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Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

The field of phylogenetics is on the cusp of a major revolution, enabled by new methods of data collection that leverage both genomic resources and recent advances in DNA sequencing. Previous phylogenetic work has required laborintensive marker development coupled with single-locus polymerase chain... Full description

Journal Title: Systematic biology 2012-10-01, Vol.61 (5), p.727-744
Main Author: Lemmon, Alan R
Other Authors: Emme, Sandra A , Lemmon, Emily Moriarty
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/22605266
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recordid: cdi_proquest_miscellaneous_1033457185
title: Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics
format: Article
creator:
  • Lemmon, Alan R
  • Emme, Sandra A
  • Lemmon, Emily Moriarty
subjects:
  • Animals
  • Biological taxonomies
  • Data collection
  • Deoxyribonucleic acid
  • DNA
  • DNA Probes - genetics
  • Gene loci
  • Genetic loci
  • Genome
  • Genomes
  • Genomics
  • High-Throughput Nucleotide Sequencing - economics
  • High-Throughput Nucleotide Sequencing - methods
  • Humans
  • Libraries
  • Phylogenetics
  • Phylogeny
  • Polymerase chain reaction
  • Sequence Analysis, DNA - economics
  • Sequence Analysis, DNA - methods
  • Sequencing
  • SOCIETY OF SYSTEMATIC BIOLOGISTS SYMPOSIUM ARTICLES
  • Taxa
  • Vertebrates
  • Vertebrates - classification
  • Vertebrates - genetics
ispartof: Systematic biology, 2012-10-01, Vol.61 (5), p.727-744
description: The field of phylogenetics is on the cusp of a major revolution, enabled by new methods of data collection that leverage both genomic resources and recent advances in DNA sequencing. Previous phylogenetic work has required laborintensive marker development coupled with single-locus polymerase chain reaction and DNA sequencing on clade-by-clade and locus-by-locus basis. Here, we present a new, cost-efficient, and rapid approach to obtaining data from hundreds of loci for potentially hundreds of individuals for deep and shallow phylogenetic studies. Specifically, we designed probes for target enrichment of > 500 loci in highly conserved anchor regions of vertebrate genomes (flanked by less conserved regions) from five model species and tested enrichment efficiency in nonmodel species up to 508 million years divergent from the nearest model. We found that hybrid enrichment using conserved probes (anchored enrichment) can recover a large number of unlinked loci that are useful at a diversity of phylogenetic timescales. This new approach has the potential not only to expedite resolution of deep-scale portions of the Tree of Life but also to greatly accelerate resolution of the large number of shallow clades that remain unresolved. The combination of low cost (~ 1% of the cost of traditional Sänger sequencing and ~ 3.5% of the cost of high-throughput amplicon sequencing for projects on the scale of 500 loci ÷ 100 individuals) and rapid data collection (~ 2 weeks of laboratory time) are expected to make this approach tractable even for researchers working on systems with limited or nonexistent genomic resources.
language: eng
source: Alma/SFX Local Collection
identifier: ISSN: 1063-5157
fulltext: fulltext
issn:
  • 1063-5157
  • 1076-836X
url: Link


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descriptionThe field of phylogenetics is on the cusp of a major revolution, enabled by new methods of data collection that leverage both genomic resources and recent advances in DNA sequencing. Previous phylogenetic work has required laborintensive marker development coupled with single-locus polymerase chain reaction and DNA sequencing on clade-by-clade and locus-by-locus basis. Here, we present a new, cost-efficient, and rapid approach to obtaining data from hundreds of loci for potentially hundreds of individuals for deep and shallow phylogenetic studies. Specifically, we designed probes for target enrichment of > 500 loci in highly conserved anchor regions of vertebrate genomes (flanked by less conserved regions) from five model species and tested enrichment efficiency in nonmodel species up to 508 million years divergent from the nearest model. We found that hybrid enrichment using conserved probes (anchored enrichment) can recover a large number of unlinked loci that are useful at a diversity of phylogenetic timescales. This new approach has the potential not only to expedite resolution of deep-scale portions of the Tree of Life but also to greatly accelerate resolution of the large number of shallow clades that remain unresolved. The combination of low cost (~ 1% of the cost of traditional Sänger sequencing and ~ 3.5% of the cost of high-throughput amplicon sequencing for projects on the scale of 500 loci ÷ 100 individuals) and rapid data collection (~ 2 weeks of laboratory time) are expected to make this approach tractable even for researchers working on systems with limited or nonexistent genomic resources.
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subjectAnimals ; Biological taxonomies ; Data collection ; Deoxyribonucleic acid ; DNA ; DNA Probes - genetics ; Gene loci ; Genetic loci ; Genome ; Genomes ; Genomics ; High-Throughput Nucleotide Sequencing - economics ; High-Throughput Nucleotide Sequencing - methods ; Humans ; Libraries ; Phylogenetics ; Phylogeny ; Polymerase chain reaction ; Sequence Analysis, DNA - economics ; Sequence Analysis, DNA - methods ; Sequencing ; SOCIETY OF SYSTEMATIC BIOLOGISTS SYMPOSIUM ARTICLES ; Taxa ; Vertebrates ; Vertebrates - classification ; Vertebrates - genetics
ispartofSystematic biology, 2012-10-01, Vol.61 (5), p.727-744
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0Copyright © 2012 Society of Systematic Biologists
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descriptionThe field of phylogenetics is on the cusp of a major revolution, enabled by new methods of data collection that leverage both genomic resources and recent advances in DNA sequencing. Previous phylogenetic work has required laborintensive marker development coupled with single-locus polymerase chain reaction and DNA sequencing on clade-by-clade and locus-by-locus basis. Here, we present a new, cost-efficient, and rapid approach to obtaining data from hundreds of loci for potentially hundreds of individuals for deep and shallow phylogenetic studies. Specifically, we designed probes for target enrichment of > 500 loci in highly conserved anchor regions of vertebrate genomes (flanked by less conserved regions) from five model species and tested enrichment efficiency in nonmodel species up to 508 million years divergent from the nearest model. We found that hybrid enrichment using conserved probes (anchored enrichment) can recover a large number of unlinked loci that are useful at a diversity of phylogenetic timescales. This new approach has the potential not only to expedite resolution of deep-scale portions of the Tree of Life but also to greatly accelerate resolution of the large number of shallow clades that remain unresolved. The combination of low cost (~ 1% of the cost of traditional Sänger sequencing and ~ 3.5% of the cost of high-throughput amplicon sequencing for projects on the scale of 500 loci ÷ 100 individuals) and rapid data collection (~ 2 weeks of laboratory time) are expected to make this approach tractable even for researchers working on systems with limited or nonexistent genomic resources.
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abstractThe field of phylogenetics is on the cusp of a major revolution, enabled by new methods of data collection that leverage both genomic resources and recent advances in DNA sequencing. Previous phylogenetic work has required laborintensive marker development coupled with single-locus polymerase chain reaction and DNA sequencing on clade-by-clade and locus-by-locus basis. Here, we present a new, cost-efficient, and rapid approach to obtaining data from hundreds of loci for potentially hundreds of individuals for deep and shallow phylogenetic studies. Specifically, we designed probes for target enrichment of > 500 loci in highly conserved anchor regions of vertebrate genomes (flanked by less conserved regions) from five model species and tested enrichment efficiency in nonmodel species up to 508 million years divergent from the nearest model. We found that hybrid enrichment using conserved probes (anchored enrichment) can recover a large number of unlinked loci that are useful at a diversity of phylogenetic timescales. This new approach has the potential not only to expedite resolution of deep-scale portions of the Tree of Life but also to greatly accelerate resolution of the large number of shallow clades that remain unresolved. The combination of low cost (~ 1% of the cost of traditional Sänger sequencing and ~ 3.5% of the cost of high-throughput amplicon sequencing for projects on the scale of 500 loci ÷ 100 individuals) and rapid data collection (~ 2 weeks of laboratory time) are expected to make this approach tractable even for researchers working on systems with limited or nonexistent genomic resources.
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