Phylogenetic informativeness reconciles ray-finned fish molecular divergence times

Catostomidae (“suckers”) is a diverse (76 species) and broadly distributed family of Holarctic freshwater fishes with a rich fossil record and a considerable number (∼35%) of threatened and imperiled species. We integrate DNA sequences (three mitochondrial genes, three nuclear genes), morphological data, and fossil information to infer sucker phylogenetic relationships and divergence times using Bayesian “total-evidence” methods, and then test hypotheses about the temporal diversification of the group. Our analyses resolved many nodes within subfamilies and clarified Catostominae relationships to be of the form ((Thoburniini, Moxostomatini), (Erimyzonini, Catostomini)). Patterns of subfamily relationships were incongruent, but mainly supported two placements of the Myxocyprininae; distinguishing these using Bayes factors lent strongest support to a model with Myxocyprininae sister to all remaining sucker lineages. We improved our Bayesian total-evidence dating analysis by excluding problematic characters, using a clock-partitioning scheme identified by Bayesian model selection, and employing a fossilized birth-death tree prior accommodating morphological data and fossils. The resulting chronogram showed that suckers evolved since the Late Cretaceous–Eocene, and that the Catostomini and Moxostomatini clades have accumulated species diversity since the early to mid-Miocene. These results agree with the fossil record and confirm previous hypotheses about dates for the origins of Catostomide and catostomine diversification, but reject previous molecular hypotheses about the timing of divergence of ictiobines, and between Asian–North American lineages. Overall, our findings from a synthesis of multiple data types enhance understanding of the phylogenetic relationships, taxonomic classification, and temporal diversification of suckers, while also highlighting practical methods for improving Bayesian divergence dating models by coupling phylogenetic informativeness profiling with relaxed-clock partitioning.

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Arthropod molecular divergence times and the Cambrian origin of pentastomids

Systematics and Biodiversity ◽

10.1080/14772000903562012 ◽

2010 ◽

Vol 8 (1) ◽

pp. 63-74 ◽

Cited By ~ 35

Author(s):

Kate L. Sanders ◽

Michael S. Y. Lee

Keyword(s):

Divergence Times ◽

Molecular Divergence

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Faculty Opinions recommendation of Chromosomal speciation and molecular divergence--accelerated evolution in rearranged chromosomes.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1013151.189304 ◽

2003 ◽

Author(s):

Thomas Mitchell-Olds

Keyword(s):

Chromosomal Speciation ◽

Accelerated Evolution ◽

Molecular Divergence

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Faculty Opinions recommendation of Evaluating phylogenetic informativeness and data-type usage for new protein-coding genes across Vertebrata.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.13360106.14730258 ◽

2011 ◽

Author(s):

Rafael Zardoya ◽

Diego San Mauro

Keyword(s):

Data Type ◽

Protein Coding ◽

Protein Coding Genes ◽

Phylogenetic Informativeness ◽

New Protein

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Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci

Genetics ◽

10.1093/genetics/164.4.1645 ◽

2003 ◽

Vol 164 (4) ◽

pp. 1645-1656 ◽

Cited By ~ 3

Author(s):

Bruce Rannala ◽

Ziheng Yang

Keyword(s):

Dna Sequences ◽

Gene Tree ◽

Species Tree ◽

Bayes Estimation ◽

Ancestral Population ◽

Divergence Times ◽

Gene Trees ◽

Species Divergence ◽

Multiple Loci ◽

Population Sizes

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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Numerical electrophoretic analysis and the behavior of larval proteins among Aedes mosquitoes

Canadian Journal of Zoology ◽

10.1139/z79-123 ◽

1979 ◽

Vol 57 (5) ◽

pp. 979-982 ◽

Cited By ~ 2

Author(s):

Emmanuel C. Igbokwe

Keyword(s):

Collective Behavior ◽

Protein Complex ◽

Related Species ◽

Electrophoretic Analysis ◽

Behavioral Profile ◽

Aedes Mosquitoes ◽

Molecular Behavior ◽

Interspecific Divergence ◽

Molecular Divergence ◽

Species Specific

Species-specific patterns of larval protein electrophoregrams obtained among three species of Aedes mosquitoes were analyzed numerically. A behavioral profile was derived and illustrated for the larval protein complex of each species. Patterns of interspecific divergence in molecular behavior not detectable otherwise from the electrophoregrams were evident in the behavioral profiles of the proteins. The degree of electrophoretic correspondence obtained from the number of shared fractions among the species differs from that derived from the collective behavior of proteins. The numerical and graphic approach to the interpretation of protein electrophoregrams offers another parameter for gauging molecular divergence among related species of insects.

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