On the other hand, some PARCEL-containing ORFs may pre-date this repertoire expansion, and their exchanges among taxa of this group, as evidenced by their presence also in M. florum.
All analyses were performed in the statistical environment R. We retrieved intronic sequences of Abp genes from mouse and rat genome sequences for use in dating the expansion of their Abp gene families (Additional file 3).
In this latter case, the majority of the copies lie at orthologous sites, allowing us to date the expansion of this lineage prior to speciation.
Our results provide a time framework for identifying ancestral and derived genomic arrangements in the APOBEC loci, and to date the expansion of this gene family for different lineages through time, as a response to changes in viral/retroviral/retrotransposon pressure.
We collected and analyzed data for Sox group B from 36 species of 12 phyla representing the major metazoan clades, with an emphasis on arthropods, to reconstruct the evolutionary history of SoxB in bilaterians and to date the expansion of Sox group B in insects.
The τ value dated the expansion to ~7 ka (Additional file 1: Table S3).
Using 534,000 years ago time of divergence of the two species as a calibration in the species tree estimated with *BEAST, we dated the expansion of the populations in both species at approximately 10,000 years ago.
The estimated starting date of this expansion varies between about 7,000 and about 35,000 years BP depending on the calibration date used for the divergence time between B. taurus and B. bison.
This expansion is dated to begin approximately 160 250 kya, corresponding to a very dry phase in the African climate (penultimate glacial/interpluvial), and predating a series of extreme droughts reported from eastern Africa [ 10], which resulted in the disappearance of several large lakes such as Lake Victoria [ 66].
Expansion within haplogroup P seems to pre-date expansion within the sub-haplogroups of macro-haplogroup T, which appears to have occurred around the time of domestication in the Near East [6], [8], [16].
