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Positive selection or natural selection within genes is the main evolutionary event for adaptation and has thus been an important focus of several comparative genomics studies (Haas et al. 2009; Schirawski et al. 2010; Kemen and Jones 2012).
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The large majority of these have only one gene, and are likely to represent errors originating in S YNM AP or OMG!, or movements of very small genomic fragments, containing little information about the main evolutionary events in these genomes.
In the study presented here, a thorough sampling of populations (including the Cretan lineage of wilkinsoni, as well as most sub-clades of pityocampa and the previously unknown ENA clade) and a Bayesian approach taking into account the gamma-distributed heterogeneity of rates, allowed us to obtain a different estimate for the age of the main evolutionary events.
Here we assess the broader phylogeographic patterns within Lacerta lepida with the specific aims to i) clarify the distribution of mtDNA phylogroups; ii) identify refugial areas within these phylogroups during the glacial periods; iii) date the main demographic and evolutionary events within Lacerta lepida; and finally iv) identify secondary contact zones between the different phylogroups.
If only a collection of gene trees is given, the new algorithm first builds a weighted consensus tree as the main evolutionary pattern and then infers the most significant alternative events.
The results obtained suggest that vertical inheritance of TCS present in the last common ancestor and lineage-specific gene losses appear as the main evolutionary forces involved in their evolution in Lactobacillaceae, although some HGT events cannot be ruled out.
IMPORTANCE Gene duplication is one of the main evolutionary paths to new protein function.
The phylogenetic context bounds the dates of each evolutionary event.
Two main evolutionary scenarios have been proposed.
The evolutionary events that originated the main extant lineages of Carabus took place according to our data during the early Miocene, between 23 and 16 Ma.
Distinct gains or losses of activity or switches in enantioselectivity coincided with the evolutionary events that led to the formation of the main subfamilies.
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