Genetic patterns in peripheral marine populations of the fusilier fish <i>Caesio cuning</i> within the Kuroshio Current

Ackiss, Amanda S.; Bird, Christopher E.; Akita, Yuichi; Santos, Mudjekeewis D.; Tachihara, Katsunori; Carpenter, Kent E.

doi:10.1002/ece3.4644

Cited by 20 publications

(19 citation statements)

References 81 publications

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“…Nucleotide diversity and F IS were lowest, and relatedness highest, in the peripheral Japanese site. These findings are congruent with the idea that edge populations are subject to higher rates of genetic drift owing to reduced N e [6,10] and match previous studies that found declining genetic diversity along the Kuroshio Current towards species' northern range margins [67]. However, our analyses also estimated similar long-term N e in all three sites and no signatures of recent bottlenecks at the range edge.…”

Section: (A) Life On the Edgesupporting

confidence: 92%

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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Section: (A) Life On the Edgesupporting

confidence: 92%

Genomic signatures of spatially divergent selection at clownfish range margins

et al. 2021

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“…To limit the influence of nonindependent loci, linkage disequilibrium (LD) was tested between all SNP pairs using the package genetics v1.3.8.1.2 (Warnes et al., 2019), and SNPs at strong linkage disequilibrium ( r 2 > 0.8) were removed (Lee et al., 2018; Tian et al., 2009). SNPs with high observed heterozygosity ( H o > 0.6) were also dropped from the dataset (e.g., Ackiss et al., 2018; Hohenlohe et al., 2010; Van Wyngaarden et al., 2017) using pegas v0.11 (Paradis, 2010), to eliminate loci exhibiting extremely high heterozygosity resulting from false SNP calls or assembly errors (Lee et al., 2018). Analyses were performed in R version 3.5.3 (R Core Team, 2019).…”

Section: Methodsmentioning

confidence: 99%

Genetic differentiation and signatures of local adaptation revealed by RADseq for a highly dispersive mud crab Scylla olivacea (Herbst, 1796) in the Sulu Sea

Mendiola

Ravago-Gotanco

2021

Ecology and Evolution

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Connectivity of marine populations is shaped by complex interactions between biological and physical processes across the seascape. The influence of environmental features on the genetic structure of populations has key implications for the dynamics and persistence of populations, and an understanding of spatial scales and patterns of connectivity is crucial for management and conservation. This study employed a seascape genomics approach combining larval dispersal modeling and population genomic analysis using single nucleotide polymorphisms (SNPs) obtained from RADseq to examine environmental factors influencing patterns of genetic structure and connectivity for a highly dispersive mud crab Scylla olivacea (Herbst, 1796) in the Sulu Sea. Dispersal simulations reveal widespread but asymmetric larval dispersal influenced by persistent southward and westward surface circulation features in the Sulu Sea. Despite potential for widespread dispersal across the Sulu Sea, significant genetic differentiation was detected among eight populations based on 1,655 SNPs (FST = 0.0057, p < .001) and a subset of 1,643 putatively neutral SNP markers (FST = 0.0042, p < .001). Oceanography influences genetic structure, with redundancy analysis (RDA) indicating significant contribution of asymmetric ocean currents to neutral genetic variation (Radj2 = 0.133, p = .035). Genetic structure may also reflect demographic factors, with divergent populations characterized by low effective population sizes (Ne < 50). Pronounced latitudinal genetic structure was recovered for loci putatively under selection (FST = 0.2390, p < .001), significantly correlated with sea surface temperature variabilities during peak spawning months for S. olivacea (Radj2 = 0.692–0.763; p < .050), suggesting putative signatures of selection and local adaptation to thermal clines. While oceanography and dispersal ability likely shape patterns of gene flow and genetic structure of S. olivacea across the Sulu Sea, the impacts of genetic drift and natural selection influenced by sea surface temperature also appear as likely drivers of population genetic structure. This study contributes to the growing body of literature documenting population genetic structure and local adaptation for highly dispersive marine species, and provides information useful for spatial management of the fishery resource.

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“…Altogether, this suggests that long distance dispersal in this species requires a strong oceanographic conduit. Using approximately 2,500 SNPs generated from RAD sequencing, Ackiss et al (2018) found evidence of reduced genetic diversity in the peripheral populations of this species in relation to the Kuroshio Current, a powerful western-boundary current in the Pacific Ocean. The authors found that sites closest to the periphery exhibited increased within-population relatedness and decreased effective population size, and potential for local adaptation.…”

Section: Transecting Geographic Rangesmentioning

confidence: 97%

Current and Forthcoming Approaches for Benchmarking Genetic and Genomic Diversity

García

Robinson

2021

Front. Ecol. Evol.

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The current attrition of biodiversity extends beyond loss of species and unique populations to steady loss of a vast genomic diversity that remains largely undescribed. Yet the accelerating development of new techniques allows us to survey entire genomes ever faster and cheaper, to obtain robust samples from a diversity of sources including degraded DNA and residual DNA in the environment, and to address conservation efforts in new and innovative ways. Here we review recent studies that highlight the importance of carefully considering where to prioritize collection of genetic samples (e.g., organisms in rapidly changing landscapes or along edges of geographic ranges) and what samples to collect and archive (e.g., from individuals of little-known subspecies or populations, even of species not currently considered endangered). Those decisions will provide the sample infrastructure to detect the disappearance of certain genotypes or gene complexes, increases in inbreeding levels, and loss of genomic diversity as environmental conditions change. Obtaining samples from currently endangered, protected, and rare species can be particularly difficult, thus we also focus on studies that use new, non-invasive ways of obtaining genomic samples and analyzing them in these cases where other sampling options are highly constrained. Finally, biological collections archiving such samples face an inherent contradiction: their main goal is to preserve biological material in good shape so it can be used for scientific research for centuries to come, yet the technologies that can make use of such materials are advancing faster than collections can change their standardized practices. Thus, we also discuss current and potential new practices in biological collections that might bolster their usefulness for future biodiversity conservation research.

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Genetic patterns in peripheral marine populations of the fusilier fish Caesio cuning within the Kuroshio Current

Cited by 20 publications

References 81 publications

Genomic signatures of spatially divergent selection at clownfish range margins

Genomic signatures of spatially divergent selection at clownfish range margins

Genetic differentiation and signatures of local adaptation revealed by RADseq for a highly dispersive mud crab Scylla olivacea (Herbst, 1796) in the Sulu Sea

Current and Forthcoming Approaches for Benchmarking Genetic and Genomic Diversity

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