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

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dc.citation.articleNumbere6399en_US
dc.citation.journalTitlePeerJen_US
dc.citation.volumeNumber7en_US
dc.contributor.authorBravo, Gustavo A.en_US
dc.contributor.authorAntonelli, Alexandreen_US
dc.contributor.authorBacon, Christine D.en_US
dc.contributor.authorBartoszek, Krzysztofen_US
dc.contributor.authorBlom, Mozes P.K.en_US
dc.contributor.authorHuynh, Stellaen_US
dc.contributor.authorJones, Grahamen_US
dc.contributor.authorKnowles, L. Laceyen_US
dc.contributor.authorLamichhaney, Sangeeten_US
dc.contributor.authorMarcussen, Thomasen_US
dc.contributor.authorMorlon, Hélèneen_US
dc.contributor.authorNakhleh, Luay K.en_US
dc.contributor.authorOxelman, Bengten_US
dc.contributor.authorPfeil, Bernarden_US
dc.contributor.authorSchliep, Alexanderen_US
dc.contributor.authorWahlberg, Niklasen_US
dc.contributor.authorWerneck, Fernanda P.en_US
dc.contributor.authorWiedenhoeft, Johnen_US
dc.contributor.authorWillows-Munro, Sandien_US
dc.contributor.authorEdwards, Scott V.en_US
dc.date.accessioned2019-12-12T17:25:37Zen_US
dc.date.available2019-12-12T17:25:37Zen_US
dc.date.issued2019en_US
dc.description.abstractBuilding 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.en_US
dc.identifier.citationBravo, Gustavo A., Antonelli, Alexandre, Bacon, Christine D., et al.. "Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics." <i>PeerJ,</i> 7, (2019) PeerJ: https://doi.org/10.7717/peerj.6399.en_US
dc.identifier.digitalpeerj-07-6399en_US
dc.identifier.doihttps://doi.org/10.7717/peerj.6399en_US
dc.identifier.urihttps://hdl.handle.net/1911/107887en_US
dc.language.isoengen_US
dc.publisherPeerJen_US
dc.rightsDistributed under Creative Commons CC-BY 4.0en_US
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en_US
dc.titleEmbracing heterogeneity: coalescing the Tree of Life and the future of phylogenomicsen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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