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Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, par... Full description

Journal Title: Systematic biology 2012-10-01, Vol.61 (5), p.717-726
Main Author: Faircloth, Brant C
Other Authors: McCormack, John E , Crawford, Nicholas G , Harvey, Michael G , Brumfield, Robb T , Glenn, Travis C
Format: Electronic Article Electronic Article
Language: English
Subjects:
DNA
Quelle: Alma/SFX Local Collection
Publisher: England: Oxford University Press
ID: ISSN: 1063-5157
Link: https://www.ncbi.nlm.nih.gov/pubmed/22232343
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recordid: cdi_proquest_miscellaneous_1033457148
title: Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales
format: Article
creator:
  • Faircloth, Brant C
  • McCormack, John E
  • Crawford, Nicholas G
  • Harvey, Michael G
  • Brumfield, Robb T
  • Glenn, Travis C
subjects:
  • Animals
  • Biological taxonomies
  • Biomarkers
  • Birds
  • Computer Simulation
  • Conserved Sequence
  • Deoxyribonucleic acid
  • DNA
  • Evolution, Molecular
  • Evolutionary biology
  • Gene loci
  • Genetic loci
  • Genetic Markers
  • Genome
  • Genomes
  • Genomics
  • High-Throughput Nucleotide Sequencing - methods
  • Libraries
  • Phylogenetics
  • Phylogeny
  • Primates
  • Sequence Alignment
  • Sequence Analysis, DNA - methods
  • Sequencing
  • SOCIETY OF SYSTEMATIC BIOLOGISTS SYMPOSIUM ARTICLES
  • Taxa
  • Vertebrates - classification
  • Vertebrates - genetics
ispartof: Systematic biology, 2012-10-01, Vol.61 (5), p.717-726
description: Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with nonmodel organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota because UCEs and phylogenetic relationships are well-known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2386 UCE-anchored loci from nine, nonmodel avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels.
language: eng
source: Alma/SFX Local Collection
identifier: ISSN: 1063-5157
fulltext: fulltext
issn:
  • 1063-5157
  • 1076-836X
url: Link


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descriptionAlthough massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with nonmodel organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota because UCEs and phylogenetic relationships are well-known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2386 UCE-anchored loci from nine, nonmodel avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels.
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subjectAnimals ; Biological taxonomies ; Biomarkers ; Birds ; Computer Simulation ; Conserved Sequence ; Deoxyribonucleic acid ; DNA ; Evolution, Molecular ; Evolutionary biology ; Gene loci ; Genetic loci ; Genetic Markers ; Genome ; Genomes ; Genomics ; High-Throughput Nucleotide Sequencing - methods ; Libraries ; Phylogenetics ; Phylogeny ; Primates ; Sequence Alignment ; Sequence Analysis, DNA - methods ; Sequencing ; SOCIETY OF SYSTEMATIC BIOLOGISTS SYMPOSIUM ARTICLES ; Taxa ; Vertebrates - classification ; Vertebrates - genetics
ispartofSystematic biology, 2012-10-01, Vol.61 (5), p.717-726
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0Copyright © 2012 Society of Systematic Biologists
1The Author(s) 2012. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com 2012
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descriptionAlthough massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with nonmodel organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota because UCEs and phylogenetic relationships are well-known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2386 UCE-anchored loci from nine, nonmodel avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels.
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abstractAlthough massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with nonmodel organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota because UCEs and phylogenetic relationships are well-known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2386 UCE-anchored loci from nine, nonmodel avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels.
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