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Microarray analysis of gene expression in testes was combined with a correction for sequence divergence derived from genomic hybridizations to identify candidate genes involved in the sterility phenotype.
Times of divergence derived from the fossil record are always underestimates of the true divergence [ 11, 41].
As shown in Figure 5B, FST values between two sub-populations of no divergence derived from the same breed resulted only in a unimodal distribution indicating a uniform mode of selection over all evaluated loci.
First, there is simple difference in calibration age between our study and the analysis of Mower et al. (2007), which utilized an age of 38 Myr for the Beta/ Silene divergence derived from a broader molecular clock analysis of the angiosperms [ 58].
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The discrepancy seen between divergence times derived from fossil materials and molecules is not unique to dog origins.
In our analyses, support for this genetic divergence derives from population genetic metrics, including genetic distance and F-statistics (Technical Appendix Table 2), PCoA, unsupervised haplotype phylogeny, and inferred population structure.
The minimum age for the Gasterosteiformes-Tetraodontiformes divergence is derived from the oldest known member of the tetraodontiform lineage, Plectocretacicus clarae, which also represents the oldest known percomorph.
Therefore, an additional measure of divergence was derived from inferred cerevisiae– paradoxus ancestral sequences using S. mikatae as an outgroup.
The estimate of divergence was derived from the mode Ks of binned values, based on a mutation rate of 5.17× 10-3 substitutions/synonymous site/Myr for the legume lineage [ 34].
It is also important to note that, because these estimates of gene divergence are derived from ESTs that represent only partial gene fragments, the estimated rates of evolution may be different when the entire protein coding sequence is evaluated.
There are numerous reasons why estimates of divergence times derived from molecular data could differ with choice of calibration point, and why molecular and fossil estimates of age might disagree.
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