Integrating phylogeographic and ecological niche approaches to delimitating cryptic lineages in the blue–green damselfish (<i>Chromis viridis</i>)

Liu, Shang-Yin Vanson; Tuanmu, Mao‐Ning; Rachmawati, Rita; Mahardika, Gusti Ngurah; Barber, Paul H.

doi:10.7717/peerj.7384

Cited by 9 publications

(8 citation statements)

References 82 publications

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“…S1). This finding is congruent with the results of connectivity studies targeting damselfishes between the SCS and Kuroshio regions which showed low and non-significant genetic structure among the Xisha (Paracel) Islands, Dongsha, and Taiwan (Liu et al, 2011(Liu et al, , 2014(Liu et al, , 2019. Failure to reject panmixia is generally common in marine species (Waples, 1998;Kinlan & Gaines, 2003), has been found consistently in the Indo-Pacific (Keyse et al, 2014;Crandall et al, 2019a), and is traditionally interpreted as evidence for relatively high levels of gene flow due to larval dispersal.…”

Section: Discussionsupporting

confidence: 84%

Dongsha Atoll is an important stepping-stone that promotes regional genetic connectivity in the South China Sea

Liu

Green

Briggs

et al. 2021

PeerJ

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Background Understanding region-wide patterns of larval connectivity and gene flow is crucial for managing and conserving marine biodiversity. Dongsha Atoll National Park (DANP), located in the northern South China Sea (SCS), was established in 2007 to study and conserve this diverse and remote coral atoll. However, the role of Dongsha Atoll in connectivity throughout the SCS is seldom studied. In this study, we aim to evaluate the role of DANP in conserving regional marine biodiversity. Methods In total, 206 samples across nine marine species were collected and sequenced from Dongsha Atoll, and these data were combined with available sequence data from each of these nine species archived in the Genomic Observatories Metadatabase (GEOME). Together, these data provide the most extensive population genetic analysis of a single marine protected area. We evaluate metapopulation structure for each species by using a coalescent sampler, selecting among panmixia, stepping-stone, and island models of connectivity in a likelihood-based framework. We then completed a heuristic graph theoretical analysis based on maximum dispersal distance to get a sense of Dongsha’s centrality within the SCS. Results Our dataset yielded 111 unique haplotypes across all taxa at DANP, 58% of which were not sampled elsewhere. Analysis of metapopulation structure showed that five out of nine species have strong regional connectivity across the SCS such that their gene pools are effectively panmictic (mean pelagic larval duration (PLD) = 78 days, sd = 60 days); while four species have stepping-stone metapopulation structure, indicating that larvae are exchanged primarily between nearby populations (mean PLD = 37 days, sd = 15 days). For all but one species, Dongsha was ranked within the top 15 out of 115 large reefs in the South China Sea for betweenness centrality. Thus, for most species, Dongsha Atoll provides an essential link for maintaining stepping-stone gene flow across the SCS. Conclusions This multispecies study provides the most comprehensive examination of the role of Dongsha Atoll in marine connectivity in the South China Sea to date. Combining new and existing population genetic data for nine coral reef species in the region with a graph theoretical analysis, this study provides evidence that Dongsha Atoll is an important hub for sustaining connectivity for the majority of coral-reef species in the region.

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Section: Discussionsupporting

confidence: 84%

Dongsha Atoll is an important stepping-stone that promotes regional genetic connectivity in the South China Sea

Liu

Green

Briggs

et al. 2021

PeerJ

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“…Chromis xanthochira XIII dorsal spines; similar to C. weberi (Moyer and Ida, 1976;Randall et al, 1981Randall et al, , 1997Myers, 1999) and C. xanthura (Moyer and Ida, 1976) S3) discovered genetically distinct populations in the Indian and Pacific basins (their ''Pattern 2''). Others have also found divergent lineages within C. atripectoralis and/or C. viridis (Hubert et al, 2012(Hubert et al, , 2017Messmer et al, 2012;Liu et al, 2019). The identity of the taxon identified as ''Chromis caerulea'' remains unclear.…”

Section: Chromis Xanthochiramentioning

confidence: 99%

Systematics of Damselfishes

Tang

Mayden

DeSalle

2021

Ichthyology & Herpetology

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The family Pomacentridae is a species-rich group of primarily marine fishes. The phylogenetic relationships of the damselfishes are examined herein using sequence data from five mitochondrial (12S, 16S, ATP synthase subunits 8/6, cytochrome b, and cytochrome c oxidase I) and three nuclear (histone H3, recombination activating gene 1 exon 3, and Tmo-4C4) loci. A combined data matrix of 6,865 base pairs was compiled for 462 taxa, representing 322 damselfish species, and used to reconstruct the phylogeny of pomacentrids via maximum likelihood. The resulting topology supports the monophyly of the family and some groups within it, corroborating some conclusions drawn by recent studies but contradicting others. We find that the family is composed of four major lineages, recognized herein as the subfamilies Chrominae, Glyphisodontinae, Microspathodontinae, and Pomacentrinae. The subfamily Microspathodontinae is sister to a clade of the other three subfamilies, and the subfamily Glyphisodontinae is sister to a clade of Chrominae and Pomacentrinae. The monotypic subfamily Lepidozyginae is recovered within Microspathodontinae and placed in the synonymy of Microspathodontinae. Species of Plectroglyphidodon and Stegastes are reassigned to maintain the monophyly of both genera. In Chrominae, the generic limits of Azurina and Chromis are revised to reflect monophyletic groups. The genus-group name Pycnochromis is resurrected to accommodate a group of former Chromis sister to Dascyllus. In Pomacentrinae, the genus Premnas is recovered within Amphiprion and placed in the synonymy of Amphiprion. The genus Chrysiptera is broadly polyphyletic within Pomacentrinae. The genus Amblypomacentrus is revised to accommodate some species formerly classified as Chrysiptera.

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“…The Kuroshio Current runs northwards to Japan from the bifurcation of the Northern Equatorial Current off the eastern coast of the Philippines [65] and may provide an avenue for migration, particularly from the core to the edge. Indeed, other damselfish show limited genetic differentiation between Japanese populations and those in the Coral Triangle [66]. However, the strong genetic differentiation seen between A. clarkii populations in Japan and the Philippines/Indonesia suggests these distinct genetic lineages may be maintained by local adaptation in addition to gene flow.…”

Section: (A) Life On the Edgementioning

confidence: 99%

Genomic signatures of spatially divergent selection at clownfish range margins

et al. 2021

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Understanding how evolutionary forces interact to drive patterns of selection and distribute genetic variation across a species' range is of great interest in ecology and evolution, especially in an era of global change. While theory predicts how and when populations at range margins are likely to undergo local adaptation, empirical evidence testing these models remains sparse. Here, we address this knowledge gap by investigating the relationship between selection, gene flow and genetic drift in the yellowtail clownfish, Amphiprion clarkii, from the core to the northern periphery of the species range. Analyses reveal low genetic diversity at the range edge, gene flow from the core to the edge and genomic signatures of local adaptation at 56 single nucleotide polymorphisms in 25 candidate genes, most of which are significantly correlated with minimum annual sea surface temperature. Several of these candidate genes play a role in functions that are upregulated during cold stress, including protein turnover, metabolism and translation. Our results illustrate how spatially divergent selection spanning the range core to the periphery can occur despite the potential for strong genetic drift at the range edge and moderate gene flow from the core populations.

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Integrating phylogeographic and ecological niche approaches to delimitating cryptic lineages in the blue–green damselfish (Chromis viridis)

Cited by 9 publications

References 82 publications

Dongsha Atoll is an important stepping-stone that promotes regional genetic connectivity in the South China Sea

Dongsha Atoll is an important stepping-stone that promotes regional genetic connectivity in the South China Sea

Systematics of Damselfishes

Genomic signatures of spatially divergent selection at clownfish range margins

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