Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools.
Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools.
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DOI：
10.1186/s12864-015-1712-0
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发表时间：
2015-07-10
期刊：
影响因子：
4.4
通讯作者：
Miller W
中科院分区：
文献类型：
--
作者：
Fuller ZL;Niño EL;Patch HM;Bedoya-Reina OC;Baumgarten T;Muli E;Mumoki F;Ratan A;McGraw J;Frazier M;Masiga D;Schuster S;Grozinger CM;Miller W
随着廉价、高通量测序技术的发展，在全基因组范围内研究与非模式物种在其生态环境中的群体遗传学和分子进化相关的问题已变得可行。在这里，我们采用了一套新开发的基于网络的集成程序，使用 FST、pN/pS 和 McDonald-Kreitman 等几种成熟的测试来检查群体动态和整个基因组的选择特征。我们应用这些技术来研究东非的蜜蜂 (Apis mellifera) 种群。在肯尼亚，有几个已描述的蜜蜂亚种，它们被认为分布在不同的生态区域。我们对来自肯尼亚各地养蜂场的 11 只工蜂进行了全基因组测序，并鉴定了 360 万个假定的单核苷酸多态性。密集的覆盖范围使我们能够应用多种计算程序来研究种群结构和种群之间的进化关系，并检测整个基因组适应性进化的迹象。虽然样本种群之间存在相当大的基因流动，但来自北部沙漠地区的种群和来自温带草原地区的种群之间存在明显的区别。我们鉴定了几个基因，这些基因显示出与非洲蜜蜂种群内以及这些种群与欧洲蜜蜂或亚洲蜜蜂群之间的正选择一致的种群遗传模式。这些结果为未来蜜蜂适应性生态进化的研究奠定了基础，并展示了新的、免费的基于网络的工具和工作流程 (http://usegalaxy.org/r/kenyanbee) 的使用，这些工具和工作流程可应用于任何具有基因组信息的模型系统。本文的在线版本 (doi:10.1186/s12864-015-1712-0) 包含补充材料，可供授权用户使用。
With the development of inexpensive, high-throughput sequencing technologies, it has become feasible to examine questions related to population genetics and molecular evolution of non-model species in their ecological contexts on a genome-wide scale. Here, we employed a newly developed suite of integrated, web-based programs to examine population dynamics and signatures of selection across the genome using several well-established tests, including FST, pN/pS, and McDonald-Kreitman. We applied these techniques to study populations of honey bees (Apis mellifera) in East Africa. In Kenya, there are several described A. mellifera subspecies, which are thought to be localized to distinct ecological regions. We performed whole genome sequencing of 11 worker honey bees from apiaries distributed throughout Kenya and identified 3.6 million putative single-nucleotide polymorphisms. The dense coverage allowed us to apply several computational procedures to study population structure and the evolutionary relationships among the populations, and to detect signs of adaptive evolution across the genome. While there is considerable gene flow among the sampled populations, there are clear distinctions between populations from the northern desert region and those from the temperate, savannah region. We identified several genes showing population genetic patterns consistent with positive selection within African bee populations, and between these populations and European A. mellifera or Asian Apis florea. These results lay the groundwork for future studies of adaptive ecological evolution in honey bees, and demonstrate the use of new, freely available web-based tools and workflows (http://usegalaxy.org/r/kenyanbee) that can be applied to any model system with genomic information. The online version of this article (doi:10.1186/s12864-015-1712-0) contains supplementary material, which is available to authorized users.
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