Complex phylogeographic patterns in the intertidal goby Chaenogobius annularis around Kyushu Island as a boundary zone of three different seas

Kato, Shuya; Arakaki, Seiji; Kikuchi, Kiyoshi; Hirase, Shotaro

doi:10.1007/s10228-020-00772-4

Cited by 10 publications

(6 citation statements)

References 67 publications

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“…With the ever‐increasing size and scope of molecular datasets, mitonuclear discordance has now been widely documented and accepted as a common phenomenon. Instances of mitonuclear discordance have been documented across the tree of life in taxa including protozoans (Kato, Cáceres, et al, 2021), algae (Kao et al, 2022), fungi (Bourret et al, 2018), arachnids (Ivanov et al, 2018), insects (Hinojosa et al, 2019; Wham et al, 2021), crabs (Shahdadi et al, 2021), fishes (Berbel‐Filho et al, 2022; Kato, Arakaki, et al, 2021), amphibians (Firneno et al, 2020), snakes (Marshall et al, 2021), mammals (Bailey & Stevison, 2021; Ge et al, 2022; Good et al, 2008) and birds (Andersen et al, 2021; Pons et al, 2014). Yet, despite the well‐documented ubiquity of mitonuclear discordance, the evolutionary mechanisms driving this phenomenon are often difficult to parse (Bonnet et al, 2017; Kimball et al, 2021).…”

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confidence: 99%

Mitonuclear discordance results from incomplete lineage sorting, with no detectable evidence for gene flow, in a rapid radiation of Todiramphus kingfishers

et al. 2023

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Many organisms possess multiple discrete genomes (i.e. nuclear and organellar), which are inherited separately and may have unique and even conflicting evolutionary histories. Phylogenetic reconstructions from these discrete genomes can yield different patterns of relatedness, a phenomenon known as cytonuclear discordance. In many animals, mitonuclear discordance (i.e. discordant evolutionary histories between the nuclear and mitochondrial genomes) has been widely documented, but its causes are often considered idiosyncratic and inscrutable. We show that a case of mitonuclear discordance in Todiramphus kingfishers can be explained by extensive genome‐wide incomplete lineage sorting (ILS), likely a result of the explosive diversification history of this genus. For these kingfishers, quartet frequencies reveal that the nuclear genome is dominated by discordant topologies, with none of the internal branches in our consensus nuclear tree recovered in >50% of genome‐wide gene trees. Meanwhile, a lack of inter‐species shared ancestry, non‐significant pairwise tests for gene flow, and little evidence for meaningful migration edges between species, leads to the conclusion that gene flow cannot explain the mitonuclear discordance we observe. This lack of evidence for gene flow combined with evidence for extensive genome‐wide gene tree discordance, a hallmark of ILS, leads us to conclude that the mitonuclear discordance we observe likely results from ILS, specifically deep coalescence of the mitochondrial genome. Based on this case study, we hypothesize that similar demographic histories in other ‘great speciator’ taxa across the Indo‐Pacific likely predispose these groups to high levels of ILS and high likelihoods of mitonuclear discordance.

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Section: Introductionmentioning

confidence: 99%

Mitonuclear discordance results from incomplete lineage sorting, with no detectable evidence for gene flow, in a rapid radiation of Todiramphus kingfishers

et al. 2023

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“…Nakano et al 2010). To grasp the process of genetic divergence and structuring in this region, the comparative phylogeographical studies are required (Kato et al 2021).…”

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confidence: 99%

“…However, some individuals of Ukujima Island and Fukuejima Island do not correspond to the above geographic haplotype distribution. Some populations of shallow water species distributed in the western coastal area of Kyushu are known to be genetically differentiated from the eastern coastal area of Kyushu due to the influence of ocean current splits that occurs in the south of Kyushu (Kojima et al 1997;Nakano et al 2010;Hirase et al 2012Hirase et al , 2014Yamazaki et al 2017Yamazaki et al , 2021aKato et al 2021). Along the western coastal area of Kyushu influenced by the Tsushima Current, Fukuejima Island populations (the Goto Islands) of some species have unique genetic components (e.g., Kato et al 2021).…”

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confidence: 99%

“…Some populations of shallow water species distributed in the western coastal area of Kyushu are known to be genetically differentiated from the eastern coastal area of Kyushu due to the influence of ocean current splits that occurs in the south of Kyushu (Kojima et al 1997;Nakano et al 2010;Hirase et al 2012Hirase et al , 2014Yamazaki et al 2017Yamazaki et al , 2021aKato et al 2021). Along the western coastal area of Kyushu influenced by the Tsushima Current, Fukuejima Island populations (the Goto Islands) of some species have unique genetic components (e.g., Kato et al 2021). This trend seems to be similar to our results of L. horikawai, which some haplotypes obtained from the Goto Islands that locate the border between the northern part of Kyushu and the central islands do not correspond to the above geographic haplotype distribution.…”

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confidence: 99%

“…This trend seems to be similar to our results of L. horikawai, which some haplotypes obtained from the Goto Islands that locate the border between the northern part of Kyushu and the central islands do not correspond to the above geographic haplotype distribution. In this area, paleoenvironmental isolation and contact events are considered to promote the complex population structure (Kato et al 2021). Alternatively, it may be caused by the migration events such as rafting among islands (e.g., Donald et al 2007) and/or the incomplete lineage sorting would cause it (Ballard & Whitlock 2004).…”

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confidence: 99%

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Genetic variation of <i>Littorina horikawai</i> endemic to the western coast and the adjacent islands around Kyushu, Japan inferred by mtDNA analyses

Yamazaki

Seo

Hirano

et al. 2022

Plankton Benthos Res

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We demonstrated the genetic variation and population structure of a direct developing marine gastropod, Littorina horikawai which is endemic species distributed in the western coast of Kyushu, Japan and is found mainly on the adjacent islands. We conducted the field survey and sampling covering most of the distribution area of L. horikawai. In total, we collected 173 individuals from 13 localities (between Tsushima Island and Yakushima Island) and determined the sequences of mitochondrial DNA, the cytochrome b (CYTB) gene. We detected a significant genetic population differentiation in L. horikawai despite the limited distribution area of the western coast of Kyushu. Also, its haplotype distribution is mainly consistent with the geographical structure: the northern part of Kyushu, the central islands, and the southern islands. However, some haplotypes obtained from the Goto Islands which is located in the border between the northern part of Kyushu and the central islands do not correspond to the above geographic distribution. The high level of genetic differentiation of L. horikawai compared to other low dispersal Littorina species despite its narrow distribution range may be due to its predominantly fragmented island habitats. Although it is necessary for understanding the detailed evolutionary history of L. horikawai to perform the high-resolution genetic analysis, our present findings indicated that a high level of genetic differentiation of L. horikawai occurred even in a narrow distribution range because of not only the ecological traits linking to dispersal ability but also its discontinuous pattern such as the island inhabitation.

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Phylogeography of Coastal Fishes of Japan

Matsui

2022

Fish Diversity of Japan

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Complex phylogeographic patterns in the intertidal goby Chaenogobius annularis around Kyushu Island as a boundary zone of three different seas

Cited by 10 publications

References 67 publications

Mitonuclear discordance results from incomplete lineage sorting, with no detectable evidence for gene flow, in a rapid radiation of Todiramphus kingfishers

Mitonuclear discordance results from incomplete lineage sorting, with no detectable evidence for gene flow, in a rapid radiation of Todiramphus kingfishers

Genetic variation of <i>Littorina horikawai</i> endemic to the western coast and the adjacent islands around Kyushu, Japan inferred by mtDNA analyses

Phylogeography of Coastal Fishes of Japan

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