Phylogenetic relationships among the European and American bison and seven cattle breeds recon structed using the Bovine SNP50 Illumina Genotyping BeadChip

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Phylogenetic relationships among the European and American bison and seven cattle breeds recon structed using the Bovine SNP50 Illumina Genotyping BeadChip. / Pertoldi, Cino; Wójcik, Jan M; Kawalko, Agata; Randi, Ettore; Kristensen, Torsten Nygård; Loeschcke, Volker; Coltman, David; Wilson, Gregory A; Gregersen, Vivi R; Bendixen, Christian.

I: Acta Theriologica, Bind 55, Nr. 2, 2010, s. 97-108.

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer review

Harvard

Pertoldi, C, Wójcik, JM, Kawalko, A, Randi, E, Kristensen, TN, Loeschcke, V, Coltman, D, Wilson, GA, Gregersen, VR & Bendixen, C 2010, 'Phylogenetic relationships among the European and American bison and seven cattle breeds recon structed using the Bovine SNP50 Illumina Genotyping BeadChip', Acta Theriologica, bind 55, nr. 2, s. 97-108. https://doi.org/10.4098/j.at.0001-7051.002.2010

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Author

Pertoldi, Cino ; Wójcik, Jan M ; Kawalko, Agata ; Randi, Ettore ; Kristensen, Torsten Nygård ; Loeschcke, Volker ; Coltman, David ; Wilson, Gregory A ; Gregersen, Vivi R ; Bendixen, Christian. / Phylogenetic relationships among the European and American bison and seven cattle breeds recon structed using the Bovine SNP50 Illumina Genotyping BeadChip. I: Acta Theriologica. 2010 ; Bind 55, Nr. 2. s. 97-108.

Bibtex

@article{8226f140472011df8b17000ea68e967b,
title = "Phylogenetic relationships among the European and American bison and seven cattle breeds recon structed using the Bovine SNP50 Illumina Genotyping BeadChip",
abstract = "Here we present the first at tempt to use the BovineSNP50 Illumina genotyping BeadChip for genome-wide screening of European bison Bisonbonasus bonasus (EB), two subspecies of American bison: the plains bison (EB), two sub species of American bison: the plains bison Bison bison bison (PB), the wood bison Bi on bison athabascae (WB) and seven (PB), the wood bison (WB) and seven cattle Bostaurus breeds. Our aims were to (1) reconstruct their evolutionary relationships, (2) detect any genetic signature of past bottlenecks and to quantify the con sequences of bottle necks on the genetic distances amongst bison subspecies and cattle, and (3) de tect loci under positive or stabilizing selection. A Bayesian clustering procedure (STRUCTURE) detected ten genetically distinct clusters, with separation among all seven cattle breeds and European and American bison, but no separation be tween plain and wood bison. A linkage disequi librium based program (LDNE) was used to estimate the effective population size (Ne) for the cattle breeds; Ne was generally low, relative to the census size of the breeds (cattle breeds: mean Ne = 299.5, min Ne = 18.1, max Ne = 755.0). BOTTLENECK 1.2 de tected signs of pop u la tion bot tle necks in = 755.0). BOTTLENECK 1.2 detected signs of population bottle necks in EB, PB and WB populations (sign test and standardized sign test: p = 0.0001). Evidence for loci under selection was found in cattle but not in bison. All extant wild populations of bison have shown to have sur vived se vere bottlenecks, which has likely had large effects on genetic diversity within and differentiation among groups.",
keywords = "SNPs, haplotypes, bottleneck, founder effect, breed comparison",
author = "Cino Pertoldi and W{\'o}jcik, {Jan M} and Agata Kawalko and Ettore Randi and Kristensen, {Torsten Nyg{\aa}rd} and Volker Loeschcke and David Coltman and Wilson, {Gregory A} and Gregersen, {Vivi R} and Christian Bendixen",
year = "2010",
doi = "10.4098/j.at.0001-7051.002.2010",
language = "English",
volume = "55",
pages = "97--108",
journal = "Acta Theriologica",
issn = "0001-7051",
publisher = "Springer",
number = "2",

}

RIS

TY - JOUR

T1 - Phylogenetic relationships among the European and American bison and seven cattle breeds recon structed using the Bovine SNP50 Illumina Genotyping BeadChip

AU - Pertoldi, Cino

AU - Wójcik, Jan M

AU - Kawalko, Agata

AU - Randi, Ettore

AU - Kristensen, Torsten Nygård

AU - Loeschcke, Volker

AU - Coltman, David

AU - Wilson, Gregory A

AU - Gregersen, Vivi R

AU - Bendixen, Christian

PY - 2010

Y1 - 2010

N2 - Here we present the first at tempt to use the BovineSNP50 Illumina genotyping BeadChip for genome-wide screening of European bison Bisonbonasus bonasus (EB), two subspecies of American bison: the plains bison (EB), two sub species of American bison: the plains bison Bison bison bison (PB), the wood bison Bi on bison athabascae (WB) and seven (PB), the wood bison (WB) and seven cattle Bostaurus breeds. Our aims were to (1) reconstruct their evolutionary relationships, (2) detect any genetic signature of past bottlenecks and to quantify the con sequences of bottle necks on the genetic distances amongst bison subspecies and cattle, and (3) de tect loci under positive or stabilizing selection. A Bayesian clustering procedure (STRUCTURE) detected ten genetically distinct clusters, with separation among all seven cattle breeds and European and American bison, but no separation be tween plain and wood bison. A linkage disequi librium based program (LDNE) was used to estimate the effective population size (Ne) for the cattle breeds; Ne was generally low, relative to the census size of the breeds (cattle breeds: mean Ne = 299.5, min Ne = 18.1, max Ne = 755.0). BOTTLENECK 1.2 de tected signs of pop u la tion bot tle necks in = 755.0). BOTTLENECK 1.2 detected signs of population bottle necks in EB, PB and WB populations (sign test and standardized sign test: p = 0.0001). Evidence for loci under selection was found in cattle but not in bison. All extant wild populations of bison have shown to have sur vived se vere bottlenecks, which has likely had large effects on genetic diversity within and differentiation among groups.

AB - Here we present the first at tempt to use the BovineSNP50 Illumina genotyping BeadChip for genome-wide screening of European bison Bisonbonasus bonasus (EB), two subspecies of American bison: the plains bison (EB), two sub species of American bison: the plains bison Bison bison bison (PB), the wood bison Bi on bison athabascae (WB) and seven (PB), the wood bison (WB) and seven cattle Bostaurus breeds. Our aims were to (1) reconstruct their evolutionary relationships, (2) detect any genetic signature of past bottlenecks and to quantify the con sequences of bottle necks on the genetic distances amongst bison subspecies and cattle, and (3) de tect loci under positive or stabilizing selection. A Bayesian clustering procedure (STRUCTURE) detected ten genetically distinct clusters, with separation among all seven cattle breeds and European and American bison, but no separation be tween plain and wood bison. A linkage disequi librium based program (LDNE) was used to estimate the effective population size (Ne) for the cattle breeds; Ne was generally low, relative to the census size of the breeds (cattle breeds: mean Ne = 299.5, min Ne = 18.1, max Ne = 755.0). BOTTLENECK 1.2 de tected signs of pop u la tion bot tle necks in = 755.0). BOTTLENECK 1.2 detected signs of population bottle necks in EB, PB and WB populations (sign test and standardized sign test: p = 0.0001). Evidence for loci under selection was found in cattle but not in bison. All extant wild populations of bison have shown to have sur vived se vere bottlenecks, which has likely had large effects on genetic diversity within and differentiation among groups.

KW - SNPs

KW - haplotypes

KW - bottleneck

KW - founder effect

KW - breed comparison

U2 - 10.4098/j.at.0001-7051.002.2010

DO - 10.4098/j.at.0001-7051.002.2010

M3 - Journal article

VL - 55

SP - 97

EP - 108

JO - Acta Theriologica

JF - Acta Theriologica

SN - 0001-7051

IS - 2

ER -