Large effective population size masks population genetic structure in Hirondellea amphipods within the deepest marine ecosystem, the Mariana Trench

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(9), P. 2206 - 2218

Published: Feb. 18, 2023

The examination of genetic structure in the deep-ocean hadal zone has focused on divergence between tectonic trenches to understand how environment and geography may drive species promote endemism. There been little attempt examine localized within trenches, partly because logistical challenges associated with sampling at an appropriate scale, large effective population sizes that can be sampled adequately mask underlying structure. Here we superabundant amphipod Hirondellea gigas Mariana Trench depths 8126-10,545 m. RAD sequencing was used identify 3182 loci containing 43,408 single nucleotide polymorphisms (SNPs) across individuals after stringent pruning prevent paralogous multicopy genomic regions being erroneously merged. Principal components analysis SNP genotypes resolved no locations, consistent a signature panmixia. However, discriminant principal identified all sites driven by 301 outlier SNPs 169 significantly latitude depth. Functional annotation differences singleton pruned from data set also nonoutlier loci, hypotheses explaining role transposable elements driving genome dynamics. This study traditional perspective highly abundant amphipods trench form panmictic population. We discuss findings relation eco-evolutionary ontogenetic processes operating deep sea, highlight key nonmodel systems inherent genomes.

Language: Английский

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Neither historical climate nor contemporary range fully explain the extant patterns of molecular diversity in marine species

Journal of Biogeography, Journal Year: 2021, Volume and Issue: 48(10), P. 2629 - 2644

Published: Aug. 10, 2021

Abstract Aim Intraspecific diversity is a significant component of adaptive potential, and thus, it important to identify the evolutionary processes that have will continue shape molecular natural populations. This study aims untangle possible drivers intraspecific by testing whether patterns historical climatic stability or contemporary range position correlate with diversity. Location South African coastline. Taxa The cape urchin ( Parechinus angulosus ), common shore crab Cyclograpsus punctatus ) granular limpet Scutellastra granularis ). Methods Species distributions were hindcasted Last Glacial Maximum assess biogeography species. Linear models built compare relationships between distributional ranges extant genetic (mtDNA) genomic (SNP) Results We found large differences in among species time periods. Regions higher habitat corresponded regions diversity, but variability was not predictor within linear models. Lower values, differentiation, detected edge populations, this consistent across marker type Main conclusions Both are potentially driving portion variation remains unexplained. Our findings suggest marine cool‐temperate bioregions Southern Hemisphere may more complex biogeographic histories than terrestrial taxa and/or coastal northern, formerly glaciated regions.

Language: Английский

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Seascape genetics in a polychaete worm: Disentangling the roles of a biogeographic barrier and environmental factors

Journal of Biogeography, Journal Year: 2022, Volume and Issue: 49(12), P. 2296 - 2308

Published: Oct. 12, 2022

Abstract Aim Seascape genomic studies aim to understand how environmental variables shape species diversity through genotype–environment associations. Identifying these effects on lecithotrophic larval that live in intertidal zones is particularly challenging because they are subject heterogeneity and anthropogenic events. Here, we evaluate biotic abiotic features the Southwest Atlantic littoral zone can affect a high dispersal species' present historical demography. Location Brazilian coast, covering more than 3000 km. Taxon Perinereis ponteni. Methods We investigated population genetic diversity, connectivity past dynamics using 23,300 single‐nucleotide polymorphisms (SNPs) generated genotyping by sequencing. tested whether could explain variance found genotype frequencies isolation‐by‐environment (IBE) landscape association approaches. These data, combined with palaeodistribution simulations oceanic circulation modelling, were used infer demographic history patterns. Results Along levels of detected, boundary southeastern region Brazil around Cabo Frio (Rio de Janeiro), cline trend for some loci. The reveal spatial refuge southeast during Last Glacial Maximum (21 kya), expansion northern region. identified 1421 SNPs associated eight variables, most which related temperature—the main factor determining IBE. Main Conclusions ponteni , polychaete gene flow capability responds biogeographic barriers, highlighting importance factors shaping connectivity. Furthermore, effect temperature indicates future climate change ocean warming hugely impact this species.

Language: Английский

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Predictors of marine genetic structure in the Indo-Australian Archipelago

Regional Studies in Marine Science, Journal Year: 2021, Volume and Issue: 47, P. 101919 - 101919

Published: July 7, 2021

Language: Английский

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Seascape genomics reveals limited dispersal and suggests spatially varying selection among European populations of sea lamprey (Petromyzon marinus)

Evolutionary Applications, Journal Year: 2023, Volume and Issue: 16(6), P. 1169 - 1183

Published: May 27, 2023

Sea lamprey Petromyzon marinus is an anadromous and semelparous fish without homing behaviors. Despite being a freshwater, free-living organism for large part of their life cycle, its adulthood spent as parasite marine vertebrates. In native European range, while it well-established that sea lampreys comprise single nearly-panmictic population, few studies have further explored the evolutionary history natural populations. Here, we performed first genome-wide characterization lamprey's genetic diversity in range. The objectives were to investigate connectivity among river basins explore processes mediating dispersal during phase, with sequencing 186 individuals from 8 locations spanning North Eastern Atlantic coast double-digest RAD-sequencing, obtaining total 30,910 bi-allelic SNPs. Population analyses reinforced existence metapopulation encompassing freshwater spawning sites within Sea, though prevalence private alleles at northern latitudes suggested some limits species' dispersal. Seascape genomics scenario where oxygen concentration runoffs impose spatially varying selection across distribution Exploring associations abundance potential hosts hake cod could also selective pressures, although nature such putative biotic interactions was unresolved. Overall, identification adaptive seascapes panmictic species contribute conservation practices by providing information restoration activities mitigate local extinctions on sites.

Language: Английский

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Management and conservation implications of cryptic population substructure for two commercially exploited fishes (Merluccius spp.) in southern Africa

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: unknown

Published: June 8, 2023

Genomic information can aid in the establishment of sustainable management plans for commercially exploited marine fishes, aiding long-term conservation these resources. The southern African hakes (Merluccius capensis and M. paradoxus) are valuable demersal fishes with similar distribution ranges but exhibiting contrasting life histories. Using a comparative framework based on Pool-Seq genome-wide SNP data, we investigated whether evolutionary processes that shaped extant patterns diversity divergence shared among two congeneric or unique to each one. Our findings revealed paradoxus show levels diversity, despite different census sizes life-history features. In addition, shows three highly structured geographic populations across Benguela Current region (one northern Benguela), no consistent genome-environment associations detected. contrast, although population structure outlier analyses suggested panmixia paradoxus, reconstruction its demographic history presence an Atlantic-Indian Ocean subtle substructuring pattern. Therefore, it appears might be composed by connected populations, one Atlantic southwest Indian Ocean. reported low genomic as well newly discovered genetically distinct both hake species thus assist informing improving important Merluccius.

Language: Английский

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Eelgrass Zostera capensis populations in KwaZulu-Natal, South Africa, harbour distinct genomic signals despite limited geographical distance

African Journal of Marine Science, Journal Year: 2023, Volume and Issue: 45(4), P. 259 - 264

Published: Oct. 2, 2023

Seagrasses are threatened by anthropogenic stressors and climate change, with numerous population declines reported. In South Africa, the eelgrass Zostera capensis is restricted to estuarine environments has a disjunct distribution declining status. With majority of Z. on west southwest coasts isolated easternmost populations in KwaZulu-Natal Province (KZN) particular interest. Following extirpation at Durban St Lucia, only five remain, which three (in Amatikulu, Mlalazi Mhlatuze estuaries) situated <50 km apart. Previous molecular analyses showed strong structure between populations, but geographically close east coast were not included. this study, using single nucleotide polymorphisms (SNPs) from 31 individual sampled plants collected northern KZN estuaries, we provide evidence for distinct clusters, unique evolutionary signals. Estuary low level genomic diversity, likely as result small, dynamic unable withstand prolonged freshwater exposure. Our results suggest that conservation efforts need consider signals even among within context restoration, where compatibility may determine persistence restored populations.

Language: Английский

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Regional population and seascape genomics of the smooth hammerhead shark Sphyrna zygaena reveals adaptive clinal variation despite high gene flow

Authorea (Authorea), Journal Year: 2024, Volume and Issue: unknown

Published: June 3, 2024

Globally, hammerhead sharks have experienced severe declines owing to continued overexploitation and anthropogenic change. The smooth shark Sphyrna zygaena remains comparatively understudied compared other members of the family Sphyrnidae, despite its Vulnerable status, a comprehensive understanding genetic landscape lacking. present study aimed conduct fine-scale genomic assessment within highly dynamic marine environment South Africa’s coastline, using thousands single nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing (3RAD). A combination differentiation-based outlier detection methods (OUTFlank pcadapt) Genotype-Environment Association (GEA) (Redundancy Analysis) analysis in were employed. Subsequent assessments putatively adaptive loci revealed distinctive south east cline. Amongst these, notable correlations between variation sea-surface dissolved oxygen salinity, addition spatial factors evident. Conversely, 110, 965 neutral SNP markers lack regional population differentiation, finding that remained consistent across various analytical approaches, including an isolation-by-distance (IBD) isolation-by-environment (IBE), clustering analyses (LEA, fastSTRUCTURE, find.clusters), discriminant principal components (DAPC). These results provide evidence for presence differential selection pressures limited range, high gene flow implied by selectively dataset. This offers insights regarding potential impacts response fluctuating environmental conditions circumglobally distributed zygaena.

Language: Английский

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Genetic diversity and connectivity of the Irrawaddy dolphin in Southern Thailand: Emphasizing the last fourteen of the Songkhla dolphin status from a microsatellite perspective

Biodiversitas Journal of Biological Diversity, Journal Year: 2024, Volume and Issue: 25(4)

Published: May 4, 2024

Abstract. Budi T, Ninwat S, Sakornwimon W, Thongcham K, Phakphien R, Kalaya C, Phavaphutanon J. 2024. Genetic diversity and connectivity of the Irrawaddy dolphin in Southern Thailand: Emphasizing last fourteen Songkhla status from a microsatellite perspective. Biodiversitas 25: 1729-1735. (Orcaella brevirostris Gray, 1866) can be found diverse aquatic environments, ranging coastal to brackish water, stretching West Bengal India central part Indonesian archipelago. Despite its widespread distribution flexible habitat tolerance, dolphins Lake, Thailand, are hypothesized isolated exhibit concerningly low population numbers, threatening their long-term survival. Limited knowledge exists regarding genetics status. This study analyzed 30 samples Lake (SKL) Lower Gulf Thailand (LGT) assess genetic diversity, structure, using 16 loci. Extremely was observed SKL (Ho = 0.039±0.039; AR 1.122±0.489) LGT 0.033±0.033; 1.141±0.566) populations. Population differentiation (FST 0.033, p>0.05) clustering analyses based on both Principal Coordinate Analysis (PCoA) Discriminant Component (DAPC) suggest limited divergence potential panmixia (single pool) between These findings highlight critical conservation concerns due despite lack isolation, emphasizing need for immediate targeted efforts ensure viability this iconic yet vulnerable population.

Language: Английский

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Trait Variation and Spatiotemporal Dynamics across Avian Secondary Contact Zones

Biology, Journal Year: 2024, Volume and Issue: 13(8), P. 643 - 643

Published: Aug. 22, 2024

A secondary contact zone (SCZ) is an area where incipient species or divergent populations may meet, mate, and hybridize. Due to the diverse patterns of interspecific hybridization, SCZs function as field labs for illuminating on-going evolutionary processes speciation establishment reproductive isolation. Interspecific hybridization widely present in avian populations, making them ideal system SCZ studies. This review exhaustively summarizes variations unique traits within (vocalization, plumage, beak, migratory traits) various movement observed previous publications. It also highlights several potential future research directions genomic era, such relationship between phenotypic differentiation SCZs, basis trait differentiation, shared by multiple species, accurate predictive models forecasting movements under climate change human disturbances. aims provide a more comprehensive understanding offers theoretical foundation conservation.

Language: Английский

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