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.评估杂交发生频率，对于理解其进化效应及对保护工作的影响具有重要意义。本研究针对两种可发生自然杂交的鸭类姊妹物种，探究了其杂交程度。本研究采用线粒体控制区（mitochondrial control region）序列与3589条双酶切限制性酶切位点相关DNA测序（double-digest restriction-associated DNA sequences，ddRADseq）数据，对野生小潜鸭（Aythya affinis）与大潜鸭（A. marila）之间的遗传混合情况进行鉴定。在111个个体中，我们在小潜鸭群体内发现1个渐渗的线粒体DNA单倍型，在大潜鸭群体内发现4个。同样，基于常染色体DNA的位点频率谱（site-frequency spectrum, SFS）分析，发现基因流存在不对称性：小潜鸭向大潜鸭的基因流水平更高。然而，利用ddRADseq核基因组数据，所有个体的物种归属后验概率均大于0.95。为了检测遗传混合的鉴定效力，我们基于实证数据构建了杂交实验模拟：首先生成F1代杂交个体，随后进行9代回交（F2至F10代）。F1代杂交个体、F2、F3以及大部分F4代回交个体均可与纯合个体明确区分，但在F4代之后，遗传混合历史的信号便基本消失。因此，我们认为：2只小潜鸭与19只大潜鸭所呈现的较低跨物种归属概率（0.011~0.043），与其在F3代之后发生遗传混合的历史相符。上述结果表明，这两种鸭类在野外的杂交倾向较低，且基因流模式整体呈不对称性。若将本研究方法应用于特定物种案例，可为保护工作中涉及的杂交相关问题提供强有力的分析工具，尤其可用于估算通过回交使遗传混合信号彻底消失所需的世代数。