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A revised list of fossil calibrations to constrain molecular dating of angiosperms
<p>Original list of calibrations used in:</p> <p><strong><strong>Ramírez-Barahona S</strong>, <strong>Sauquet H</strong>, <strong>Magallón S</strong></strong>. <strong>2020</strong>. The delayed and geographically heterogenous diversification of flowering plant families. <em>Nature Ecology & Evolution</em>: 10.1038/s41559-020-1241–3.</p>
Data from: Molecular Dating of Phylogeny of Sturgeons (Acipenseridae) Based on Total Evidence Analysis
<p>Bayesian chronograms (original and updated 08.10.2022) of cladogenesis of fossil and recent Acipenseriformes reconstructed on the basis of combined (mtDNA, morphological characters) data.</p>
FIGURE 8 in A new perspective on the molecular dating of the brown trout complex with an extended phylogeographic information on the species in Serbia
FIGURE 8 Simplified palinspastic map for the Pliocene (compiled and modified after Popov et al., 2004, 2006; Neubauer et al., 2015) with the indication of hypothetic BT colonization routes (arrows). Interrupted lines mark migration routes that are, in our opinion, less likely. Green areas represent brackish environments, light blue freshwater lakes or marshes and rivers, dark blue seas, dark gray mountain ranges, and light gray land mass; all geographic features are tentatively positioned. 1 – Ancestral trout originated in the Ponto-Caspian system and crossed from the paleo-Danube into the Western Mediterranean basin via stream capture of Alpine rivers in Pliocene; 2 – Ancestral trout originated in the Balkans basin and colonized other parts of the Mediterranean Basin from here; 3 – Colonization of the Central Alps took place in the Pliocene after the paleo-Rhône separated from the paleo-Danube and reached the Mediterranean; 4 – Atlantic basin was colonized when the Rhine captured Central Alpine rivers; 5 – Atlantic basin was colonized along the Mediterranean coastline and via Gibraltar; 6 – Ponto-Caspian basin was colonized from the Mediterranean basin following a presumed sea corridor in the upper Euphrates valley or using the paleo-Euphrates, which might have been connected with the Mediterranean until the Middle Pliocene; 7 – Ponto-Caspian basin was colonized via a possible Pliocene gateway that connected the Dacic basin and the Aegean Sea; 8 – Ponto-Caspian basin was colonized through the Bosphorus gateway.
FIGURE 6 in A new perspective on the molecular dating of the brown trout complex with an extended phylogeographic information on the species in Serbia
FIGURE 6 Split graph of the Neighbor-Net phylogenetic network analysis of brown trout lineages. The colors of the haplotypes represent different lineages, and the scale bar represents the nucleotide substitutions per site.
FIGURE 4 in A new perspective on the molecular dating of the brown trout complex with an extended phylogeographic information on the species in Serbia
FIGURE 4 Median-joining network of CR mtDNA sequences belonging to Danubian haplogroups. Haplotypes are represented by colored circles whose size is proportional to haplotype frequencies detected and taken from the literature (supplementary tables S2 and S3). Haplotypes from this study are bolded and framed. Mutations are represented by hatch marks on the lines connecting the haplotypes. Missing or theoretical haplotypes are shown as black dots. The maps show the distribution of haplotypes from the network (A – DA-ES haplotypes, B – DA-INT haplotypes, C – DA-BS haplotypes), and their numbering corresponds to that in supplementary table S2.
FIGURE 3 in A new perspective on the molecular dating of the brown trout complex with an extended phylogeographic information on the species in Serbia
FIGURE 3 Reconstruction of the sequence evolution in the Danubian lineage. Defining variable nucleotide sites in the control region are all placed nearby in the central part of the control region, between the nucleotide positions 540-550 of our alignment. The 542 G → C transversion defines the split of the DAES + DA-INT and the DA-BS; 541 G → A split of the DA-ES + DA-INT (excluding DaBS9) from the DaBS9 haplotype; and 548 C → T defines the DA-ES.
FIGURE 7 in A new perspective on the molecular dating of the brown trout complex with an extended phylogeographic information on the species in Serbia
FIGURE 7 Fossil and geologically calibrated chronogram of the genus Salmo created with a relaxed clock in BEAST 2. 95% highest posterior density (HPD) intervals are shown as gray bars at the nodes. Calibration points are indicated by arrows. Median node ages are shown as node labels. Time estimates are given in millions of years. Clades, that were a priori treated as monophyletic are indicated with a black star, while a red star indicates the clade, where posterior probability was> 90% only in BEAST analysis.
Code and data for molecular dating benchmark based on real and simulated Primates gene trees
<p>Benchmark of molecular clock dating applied to single gene trees separately, whose results are described in “Factors influencing the accuracy and precision in dating single gene trees” by Guillaume Louvel and Hugues Roest Crollius.</p> <ol> <li>Real Primates gene trees are analyzed to identify what characteristics of a gene tree are related to the precision of dating; </li> <li>alignments are also simulated on the tree of Primates to measure the accuracy of dating under controlled parameters such as the degree of rate variation and the length of the alignment.</li> </ol> <p><strong>Content</strong></p> <p><code>Louvel_Accuracy-dating_results_2024.tar.gz</code>:<br> - <code>notebook/</code>: statistical analyses in Python;<br> - <code>outputs/</code>: html reports with figures/tables resulting from the analysis;<br> - <code>lib/</code>: required libraries.<br> - <code>data/</code>: intermediate data needed for the final analysis (dates, gene tree features);</p> <p><code>Louvel_Accuracy-dating_dating-source_2024.tar.gz</code>:<br> - <code>dating-source/</code>: input data and config files necessary to reproduce <code>data</code>;</p> <p><code>Louvel_Accuracy-dating_raw-data-preparation_2024.tar.gz</code>:<br> - <code>raw-data-preparation/</code>: raw data and steps to produce <code>dating-source</code>.<br><br><strong>Requirements</strong><br><br>This code requires the libraries developed in the lab for this project,<br>available at <a href="https://github.com/DyogenIBENS/">github.com/DyogenIBENS/</a>, but also included here in <code>lib/</code>.<br><br>- <a href="https://github.com/DyogenIBENS/Phylorgs">Phylorgs</a><br>- <a href="https://github.com/DyogenIBENS/LibsDyogen_py3">LibsDyogen_py3</a><br>- <a href="https://github.com/DyogenIBENS/ToolsDyogen_py3">ToolsDyogen_py3</a>.</p>
FIGURE 2 in Dating the origin and diversiFIcation of Pan-Chelidae (Testudines, Pleurodira) under multiple molecular clock approaches
FIGURE 2 Opening of Tasman Sea; Pal., Paleocene; P, Pliocene; Pe, Pelomedusa; Pel, Pelusios; Pelt, Peltocephalus; (cont.) Ph, Phrynops; Pl, Platemys; Ple, Pleurodira; Po, Podocnemis; Ps, Pseudemydura; Q, Quaternary; R, Rheodytes; Rh, Rhinemys. *, constrained nodes based on the TE MP topology; †, extinct taxa; ↑, origin of total groups Pan-Chelidae and Pan-Pelomedusioides. Downloaded from Brill.com10/07/2022 07:36:56PM via free access
FIGURE 3 in Dating the origin and diversiFIcation of Pan-Chelidae (Testudines, Pleurodira) under multiple molecular clock approaches
FIGURE 3 Comparison of the three dating analyses performed in this study (simplified trees). Node number as in table 2. Abbreviations of analyses as in table 1. Abbreviations of geological events as in fig. 2. Abbrevia- tions of genera as in figs. 1 and 2. * constrained nodes based on the MP topologies; ↑, origin of total groups Pan-Chelidae and Pan- Pelomedusioides.
FIGURE 4 in Dating the origin and diversiFIcation of Pan-Chelidae (Testudines, Pleurodira) under multiple molecular clock approaches
FIGURE 4 Comparison of dates produced by the three analyses of this study and four previous molecular clock studies. Abbreviations: Dea (2011), Dornburg et al. (2011); Jea (2013), Joyce et al. (2013); Pea (2017), Pereira et al. (2017); TS-M TD, This study morphological tip-dating; TS- ND, This study node-dating; TS-TE TD, This study total-evidence tip- dating; R&DF (2016), Rodrigues & Diniz-Filho (2016). Node numbers as in table 2.
Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches
<p><span><span><span><span><span><span><span><span><span><span><span>Simultaneous molecular dating of population and species divergences is essential in many biological investigations, including phylogeography, phylodynamics, and species delimitation studies. In these investigations, multiple sequence alignments consist of both intra- and inter-species samples (mixed samples). As a result, the phylogenetic trees contain inter-species, inter-population, and within-population divergences. Bayesian relaxed clock methods are often employed in these analyses, but they assume the same tree prior for both inter- and intra-species branching processes and require specification of a clock model for branch rates (independent vs. autocorrelated rates models). We evaluated the impact of a single tree prior onBayesian divergence time estimates by analyzing computer-simulated datasets. We also examined the effectof the assumption of independence of evolutionary rate variation among branches when the branch rates are autocorrelated. Bayesian approach with coalescent tree priors generally produced excellent molecular dates and highest posterior densities with high coverage probabilities. We also evaluated the performance of a non-Bayesian method, RelTime, which does not require the specification of a tree prior or a clock model. RelTime's performance was similar to that of the Bayesian approach, suggesting that it is also suitable to analyze datasets containing both populations and species variation when its computational-efficiency is needed.</span></span></span></span></span></span></span></span></span></span></span></p>
Treelists, constraints and logfiles for: Relative time constraints improve molecular dating
<p>Dating the tree of life is central to understanding the evolution of life on Earth. Molecular clocks calibrated with fossils represent the state of the art for inferring the ages of major groups. Yet, other information on the timing of species diversification can be used to date the tree of life. This is the case for instance for horizontal gene transfer events and ancient coevolutionary relationships such as (endo)symbioses, which can imply temporal relationships between two nodes in a phylogeny (Davin et al. 2018). This can be particularly helpful when the geological record is sparse, e.g. for microorganisms, which represent the vast majority of extant and extinct biodiversity. Here, we demonstrate that relative age constraints, when combined with fossil calibrations, can significantly improve both the accuracy and resolution of molecular clock estimates. We provide an implementation of relative age constraints in RevBayes (Hoehna et al. 2016) that can be combined in a modular manner with the wide range of molecular dating methods available in the software. To validate our method in a realistic data setting we apply it to two data sets of 40 Cyanobacteria and 62 Archaea respectively, and provide cross-validations of fossil calibrations and relative age constraints.</p>
Comparative analysis of chloroplast genomes of Sanguisorba species and insights into phylogenetic implications and molecular dating
<pre class="js_message_plain ng-binding"><em>Sanguisorba</em> is a small genus, which consists of about 15 species widely distributed in North America and Eurasia. Previous studies on <em>Sanguisorba</em> are useful for understanding of phylogeny and chloroplast (cp) genome evolution of <em>Sanguisorba</em>. However, the cp genome resources of <em>Sanguisorba</em> are still limited, and the phylogeny and molecular dating for <em>Sanguisorba</em> and its relatives still need further explored. Here, we reported four cp genomes of <em>Sanguisorba</em> and conducted comparative analysis of the four <em>Sanguisorba</em> cp genomes plus five previously published ones. The nine cp genomes of <em>Sanguisorba</em> have typical tetrad quadripartite structure, with a total length of 154 282 to 155 730 bp, and their gene content, gene structure, and gene order are relatively conservative. The analysis of single copy (SC)/inverted repeat (IR) boundaries shows very slight boundary differences in <em>Sanguisorba</em> cp genomes. Eight variation hotspots were screened as excellent candidate markers of <em>Sanguisorba</em>. Phylogenetic analysis indicated <em>Sanguisorba</em> was monophyletic and was a member of tribe Agrimonieae subtribe Sanguisorbinae. Within <em>Sanguisorba</em>, <em>S. filiformis</em> is a sister group of six other taxa in the present sampling. Estimation of the divergence times indicated that subtribes Agrimoniinae and Sanguisorbinae diverged at the transition between the Oligocene and the Miocene, and divergent times of Agrimonieae genera ranged from the late Miocene to the Middle Pleistocene. This study enriches the available cp genome resources of <em>Sanguisorba</em>, and it is of great significance to further study the phylogeny and evolution of <em>Sanguisorba</em> and its relatives.</pre>
Data for dating in the dark: Elevated substitution rates in cave cockroaches (Blattodea: Nocticolidae) have negative impacts on molecular date estimates
<p>Rates of nucleotide substitution vary substantially across the Tree of Life, with potentially confounding effects on phylogenetic and evolutionary analyses. A large acceleration in mitochondrial substitution rate occurs in the cockroach family Nocticolidae, which predominantly inhabit subterranean environments. To evaluate the impacts of this among-lineage rate heterogeneity on estimates of phylogenetic relationships and evolutionary timescales, we analysed nuclear ultraconserved elements (UCEs) and mitochondrial genomes from nocticolids and other cockroaches. Substitution rates were substantially elevated in nocticolid lineages compared with other cockroaches, especially in mitochondrial protein-coding genes. This disparity in evolutionary rates is likely to have led to different evolutionary relationships being supported by mitochondrial genomes and UCE loci. Furthermore, analyses using relaxed-clock models inferred much deeper divergence times compared with a flexible local clock. Our phylogenetic analysis of UCEs, which is the first genome-scale study to include all nine major cockroach families, unites Corydiidae and Nocticolidae and places Anaplectidae as the sister lineage to the rest of Blattoidea. We uncover an extraordinary level of genetic divergence in Nocticolidae, including two highly distinct clades that separated ~115 million years ago despite both containing representatives of the genus <em>Nocticola</em>. The results of our study highlight the potential impacts of high among-lineage rate variation on estimates of phylogenetic relationships and evolutionary timescales.</p>
Data for dating in the dark: Elevated substitution rates in cave cockroaches (Blattodea: Nocticolidae) have negative impacts on molecular date estimates
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Comparative analysis of chloroplast genomes of Sanguisorba species and insights into phylogenetic implications and molecular dating
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Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches
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Treelists, constraints and logfiles for: Relative time constraints improve molecular dating
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Data from: Inflation of molecular clock rates and dates: molecular phylogenetics, biogeography, and diversification of a global cicada radiation from Australasia (Hemiptera: Cicadidae: Cicadettini)
Dated phylogenetic trees are important for studying mechanisms of diversification, and molecular clocks are important tools for studies of organisms lacking good fossil records. However, studies have begun to identify problems in molecular clock dates caused by uncertainty of the modeled molecular substitution process. Here we explore Bayesian relaxed-clock molecular dating while studying the biogeography of ca. 200 species from the global cicada tribe Cicadettini. Because the available fossils are few and uninformative, we calibrate our trees in part with a cytochrome oxidase I (COI) clock prior encompassing a range of literature estimates for arthropods. We show that tribe-level analyses calibrated solely with the COI clock recover extremely old dates that conflict with published estimates for two well-studied New Zealand subclades within Cicadettini. Additional subclade analyses suggest that COI relaxed-clock rates and maximum-likelihood branch lengths become inflated relative to EF-1α intron and exon rates and branch lengths as clade age increases. We present corrected estimates derived from (1) an extrapolated EF-1α exon clock derived from COI-calibrated analysis within the largest New Zealand subclade, (2) post-hoc scaling of the tribe-level chronogram using results from subclade analyses, and (3) exploitation of a geological calibration point associated with New Caledonia. We caution that considerable uncertainty is generated due to dependence of substitution estimates on both the taxon sample and the choice of model, including gamma category number and the choice of empirical versus estimated base frequencies. Our results suggest that diversification of the tribe Cicadettini commenced in the early- to mid-Cenozoic and continued with the development of open, arid habitats in Australia and worldwide. We find that Cicadettini is a rare example of a global terrestrial animal group with an Australasian origin, with all non-Australasian genera belonging to two distal clades. Within Australia, we show that Cicadettini is more widely distributed than any other cicada tribe, diverse in temperate, arid and monsoonal habitats, and nearly absent from rainforests. We comment on the taxonomic implications of our findings for thirteen cicada genera.
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