This paper discovered that both haplotype sharing and recombination rate were correlated with genetic divergence between populations. The authors consider that haplotype sharing can be attributed to both drift and recombination, and study haplotype sharing for haplotypes of different lengths.
A potential problem is that humans may harbor archaic DNA sequences. Depending on when admixture with archaic humans took place, recombination may have reduced these archaic sequences to very small lengths. It is no longer tenable to suppose that only drift and recombination have affected haplotypes, the former removing some, the latter re-arranging others.
We must take into account the possibility that genetic divergence between human groups is partly the result of admixture with species outside the main H. sapiens phyletic line. Immediately following such admixture, there would have been long archaic haplotypes in affected humans, but -with enough time- these would have been reduced in size due to recombination.
Annals of Human Genetics doi: 10.1111/j.1469-1809.2011.00678.x
Chromosome-Wide Haplotype Sharing: A Measure Integrating Recombination Information to Reconstruct the Phylogeny of Human Populations
Shuhua Xu and Li Jin
The vast amount of recombination information in the human genome has long been ignored or deliberately avoided in studies on human population genetic relationships. One reason is that estimation of the recombination parameter from genotyping data is computationally challenging and practically difficult. Here we propose chromosome-wide haplotype sharing (CHS) as a measure of genetic similarity between human populations, which is an indirect approach to integrate recombination information. We showed in both empirical and simulated data that recombination differences and genetic differences between human populations are strongly correlated, indicating that recombination events in different human populations are evolutionarily related. We further demonstrated that CHS can be used to reconstruct reliable phylogenies of human populations and the majority of the variation in CHS matrix can be attributed to recombination. However, for distantly related populations, the utility of CHS to reconstruct correct phylogeny is limited, suggesting that the linear correlation of CHS and population divergence could have been disturbed by recurrent recombination events over a large time scale. The CHS we proposed in this study is a practical approach without involving computationally challenging and time-consuming estimation of recombination parameter. The advantage of CHS is rooted in its integration of both drift and recombination information, therefore providing additional resolution especially for populations separated recently.