Divergence Time and Evolutionary Rate Estimation with Multilocus Data

Abstract

Bayesian methods for estimating evolutionary divergence times are extended to multigene data sets, and a technique is described for detecting correlated changes in evolutionary rates among genes. Simulations are employed to explore the effect of multigene data on divergence time estimation, and the methodology is illustrated with a previously published data set representing diverse plant taxa. The fact that evolutionary rates and times are confounded when sequence data are compared is emphasized and the importance of fossil information for disentangling rates and times is stressed.

Δ6-Desaturase sequence evidence for explosive Pliocene radiations within the adaptive radiation of Macaronesian Echium (Boraginaceae)

“…Additionally, a Bayesian dating method was used to infer divergence time estimates and associated confidence intervals (Kishino et al, 2001). The procedure outlined in Rutschmann (2005) was followed, which involves the use of three programs: Baseml (PAML3.15; Yang, 1997), Estbranches (Thorne et al, 1998), and Multidivtime (Thorne and Kishino, 2002). Model parameters (base frequencies, transition/transversion ratio, and alpha shape parameter of the gamma distribution accounting for among-site rate heterogeneity) were estimated using the most complex substitution model implemented in Baseml, F84+G.…”

Age and biogeography of major clades in sturgeons and paddlefishes (Pisces: Acipenseriformes)

“…Second, we used Ludwig et al's (2001) phylogeny among extant acipenseriform species to estimate the divergence time among these groups using mitochondrial cytochrome b gene sequences data retrieved from GenBank (Table 2-including inferred ploidy levels of acipenseriforms). Bayesian approaches (Thorne et al, 1998;Thorne and Kishino, 2002), one of the relaxed molecular clock methods, were used for the two dating analyses, the setting for Bayesian approaches were as follows.…”

“…Divergence times were determined using a Bayesian approach that incorporates variation of rates of evolution among genes and among lineages (Thorne et al, 1998;Thorne and Kishino, 2002), which were estimated with MULTIDIVTIME program (available from J. Thorne). This parametric approach relaxes the assumption of a strict Table 2 Twenty-four mitochondrial cytochrome b gene sequences used for dating the divergence time of acipenseriform species retrieved from GenBank for the second dating analysis a Nine distribution areas were coded from A to I according to the analysis of Bemis and Kynard (1997) (Yang, 1994) along with their variance-covariance matrix.…”

Molecular phylogeny of the Cricetinae subfamily based on the mitochondrial cytochrome b and 12S rRNA genes and the nuclear vWF gene

“…We also estimated divergence times using the relaxed Bayesian clock method for multigene data (multidivtime program; Thorne and Kishino, 2002). The ML topology for the combined data were used as the reference tree.…”

“…Model parameters were estimated with the use of baseml software (PAML version 3.14; Yang, 1997). Branch lengths and their covariance matrices were calculated with estbranche-dna program (Multidistribute package; Thorne and Kishino, 2002). Multidivtime program was run with the Markov chain sampled 10,000 times, every 100th generation.…”