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  • Antonelli, Alexandre,1978Gothenburg University,Göteborgs universitet,University of Gothenburg,Harvard University,Harvard Univ, MA 02138 USA; Gothenburg Global Biodivers Ctr, Sweden; Univ Gothenburg, Sweden; Gothenburg Bot Garden, Sweden,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences,Göteborgs botaniska trädgård,Gothenburg Botanical Garden (author)

Embracing heterogeneity: Coalescing the tree of life and the future of phylogenomics

  • Article/chapterEnglish2019

Publisher, publication year, extent ...

  • 2019-02-14
  • PeerJ,2019
  • electronicrdacarrier

Numbers

  • LIBRIS-ID:oai:research.chalmers.se:a8952ec8-e4f4-486b-b7c5-78d21c70fc40
  • https://research.chalmers.se/publication/520650URI
  • https://doi.org/10.7717/peerj.6399DOI
  • https://lup.lub.lu.se/record/ab028233-5020-41d1-9d2f-3a461d2291f4URI
  • https://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-155004URI
  • https://gup.ub.gu.se/publication/328895URI

Supplementary language notes

  • Language:English
  • Summary in:English

Part of subdatabase

Classification

  • Subject category:art swepub-publicationtype
  • Subject category:ref swepub-contenttype

Notes

  • Funding Agencies|Chalmers University of Technology; University of Gothenburg; Swedish Research Council; U.S. National Science Foundation; European Research Council under the European Unions Seventh Framework Programme (FP/2007-2013, ERC) [331024]; Swedish Foundation for Strategic Research; Wallenberg Academy Fellowship; Conselho Nacional de Desenvolvimento Cientifico e Tecnologico-CNPq; U.S. National Academy of Sciences; U.S. Agency of International Development-PEER NAS/USAID; LOreal-Unesco For Women in Science Program
  • 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.

Subject headings and genre

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  • Antonelli, Alexandre,1978Harvard University,Göteborgs universitet,University of Gothenburg,Göteborgs botaniska trädgård,Gothenburg Botanical Garden (author)
  • Bacon, Christine D.Gothenburg University,Göteborgs universitet,University of Gothenburg,Gothenburg Global Biodivers Ctr, Sweden; Univ Gothenburg, Sweden,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences(Swepub:gu)xbacoc (author)
  • Bartoszek, Krzysztof,1984Linköpings universitet,Linköping University,Statistik och maskininlärning,Filosofiska fakulteten(Swepub:liu)krzba67 (author)
  • Blom, Mozes P.K.Swedish Museum of Natural History,Swedish Museum Nat Hist, Sweden,Naturhistoriska riksmuseet (author)
  • Huynh, StellaUniversité de Neuchâtel,University of Neuchatel,Univ Neuchatel, Switzerland (author)
  • Jones, Robert Graham,1959Gothenburg University,Göteborgs universitet,University of Gothenburg,Univ Gothenburg, Sweden,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences(Swepub:gu)xjongr (author)
  • Lacey Knowles, L.University of Michigan,Univ Michigan, MI 48109 USA (author)
  • Lamichhaney, SangeetHarvard University,Harvard Univ, MA 02138 USA (author)
  • Marcussen, Thomas,1971Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences,Universitetet i Oslo,University of Oslo(Swepub:gu)xmarct (author)
  • Morlon, HélèneEcole Normale Superieure (ENS),École Normale Supérieure,Ecole Normale Super Paris, France (author)
  • Nakhleh, Luay K.Rice University,Rice Univ, TX USA (author)
  • Oxelman, Bengt,1958Gothenburg University,Göteborgs universitet,University of Gothenburg,Gothenburg Global Biodivers Ctr, Sweden; Univ Gothenburg, Sweden,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences(Swepub:gu)xoxebe (author)
  • Pfeil, Bernard E.,1975Gothenburg University,Göteborgs universitet,University of Gothenburg,Univ Gothenburg, Sweden,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences(Swepub:gu)xpfebe (author)
  • Schliep, AlexanderChalmers University of Technology,Chalmers Univ Technol, Sweden; Univ Gothenburg, Sweden (author)
  • Wahlberg, NiklasLund University,Lunds universitet,Biodiversitet,Biologiska institutionen,Naturvetenskapliga fakulteten,BECC: Biodiversity and Ecosystem services in a Changing Climate,Centrum för miljö- och klimatvetenskap (CEC),Biodiversity,Department of Biology,Faculty of Science,Centre for Environmental and Climate Science (CEC),Lund Univ, Sweden(Swepub:lu)biol-nlw (author)
  • Werneck, Fernanda P.Instituto Nacional de Pesquisas da Amazonia,National Institute of Amazonian Research,Inst Nacl de Pesquisas da Amazonia, Brazil (author)
  • Wiedenhoeft, John,1982Chalmers University of Technology,Rutgers University: The State University of New Jersey,Chalmers Univ Technol, Sweden; Univ Gothenburg, Sweden; Rutgers State Univ, NJ USA,Rutgers University,Chalmers tekniska högskola(Swepub:cth)johnwi (author)
  • Willows-Munro, SandiUniversity of KwaZulu-Natal,Univ Kwazulu Natal, South Africa (author)
  • Edwards, Scott,1963Chalmers University of Technology,Harvard University,Harvard Univ, MA 02138 USA; Univ Gothenburg, Sweden; Chalmers Univ Technol, Sweden,Chalmers tekniska högskola(Swepub:cth)scotte (author)
  • University of GothenburgHarvard University (creator_code:org_t)

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