Data from: Deep mitochondrial divergence in Baja California populations of an aquilopelagic elasmobranch: the golden cownose ray

Assessing the realized effect of dispersal in the genetic makeup of a species has significant evolutionary, ecological, and economical consequences. Here, we investigate the genetic diversity and population differentiation in the aquilopelagic golden cownose ray Rhinoptera steindachneri from the Gulf of California (GC) and the Pacific coast of Baja California (PCBC) using the mitochondrial NADH2 gene. Low levels of genetic diversity were found with only 4 polymerase chain reaction-restriction fragment length polymorphism haplotypes among 76 specimens. Pacific coast organisms were fixed for a unique haplotype not shared with rays from the gulf; 92% of GC rays possessed a single NADH2 haplotype not found in the Pacific. This produced significant differentiation between the GC and the PCBC (ΦCT = 0.972, P < 0.001). A pronounced phylogeographic pattern was found in which GC haplotypes were reciprocally monophyletic relative to a very divergent Pacific lineage (d = 10%). Our results indicate that despite high dispersal potential, GC and PCBC golden cownose ray populations are characterized by highly divergent mitochondrial lineages. Although more evidence is needed to corroborate the genetic isolation and systematic status of PCBC and GC golden cownose rays, our results suggest a possible cryptic species in the region.评估扩散对物种遗传构成的实际效应，具有重要的进化、生态与经济意义。本研究针对加利福尼亚湾（Gulf of California, GC）及下加利福尼亚太平洋沿岸（Pacific coast of Baja California, PCBC）的远洋金牛鼻鲼（Rhinoptera steindachneri），利用线粒体NADH脱氢酶亚基2基因（mitochondrial NADH2 gene）开展遗传多样性与种群分化分析。研究共获取76份样本，仅检测到4个聚合酶链式反应-限制性片段长度多态性（polymerase chain reaction-restriction fragment length polymorphism）单倍型，整体遗传多样性水平较低。太平洋沿岸种群仅固定存在1种特有单倍型，未与海湾种群共享；92%的加利福尼亚湾个体携带1种太平洋种群未检出的NADH2单倍型。上述特征导致GC与PCBC种群间出现显著遗传分化（ΦCT = 0.972, P < 0.001）。研究发现显著的系统地理格局：加利福尼亚湾种群的单倍型与高度分化的太平洋支系（d = 10%）互为单系群。本研究结果表明，尽管金牛鼻鲼具备较强的扩散潜力，GC与PCBC种群仍呈现高度分化的线粒体谱系。尽管需要更多证据验证GC与PCBC金牛鼻鲼种群的遗传隔离状况及分类学地位，本研究结果提示该区域可能存在隐存种。