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Comparative phylogeography of coastal gobies in the Japanese Archipelago: future perspectives for the study of adaptive divergence and speciation

Abstract

Phylogeography infers the demographic history of various species by resolving genetic relationships among populations across a geographic range. Comparison of phylogeographic patterns of multiple species with similar geographic distributions, i.e., comparative phylogeography, allows us to assess the roles of regional historical events and species-specific ecological factors in shaping intraspecific genetic diversity, providing model systems for studying the processes and genetic basis of adaptive evolution and speciation. In addition, these patterns can also be compared among species from different regions to infer the impact of global-scale historical and present events, such as Pleistocene glacial cycles, on current biodiversity. In this review, I summarize and integrate recent findings of phylogeographic studies for two geographic lineages, Pacific Ocean (PO) and Sea of Japan (SJ) lineages, of five coastal gobies distributed around the Japanese Archipelago. Using mitochondrial and nuclear DNA markers, these studies revealed genetic divergences of the PO and SJ lineages in the coastal gobies. However, the two types of markers showed discordant patterns for genetic divergences between the two lineages (mitonuclear discordance), suggesting different coalescent processes between these genetic markers. Ecological features that depend on shallow coastal resources may contribute to restricted gene flow and be responsible for the existence of the two lineages that are predominantly found in the coastal gobies. All coastal gobies shared sharp contrasts in genetic diversity between the two lineages, with the SJ lineages rapidly expanding during Pleistocene interglacial periods. Such rapid population expansions can provide alternative ways to obtain recent calibration points to estimate divergence times of the two lineages. A comparison of the geographic distributions between the two lineages indicated that the centers of their secondary contact zones vary, which may appear to represent the continuous transition process of the two lineage distributions. Compared with results of phylogeographic studies from other oceans, multiple divergence times, sharply contrasting demographic histories, and two independent secondary contact zones are unique characteristics of the divergence between the PO and SJ lineages. These characteristics will allow us to test the continuous processes of genomic divergence during geographical isolation with environmental fluctuations and the consequences of hybridization of divergent lineages in independent secondary contact zones with different environmental settings.

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Acknowledgements

I sincerely thank Seishi Kimura and other organizing committee members of the Commemoration of the 50th Anniversary of the Ichthyological Society of Japan for providing me with an opportunity for writing this review article. I am grateful to Carol A. Stepien and Kiyoshi Kikuchi for their constructive feedback and language improvements. I am grateful to Shuya Kato for providing me with the photos of the five gobies. I would like to thank all my collaborators. This work was supported by the Japan Society for the Promotion of Science (KAKENHI 18H02493). Publication of this article was also supported by the Commemoration of the 50th Anniversary of the Ichthyological Society of Japan Society. I would like to thank the editor and two anonymous reviewers for their helpful comments on earlier versions of this article.

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Correspondence to Shotaro Hirase.

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Hirase, S. Comparative phylogeography of coastal gobies in the Japanese Archipelago: future perspectives for the study of adaptive divergence and speciation. Ichthyol Res (2021). https://doi.org/10.1007/s10228-021-00824-3

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Keywords

  • Mitonuclear discordance
  • Sea of Japan
  • Hybridization
  • Speciation continuum