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（Mugil cephalus）渔业的可持续管理需考量近期观测到的区域尺度种群分化现象。针对澳大利亚东部海域这一兼具生态与经济价值的重要鱼类，亟需开展种群遗传学分析以评估其种群现状。本研究报道了三项核心内容：(i) 新型种群遗传标记——单核苷酸多态性（single nucleotide polymorphisms, SNPs）及潜在微卫星位点；(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功效检验。 我们从澳大利亚东海岸的三个采样区域（昆士兰州北部、昆士兰州南部以及新南威尔士州中部）采集了6份DNA样本，利用限制性内切酶EcoRI与MseI对基因组DNA进行酶切，制备限制性酶切位点相关DNA（restriction site associated DNA, RAD）标签文库。将混合后的区域RAD标签文库采用罗氏GS-FLX Titanium测序平台进行测序，共获得172 837条原始测序reads（总长度17.4 Mbp），其中95 500条reads用于发掘1267个SNPs位点与1417个微卫星位点。 选取161个SNPs位点，利用Sequenom MassArray（iPLEX Gold 试剂盒）对额外63份DNA样本进行基因分型以验证其有效性。最终共确认92个SNPs位点（占比57%），其中40%的位点为南北采样区域间的固定变异位点。 本研究初步结果显示，澳大利亚东部海域的鲻鱼渔业种群呈现多群体结构，但主要渔场北部存在显著的遗传分化。在主要渔场内部，极低的潜在遗传分化（如固定指数FST=0.0025）可通过采用标准样本量50及经过验证的可用标记子集，以≥67%的检验效力得以分辨。