Biogeographic Dating of Phylogenetic Divergence Times Using Priors and Processes

Abstract The effective population sizes of ancestral as well as modern species are important parameters in models of population genetics and human evolution. The commonly used method for estimating ancestral population sizes, based on counting mismatches between the species tree and the inferred gene trees, is highly biased as it ignores uncertainties in gene tree reconstruction. In this article, we develop a Bayes method for simultaneous estimation of the species divergence times and current and ancestral population sizes. The method uses DNA sequence data from multiple loci and extracts information about conflicts among gene tree topologies and coalescent times to estimate ancestral population sizes. The topology of the species tree is assumed known. A Markov chain Monte Carlo algorithm is implemented to integrate over uncertain gene trees and branch lengths (or coalescence times) at each locus as well as species divergence times. The method can handle any species tree and allows different numbers of sequences at different loci. We apply the method to published noncoding DNA sequences from the human and the great apes. There are strong correlations between posterior estimates of speciation times and ancestral population sizes. With the use of an informative prior for the human-chimpanzee divergence date, the population size of the common ancestor of the two species is estimated to be ∼20,000, with a 95% credibility interval (8000, 40,000). Our estimates, however, are affected by model assumptions as well as data quality. We suggest that reliable estimates have yet to await more data and more realistic models.

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Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

Scientific Reports ◽

10.1038/s41598-021-83664-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Maria Alejandra Serna-Sánchez ◽

Oscar A. Pérez-Escobar ◽

Diego Bogarín ◽

María Fernanda Torres-Jimenez ◽

Astrid Catalina Alvarez-Yela ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Divergence Times ◽

Molecular Clocks ◽

Phylogenetic Placement ◽

Plastid Genomes ◽

Phylogenetic Reconstructions ◽

A Genome ◽

Tree Models ◽

Phylogenomic Analyses ◽

First Time

AbstractRecent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth–death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.

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Phylogeny and divergence times of some racerunner lizards (Lacertidae: Eremias) inferred from mitochondrial 16S rRNA gene segments

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2011.06.022 ◽

2011 ◽

Vol 61 (2) ◽

pp. 400-412 ◽

Cited By ~ 26

Author(s):

Xianguang Guo ◽

Xin Dai ◽

Dali Chen ◽

Theodore J. Papenfuss ◽

Natalia B. Ananjeva ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Divergence Times ◽

Rrna Gene ◽

Mitochondrial 16S Rrna Gene

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Phylogenetic diversification patterns and divergence times in ground beetles (Coleoptera: Carabidae: Harpalinae)

BMC Evolutionary Biology ◽

10.1186/1471-2148-10-262 ◽

2010 ◽

Vol 10 (1) ◽

pp. 262 ◽

Cited By ~ 17

Author(s):

Karen A Ober ◽

Thomas N Heider

Keyword(s):

Ground Beetles ◽

Divergence Times

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Molecular clocks and the early evolution of metazoan nervous systems

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2015.0046 ◽

2015 ◽

Vol 370 (1684) ◽

pp. 20150046 ◽

Cited By ~ 23

Author(s):

Gregory A. Wray

Keyword(s):

Sensory Processing ◽

Fossil Record ◽

Sequence Data ◽

Divergence Times ◽

Molecular Clocks ◽

Sense Organs ◽

Animal Evolution ◽

Nervous Systems ◽

Nervous System Evolution ◽

Fossil Records

The timing of early animal evolution remains poorly resolved, yet remains critical for understanding nervous system evolution. Methods for estimating divergence times from sequence data have improved considerably, providing a more refined understanding of key divergences. The best molecular estimates point to the origin of metazoans and bilaterians tens to hundreds of millions of years earlier than their first appearances in the fossil record. Both the molecular and fossil records are compatible, however, with the possibility of tiny, unskeletonized, low energy budget animals during the Proterozoic that had planktonic, benthic, or meiofaunal lifestyles. Such animals would likely have had relatively simple nervous systems equipped primarily to detect food, avoid inhospitable environments and locate mates. The appearance of the first macropredators during the Cambrian would have changed the selective landscape dramatically, likely driving the evolution of complex sense organs, sophisticated sensory processing systems, and diverse effector systems involved in capturing prey and avoiding predation.

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Biogeography, reproductive biology and phylogenetic divergence within the Fungiidae (mushroom corals)

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2021.107265 ◽

2021 ◽

pp. 107265

Author(s):

Mila Grinblat ◽

Ira Cooke ◽

Tom Shlesinger ◽

Or Ben-Zvi ◽

Yossi Loya ◽

...

Keyword(s):

Reproductive Biology ◽

Phylogenetic Divergence

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Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated

Bioinformatics ◽

10.1093/bioinformatics/btaa820 ◽

2020 ◽

Vol 36 (Supplement_2) ◽

pp. i884-i894

Author(s):

Jose Barba-Montoya ◽

Qiqing Tao ◽

Sudhir Kumar

Keyword(s):

Divergence Time ◽

Sequence Divergence ◽

Molecular Dating ◽

Divergence Times ◽

Time Reversibility ◽

Sequence Alignments ◽

Divergence Time Estimates ◽

Time Estimates ◽

Substitution Process ◽

The Impact

Abstract Motivation As the number and diversity of species and genes grow in contemporary datasets, two common assumptions made in all molecular dating methods, namely the time-reversibility and stationarity of the substitution process, become untenable. No software tools for molecular dating allow researchers to relax these two assumptions in their data analyses. Frequently the same General Time Reversible (GTR) model across lineages along with a gamma (+Γ) distributed rates across sites is used in relaxed clock analyses, which assumes time-reversibility and stationarity of the substitution process. Many reports have quantified the impact of violations of these underlying assumptions on molecular phylogeny, but none have systematically analyzed their impact on divergence time estimates. Results We quantified the bias on time estimates that resulted from using the GTR + Γ model for the analysis of computer-simulated nucleotide sequence alignments that were evolved with non-stationary (NS) and non-reversible (NR) substitution models. We tested Bayesian and RelTime approaches that do not require a molecular clock for estimating divergence times. Divergence times obtained using a GTR + Γ model differed only slightly (∼3% on average) from the expected times for NR datasets, but the difference was larger for NS datasets (∼10% on average). The use of only a few calibrations reduced these biases considerably (∼5%). Confidence and credibility intervals from GTR + Γ analysis usually contained correct times. Therefore, the bias introduced by the use of the GTR + Γ model to analyze datasets, in which the time-reversibility and stationarity assumptions are violated, is likely not large and can be reduced by applying multiple calibrations. Availability and implementation All datasets are deposited in Figshare: https://doi.org/10.6084/m9.figshare.12594638.

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Reclassification of Rhodospirillum photometricum Molisch 1907, Rhodospirillum sulfurexigens Anil Kumar et al. 2008 and Rhodospirillum oryzae Lakshmi et al. 2013 in a new genus, Pararhodospirillum gen. nov., as Pararhodospirillum photometricum comb. nov., Pararhodospirillum sulfurexigens comb. nov. and Pararhodospirillum oryzae comb. nov., respectively, and emended description of the genus Rhodospirillum

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.059147-0 ◽

2014 ◽

Vol 64 (Pt_4) ◽

pp. 1154-1159 ◽

Cited By ~ 20

Author(s):

K. V. N. S. Lakshmi ◽

B. Divyasree ◽

E. V. V. Ramprasad ◽

Ch. Sasikala ◽

Ch. V. Ramana

Keyword(s):

Type Species ◽

New Genus ◽

Rhodospirillum Rubrum ◽

Phenotypic Properties ◽

Content Type ◽

Link Type ◽

Carotenoid Composition ◽

Emended Description ◽

Phylogenetic Divergence ◽

Diagnostic Properties

The genus Rhodospirillum is represented by four species, with three of them showing phylogenetic divergence compared to the type species, Rhodospirillum rubrum . Differences in the major diagnostic properties such as internal photosynthetic membranes, quinones, fatty acids, carotenoid composition and a few other phenotypic properties warrant the reclassification of members of this genus. Resultantly, a new genus, Pararhodospirillum gen. nov., is proposed based on the analysis of nine strains to accommodate Rhodospirillum photometricum , Rhodospirillum sulfurexigens and Rhodospirillum oryzae as Pararhodospirillum photometricum comb. nov., Pararhodospirillum sulfurexigens comb. nov. and Pararhodospirillum oryzae comb. nov., respectively. The type species of the genus is Pararhodospirillum photometricum comb. nov. An emended description of the genus Rhodospirillum is also proposed.

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