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Our results suggest that divergence dating methods produce results that are correlated, but that older nodes are more variable and more difficult to estimate with precision and accuracy.We also find that models incorporating less rate heterogeneity estimate older dates of divergence than more complex models, as node age increases.Understanding the impact of gene and/or lineage rate heterogeneity is paramount for understanding variation among divergence date estimates. the process of molecular evolution is poorly characterized and the relative contributions of gene-specific versus lineage-specific factors toward rate variation over time are unclear.” In this study, we explore the relative contributions of modeling gene and lineage rate heterogeneity to divergence date estimates and investigate the impact of time by dating divergences of various ages under three frameworks: 1) a global molecular clock framework that assumes a single rate across both genes and lineages, 2) a genic molecular clock framework that assumes rate constancy across lineages but allows an evolutionary rate specific to each gene, and 3) a relaxed clock framework that allows rate differences across both genes and lineages.We employ a mixed model nested analysis of variance (ANOVA) approach for assessing the relative contributions of gene, method, and framework to the overall variation among date estimates by treating these different variables as categorical—a novel approach for comparing divergence dating methods—and estimating the relative impact of different types of rate heterogeneity on divergence dating.If rate differences among genes are the rule, it is clear that the application of a global clock to estimate homoeologue divergence dates will produce wildly different results across genes, calling into question the accuracy of dates based on the mode of a polyploid peak. More recent work used synonymous global clock dating via the peak approach (Blanc and Wolfe 2004, Schlueter et al. 2007), reducing the confounding affects of recombination.To the extent that relaxed clock methods better model rate differences across lineages and genes, it would seem useful to apply them to the problem of dating homoeologue divergences and to assess how they compare with is known to be an ancient polyploid based on chromosome number (Goldblatt 1981), genetic mapping (Shoemaker et al. 2004) and comparisons of individual homoeologous pairs (Pfeil et al. Genes in this region, however, show different synonymous distances between homoeologue pairs that trace their divergence to the same event (Innes et al.We also examine different strategies for dealing with multiple genes.

1999), across lineages (Smith and Donoghue 2008), and over time (Fitch and Markowitz 1970, Lopez et al.

2008), making this a useful study system for our purposes.

As genomic analyses become more prevalent, more studies will begin to incorporate phylogenetic information with comparative genomic data (e.g., Fawcett et al. It is thus important to understand the relative application and power of various divergence dating methods across scientific disciplines.

Gene by taxon sampling and phylogenetic relationships of orthologous and homoeologous sequences are outlined in Figure 2.

All genes in (GP) are syntenic, thereby providing evidence for orthology/paralogy.

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