Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges

Sarah Helyar; J. Hemmer-Hansen; Dorte Bekkevold; Martin I. Taylor; Rob Ogden; Morten T Limborg; Alessia Cariani; Gregory E. Maes; Eveine  Diopere; Gary Carvalho; Anders Nielsen

doi:10.1111/j.1755-0998.2010.02943.x

Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges

Sarah Helyar
, J. Hemmer-Hansen
, Dorte Bekkevold
, Martin I. Taylor
, Rob Ogden
, Morten T Limborg
, Alessia Cariani
, Gregory E. Maes
, Eveine Diopere
, Gary Carvalho
, Anders Nielsen

Technical University of Denmark, Lyngby
Royal Zoological Society of Scotland, Edinburgh
University of Bologna
University of Leuven

Allbwn ymchwil: Cyfraniad at gyfnodolyn › Erthygl › adolygiad gan gymheiriaid

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Recent improvements in the speed, cost and accuracy of next generation sequencing are revolutionizing the discovery of single nucleotide polymorphisms (SNPs). SNPs are increasingly being used as an addition to the molecular ecology toolkit in nonmodel organisms, but their efficient use remains challenging. Here, we discuss common issues when employing SNP markers, including the high numbers of markers typically employed, the effects of ascertainment bias and the inclusion of nonneutral loci in a marker panel. We provide a critique of considerations specifically associated with the application and population genetic analysis of SNPs in nonmodel taxa, focusing specifically on some of the most commonly applied methods

Iaith wreiddiol	Saesneg
Tudalennau (o-i)	123-136
Cyfnodolyn	Molecular Ecology Resources
Cyfrol	11
Rhif cyhoeddi	S1
Dynodwyr Gwrthrych Digidol (DOIs)	https://doi.org/10.1111/j.1755-0998.2010.02943.x
Statws	Cyhoeddwyd - Maw 2011

Mynediad at Ddogfen

10.1111/j.1755-0998.2010.02943.x

New DNA forensics tools improve sustainable fisheries management and reduce wildlife crime
Dawnay, N. (Cyfranogwr), Carvalho, G. (Cyfranogwr), Thorpe, R. (Cyfranogwr), Peppin, L. (Cyfranogwr), Helyar, S. (Cyfranogwr) & DeBruyn, M. (Cyfranogwr)
Effaith

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Dyfynnu hyn

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title = "Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges",

abstract = "Recent improvements in the speed, cost and accuracy of next generation sequencing are revolutionizing the discovery of single nucleotide polymorphisms (SNPs). SNPs are increasingly being used as an addition to the molecular ecology toolkit in nonmodel organisms, but their efficient use remains challenging. Here, we discuss common issues when employing SNP markers, including the high numbers of markers typically employed, the effects of ascertainment bias and the inclusion of nonneutral loci in a marker panel. We provide a critique of considerations specifically associated with the application and population genetic analysis of SNPs in nonmodel taxa, focusing specifically on some of the most commonly applied methods",

keywords = "ascertainment bias, nonneutral loci, outlier detection, population genomics, population structure, software",

author = "Sarah Helyar and J. Hemmer-Hansen and Dorte Bekkevold and Taylor, \{Martin I.\} and Rob Ogden and Limborg, \{Morten T\} and Alessia Cariani and Maes, \{Gregory E.\} and Eveine Diopere and Gary Carvalho and Anders Nielsen",

year = "2011",

month = mar,

doi = "10.1111/j.1755-0998.2010.02943.x",

language = "English",

volume = "11",

pages = "123--136",

journal = "Molecular Ecology Resources",

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T1 - Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges

AU - Helyar, Sarah

AU - Hemmer-Hansen, J.

AU - Bekkevold, Dorte

AU - Taylor, Martin I.

AU - Ogden, Rob

AU - Limborg, Morten T

AU - Cariani, Alessia

AU - Maes, Gregory E.

AU - Diopere, Eveine

AU - Carvalho, Gary

AU - Nielsen, Anders

PY - 2011/3

Y1 - 2011/3

N2 - Recent improvements in the speed, cost and accuracy of next generation sequencing are revolutionizing the discovery of single nucleotide polymorphisms (SNPs). SNPs are increasingly being used as an addition to the molecular ecology toolkit in nonmodel organisms, but their efficient use remains challenging. Here, we discuss common issues when employing SNP markers, including the high numbers of markers typically employed, the effects of ascertainment bias and the inclusion of nonneutral loci in a marker panel. We provide a critique of considerations specifically associated with the application and population genetic analysis of SNPs in nonmodel taxa, focusing specifically on some of the most commonly applied methods

AB - Recent improvements in the speed, cost and accuracy of next generation sequencing are revolutionizing the discovery of single nucleotide polymorphisms (SNPs). SNPs are increasingly being used as an addition to the molecular ecology toolkit in nonmodel organisms, but their efficient use remains challenging. Here, we discuss common issues when employing SNP markers, including the high numbers of markers typically employed, the effects of ascertainment bias and the inclusion of nonneutral loci in a marker panel. We provide a critique of considerations specifically associated with the application and population genetic analysis of SNPs in nonmodel taxa, focusing specifically on some of the most commonly applied methods

KW - ascertainment bias

KW - nonneutral loci

KW - outlier detection

KW - population genomics

KW - population structure

KW - software

U2 - 10.1111/j.1755-0998.2010.02943.x

DO - 10.1111/j.1755-0998.2010.02943.x

M3 - Article

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VL - 11

SP - 123

EP - 136

JO - Molecular Ecology Resources

JF - Molecular Ecology Resources

IS - S1

ER -

Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges

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Mynediad at Ddogfen

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New DNA forensics tools improve sustainable fisheries management and reduce wildlife crime

Dyfynnu hyn