Data from: Distinguishing migration events of different timing for wild boar in the Balkans

Aim: We compared the power of different nuclear markers to investigate genetic structure of southern Balkan wild boar. We distinguished between historic events, such as isolation in different refugia during glacial periods, from recent demographic processes, such as naturally occurring expansions. Location: Southern Balkans/Greece. Methods: We sampled 555 wild boars from 20 different locations in southern Balkans/Greece. All individuals were analysed with 10 microsatellites and a subgroup of 91 with 49,508 single nucleotide polymorphisms (SNPs). Patterns of genetic structure and demographic processes were assessed with Bayesian clustering, linkage disequilibrium and past effective population size estimation analysis. Results: Both microsatellite and SNP data analyses detected genetic structure caused by historic events and support the existence of three groups in the studied area. A hybrid zone between two of the groups was also detected. We also showed that genome-wide SNP data analysis can identify recent events in bottlenecked populations. Main conclusions: We inferred the three groups diverged ~50,000–10,000 yr bp when populations contracted to different refugia. Our findings strengthened the evidence that the southern Balkan area was a glacial refugium including further local smaller refugia. Genome-wide genotyping inferred a recent population expansion that can mimic a ‘refugium within refugium’ scenario. It seems that microsatellite data tend to overestimate genetic structure when genetic drift happens in bottlenecked populations over a short distance. Therefore, genome-wide SNPs are more powerful at inferring phylogeography in natural populations, resolving inconsistencies from mitochondrial and microsatellite data sets.研究目的：本研究旨在比较不同核标记在探究巴尔干南部野猪遗传结构中的应用效能，区分冰川时期不同避难所隔离等历史事件与自然种群扩张等近期动态过程。 研究区域：巴尔干南部/希腊。 研究方法：我们从巴尔干南部/希腊的20个不同采样点位共采集555头野猪样本。对所有个体采用10个微卫星（microsatellite）标记进行基因分型，其中91个个体额外使用49508个单核苷酸多态性（single nucleotide polymorphisms, SNPs）标记开展分析。遗传结构与种群动态模式通过贝叶斯聚类、连锁不平衡及历史有效种群大小估算分析进行评估。 研究结果：微卫星与SNP数据分析均检测到由历史事件引发的遗传结构，证实研究区域内存在3个野猪种群类群，同时还检测到两类群之间的杂交带。本研究同时证明，全基因组SNP数据分析可识别瓶颈种群中的近期动态事件。 主要结论：本研究推断，3个类群的分化时间约为距今50000至10000年前，对应种群收缩至不同避难所的时期。本研究结果进一步支撑巴尔干南部区域作为冰期避难所，且包含多个局部小型避难所的结论。全基因组基因分型结果显示存在近期种群扩张事件，该现象可模拟"避难所内避难所"的场景。研究还发现，当瓶颈种群在短距离内发生遗传漂变时，微卫星数据往往会高估遗传结构。因此，全基因组SNP标记在推断系统地理学（phylogeography）方面具有更优效能，可解决线粒体及微卫星数据集存在的不一致性问题。