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Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics

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...

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Autores principales: Bravo, Gustavo A., Antonelli, Alexandre, Bacon, Christine D., Bartoszek, Krzysztof, Blom, Mozes P. K., Huynh, Stella, Jones, Graham, Knowles, L. Lacey, Lamichhaney, Sangeet, Marcussen, Thomas, Morlon, Hélène, Nakhleh, Luay K., Oxelman, Bengt, Pfeil, Bernard, Schliep, Alexander, Wahlberg, Niklas, Werneck, Fernanda P., Wiedenhoeft, John, Willows-Munro, Sandi, Edwards, Scott V.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6378093/
https://www.ncbi.nlm.nih.gov/pubmed/30783571
http://dx.doi.org/10.7717/peerj.6399
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author Bravo, Gustavo A.
Antonelli, Alexandre
Bacon, Christine D.
Bartoszek, Krzysztof
Blom, Mozes P. K.
Huynh, Stella
Jones, Graham
Knowles, L. Lacey
Lamichhaney, Sangeet
Marcussen, Thomas
Morlon, Hélène
Nakhleh, Luay K.
Oxelman, Bengt
Pfeil, Bernard
Schliep, Alexander
Wahlberg, Niklas
Werneck, Fernanda P.
Wiedenhoeft, John
Willows-Munro, Sandi
Edwards, Scott V.
author_facet Bravo, Gustavo A.
Antonelli, Alexandre
Bacon, Christine D.
Bartoszek, Krzysztof
Blom, Mozes P. K.
Huynh, Stella
Jones, Graham
Knowles, L. Lacey
Lamichhaney, Sangeet
Marcussen, Thomas
Morlon, Hélène
Nakhleh, Luay K.
Oxelman, Bengt
Pfeil, Bernard
Schliep, Alexander
Wahlberg, Niklas
Werneck, Fernanda P.
Wiedenhoeft, John
Willows-Munro, Sandi
Edwards, Scott V.
author_sort Bravo, Gustavo A.
collection PubMed
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.
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spelling pubmed-63780932019-02-19 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 Knowles, L. Lacey Lamichhaney, Sangeet Marcussen, Thomas Morlon, Hélène Nakhleh, Luay K. Oxelman, Bengt Pfeil, Bernard Schliep, Alexander Wahlberg, Niklas Werneck, Fernanda P. Wiedenhoeft, John Willows-Munro, Sandi Edwards, Scott V. PeerJ Biodiversity 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. PeerJ Inc. 2019-02-14 /pmc/articles/PMC6378093/ /pubmed/30783571 http://dx.doi.org/10.7717/peerj.6399 Text en © 2019 Bravo et al. http://creativecommons.org/licenses/by/4.0/ 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 use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Biodiversity
Bravo, Gustavo A.
Antonelli, Alexandre
Bacon, Christine D.
Bartoszek, Krzysztof
Blom, Mozes P. K.
Huynh, Stella
Jones, Graham
Knowles, L. Lacey
Lamichhaney, Sangeet
Marcussen, Thomas
Morlon, Hélène
Nakhleh, Luay K.
Oxelman, Bengt
Pfeil, Bernard
Schliep, Alexander
Wahlberg, Niklas
Werneck, Fernanda P.
Wiedenhoeft, John
Willows-Munro, Sandi
Edwards, Scott V.
Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics
title 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_short 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
topic Biodiversity
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6378093/
https://www.ncbi.nlm.nih.gov/pubmed/30783571
http://dx.doi.org/10.7717/peerj.6399
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