Both Structural Variant and Single Nucleotide Polymorphism Load Impact Lifetime Fitness in a Threatened Bird Species DOI
Katarina C. Stuart, Hui Zhen Tan, Annabel Whibley

и другие.

Molecular Ecology, Год журнала: 2024, Номер unknown

Опубликована: Дек. 17, 2024

ABSTRACT The field of conservation genomics is becoming increasingly interested in whether, and how, structural variant (SV) genotype information can be leveraged the management threatened species. functional consequences SVs are more complex than for single nucleotide polymorphisms (SNPs), as typically impact a larger proportion genome due to their size thus may likely contribute load. While impacts SV‐specific genetic load less consequential large populations, interplay between weakened selection stochastic processes means that smaller such those Aotearoa hihi/New Zealand stitchbird ( Notiomystis cincta ), harbour high SV Hihi were once confined remnant population, but have been reestablished into six sanctuaries reserves, often via secondary bottlenecks, resulting low diversity, adaptive potential, inbreeding depression. In this study, we use whole resequencing 30 individuals from Tiritiri Matangi population identify nature distribution both SNPs within small avian population. We find SNP individual mutation only moderately correlated, because arise regions recombination evolutionarily conserved. Finally, leverage long‐term monitoring dataset pedigree fitness data assess loads on fitness, realised had similar negative correlations with lifetime fitness. However, masked metrics, positive significant correlation indicating masking deleterious alleles important SNPs. results study indicate examining neglects aspects intra‐specific variation studying has direct implications linking diversity genomic health inform decisions.

Язык: Английский

Structural genomic variation in the inbred Scandinavian wolf population contributes to the realized genetic load but is positively affected by immigration DOI Creative Commons
Linnéa Smeds,

Lars S. A. Huson,

Hans Ellegren

и другие.

Evolutionary Applications, Год журнала: 2024, Номер 17(2)

Опубликована: Фев. 1, 2024

When populations decrease in size and may become isolated, genomic erosion by loss of diversity from genetic drift accumulation deleterious mutations is likely an inevitable consequence. In such cases, immigration (genetic rescue) necessary to restore levels counteract inbreeding depression. Recent work conservation genomics has studied these processes focusing on the single nucleotide polymorphisms. contrast, our knowledge about structural variation (insertions, deletions, duplications inversions) endangered species limited. We analysed whole-genome, short-read sequences 212 wolves inbred Scandinavian population neighbouring Finland Russia, detected >35,000 variants (SVs) after stringent quality genotype frequency filtering; >26,000 high-confidence remained manual curation. The majority were shorter than 1 kb, with a distinct peak length distribution deletions at 190 bp, corresponding insertion events SINE/tRNA-Lys elements. site spectrum SVs protein-coding regions was significantly shifted towards rare alleles compared putatively neutral variants, consistent purifying selection. realized load increased population, but provided rescue effect lowering reintroducing ancestral loci fixed for derived SVs. Our study shows that comprises common type part establishing gene flow mitigate negative consequences diversity.

Язык: Английский

Процитировано

4
Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations DOI Creative Commons
Gabriel David,

Alicia Bertolotti,

Ryan M. Layer

и другие.

Genome Biology and Evolution, Год журнала: 2024, Номер 16(4)

Опубликована: Март 15, 2024

Abstract Comprehensive characterization of structural variation in natural populations has only become feasible the last decade. To investigate population genomic nature variation, reproducible and high-confidence callsets are first required. We created a population-scale reference genome-wide landscape across 33 Nordic house sparrows (Passer domesticus). produce consensus callset all samples using short-read data, we compare heuristic-based quality filtering visual curation (Samplot/PlotCritic Samplot-ML) approaches. demonstrate that variants is important for reducing putative false positives time invested this step outweighs potential costs analyzing short-read–discovered data sets include many positives. find even lenient manual strategy (e.g. applied by single curator) can reduce proportion up to 80%, thus enriching variants. Crucially, applying with curator, nearly (>99%) rejected as were also classified such more stringent three additional curators. Furthermore, failed reflect expected structure from SNPs, whereas passing did. Combining rapid therefore time- cost-effective functional studies requiring callsets.

Язык: Английский

Процитировано

0
What Can Genome Sequence Data Reveal About Population Viability? DOI
Marty Kardos, Lukas F. Keller, W. Chris Funk

и другие.

Molecular Ecology, Год журнала: 2024, Номер unknown

Опубликована: Дек. 16, 2024

ABSTRACT Biologists have long sought to understand the impacts of deleterious genetic variation on fitness and population viability. However, our understanding these effects in wild is incomplete, part due rarity sufficient demographic data needed measure their impact. The genomics revolution promising a potential solution by predicting variants (genetic load) bioinformatically from genome sequences alone bypassing need for costly data. After historical perspective theoretical empirical basis dynamics variation, we evaluate new genomic measures load predict We argue that current analyses cannot reliably growth, because depend demographic, ecological parameters more than just sequence be measured. Thus, while purely promise improve composition load, they are currently little use evaluating Demographic context remain crucial consequences fitness. when combined with such data, information can offer important insights into inbreeding conservation decision making.

Язык: Английский

Процитировано

0
Both Structural Variant and Single Nucleotide Polymorphism Load Impact Lifetime Fitness in a Threatened Bird Species DOI
Katarina C. Stuart, Hui Zhen Tan, Annabel Whibley

и другие.

Molecular Ecology, Год журнала: 2024, Номер unknown

Опубликована: Дек. 17, 2024

ABSTRACT The field of conservation genomics is becoming increasingly interested in whether, and how, structural variant (SV) genotype information can be leveraged the management threatened species. functional consequences SVs are more complex than for single nucleotide polymorphisms (SNPs), as typically impact a larger proportion genome due to their size thus may likely contribute load. While impacts SV‐specific genetic load less consequential large populations, interplay between weakened selection stochastic processes means that smaller such those Aotearoa hihi/New Zealand stitchbird ( Notiomystis cincta ), harbour high SV Hihi were once confined remnant population, but have been reestablished into six sanctuaries reserves, often via secondary bottlenecks, resulting low diversity, adaptive potential, inbreeding depression. In this study, we use whole resequencing 30 individuals from Tiritiri Matangi population identify nature distribution both SNPs within small avian population. We find SNP individual mutation only moderately correlated, because arise regions recombination evolutionarily conserved. Finally, leverage long‐term monitoring dataset pedigree fitness data assess loads on fitness, realised had similar negative correlations with lifetime fitness. However, masked metrics, positive significant correlation indicating masking deleterious alleles important SNPs. results study indicate examining neglects aspects intra‐specific variation studying has direct implications linking diversity genomic health inform decisions.

Язык: Английский

Процитировано

0