Genomic atolls of differentiation in coral reef fishes (<i><scp>H</scp>ypoplectrus</i>spp.,<i>Serranidae</i>)

Puebla, Oscar; Bermingham, Eldredge; McMillan, W. Owen

doi:10.1111/mec.12926

Cited by 52 publications

(102 citation statements)

References 55 publications

(106 reference statements)

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“…Recent studies by Puebla et al . () and Keller et al . () obtained the best phylogenetic signal among recently diverged fish taxa when using only the top 10% and 25% of the global F ST distribution, respectively.…”

Section: Discussionmentioning

confidence: 88%

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Rapid postglacial diversification and long‐term stasis within the songbird genus Junco: phylogeographic and phylogenomic evidence

et al. 2016

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Natural systems composed of closely related taxa that vary in the degree of phenotypic divergence and geographic isolation provide an opportunity to investigate the rate of phenotypic diversification and the relative roles of selection and drift in driving lineage formation. The genus Junco (Aves: Emberizidae) of North America includes parapatric northern forms that are markedly divergent in plumage pattern and colour, in contrast to geographically isolated southern populations in remote areas that show moderate phenotypic divergence. Here, we quantify patterns of phenotypic divergence in morphology and plumage colour and use mitochondrial DNA genes, a nuclear intron, and genomewide SNPs to reconstruct the demographic and evolutionary history of the genus to infer relative rates of evolutionary divergence among lineages. We found that geographically isolated populations have evolved independently for hundreds of thousands of years despite little differentiation in phenotype, in sharp contrast to phenotypically diverse northern forms, which have diversified within the last few thousand years as a result of the rapid postglacial recolonization of North America. SNP data resolved young northern lineages into reciprocally monophyletic lineages, indicating low rates of gene flow even among closely related parapatric forms, and suggesting a role for strong genetic drift or multifarious selection acting on multiple loci in driving lineage divergence. Juncos represent a compelling example of speciation in action, where the combined effects of historical and selective factors have produced one of the fastest cases of speciation known in vertebrates.

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Section: Discussionmentioning

confidence: 88%

“…; Puebla et al . ). We tested the phylogenetic resolution of neutral SNPs using three different F ST intervals: (i) 100% of the SNP data set, (ii) top 25% F ST SNPs and (iii) top 10% F ST SNPs (Table ).…”

Section: Methodsmentioning

confidence: 97%

Rapid postglacial diversification and long‐term stasis within the songbird genus Junco: phylogeographic and phylogenomic evidence

et al. 2016

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“…These results add to the growing literature that highlights the use of RAD sequencing in delimiting closely related species and identifying cryptic species (Puebla et al . ; Gaither et al . ; Pante et al .…”

Section: Discussionmentioning

confidence: 99%

Seascape genetics along environmental gradients in the Arabian Peninsula: insights from ddRAD sequencing of anemonefishes

et al. 2015

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Understanding the processes that shape patterns of genetic structure across space is a central aim of landscape genetics. However, it remains unclear how geographical features and environmental variables shape gene flow, particularly for marine species in large complex seascapes. Here, we evaluated the genomic composition of the two-band anemonefish Amphiprion bicinctus across its entire geographical range in the Red Sea and Gulf of Aden, as well as its close relative, Amphiprion omanensis endemic to the southern coast of Oman. Both the Red Sea and the Arabian Sea are complex and environmentally heterogeneous marine systems that provide an ideal scenario to address these questions. Our findings confirm the presence of two genetic clusters previously reported for A. bicinctus in the Red Sea. Genetic structure analyses suggest a complex seascape configuration, with evidence of both isolation by distance (IBD) and isolation by environment (IBE). In addition to IBD and IBE, genetic structure among sites was best explained when two barriers to gene flow were also accounted for. One of these coincides with a strong oligotrophic-eutrophic gradient at around 16-20˚N in the Red Sea. The other agrees with a historical bathymetric barrier at the straight of Bab al Mandab. Finally, these data support the presence of interspecific hybrids at an intermediate suture zone at Socotra and indicate complex patterns of genomic admixture in the Gulf of Aden with evidence of introgression between species. Our findings highlight the power of recent genomic approaches to resolve subtle patterns of gene flow in marine seascapes.

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“…Next-generation technologies like RAD sequencing provide a promising and cost-effective solution to this obstacle by uncovering restriction site associated SNPs across the entire genome without the need for completely sequencing it (Davey et al 2011;Wang et al 2012;Reitzel et al 2013). Future studies could exploit this method to reveal genomic differentiation, unambiguously assigning natal origins of recruiting larvae, and identifying genes involved in speciation (e.g., Puebla et al 2014), thereby helping to understand the molecular mechanisms that underlie biodiversity dynamics at hydrothermal vents and improving attempts to mitigate impacts of deep-sea mining in these unique ecosystems.…”

Section: Discussionmentioning

confidence: 99%

Population structure and connectivity in Indo-Pacific deep-sea mussels of the Bathymodiolus septemdierum complex

et al. 2015

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Current pressures to mine polymetallic sulfide deposits pose threats to the animal communities found at deep-sea hydrothermal vents. Management plans aimed at preserving these unusual communities require knowledge of historical and contemporary forces that shaped the distributions and connectivity of associated species. As most vent research has focused on the eastern Pacific and mid-Atlantic ridge systems less is known about Indo-Pacific vents, where mineral extraction activities are imminent. Deep-sea mussels (Bivalvia: Mytilidae) of the genus Bathymodiolus include the morphotypic species B. septemdierum, B. brevior, B. marisindicus, and B. elongatus which are among the dominant vent taxa in western Pacific back-arc basins and the Central Indian Ridge. To assess their interpopulational relationships, we examined multilocus genotypes based on DNA sequences from four nuclear and four mitochondrial genes, and allozyme variation encoded by eleven genes. Bayesian assignment methods grouped mussels from seven widespread western Pacific localities into a single cluster, whereas the Indian Ocean mussels were clearly divergent. Thus, we designate two regional metapopulations. Notably, contemporary migration rates among all sites appeared to be low despite limited population differentiation, which highlights the necessity of obtaining realistic data on recovery times and fine-scale population structure to develop and manage conservation units effectively. Future studies using population genomic methods to address these issues in a range of species will help to inform management plans aimed at mitigating potential impacts of deep-sea mining in the Indo-Pacific region.

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Genomic atolls of differentiation in coral reef fishes (Hypoplectrusspp.,Serranidae)

Cited by 52 publications

References 55 publications

Rapid postglacial diversification and long‐term stasis within the songbird genus Junco: phylogeographic and phylogenomic evidence

Rapid postglacial diversification and long‐term stasis within the songbird genus Junco: phylogeographic and phylogenomic evidence

Seascape genetics along environmental gradients in the Arabian Peninsula: insights from ddRAD sequencing of anemonefishes

Population structure and connectivity in Indo-Pacific deep-sea mussels of the Bathymodiolus septemdierum complex

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