Recombination map tailored to Native Hawaiians reduces false positive findings in genomic scans of positive selection.

Recombination events establish the patterns of haplotypic structure in a population and estimates of recombination rates are used in several downstream population and statistical genetic analyses. However, the recombination landscape of populations not represented in the 1000 Genomes Project (1KGP) is poorly understood. Using suboptimal maps from distantly related populations reduces the efficacy of extending genomic analyses to underrepresented populations, including Native Hawaiians. To overcome this challenge, we constructed linkage disequilibrium (LD)- and Identity-by-Descent (IBD)-based recombination maps specifically for Native Hawaiians. We created and characterized two recombination maps from our study sample: one based on a random subset of our sample reflecting the current admixed state of Native Hawaiians (NH map), and one based on a subset of individuals with enriched Polynesian ancestries (PNS map) with potential to be used for less admixed Polynesian populations such as the Samoans. We found the recombination landscape to be less correlated with those from other 1KGP populations (e.g. Spearman's rho = 0.79 between PNS and CEU (Utah residents with Northern and Western European ancestry) compared to 0.92 between YRI (Yoruba in Ibadan, Nigeria) and CEU at 50 kb resolution. PNS shared the fewest recombination hotspots with other populations from 1KGP (e.g. 8% of hotspots shared between PNS and CEU compared to 27% of hotspots shared between YRI and CEU). We found that downstream analysis in the Native Hawaiian population, such as local ancestry inference, imputation, and IBD segment and relatedness detections, would achieve similar efficacy when using the NH map compared to an omnibus map. However, for genome scans of adaptive loci using integrated haplotype scores, we found several loci with apparent genome-wide significant signals (|Z-score| > 4) in Native Hawaiians that would not have been significant when analyzed using NH-specific maps. Therefore, population-specific recombination maps improve the robustness of haplotype-based statistics and help us better characterize the evolutionary history that may underlie Native Hawaiian-specific health conditions that persist today.