Cryptic genetic diversity in the mottled rabbitfish Siganus fuscescens with mitochondrial introgression at a contact zone in the South China Sea

The taxonomy of the mottled rabbitfish Siganus fuscescens species complex has long been challenging. In this study, we analyzed microsatellite genotypes, mitochondrial lineages, and morphometric data from 373 S. fuscescens individuals sampled from the northern Philippines and Hong Kong (South China Sea, Philippine Sea and Sulu Sea basins), to examine putative species boundaries in samples comprising three co-occurring mitochondrial lineages previously reported to characterize S. fuscescens (Clade A and Clade B) or S. canaliculatus (Clade C). We report the existence of two cryptic species within S. fuscescens in the northeast region of the South China Sea and northern Philippine Sea, supported by genetic and morphological differences. Individual-based assignment methods recovered concordant groupings of individuals into two nuclear genotype clusters (Cluster 1, Cluster 2) with (1) limited gene flow, if any, between them (FST = 0.241; P &lt; 0.001); (2) low frequency of later-generation...带纹篮子鱼（Siganus fuscescens）物种复合群的分类学研究长期以来颇具挑战。本研究分析了采自菲律宾北部及香港（覆盖南海、菲律宾海与苏禄海海域）的373尾S. fuscescens个体的微卫星基因型（microsatellite genotypes）、线粒体谱系（mitochondrial lineages）及形态测量数据（morphometric data），旨在探究此前报道的、以S. fuscescens（支系A与支系B）或S. canaliculatus（支系C）为特征的3种共存线粒体谱系样本中的推定物种边界。本研究证实，南海东北部及菲律宾海北部区域的S. fuscescens种群内存在2种隐存种（cryptic species），该结论得到遗传与形态差异的支持。基于个体的归属分析方法（individual-based assignment methods）得到了一致的聚类结果，将个体划分为2个核基因型簇（nuclear genotype clusters，簇1、簇2）：（1）二者间即便存在基因流（gene flow）也极为有限（遗传分化系数FST=0.241；P<0.001）；（2）晚世代个体的出现频率较低……