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Second, what traditionally is considered a gene duplication event, in many instances upon closer inspection will reveal itself to be the result of divergence followed by gene transfer and non-homologous recombination of the divergent copy [ 66, 67].
Our results therefore highlight the fact that speciation is the combined result of divergence along multiple phenotypic axes.
As suggested for other gymnosperms, the large amount of SL DNA in Taxodium is likely the result of divergence among ancient repeat copies and gene/pseudogene duplication.
These non-plant proteins have not been related to Snf1-associated gene regulation, possibly as a result of divergence with PRL1 in the amino-terminal regions of the proteins.
The repeated observation that stronger assortative mating is found between populations of flies that are in close contact in the wild (C&O, p 357-365) brings very strong support to the idea that reproductive isolation is a phenotype that is selected for, and not just the result of divergence between populations that are not in contact with one another.
Whereas interspecific comparisons reveal only the ultimate outcome or regulatory divergence (expression level), comparisons between hybrids and their parents allow us to observe the result of divergence at all levels of gene regulation, from cis-regulatory elements to the feedback/forward regulation occurring in the overall hybrid regulatory network.
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Results of divergence time analyses were evaluated by examining effective samples sizes and burn-in using Tracer and then calculating the median node heights using TreeAnnotator.
Results of divergence time estimates are in agreement with the fossil records of Hydrocharitaceae.
Results of divergence date estimates from individual genes showed that the oldest dates for all nodes were inferred from the wg gene and the youngest dates for all nodes were inferred from the 18S gene with r8s (Table 2).
The degree of similarity of coding sequences in these elements, their discontinuous distribution, and the results of divergence-versus-age analysis, make it highly unlikely that these sequences diverged at the same time as their host taxa.
The degree of coding sequence similarity of the studied elements, their discontinuous distribution, and results of divergence-versus-age analysis make it highly unlikely that these sequences diverged at the same time as their host taxa.
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