Planning and implementing genetic rescue of an endangered freshwater fish population in a regulated river, where low flow reduces breeding opportunities and may trigger inbreeding depression

Evolutionary Applications, Journal Year: 2024, Volume and Issue: 17(4)

Published: April 1, 2024

Abstract Augmenting depleted genetic diversity can improve the fitness and evolutionary potential of wildlife populations, but developing effective management approaches requires genetically monitored test cases. One such case is small, isolated inbred Cotter River population an endangered Australian freshwater fish, Macquarie perch Macquaria australasica , which over 3 years (2017–2019) received 71 translocated migrants from a closely related, more diverse population. We used monitoring to whether immigrants bred, interbred with local fish augmented diversity. also investigated levels river flow affected recruitment, inbreeding depression juvenile dispersal. Fish length was estimate age, birth year cohort growth 524 individuals born between 2016 2020 under variable conditions. DArT genome‐wide genotypes were assess individual ancestry, heterozygosity, short‐term size identify parent‐offspring full‐sibling families. Of 442 after translocations commenced, only two (0.45%) mixed ancestry; these half‐sibs one parent in common. Numbers breeders for five cohorts low, especially low‐flow years. Additionally, lowest evidently suffered growth. The highest associated largest number breeders, offspring greatest dispersal distances. Genetic decreased upstream direction, flagging restricted access most breeding sites, exacerbated by low flow. Our results suggest that effectiveness could be increased focussing on sites moving per year; using riverine sources should considered. indicate sufficient facilitate movement through system would increase promote individuals' growth, reduce rescue.

Language: Английский

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Genomic repercussions of landscape modification on three lizard species

Conservation Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: March 14, 2025

Language: Английский

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Accurate Bayesian inference of sex chromosome karyotypes and sex‐linked scaffolds from low‐depth sequencing data

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(3)

Published: Jan. 3, 2024

Abstract The identification of sex‐linked scaffolds and the genetic sex individuals, i.e. their karyotype, is a fundamental step in population genomic studies. If are known, single individuals may be sexed based on read counts next‐generation sequencing data. both as well karyotypes unknown, often case for non‐model organisms, they have to jointly inferred. For cases, current methods rely arbitrary thresholds, which limits power low‐depth In addition, most limited euploid (XX XY). Here we develop BeXY , fully Bayesian method infer posterior probabilities each scaffold autosomal, X‐ or Y‐linked individual any XX, XY, X0, XXX, XXY, XYY XXYY. it also identifies autosomal trisomies estimates karyotype individuals. As show with downsampling experiments, has higher than all existing methods. It accurately infers ancient human samples few 20,000 reads from data sets just handful highly imbalanced ratios, low‐quality reference assemblies. We illustrate by applying whole‐genome shotgun target enrichment modern humans, several organisms.

Language: Английский

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dartR.sexlinked: Analysing SNP Data to Identify Sex-Linked Markers

Published: June 24, 2024

Description Identifies, filters and exports sex linked markers using 'SNP'(single nucleotide polymorphism) data.To install the other packages, we recommend to 'dartRverse' package, that supports installation of all packages in 'dartRverse'.If you want understand applied rational identify sexlinked and/or cite 'dartR.sexlinked',you find information by typing citation('dartR.sexlinked') console.

Language: Английский

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Immediate Genetic Augmentation and Enhanced Habitat Connectivity Are Required to Secure the Future of an Iconic Endangered Freshwater Fish Population

Evolutionary Applications, Journal Year: 2024, Volume and Issue: 17(10)

Published: Oct. 1, 2024

ABSTRACT Genetic diversity is rapidly lost from small, isolated populations by genetic drift. Measuring the level of drift using effective population size ( N e ) highly useful for management. Single‐cohort estimators approximate number breeders in one season b ): a value < 100 signals likely inbreeding depression. Per‐generation 1000 estimated multiple cohort reduced adaptive potential. Natural rarely meet assumptions ‐estimation, so interpreting estimates challenging. Macquarie perch an endangered Australian freshwater fish threatened severely range, habitat loss, and fragmentation. To counteract low , augmented gene flow being implemented several populations. In Murrumbidgee River, unknown effects water management on among‐site connectivity impede design interventions. Using DArT SNPs 328 individuals sampled across sites years with different conditions, we assessed structure, site isolation, heterozygosity, inbreeding, . We tested depression, dispersal, evaluated whether translocated Cataract Reservoir to River bred, interbred local fish. found strong indicating complete or partial isolation river fragments. This structure violates estimation, resulting strongly downwardly biased unless per‐site, highlighting necessity account while estimating Inbreeding depression was not detected, but at each site, are likely. These results flagged address within‐river through mixing translocations among other Three detected genetically diverse offspring parent indicated that progress. Including admixed yielded lower higher suggesting heterozygosity preferable indicator augmentation.

Language: Английский

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Seascape Genomics of the Smooth Hammerhead Shark Sphyrna zygaena Reveals Regional Adaptive Clinal Variation

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(12)

Published: Dec. 1, 2024

ABSTRACT Globally, hammerhead sharks have experienced severe declines owing to continued overexploitation and anthropogenic change. The smooth shark Sphyrna zygaena remains understudied compared other members of the family Sphyrnidae. Despite its vulnerable status, a comprehensive understanding genetic landscape lacking in many regions worldwide. 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 genotype‐environment association (GEA) analysis was employed . Subsequent assessments putatively adaptive loci revealed distinctive south east cline. Among these, notable correlations between variation sea‐surface dissolved oxygen salinity were evident. Conversely, 111,243 neutral SNP markers lack regional population differentiation, finding that remained consistent across various analytical approaches. These results provide evidence for presence differential selection pressures limited spatial range, despite high gene flow implied by selectively dataset. This offers insights regarding potential impacts response fluctuating environmental conditions circumglobally distributed

Language: Английский

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Accurate Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Sept. 17, 2023

1 Abstract The identification of sex-linked scaffolds and the genetic sex individuals, i.e. their karyotype, is a fundamental step in population genomic studies. If are known, single individuals may be sexed based on read counts next-generation sequencing data. both as well karyotypes unknown, often case for non-model organisms, they have to jointly inferred. For cases, current methods rely arbitrary thresholds, which limits power low-depth In addition, most limited euploid (XX XY). Here we develop BeXY , fully Bayesian method infer posterior probabilities each scaffold autosomal, X-or Y-linked individual any XX, XY, X0, XXX, XXY, XYY XXYY. it also identifies autosomal trisomies estimates karyotype individuals. As show with downsampling experiments, has higher than all existing methods. It accurately infers ancient human samples few 20,000 reads from data sets just handful or highly imbalanced ratios, low-quality reference assemblies. We illustrate by applying whole-genome shotgun target enrichment modern humans, several organisms.

Language: Английский

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dartR.data: Auxiliary Data Package for Our Main Package 'dartR'

Published: Nov. 16, 2022

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