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Critiquing blind dating: the dangers of over-confident date estimates in comparative genomics

2013; Elsevier BV; Volume: 28; Issue: 11 Linguagem: Inglês

10.1016/j.tree.2013.07.007

1872-8383

Christopher W. Wheat, Niklas Wahlberg,

Genetic diversity and population structure

Phylogenomic advances provide more rigorous estimates for the timing of evolutionary divergences than previously available (e.g., Bayesian relaxed-clock estimates with soft fossil constraints). However, because many family-level clades and higher, as well as model species within those clades, have not been included in phylogenomic studies, the literature presents temporal estimates likely harboring substantial errors. Blindly using such dates can substantially retard scientific advancement. We suggest a way forward by conducting analyses that minimize prior assumptions and use large datasets, and demonstrate how using such a phylogenomic approach can lead to significantly more parsimonious conclusions without a good fossil record. We suggest that such an approach calls for research into the biological causes of conflict between molecular and fossil signatures. Phylogenomic advances provide more rigorous estimates for the timing of evolutionary divergences than previously available (e.g., Bayesian relaxed-clock estimates with soft fossil constraints). However, because many family-level clades and higher, as well as model species within those clades, have not been included in phylogenomic studies, the literature presents temporal estimates likely harboring substantial errors. Blindly using such dates can substantially retard scientific advancement. We suggest a way forward by conducting analyses that minimize prior assumptions and use large datasets, and demonstrate how using such a phylogenomic approach can lead to significantly more parsimonious conclusions without a good fossil record. We suggest that such an approach calls for research into the biological causes of conflict between molecular and fossil signatures. a part of a phylogenetic tree where independent branches connect, usually bifurcating, and representative of an evolutionary divergence event. analyzing data to estimate the evolutionary relationships of a group of organisms. Modern techniques are based on increasingly sophisticated models of evolution, primarily relying on DNA sequence data. phylogenetics based on genomic-level data. In practice, any study that uses multiple (10s to 100s) molecular markers (e.g., protein-coding genes) to infer phylogenetic relationships. a single date assigned to a given node with no associated error. When used in analyses, this makes a strong claim that the exact time of divergence between two lineages is known without error. the use of fossil or other extrinsic information to calibrate relaxed clock models to estimate absolute times of divergence of lineages. the distribution of dates from which values are drawn that are used in an analysis to construct, together with the likelihood calculated from the data, the posterior distribution. In the context of a Bayesian relaxed-clock analysis, prior distributions reflect the range of age values from which an analysis program will sample values, assess them based on their likelihood, and produce a set of values of the posterior distribution for estimation of the ages in question. the use of results from previous studies (that used primary calibrations) to calibrate relaxed clock models to estimate absolute times of divergence of lineages.