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 ...评估杂交发生频率，对于理解其进化效应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种，探究其杂交程度。我们采用线粒体控制区序列与3589条双酶切限制性位点相关DNA测序（double-digest restriction-associated DNA sequences, ddRADseq）数据，对野生斑背潜鸭（Aythya affinis）与大潜鸭（A. marila）之间的遗传混合现象进行鉴定。在111份个体样本中，我们于斑背潜鸭体内检出1个渐渗的线粒体DNA单倍型，于大潜鸭体内检出4个。同理，基于常染色体DNA的位点频率谱（site-frequency spectrum, SFS）分析结果，二者间的基因流呈不对称模式：斑背潜鸭向大潜鸭的基因流速率更高。然而，利用ddRADseq核基因组数据进行分析时，所有个体均被以大于0.95的后验分配概率归类至其所属物种。为验证本研究检测遗传混合的效能，我们基于实证数据构建了F1代杂交个体的繁育模拟实验……