Molecular Phylogeny and Divergence Time Estimates for Major Rodent Groups: Evidence from Multiple Genes

Fossil record of penaeids indicates that the family exists since the Triassic period, but extant genera appeared only recently in Tertiary strata. Molecular based divergence time estimates on the matter of penaeid radiation were never properly addressed, due to shortcomings of the global molecular clock assumptions. Here, we studied the diversification patterns of the family, uncovering, more specifically, a correlation between fossil and extant Penaeid fauna. For this, we have used a Bayesian framework that does not assume a global clock. Our results suggest that Penaeid genera originated between 20 million years ago and 43 million years ago, much earlier than expected by previous molecular studies. Altogether, these results promptly discard late Tertiary or even Quaternary hypotheses that presumed a major glaciations influence on the diversification patterns of the family.

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Out of the Neotropics: Late Cretaceous colonization of Australasia by American arthropods

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2012.0675 ◽

2012 ◽

Vol 279 (1742) ◽

pp. 3501-3509 ◽

Cited By ~ 41

Author(s):

Prashant P. Sharma ◽

Gonzalo Giribet

Keyword(s):

Late Cretaceous ◽

Divergence Time ◽

Disjunct Distribution ◽

Continental Margins ◽

Divergence Time Estimates ◽

Evolutionary Origins ◽

Source Regions ◽

Time Estimates ◽

Fiji Islands ◽

The Pacific

The origins of tropical southwest Pacific diversity are traditionally attributed to southeast Asia or Australia. Oceanic and fragment islands are typically colonized by lineages from adjacent continental margins, resulting in attrition of diversity with distance from the mainland. Here, we show that an exceptional tropical family of harvestmen with a trans-Pacific disjunct distribution has its origin in the Neotropics. We found in a multi-locus phylogenetic analysis that the opilionid family Zalmoxidae, which is distributed in tropical forests on both sides of the Pacific, is a monophyletic entity with basal lineages endemic to Amazonia and Mesoamerica. Indo-Pacific Zalmoxidae constitute a nested clade, indicating a single colonization event. Lineages endemic to putative source regions, including Australia and New Guinea, constitute derived groups. Divergence time estimates and probabilistic ancestral area reconstructions support a Neotropical origin of the group, and a Late Cretaceous ( ca 82 Ma) colonization of Australasia out of the Fiji Islands and/or Borneo, which are consistent with a transoceanic dispersal event. Our results suggest that the endemic diversity within traditionally defined zoogeographic boundaries might have more complex evolutionary origins than previously envisioned.

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Phylogenetic relationships and divergence time estimates in the genus Echinops L. (Asteraceae)

Nordic Journal of Botany ◽

10.1111/njb.03081 ◽

2021 ◽

Vol 39 (3) ◽

Author(s):

Handan Şapci Selamoğlu

Keyword(s):

Phylogenetic Relationships ◽

Divergence Time ◽

Divergence Time Estimates ◽

Time Estimates

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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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