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

doi:10.17520/biods.2017097

Abstract

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

Jian-Feng Mao, Yongpeng Ma, Renchao Zhou. Approaches used to detect and test hybridization: combining phylogenetic and population genetic analyses[J]. Biodiv Sci, 2017, 25(6): 577-599.

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URL: https://www.biodiversity-science.net/EN/10.17520/biods.2017097

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

Figures/Tables 3

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.

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.

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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