Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds"

Joel Cracraft¹, Peter Houde², Simon Y W Ho³, David P Mindell⁴, Jon Fjeldså⁵, Bent Lindow⁶, Scott V Edwards⁷, Carsten Rahbek⁸, Siavash Mirarab⁹, Tandy Warnow¹⁰, M Thomas P Gilbert¹¹, Guojie Zhang¹², Edward L Braun¹³, Erich D Jarvis¹⁴

Affiliations

¹ Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA. jlc@amnh.org ebraun68@ufl.edu jarvis@neuro.duke.edu.
² Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA.
³ School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia.
⁴ Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA.
⁵ Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark.
⁶ Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
⁷ Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA.
⁸ Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark. Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK.
⁹ Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA.
¹⁰ Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA. Departments of Bioengineering and Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
¹¹ Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia.
¹² China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.
¹³ Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA. jlc@amnh.org ebraun68@ufl.edu jarvis@neuro.duke.edu.
¹⁴ Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA. Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. jlc@amnh.org ebraun68@ufl.edu jarvis@neuro.duke.edu.

PMID: 26404820
DOI: 10.1126/science.aab1578

Comment

Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds"

Joel Cracraft et al. Science. 2015.

. 2015 Sep 25;349(6255):1460.

doi: 10.1126/science.aab1578.

Authors

Affiliations

¹ Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA. jlc@amnh.org ebraun68@ufl.edu jarvis@neuro.duke.edu.
² Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA.
³ School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia.
⁴ Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA.
⁵ Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark.
⁶ Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
⁷ Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA.
⁸ Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark. Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK.
⁹ Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA.
¹⁰ Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA. Departments of Bioengineering and Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
¹¹ Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia.
¹² China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.
¹³ Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA. jlc@amnh.org ebraun68@ufl.edu jarvis@neuro.duke.edu.
¹⁴ Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA. Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. jlc@amnh.org ebraun68@ufl.edu jarvis@neuro.duke.edu.

PMID: 26404820
DOI: 10.1126/science.aab1578

Abstract

Mitchell et al. argue that divergence-time estimates for our avian phylogeny were too young because of an "inappropriate" maximum age constraint for the most recent common ancestor of modern birds and that, as a result, most modern bird orders diverged before the Cretaceous-Paleogene mass extinction event 66 million years ago instead of after. However, their interpretations of the fossil record and timetrees are incorrect.

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Comment on

Whole-genome analyses resolve early branches in the tree of life of modern birds.
Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MP, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G. Jarvis ED, et al. Science. 2014 Dec 12;346(6215):1320-31. doi: 10.1126/science.1253451. Science. 2014. PMID: 25504713 Free PMC article.
Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds".
Mitchell KJ, Cooper A, Phillips MJ. Mitchell KJ, et al. Science. 2015 Sep 25;349(6255):1460. doi: 10.1126/science.aab1062. Science. 2015. PMID: 26404819

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Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds"

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Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds"

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Affiliations

Abstract

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