Data from: Becoming pure: identifying generational classes of admixed individuals within lesser and greater scaup populations

Estimating the frequency of hybridization is important to understand its evolutionary consequences and its effects on conservation efforts. In this study, we examined the extent of hybridization in two sister species of ducks that hybridize. We used mitochondrial control region sequences and 3,589 double-digest restriction-associated DNA sequences (ddRADseq) to identify admixture between wild lesser scaup (Aythya affinis) and greater scaup (A. marila). Among 111 individuals, we found one introgressed mitochondrial DNA haplotype in lesser scaup and four in greater scaup. Likewise, based on the site-frequency spectrum from autosomal DNA, gene flow was asymmetrical, with higher rates from lesser into greater scaup. However, using ddRADseq nuclear DNA all individuals were assigned to their respective species with > 0.95 posterior assignment probability. To examine the power for detecting admixture, we simulated a breeding experiment in which empirical data were used to create F1 hybrids and nine generations (F2-F10) of backcrossing. F1 hybrids and F2, F3, and most F4 backcrosses were clearly distinguishable from pure individuals, but evidence of admixed histories was effectively lost after the fourth generation. Thus, we conclude that low interspecific assignment probabilities (0.011 – 0.043) for two lesser and nineteen greater scaup were consistent with admixed histories beyond the F3 generation. These results indicate that the propensity of these species to hybridize in the wild is low and largely asymmetric. When applied to species-specific cases, our approach offers powerful utility for examining concerns of hybridization in conservation efforts, especially for determining the generational time until admixed histories are effectively lost through backcrossing.

估算杂交（hybridization）发生频率，对于阐明其演化后果及对物种保护工作的影响至关重要。本研究针对两种可发生杂交的鸭类姊妹物种（sister species），探究其杂交程度。本研究采用线粒体控制区序列（mitochondrial control region sequences）与3589条双酶切限制性位点关联DNA序列（double-digest restriction-associated DNA sequences, ddRADseq），鉴定野生小斑背潜鸭（lesser scaup, Aythya affinis）与大斑背潜鸭（greater scaup, A. marila）之间的遗传渐渗情况。在111个个体中，我们于小斑背潜鸭中检出1个渐渗线粒体DNA（mitochondrial DNA）单倍型，大斑背潜鸭中检出4个。同样，基于常染色体DNA的位点频率频谱（site-frequency spectrum）开展分析，结果显示基因流呈现不对称性，小斑背潜鸭向大斑背潜鸭的基因流水平更高。然而，利用ddRADseq核基因组测序数据，所有个体均被以>0.95的后验分配概率归至其所属物种。为检测杂交渐渗的检出效力，我们基于实测数据构建了F1杂交个体及9代回交群体（F2至F10）的繁殖模拟实验。F1杂交个体、F2、F3及多数F4回交个体均可与纯合个体明确区分，但回交至第4代后，杂交起源的遗传痕迹基本丢失。据此我们认为，2只小斑背潜鸭与19只大斑背潜鸭的种间分配概率较低（0.011~0.043），这与其回交至F3代之后的杂交起源历史相符。上述结果表明，这两个物种在野外的杂交倾向较低，且基因流整体呈不对称性。将本研究方法应用于特定物种案例时，可为评估物种保护中的杂交相关风险提供有力工具，尤其可用于估算通过回交使杂交起源的遗传痕迹完全丢失所需的世代数。