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At later stages of ecological speciation, as many loci diverge among incipient species, genome-wide effective gene flow will be reduced even at unlinked loci: divergence hitchhiking being superseded by genome hitchhiking (GH) [ 16].
Previous work, based on ITS and MAT loci divergence, has established that most C. orthopsilosis strains belong to two clearly distinct subspecies, referred to as Type 1 and Type 2 (Sai et al. 2011).
The divergence (FST and RST) estimates between seasons, districts and altitude classes for each of the SSR loci analysed are given in Additional file 2. The individual SSR loci divergence (FST,) between seasons was significant for four loci (Bmag0013, HVM67, Bmac0040, and Bmac0134), even if the values were low, and varied from 0.02 to 0.05 (Additional file 2).
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Thus the absolute conversion rate is estimated by μ multiplied by this locus divergence rate.
Our data showed that deletions also accounted for part of the I2 locus divergence between different species.
Neutral locus divergence is a poor predictor of outbreeding depression (McClelland and Naish 2007), but rather shows a positive relationship with F1 mean for quantitative characters (McClelland and Naish 2007), predicting heterosis rather than outbreeding depression.
For breeds that are commonly available one could identify the Angus, Brahman and Holstein as a minimum group for studies of breed or locus divergence based on the similarity between the two studies.
In contrast to the included human DRB and DQB alleles, which showed strong locus divergence, the murid alleles did not cluster in a significant pattern (Fig. 1), suggesting that the DRB and DQB lineages in murids are not as differentiated as they are in primates.
Based on substitution rates at the endo-polygalacturonase locus, divergence of the citrus 2 and the 1 and 3 lineages was estimated to have occurred at least 5, 400 years before present, predating the human-mediated movement of citrus and associated pathogens out of SE Asia.
Thus, the novel prediction we test here is that there will be an association between locus-specific divergence and locus-specific introgression, consistent with highly differentiated loci contributing to reproductive isolation.
These are the conditions under which variation in introgression will more closely reflect locus-specific contributions to reproductive isolation, resulting in correspondence between locus-specific divergence and locus-specific introgression [ 52].
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