It is known that the rate of molecular evolution differs across the genome (Matassi et al.1999), across lineages (Smith and Donoghue 2008), and over time (Fitch and Markowitz 1970, Lopez et al.
pulse speed dating - Dating origins polyploidy events
But how effective is this more rigorous, complex approach in obtaining a reliable date for the same event from multiple genes? (2005) obtained different but correlated dates for legume divergences from two regions of the effectively nonrecombining chloroplast genome. 2008) to identify and date two rounds of polyploidy in soybean: a more recent event in (Pfeil et al.
With recombinational jumbling of evolutionary histories, the situation is likely to be worse for nuclear genes. (2002) reported synonymous substitution rate differences of up to 13.8-fold among homoeologous genes duplicated in . 2005), which diverged from soybean ∼54 Ma (Lavin et al. We date homoeologue and orthologue divergences using multiple genes linked in a 1-Mb region of the soybean genome (Innes et al. The predominately selfing breeding system of soybean causes strong linkage among genes (Hyten et al.
Such global rates are often generalizations of questionable relevance to the taxa under study and can lead to very different interpretations of the same data. (2004) and Blanc and Wolfe (2004) reported similar modal values for polyploid peaks in several crop plants but estimated very different homoeologue divergence dates due to the use of different substitution rates. (2009) criticized the methodologies of these and other studies that led to such conflicting results and instead used a relaxed clock method to obtain dates for a number of polyploid events in angiosperms.
The use of relaxed methods eliminates one source of potential error, and the assumption that a global rate is appropriate to transform synonymous distances to dates.
We also examine different strategies for dealing with multiple genes.
Some scientists recommend concatenation as the best method (e.g., Thorne and Kishino 2005), and many studies do so without examining independent data sets, whereas other researchers disagree (e.g., Rodriquez-Trelles et al. Here, we compare the results of estimating divergence dates by using individual genes, averaging across independent gene estimates, and by concatenation of multiple genes.
A mixed model nested analysis of variance testing the effects of framework, method, and gene found that framework had a significant effect on the divergence date estimates but that most variation among dates is due to variation among genes, suggesting a need to further characterize and understand the evolutionary phenomena underlying rate variation within genomes, among genes, and across lineages.
In systematics, the use of a molecular clock for dating divergences has been considered problematic for some time (Graur and Li 2000).
This sampling scheme enables various sets of comparisons, such as across methods and frameworks but within node (shown by the series of dotted lines), among methods within framework (suggested by the gray boxes inclusive of two methods) and by using a mixed model nested ANOVA to compare within and among gene, method, and framework on a node by node basis (suggested by the concentric solid line groups).
This sampling scheme enables various sets of comparisons, such as across methods and frameworks but within node (shown by the series of dotted lines), among methods within framework (suggested by the gray boxes inclusive of two methods) and by using a mixed model nested ANOVA to compare within and among gene, method, and framework on a node by node basis (suggested by the concentric solid line groups)., available from for Gen Bank numbers; available at
Gene by taxon sampling and phylogenetic relationships of orthologous and homoeologous sequences are outlined in Figure 2.