Embracing heterogeneity: Coalescing the tree of life and the future of phylogenomics
Artikel i vetenskaplig tidskrift, 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.
Retroelement
Gene flow
Transcriptome
Speciation
Multispecies coalescent model
Genome
Författare
Gustavo A. Bravo
Harvard University
Alexandre Antonelli
Göteborgs universitet
Göteborgs botaniska trädgård
Gothenburg Global Biodiversity Centre
Harvard University
Christine D. Bacon
Göteborgs universitet
Gothenburg Global Biodiversity Centre
Krzysztof Bartoszek
Linköpings universitet
Mozes P.K. Blom
Naturhistoriska riksmuseet
Stella Huynh
Université de Neuchâtel
Robert Graham Jones
Göteborgs universitet
L. Lacey Knowles
University of Michigan
Sangeet Lamichhaney
Harvard University
Thomas Marcussen
Universitetet i Oslo
Hélène Morlon
Ecole Normale Superieure (ENS)
Luay K. Nakhleh
Rice University
Bengt Oxelman
Gothenburg Global Biodiversity Centre
Göteborgs universitet
Bernard Pfeil
Göteborgs universitet
Alexander Schliep
Chalmers, Data- och informationsteknik
Niklas Wahlberg
Lunds universitet
Fernanda P. Werneck
Instituto Nacional de Pesquisas da Amazonia
John Wiedenhoeft
Rutgers University
Chalmers, Data- och informationsteknik, Data Science
Sandi Willows-Munro
University of KwaZulu-Natal
Scott Edwards
Harvard University
Chalmers, Matematiska vetenskaper
PeerJ
21678359 (eISSN)
Vol. 2019 2 6399Ämneskategorier (SSIF 2011)
Evolutionsbiologi
Bioinformatik (beräkningsbiologi)
Bioinformatik och systembiologi
DOI
10.7717/peerj.6399