Post by djoser-xyyman on Dec 13, 2018 12:39:48 GMT -5
Resolving the insertion sites of polymorphic duplications reveals a HERC2 haplotype under selection
Authors SAITOU, M.1, GOKCUMEN, O.1
We found that [b**]linkage disequilibrium was strongest in European populations** and weaker in Asian and African
populations.[/b] To understand the ancestral state of the haplotypes harboring the duplication, we
we investigated 17 variants that have strong linkage disequilibrium defining this haplotype
(R2>0.75 with the duplication in European populations) in chimpanzee, Neanderthal, and
Denisovan genomes. This analysis suggests that the duplication is likely derived in the human
lineage as compared to chimpanzees. Intriguingly we found that the Neanderthal genome is
heterozygous at this locus, carrying both duplicated and non-duplicated haplotypes (
A significant positive XP-EHH score is indicative of positive selection
in the first population, while a negative score indicates positive selection in the second
population (Sabeti et al. 2007). Based on this calculation, we found no clear population
differentiation between the representative African (YRI) and East Asian (CHB) populations.
However, we found the representative European population (Central European from Utah, CEU)
to be significantly differentiated from CHB and YRI (>99th, and >95th percentile, respectively)
(fig. 4B). This means that there are relatively ***long runs of homozygosity**** in this region in CEU
population as compared to CHB and YRI, concordant with the excess of rare variants suggested
by Tajima’s D comparisons. In sum, these results are in line with a scenario that a** recent**
selection event in Europe favors non-duplicated haplotypes over duplicated-haplotypes
Authors SAITOU, M.1, GOKCUMEN, O.1
We found that [b**]linkage disequilibrium was strongest in European populations** and weaker in Asian and African
populations.[/b] To understand the ancestral state of the haplotypes harboring the duplication, we
we investigated 17 variants that have strong linkage disequilibrium defining this haplotype
(R2>0.75 with the duplication in European populations) in chimpanzee, Neanderthal, and
Denisovan genomes. This analysis suggests that the duplication is likely derived in the human
lineage as compared to chimpanzees. Intriguingly we found that the Neanderthal genome is
heterozygous at this locus, carrying both duplicated and non-duplicated haplotypes (
A significant positive XP-EHH score is indicative of positive selection
in the first population, while a negative score indicates positive selection in the second
population (Sabeti et al. 2007). Based on this calculation, we found no clear population
differentiation between the representative African (YRI) and East Asian (CHB) populations.
However, we found the representative European population (Central European from Utah, CEU)
to be significantly differentiated from CHB and YRI (>99th, and >95th percentile, respectively)
(fig. 4B). This means that there are relatively ***long runs of homozygosity**** in this region in CEU
population as compared to CHB and YRI, concordant with the excess of rare variants suggested
by Tajima’s D comparisons. In sum, these results are in line with a scenario that a** recent**
selection event in Europe favors non-duplicated haplotypes over duplicated-haplotypes