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Vigors, S., O'Doherty, J. V., Kelly, A. K., O'Shea, C. J. & Sweeney, T. The Effect of Divergence in Feed Efficiency on the Intestinal Microbiota and the Intestinal Immune Response in Both Unchallenged and Lipopolysaccharide Challenged Ileal and Colonic Explants.
To explore the effect of divergence time and gene flow on the success rate of species identification, we conducted a series of simulations using twenty thousand loci for two species with a range of splitting times and migration profiles.
Guided by the patterns seen in the empirical data, we simulated sequences with different splitting times and migration rates, and explored the effect of divergence time and gene flow on the success rate of species identification over a broader range of the relevant parameter space.
Similarly, we also evaluated the effect of divergence time on our results.
Using these estimates we failed to find a persuasive effect of divergence on level of genetic diversity.
To detect the effect of divergence on functional role, we plotted the distribution of functional classes by the %chSp.
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To discriminate between the relative effects of divergence and gene flow on the speciation process, we analysed our data set under the Isolation with Migration model [45].
These experiments could more precisely tease apart the effects of divergence and such locus-specific factors as proximity to the origin of DNA replication or the effects of chromosome structural proteins (Ray et al. 2009).
Thus, interspecific mating propensity was significantly affected by cuticular hydrocarbon profile divergence, even after correction for genetic divergence (glm with quasibinomial error distribution; effect of genetic divergence: t= −5.5, p< 0.0001, hydrocarbon divergence: t= −2.9, p= 0.006).
In fact, the effect size of divergence across these populations in the SF proteome is much larger than those seen previously for other phenotypes such as morphology [ 59, 60] and life-history traits [ 34, 61].
We analysed the relationship between amino acid sequence divergence and variation in GC3, to test the effect of evolutionary divergence on codon usage.
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