Data from: New SNPs for population genetic analysis reveal possible cryptic speciation of eastern Australian sea mullet (Mugil cephalus)

Sustainable management of sea mullet (Mugil cephalus) fisheries needs to account for recent observations of regional-scale differentiation. Population genetic analysis is sought to assess the situation of this ecologically and economically important fish species in eastern Australian waters. Here, we report (i) new population genetic markers [single nucleotide polymorphisms (SNPs) and potential microsatellites], (ii) first estimates of spatial genetic differentiation and (iii) prospective power tests for designing more comprehensive studies. Six DNA samples from three sampling regions (North Queensland, South Queensland and central New South Wales) on the eastern coast of Australia were used to prepare restriction site associated DNA (RAD) tag libraries from genomic DNA digested with EcoRI and MseI. A pooled sample of regional RAD tag libraries was sequenced using the Roche GS-FLX Titanium platform. A total of 172 837 raw reads (17.4 Mbp) were retrieved, 95 500 of which were used to discover 1267 SNPs and 1417 microsatellites. A subset of 161 SNPs was validated based on 63 additional DNA samples genotyped using the Sequenom MassArray (iPLEX Gold chemistry). Altogether 92 SNPs (57%) were confirmed, with 40% of these marking fixed variants between northern and southern sampling regions. Our preliminary findings indicate a multispecies fishery stock of M. cephalus in eastern Australian waters, but suggest that strong genetic differentiation occurs north of major fishing grounds. Low potential differentiation within major fishing grounds (e.g. FST = 0.0025) can be resolved with a likely power ≥67% by using standard sample sizes of 50 and validated subsets of available markers.

鲻鱼（Mugil cephalus）渔业的可持续管理，需纳入近期观测到的区域尺度遗传分化相关考量。本研究旨在通过种群遗传学分析，评估澳大利亚东部海域这一兼具生态与经济价值的鱼类的种群现状。本研究报道了三方面核心内容：(i) 新型种群遗传标记[单核苷酸多态性（single nucleotide polymorphisms, SNPs）与潜在微卫星标记]；(ii) 空间遗传分化的首次估算结果；(iii) 用于设计更全面研究的前瞻性检验效力方案。本研究从澳大利亚东海岸的3个采样区域（昆士兰州北部、昆士兰州南部与新南威尔士州中部）获取了6份DNA样品，以经EcoRI与MseI酶切的基因组DNA构建限制性酶切位点相关DNA（restriction site associated DNA, RAD）标签文库。将各区域的RAD标签文库混合后，采用罗氏（Roche）GS-FLX Titanium测序平台进行测序。最终共获得172837条原始读段（17.4 Mbp），其中95500条被用于发掘1267个单核苷酸多态性位点与1417个微卫星位点。选取161个单核苷酸多态性位点作为验证子集，利用额外的63份DNA样品，采用Sequenom MassArray（iPLEX Gold 化学反应体系）完成基因分型以验证标记有效性。最终确认92个位点（占比57%）有效，其中40%的位点为北部与南部采样区域间的固定变异位点。本研究的初步结果显示，澳大利亚东部海域的鲻鱼渔业种群为混合遗传群体，但主要渔场以北区域存在显著的遗传分化。主要渔场内部的遗传分化程度较低（如遗传分化固定指数（Fixation Index, FST）=0.0025），若采用标准样本量50份与经过验证的可用标记子集，即可达到≥67%的检验效力。