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Current theories suggest a two step evolution of the locus, one to explain the early evolution of the human alleles and a second step to account for their current global frequencies.
Matches of ESTs to intergenic regions of the 5.2 kb repetitive unit likely represent fragments of transposable sequences that may have played a role in the evolution of the locus.
Statistical significance for deviation from the standard neutral model was only obtained from TYRP1, but since this is based on 4 SNPs in just 267 bp, we are careful in interpreting this result as non-neutral evolution of the locus.
Phylogenetic analysis of the domains and modules across pMUM001 and pMUM002 emphasise the high degree of relatedness between these genetic loci but also show that they cluster by strain, suggesting that evolution of the locus is occurring vertically rather than via horizontal exchanges between strains.
However, a microsatellite can also be comprised of adjacent tandem arrays of different repeat motifs (termed "compound" [ 69]) or "interrupted" as a result of point mutations and small insertions or deletions that have occurred during the evolution of the locus (also termed "imperfect").
However, Solanaceae microstructures appear much more different that the conservation between coffee tree and grapevine, suggesting a divergent and specific evolution of the locus in the Solanaceae prior to the separation with the Rubiaceae and that time factor alone does not explain the divergences.
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Finally, we propose that adaptation is most likely involved in the evolution of the loci that covary with the Pygmy phenotype.
Towards this aim we have determined the complete genomic organization, content and evolution of the loci encoding both the conventional TCRs (TRA, TRB, TRG and TRD) and the recently discovered TRM locus in the opossum Monodelphis domestica.
Either S. japonicum and other Asian species in the S. japonicum group evolved independently from a common ancestor, or the evolution of this locus and the subsequent dispersed duplication occurred recently after the other Asian forms have diverged (see phylogenetic relationship in Additional file 3).
Despite finding strong evidence for positive selection having acted on a gene which has a key role in brain development, we found no compelling evidence to support the hypothesis that there is an association between the evolution of this locus and the evolution of brain size in cetaceans.
Because both genes map to human chromosome 22, we wanted to gain more insight in the evolution of this locus by studying the genome organisation of zebrafish, another teleost fish.
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