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PeerJ. 2019 Feb 14;7:e6399. doi: 10.7717/peerj.6399. eCollection 2019.

Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics.

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Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA.
Gothenburg Global Biodiversity Centre, Göteborg, Sweden.
Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden.
Gothenburg Botanical Garden, Göteborg, Sweden.
Department of Computer and Information Science, Linköping University, Linköping, Sweden.
Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland.
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.
Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway.
Institut de Biologie, Ecole Normale Supérieure de Paris, Paris, France.
Department of Computer Science, Rice University, Houston, TX, USA.
Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden.
Department of Biology, Lund University, Lund, Sweden.
Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisa da Amazônia, Manaus, AM, Brazil.
Department of Computer Science, Rutgers University, Piscataway, NJ, USA.
School of Life Sciences, University of Kwazulu-Natal, Pietermaritzburg, South Africa.
Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden.


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.


Gene flow; Genome; Multispecies coalescent model; Retroelement; Speciation; Transcriptome

Conflict of interest statement

Alexander Schliep and Scott V. Edwards are Academic Editors for PeerJ.

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