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Population genomics of the killer whale; SNP discovery towards the assessment of population structure at functional genes

虎鲸的种群基因组学；

基本信息

批准号：
NE/J014443/1
负责人：
Alan Hoelzel
金额：
$ 6.66万
依托单位：
Durham University
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2012
资助国家：
英国
起止时间：
2012 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=NE%2FJ014443%2F1
关键词：
Population genomics killer whale SNP

项目摘要

Since a Canadian research project in the 1970s first showed how the regional killer whale population could be tracked over time using photographs to identify and follow the associations and movement of individual whales, it has become increasingly apparent that this species offers great potential for advancing our understanding of key evolutionary and ecological processes. Despite their tremendous potential for long-distance dispersion, with social groups travelling 1000s of km in a season, identified populations of associating individuals (divided into social units of 20-50 individuals) are genetically differentiated at neutral markers over small geographic scales. The apparent mechanism is dependence on local or seasonal habitat resources, and in particular, prey resources. In this way picivorous populations can be separated by the direction of migration in their anadromous salmonid prey (migrating north or south of an estuary), and picivorous populations can be isolated from marine-mammal-eating populations even in sympatry. There is a pattern of differentiation associated with geographic distance (as seen for many species), but only within an ecotype. Differentiation among ecotypes is based on biological factors (especially behaviour associated with foraging and social structure). Although the effective size of regional populations is likely small, there are sometimes physical differences that may be associated with resource exploitation (as seen in various other delphinid species, especially associated with buccal morphology), suggesting local adaptation. In this study we will identify genes that are apparently under selection, and associate them where possible with ecological characteristics, especially known aspect of the life history of the different ecotype populations. A key deliverable will be an extensive set of SNP markers, with some identified as likely under selection, to be applied in a follow-on study to an extensive program of population screening. A preliminary assessment based on these SNP markers will be undertaken in the current study as part of the SNP discovery process. This is made possible by the chosen methodology. The initial step will be the sequencing of the full genome for one sample to a quality level sufficient to use as a reference scaffold (to be done through the commercial provider, Eurofins MWG/ Operon). This will then be used to facilitate the RAD-Tag sequencing work and the associated bio-informatics (to be undertaken under the supervision of partner Neil Hall at CGR Liverpool). The RAD-Tag data will then be analysed by the PI in Durham in collaboration with Prof. Hall and with the assistance of the RA. The RAD-Tag sequences will permit the identification of SNP markers, and the reference genome would permit identification of their location and linkage within the killer whale genome. Analysis of an initial 150 whales from 5 populations will provide the preliminary data on signals for selection and a high-resolution assessment of patterns of differentiation. Bayesian and multiple regression methods will be applied to allow interpretation of genetic variation in the context of environmental variables, and to assess which variables explain the largest proportion of the genetic variance. Taken together these analyses will advance our understanding of the evolutionary processes that generate biodiversity within and among species, facilitate more effective programs of biodiversity conservation, and provide the raw material for future studies that will advance these objectives further.

自从20世纪70年代加拿大的一个研究项目首次展示了如何使用照片来识别和跟踪单个鲸鱼的联系和运动来跟踪区域虎鲸数量以来，越来越明显的是，这个物种为促进我们对关键进化和生态过程的理解提供了巨大的潜力。尽管它们具有远距离分散的巨大潜力，社会群体在一个季节内移动数千公里，但已确定的关联个体群体（分为20-50个个体的社会单位）在小地理尺度上以中性标记进行遗传分化。明显的机制是对当地或季节性栖息地资源，特别是猎物资源的依赖。通过这种方式，可以根据其溯河鲑鱼猎物的迁徙方向（向河口的北部或南部迁移）来区分食鱼种群，并且可以将食鱼种群与海洋哺乳动物种群分开，即使是在同栖环境中。有一种与地理距离相关的分化模式（如许多物种所见），但仅在一个生态型内。生态型之间的分化是基于生物因素（特别是与觅食和社会结构相关的行为）。虽然区域种群的有效规模可能很小，但有时存在与资源开发有关的物理差异（如在各种其他海豚物种中所见，特别是与颊形态有关），这表明局部适应。在这项研究中，我们将识别明显处于选择中的基因，并尽可能将它们与生态特征联系起来，特别是不同生态型种群的生活史的已知方面。一个关键的成果将是一套广泛的SNP标记，其中一些被确定为可能处于选择状态，将应用于广泛的人群筛查项目的后续研究中。基于这些SNP标记的初步评估将在当前的研究中进行，作为SNP发现过程的一部分。所选择的方法使这成为可能。第一步将是对一个样本进行全基因组测序，使其达到足以用作参考支架的质量水平（通过商业供应商Eurofins MWG/ Operon完成）。然后，这将用于促进rad标签测序工作和相关的生物信息学（将在CGR利物浦的合作伙伴Neil Hall的监督下进行）。然后，达勒姆的PI将与Hall教授合作，在RA的协助下，对RAD-Tag数据进行分析。RAD-Tag序列将允许鉴定SNP标记，而参考基因组将允许鉴定它们在虎鲸基因组中的位置和联系。对来自5个种群的150头鲸鱼的初步分析将提供关于选择信号的初步数据和对分化模式的高分辨率评估。将应用贝叶斯和多元回归方法来解释环境变量背景下的遗传变异，并评估哪些变量解释了遗传变异的最大比例。综上所述，这些分析将促进我们对物种内部和物种之间产生生物多样性的进化过程的理解，促进更有效的生物多样性保护计划，并为进一步推进这些目标的未来研究提供原材料。

项目成果

期刊论文数量（5）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Phylogenomics of the killer whale indicates ecotype divergence in sympatry.

虎鲸的系统基因组学表明同源生态型存在差异。

DOI：
10.1038/hdy.2014.67
发表时间：
2015
期刊：
Heredity
影响因子：
3.8
作者：
Moura AE
通讯作者：
Moura AE

Population genomics of the killer whale indicates ecotype evolution in sympatry involving both selection and drift.

DOI：
10.1111/mec.12929
发表时间：
2014-11
期刊：
Molecular ecology
影响因子：
4.9
作者：
Moura AE;Kenny JG;Chaudhuri R;Hughes MA;J Welch A;Reisinger RR;de Bruyn PJ;Dahlheim ME;Hall N;Hoelzel AR
通讯作者：
Hoelzel AR

Killer whale nuclear genome and mtDNA reveal widespread population bottleneck during the last glacial maximum.

DOI：
10.1093/molbev/msu058
发表时间：
2014-05
期刊：
Molecular biology and evolution
影响因子：
10.7
作者：
Moura AE;Janse van Rensburg C;Pilot M;Tehrani A;Best PB;Thornton M;Plön S;de Bruyn PJ;Worley KC;Gibbs RA;Dahlheim ME;Hoelzel AR
通讯作者：
Hoelzel AR

Resource specialisation and the divergence of killer whale populations.

资源专业化和虎鲸种群的分化。