Next-generation data filtering in the genomics era

Nature Reviews Genetics, Год журнала: 2024, Номер unknown

Опубликована: Июнь 14, 2024

Язык: Английский

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Cold, creeping things: deep phylogeographic structure in a naturally fragmented cool-adapted skink (Scincidae; Anepischetosia) from south-eastern Australia

Conservation Genetics, Год журнала: 2025, Номер unknown

Опубликована: Апрель 24, 2025

Abstract The temperate forests of eastern Australia have been extensively fragmented over the last 200 years and are now increasingly threatened by fire climate change. To understand manage impacts these threats, there is a need to patterns endemism diversity across an array ecologically divergent taxa. Anepischetosia monotypic genus scincid lizards that adapted cool, wet forest habitats in far south-eastern mainland Australia. Here we use reduced representation genomic data sequencing mitochondrial ND4 locus from museum tissue samples characterise phylogeographic structure population-level genetic this taxon. These reveal novel deep geographically localised structuring, including at least six ESUs spanning several candidate species. Many lineages associated with patches mesic habitat, especially north range, suggesting long histories persistence through major environmental change Plio-Pleistocene, similar observed some taxa non-glaciated landscapes northern hemisphere. Two putative ESUs, whose ranges overlap areas impacted recent high-intensity bushfires, low may be conservation concern. Additional seemingly isolated populations western Victoria remain poorly sampled comprise yet further or results highlight how analyses can overlooked concern leveraging collections – as well-sampled accessible even considered comparatively “well known”.

Язык: Английский

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Genetic analysis of selective breeding population and introduced population in Litopenaeus vannamei using SSRs and SNPs

Gene Reports, Год журнала: 2025, Номер unknown, С. 102251 - 102251

Опубликована: Май 1, 2025

Язык: Английский

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Previously unmeasured genetic diversity explains part of Lewontin's paradox in a k-mer-based meta-analysis of 112 plant species

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Май 19, 2024

Abstract At the molecular level, most evolution is expected to be neutral. A key prediction of this expectation that level genetic diversity in a population should scale with size. However, as was noted by Richard Lewontin 1974 and reaffirmed later studies, slope size-diversity relationship nature much weaker than under neutral theory. We hypothesize one contributor paradox current methods relying on single nucleotide polymorphisms (SNPs) called from aligning short reads reference genome underestimate levels many species. To test idea, we calculated ( π ) k -mer-based metrics across 112 plant species, amounting over 205 terabases DNA sequencing data 27,488 individual plants. then compared how these different correlated proxies size account for both range density variation found our scaled anywhere about 3 20 times faster -mer after adjusting evolutionary history, mating system, life cycle habit, cultivation status, invasiveness. The between also remains significant correcting size, whereas analogous does not. These results suggest not captured common SNP-based analyses explains part Lewontin’s Lay Summary Even revolutions ability sequence understand DNA, important biological questions remain unsolved. One such problem paradox, named who first described it 1974. core simple idea: species more individuals genetically diverse. reasoning means replication thus opportunities mutation create new variation. differ massively often have similar levels. has several potential, previously investigated mechanisms but what if simply measurements are off? Most studies estimate comparing sample genomes standard genome. While approach useful, impossible measure represented - phenomenon known bias. free reference-bias re-investigate Overall, find reference-free reference-biased approach. unlikely fully plays an role.

Язык: Английский

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Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe

Genome Research, Год журнала: 2024, Номер 34(11), С. 2094 - 2107

Опубликована: Ноя. 1, 2024

Genomic resources are important for evaluating genetic diversity and supporting conservation efforts. The garden dormouse ( Eliomys quercinus ) is a small rodent that has experienced one of the most severe modern population declines in Europe. We present high-quality haplotype-resolved reference genome dormouse, combine comprehensive short long-read transcriptomics data sets with homology-based methods to generate highly complete gene annotation. Demographic history analysis reveal sharp decline since last interglacial, indicating an association between colder climates before anthropogenic influence. Using our from 100 individuals, largely sampled citizen-science project across contemporary range, we conduct first genomic this species. find clear evidence structure species’ core Central European range. Notably, show Alpine population, characterized by strong differentiation reduced diversity, reproductively isolated other regions likely represents differentiated evolutionary significant unit (ESU). predominantly declining Eastern populations also signs recent isolation, pattern consistent range expansion Western Europe during Holocene, leaving relict now facing local extinction. Overall, findings suggest may be enhanced through designation ESUs.

Язык: Английский

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Dartseq-Generated Snps Revealed Low Genetic Diversity and Genetic Erosion Along Life Stages in Fragmented Populations of Afrocarpus Gracilior (Pilg.) C.N.Page in Southern Ethiopia

Опубликована: Янв. 1, 2024

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Язык: Английский

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Divergent lineages in a young species: The case of datilillo (Yucca valida), a broadly distributed plant from the Baja California Peninsula

American Journal of Botany, Год журнала: 2024, Номер 111(9)

Опубликована: Авг. 7, 2024

Abstract Premise Globally, barriers triggered by climatic changes have caused habitat fragmentation and population allopatric divergence. Across North America, oscillations during the Quaternary played important roles in distribution of wildlife. Notably, diverse plant species from Baja California Peninsula western isolated Pleistocene glacial–interglacial cycles, exhibit strong genetic structure highly concordant divergent lineages across their ranges. A representative genus peninsula is Yucca , with Y. valida having widest range. Although a dominant species, it has an extensive discontinuity between 26° N 27° N, suggesting restricted gene flow. Moreover, historical models indicate absence area suitable conditions for Last Interglacial, making interesting model studying Methods We assembled 4411 SNPs 147 plants throughout its range to examine phylogeography identify number lineages, quantify differentiation, reconstruct demographic history estimate age species. Results Three were identified based on SNPs. Our analyses support that drift driver differentiation among these lineages. estimated less than 1 million years common ancestor sister Conclusions Habitat changes, low dispersal, geographical gap acted as cumulative mechanisms leading divergence .

Язык: Английский

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Ecological opportunity leads to higher diversity and probability of trophic specialisation in Arctic charr

Evolutionary Journal of the Linnean Society, Год журнала: 2024, Номер 3(1)

Опубликована: Янв. 1, 2024

Abstract Understanding the extrinsic factors that drive emergence of biological diversity is critical to its protection and management. However, even superficially similar local environments can vary considerably, so large-scale datasets are needed understand key drivers across a representative portion species distribution. Arctic charr (Salvelinus alpinus) widespread salmonid fish represents an excellent study system for these processes because shows substantial diversification range freshwater multiple instances trophic specialization in form sympatric ecotype populations. behind this variation remain largely unknown due lack broad-scale studies. To address this, we investigated via national-scale 64 populations lakes Scotland using genome-wide dataset single nucleotide polymorphisms (N = 24 878) phenotypic data head depth relative body size. We found extent genetic was predicted by ecosystem size (a proxy lake size, depth, complexity). suggest larger, deeper generally provided more ecological opportunity potential. Additionally, environmental from all 187 containing Scotland, strongly potential presence divergent ecotypes. Our results show importance underlying adaptive radiations.

Язык: 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, Год журнала: 2024, Номер 17(10)

Опубликована: Окт. 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.

Язык: Английский

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Genetic diversity and population structure of pedunculate oaks (Quercus robur) in Wytham Woods

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Окт. 31, 2024

Summary Genetic diversity is fundamental for adaptation to changing environments. It particularly important in forest trees because of their significant role nature’s contribution people. However, genetic has been significantly changed by human activities the past centuries. This paper investigates a focal site, Wytham Woods, one most researched woodlands on Earth, and presents population study pedunculate oaks ( Quercus robur ), keystone species ecosystem. We characterised 210 with Genotyping Sequencing (GbS) quantified levels across stands different histories management regimes. detected only weak structure within 218,567 SNPs, such that variation occurred but not among stands, which included semi-natural woodland areas plantations aged between 200 50 years ago. also observed little difference expected heterozygosity stand types, some inbreeding youngest plantation. discovered 26,174 SNPs (11.98%) were highly differentiated under potential selection. suggest life history traits oak contribute its resistance against erosion, beeches, spruces, pines. Preference as timber tree tendency use local seed source might have resulted homogeneous structure. tree-to-tree differences may harbour putative adaptive loci. Our contributes crucial baseline information conservation human-modified woodlands, addition supporting long-term ecological studies many other species, depend this species. Societal Impact Statement highlights importance monitoring preserving trees, like oaks. Human activities, including land changes forestry practices, could influence potentially alter demonstrate how understanding ranging from (1) shed light natural consequence (2) support continuing, adaptational population, (3) be translated co-occurring effective at large.

Язык: Английский

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