Genetic structure of Pacific crown-of-thorns starfish (Acanthaster cf. solaris) in southern Japan based on genome-wide RADseq analysis

Iguchi, Akira; Tada, Isao; Nagano, Atsushi J.; Yasuda, Nina

doi:10.1007/s00338-021-02145-3

Cited by 6 publications

(4 citation statements)

References 48 publications

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“…Several recent studies, conducted with either genomic‐scale data (Chang et al., 2022; Iguchi et al., 2021; Okuyama et al., 2020) or involving limited numbers of Sanger sequence loci (Kumekawa et al., 2021; Su et al., 2016) have found similar patterns, but have been restricted in geographical focus on Taiwan and the Ryukyu Island Chain. Here, we used both genome‐wide, and Sanger DNA sequence data, to further extend inference of patterns to the broader regional scales of the tropical Southwest Pacific, including the Philippines and Australia (Brown et al., 2013; Lohman et al., 2011).…”

Section: Discussionmentioning

confidence: 91%

“…Several recent studies, conducted with either genomic-scale data (Chang et al, 2022;Iguchi et al, 2021;Okuyama et al, 2020) or involving limited numbers of Sanger sequence loci (Kumekawa et al, 2021;Su et al, 2016) shows the number of events through time; the y-axis represents the number of events, and the x-axis represents the corresponding divergence time in the phylogenomic tree above. The blue line is the number of dispersal events, the purple line is the number of vicariances, and the red line is the standard events, which represent the summary of all kinds of events.…”

Section: Discussionmentioning

confidence: 99%

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A shift in the host web occupancy of dew‐drop spiders associated with genetic divergence in the Southwest Pacific

Elias,

Responte,

et al. 2024

Journal of Biogeography

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AimWe assessed the population genetic structure of the kleptoparasitic spider Argyrodes bonadea across the Southwestern Pacific islands. Our aim is to evaluate the impact of overseas distances and, in particular, the Kerama gap, as potential drivers of genetic differentiation. If no relationship exists, then we assume dispersal following adaptive change as alternative non‐vicariant mechanism that generates divergence.LocationSouthwestern Pacific Islands.Taxon Argyrodes bonadea. MethodsWe used mitochondrial Cytochrome Oxidase 1 (CO1) gene sequences and Restriction Site‐associated DNA Sequencing (RAD‐seq) for our analyses.ResultsTwo strongly supported lineages, an Amami‐Okinawa Lineage (AOL) and an Austral‐Asia Lineage (AAL), correspond to two separate clades, roughly divided by the Kerama Gap, in phylogenetic trees estimated here. However, species delimitation led to the interpretation of only a single species present. The AOL exhibits complex, geographically structured host web spider species specificity, wherein the Amami population utilizes Cyrtophora, but AOL samples in Okinawa associate exclusively with Nephila—and yet all broadly distributed AAL populations show no evidence of host web spider species specificity.Main ConclusionThe population boundary between AOL and AAL likely results from local adaptation to novel hosts—instead of isolation by the Kerama Gap—following long‐distance dispersal and range expansion. Our results suggest kleptoparasitic spiders have the capacity to overcome permanent deep‐sea barriers and colonize distant landmasses. Whereas peripheral populations (AOL) demonstrate the capacity for specialization to a single host, which may have contributed to genetic differentiation and isolation, the broadly distributed AAL persists and has successfully expanded its geographical range as a host generalist, which may contribute to ongoing gene flow inferred in this study.

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Section: Discussionmentioning

confidence: 91%

Section: Discussionmentioning

confidence: 99%

A shift in the host web occupancy of dew‐drop spiders associated with genetic divergence in the Southwest Pacific

Elias,

Responte,

et al. 2024

Journal of Biogeography

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“…Several recent studies, conducted with either genomic-scale data (Okuyama et al, 2020; Iguchi, Tada, Nagano, & Yasuda, 2021; Chang et al, 2022) or involving limited numbers of Sanger sequence loci (Su et al, 2016; Kumekawa et al, 2021) have found similar patterns, but have been restricted in geographical focus on Taiwan and the Ryukyu Island Chain. Here, we used both genome-wide, and Sanger DNA sequence data, to further extended inference of patterns to the broader regional scales of the tropical Southwest Pacific, including the Philippines and Australia (Brown et al, 2013; Lohman et al, 2011).…”

Section: Discussionmentioning

confidence: 93%

A shift in the host web occupancy of dew-drop spiders associated with genetic divergence in the Southwest Pacific

Elias,

Responte,

et al. 2023

Preprint

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AimWe assessed the population genetic structure of the kleptoparasitic spiderArgyrodes bonadeaacross the Southwestern Pacific islands. Our focus is on assessing the impact of overseas distances and, in particular, the Kerama gap, as potential drivers of genetic differentiation. We found that the spider kleptoparasite’s switch to a specific host species is associated with significant genetic variation at fine scales, whereas the same species adoption of a generalist host strategy has likely facilitated its broad dispersal, colonization, and recent range expansion across the southwestern Pacific, and is associated with a lack of geographically– structured genetic variation in these latter, subsequently-colonized landmasses.LocationSouthwestern Pacific IslandsTaxonArgyrodes bonadeaMethodsWe used mitochondrial Cytochrome Oxidase 1 (CO1) gene sequences, and Restriction Site-associated DNA Sequencing (RAD-seq) for our analyses.ResultsTwo strongly supported lineages, an Amami-Okinawa Lineage (AOL) and an Austral-Asia Lineage (AAL) correspond to two separate clades, roughly divided by the Kerama Gap, in phylogenetic trees estimated here. However, species delimitation led to the interpretation of only a single species present. The AOL exhibits complex, geographically-structured host web spider species specificity, wherein the Amami population utilizesCyrtophora, but AOL samples in Okinawa associates exclusively withNephila—and yet all broadly distributed AAL populations show no evidence of host web spider species specificity.Main conclusionThe population boundary between AOL and AAL likely results from local adaptation to novel hosts—instead of isolation by the Kerama Gap—following long-distance dispersal and range expansion. Our results suggest kleptoparasitic spiders have the capacity to overcome permanent deep-sea barriers and colonize distant landmasses. Whereas peripheral populations (AOL) demonstrate the capacity for specialization to a single host, which may have contributed to genetic differentiation and isolation, the broadly-distributed AAL persists and has successfully expanded its geographical range as a host generalist, which may contribute to ongoing gene flow inferred in this study.

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“…To overcome this problem, population genomic studies have been using restriction site associated DNA sequencing (RADseq) techniques to obtain reduced representations of genomes to diminish costs (Pecoraro et al, 2018;Casso et al, 2019). These techniques use restriction enzymes that cleave the genome into several targeted fragments ranging from tens to more than a thousand base pairs (Iguchi et al, 2021;Tonzo and Ortego, 2021;Hernandez-Castro et al, 2022;Min et al, 2022). Particularly, 2b-RAD uses IIb-enzymes that cleave at both sides of the recognition site (Wang et al, 2012), generating sticky ends with few random nucleotides depending on the enzyme.…”

Section: Introductionmentioning

confidence: 99%

The impact of adaptor selection on genotyping in 2b-RAD studies

et al. 2022

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Population genomic studies have increased in the last decade, showing great potential to understand the evolutionary patterns in a great variety of organisms, mostly relying on RAD sequencing techniques to obtain reduced representations of the genomes. Among them, 2b-RAD can provide further secondary reduction to adjust experimental costs by using base-selective adaptors, although its impact on genotyping is unknown. Here we provide empirical comparisons on genotyping and genetic differentiation when using fully degenerate or base-selective adaptors and assess the impact of missing data. We built libraries with the two types of adaptors for the same individuals and generated independent and combined datasets with different missingness filters (presence in 100%, 75% and 50% of the libraries). Our approach, by exploring locus-by-locus, found 92% of identical genotypes between the two libraries of the same individual when using loci shared among 100% of the libraries, which decreased to 35% when working with loci present in at least 50% of them. We show that missing data is a major source of individual genetic differentiation. The loci discordant by genotyping were in low frequency (7.67%) in all filtered files. Only 0.96% of them were directly attributable to base-selective adaptors reducing heterozygosity. An underestimation of heterozygosity in 6.44% of genotypes was found in libraries generated with fully degenerated adaptors, of which ca. 70% had <10 reads per locus indicating that sufficient read depth should be ensured for a correct genotyping. Base-selective adaptors reduce the number of loci, increase their coverage, and provide a reliable genotyping with no heterozygosity underestimation at a lower sequencing cost. We demonstrate that missing data is a major concern for a correct identification of genetic differentiation, and should not be neglected in genomic studies. Thus, we conclude that 2b-RAD libraries using base-selective adaptors are a robust tool to use in population genomics regardless the target species genome size, promoting their use in future studies.

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Genetic structure of Pacific crown-of-thorns starfish (Acanthaster cf. solaris) in southern Japan based on genome-wide RADseq analysis

Cited by 6 publications

References 48 publications

A shift in the host web occupancy of dew‐drop spiders associated with genetic divergence in the Southwest Pacific

A shift in the host web occupancy of dew‐drop spiders associated with genetic divergence in the Southwest Pacific

A shift in the host web occupancy of dew-drop spiders associated with genetic divergence in the Southwest Pacific

The impact of adaptor selection on genotyping in 2b-RAD studies

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