Cargando…
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...
Autores principales: | , , , , , , , , , , , , , , , , , , , |
---|---|
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 |
_version_ | 1783395866219905024 |
---|---|
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. |
format | Online Article Text |
id | pubmed-6378093 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT bravogustavoa embracingheterogeneitycoalescingthetreeoflifeandthefutureofphylogenomics AT antonellialexandre embracingheterogeneitycoalescingthetreeoflifeandthefutureofphylogenomics AT baconchristined embracingheterogeneitycoalescingthetreeoflifeandthefutureofphylogenomics AT bartoszekkrzysztof embracingheterogeneitycoalescingthetreeoflifeandthefutureofphylogenomics AT blommozespk embracingheterogeneitycoalescingthetreeoflifeandthefutureofphylogenomics AT huynhstella embracingheterogeneitycoalescingthetreeoflifeandthefutureofphylogenomics AT jonesgraham embracingheterogeneitycoalescingthetreeoflifeandthefutureofphylogenomics AT knowlesllacey embracingheterogeneitycoalescingthetreeoflifeandthefutureofphylogenomics AT lamichhaneysangeet embracingheterogeneitycoalescingthetreeoflifeandthefutureofphylogenomics AT marcussenthomas embracingheterogeneitycoalescingthetreeoflifeandthefutureofphylogenomics AT morlonhelene embracingheterogeneitycoalescingthetreeoflifeandthefutureofphylogenomics AT nakhlehluayk embracingheterogeneitycoalescingthetreeoflifeandthefutureofphylogenomics AT oxelmanbengt embracingheterogeneitycoalescingthetreeoflifeandthefutureofphylogenomics AT pfeilbernard embracingheterogeneitycoalescingthetreeoflifeandthefutureofphylogenomics AT schliepalexander embracingheterogeneitycoalescingthetreeoflifeandthefutureofphylogenomics AT wahlbergniklas embracingheterogeneitycoalescingthetreeoflifeandthefutureofphylogenomics AT werneckfernandap embracingheterogeneitycoalescingthetreeoflifeandthefutureofphylogenomics AT wiedenhoeftjohn embracingheterogeneitycoalescingthetreeoflifeandthefutureofphylogenomics AT willowsmunrosandi embracingheterogeneitycoalescingthetreeoflifeandthefutureofphylogenomics AT edwardsscottv embracingheterogeneitycoalescingthetreeoflifeandthefutureofphylogenomics |