结合系统发育与群体遗传学分析检验杂交是否存在的技术策略

doi:10.17520/biods.2017097

生物多样性 ›› 2017, Vol. 25 ›› Issue (6): 577-599. DOI: 10.17520/biods.2017097

所属专题：物种形成与系统进化

结合系统发育与群体遗传学分析检验杂交是否存在的技术策略

毛建丰^1,^*(), 马永鹏², 周仁超³

1 北京林业大学生物科学与技术学院林木育种国家工程实验室和林木花卉育种教育部重点实验室, 北京 100083
2 中国科学院昆明植物研究所东亚植物多样性与生物地理学重点实验室, 昆明 650201
3 中山大学生命科学学院, 广州 510275

收稿日期:2017-03-26 接受日期:2017-05-04 出版日期:2017-06-20 发布日期:2017-07-10
通讯作者: 毛建丰
基金资助:
国家自然科学基金(31370255;31670664)

Approaches used to detect and test hybridization: combining phylogenetic and population genetic analyses

Jian-Feng Mao^1,^*(), Yongpeng Ma², Renchao Zhou³

1 National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083
2 Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201
3 School of Life Sciences, Sun Yat-sen University, Guangzhou 510275

Received:2017-03-26 Accepted:2017-05-04 Online:2017-06-20 Published:2017-07-10
Contact: Mao Jian-Feng

摘要/Abstract

摘要：

杂交通常指不同类群间(种间或种内)经有性途径的遗传交流。越来越多的研究表明, 作为一种遗传交换过程, 杂交是生物多样性形成、维持和丧失的重要机制, 它广泛参与了动物、植物、微生物等的类群分化。然而, 我们对杂交过程中遗传交换的普遍性、存在模式、产生机制的认识还非常有限。当前, 高通量测序技术的飞速发展和基因组学研究技术的普遍应用, 为深入评价遗传交换的普遍性和进化意义提供了前所未有的契机。如何选用恰当的研究技术与策略检验潜在的杂交并评价它的特征, 成为大家普遍面临的问题。本文试图综合来自系统发育和群体遗传等相互关联学科中不同的技术策略, 以当前流行的高通量测序技术为核心, 结合表型和细胞遗传学等多种数据获取和分析手段, 概括不同分析策略的特点, 联系必要的实例研究, 为生物多样性与进化领域的学者提供检测遗传交换的参考。

关键词: 遗传交换, 基因流, 生物多样性, 系统发育, 群体遗传

Abstract

Hybridization among diverging (interspecific or intraspecific) groups involves gene flow and genetic recombination. Increasingly, studies have shown that hybridization, a process of genetic exchanges, occurs widely in the divergence and unity of animals, plants, and microorganisms, and acts as an important mechanism for the formation and maintenance of biological diversity. The rapid development of high-throughput sequencing technology and the widespread application of genome-level techniques provides an unprecedented opportunity for us to further evaluate the universality and evolutionary significance of hybridization. However, selecting appropriate research techniques and strategies to detect the potential hybridization and evaluate its characteristics becomes a common question. In this review, we attempt to synthesize methods from phylogenetics and population genetics of the genomic era to provide biodiversity and evolutionary researchers a practical reference for testing hybridization.

Key words: genetic exchange, gene flow, biodiversity, phylogenetics, population genetics

毛建丰, 马永鹏, 周仁超 (2017) 结合系统发育与群体遗传学分析检验杂交是否存在的技术策略. 生物多样性, 25, 577-599. DOI: 10.17520/biods.2017097.

Jian-Feng Mao, Yongpeng Ma, Renchao Zhou (2017) Approaches used to detect and test hybridization: combining phylogenetic and population genetic analyses. Biodiversity Science, 25, 577-599. DOI: 10.17520/biods.2017097.

导出引用管理器 EndNote|Ris|BibTeX

链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2017097

https://www.biodiversity-science.net/CN/Y2017/V25/I6/577

图/表 3

图1 基因组时代的分子标记技术(改编自Lemmon & Lemmon, 2013)。图中简要列出了各测序技术的特点、操作流程和数据特征。

Fig. 1 Molecular genotyping technologies in the genomic era (adapted from Lemmon & Lemmon, 2013). The figure lists the features, operating procedures and data processing of each sequencing technique.

图2 系统发育策略检验杂交存在的基本流程(改编自Lemmon & Lemmon, 2013)。图中给出了利用基因组水平测序技术, 通过数据处理、数据质量评估、数据筛选、直系同源基因识别、序列分析、碱基替代模型选取、系统发育树及系统发育网络重建等多个步骤的简要流程和相关的分析软件。依据操作的难易程度、数据的可靠性、是否能区分杂交和不完全谱系分选等因素, 我们将各技术环节区分为“推荐”、“次优”和“不推荐”等等级, 并列举了各环节部分可利用的软件。

Fig. 2 The brief work-flow of phylogenetic strategy used to test hybridization (adapted from Lemmon & Lemmon, 2013). The work-flow contains multiple steps including data processing, data quality evaluation, data screening, orthologous gene identification, sequence analysis, selection of base substitution model, phylogenetic tree and phylogenetic network reconstruction. We sort out the hierarchy of recommended, suboptimal or requires validation and not recommended, in consideration of the degree of operation, the reliability of the data, whether can distinguish hybridization, incomplete lineage sorting and other factors. And we list the available softwares for each step.

图3 检验杂交群体遗传分析的基本流程。图中给出了利用当前流行的群体基因组学技术, 通过数据收集、数据处理和分析等环节, 对杂交的存在和模式进行全局和局部检验的基本流程, 并列举出了数据格式类型和部分可利用的软件。

Fig. 3 The current population genomic work-flow used to test hybridization. The basic process of global and local testing for the existence and mode of hybridization through data collection, data processing and analysis are presented. The data format and some of the available softwares are listed.

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结合系统发育与群体遗传学分析检验杂交是否存在的技术策略

Approaches used to detect and test hybridization: combining phylogenetic and population genetic analyses

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