Estimating Divergence Times from Molecular Data on Phylogenetic and Population Genetic Timescales

By B. Arbogast, S. Edwards, John Wakeley, Peter Beerli, J. Slowinski. 2002

596 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/7c89d3257115c295c72928190fe44d024f777311

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Citations in the corpus

The role of molecular genetics in sculpting the future of integrative biogeography (2008, background): “Given the importance of divergence time estimates in comparative phylogeographic studies, rigorous methods using modeling approaches that incorporate the coalescent variation among and within lineages are needed to prevent misleading inferences about community history (Arbogast et al., 2002).”
Footprints on water: the genetic wake of dispersal among reefs (2007, background): “Interpretation of these analyses warrants some caveats however (see Arbogast et al. 2002 ).”
Disentangling taxonomy within the Rhabditis (Pellioditis) marina (Nematoda, Rhabditidae) species complex using molecular and morhological tools (2008, background): “Saturation (multiple substitutions at the same sites) masks the true levels of sequence divergence and obscures the deeper phylogenetic relationships among sequences (Arbogast et al., 2002).”
MTML-msBayes: Approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity (2011, methodology): “divergence and divergence time estimation are dependent on model assumptions about post-divergence migration [54-56] and therefore we initially used ABC model choice [32,58] to compare the posterior probability of two models; complete isolation and post-divergence migration across all three taxon-pa”
Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA (2006, methodology): “The past several years have seen a renewed interest in methods for attaching time estimates to phylogenetic trees (Arbogast et al. 2002, Welch & Bromham 2005).”
Calibrating the avian molecular clock (2008, background): “Multiple mutations at a single site (‘saturation’) confound genetic distance estimates (Arbogast et al. 2002).”
Is there a universal mtDNA clock for birds (2004, unknown): “linear fashion (Arbogast et al. 2002).”
Evolution and phylogeny of the genus Natrix (Serpentes: Colubridae) (2006, methodology): “There are many ambiguities in the application of any molecular clock (for reviews see Avise et al., 1992; Easteal, Collet & Betty, 1995; Arbogast et al., 2002), and most phylogeographical scenarios can provide only approximations of divergence times.”
Isolation with migration models for more than two populations. (2010, background): “The discernment of recent evolutionary history for closely related populations or species presents challenges that fall in the area of population genetics (Gillespie and Langley 1979; Pamilo and Nei 1988; Hudson 1992; Nielsen 1998; Rannala and Yang 2003; Degnan and Salter 2005), and evolutionary bio”
Is a new paradigm emerging for oceanic island biogeography? (2007, methodology): “…of those robust phylogenies; the ability to make rough but reasonable estimates of the timing of phylogenetic events using DNA sequence data (e.g. Arbogast et al., 2002); the availability of some well-dated fossil material; and the existence of increasingly detailed and reliable geological…”
Molecular phylogeny and systematics of the Pieridae (Lepidoptera: Papilionoidea): higher classification and biogeography (2006, background): “…dated fossils, rather than ages of vicariance events inferred from biogeography and geological data, to estimate minimum divergence times of lineages within the framework of our phylogenetic hypothesis (Hillis, Mable & Moritz, 1996b; Arbogast et al., 2002; Hedges & Kumar, 2003; Magallón, 2004).”
As Time Goes by: A Simple Fool's Guide to Molecular Clock Approaches in Invertebrates* (2009, background): “Several studies, however, indicated that in many cases the assumption of rate constancy is violated (e.g., Arbogast et al. 2002, Pulquerio and Nichols 2007).”
Barley yellow dwarf viruses (BYDVs) preserved in herbarium specimens illuminate historical disease ecology of invasive and native grasses (2007, methodology): “Divergence times estimated with three different models of nucleotide sequence evolution (to account for multiple substitutions and non-uniform substitution rates across sites; Arbogast et al. 2002) suggest that virus may have dispersed from California to Australia in the 1890s.”