Embracing heterogeneity: Building the Tree of Life and the future of phylogenomics
- Published
- Accepted
- Subject Areas
- Biodiversity, Computational Biology, Evolutionary Studies, Genomics
- Keywords
- gene flow, genome, multispecies coalescent model, retroelement, speciation, transcriptome
- Copyright
- © 2018 Bravo et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2018. Embracing heterogeneity: Building the Tree of Life and the future of phylogenomics. PeerJ Preprints 6:e26449v3 https://doi.org/10.7287/peerj.preprints.26449v3
Abstract
Building the Tree of Life (ToL) is a major challenge of modern biology, requiring major 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. 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 major model supporting innovation in phylogenomics today, the multispecies coalescent model. 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 to each step, are essential for progress.
Author Comment
This version contains an updated version of Supplementary Table S1 and Figure 2 after removal of two data sets. Also, it contains other minor edits in the references and a section on Heterozygosity and Intra-Individual Site Polymorphisms following suggestions made by Thomas Couvreur and Tobias Andermann.
Supplemental Information
Supplementary Table S1: Information on number of species, number of loci, and data set size contained in 164 phylogenomic data sets
Each row represents a data set included in Figure 2. For further details on how this table was built, please see section "Compilation of data in Supplementary Table S1" in the Supplementary Material.