The Implications of Lineage-Specific Rates for Divergence Time Estimation. [PDF]
Syst Biol, 2020 Abstract Rate variation adds considerable complexity to divergence time estimation in molecular phylogenies. Here, we evaluate the impact of lineage-specific rates—which we define as among-branch-rate-variation that acts consistently across the entire genome.
Carruthers T, Sanderson MJ, Scotland RW.
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So many genes, so little time: A practical approach to divergence-time estimation in the genomic era. [PDF]
PLoS ONE, 2018 Phylogenomic datasets have been successfully used to address questions involving evolutionary relationships, patterns of genome structure, signatures of selection, and gene and genome duplications.
Stephen A Smith +2 more
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Uncertainty in Divergence Time Estimation [PDF]
Systematic Biology, 2020 Abstract Understanding and representing uncertainty is crucial in academic research because it enables studies to build on the conclusions of previous studies, leading to robust advances in a particular field. Here, we evaluate the nature of uncertainty and the manner by which it is represented in divergence time estimation, a field that
Carruthers, T, Scotland, RW
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Estimating parameters of speciation models based on refined summaries of the joint site-frequency spectrum. [PDF]
PLoS ONE, 2011 Understanding the processes and conditions under which populations diverge to give rise to distinct species is a central question in evolutionary biology.
Aurélien Tellier +7 more
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Dating Tips for Divergence-Time Estimation [PDF]
Trends in Genetics, 2015 The molecular clock is the only viable means of establishing an accurate timescale for Life on Earth, but it remains reliant on a capricious fossil record for calibration. 'Tip-dating' promises a conceptual advance, integrating fossil species among their living relatives using molecular/morphological datasets and evolutionary models.
O'Reilly, Joseph E. +2 more
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Taxonomy, Phylogeny, Divergence Time Estimation, and Biogeography of the Family Pseudoplagiostomataceae (Ascomycota, Diaporthales) [PDF]
Journal of Fungi, 2023 Species of Pseudoplagiostomataceae were mainly introduced as endophytes, plant pathogens, or saprobes from various hosts. Based on multi-locus phylogenies from the internal transcribed spacers (ITS), the large subunit of nuclear ribosomal RNA gene (LSU),
Zhaoxue Zhang +6 more
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CladeDate: Calibration information generator for divergence time estimation
Methods in Ecology and Evolution, 2022 Time‐scaled phylogenetic trees are essential tools in modern biology and node‐based calibrations have been the main approach to time‐tree estimation. But methods for generating the required calibration information are scarce and difficult to parameterize.
Santiago Claramunt
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Mitogenome of a cryptic species within Uropsilus and divergence time estimation [PDF]
Mitochondrial DNA. Part B. Resources, 2017 Uropsilus sp. 4 is a new cryptic species, collected in Changyang county, Hubei province, China. In this study, the whole mitochondrial genome of Uropsilus sp. 4 was first determined and characterized.
Yu Xu, Yunting Hu, Feiyun Tu
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Phylogenetic relations among Mexican phlebotomine sand flies (Diptera: Psychodidae) and their divergence time estimation. [PDF]
PLoS ONE, 2023 Phlebotomine sand flies (Diptera: Psychodidae: Phlebotominae) have biological relevance as vectors of several pathogens. To ensure periodic entomological monitoring it is necessary to have efficient and accurate tools for an adequate taxonomic ...
Yokomi N Lozano-Sardaneta +10 more
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Probabilistic divergence time estimation without branch lengths: dating the origins of dinosaurs, avian flight and crown birds. [PDF]
Biol Lett, 2016 Branch lengths—measured in character changes—are an essential requirement of clock-based divergence estimation, regardless of whether the fossil calibrations used represent nodes or tips.
Lloyd GT +3 more
europepmc +4 more sources