A Pipeline and Recommendations for Population and Individual Diagnostic SNP Selection in Non‐Model Species DOI Creative Commons
Ellie E. Armstrong, Chenyang Li, Michael G. Campana

et al.

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

Published: Nov. 29, 2024

ABSTRACT Despite substantial reductions in the cost of sequencing over last decade, genetic panels remain relevant due to their cost‐effectiveness and flexibility across a variety sample types. In particular, single nucleotide polymorphism (SNP) are increasingly favoured for conservation applications. SNP often used because adaptability, effectiveness with low‐quality samples, cost‐efficiency population monitoring forensics. However, selection diagnostic SNPs assignment individual identification can be challenging. The consequences poor under‐powered panels, inaccurate results, monetary loss. Here, we develop novel user‐friendly pipeline (mPCRselect) that select and/or identification. mPCRselect allows any researcher, who has sufficient SNP‐level data, design successful cost‐effective panel diploid species concern.

Language: Английский

Unraveling the genomic diversity and admixture history of captive tigers in the United States DOI Creative Commons
Ellie E. Armstrong, Jazlyn A. Mooney, Katherine A. Solari

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(39)

Published: Sept. 19, 2024

Genomic studies of endangered species have primarily focused on describing diversity patterns and resolving phylogenetic relationships, with the overarching goal informing conservation efforts. However, few investigated genomic housed in captive populations. For tigers ( Panthera tigris ), individuals vastly outnumber those wild, but their remains largely unexplored. Privately owned tiger populations remained an enigma community, some believing that these are severely inbred, while others believe they may be a source now-extinct diversity. Here, we present large-scale genetic study private (non-zoo) population United States, also known as “Generic” tigers. We find Generic has admixture fingerprint comprising all six extant wild subspecies. Of 138 sequenced for purpose this study, no individual had ancestry from only one show comparable amount relative to most subspecies, variants, fewer deleterious mutations. observe inbreeding coefficients similar populations, although there within both substantially inbred. Additionally, develop reference panel can used imputation accurately distinguish assign ultralow coverage (0.25×) data. By providing cost-effective alternative whole-genome sequencing (WGS), provides resource assist efforts ex- situ

Language: Английский

Citations

3
Revealing extensive inbreeding and less-efficient purging of deleterious mutations in wild Amur tigers in China DOI Creative Commons
Tianming Lan, Haimeng Li,

Boyang Liu

et al.

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 1, 2024

Inbreeding increases genome homozygosity within populations, which can exacerbate inbreeding depression by exposing homozygous deleterious alleles that are responsible for declines in fitness traits. In small genetic purging occurs under pressure of natural selection acts as an opposing force, contributing to a reduction alleles. Both and paramount the field conservation genomics. The Amur tiger (Panthera tigris altaica) lives populations forests Northeast Asia is among most endangered animals on planet. Using genome-wide assessment comparison, we reveal substantially higher more extensive wild tigers (F

Language: Английский

Citations

2
A Pipeline and Recommendations for Population and Individual Diagnostic SNP Selection in Non‐Model Species DOI Creative Commons
Ellie E. Armstrong, Chenyang Li, Michael G. Campana

et al.

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

Published: Nov. 29, 2024

ABSTRACT Despite substantial reductions in the cost of sequencing over last decade, genetic panels remain relevant due to their cost‐effectiveness and flexibility across a variety sample types. In particular, single nucleotide polymorphism (SNP) are increasingly favoured for conservation applications. SNP often used because adaptability, effectiveness with low‐quality samples, cost‐efficiency population monitoring forensics. However, selection diagnostic SNPs assignment individual identification can be challenging. The consequences poor under‐powered panels, inaccurate results, monetary loss. Here, we develop novel user‐friendly pipeline (mPCRselect) that select and/or identification. mPCRselect allows any researcher, who has sufficient SNP‐level data, design successful cost‐effective panel diploid species concern.

Language: Английский

Citations

1