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Such a reconciliation between T and S implies an unambiguous evolution scenario for the gene family, where a vertex of R(T, S) that satisfies property (D) represents a duplication (duplication vertex), a vertex that satisfies property (S) represents a speciation (speciation vertex), and an inserted subtree represents a gene loss.
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Our survey of the literature indicates that the opportunity for fishing selection is amply demonstrated, even if it does not yet provide unambiguous evidence for rapid evolution.
As Table 2 shows, AAT2Tb and AAT5Tb gave unambiguous evidence for concert evolution of gene duplicates; where homoeologs from the various species were constrained to show orthologous relationships, this topology was significantly less likely than the optimal tree topology, unlike the topology constrained to show sequences clustering by species.
In the T7 study, there was direct evidence of beneficial mutations ascending during the period of evolution but no unambiguous way to determine how much fitness benefit they contributed.
The need for a direct genetic approach has been noted (Kuparinen and Merilä 2007; Allendorf et al. 2008), but unambiguous genetic evidence of contemporary evolution in marine fish populations has proven elusive because of the limited availability of adaptive variation estimates, as well as historical molecular data sets (Conover et al. 2006).
The current variations with respect to time provided an unambiguous characterization of the single pit evolution.
For the remaining pairs of unambiguous conserved orthologous ORFs, we analyze evolution of TATA box consensus sequences in their upstream regions.
First, this gene has very few indels in its evolution across vertebrates, making for a largely unambiguous alignment, and it is a single copy nuclear gene with no paralogs of high sequence similarity.
However, unambiguous evidence regarding the recurrence of this model in compensatory evolution still awaits large-scale analyses.
Two example ortholog groups were chosen due to their unambiguous evolutionary history: for most groups it is difficult to unambiguously reconstruct the full evolution due to the presence of intermingled events.
Holometabolic insects such as Drosophila provide an excellent model for studying gene evolution over ontogeny as they pass through four separate, unambiguous developmental stages (embryo, larva, pupa, and adult).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com