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

2167-8359 (ISSN)

Vol. 2019 2 6399

Subject Categories

Evolutionary Biology

Bioinformatics (Computational Biology)

Bioinformatics and Systems Biology

DOI

10.7717/peerj.6399

More information

Latest update

12/9/2020