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

et al.

Molecular Ecology, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 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.

Language: Английский

Germline mutation rates and fine-scale recombination parameters in zebra finch DOI Creative Commons
Djivan Prentout, Daria Bykova, Carla Hoge

et al.

PLoS Genetics, Journal Year: 2025, Volume and Issue: 21(4), P. e1011661 - e1011661

Published: April 15, 2025

Most of our understanding the fundamental processes mutation and recombination stems from a handful disparate model organisms pedigree studies mammals, with little known about other vertebrates. To gain broader comparative perspective, we focused on zebra finch ( Taeniopygia castanotis ), which, like birds, differs mammals in its karyotype (which includes many micro-chromosomes), mechanism by which is directed to genome, aspects ontogenesis. We collected genome sequences three generation pedigrees that provide information 80 meioses, inferring 202 single-point de novo mutations, 1,088 crossovers, 275 non-crossovers. On basis, estimated sex-averaged rate 5.0 × 10 -9 per base pair generation, par have similar time (~2–3 years). Also as found paternal germline bias at later stages gametogenesis (of 1.7:1) but no discernible difference between sexes early development. Examining patterns, crossover macro-chromosomes 0.93 cM/Mb, pronounced enrichment crossovers near telomeres. In contrast, non-crossover rates are more uniformly distributed. micro-chromosomes, substantially higher (3.96 cM/Mb), accordance homeostasis, both events At finer scale, overlap CpG islands often than expected chance, absence PRDM9. Estimates degree GC-biased gene conversion (59%), mean tract length (~32 bp), non-crossover-to-crossover ratio (5.4:1) all comparable those reported primates mice. Therefore, properties resolutions remain over large phylogenetic distances.

Language: Английский

Citations

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

et al.

Molecular Ecology, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 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.

Language: Английский

Citations

0