Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements

Abstract Marker selection has emerged as an important component of phylogenomic study design due to rising concerns of the effects of gene tree estimation error, model misspecification, and data-type differences. Researchers must balance various trade-offs associated with locus length and evolutiona...

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Veröffentlicht in:Molecular biology and evolution Jg. 37; H. 3; S. 904 - 922
Hauptverfasser: Karin, Benjamin R, Gamble, Tony, Jackman, Todd R
Format: Journal Article
Sprache:Englisch
Veröffentlicht: United States Oxford University Press 01.03.2020
Schlagworte:
Animals
Bayes Theorem
Bayesian analysis
Biology
Computational Biology - methods
Datasets
Evolution
Evolution, Molecular
Exons
Genetic diversity
Genetic Loci
Genomes
Lizards
Methods
Optimization
Orthology
Phylogenetics
Phylogeny
RAG1 protein
Reptiles
Reptiles - classification
Reptiles - genetics
Sequence Alignment
Snakes
Whole Genome Sequencing - methods
sequence capture
phylogenetics
anchored hybrid enrichment
marker selection
reduced representation
ultraconserved elements
ISSN:0737-4038, 1537-1719, 1537-1719
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Abstract Abstract Marker selection has emerged as an important component of phylogenomic study design due to rising concerns of the effects of gene tree estimation error, model misspecification, and data-type differences. Researchers must balance various trade-offs associated with locus length and evolutionary rate among other factors. The most commonly used reduced representation data sets for phylogenomics are ultraconserved elements (UCEs) and Anchored Hybrid Enrichment (AHE). Here, we introduce Rapidly Evolving Long Exon Capture (RELEC), a new set of loci that targets single exons that are both rapidly evolving (evolutionary rate faster than RAG1) and relatively long in length (>1,500 bp), while at the same time avoiding paralogy issues across amniotes. We compare the RELEC data set to UCEs and AHE in squamate reptiles by aligning and analyzing orthologous sequences from 17 squamate genomes, composed of 10 snakes and 7 lizards. The RELEC data set (179 loci) outperforms AHE and UCEs by maximizing per-locus genetic variation while maintaining presence and orthology across a range of evolutionary scales. RELEC markers show higher phylogenetic informativeness than UCE and AHE loci, and RELEC gene trees show greater similarity to the species tree than AHE or UCE gene trees. Furthermore, with fewer loci, RELEC remains computationally tractable for full Bayesian coalescent species tree analyses. We contrast RELEC to and discuss important aspects of comparable methods, and demonstrate how RELEC may be the most effective set of loci for resolving difficult nodes and rapid radiations. We provide several resources for capturing or extracting RELEC loci from other amniote groups.
AbstractList Marker selection has emerged as an important component of phylogenomic study design due to rising concerns of the effects of gene tree estimation error, model misspecification, and data-type differences. Researchers must balance various trade-offs associated with locus length and evolutionary rate among other factors. The most commonly used reduced representation data sets for phylogenomics are ultraconserved elements (UCEs) and Anchored Hybrid Enrichment (AHE). Here, we introduce Rapidly Evolving Long Exon Capture (RELEC), a new set of loci that targets single exons that are both rapidly evolving (evolutionary rate faster than RAG1) and relatively long in length (>1,500 bp), while at the same time avoiding paralogy issues across amniotes. We compare the RELEC data set to UCEs and AHE in squamate reptiles by aligning and analyzing orthologous sequences from 17 squamate genomes, composed of 10 snakes and 7 lizards. The RELEC data set (179 loci) outperforms AHE and UCEs by maximizing per-locus genetic variation while maintaining presence and orthology across a range of evolutionary scales. RELEC markers show higher phylogenetic informativeness than UCE and AHE loci, and RELEC gene trees show greater similarity to the species tree than AHE or UCE gene trees. Furthermore, with fewer loci, RELEC remains computationally tractable for full Bayesian coalescent species tree analyses. We contrast RELEC to and discuss important aspects of comparable methods, and demonstrate how RELEC may be the most effective set of loci for resolving difficult nodes and rapid radiations. We provide several resources for capturing or extracting RELEC loci from other amniote groups.
Marker selection has emerged as an important component of phylogenomic study design due to rising concerns of the effects of gene tree estimation error, model misspecification, and data-type differences. Researchers must balance various trade-offs associated with locus length and evolutionary rate among other factors. The most commonly used reduced representation data sets for phylogenomics are ultraconserved elements (UCEs) and Anchored Hybrid Enrichment (AHE). Here, we introduce Rapidly Evolving Long Exon Capture (RELEC), a new set of loci that targets single exons that are both rapidly evolving (evolutionary rate faster than RAG1) and relatively long in length (>1,500 bp), while at the same time avoiding paralogy issues across amniotes. We compare the RELEC data set to UCEs and AHE in squamate reptiles by aligning and analyzing orthologous sequences from 17 squamate genomes, composed of 10 snakes and 7 lizards. The RELEC data set (179 loci) outperforms AHE and UCEs by maximizing per-locus genetic variation while maintaining presence and orthology across a range of evolutionary scales. RELEC markers show higher phylogenetic informativeness than UCE and AHE loci, and RELEC gene trees show greater similarity to the species tree than AHE or UCE gene trees. Furthermore, with fewer loci, RELEC remains computationally tractable for full Bayesian coalescent species tree analyses. We contrast RELEC to and discuss important aspects of comparable methods, and demonstrate how RELEC may be the most effective set of loci for resolving difficult nodes and rapid radiations. We provide several resources for capturing or extracting RELEC loci from other amniote groups.Marker selection has emerged as an important component of phylogenomic study design due to rising concerns of the effects of gene tree estimation error, model misspecification, and data-type differences. Researchers must balance various trade-offs associated with locus length and evolutionary rate among other factors. The most commonly used reduced representation data sets for phylogenomics are ultraconserved elements (UCEs) and Anchored Hybrid Enrichment (AHE). Here, we introduce Rapidly Evolving Long Exon Capture (RELEC), a new set of loci that targets single exons that are both rapidly evolving (evolutionary rate faster than RAG1) and relatively long in length (>1,500 bp), while at the same time avoiding paralogy issues across amniotes. We compare the RELEC data set to UCEs and AHE in squamate reptiles by aligning and analyzing orthologous sequences from 17 squamate genomes, composed of 10 snakes and 7 lizards. The RELEC data set (179 loci) outperforms AHE and UCEs by maximizing per-locus genetic variation while maintaining presence and orthology across a range of evolutionary scales. RELEC markers show higher phylogenetic informativeness than UCE and AHE loci, and RELEC gene trees show greater similarity to the species tree than AHE or UCE gene trees. Furthermore, with fewer loci, RELEC remains computationally tractable for full Bayesian coalescent species tree analyses. We contrast RELEC to and discuss important aspects of comparable methods, and demonstrate how RELEC may be the most effective set of loci for resolving difficult nodes and rapid radiations. We provide several resources for capturing or extracting RELEC loci from other amniote groups.
Abstract Marker selection has emerged as an important component of phylogenomic study design due to rising concerns of the effects of gene tree estimation error, model misspecification, and data-type differences. Researchers must balance various trade-offs associated with locus length and evolutionary rate among other factors. The most commonly used reduced representation data sets for phylogenomics are ultraconserved elements (UCEs) and Anchored Hybrid Enrichment (AHE). Here, we introduce Rapidly Evolving Long Exon Capture (RELEC), a new set of loci that targets single exons that are both rapidly evolving (evolutionary rate faster than RAG1) and relatively long in length (>1,500 bp), while at the same time avoiding paralogy issues across amniotes. We compare the RELEC data set to UCEs and AHE in squamate reptiles by aligning and analyzing orthologous sequences from 17 squamate genomes, composed of 10 snakes and 7 lizards. The RELEC data set (179 loci) outperforms AHE and UCEs by maximizing per-locus genetic variation while maintaining presence and orthology across a range of evolutionary scales. RELEC markers show higher phylogenetic informativeness than UCE and AHE loci, and RELEC gene trees show greater similarity to the species tree than AHE or UCE gene trees. Furthermore, with fewer loci, RELEC remains computationally tractable for full Bayesian coalescent species tree analyses. We contrast RELEC to and discuss important aspects of comparable methods, and demonstrate how RELEC may be the most effective set of loci for resolving difficult nodes and rapid radiations. We provide several resources for capturing or extracting RELEC loci from other amniote groups.
Author Jackman, Todd R
Karin, Benjamin R
Gamble, Tony
AuthorAffiliation 4 Milwaukee Public Museum , Milwaukee, WI
1 Department of Biology, Villanova University , Villanova, PA
5 Bell Museum of Natural History, University of Minnesota , St. Paul, MN
3 Department of Biological Sciences, Marquette University , Milwaukee, WI
2 Museum of Vertebrate Zoology and Department of Integrative Biology , University of California, Berkeley, CA
AuthorAffiliation_xml – name: 5 Bell Museum of Natural History, University of Minnesota , St. Paul, MN
– name: 4 Milwaukee Public Museum , Milwaukee, WI
– name: 2 Museum of Vertebrate Zoology and Department of Integrative Biology , University of California, Berkeley, CA
– name: 1 Department of Biology, Villanova University , Villanova, PA
– name: 3 Department of Biological Sciences, Marquette University , Milwaukee, WI
Author_xml – sequence: 1
  givenname: Benjamin R
  orcidid: 0000-0001-7936-7099
  surname: Karin
  fullname: Karin, Benjamin R
  email: benkarin@berkeley.edu
  organization: Department of Biology, Villanova University, Villanova, PA
– sequence: 2
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  surname: Gamble
  fullname: Gamble, Tony
  organization: Department of Biological Sciences, Marquette University, Milwaukee, WI
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  surname: Jackman
  fullname: Jackman, Todd R
  organization: Department of Biology, Villanova University, Villanova, PA
BackLink https://www.ncbi.nlm.nih.gov/pubmed/31710677$$D View this record in MEDLINE/PubMed
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ContentType Journal Article
Copyright The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. 2019
The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
Copyright_xml – notice: The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. 2019
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1537-1719
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Issue 3
Keywords sequence capture
phylogenetics
anchored hybrid enrichment
marker selection
reduced representation
ultraconserved elements
Language English
License This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
http://creativecommons.org/licenses/by/4.0
The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
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PublicationTitle Molecular biology and evolution
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Publisher Oxford University Press
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Snippet Abstract Marker selection has emerged as an important component of phylogenomic study design due to rising concerns of the effects of gene tree estimation...
Marker selection has emerged as an important component of phylogenomic study design due to rising concerns of the effects of gene tree estimation error, model...
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Enrichment Source
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StartPage 904
SubjectTerms Animals
Bayes Theorem
Bayesian analysis
Biology
Computational Biology - methods
Datasets
Evolution
Evolution, Molecular
Exons
Genetic diversity
Genetic Loci
Genomes
Lizards
Methods
Optimization
Orthology
Phylogenetics
Phylogeny
RAG1 protein
Reptiles
Reptiles - classification
Reptiles - genetics
Sequence Alignment
Snakes
Whole Genome Sequencing - methods
Title Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements
URI https://www.ncbi.nlm.nih.gov/pubmed/31710677
https://www.proquest.com/docview/3171297905
https://www.proquest.com/docview/2314012846
https://pubmed.ncbi.nlm.nih.gov/PMC7038749
Volume 37
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