Phylogeography of two marine predators, giant trevally (Caranx ignobilis) and bluefin trevally (Caranx melampygus), across the Indo-Pacific

For economically valuable marine fishes, identifying biogeographic barriers and estimating the extent of gene flow are critical components of fisheries management. We examined the population genetic structure of two commercially important reef-associated predators, the giant trevally ( Caranx ignobilis) and bluefin trevally (Caranx melampygus). We sampled 225 individuals and 32,798 single nucleotide polymorphisms (SNPs) of C. ignobilis, and 74 individuals and 43,299 SNPs of C. melampygus. Analyses of geographic population structure indicate the two species display subtly different phylogeographic patterns. Caranx ignobilis comprises two to three putative populations—one in the Central Pacific, one inhabiting the Western Pacific and Eastern Indian oceans, and one in the Western Indian Ocean—with some restricted gene flow between them. Caranx melampygus shows evidence of restricted gene flow from Hawaii to the West Pacific and Indian oceans, as well as limited genetic connectivity across the Indo- Pacific Barrier. Both species exhibit patterns characteristic of other large, reef-associated predators such as deepwater snappers and the great barracuda. This study contributes to ongoing assessments of the role of the Indo-Pacific Barrier in shaping patterns of phylogeography for large reef-associated fishes. Furthermore, by identifying putative populations of C. ignobilis and C. melampygus in the Central Pacific, our findings serve to improve future management measures for these economically important, data-limited species, particularly in light of historic and contemporary overfishing in Hawaii.

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By Animal, Water, or Wind: Can Dispersal Mode Predict Genetic Connectivity in Riverine Plant Species?

Frontiers in Plant Science ◽

10.3389/fpls.2021.626405 ◽

2021 ◽

Vol 12 ◽

Author(s):

Alison G. Nazareno ◽

L. Lacey Knowles ◽

Christopher W. Dick ◽

Lúcia G. Lohmann

Keyword(s):

Gene Flow ◽

Seed Dispersal ◽

Plant Species ◽

Amazon Basin ◽

Geographic Distance ◽

Genetic Connectivity ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Deforestation Rates ◽

History Of

Seed dispersal is crucial to gene flow among plant populations. Although the effects of geographic distance and barriers to gene flow are well studied in many systems, it is unclear how seed dispersal mediates gene flow in conjunction with interacting effects of geographic distance and barriers. To test whether distinct seed dispersal modes (i.e., hydrochory, anemochory, and zoochory) have a consistent effect on the level of genetic connectivity (i.e., gene flow) among populations of riverine plant species, we used unlinked single-nucleotide polymorphisms (SNPs) for eight co-distributed plant species sampled across the Rio Branco, a putative biogeographic barrier in the Amazon basin. We found that animal-dispersed plant species exhibited higher levels of genetic diversity and lack of inbreeding as a result of the stronger genetic connectivity than plant species whose seeds are dispersed by water or wind. Interestingly, our results also indicated that the Rio Branco facilitates gene dispersal for all plant species analyzed, irrespective of their mode of dispersal. Even at a small spatial scale, our findings suggest that ecology rather than geography play a key role in shaping the evolutionary history of plants in the Amazon basin. These results may help improve conservation and management policies in Amazonian riparian forests, where degradation and deforestation rates are high.

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Genome Assembly of the Roundjaw Bonefish (Albula glossodonta), a Vulnerable Circumtropical Sportfish

10.1101/2021.09.10.458299 ◽

2021 ◽

Author(s):

Brandon D. Pickett ◽

Sheena Talma ◽

Jessica R. Glass ◽

Daniel Ence ◽

Paul D. Cowley ◽

...

Keyword(s):

Population Structure ◽

Gene Flow ◽

Indian Ocean ◽

Genome Assembly ◽

Anthropogenic Activities ◽

Western Indian Ocean ◽

Genetic Connectivity ◽

High Quality ◽

Widespread Species ◽

High Quality Genome

ABSTRACTBackgroundBonefishes are cryptic species indiscriminately targeted by subsistence and recreational fisheries worldwide. The roundjaw bonefish, Albula glossodonta is the most widespread bonefish species in the Indo-Pacific and is listed as vulnerable to extinction by the IUCN’s Red List due to anthropogenic activities. Whole-genome datasets allow for improved population and species delimitation, which – prior to this study – were lacking for Albula species.ResultsWe generated a high-quality genome assembly of an A. glossodonta individual from Hawai‘i, USA. The assembled contigs had an NG50 of 4.75 Mbp and a maximum length of 28.2 Mbp. Scaffolding yielded an NG50 of 14.49 Mbp, with the longest scaffold reaching 42.29 Mbp. Half the genome was contained in 20 scaffolds. The genome was annotated with 28.3 K protein-coding genes. We then analyzed 66 A. glossodonta individuals and 38,355 SNP loci to evaluate population genetic connectivity between six atolls in Seychelles and Mauritius in the Western Indian Ocean. We observed genetic homogeneity between atolls in Seychelles and evidence of reduced gene flow between Seychelles and Mauritius. The South Equatorial Current could be one mechanism limiting gene flow of A. glossodonta populations between Seychelles and Mauritius.ConclusionsQuantifying the spatial population structure of widespread fishery species such as bonefishes is necessary for effective transboundary management and conservation. This population genomic dataset mapped to a high-quality genome assembly allowed us to discern shallow population structure in a widespread species in the Western Indian Ocean. The genome assembly will be useful for addressing the taxonomic uncertainties of bonefishes globally.

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Increased individual homozygosity is correlated with low fitness in a fragmented lizard population

Biological Journal of the Linnean Society ◽

10.1093/biolinnean/blz144 ◽

2019 ◽

Vol 128 (4) ◽

pp. 952-962 ◽

Cited By ~ 1

Author(s):

Javier Pérez-Tris ◽

Alejandro Llanos-Garrido ◽

Paul Bloor ◽

Roberto Carbonell ◽

José Luis Tellería ◽

...

Keyword(s):

Gene Flow ◽

Restricted Gene Flow ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genome Wide ◽

Anthropogenic Habitat ◽

Geographical Scale ◽

Psammodromus Algirus ◽

Fragmented Population ◽

The Impact

Abstract Isolation owing to anthropogenic habitat fragmentation is expected to increase the homozygosity of individuals, which might reduce their fitness as a result of inbreeding depression. Using samples from a fragmented population of the lizard Psammodromus algirus, for which we had data about two correlates of fitness, we genotyped individuals for six microsatellite loci that correctly capture genome-wide individual homozygosity of these lizards (as validated with an independent sample of lizards genotyped for both these microsatellites and > 70 000 single nucleotide polymorphisms). Our data revealed genetic structure at a very small geographical scale, which was compatible with restricted gene flow among populations disconnected in a matrix of inhospitable habitat. Lizards from the same fragment were genetically more related to one another than expected by chance, and individual homozygosity was greater in small than in large fragments. Within fragments, individual homozygosity was negatively associated with adult body size and clutch mass, revealing a link among reduced gene flow, increased homozygosity and lowered fitness that might reduce population viability deterministically. Our results contribute to mounting evidence of the impact of the loss of genetic diversity on fragmented wild populations.

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RADseq analyses reveal concordant Indian Ocean biogeographic and phylogeographic boundaries in the reef fish Dascyllus trimaculatus

Royal Society Open Science ◽

10.1098/rsos.172413 ◽

2019 ◽

Vol 6 (5) ◽

pp. 172413 ◽

Cited By ~ 2

Author(s):

E. M. Salas ◽

G. Bernardi ◽

M. L. Berumen ◽

M. R. Gaither ◽

L. A. Rocha

Keyword(s):

Indian Ocean ◽

Red Sea ◽

Arabian Sea ◽

Population Level ◽

Western Indian Ocean ◽

Genetic Connectivity ◽

Nucleotide Polymorphisms ◽

Population Genetic Analysis ◽

Outlier Loci ◽

Biogeographic Provinces

Population genetic analysis is an important tool for estimating the degree of evolutionary connectivity in marine organisms. Here, we investigate the population structure of the three-spot damselfish Dascyllus trimaculatus in the Red Sea, Arabian Sea and Western Indian Ocean, using 1174 single nucleotide polymorphisms (SNPs). Neutral loci revealed a signature of weak genetic differentiation between the Northwestern (Red Sea and Arabian Sea) and Western Indian Ocean biogeographic provinces. Loci potentially under selection (outlier loci) revealed a similar pattern but with a much stronger signal of genetic structure between regions. The Oman population appears to be genetically distinct from all other populations included in the analysis. While we could not clearly identify the mechanisms driving these patterns (isolation, adaptation or both), the datasets indicate that population-level divergences are largely concordant with biogeographic boundaries based on species composition. Our data can be used along with genetic connectivity of other species to identify the common genetic breaks that need to be considered for the conservation of biodiversity and evolutionary processes in the poorly studied Western Indian Ocean region.

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Restricted gene flow among western Indian Ocean populations of the mangrove whelk Terebralia palustris (Linnaeus, 1767) (Caenogastropoda: Potamididae)

Journal of Molluscan Studies ◽

10.1093/mollus/eyy001 ◽

2018 ◽

Vol 84 (2) ◽

pp. 163-169 ◽

Cited By ~ 1

Author(s):

Hajaniaina Andrianavalonarivo Ratsimbazafy ◽

Marc Kochzius

Keyword(s):

Gene Flow ◽

Indian Ocean ◽

Western Indian Ocean ◽

Restricted Gene Flow

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Highly restricted dispersal in habitat-forming seaweed may impede natural recovery of disturbed populations

Scientific Reports ◽

10.1038/s41598-021-96027-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Florentine Riquet ◽

Christiane-Arnilda De Kuyper ◽

Cécile Fauvelot ◽

Laura Airoldi ◽

Serge Planes ◽

...

Keyword(s):

Genetic Structure ◽

Spatial Scales ◽

Mediterranean Ecosystems ◽

Dispersal Distance ◽

Genetic Connectivity ◽

Restricted Gene Flow ◽

Isolated Populations ◽

Natural Recovery ◽

Limited Dispersal ◽

Ecological Importance

AbstractCystoseira sensu lato (Class Phaeophyceae, Order Fucales, Family Sargassaceae) forests play a central role in marine Mediterranean ecosystems. Over the last decades, Cystoseira s.l. suffered from a severe loss as a result of multiple anthropogenic stressors. In particular, Gongolaria barbata has faced multiple human-induced threats, and, despite its ecological importance in structuring rocky communities and hosting a large number of species, the natural recovery of G. barbata depleted populations is uncertain. Here, we used nine microsatellite loci specifically developed for G. barbata to assess the genetic diversity of this species and its genetic connectivity among fifteen sites located in the Ionian, the Adriatic and the Black Seas. In line with strong and significant heterozygosity deficiencies across loci, likely explained by Wahlund effect, high genetic structure was observed among the three seas (ENA corrected FST = 0.355, IC = [0.283, 0.440]), with an estimated dispersal distance per generation smaller than 600 m, both in the Adriatic and Black Sea. This strong genetic structure likely results from restricted gene flow driven by geographic distances and limited dispersal abilities, along with genetic drift within isolated populations. The presence of genetically disconnected populations at small spatial scales (< 10 km) has important implications for the identification of relevant conservation and management measures for G. barbata: each population should be considered as separated evolutionary units with dedicated conservation efforts.

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