Adaptive introgression of the beta-globin cluster in two Andean waterfowl

Introgression of alleles has emerged as an important avenue for genetic adaptation in both plant and animal populations. In vertebrates, adaptation to hypoxic high-altitude environments involves the coordination of multiple molecular and cellular mechanisms, including selection on the Hypoxia-Inducible Factor (HIF) pathway and the blood-O2 transport protein hemoglobin (Hb). In two Andean duck species, a striking DNA sequence similarity reflecting identity by descent is present across the ~20 kb b-globin cluster including both embryonic (HBE) and adult (HBB) paralogs, though it was yet untested whether this is due to independent parallel evolution or adaptive introgression. In this study, we find that identical amino acid substitutions in the b-globin cluster that increase Hb-O2 affinity have likely resulted from historical interbreeding between high-altitude populations of two different distantly-related species. We examined the direction of introgression and discovered that the species with a deeper mtDNA divergence that colonized high altitude earlier in history (Anas flavirostris) transferred adaptive genetic variation to the species with a shallower divergence (A. georgica) that likely colonized high altitude more recently possibly following the range shift into a novel environment. As a consequence, the species that received these b-globin variants through hybridization might have adapted to the high-altitude environment more quickly through acquiring beneficial alleles from the new, hybrid-origin variation, leading to faster evolution.

Methods
A custom pipeline (https://github.com/amgraham07) was created to remove orphan sequences and assemble sequences against the α-globin (NW_004678373, scaffold 2065) and β-globin (NW_004682656, scaffold 6035) sequences of the mallard reference, using BWA v0.7.15 (Li and Durbin, 2009). The Samtools package v1.3.1, including BCFtools v.1.3.1 (Li et al, 2009) was then used to create a VCF file and to provide assembly statistics (i.e., bp-by-bp coverage). These programs used in the pipeline called SNP variants against the mallard reference, including indels (insertion/deletion); however, indels were excluded in the final dataset as were sites with missing data.

等位基因渐渗已成为动植物种群遗传适应的重要途径。在脊椎动物中，适应低氧高海拔环境需要协同调控多种分子与细胞机制，包括对缺氧诱导因子（Hypoxia-Inducible Factor，HIF）通路以及血液氧转运蛋白血红蛋白（hemoglobin，Hb）的选择压。在两种安第斯鸭物种中，一段约20 kb的β-珠蛋白基因簇（包含胚胎型HBE与成年型HBB旁系同源基因）呈现出显著的、由共同祖先衍生的DNA序列相似性，但此前尚未明确该现象源于独立平行进化还是适应性渐渗。本研究发现，该β-珠蛋白基因簇中可提升Hb-O₂结合亲和力的相同氨基酸替换，极有可能源自两个远缘物种的高海拔种群间的历史杂交事件。我们探究了渐渗的方向，结果发现，线粒体DNA分化程度更深、更早定居高海拔环境的物种（黄嘴凫*Anas flavirostris*），将适应性遗传变异传递给了线粒体DNA分化程度较浅、推测较晚才迁入高海拔环境（可能是在拓展至新生存环境后）的物种（*A. georgica*）。因此，通过杂交获得该β-珠蛋白变异的物种，可通过从新的杂交起源变异中获取有益等位基因，更快地适应高海拔环境，进而加速进化进程。

方法
本研究构建了一套自定义分析流程（https://github.com/amgraham07），用于剔除孤儿序列，并将测序序列比对至绿头鸭参考基因组的α-珠蛋白（NW_004678373，scaffold 2065）与β-珠蛋白（NW_004682656，scaffold 6035）序列，比对工具采用BWA v0.7.15（Li与Durbin，2009）。随后使用Samtools工具包v1.3.1（包含BCFtools v1.3.1，Li等人，2009）生成变异识别格式（Variant Call Format，VCF）文件，并提供组装统计信息（即逐碱基覆盖度）。该流程中的程序以绿头鸭参考基因组为基准调用SNP变异（包括插入/缺失（indel，insertion/deletion）变异），但最终数据集仅保留了无缺失数据的位点，且剔除了所有indel变异。