Genomic Footprints of Hybridisation in North Atlantic Eels (Anguilla anguilla and A. rostrata)

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 29, 2025

ABSTRACT Understanding interspecific introgressive hybridisation and the biological significance of introgressed variation remains an important goal in population genomics. European ( Anguilla anguilla ) American eel A. rostrata represent a remarkable case hybridisation. Both are panmictic spawn partial sympatry Sargasso Sea, occasionally producing viable, fertile hybrids, primarily found Iceland. We studied from into using whole‐genome sequences 78 individuals, including European, 21 putative hybrid eels. Previous studies few genetic markers could not resolve whether involved simple unidirectional backcrossing or more complex swarm scenario. However, local ancestry inference along individual chromosomes revealed that Icelandic hybrids were F1 first‐generation backcrosses towards eel, with some showing backcrossing. All eels outside Iceland contained short chromosomal blocks indicating porous genome. no evidence for previously hypothesised geographical gradients introgression Several regions showed high divergence, but haplotype identified both within these regions. There was little correspondence between relative F ST absolute divergence d XY ), former reflecting selective sweeps species reduced recombination rather than barrier loci. A single genomic region repeated under positive selection species. The study illustrates can maintain integrity despite genomes standing one potentially be available future adaptive responses other

Language: Английский

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Panmixia in the American eel extends to its tropical range of distribution: Biological implications and policymaking challenges

Evolutionary Applications, Journal Year: 2023, Volume and Issue: 16(12), P. 1872 - 1888

Published: Nov. 17, 2023

Abstract The American eel ( Anguilla rostrata ) has long been regarded as a panmictic fish and confirmed such in the northern part of its range. In this paper, we tested for first time whether panmixia extends to tropical range species. To do so, assembled reference genome (975 Mbp, 19 chromosomes) combining (PacBio Nanopore short (Illumina paired‐end) reads technologies support both study future research. test population structure, estimated genotype likelihoods from low‐coverage whole‐genome sequencing 460 eels, collected at 21 sampling sites (in seven geographic regions) ranging Canada Trinidad Tobago. We genetic distance between regions, performed ADMIXTURE‐like clustering analysis multivariate analysis, found no evidence thus confirming that addition, two genomic regions with putative inversions were observed, geographically widespread present similar frequencies all regions. discuss implications lack structure Our results are key research implementation conservation measures throughout Additionally, our can be applied fisheries management aquaculture

Language: Английский

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Putting Structural Variants Into Practice: The Role of Chromosomal Inversions in the Management of Marine Environments

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: May 8, 2025

ABSTRACT Major threats to marine species and ecosystems include overfishing, invasive species, pollution climate change. The changing not only imposes direct through the impacts of severe heatwaves, cyclones ocean acidification but also complicates fisheries management by driving range shifts. dynamic nature these means that future our oceans will depend on ability adapt. This has led calls for genetic interventions focussed enhancing species' adaptive capacity, including translocations, restocking selective breeding. Assessing benefits risks such approaches requires an improved understanding architecture variation, in relation climate‐resilient phenotypes locally adapted populations fitness hybrids. Large structural variants as chromosomal inversions play important role local adaptation linking multiple loci. Consequently, are likely be particularly when managing capacity. However, under some circumstances, they accumulate deleterious mutations, potentially increasing risk inbreeding depression. Genetic takes account dual roles is more effective at ensuring population persistence. We summarise evolutionary factors influencing variation inversions, review found taxa, provide a framework predict consequences ignoring key scenarios. conclude describing practical methods bridge gap between theory application conservation.

Language: Английский

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Widespread Deviant Patterns of Heterozygosity in Whole-Genome Sequencing Due to Autopolyploidy, Repeated Elements, and Duplication

Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 15(12)

Published: Dec. 1, 2023

Abstract Most population genomic tools rely on accurate single nucleotide polymorphism (SNP) calling and filtering to meet their underlying assumptions. However, complexity, resulting from structural variants, paralogous sequences, repetitive elements, presents significant challenges in assembling contiguous reference genomes. Consequently, short-read resequencing studies can encounter mismapping issues, leading SNPs that deviate Mendelian expected patterns of heterozygosity allelic ratio. In this study, we employed the ngsParalog software identify such deviant whole-genome sequencing (WGS) data with low (1.5×) intermediate (4.8×) coverage for four species: Arctic Char (Salvelinus alpinus), Lake Whitefish (Coregonus clupeaformis), Atlantic Salmon (Salmo salar), American Eel (Anguilla rostrata). The analyses revealed accounted 22% 62% all salmonid datasets approximately 11% dataset. These were particularly concentrated within elements regions had recently undergone rediploidization salmonids. Additionally, narrow peaks elevated ubiquitous along genomes, encompassed most SNPs, could be partially associated transposons tandem repeats. Including these led highly distorted site frequency spectra, underestimated pairwise FST values, overestimated diversity. Considering widespread occurrence arising a variety sources, important impact estimating parameters, availability effective them, propose excluding WGS is required improve inferences wide range taxa depths.

Language: Английский

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Whole genome resequencing of sablefish at the northern end of their range reveals genetic panmixia and large putative inversions

ICES Journal of Marine Science, Journal Year: 2024, Volume and Issue: 81(6), P. 1096 - 1110

Published: June 5, 2024

Abstract Sablefish (Anoplopoma fimbria) are a highly mobile species that support important commercial fisheries in the North Pacific Ocean. Information on genetic stock structure of sablefish is vital for constructing management strategies ensure long-term viability species. Most previous studies have found panmixia throughout majority their range, but recent study suggested population may exist. Here, we use low-coverage whole genome resequencing to investigate northern end species’ range (from Washington State, USA Bering Sea and Aleutian Islands, AK, USA). Additionally, reanalyzed an existing genomic dataset containing 2661 markers test specific hypotheses about by sex. Genome data from 119 individuals screened at 7 110 228 revealed no evidence structure, reanalysis supported same conclusion. Differentiation across was largely driven variation two putative inversions located ∼1 megabase apart, which did not display any signals geographic differentiation. Our further supports conclusion its range.

Language: Английский

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Demographic History and Inbreeding in Two Declining Sea Duck Species Inferred From Whole‐Genome Sequence Data

Evolutionary Applications, Journal Year: 2024, Volume and Issue: 17(9)

Published: Sept. 1, 2024

ABSTRACT Anthropogenic impact has transitioned from threatening already rare species to causing significant declines in once numerous organisms. Long‐tailed duck ( Clangula hyemalis ) and velvet scoter Melanitta fusca were important quarry sea NW Europe, but recent resulted their reclassification as vulnerable on the IUCN Red List. We sequenced assembled genomes for both resequenced 15 individuals of each. Using analyses based site frequency spectra sequential Markovian coalescence, we found C . show more historical demographic stability, whereas M. was affected particularly by Last (Weichselian) Glaciation. This likely reflects breeding continuously across Arctic, with cycles glaciation primarily shifting areas south or north without major population declines, restricted southern range would lead contraction during glaciations. Both showed evidence over past thousands years, potentially reflecting anthropogenic pressures decline indicating an accelerated process. Analysis runs homozygosity (ROH) low nontrivial inbreeding, F ROH 0.012 0.063 ranging 0 0.047 Lengths suggested that this due ongoing background inbreeding rather than declines. Overall, despite demographically not yet led strong genetic erosion, most pressing conservation concern may be risk density‐dependent (Allee) effects. recommend monitoring using analysis a cost‐efficient method track future developments support effective these species.

Language: Английский

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loco-pipe: an automated pipeline for population genomics with low-coverage whole-genome sequencing

Bioinformatics Advances, Journal Year: 2024, Volume and Issue: 4(1)

Published: Jan. 1, 2024

Abstract Summary We developed loco-pipe, a Snakemake pipeline that seamlessly streamlines set of essential population genomic analyses for low-coverage whole genome sequencing (lcWGS) data. loco-pipe is highly automated, easily customizable, massively parallelized, and thus valuable tool both new experienced users lcWGS. Availability implementation published under the GPLv3. It freely available on GitHub (github.com/sudmantlab/loco-pipe) archived Zenodo (doi.org/10.5281/zenodo.10425920).

Language: Английский

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Characterizing Sex Ratios of American Eels (

PubMed, Journal Year: 2024, Volume and Issue: 2024

Published: Jan. 1, 2024

The American eel (

Language: Английский

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Age and growth of American Eel in lower St. Johns River in northeast Florida

North American Journal of Fisheries Management, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 8, 2024

Abstract Objective Little is known about American Eel Anguilla rostrata populations across much of the species' large geographic range. This study aimed to collect important information on life history and population biology in a northeast Florida river. Methods During two 12‐week periods, from August November 2021 September December 2022, were collected ~90‐km stretch lower St. Johns River via boat electrofishing. Data length, weight, age, Anguillicoloides crassus parasite infection, swim bladder condition recorded for both years, additional data sex, sexual maturity, fin eye morphology 2022. Result Overall, biologists spent more than 63.5 h effort over 42 sampling days 297 Eel, ranging size 150 705 mm total length (TL) with continental age 0 8 years. catches low varied by section river time; however, no differences length–weight relationship or structure observed between sections. Adult parasites bladders 36% 57% eel exhibited some level damage. Although relationships similar regardless condition, relative was fish severe Histological examination gonads 160 2022 revealed that male : female sex ratio 0.9:1 nearly all sexually immature. The majority 2–4 years age; average growth modeled von Bertalanffy curve aged 1–8: TL = 740 × [1 – e −0.12(age + 1.98) ]. Conclusion Given paucity this region, provided will be critical informing future decisions management stock.

Language: Английский

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Bridging species boundaries: eDNA and genetic analysis reveal hybrid settlement at the very end of American eel distribution

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 9, 2024

Abstract Documenting species distributions and hybridization patterns is paramount for elucidating biogeography understanding speciation processes. Here we combined genetic specimen analysis environmental DNA (eDNA) to investigate the presence of American eel ( Anguilla rotrata ) × European anguilla hybrids in Greenland freshwater. We further tested use eDNA document by using mtDNA as a proxy hybrid occurrence. Overall, detected mainly but also mtDNA. This finding was validated sequencing, which identified 3 out 26 captured eels (14.3%) carrying Five (19.2%), including all three with mtDNA, were heterozygous species-specific nuclear gene variants, supporting ancestry. Further, successfully lakes where they caught fyke net fishing, extending their confirmed northern range 40 km, indicated >200km north. The study provides an empirical demonstration occurrence extends reported distribution significantly beyond previous observations. existence may be key complex mechanisms between eels.

Language: Английский

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