Fernández R, Schubert M, Vargas-Velázquez A M, Brownlow A, Víkingsson G A, Siebert U, Jensen L F, Øien N, Wall D, Rogan E, Mikkelsen B, Dabin W, Alfarhan A H, Alquraishi S A, Al-Rasheid K A S, Guillot G, Orlando L
Centre for GeoGenetics, University of Copenhagen, Øster Volgade 5-7, 1350K, Copenhagen, Denmark.
Wildlife Unit, SAC Veterinary Services, Drummondhill, Stratherrick Road, Inverness, UK.
Mol Ecol Resour. 2016 Jan;16(1):266-76. doi: 10.1111/1755-0998.12427. Epub 2015 May 29.
The field of population genetics is rapidly moving into population genomics as the quantity of data generated by high-throughput sequencing platforms increases. In this study, we used restriction-site-associated DNA sequencing (RADSeq) to recover genomewide genotypes from 70 white-beaked (Lagenorhynchus albirostris) and 43 Atlantic white-sided dolphins (L. acutus) gathered throughout their north-east Atlantic distribution range. Both species are at a high risk of being negatively affected by climate change. Here, we provide a resource of 38,240 RAD-tags and 52,981 nuclear SNPs shared between both species. We have estimated overall higher levels of nucleotide diversity in white-sided (π = 0.0492 ± 0.0006%) than in white-beaked dolphins (π = 0.0300 ± 0.0004%). White-sided dolphins sampled in the Faroe Islands, belonging to two pods (N = 7 and N = 11), showed similar levels of diversity (π = 0.0317 ± 0.0007% and 0.0267 ± 0.0006%, respectively) compared to unrelated individuals of the same species sampled elsewhere (e.g. π = 0.0285 ± 0.0007% for 11 Scottish individuals). No evidence of higher levels of kinship within pods can be derived from our analyses. When identifying the most likely number of genetic clusters among our sample set, we obtained an estimate of two to four clusters, corresponding to both species and possibly, two further clusters within each species. A higher diversity and lower population structuring was encountered in white-sided dolphins from the north-east Atlantic, in line with their preference for pelagic waters, as opposed to white-beaked dolphins that have a more patchy distribution, mainly across continental shelves.
随着高通量测序平台产生的数据量不断增加，群体遗传学领域正迅速迈向群体基因组学。在本研究中，我们使用限制性位点相关DNA测序（RADSeq）技术，从分布于东北大西洋的70只白喙斑纹海豚（Lagenorhynchus albirostris）和43只大西洋白侧海豚（L. acutus）中获取全基因组基因型。这两个物种都面临着气候变化带来负面影响的高风险。在此，我们提供了一个包含38240个RAD标签和52981个两个物种共有的核单核苷酸多态性（SNP）的资源。我们估计，白侧海豚的总体核苷酸多样性水平（π = 0.0492 ± 0.0006%）高于白喙斑纹海豚（π = 0.0300 ± 0.0004%）。在法罗群岛采样的白侧海豚，分属于两个鲸群（N = 7和N = 11），与在其他地方采样的同物种无亲缘关系个体相比，其多样性水平相似（分别为π = 0.0317 ± 0.0007%和0.0267 ± 0.0006%）（例如，11只苏格兰个体的π = 0.0285 ± 0.0007%）。我们的分析未发现鲸群内存在更高亲缘关系水平的证据。在确定样本集中最可能的遗传簇数量时，我们估计为两到四个簇，对应两个物种，并且每个物种内可能还有另外两个簇。东北大西洋的白侧海豚具有更高的多样性和更低的群体结构，这与其对远洋水域的偏好一致，而白喙斑纹海豚的分布则更为零散，主要分布在大陆架上。
