Performance of a Divergence Time Estimation Method under a Probabilistic Model of Rate Evolution

Abstract

Rates of molecular evolution vary over time and, hence, among lineages. In contrast, widely used methods for estimating divergence times from molecular sequence data assume constancy of rates. Therefore, methods for estimation of divergence times that incorporate rate variation are attractive. Improvements on a previously proposed Bayesian technique for divergence time estimation are described. New parameterization more effectively captures the phylogenetic structure of rate evolution on a tree. Fossil information and other evidence can now be included in Bayesian analyses in the form of constraints on divergence times. Simulation results demonstrate that the accuracy of divergence time estimation is substantially enhanced when constraints are included.

Dated historical biogeography of the temperate Loliinae (Poaceae, Pooideae) grasses in the northern and southern hemispheres

“…Due to the lack of crown Loliinae fossils, we first estimated the divergence time of the grass family and that dated the divergence of the Triticeae tribe from the Aveneae-Poeae tribe (which include both our outgroup and ingroup taxa) using Bayesian dating methods (Thorne et al, 1998;Kishino et al, 2001;Thorne and Kishino, 2002) as indicated in and Forest et al (2007). Following Gaut (2002), the inferred dates were derived from the plastid gene ndhV of nine Poaceae representatives [Anomochloa (Anomochloeae), Leersia (Oryzeae); Avena (Aveneae); Poa (Poeae); Hordeum (Triticeae); Setaria and Pennisetum (Paniceae); Sorghum and Zea (Andropogoneae) plus Joinvillea (Joinvilleaceae; outgroup)], and a phylogeny of the family concordant with that presented by Clark et al (1995) and the Grass Phylogeny Working Group (GPWG, 2001).…”

“…We used as calibration lower and upper bounds previously reported on the age of the family based on pollen (Linder, 1987;Jacobs et al, 1999;Kellogg, 2002Kellogg, , 2001) and phytoliths (Prasad et al, 2005) fossil records that varied between 55-80 My and that were imposed as minimum and maximum constraints to the crown node of the Poaceae, respectively. Divergence times and additional parameters (based on the F84 + G model and 100,000 MCMC iterations, with rttm and rttmsd set at 6.0, rtrate and rtratesd set at 0.02, brownmean and brownsd set at 0.16, and big time set at 100, see below) were calculated using the programs Baseml (PAML package, Yang, 1997), Estbranches (Thorne et al, 1998) and Multidivtime (Kishino et al, 2001).…”

A multi-locus time-calibrated phylogeny of the siphonous green algae

“…Node age estimates were therefore obtained by fitting a relaxed clock model to our molecular data. The assumption of the molecular clock was relaxed by allowing rates of molecular evolution to vary along the tree according to a Brownian motion model (Kishino et al, 2001;Thorne et al, 1998). First, an F84 model with rate variation across sites following a discrete gamma distribution with 20 rate categories was optimized in PAML v.4 (Yang, 2007), using the topology obtained with Bayesian inference from which all but two outgroups were removed (Trentepohlia and Oltmannsiellopsis).…”

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).…”