ABSTRACT Much progress has been achieved in disentangling evolutionary relationships among species in the tree of life, but some taxonomic groups remain difficult to resolve despite

increasing availability of genome-scale data sets. Here we present a practical approach to studying ancient divergences in the face of high levels of conflict, based on explicit gene

genealogy interrogation (GGI). We show its efficacy in resolving the controversial relationships within the largest freshwater fish radiation (Otophysi) based on newly generated DNA

sequences for 1,051 loci from 225 species. Initial results using a suite of standard methodologies revealed conflicting phylogenetic signal, which supports ten alternative evolutionary

ctenophores are the earliest-branching animal lineage, and adds insight into relationships within clades of yeasts, birds and mammals. GGI opens up a promising avenue to account for

incompatible signals in large data sets and to discern between estimation error and actual biological conflict explaining gene tree discordance. Access through your institution Buy or

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PHYLOGENOMICS ERA Article 27 June 2023 A SPECIES-LEVEL TIMELINE OF MAMMAL EVOLUTION INTEGRATING PHYLOGENOMIC DATA Article 22 December 2021 INFERENCE AND RECONSTRUCTION OF THE

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phylogenomics and the multispecies coalescent modeL. _Proc. Natl Acad. Sci. USA_ 2012 (2012). Download references ACKNOWLEDGEMENTS We dedicate this contribution in honour and memory of our

friend and valued colleague Richard Vari whose untimely death has left a huge lacuna in the world of otophysan systematics. We thank D. Maddison, for helping with the MDS analyses in

Mesquite, and R. Rivero, for helping with illustrations. We also thank S. Edwards and T. Warnow for providing extensive comments on earlier versions of the paper. J. P. Sullivan kindly

provided a photograph for Citharinoidei. This work was supported by National Science Foundation (NSF) grants (DEB-147184, DEB-1541491) to R.B.R., (DEB-1457426 and DEB-1541554) to G.O.,

(DEB-0315963 and DEB-1023403) to J.W.A., and (DEB-1350474) to L.J.R. This project was also funded by the Opportunity Research Program between George Washington University and the Natural

History Museum (Smithsonian) to G.O. and R.V and the Smithsonian Peter Buck fellowship to R.B.R. AUTHOR INFORMATION Author notes * Richard Vari: Deceased. AUTHORS AND AFFILIATIONS *

Department of Biological Sciences, The George Washington University, 2023 G Street NW, Washington, 20052, DC, USA Dahiana Arcila, Guillermo Ortí & Kyung D. Ko * Department of Vertebrate

Zoology, National Museum of Natural History Smithsonian Institution, PO Box 37012, MRC 159, Washington, 20013, DC, USA Dahiana Arcila, Richard Vari & Ricardo Betancur-R. * Department of

Biological Sciences, Auburn University, Auburn, 36849, Alabama, USA Jonathan W. Armbruster * Department of Ichthyology, Division of Vertebrate Zoology, American Museum of Natural History,

New York, 10024, New York, USA Melanie L. J. Stiassny * Department of Ichthyology, The Academy of Natural Sciences, 1900 Benjamin Franklin Parkway, Philadelphia, 19103, Pennsylvania, USA

Mark H. Sabaj & John Lundberg * Department of Biology, University of Massachusetts Boston, Boston, 02125, Massachusetts, USA Liam J. Revell * Department of Biology, University of Puerto

Rico – Río Piedras, PO Box 23360, San Juan, Puerto Rico Ricardo Betancur-R. Authors * Dahiana Arcila View author publications You can also search for this author inPubMed Google Scholar *

Guillermo Ortí View author publications You can also search for this author inPubMed Google Scholar * Richard Vari View author publications You can also search for this author inPubMed 

Google Scholar * Jonathan W. Armbruster View author publications You can also search for this author inPubMed Google Scholar * Melanie L. J. Stiassny View author publications You can also

search for this author inPubMed Google Scholar * Kyung D. Ko View author publications You can also search for this author inPubMed Google Scholar * Mark H. Sabaj View author publications You

can also search for this author inPubMed Google Scholar * John Lundberg View author publications You can also search for this author inPubMed Google Scholar * Liam J. Revell View author

publications You can also search for this author inPubMed Google Scholar * Ricardo Betancur-R. View author publications You can also search for this author inPubMed Google Scholar

CONTRIBUTIONS D.A., R.B.R., R.V. and G.O. planned the project; R.B.R., K.K and G.O. conducted the pilot experiment; D.A. and R.B.R. carried out the experiments and collected the data; D.A.,

R.B.R., L.J.R., and G.O. conceived the GGI method; D.A. and R.B.R. analysed data; J.W.A., J.L., M.L.J.S., and M.H.S. collected, identified and curated the fish specimens examined; R.B.R.,

D.A. and G.O. wrote the paper and all other authors contributed to the writing. CORRESPONDING AUTHOR Correspondence to Ricardo Betancur-R.. ETHICS DECLARATIONS COMPETING INTERESTS The

authors declare no competing financial interests. SUPPLEMENTARY INFORMATION SUPPLEMENTARY INFORMATION Supplementary Methods, Supplementary Notes, Supplementary Figures 1–7 and Supplementary

Tables 1–8. (PDF 1912 kb) RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Arcila, D., Ortí, G., Vari, R. _et al._ Genome-wide interrogation advances

resolution of recalcitrant groups in the tree of life. _Nat Ecol Evol_ 1, 0020 (2017). https://doi.org/10.1038/s41559-016-0020 Download citation * Received: 10 June 2016 * Accepted: 25

October 2016 * Published: 13 January 2017 * DOI: https://doi.org/10.1038/s41559-016-0020 SHARE THIS ARTICLE Anyone you share the following link with will be able to read this content: Get

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