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. Using suboptimal maps from distantly related populations may reduce the efficacy of genomic analyses, particularly for underrepresented populations such as the Native Hawaiians. To overcome this challenge, we constructed recombination maps using genome-wide array data from two study samples of Native Hawaiians: one reflecting the current admixed state of Native Hawaiians (NH map) and one based on individuals of enriched Polynesian ancestries (PNS map) with the 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 continental 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), likely driven by the unique demographic history of the Native Hawaiians. PNS also shared the fewest recombination hotspots with other populations (e.g. 8% of hotspots shared between PNS and CEU compared to 27% of hotspots shared between YRI and CEU). We found that downstream analyses 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. Population-specific recombination maps may therefore 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.

重组事件建立了群体中单倍型结构的模式，并且重组率的估计用于几个下游群体和统计遗传分析。使用远亲群体的次优地图可能会降低基因组分析的效率，特别是对于夏威夷原住民等代表性不足的群体。为了克服这一挑战，我们使用来自两个夏威夷原住民研究样本的全基因组阵列数据构建了重组图谱：一个反映了夏威夷原住民当前的混合状态（NH 图），另一个基于丰富的波利尼西亚血统个体（PNS 图），可能用于混合程度较低的波利尼西亚人，例如萨摩亚人。我们发现重组景观与其他大陆人群的相关性较低（例如，PNS 和 CEU（具有北欧和西欧血统的犹他州居民）之间的 Spearman's rho = 0.79，而 YRI（尼日利亚伊巴丹的约鲁巴人）和 CEU 之间的相关性为 0.92。 50 kb 分辨率），可能是由夏威夷原住民独特的人口历史驱动的。PNS 还与其他群体共享最少的重组热点（例如，PNS 和 CEU 之间共享的热点为 8%，而 YRI 和 CEU 之间共享的热点为 27%）。我们发现，与综合地图相比，使用 NH 地图时，对夏威夷原住民群体的下游分析（例如当地血统推断、插补以及 IBD 片段和相关性检测）将达到类似的效果。然而，对于使用整合单倍型评分对适应性基因座进行基因组扫描，我们发现夏威夷原住民中的几个基因座具有明显的全基因组显着信号（| Z评分|> 4），而当使用 NH 特异性图谱进行分析时，这些信号并不显着。因此，特定人群的重组图谱可能会提高基于单倍型统计数据的稳健性，并帮助我们更好地描述可能构成当今持续存在的夏威夷原住民特定健康状况的进化历史。