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Because the troglomorphs are extremely rare – we have visited this site on four separate occasions and have collected a total of 3 specimens (no adult males) – we are uncertain of both the full geographic distribution of this form, and the geographic context of divergence from surface ancestors (e.g., in allopatry versus parapatry).
The methods used here can be easily applied to address similar evolutionary questions in other systems to help elucidate the geographic context of divergence and speciation.
Our data concur with other studies on comparative phylogeography in Europe [ 9, 10] in explaining the divergence between lineages in the context of divergence among three main areas and of the effect of the Alpine barrier in population differentiation.
New algorithms can effectively estimate demographic parameters on a species tree to help disentangle the historical context of divergence and speciation and to test the plausibility of a peripatric scenario in comparison with the generally accepted null model of allopatric divergence [ 2, 3, 9].
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In this context, dates of divergence for particular clades can be estimated.
The five species pairs of Sceloporus that support divergence with gene flow have not been previously studied in the context of population divergence genetics.
This unique dataset provides an opportunity to examine the strength of reproductive isolation, the development and sex ratios of hybrid offspring, patterns of fertility and infertility, and polyploidization in hybrids all in the context of genetic divergence between parental species.
Finally a model of PTH gene family evolution is proposed and discussed in the context of functional divergence.
A hypothesis of the phylogenetic position of adaptive peak shifts also provides a framework for future assessments of the ecological context of phenotypic divergence in adaptive radiations.
When differential levels of OR transcripts were viewed within the context of molecular divergence, there was no significant correlation between transcript enrichment and dN/dS ratio.
The phylogenetic origin of Hydatellaceae near the root of angiosperm phylogeny [ 10] and lack of reliable fossils [ 7] make consideration of the family age infeasible outside the context of angiosperm divergence times.
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