Conservation Genetics Resources, Journal Year: 2023, Volume and Issue: 15(1-2), P. 15 - 20
Published: April 1, 2023
Language: Английский
Molecular Ecology Resources, Journal Year: 2025, Volume and Issue: unknown
Published: Jan. 31, 2025
ABSTRACT In recent years, numerous single nucleotide polymorphism (SNP) panel methods to genotype non‐invasive faecal samples have been developed. However, none of these existing fit all the criteria necessary make a SNP broadly usable for conservation projects in any country—cost effective, streamlined lab protocol and user‐friendly open‐source bioinformatics protocols design analysis. Here, we present such method display its utility by developing multiplex PCR conducting individual ID snow leopards, Panthera uncia , from samples. The consists 144 SNPs utilises next‐generation sequencing technology. We validate our with paired tissue zoo individuals, showing minimum 96.7% accuracy allele calls per run. then generate data 235 field‐collected across Pakistan show that can reliably identify individuals low‐quality unknown age is robust contamination. also has capability first‐order relatives among sampled provides insights into geographic origin This will empower leopard research community their efforts assess local global population sizes. More broadly, development be used species interest which adequate genomic reference available.
Language: Английский
Citations
0
International Journal of Primatology, Journal Year: 2024, Volume and Issue: unknown
Published: May 21, 2024
Language: Английский
Citations
3
Evolutionary Applications, Journal Year: 2023, Volume and Issue: 16(12), P. 1937 - 1955
Published: Nov. 20, 2023
North America is recognized for the exceptional richness of rabies virus (RV) wildlife reservoir species. Management RV accomplished through vaccination targeting mesocarnivore populations, such as raccoon (
Language: Английский
Citations
4
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: July 6, 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 favored for conservation applications. SNP often used because adaptability, effectiveness with low-quality samples, cost-efficiency use 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 identification, mPCRselect. mPCRselect allows any researcher, who has sufficient SNP-level data, design successful cost-effective panel species concern.
Language: Английский
Citations
1
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
Journal of Heredity, Journal Year: 2023, Volume and Issue: 114(5), P. 529 - 538
Published: May 29, 2023
Abstract We provide novel genomic resources to help understand the traits involved in elephant health and aid conservation efforts. sequence 11 genomes (5 African savannah, 6 Asian) from North American zoos, including 9 de novo assemblies. estimate germline mutation rates reconstruct demographic histories. Finally, we an in-solution capture assay genotype Asian elephants. This is suitable for analyzing degraded museum noninvasive samples, such as feces hair. The present here should allow more detailed uniform studies future efforts disease research.
Language: Английский
Citations
2
PeerJ, Journal Year: 2022, Volume and Issue: 10, P. e14428 - e14428
Published: Dec. 6, 2022
The Amur or Siberian tiger Panthera tigris altaica (Temminck, 1844) is currently restricted to a small region of its original geographical range in northwestern Asia and considered 'endangered' by the IUCN Red List Threatened Species. This solitary, territorial, large top predator major need genomic resources inform conservation management strategies. study formally tested if complete mitochondrial genomes P. can be assembled from non-enriched metagenomic libraries generated scat eDNA samples using Illumina sequencing platform open-access bioinformatics pipelines. mitogenome was circularized pipeline GetOrganelle with coverage ranging 322.7x 17.6x four different samples. A nearly genome (101x) retrieved fifth sample. were AT-rich composed 13 protein coding genes (PCGs), 22 transfer RNA genes, two ribosomal putative control region. Synteny observed all mitogenomes identical that reported before for other felids. phylogenomic analysis based on PCGs demonstrated reliably identify sequenced as belonging distinguished same closely distantly related congeneric species. demonstrates it viable retrieve accurate whole (and probably felids) without library enrichment protocols workflows. new resource represents tool support strategies (bio-prospecting bio-monitoring) this iconic cat.
Language: Английский
Citations
3
Canadian Journal of Zoology, Journal Year: 2024, Volume and Issue: 102(11), P. 859 - 870
Published: July 11, 2024
Smaller canids, such as most foxes, individually hunt small prey, and therefore, social groups typically consist of just a mated pair. However, these smaller canids occasionally form in which the members have been presumed to be genetically or socially related. We studied genetic relationships among urban San Joaquin kit fox ( Vulpes macrotis mutica Merriam, 1902) Bakersfield, California. Of 59 groups, 42.4% had extra adults addition parents. Foxes were field classified either mothers, fathers, helpers (extra adults), pups. then assessed relatedness foxes within using 11 microsatellites DNA from tissue hair samples. Mated pairs significantly less related than mothers helpers, with fathers being intermediate. Twelve females mother–daughter dyads, but we also found two cases sisters where unrelated. Pups always female identified their mother. Father–pup mother–pup pairs, helper–pup The extra-pair paternity rate (multiple per litter) was 39%. flexibility exhibited by may increase resiliency marked fluctuations resource availability, thereby reducing extinction risk.
Language: Английский
Citations
0
Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(7)
Published: July 26, 2024
Abstract High‐density genotyping methods have revolutionized the field of population and conservation genetics in past decade. To exploit technological analytical advances field, access to high‐quality genetic material is a key component. However, such samples endangered rare animals often challenging or even impossible. Here, we used minimally invasive sampling method (MIS) cave salamander Proteus anguinus , olm, generate thousands markers using ddRADseq for genomic analyses. Using tail clips MIS skin swabs taken from same individual, investigated data properties two different types. We found that sufficient DNA can be extracted swab up 200,000 polymorphic SNPs divergent lineages. Swab tissue were highly reproducible exhibiting low SNP error rates. most frequently (~50%) located within genic regions, while rest mapped mostly flanking regions repetitive DNA. The vast majority recovered swabbing was host fraction contained additional ecological information on species, including eDNA surrounding environment bacterial fauna. Most exogenous bacteria (~80%), followed by vertebrates (~20%). Our results demonstrate (i) tens analyses (ii) inform species health status ecology
Language: Английский
Citations
0
Southeastern Naturalist, Journal Year: 2024, Volume and Issue: 23(3)
Published: Aug. 9, 2024
Neotoma magister (Allegheny Woodrat) has a conservation status of vulnerable or at even greater risk across 13 eastern US states. A lack recent museum vouchers the southern limit its distribution, where sister species floridana (Eastern occurs, creates uncertainty as to current range Allegheny Woodrat in Alabama. We opportunistically collected woodrat scat samples for identification using mitochondrial cytochrome b comparisons that provided genetic evidence Woodrats Alabama north Tennessee River, consistent with recognized distribution. These new are most closely related from Pennsylvania, Virginia, and West intraspecific cyt variation (5%) than previously reported. Comparisons between our (2 2 south River), published Eastern sequences revealed clear distinction small geographic distances, mean interspecific divergence values over 8%. add known Woodrats, further characterize their differentiation Woodrats. Additional data needed delimit distributional boundaries beyond.
Language: Английский
Citations
0