Molecular phylogeny and snp variation of polar bears (ursus maritimus), brown bears (u. arctos), and black bears (u. americanus) derived from genome sequences

Matthew A. Cronin, Gonzalo Rincon, Robert Meredith, Michael D. Macneil, Alma Islas-Trejo, Angela Cánovas, Juan F. Medrano

Research output: Contribution to journalArticleResearchpeer-review

13 Citations (Scopus)

Abstract

We assessed the relationships of polar bears (Ursus maritimus), brown bears (U. arctos), and black bears (U. americanus) with high throughput genomic sequencing data with an average coverage of 25× for each species. A total of 1.4 billion 100-bp paired-end reads were assembled using the polar bear and annotated giant panda (Ailuropoda melanoleuca) genome sequences as references. We identified 13.8 million single nucleotide polymorphisms (SNP) in the 3 species aligned to the polar bear genome. These data indicate that polar bears and brown bears share more SNP with each other than either does with black bears. Concatenation and coalescence-based analysis of consensus sequences of approximately 1 million base pairs of ultraconserved elements in the nuclear genome resulted in a phylogeny with black bears as the sister group to brown and polar bears, and all brown bears are in a separate clade from polar bears. Genotypes for 162 SNP loci of 336 bears from Alaska and Montana showed that the species are genetically differentiated and there is geographic population structure of brown and black bears but not polar bears.

Original languageEnglish
Pages (from-to)312-323
Number of pages12
JournalJournal of Heredity
Volume105
Issue number3
DOIs
StatePublished - 1 Jan 2014

Fingerprint

Ursidae
Phylogeny
Genome
Single Nucleotide Polymorphism
Consensus Sequence
Base Pairing

Keywords

  • Phylogeny
  • Ursus
  • black bears
  • brown
  • molecular clock
  • polar
  • single nucleotide polymorphism
  • ultraconserved elements

Cite this

Cronin, Matthew A. ; Rincon, Gonzalo ; Meredith, Robert ; Macneil, Michael D. ; Islas-Trejo, Alma ; Cánovas, Angela ; Medrano, Juan F. / Molecular phylogeny and snp variation of polar bears (ursus maritimus), brown bears (u. arctos), and black bears (u. americanus) derived from genome sequences. In: Journal of Heredity. 2014 ; Vol. 105, No. 3. pp. 312-323.
@article{fffdeddcfd014bd48507e2372d835d8e,
title = "Molecular phylogeny and snp variation of polar bears (ursus maritimus), brown bears (u. arctos), and black bears (u. americanus) derived from genome sequences",
abstract = "We assessed the relationships of polar bears (Ursus maritimus), brown bears (U. arctos), and black bears (U. americanus) with high throughput genomic sequencing data with an average coverage of 25× for each species. A total of 1.4 billion 100-bp paired-end reads were assembled using the polar bear and annotated giant panda (Ailuropoda melanoleuca) genome sequences as references. We identified 13.8 million single nucleotide polymorphisms (SNP) in the 3 species aligned to the polar bear genome. These data indicate that polar bears and brown bears share more SNP with each other than either does with black bears. Concatenation and coalescence-based analysis of consensus sequences of approximately 1 million base pairs of ultraconserved elements in the nuclear genome resulted in a phylogeny with black bears as the sister group to brown and polar bears, and all brown bears are in a separate clade from polar bears. Genotypes for 162 SNP loci of 336 bears from Alaska and Montana showed that the species are genetically differentiated and there is geographic population structure of brown and black bears but not polar bears.",
keywords = "Phylogeny, Ursus, black bears, brown, molecular clock, polar, single nucleotide polymorphism, ultraconserved elements",
author = "Cronin, {Matthew A.} and Gonzalo Rincon and Robert Meredith and Macneil, {Michael D.} and Alma Islas-Trejo and Angela C{\'a}novas and Medrano, {Juan F.}",
year = "2014",
month = "1",
day = "1",
doi = "10.1093/jhered/est133",
language = "English",
volume = "105",
pages = "312--323",
journal = "Journal of Heredity",
issn = "0022-1503",
publisher = "Oxford University Press",
number = "3",

}

Molecular phylogeny and snp variation of polar bears (ursus maritimus), brown bears (u. arctos), and black bears (u. americanus) derived from genome sequences. / Cronin, Matthew A.; Rincon, Gonzalo; Meredith, Robert; Macneil, Michael D.; Islas-Trejo, Alma; Cánovas, Angela; Medrano, Juan F.

In: Journal of Heredity, Vol. 105, No. 3, 01.01.2014, p. 312-323.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Molecular phylogeny and snp variation of polar bears (ursus maritimus), brown bears (u. arctos), and black bears (u. americanus) derived from genome sequences

AU - Cronin, Matthew A.

AU - Rincon, Gonzalo

AU - Meredith, Robert

AU - Macneil, Michael D.

AU - Islas-Trejo, Alma

AU - Cánovas, Angela

AU - Medrano, Juan F.

PY - 2014/1/1

Y1 - 2014/1/1

N2 - We assessed the relationships of polar bears (Ursus maritimus), brown bears (U. arctos), and black bears (U. americanus) with high throughput genomic sequencing data with an average coverage of 25× for each species. A total of 1.4 billion 100-bp paired-end reads were assembled using the polar bear and annotated giant panda (Ailuropoda melanoleuca) genome sequences as references. We identified 13.8 million single nucleotide polymorphisms (SNP) in the 3 species aligned to the polar bear genome. These data indicate that polar bears and brown bears share more SNP with each other than either does with black bears. Concatenation and coalescence-based analysis of consensus sequences of approximately 1 million base pairs of ultraconserved elements in the nuclear genome resulted in a phylogeny with black bears as the sister group to brown and polar bears, and all brown bears are in a separate clade from polar bears. Genotypes for 162 SNP loci of 336 bears from Alaska and Montana showed that the species are genetically differentiated and there is geographic population structure of brown and black bears but not polar bears.

AB - We assessed the relationships of polar bears (Ursus maritimus), brown bears (U. arctos), and black bears (U. americanus) with high throughput genomic sequencing data with an average coverage of 25× for each species. A total of 1.4 billion 100-bp paired-end reads were assembled using the polar bear and annotated giant panda (Ailuropoda melanoleuca) genome sequences as references. We identified 13.8 million single nucleotide polymorphisms (SNP) in the 3 species aligned to the polar bear genome. These data indicate that polar bears and brown bears share more SNP with each other than either does with black bears. Concatenation and coalescence-based analysis of consensus sequences of approximately 1 million base pairs of ultraconserved elements in the nuclear genome resulted in a phylogeny with black bears as the sister group to brown and polar bears, and all brown bears are in a separate clade from polar bears. Genotypes for 162 SNP loci of 336 bears from Alaska and Montana showed that the species are genetically differentiated and there is geographic population structure of brown and black bears but not polar bears.

KW - Phylogeny

KW - Ursus

KW - black bears

KW - brown

KW - molecular clock

KW - polar

KW - single nucleotide polymorphism

KW - ultraconserved elements

UR - http://www.scopus.com/inward/record.url?scp=84899015956&partnerID=8YFLogxK

U2 - 10.1093/jhered/est133

DO - 10.1093/jhered/est133

M3 - Article

VL - 105

SP - 312

EP - 323

JO - Journal of Heredity

JF - Journal of Heredity

SN - 0022-1503

IS - 3

ER -