A panel of 96 SNPs to identify individuals and differentiate subspecies of elk (Cervus canadensis) for microfluidic and other genotyping platforms

Benjamin N. Sacks; Gunmeet K. Bali; Zachary T. Lounsberry; Stevi Lee Vanderzwan

doi:10.1007/s12686-020-01184-2

A panel of 96 SNPs to identify individuals and differentiate subspecies of elk (Cervus canadensis) for microfluidic and other genotyping platforms

Benjamin N. Sacks, Gunmeet K. Bali, Zachary T. Lounsberry, Stevi Lee Vanderzwan

School of Veterinary Medicine

Research output: Contribution to journal › Article › peer-review

Abstract

The tule elk (Cervus canadensis nannodes) is endemic to California, USA, where it experienced an extreme genetic bottleneck in the 1870s. Two other subspecies of elk co-occur in California, Roosevelt (C. c. roosevelti) and Rocky Mountain (C. c. nelsoni) elk. These subspecies potentially interbreed in contact zones. For monitoring and genetic management of fragmented populations, markers are needed to differentiate both individuals and subspecies. Using Illumina HiSeq sequencing of 12 individuals, including four from each subspecies, we developed a suite of 96 SNP markers for a Fluidigm platform. This marker set enabled differentiation of individuals and subspecies with high confidence and will facilitate genetic monitoring of elk throughout their range.

Original language	English (US)
Journal	Conservation Genetics Resources
DOIs	https://doi.org/10.1007/s12686-020-01184-2
State	Accepted/In press - 2021

Keywords

Cervus canadensis
Fluidigm
Rocky mountain elk
Roosevelt elk
Single nucleotide polymorphism
Tule elk
WGS

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics

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title = "A panel of 96 SNPs to identify individuals and differentiate subspecies of elk (Cervus canadensis) for microfluidic and other genotyping platforms",

abstract = "The tule elk (Cervus canadensis nannodes) is endemic to California, USA, where it experienced an extreme genetic bottleneck in the 1870s. Two other subspecies of elk co-occur in California, Roosevelt (C. c. roosevelti) and Rocky Mountain (C. c. nelsoni) elk. These subspecies potentially interbreed in contact zones. For monitoring and genetic management of fragmented populations, markers are needed to differentiate both individuals and subspecies. Using Illumina HiSeq sequencing of 12 individuals, including four from each subspecies, we developed a suite of 96 SNP markers for a Fluidigm platform. This marker set enabled differentiation of individuals and subspecies with high confidence and will facilitate genetic monitoring of elk throughout their range.",

keywords = "Cervus canadensis, Fluidigm, Rocky mountain elk, Roosevelt elk, Single nucleotide polymorphism, Tule elk, WGS",

author = "Sacks, {Benjamin N.} and Bali, {Gunmeet K.} and Lounsberry, {Zachary T.} and Vanderzwan, {Stevi Lee}",

note = "Funding Information: Funding was from the Rocky Mountain Elk Foundation (RMEF Project #CA160553), the California Department of Fish and Wildlife, Big Game Management Program (Grant No. P1580009), and the University of California, Davis, Forensic Sciences Graduate Group. Cristen Langner and Erin Meredith of CDFW provided samples. ",

year = "2021",

doi = "10.1007/s12686-020-01184-2",

language = "English (US)",

journal = "Conservation Genetics Resources",

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AU - Sacks, Benjamin N.

AU - Bali, Gunmeet K.

AU - Lounsberry, Zachary T.

AU - Vanderzwan, Stevi Lee

N1 - Funding Information: Funding was from the Rocky Mountain Elk Foundation (RMEF Project #CA160553), the California Department of Fish and Wildlife, Big Game Management Program (Grant No. P1580009), and the University of California, Davis, Forensic Sciences Graduate Group. Cristen Langner and Erin Meredith of CDFW provided samples.

PY - 2021

Y1 - 2021

N2 - The tule elk (Cervus canadensis nannodes) is endemic to California, USA, where it experienced an extreme genetic bottleneck in the 1870s. Two other subspecies of elk co-occur in California, Roosevelt (C. c. roosevelti) and Rocky Mountain (C. c. nelsoni) elk. These subspecies potentially interbreed in contact zones. For monitoring and genetic management of fragmented populations, markers are needed to differentiate both individuals and subspecies. Using Illumina HiSeq sequencing of 12 individuals, including four from each subspecies, we developed a suite of 96 SNP markers for a Fluidigm platform. This marker set enabled differentiation of individuals and subspecies with high confidence and will facilitate genetic monitoring of elk throughout their range.

AB - The tule elk (Cervus canadensis nannodes) is endemic to California, USA, where it experienced an extreme genetic bottleneck in the 1870s. Two other subspecies of elk co-occur in California, Roosevelt (C. c. roosevelti) and Rocky Mountain (C. c. nelsoni) elk. These subspecies potentially interbreed in contact zones. For monitoring and genetic management of fragmented populations, markers are needed to differentiate both individuals and subspecies. Using Illumina HiSeq sequencing of 12 individuals, including four from each subspecies, we developed a suite of 96 SNP markers for a Fluidigm platform. This marker set enabled differentiation of individuals and subspecies with high confidence and will facilitate genetic monitoring of elk throughout their range.

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