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recordtype dspace
spelling oai:repositorio:1-15348 Embracing heterogeneity: Coalescing the tree of life and the future of phylogenomics Bravo, Gustavo A. Antonelli, Alexandre Bacon, Christine D. Bartoszek, Krzysztof Blom, Mozes P.K. Huynh, Stella Jones, Graham R. Lacey Knowles, L. Lamichhaney, Sangeet Marcussen, Thomas Morlon, Hélène Nakhleh, Luay K. Oxelman, Bengt Pfeil, Bernard E. Schliep, Alexander Wahlberg, Niklas Werneck, F. P. Wiedenhoeft, John Willows-Munro, Sandi Edwards, Scott V. Ancient Dna Transcriptome Arabidopsis Thaliana Biogeography Copy Number Variation Gene Duplication Gene Flow Gene Locus Gene Loss Gene Mapping Gene Order Genetic Parameters Recombination, Genetic Genotype Heredity Heterozygosity High Throughput Sequencing Gene Transfer, Horizontal Human Hybridization Introgression Phylogenomics Phylogeny Phylogeography Polymerase Chain Reaction Polyploidy Sanger Sequencing Polymorphism, Single Nucleotide Species Differentiation Synteny Tree Of Life Whole Genome Sequencing Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress. © 2019 Bravo et al. 2020-05-08T20:19:07Z 2020-05-08T20:19:07Z 2019 Artigo https://repositorio.inpa.gov.br/handle/1/15348 10.7717/peerj.6399 en Volume 2019, Número 2 Attribution-NonCommercial-NoDerivs 3.0 Brazil http://creativecommons.org/licenses/by-nc-nd/3.0/br/ application/pdf PeerJ
institution Instituto Nacional de Pesquisas da Amazônia - Repositório Institucional
collection INPA-RI
language English
topic Ancient Dna
Transcriptome
Arabidopsis Thaliana
Biogeography
Copy Number Variation
Gene Duplication
Gene Flow
Gene Locus
Gene Loss
Gene Mapping
Gene Order
Genetic Parameters
Recombination, Genetic
Genotype
Heredity
Heterozygosity
High Throughput Sequencing
Gene Transfer, Horizontal
Human
Hybridization
Introgression
Phylogenomics
Phylogeny
Phylogeography
Polymerase Chain Reaction
Polyploidy
Sanger Sequencing
Polymorphism, Single Nucleotide
Species Differentiation
Synteny
Tree Of Life
Whole Genome Sequencing
spellingShingle Ancient Dna
Transcriptome
Arabidopsis Thaliana
Biogeography
Copy Number Variation
Gene Duplication
Gene Flow
Gene Locus
Gene Loss
Gene Mapping
Gene Order
Genetic Parameters
Recombination, Genetic
Genotype
Heredity
Heterozygosity
High Throughput Sequencing
Gene Transfer, Horizontal
Human
Hybridization
Introgression
Phylogenomics
Phylogeny
Phylogeography
Polymerase Chain Reaction
Polyploidy
Sanger Sequencing
Polymorphism, Single Nucleotide
Species Differentiation
Synteny
Tree Of Life
Whole Genome Sequencing
Bravo, Gustavo A.
Embracing heterogeneity: Coalescing the tree of life and the future of phylogenomics
topic_facet Ancient Dna
Transcriptome
Arabidopsis Thaliana
Biogeography
Copy Number Variation
Gene Duplication
Gene Flow
Gene Locus
Gene Loss
Gene Mapping
Gene Order
Genetic Parameters
Recombination, Genetic
Genotype
Heredity
Heterozygosity
High Throughput Sequencing
Gene Transfer, Horizontal
Human
Hybridization
Introgression
Phylogenomics
Phylogeny
Phylogeography
Polymerase Chain Reaction
Polyploidy
Sanger Sequencing
Polymorphism, Single Nucleotide
Species Differentiation
Synteny
Tree Of Life
Whole Genome Sequencing
description Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress. © 2019 Bravo et al.
format Artigo
author Bravo, Gustavo A.
author2 Antonelli, Alexandre
Bacon, Christine D.
Bartoszek, Krzysztof
Blom, Mozes P.K.
Huynh, Stella
Jones, Graham R.
Lacey Knowles, L.
Lamichhaney, Sangeet
Marcussen, Thomas
Morlon, Hélène
Nakhleh, Luay K.
Oxelman, Bengt
Pfeil, Bernard E.
Schliep, Alexander
Wahlberg, Niklas
Werneck, F. P.
Wiedenhoeft, John
Willows-Munro, Sandi
Edwards, Scott V.
author2Str Antonelli, Alexandre
Bacon, Christine D.
Bartoszek, Krzysztof
Blom, Mozes P.K.
Huynh, Stella
Jones, Graham R.
Lacey Knowles, L.
Lamichhaney, Sangeet
Marcussen, Thomas
Morlon, Hélène
Nakhleh, Luay K.
Oxelman, Bengt
Pfeil, Bernard E.
Schliep, Alexander
Wahlberg, Niklas
Werneck, F. P.
Wiedenhoeft, John
Willows-Munro, Sandi
Edwards, Scott V.
title Embracing heterogeneity: Coalescing the tree of life and the future of phylogenomics
title_short Embracing heterogeneity: Coalescing the tree of life and the future of phylogenomics
title_full Embracing heterogeneity: Coalescing the tree of life and the future of phylogenomics
title_fullStr Embracing heterogeneity: Coalescing the tree of life and the future of phylogenomics
title_full_unstemmed Embracing heterogeneity: Coalescing the tree of life and the future of phylogenomics
title_sort embracing heterogeneity: coalescing the tree of life and the future of phylogenomics
publisher PeerJ
publishDate 2020
url https://repositorio.inpa.gov.br/handle/1/15348
_version_ 1787145066932862976
score 11.755432

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