Stobie Cora Sabriel, Oosthuizen Carel J, Cunningham Michael J, Bloomer Paulette
Molecular Ecology and Evolution Programme Department of Genetics University of Pretoria Pretoria South Africa.
Ecol Evol. 2018 Jan 28;8(4):2326-2342. doi: 10.1002/ece3.3821. eCollection 2018 Feb.
The KwaZulu-Natal yellowfish () is an abundant cyprinid, endemic to KwaZulu-Natal Province, South Africa. In this study, we developed a single-nucleotide polymorphism (SNP) dataset from double-digest restriction site-associated DNA (ddRAD) sequencing of samples across the distribution. We addressed several hidden challenges, primarily focusing on proper filtering of RAD data and selecting optimal parameters for data processing in polyploid lineages. We used the resulting high-quality SNP dataset to investigate the population genetic structure of . A small number of mitochondrial markers present in these data had disproportionate influence on the recovered genetic structure. The presence of singleton SNPs also confounded genetic structure. We found a well-supported division into northern and southern lineages, with further subdivision into five populations, one of which reflects north-south admixture. Approximate Bayesian Computation scenario testing supported a scenario where an ancestral population diverged into northern and southern lineages, which then diverged to yield the current five populations. All river systems showed similar levels of genetic diversity, which appears unrelated to drainage system size. Nucleotide diversity was highest in the smallest river system, the Mbokodweni, which, together with adjacent small coastal systems, should be considered as a key catchment for conservation.
夸祖鲁 - 纳塔尔黄鱼（）是一种数量丰富的鲤科鱼类，原产于南非夸祖鲁 - 纳塔尔省。在本研究中，我们通过对分布范围内的样本进行双酶切限制性位点关联DNA（ddRAD）测序，开发了一个单核苷酸多态性（SNP）数据集。我们解决了几个潜在的挑战，主要集中在对RAD数据进行适当过滤以及为多倍体系谱中的数据处理选择最佳参数。我们使用得到的高质量SNP数据集来研究的种群遗传结构。这些数据中存在的少量线粒体标记对恢复的遗传结构产生了不成比例的影响。单例SNP的存在也混淆了遗传结构。我们发现有充分证据支持将其分为北部和南部谱系，并进一步细分为五个种群，其中一个反映了南北混合情况。近似贝叶斯计算情景测试支持这样一种情景：一个祖先种群分化为北部和南部谱系，然后这些谱系再分化产生当前的五个种群。所有河流系统都表现出相似水平的遗传多样性，这似乎与排水系统大小无关。核苷酸多样性在最小的河流系统姆博科德韦尼中最高，该河流系统与相邻的小型沿海系统一起，应被视为保护的关键集水区。
