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Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics
Harvard Univ, MA 02138 USA.
Harvard Univ, MA 02138 USA; Gothenburg Global Biodivers Ctr, Sweden; Univ Gothenburg, Sweden; Gothenburg Bot Garden, Sweden.
Gothenburg Global Biodivers Ctr, Sweden; Univ Gothenburg, Sweden.
Linköping University, Department of Computer and Information Science, The Division of Statistics and Machine Learning. Linköping University, Faculty of Arts and Sciences.ORCID iD: 0000-0002-5816-4345
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2019 (English)In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 7, article id e6399Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
PEERJ INC , 2019. Vol. 7, article id e6399
Keywords [en]
Gene flow; Genome; Multispecies coalescent model; Retroelement; Speciation; Transcriptome
National Category
Evolutionary Biology
Identifiers
URN: urn:nbn:se:liu:diva-155004DOI: 10.7717/peerj.6399ISI: 000458746400004PubMedID: 30783571OAI: oai:DiVA.org:liu-155004DiVA, id: diva2:1297526
Note

Funding Agencies|Chalmers University of Technology; University of Gothenburg; Swedish Research Council; U.S. National Science Foundation; European Research Council under the European Unions Seventh Framework Programme (FP/2007-2013, ERC) [331024]; Swedish Foundation for Strategic Research; Wallenberg Academy Fellowship; Conselho Nacional de Desenvolvimento Cientifico e Tecnologico-CNPq; U.S. National Academy of Sciences; U.S. Agency of International Development-PEER NAS/USAID; LOreal-Unesco For Women in Science Program

Available from: 2019-03-20 Created: 2019-03-20 Last updated: 2019-09-04

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