干旱区生态环境知识资源中心(Arid): An efficient method for simultaneous species, individual, and sex identification via in-solution single nucleotide polymorphism capture from low-quality scat samples

Arid

DOI	10.1111/1755-0998.13552
	An efficient method for simultaneous species, individual, and sex identification via in-solution single nucleotide polymorphism capture from low-quality scat samples
	Parker, Lillian D.; Campana, Michael G.; Quinta, Jessica D.; Cypher, Brian; Rivera, Isabel; Fleischer, Robert C.; Ralls, Katherine; Wilbert, Tammy R.; Boarman, Ryan; Boarman, William, I; Maldonado, Jesus E.
通讯作者	Parker, LD (corresponding author), Smithsonian Conservat Biol Inst, Ctr Conservat Genom, Washington, DC 20008 USA. ; Parker, LD (corresponding author), Natl Zool Pk, Washington, DC 20008 USA.
来源期刊	MOLECULAR ECOLOGY RESOURCES
ISSN	1755-098X
EISSN	1755-0998
出版年	2021-11
英文摘要	Understanding predator population dynamics is important for conservation management because of the critical roles predators play within ecosystems. Noninvasive genetic sampling methods are useful for the study of predators like canids that can be difficult to capture or directly observe. Here, we introduce the FAECES* method (Fast and Accurate Enrichment of Canid Excrement for Species* and other analyses) which expands the toolbox for canid researchers and conservationists by using in-solution hybridization sequence capture to produce single nucleotide polymorphism (SNP) genotypes for multiple canid species from scat-derived DNA using a single enrichment. We designed a set of hybridization probes to genotype both coyotes (Canis latrans) and kit foxes (Vulpes macrotis) at hundreds of polymorphic SNP loci and we tested the probes on both tissues and field-collected scat samples. We enriched and genotyped by sequencing 52 coyote and 70 kit fox scats collected in and around a conservation easement in the Nevada Mojave Desert. We demonstrate that the FAECES* method produces genotypes capable of differentiating coyotes and kit foxes, identifying individuals and their sex, and estimating genetic diversity and effective population sizes, even using highly degraded, low-quantity DNA extracted from scat. We found that the study area harbours a large and diverse population of kit foxes and a relatively smaller population of coyotes. By replicating our methods in the future, conservationists can assess the impacts of management decisions on canid populations. The method can also be adapted and applied more broadly to enrich and sequence multiple loci from any species of interest using scat or other noninvasive genetic samples.
英文关键词	canid conservation genetics coyote (Canis latrans) hybridization capture kit fox (Vulpes macrotis) noninvasive genetic sampling
类型	Article ; Early Access
语种	英语
收录类别	SCI-E
WOS记录号	WOS:000722176600001
WOS关键词	JOAQUIN KIT FOXES ; EFFECTIVE POPULATION-SIZE ; VULPES-MACROTIS-MUTICA ; NONINVASIVE METHOD ; MOJAVE DESERT ; FECAL SAMPLES ; DNA ; COYOTE ; CONSERVATION ; INFERENCE
WOS类目	Biochemistry & Molecular Biology ; Ecology ; Evolutionary Biology
WOS研究方向	Biochemistry & Molecular Biology ; Environmental Sciences & Ecology ; Evolutionary Biology
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/374628
作者单位	[Parker, Lillian D.; Campana, Michael G.; Quinta, Jessica D.; Rivera, Isabel; Fleischer, Robert C.; Ralls, Katherine; Wilbert, Tammy R.; Maldonado, Jesus E.] Smithsonian Conservat Biol Inst, Ctr Conservat Genom, Washington, DC 20008 USA; [Parker, Lillian D.; Campana, Michael G.; Quinta, Jessica D.; Rivera, Isabel; Fleischer, Robert C.; Ralls, Katherine; Wilbert, Tammy R.; Maldonado, Jesus E.] Natl Zool Pk, Washington, DC 20008 USA; [Parker, Lillian D.; Campana, Michael G.; Maldonado, Jesus E.] George Mason Univ, Sch Syst Biol, Fairfax, VA 22030 USA; [Campana, Michael G.; Maldonado, Jesus E.] George Mason Univ, Dept Environm Sci & Policy, Fairfax, VA 22030 USA; [Cypher, Brian] Calif State Univ, Endangered Species Recovery Program, Turlock, CA USA; [Boarman, Ryan; Boarman, William, I] Conservat Sci Res & Consultat, Spring Valley, CA USA
推荐引用方式 GB/T 7714	Parker, Lillian D.,Campana, Michael G.,Quinta, Jessica D.,et al. An efficient method for simultaneous species, individual, and sex identification via in-solution single nucleotide polymorphism capture from low-quality scat samples[J],2021.
APA	Parker, Lillian D..,Campana, Michael G..,Quinta, Jessica D..,Cypher, Brian.,Rivera, Isabel.,...&Maldonado, Jesus E..(2021).An efficient method for simultaneous species, individual, and sex identification via in-solution single nucleotide polymorphism capture from low-quality scat samples.MOLECULAR ECOLOGY RESOURCES.
MLA	Parker, Lillian D.,et al."An efficient method for simultaneous species, individual, and sex identification via in-solution single nucleotide polymorphism capture from low-quality scat samples".MOLECULAR ECOLOGY RESOURCES (2021).