Embracing heterogeneity: Coalescing the tree of life and the future of phylogenomics
Journal article, 2019
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.
Genome
Gene flow
Speciation
Retroelement
Multispecies coalescent model
Transcriptome
Author
Gustavo A. Bravo
Harvard University
Alexandre Antonelli
Harvard University
Gothenburg Global Biodiversity Centre
University of Gothenburg
Gothenburg Botanical Garden
Christine D. Bacon
Gothenburg Global Biodiversity Centre
University of Gothenburg
Krzysztof Bartoszek
Linköping University
Mozes P.K. Blom
Naturhistoriska riksmuseet
Stella Huynh
University of Neuchatel
Robert Graham Jones
University of Gothenburg
L. Lacey Knowles
University of Michigan
Sangeet Lamichhaney
Harvard University
Thomas Marcussen
University of Oslo
Hélène Morlon
Ecole Normale Superieure (ENS)
Luay K. Nakhleh
Rice University
Bengt Oxelman
University of Gothenburg
Gothenburg Global Biodiversity Centre
Bernard Pfeil
University of Gothenburg
Alexander Schliep
Niklas Wahlberg
Lund University
Fernanda P. Werneck
Instituto Nacional de Pesquisas da Amazonia
John Wiedenhoeft
Rutgers University
Chalmers, Computer Science and Engineering (Chalmers), Data Science
Sandi Willows-Munro
University of KwaZulu-Natal
Scott Edwards
Harvard University
Chalmers, Mathematical Sciences
PeerJ
21678359 (eISSN)
Vol. 2019 2 6399Subject Categories
Evolutionary Biology
Bioinformatics (Computational Biology)
Bioinformatics and Systems Biology
DOI
10.7717/peerj.6399