossils, molecules, divergence times, and the origin of Salamandroidea. Proceedings of the National Academy of Sciences, Quarterly Journal of the Geological Society, Reassessment of the phylogenetic interrelationships of basal turtles Testudinata. Journal of Systematic Palaeontology, A new stem turtle from the Middle Jurassic of Scotland: New insights into the evolution and palaeoecology of basal turtles.

Proceedings of the Royal Society B: Fourteen nuclear genes provide phylogenetic resolution for difficult nodes in the turtle tree of life. Molecular Phylogenetics and Evolution, A program that uses blast to align problematic nucleotide sequences.

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Author Affiliations Walter G. Donoghue Department of Earth Sciences, University of Bristol, Bristol, UK Abstract Turtles have served as a model system for molecular divergence dating studies using fossil calibrations. However, because some parts of the fossil record of turtles are very well known, divergence age estimates from molecular phylogenies often do not differ greatly from those observed directly from the fossil record alone.

Although challenges in dating analysis are apparent, the use of divergence times into systematics, coupled with a robust phylogeny, will provide extra evidence to better assign taxa to specific taxonomic ranks and revise their classification.

Symposium 3 Friday, November 7, , These support very different historical biogeographic scenarios; either the two gharials share an Asian freshwater-dwelling ancestor during the Cenozoic, or they last shared a common ancestor in the Late Cretaceous and independently became limited to nonmarine settings from North Atlantic shallow marine ancestors. Combined-data and molecular scaffold analyses including fossils both support the close relationship between Gavialis and Tomistoma preferred by molecular data, but they also put the Late Cretaceous through Paleocene ‘thoracosaurs’ on the Gavialis line, as supported by morphological data, suggesting that the common gharial ancestor was a coastal Laurasian crocodylian.

But whether these reflect actual relationships or a topological compromise between strongly conflicting signals is an open question — they support a clade recovered in molecular analyses, but with a divergence time 20 or more million years older than the dates supported by the same data. Analyses with fossils that constrain Gavialis and Tomistoma to a late Paleogene split may more precisely reflect molecular evidence, but they require arbitrary decisions about clade membership not independently supported by either data set.

They do, however, continue to support a common gharial ancestor that was at least capable of crossing substantial marine barriers, which is consistent with the presence of oral and glandular features in both gharials that allow tolerance of salt water. Studies using the results of phylogenetic analyses often use one tree, but in cases like this, it might be more advisable to consider trees supported by different data sets and combined-data trees independently, and to regard different scenarios supported by these trees as equally viable, while further information is collected to resolve remaining conflicts intrinsic to the data.

Yet, certain aspects of their evolutionary history remain obscure, including: We examined these issues using recent advances in phylogenetic and paleobiogeographic analyses that utilize a morphological clock and tip-dating of non-contemporaneous taxa.

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