PT  - JOURNAL ARTICLE
AU  - Brian Arnold
AU  - Mashaal Sohail
AU  - Crista Wadsworth
AU  - Jukka Corander
AU  - William P. Hanage
AU  - Shamil Sunyaev
AU  - Yonatan H. Grad
TI  - Fine-scale haplotype structure reveals strong signatures of positive selection in a recombining bacterial pathogen
AID  - 10.1101/634147
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 634147
4099  - http://biorxiv.org/content/early/2019/05/10/634147.short
4100  - http://biorxiv.org/content/early/2019/05/10/634147.full
AB  - Identifying the forces that create and shape ecologically meaningful variation in bacteria remains an important challenge. For recombining bacteria, the sign and strength of linkage provide a unique lens into ongoing selection. We show derived alleles less than 300bp apart in Neisseria gonorrhoeae exhibit more coupling linkage than repulsion linkage, a pattern that cannot be explained by limited recombination or neutrality as these couplings are significantly stronger for nonsynonymous alleles compared to synonymous alleles. While linkage is shaped by many evolutionary processes, extensive simulations show only two distinct forms of positive selection can drive an excess of coupling linkage between neighboring nonsynonymous alleles: directional selection on introgressed alleles or selection that maintains distinct haplotypes in the presence of recombination. Our results establish a framework for identifying patterns of selection in fine-scale haplotype structure that indicate specific ecological processes in species that recombine with distantly related lineages or possess coexisting adaptive haplotypes.