Next-generation snow leopard population assessment tool: multiplex-PCR SNP panel for individual identification from feces

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 24, 2024

Abstract Snow leopards, Panthera uncia , are under threat from numerous pressures and the focus of a great deal conservation efforts. However, their elusive nature makes it difficult to estimate population sizes. Current methods used monitor local sizes include visually identifying individuals camera trap photos genetically fecal samples using microsatellite loci. Here, we present new method for snow leopard multiplex PCR single nucleotide polymorphism (SNP) panel method. The SNP consists 144 SNPs utilizes next-generation sequencing technology, making cheaper easier than current methods. We validate our with paired tissue zoo individuals, showing minimum 96.7% accuracy in allele calls per run. then generate data 235 field-collected across Pakistan show that can reliably identify low-quality unknown age is robust contamination. also has capability first-order relatives provides insights into geographic origin samples. This will empower research community efforts assess global More broadly, developing open source software selection primer design, Illumina streamlined lab bioinformatics protocol which be create similar panels any species interest adequate genomic reference available.

Language: Английский

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Genomic Resources for Asian (Elephas maximus) and African Savannah Elephant (Loxodonta africana) Conservation and Health Research

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Feb. 13, 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 non-invasive samples, such as feces hair. The present here should allow more detailed uniform studies future efforts disease research.

Language: Английский

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Genetic analyses are more sensitive than morphological inspection at detecting the presence of threatened Mojave desert tortoise (Gopherus agassizii) remains in canid scat and raven pellets

Conservation Science and Practice, Journal Year: 2022, Volume and Issue: 4(6)

Published: April 7, 2022

Abstract Subsidization of predator populations increases predation pressure on prey species, which is exacerbated when natural resources are scarce. Estimating the frequency by subsidized predators vulnerable especially low‐density, long‐lived species such as federally threatened Mojave desert tortoise ( Gopherus agassizii ), allows landscape managers to evaluate need for actions like reducing subsidies, discouraging taste aversion, or removal. Most studies have relied morphological analysis identify hard parts in scat. Here, we developed and validated a qPCR assay test presence DNA extracted from scat pellets. We used detect pellets collected conservation easement adjacent Boulder City, Nevada, three predators: coyotes Canis latrans kit foxes Vulpes macrotis arsipus common ravens Corvus corax )—all consume anthropogenic resources. compared results our same samples found that method much more sensitive at detecting remains. Although neither can determine whether consumption was result scavenging, nor how many individual tortoises were consumed, findings indicate may benefit focusing efforts subsidies attract support mortality predation.

Language: Английский

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Shallow sequencing can mislead when evaluating hybridization capture methods

Conservation Genetics Resources, Journal Year: 2023, Volume and Issue: 15(1-2), P. 15 - 20

Published: April 1, 2023

Language: Английский

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