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In addition, allopatric divergence in rainforest refugia does not seem a likely mechanism to explain divergence of the lowland tapir as the species' distribution ranges across South America [ 13] including large areas of savanna [ 31].
Specifically, we observed strong additive effects for each trait measured, and a simple additive model was sufficient to explain divergence in important body size attributes (e.g., snout-vent length, mass, growth).
If the fitness landscape is similarly rugged within G. manniand Gambusiasp, then the latter two mechanisms could explain divergence in the face of similar selection – because multiple adaptive solutions to environmental constraints on signal transmission exist.
Other isolating mechanisms are appropriate to explore in this system to help explain divergence patterns not well supported by vicariance, such as the effects of rapidly evolving gamete recognition proteins on isolating populations.
Covarion models are useful not only because of improved phylogenetic estimation; they can also be used to identify patterns of sequence evolution that explain divergence in protein function or structure.
In cases where distance does not explain divergence, it has been suggested that circulation patterns, such as recirculation in a coastal fjord, may provide a sufficient barrier to gene flow, allowing populations to diverge and perhaps adapt to local conditions (Rynearson and Armbrust 2004).
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At the ovate locus, conservation did not decline in relation to increasing phylogenetic distance, suggesting that the time factor alone does not explain divergences.
European Pleistocene refugia have been suggested to explain divergences within cantillans [ 34], although that study did not attempt to date lineage divergences; our results suggest that very late Pliocene events might also have been important for atricapilla and borin.
Pairwise Fst and Rst statistics were used to compare population genetic models explaining divergence among subpopulations (step-wise mutation vs geneflow or drift) based on nuclear microsatellite markers (amplicon length) (Slatkin [1995]; Hardy et al. [2003]) using Arlequin v3.5 (Excoffier and Lischer [2010]).
We suggest that a constraint early/opportunity late model best explains divergence over ontogeny.
Duplication induced mutations explaining divergence; and recombination harbored new folds of new proteins with new functions that evolved from common ancestors [ 40, 46].
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