These field data contrast sharply with the results from experimental hybridization in anurans, which show that some lineages may still produce viable F1 offspring after ca. 20 My of divergence (see Background).
Importantly, these systems also offer an opportunity to identify the genetic changes that underlie species-level divergence, because background differentiation at neutral sites is reduced by persistent hybridization and interspecific gene flow (Nosil et al., 2009; Via, 2009).
Some of the respondents suggested that given the divergence of backgrounds the project should have invested more energy in ensuring common understanding at the outset.
Divergence-based approaches additionally rely on recurrent fixations of beneficial mutations to detect significantly elevated levels of divergence relative to background substitution patterns (Nielsen 2005).
In addition, we assess the divergence in genetic background between the S and NS lines, by comparing the left domain of the mitochondrial DNA (mtDNA) control region.
A control simulation without selection was performed for each simulation to estimate the potential increase in background divergence due to selection.
As an estimate for the background divergence pattern, all coding (synonymous and nonsynonymous) bases were placed in 3 × 1 'coding GERP matrix' which was binned as conserved (GERP score < -1), intermediate (GERP score: -1.0 – 1.0) and divergent (GERP score: >1.0).
Each chromosome was divided into 100 windows spanning 18 cM each; these parameters were optimized to detect small regions of divergence but minimize background noise due to sampling variance.
For instance, the background divergence between non-hybridizing races with different color patterns from Peru and French Guiana (0.191; 95 % CI: 0.182-0.200) isignificantlylowerwer than the divergence between the incipient species (0.519; 95 % CI: 0.507-0.531), despite higher realized rates of gene flow between the incipient species than the non-hybridizing races.
As shown in Fig. 5, this was the case for the majority of the codons and expression bins in both Arabidopsis and rice, with the latter featuring wider divergence from the background in accordance with previous reports of gBGC in grasses.
