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Article|03 Mar 2022|OPEN
Patterns of genomic divergence in sympatric and allopatric speciation of three Mihoutao (Actinidia) species 
Yongbo Liu1 , , Wenhao Yu1 , Baofeng Wu1 and Junsheng Li,1
1State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, Beijing 100012, China
*Corresponding author. E-mail: liuyb@craes.org.cn

Horticulture Research 9,
Article number: uhac054 (2022)
doi: https://doi.org/10.1093/hr/uhac054
Views: 17

Received: 01 Nov 2021
Accepted: 19 Feb 2022
Published online: 03 Mar 2022

Abstract

Isolation by geographic distance is involved in the formation of potential genomic islands and the divergence of genomes, which often result in speciation. The mechanisms of sympatric and allopatric speciation associated with geographic distance remain a topic of interest to evolutionary biologists. Here, we examined genomic divergence in three Actinidia species from large-scale sympatric and allopatric regions. Genome sequence data revealed that hexaploid Actinidia deliciosa originated from Actinidia chinensis and supported the speciation-with-gene-flow model in sympatric regions. The common ancestor of Actinidia setosa and A. deliciosa migrated from the mainland to the Taiwan Island ~2.91 Mya and formed A. setosa ~0.92 Mya, and the speciation of A. setosa is consistent with the divergence-after-speciation model with selective sweeps. Geographic isolation resulted in population contraction and accelerated the process of lineage sorting and speciation due to natural selection. Genomic islands contained genes associated with organ development, local adaptation, and stress resistance, indicating selective sweeps on a specific set of traits. Our results highlight the patterns of genomic divergence in sympatric and allopatric speciation, with the mediation of geographic isolation in the formation of genomic islands during Actinidia speciation.