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Blackburn DC, Boyer DM, Gray JA, Winchester J, Bates JM, Baumgart SL, Braker E, Coldren D, Conway KW, Rabosky AD, de la Sancha N, Dillman CB, Dunnum JL, Early CM, Frable BW, Gage MW, Hanken J, Maisano JA, Marks BD, Maslenikov KP, McCormack JE, Nagesan RS, Pandelis GG, Prestridge HL, Rabosky DL, Randall ZS, Robbins MB, Scheinberg LA, Spencer CL, Summers AP, Tapanila L, Thompson CW, Tornabene L, Watkins-Colwell GJ, Welton LJ, Stanley EL. Increasing the impact of vertebrate scientific collections through 3D imaging: The openVertebrate (oVert) Thematic Collections Network. Bioscience 2024; 74:169-186. [PMID: 38560620 PMCID: PMC10977868 DOI: 10.1093/biosci/biad120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/08/2023] [Indexed: 04/04/2024] Open
Abstract
The impact of preserved museum specimens is transforming and increasing by three-dimensional (3D) imaging that creates high-fidelity online digital specimens. Through examples from the openVertebrate (oVert) Thematic Collections Network, we describe how we created a digitization community dedicated to the shared vision of making 3D data of specimens available and the impact of these data on a broad audience of scientists, students, teachers, artists, and more. High-fidelity digital 3D models allow people from multiple communities to simultaneously access and use scientific specimens. Based on our multiyear, multi-institution project, we identify significant technological and social hurdles that remain for fully realizing the potential impact of digital 3D specimens.
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Affiliation(s)
- David C Blackburn
- Florida Museum of Natural History (FLMNH), University of Florida, Gainesville, Florida, United States
- Blackburn served as the lead principal investigator for the oVert Thematic Collections Network
| | - Doug M Boyer
- Duke University, Durham, North Carolina, United States
| | - Jaimi A Gray
- Florida Museum of Natural History (FLMNH), University of Florida, Gainesville, Florida, United States
- Blackburn served as the lead principal investigator for the oVert Thematic Collections Network
| | | | - John M Bates
- Field Museum of Natural History, Chicago, Illinois, United States
| | - Stephanie L Baumgart
- University of Chicago and University of Florida, Gainesville, Florida, United States
| | - Emily Braker
- University of Colorado, Boulder, Colorado, United States
| | - Daryl Coldren
- Field Museum of Natural History, Chicago, Illinois, United States
| | - Kevin W Conway
- Texas A&M University, College Station, Texas, United States
| | | | - Noé de la Sancha
- Chicago State University DePaul University, Chicago, Illinois, United States
| | | | - Jonathan L Dunnum
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States
| | - Catherine M Early
- FLMNH Science Museum of Minnesota, St. Paul, Minnesota, United States
| | - Benjamin W Frable
- Scripps Institute of Oceanography, University of California, San Diego, San Diego, California, United States
| | - Matt W Gage
- Harvard University, Cambridge, Massachusetts, United States
| | - James Hanken
- Harvard University, Cambridge, Massachusetts, United States
| | | | - Ben D Marks
- Field Museum of Natural History, Chicago, Illinois, United States
| | | | | | | | | | | | | | - Zachary S Randall
- Florida Museum of Natural History (FLMNH), University of Florida, Gainesville, Florida, United States
- Blackburn served as the lead principal investigator for the oVert Thematic Collections Network
| | | | | | - Carol L Spencer
- University of California, Berkeley, in Berkeley, California, United States
| | - Adam P Summers
- University of Washington, Seattle, Washington, United States
| | - Leif Tapanila
- Idaho State University, Pocatello, Idaho, United States
| | | | - Luke Tornabene
- University of Washington, Seattle, Washington, United States
| | | | - Luke J Welton
- University of Kansas, Lawrence, Kansas, United States
| | | | - Edward L Stanley
- Florida Museum of Natural History (FLMNH), University of Florida, Gainesville, Florida, United States
- Blackburn served as the lead principal investigator for the oVert Thematic Collections Network
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Title PO, Singhal S, Grundler MC, Costa GC, Pyron RA, Colston TJ, Grundler MR, Prates I, Stepanova N, Jones MEH, Cavalcanti LBQ, Colli GR, Di-Poï N, Donnellan SC, Moritz C, Mesquita DO, Pianka ER, Smith SA, Vitt LJ, Rabosky DL. The macroevolutionary singularity of snakes. Science 2024; 383:918-923. [PMID: 38386744 DOI: 10.1126/science.adh2449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 01/02/2024] [Indexed: 02/24/2024]
Abstract
Snakes and lizards (Squamata) represent a third of terrestrial vertebrates and exhibit spectacular innovations in locomotion, feeding, and sensory processing. However, the evolutionary drivers of this radiation remain poorly known. We infer potential causes and ultimate consequences of squamate macroevolution by combining individual-based natural history observations (>60,000 animals) with a comprehensive time-calibrated phylogeny that we anchored with genomic data (5400 loci) from 1018 species. Due to shifts in the dynamics of speciation and phenotypic evolution, snakes have transformed the trophic structure of animal communities through the recurrent origin and diversification of specialized predatory strategies. Squamate biodiversity reflects a legacy of singular events that occurred during the early history of snakes and reveals the impact of historical contingency on vertebrate biodiversity.
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Affiliation(s)
- Pascal O Title
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
- Environmental Resilience Institute, Indiana University, Bloomington, IN 47408, USA
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sonal Singhal
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biology, California State University, Dominguez Hills, Carson, CA 90747, USA
| | - Michael C Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gabriel C Costa
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biology and Environmental Sciences, Auburn University at Montgomery, Montgomery, AL 36117, USA
| | - R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA
| | - Timothy J Colston
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00680, Puerto Rico
| | - Maggie R Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ivan Prates
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Natasha Stepanova
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marc E H Jones
- Science Group: Fossil Reptiles, Amphibians and Birds Section, Natural History Museum, London SW7 5BD, UK
- Research Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
- Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Lucas B Q Cavalcanti
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, Paraíba 58051-900, Brazil
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Distrito Federal 70910-900, Brazil
| | - Nicolas Di-Poï
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | | | - Craig Moritz
- Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
| | - Daniel O Mesquita
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, Paraíba 58051-900, Brazil
| | - Eric R Pianka
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laurie J Vitt
- Sam Noble Museum and Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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3
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Nachman MW, Beckman EJ, Bowie RCK, Cicero C, Conroy CJ, Dudley R, Hayes TB, Koo MS, Lacey EA, Martin CH, McGuire JA, Patton JL, Spencer CL, Tarvin RD, Wake MH, Wang IJ, Achmadi A, Álvarez-Castañeda ST, Andersen MJ, Arroyave J, Austin CC, Barker FK, Barrow LN, Barrowclough GF, Bates J, Bauer AM, Bell KC, Bell RC, Bronson AW, Brown RM, Burbrink FT, Burns KJ, Cadena CD, Cannatella DC, Castoe TA, Chakrabarty P, Colella JP, Cook JA, Cracraft JL, Davis DR, Davis Rabosky AR, D’Elía G, Dumbacher JP, Dunnum JL, Edwards SV, Esselstyn JA, Faivovich J, Fjeldså J, Flores-Villela OA, Ford K, Fuchs J, Fujita MK, Good JM, Greenbaum E, Greene HW, Hackett S, Hamidy A, Hanken J, Haryoko T, Hawkins MTR, Heaney LR, Hillis DM, Hollingsworth BD, Hornsby AD, Hosner PA, Irham M, Jansa S, Jiménez RA, Joseph L, Kirchman JJ, LaDuc TJ, Leaché AD, Lessa EP, López-Fernández H, Mason NA, McCormack JE, McMahan CD, Moyle RG, Ojeda RA, Olson LE, Kin Onn C, Parenti LR, Parra-Olea G, Patterson BD, Pauly GB, Pavan SE, Peterson AT, Poe S, Rabosky DL, Raxworthy CJ, Reddy S, Rico-Guevara A, Riyanto A, Rocha LA, Ron SR, Rovito SM, Rowe KC, Rowley J, Ruane S, Salazar-Valenzuela D, Shultz AJ, Sidlauskas B, Sikes DS, Simmons NB, Stiassny MLJ, Streicher JW, Stuart BL, Summers AP, Tavera J, Teta P, Thompson CW, Timm RM, Torres-Carvajal O, Voelker G, Voss RS, Winker K, Witt C, Wommack EA, Zink RM. Specimen collection is essential for modern science. PLoS Biol 2023; 21:e3002318. [PMID: 37992027 PMCID: PMC10664955 DOI: 10.1371/journal.pbio.3002318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/30/2023] [Indexed: 11/24/2023] Open
Abstract
Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.
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Affiliation(s)
- Michael W. Nachman
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Elizabeth J. Beckman
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Rauri CK Bowie
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Carla Cicero
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Chris J. Conroy
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Robert Dudley
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Tyrone B. Hayes
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Michelle S. Koo
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Eileen A. Lacey
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Christopher H. Martin
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Jimmy A. McGuire
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - James L. Patton
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Carol L. Spencer
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Rebecca D. Tarvin
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Marvalee H. Wake
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Ian J. Wang
- Museum of Vertebrate Zoology, UC Berkeley, Berkeley, California, United States of America
| | - Anang Achmadi
- Museum Zoologicum Bogoriense, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | | | - Michael J. Andersen
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Jairo Arroyave
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Christopher C. Austin
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - F Keith Barker
- Bell Museum of Natural History, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Lisa N. Barrow
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | | | - John Bates
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | - Aaron M. Bauer
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
| | - Kayce C. Bell
- Natural History Museum of Los Angeles County, Los Angeles, California, United States of America
| | - Rayna C. Bell
- California Academy of Sciences, San Francisco, California, United States of America
| | - Allison W. Bronson
- Biological Sciences, California State Polytechnic University, Humboldt, Arcata, California, United States of America
| | - Rafe M. Brown
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, United States of America
| | - Frank T. Burbrink
- American Museum of Natural History, New York, New York, United States of America
| | - Kevin J. Burns
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | | | - David C. Cannatella
- Biodiversity Center & Dept. of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Todd A. Castoe
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Prosanta Chakrabarty
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Jocelyn P. Colella
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, United States of America
| | - Joseph A. Cook
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Joel L. Cracraft
- American Museum of Natural History, New York, New York, United States of America
| | - Drew R. Davis
- Natural History Museum and Dept. of Biology, Eastern New Mexico University, Portales, New Mexico, United States of America
| | | | - Guillermo D’Elía
- Instituto de Cs. Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - John P. Dumbacher
- California Academy of Sciences, San Francisco, California, United States of America
| | - Jonathan L. Dunnum
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Scott V. Edwards
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Jacob A. Esselstyn
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Julián Faivovich
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia", Buenos Aires, Argentina
| | - Jon Fjeldså
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Kassandra Ford
- Bell Museum of Natural History, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Jérôme Fuchs
- ISYEB, Muséum national d’Histoire naturelle, Paris, France
| | - Matthew K. Fujita
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Jeffrey M. Good
- Philip L. Wright Zoological Museum, University of Montana, Missoula, Montana, United States of America
| | - Eli Greenbaum
- Biodiversity Collections and Dept. of Biological Sciences, University of Texas at El Paso, El Paso, Texas, United States of America
| | - Harry W. Greene
- Biodiversity Center & Dept. of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Shannon Hackett
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | - Amir Hamidy
- Museum Zoologicum Bogoriense, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - James Hanken
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Tri Haryoko
- Museum Zoologicum Bogoriense, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Melissa TR Hawkins
- Smithsonian Institution, National Museum of Natural History, Washington, DC, United States of America
| | - Lawrence R. Heaney
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | - David M. Hillis
- Biodiversity Center & Dept. of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | | | - Angela D. Hornsby
- Philip L. Wright Zoological Museum, University of Montana, Missoula, Montana, United States of America
| | - Peter A. Hosner
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Mohammad Irham
- Museum Zoologicum Bogoriense, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Sharon Jansa
- Bell Museum of Natural History, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Rosa Alicia Jiménez
- Escuela de Biología, Universidad de San Carlos de Guatemala, Ciudad de Guatemala, Guatemala
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO, Canberra, Australia
| | | | - Travis J. LaDuc
- Biodiversity Center & Dept. of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Adam D. Leaché
- Burke Museum, University of Washington, Seattle, Washington, United States of America
| | - Enrique P. Lessa
- Departamento de Ecología y Evolución, Universidad de la República, Montevideo, Uruguay
| | - Hernán López-Fernández
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Nicholas A. Mason
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - John E. McCormack
- Moore Laboratory of Zoology, Occidental College, Los Angeles, California, United States of America
| | - Caleb D. McMahan
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | - Robert G. Moyle
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, United States of America
| | - Ricardo A. Ojeda
- CONICET, Centro de Ciencia y Técnica Mendoza, Mendoza, Argentina
| | - Link E. Olson
- University of Alaska Museum, Fairbanks, Alaska, United States of America
| | | | - Lynne R. Parenti
- Smithsonian Institution, National Museum of Natural History, Washington, DC, United States of America
| | - Gabriela Parra-Olea
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Bruce D. Patterson
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | - Gregory B. Pauly
- Natural History Museum of Los Angeles County, Los Angeles, California, United States of America
| | - Silvia E. Pavan
- Biological Sciences, California State Polytechnic University, Humboldt, Arcata, California, United States of America
| | - A Townsend Peterson
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, United States of America
| | - Steven Poe
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Daniel L. Rabosky
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, United States of America
| | | | - Sushma Reddy
- Bell Museum of Natural History, University of Minnesota, Saint Paul, Minnesota, United States of America
| | | | - Awal Riyanto
- Museum Zoologicum Bogoriense, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Luiz A. Rocha
- California Academy of Sciences, San Francisco, California, United States of America
| | - Santiago R. Ron
- Museo de Zoología, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | | | - Kevin C. Rowe
- Museums Victoria Research Institute, Melbourne, Australia
| | - Jodi Rowley
- Australian Museum Research Institute, Australian Museum, Sydney, Australia
| | - Sara Ruane
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | | | - Allison J. Shultz
- Natural History Museum of Los Angeles County, Los Angeles, California, United States of America
| | - Brian Sidlauskas
- Dept. of Fisheries, Wildlife & Conservation Sciences, Oregon State University, Corvallis, Oregon, United States of America
| | - Derek S. Sikes
- University of Alaska Museum, Fairbanks, Alaska, United States of America
| | - Nancy B. Simmons
- American Museum of Natural History, New York, New York, United States of America
| | | | | | - Bryan L. Stuart
- North Carolina Museum of Natural Sciences, Raleigh, North Carolina, United States of America
| | - Adam P. Summers
- Friday Harbor Laboratories, University of Washington, Friday Harbor, Washington, United States of America
| | | | - Pablo Teta
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia", Buenos Aires, Argentina
| | - Cody W. Thompson
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Robert M. Timm
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, United States of America
| | | | - Gary Voelker
- Dept. Ecology and Conservation Biology, Texas A&M University, College Station, Texas, United States of America
| | - Robert S. Voss
- American Museum of Natural History, New York, New York, United States of America
| | - Kevin Winker
- University of Alaska Museum, Fairbanks, Alaska, United States of America
| | - Christopher Witt
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Elizabeth A. Wommack
- University of Wyoming Museum of Vertebrates, University of Wyoming, Laramie, Wyoming, United States of America
| | - Robert M. Zink
- University of Nebraska State Museum, Lincoln, Nebraska, United States of America
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4
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Pandelis GG, Grundler MC, Rabosky DL. Ecological correlates of cranial evolution in the megaradiation of dipsadine snakes. BMC Ecol Evol 2023; 23:48. [PMID: 37679675 PMCID: PMC10485986 DOI: 10.1186/s12862-023-02157-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 08/22/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Dipsadine snakes represent one of the most spectacular vertebrate radiations that have occurred in any continental setting, with over 800 species in South and Central America. Their species richness is paralleled by stunning ecological diversity, ranging from arboreal snail-eating and aquatic eel-eating specialists to terrestrial generalists. Despite the ecological importance of this clade, little is known about the extent to which ecological specialization shapes broader patterns of phenotypic diversity within the group. Here, we test how habitat use and diet have influenced morphological diversification in skull shape across 160 dipsadine species using micro-CT and 3-D geometric morphometrics, and we use a phylogenetic comparative approach to test the contributions of habitat use and diet composition to variation in skull shape among species. RESULTS We demonstrate that while both habitat use and diet are significant predictors of shape in many regions of the skull, habitat use significantly predicts shape in a greater number of skull regions when compared to diet. We also find that across ecological groupings, fossorial and aquatic behaviors result in the strongest deviations in morphospace for several skull regions. We use simulations to address the robustness of our results and describe statistical anomalies that can arise from the application of phylogenetic generalized least squares to complex shape data. CONCLUSIONS Both habitat and dietary ecology are significantly correlated with skull shape in dipsadines; the strongest relationships involved skull shape in snakes with aquatic and fossorial lifestyles. This association between skull morphology and multiple ecological axes is consistent with a classic model of adaptive radiation and suggests that ecological factors were an important component in driving morphological diversification in the dipsadine megaradiation.
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Affiliation(s)
- Gregory G Pandelis
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA.
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, 48109, USA.
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019, USA.
| | - Michael C Grundler
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, 48109, USA
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5
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Jiménez-Ortega D, Valente L, Dugo-Cota Á, Rabosky DL, Vilà C, Gonzalez-Voyer A. Diversification dynamics in Caribbean rain frogs ( Eleutherodactylus) are uncoupled from the anuran community and consistent with adaptive radiation. Proc Biol Sci 2023; 290:20222171. [PMID: 36629104 PMCID: PMC9832552 DOI: 10.1098/rspb.2022.2171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/08/2022] [Indexed: 01/12/2023] Open
Abstract
Adaptive radiation is proposed to play a key role in generating differences in species richness among lineages and geographical regions. Due to the importance of ecological divergence in adaptive radiation, species richness is predicted to be influenced by equilibrium diversity dynamics, although the concept continues to generate much debate. An additional important question is whether radiating clades have intrinsic biological characteristics that make them particularly prone to diversify. We tackle these questions by analysing (i) the temporal patterns of diversification of Caribbean Eleutherodactylus frogs, and (ii) assembly of the complete native anuran community of the Caribbean archipelago (197 species), testing for the presence of equilibrium dynamics and whether diversification patterns of Eleutherodactylus differ from those of the rest of the Caribbean anurans. Diversification rates follow the predicted pattern of rapid diversification early in the radiation which gradually decreases towards the present. Eleutherodactylus diversification is significantly faster than that of the Caribbean anuran community, and although equilibrium dynamics influence richness of all Caribbean anurans, Eleutherodactylus shows higher carrying capacity. Our results indicate that ecological opportunity per se is not sufficient for adaptive radiation and that diverse lineages present intrinsic characteristics that enable them to make the most of available opportunity.
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Affiliation(s)
- Dante Jiménez-Ortega
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, México
| | - Luis Valente
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Álvaro Dugo-Cota
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville 41092, Spain
| | - Daniel L. Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Carles Vilà
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville 41092, Spain
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6
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Rabosky DL. Evolutionary time and species diversity in aquatic ecosystems worldwide. Biol Rev Camb Philos Soc 2022; 97:2090-2105. [PMID: 35899476 PMCID: PMC9796449 DOI: 10.1111/brv.12884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 01/01/2023]
Abstract
The latitudinal diversity gradient (LDG) is frequently described as the most dramatic biodiversity pattern on Earth, yet ecologists and biogeographers have failed to reach consensus on its primary cause. A key problem in explaining the LDG involves collinearity between multiple factors that are predicted to affect species richness in the same direction. In terrestrial systems, energy input, geographic area, and evolutionary time for species accumulation tend to covary positively with species richness at the largest spatial scales, such that their individual contributions to the LDG are confounded in global analyses. I review three diversity patterns from marine and freshwater systems that break this collinearity and which may thus provide stronger tests of the influence of time on global richness gradients. Specifically, I contrast biodiversity patterns along oceanic depth gradients, in geologically young versus ancient lakes, and in the north versus south polar marine biomes. I focus primarily on fishes due to greater data availability but synthesize patterns for invertebrates where possible. I find that regional-to-global species richness generally declines with depth in the oceans, despite the great age and stability of the deep-sea biome. Geologically ancient lakes generally do not contain more species than young lakes, and the Antarctic marine biome is not appreciably more species rich than the much younger Arctic marine biome. However, endemism is consistently higher in older systems. Patterns for invertebrate groups are less clear than for fishes and reflect a critical need for primary biodiversity data. In summary, the available data suggest that species richness is either decoupled from or only weakly related to the amount of time for diversification. These results suggest that energy, productivity, or geographic area are the primary drivers of large-scale diversity gradients. To the extent that marine and terrestrial diversity gradients result from similar processes, these examples provide evidence against a primary role for evolutionary time as the cause of the LDG.
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Affiliation(s)
- Daniel L. Rabosky
- Museum of Zoology & Department of Ecology and Evolutionary BiologyUniversity of Michigan2032 Biological Sciences BuildingAnn ArborMI48109USA
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7
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Prates I, Doughty P, Rabosky DL. Subspecies at crossroads: the evolutionary significance of genomic and phenotypic variation in a wide-ranging Australian lizard ( Ctenotus pantherinus). Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Many subspecies were described to capture phenotypic variation in wide-ranging taxa, with some later being found to correspond to divergent genetic lineages. We investigate whether currently recognized subspecies correspond to distinctive and coherent evolutionary lineages in the widespread Australian lizard Ctenotus pantherinus based on morphological, mitochondrial and genome-wide nuclear variation. We find weak and inconsistent correspondence between morphological patterns and the presumed subspecies ranges, with character polymorphism within regions and broad morphological overlap across regions. Phylogenetic analyses suggest paraphyly of populations assignable to each subspecies, mitonuclear discordance and little congruence between subspecies ranges and the distribution of inferred clades. Genotypic clustering supports admixture across regions. These results undermine the presumed phenotypic and genotypic coherence and distinctiveness of C. pantherinus subspecies. Based on our findings, we comment on the operational and conceptual shortcomings of morphologically defined subspecies and discuss practical challenges in applying the general notion of subspecies as incompletely separated population lineages. We conclude by highlighting a historical asymmetry that has implications for ecology, evolution and conservation: subspecies proposed in the past are difficult to falsify even in the face of new data that challenge their coherence and distinctiveness, whereas modern researchers appear hesitant to propose new subspecies.
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Affiliation(s)
- Ivan Prates
- Department of Ecology and Evolutionary Biology, University of Michigan , Ann Arbor, MI , USA
- Museum of Zoology, University of Michigan , Ann Arbor, MI , USA
| | - Paul Doughty
- Collections & Research, Western Australian Museum , Welshpool , WA 6106 , Australia
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8
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Ahluwalia S, Holmes I, von May R, Rabosky DL, Davis Rabosky AR. Assembling microbial communities: a genomic analysis of a natural experiment in neotropical bamboo internodes. PeerJ 2022; 10:e13958. [PMID: 36132220 PMCID: PMC9484453 DOI: 10.7717/peerj.13958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/06/2022] [Indexed: 01/19/2023] Open
Abstract
Microbes participate in ecological communities, much like multicellular organisms. However, microbial communities lack the centuries of observation and theory describing and predicting ecological processes available for multicellular organisms. Here, we examine early bacterial community assembly in the water-filled internodes of Amazonian bamboos from the genus Guadua. Bamboo stands form distinct habitat patches within the lowland Amazonian rainforest and provide habitat for a suite of vertebrate and invertebrate species. Guadua bamboos develop sealed, water-filled internodes as they grow. Internodes are presumed sterile or near sterile while closed, but most are eventually opened to the environment by animals, after which they are colonized by microbes. We find that microbial community diversity increases sharply over the first few days of environmental exposure, and taxonomic identity of the microbes changes through this time period as is predicted for early community assembly in macroscopic communities. Microbial community taxonomic turnover is consistent at the bacteria phylum level, but at the level of Operational Taxonomic Units (OTUs), internode communities become increasingly differentiated through time. We argue that these tropical bamboos form an ideal study system for microbial community ecology due to their near-sterile condition prior to opening, relatively consistent environment after opening, and functionally limitless possibilities for replicates. Given the possible importance of opened internode habitats as locations of transmission for both pathogenic and beneficial microbes among animals, understanding the microbial dynamics of the internode habitat is a key conservation concern for the insect and amphibian species that use this microhabitat.
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Affiliation(s)
- Sonia Ahluwalia
- Department of Ecology and Evolutionary Biology & Museum of Zoology, University of Michigan – Ann Arbor, Ann Arbor, Michigan, United States,Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Iris Holmes
- Department of Ecology and Evolutionary Biology & Museum of Zoology, University of Michigan – Ann Arbor, Ann Arbor, Michigan, United States,Cornell Institute of Host Microbe Interactions and Disease and Department of Microbiology, Cornell University, Ithaca, New York, United States
| | - Rudolf von May
- Department of Ecology and Evolutionary Biology & Museum of Zoology, University of Michigan – Ann Arbor, Ann Arbor, Michigan, United States,Biology Program, California State University, Channel Islands, Camarillo, California, USA
| | - Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology & Museum of Zoology, University of Michigan – Ann Arbor, Ann Arbor, Michigan, United States
| | - Alison R. Davis Rabosky
- Department of Ecology and Evolutionary Biology & Museum of Zoology, University of Michigan – Ann Arbor, Ann Arbor, Michigan, United States
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9
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Singhal S, Wrath J, Rabosky DL. Genetic variability and the ecology of geographic range: A test of the central-marginal hypothesis in Australian scincid lizards. Mol Ecol 2022; 31:4242-4253. [PMID: 35779002 PMCID: PMC9545263 DOI: 10.1111/mec.16589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 11/27/2022]
Abstract
For many species, both local abundance and regional occupancy are highest near the centre of their geographic distributions. One hypothesis for this pattern is that niche suitability declines with increasing distance from a species geographic centre, such that populations near range margins are characterized by reduced density and increased patchiness. In these smaller edge populations, genetic drift is more powerful, leading to the loss of genetic diversity. This simple verbal model has been formalized as the central-marginal hypothesis, which predicts that core populations should have greater genetic diversity than edge populations. Here, we tested the central-marginal hypothesis using a genomic data set of 25 species-level taxa of Australian scincid lizards in the genera Ctenotus and Lerista. A majority of taxa in our data set showed range-wide patterns of genetic variation consistent with central-marginal hypothesis, and eight of 25 taxa showed significantly greater genetic diversity in the centre of their range. We then explored biological, historical, and methodological factors that might predict which taxa support the central-marginal hypothesis. We found that taxa with the strongest evidence for range expansion were the least likely to follow predictions of the central-marginal hypothesis. The majority of these taxa had range expansions that originated at the range edge, which led to a gradient of decreasing genetic diversity from the range edge to the core, contrary to the central-marginal hypothesis.
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Affiliation(s)
- Sonal Singhal
- Department of BiologyCSU Dominguez HillsCarsonCaliforniaUSA
| | - John Wrath
- Department of BiologyCSU Dominguez HillsCarsonCaliforniaUSA
| | - Daniel L. Rabosky
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMichiganUSA
- Museum of ZoologyUniversity of MichiganAnn ArborMichiganUSA
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10
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Grundler MC, Rabosky DL, Zapata F. Fast Likelihood Calculations for Automatic Identification of Macroevolutionary Rate Heterogeneity in Continuous and Discrete Traits. Syst Biol 2022; 71:1307-1318. [DOI: 10.1093/sysbio/syac035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 04/28/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Understanding phenotypic disparity across the tree of life requires identifying where and when evolutionary rates change on phylogeny. A primary methodological challenge in macroevolution is therefore to develop methods for accurate inference of among-lineage variation in rates of phenotypic evolution. Here, we describe a method for inferring among-lineage evolutionary rate heterogeneity in both continuous and discrete traits. The method assumes that the present-day distribution of a trait is shaped by a variable-rate process arising from a mixture of constant-rate processes and uses a single-pass tree traversal algorithm to estimate branch-specific evolutionary rates. By employing dynamic programming optimization techniques and approximate maximum likelihood estimators where appropriate, our method permits rapid exploration of the tempo and mode of phenotypic evolution. Simulations indicate that the method reconstructs rates of trait evolution with high accuracy. Application of the method to datasets on squamate reptile reproduction and turtle body size recovers patterns of rate heterogeneity identified by previous studies but with computational costs reduced by many orders of magnitude. Our results expand the set of tools available for detecting macroevolutionary rate heterogeneity and point to the utility of fast, approximate methods for studying large scale biodiversity dynamics.
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Affiliation(s)
- Michael C Grundler
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Felipe Zapata
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
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11
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Singhal S, Colli GR, Grundler MR, Costa GC, Prates I, Rabosky DL. No link between population isolation and speciation rate in squamate reptiles. Proc Natl Acad Sci U S A 2022; 119:e2113388119. [PMID: 35058358 PMCID: PMC8795558 DOI: 10.1073/pnas.2113388119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/19/2021] [Indexed: 11/26/2022] Open
Abstract
Rates of species formation vary widely across the tree of life and contribute to massive disparities in species richness among clades. This variation can emerge from differences in metapopulation-level processes that affect the rates at which lineages diverge, persist, and evolve reproductive barriers and ecological differentiation. For example, populations that evolve reproductive barriers quickly should form new species at faster rates than populations that acquire reproductive barriers more slowly. This expectation implicitly links microevolutionary processes (the evolution of populations) and macroevolutionary patterns (the profound disparity in speciation rate across taxa). Here, leveraging extensive field sampling from the Neotropical Cerrado biome in a biogeographically controlled natural experiment, we test the role of an important microevolutionary process-the propensity for population isolation-as a control on speciation rate in lizards and snakes. By quantifying population genomic structure across a set of codistributed taxa with extensive and phylogenetically independent variation in speciation rate, we show that broad-scale patterns of species formation are decoupled from demographic and genetic processes that promote the formation of population isolates. Population isolation is likely a critical stage of speciation for many taxa, but our results suggest that interspecific variability in the propensity for isolation has little influence on speciation rates. These results suggest that other stages of speciation-including the rate at which reproductive barriers evolve and the extent to which newly formed populations persist-are likely to play a larger role than population isolation in controlling speciation rate variation in squamates.
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Affiliation(s)
- Sonal Singhal
- Department of Biology, California State University, Dominguez Hills, Carson, CA 90747;
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Distrito Federal 70910-900, Brazil
| | - Maggie R Grundler
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, CA 94720
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720
| | - Gabriel C Costa
- Department of Biology and Environmental Sciences, Auburn University at Montgomery, Montgomery, AL 36117
| | - Ivan Prates
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48109
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109;
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48109
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12
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Prates I, Singhal S, Marchán-Rivadeneira MR, Grundler MR, Moritz C, Donnellan SC, Rabosky DL. Genetic and Ecogeographic Controls on Species Cohesion in Australia’s Most Diverse Lizard Radiation. Am Nat 2022; 199:E57-E75. [DOI: 10.1086/717411] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Ivan Prates
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, Michigan 48109
| | - Sonal Singhal
- Department of Biology, California State University–Dominguez Hills, Carson, California 90747
| | | | - Maggie R. Grundler
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720; and Museum of Vertebrate Zoology, University of California, Berkeley, California 94720
| | - Craig Moritz
- Division of Ecology and Evolution and Centre for Biodiversity Analysis, Australian National University, Camberra, Australian Capital Territory, Australia
| | | | - Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, Michigan 48109
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13
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Abstract
The fossil record is the primary source of information on how biodiversity has varied in deep time, providing unique insight on the long-term dynamics of diversification and their drivers. However, interpretations of fossil record diversity patterns have been much debated, with a traditional focus on global diversity through time. Problems arise because the fossil record is spatially and temporally patchy, so 'global' diversity estimates actually represent the summed diversity across a set of geographically and environmentally distinct regions that vary substantially in number and identity through time. Furthermore, a focus on global diversity lumps the signal of ecological drivers at local and regional scales with the signal of global-scale processes, including variation in the distribution of environments and in provincialism (the extent of subdivision into distinct biogeographic regions). These signals cannot be untangled by studying global diversity measures alone. These conceptual and empirical concerns necessitate a shift away from the study of 'biodiversity through time' and towards the study of 'biodiversity across time and space'. Spatially explicit investigations, including analyses of local- and regional-scale datasets, are central to achieving this and allow analysis of geographic scale, location and the environmental parameters directly experienced by organisms. So far, research in this area has revealed the stability of species richness variation among environments through time, and the potential climatic and Earth-system drivers of changing biodiversity. Ultimately, this research program promises to address key questions regarding the assembly of biodiversity, and the contributions of local-, regional- and global-scale processes to the diversification of life on Earth.
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Affiliation(s)
- Roger B J Benson
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK.
| | - Richard Butler
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Roger A Close
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Erin Saupe
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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14
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Abstract
An influential hypothesis proposes that the tempo of evolution is faster in the tropics. Emerging evidence, including a study in this issue of PLOS Biology, challenges this view, raising new questions about the causes of Earth’s iconic latitudinal diversity gradient (LDG).
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Affiliation(s)
- Daniel L. Rabosky
- Museum of Zoology & Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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15
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Melville J, Chapple DG, Keogh JS, Sumner J, Amey A, Bowles P, Brennan IG, Couper P, Donnellan SC, Doughty P, Edwards DL, Ellis RJ, Esquerré D, Fenker J, Gardner MG, Georges A, Haines ML, Hoskin CJ, Hutchinson M, Moritz C, Nankivell J, Oliver P, Pavón-Vázquez CJ, Pepper M, Rabosky DL, Sanders K, Shea G, Singhal S, Worthington Wilmer J, Tingley R. A return-on-investment approach for prioritization of rigorous taxonomic research needed to inform responses to the biodiversity crisis. PLoS Biol 2021; 19:e3001210. [PMID: 34061821 PMCID: PMC8168848 DOI: 10.1371/journal.pbio.3001210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/29/2021] [Indexed: 11/19/2022] Open
Abstract
Global biodiversity loss is a profound consequence of human activity. Disturbingly, biodiversity loss is greater than realized because of the unknown number of undocumented species. Conservation fundamentally relies on taxonomic recognition of species, but only a fraction of biodiversity is described. Here, we provide a new quantitative approach for prioritizing rigorous taxonomic research for conservation. We implement this approach in a highly diverse vertebrate group-Australian lizards and snakes. Of 870 species assessed, we identified 282 (32.4%) with taxonomic uncertainty, of which 17.6% likely comprise undescribed species of conservation concern. We identify 24 species in need of immediate taxonomic attention to facilitate conservation. Using a broadly applicable return-on-investment framework, we demonstrate the importance of prioritizing the fundamental work of identifying species before they are lost.
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Affiliation(s)
- Jane Melville
- Department of Sciences, Museums Victoria, Melbourne, Australia
- Department of Biology, Washington University, St. Louis, MI, United States of America
- School of Biological Sciences, Monash University, Clayton, Australia
| | - David G. Chapple
- School of Biological Sciences, Monash University, Clayton, Australia
| | - J. Scott Keogh
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Joanna Sumner
- Department of Sciences, Museums Victoria, Melbourne, Australia
| | - Andrew Amey
- Biodiversity & Geosciences Program, Queensland Museum, Brisbane, Australia
| | - Phil Bowles
- Snake & Lizard Red List Authority, CI-IUCN Biodiversity Assessment Unit, IUCN North America Office, Washington, DC, United States of America
| | - Ian G. Brennan
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Patrick Couper
- Biodiversity & Geosciences Program, Queensland Museum, Brisbane, Australia
| | | | - Paul Doughty
- Collections & Research, Western Australian Museum, Welshpool, Australia
| | - Danielle L. Edwards
- Department of Life & Environmental Sciences, University of California, Merced, Merced, CA, United States of America
| | - Ryan J. Ellis
- Collections & Research, Western Australian Museum, Welshpool, Australia
- Biologic Environmental Survey, East Perth, Australia
| | - Damien Esquerré
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Jéssica Fenker
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Michael G. Gardner
- South Australian Museum, North Terrace, Adelaide, Australia
- College of Science & Engineering, Flinders University, Adelaide, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | | | - Conrad J. Hoskin
- College of Science & Engineering, James Cook University, Townsville, Australia
| | | | - Craig Moritz
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - James Nankivell
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Paul Oliver
- Biodiversity & Geosciences Program, Queensland Museum, Brisbane, Australia
- Environmental Futures Research Institute, Griffith University, Australia
| | - Carlos J. Pavón-Vázquez
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Mitzy Pepper
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Daniel L. Rabosky
- Museum of Zoology & Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Kate Sanders
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Glenn Shea
- School of Veterinary Science, University of Sydney, Sydney, Australia
- Australian Museum Research Institute, The Australian Museum, Sydney, Australia
| | - Sonal Singhal
- Department of Biology, California State University, Dominguez Hills, Carson, CA, United States of America
| | | | - Reid Tingley
- School of Biological Sciences, Monash University, Clayton, Australia
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16
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Shi JJ, Westeen EP, Rabosky DL. A test for rate-coupling of trophic and cranial evolutionary dynamics in New World bats. Evolution 2021; 75:861-875. [PMID: 33565084 DOI: 10.1111/evo.14188] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 01/15/2021] [Accepted: 01/30/2021] [Indexed: 01/19/2023]
Abstract
Morphological evolution is often assumed to be causally related to underlying patterns of ecological trait evolution. However, few studies have directly tested whether evolutionary dynamics of-and major shifts in-ecological resource use are coupled with morphological shifts that may facilitate trophic innovation. Using diet and multivariate cranial (microCT) data, we tested whether rates of trophic and cranial evolution are coupled in the radiation of New World bats. We developed a generalizable information-theoretic method for describing evolutionary rate heterogeneity across large candidate sets of multirate evolutionary models, without relying on a single best-fitting model. We found considerable variation in trophic evolutionary dynamics, in sharp contrast to a largely homogeneous cranial evolutionary process. This dichotomy is surprising given established functional associations between overall skull morphology and trophic ecology. We suggest that assigning discrete trophic states may underestimate trophic generalism and opportunism, and that this radiation could be characterized by labile crania and a homogeneous dynamic of generally high morphological rates. Overall, we discuss how trophic classifications could substantively impact our interpretation of how these dynamics covary in adaptive radiations.
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Affiliation(s)
- Jeff J Shi
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, 55455.,Museum of Zoology, University of Michigan, Ann Arbor, Michigan, 48109.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109
| | - Erin P Westeen
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, 48109.,Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, 94720.,Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, 94720
| | - Daniel L Rabosky
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, 48109.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109
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17
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Laudanno G, Haegeman B, Rabosky DL, Etienne RS. Detecting Lineage-Specific Shifts in Diversification: A Proper Likelihood Approach. Syst Biol 2021; 70:389-407. [PMID: 32617585 PMCID: PMC7875465 DOI: 10.1093/sysbio/syaa048] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 06/11/2020] [Accepted: 06/23/2020] [Indexed: 11/25/2022] Open
Abstract
The branching patterns of molecular phylogenies are generally assumed to contain information on rates of the underlying speciation and extinction processes. Simple birth-death models with constant, time-varying, or diversity-dependent rates have been invoked to explain these patterns. They have one assumption in common: all lineages have the same set of diversification rates at a given point in time. It seems likely, however, that there is variability in diversification rates across subclades in a phylogenetic tree. This has inspired the construction of models that allow multiple rate regimes across the phylogeny, with instantaneous shifts between these regimes. Several methods exist for calculating the likelihood of a phylogeny under a specified mapping of diversification regimes and for performing inference on the most likely diversification history that gave rise to a particular phylogenetic tree. Here, we show that the likelihood computation of these methods is not correct. We provide a new framework to compute the likelihood correctly and show, with simulations of a single shift, that the correct likelihood indeed leads to parameter estimates that are on average in much better agreement with the generating parameters than the incorrect likelihood. Moreover, we show that our corrected likelihood can be extended to multiple rate shifts in time-dependent and diversity-dependent models. We argue that identifying shifts in diversification rates is a nontrivial model selection exercise where one has to choose whether shifts in now-extinct lineages are taken into account or not. Hence, our framework also resolves the recent debate on such unobserved shifts. [Diversification; macroevolution; phylogeny; speciation].
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Affiliation(s)
- Giovanni Laudanno
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC, Groningen, The Netherlands
| | - Bart Haegeman
- Centre for Biodiversity Theory and Modelling, Theoretical and Experimental Ecology Station, CNRS and Paul Sabatier University, 09200, Moulis, France
| | - Daniel L Rabosky
- Museum of Zoology & Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC, Groningen, The Netherlands
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18
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Chang J, Rabosky DL, Alfaro ME. Estimating Diversification Rates on Incompletely Sampled Phylogenies: Theoretical Concerns and Practical Solutions. Syst Biol 2020; 69:602-611. [PMID: 31804691 DOI: 10.1093/sysbio/syz081] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 11/12/2019] [Accepted: 12/01/2019] [Indexed: 11/13/2022] Open
Abstract
Molecular phylogenies are a key source of information about the tempo and mode of species diversification. However, most empirical phylogenies do not contain representatives of all species, such that diversification rates are typically estimated from incompletely sampled data. Most researchers recognize that incomplete sampling can lead to biased rate estimates, but the statistical properties of methods for accommodating incomplete sampling remain poorly known. In this point of view, we demonstrate theoretical concerns with the widespread use of analytical sampling corrections for sparsely sampled phylogenies of higher taxonomic groups. In particular, corrections based on "sampling fractions" can lead to low statistical power to infer rate variation when it is present, depending on the likelihood function used for inference. In the extreme, the sampling fraction correction can lead to spurious patterns of diversification that are driven solely by unbalanced sampling across the tree in concert with low overall power to infer shifts. Stochastic polytomy resolution provides an alternative to sampling fraction approaches that avoids some of these biases. We show that stochastic polytomy resolvers can greatly improve the power of common analyses to estimate shifts in diversification rates. We introduce a new stochastic polytomy resolution method (Taxonomic Addition for Complete Trees [TACT]) that uses birth-death-sampling estimators across an ultrametric phylogeny to estimate branching times for unsampled taxa, with taxonomic information to compatibly place new taxa onto a backbone phylogeny. We close with practical recommendations for diversification inference under several common scenarios of incomplete sampling. [Birth-death process; diversification; incomplete sampling; phylogenetic uncertainty; rate heterogeneity; rate shifts; stochastic polytomy resolution.].
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Affiliation(s)
- Jonathan Chang
- School of Biological Sciences, Monash University, 25 Rainforest Walk, Melbourne, VIC 3800, Australia.,Department of Ecology and Evolutionary Biology & Museum of Zoology, University of Michigan, 1105 North University Ave, Ann Arbor, MI 48109, USA.,Department of Ecology and Evolutionary Biology, University of California, 612 Charles E Young Dr S, Los Angeles, CA 90095, USA
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology & Museum of Zoology, University of Michigan, 1105 North University Ave, Ann Arbor, MI 48109, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, 612 Charles E Young Dr S, Los Angeles, CA 90095, USA
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Singhal S, Colston TJ, Grundler MR, Smith SA, Costa GC, Colli GR, Moritz C, Pyron RA, Rabosky DL. Congruence and Conflict in the Higher-Level Phylogenetics of Squamate Reptiles: An Expanded Phylogenomic Perspective. Syst Biol 2020; 70:542-557. [PMID: 32681800 DOI: 10.1093/sysbio/syaa054] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 05/05/2020] [Accepted: 07/05/2020] [Indexed: 12/16/2022] Open
Abstract
Genome-scale data have the potential to clarify phylogenetic relationships across the tree of life but have also revealed extensive gene tree conflict. This seeming paradox, whereby larger data sets both increase statistical confidence and uncover significant discordance, suggests that understanding sources of conflict is important for accurate reconstruction of evolutionary history. We explore this paradox in squamate reptiles, the vertebrate clade comprising lizards, snakes, and amphisbaenians. We collected an average of 5103 loci for 91 species of squamates that span higher-level diversity within the clade, which we augmented with publicly available sequences for an additional 17 taxa. Using a locus-by-locus approach, we evaluated support for alternative topologies at 17 contentious nodes in the phylogeny. We identified shared properties of conflicting loci, finding that rate and compositional heterogeneity drives discordance between gene trees and species tree and that conflicting loci rarely overlap across contentious nodes. Finally, by comparing our tests of nodal conflict to previous phylogenomic studies, we confidently resolve 9 of the 17 problematic nodes. We suggest this locus-by-locus and node-by-node approach can build consensus on which topological resolutions remain uncertain in phylogenomic studies of other contentious groups. [Anchored hybrid enrichment (AHE); gene tree conflict; molecular evolution; phylogenomic concordance; target capture; ultraconserved elements (UCE).].
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Affiliation(s)
- Sonal Singhal
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.,Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Biology, CSU Dominguez Hills, Carson, CA 90747, USA
| | - Timothy J Colston
- Department of Biological Sciences, The George Washington University, Washington D.C. 20052, USA.,Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Maggie R Grundler
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.,Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Environmental Science, Policy, & Management, University of California Berkeley, Berkeley, CA 94720, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gabriel C Costa
- Department of Biology and Environmental Sciences, Auburn University at Montgomery, Montgomery, AL, USA
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, DF, Brazil
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, The Australian National University, 46 Sullivans Creek Road, Acton, ACT 2601, Australia
| | - R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington D.C. 20052, USA
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.,Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
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20
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Westeen EP, Durso AM, Grundler MC, Rabosky DL, Davis Rabosky AR. What makes a fang? Phylogenetic and ecological controls on tooth evolution in rear-fanged snakes. BMC Evol Biol 2020; 20:80. [PMID: 32646372 PMCID: PMC7346461 DOI: 10.1186/s12862-020-01645-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 06/22/2020] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Fangs are a putative key innovation that revolutionized prey capture and feeding in snakes, and - along with their associated venom phenotypes - have made snakes perhaps the most medically-significant vertebrate animals. Three snake clades are known for their forward-positioned fangs, and these clades (Elapidae, Viperidae, and Atractaspidinae) contain the majority of snakes that are traditionally considered venomous. However, many other snakes are "rear-fanged": they possess potentially venom-delivering teeth situated at the rear end of the upper jaw. Quantification of fang phenotypes - and especially those of rear-fanged species - has proved challenging or impossible owing to the small size and relative rarity of many such snakes. Consequently, it has been difficult to understand the evolutionary history of both venom and prey-capture strategies across extant snakes. We quantified variation in the dentition of 145 colubriform ("advanced") snake species using microCT scanning and compared dental characters with ecological data on species' diet and prey capture method(s) to understand broader patterns in snake fang evolution. RESULTS Dental traits such as maxilla length, tooth number, and fang size show strong phylogenetic signal across Colubriformes. We find extreme heterogeneity and evolutionary lability in the rear-fanged phenotype in colubrid (colubrine, dipsadine, and natricine lineages) and lamprophiid snakes, in contrast to relative uniformity in the front fanged phenotypes of other groups (vipers and, to a lesser extent, elapids). Fang size and position are correlated with venom-use in vipers, elapids, and colubrid snakes, with the latter group shifting fangs anteriorly by shortening the entire maxillary bone. We find that maxilla length and tooth number may also be correlated with the evolution of dietary specialization. Finally, an ancestral state reconstruction suggests that fang loss is a recurring phenomenon in colubrid snakes, likely accompanied by shifts in diet and prey capture mode. CONCLUSIONS Our study provides a framework for quantifying the complex morphologies associated with venom use in snakes. Our results suggest that fang phenotypes, and particularly the rear-fanged phenotype, in snakes are both diverse and labile, facilitating a wide range of ecological strategies and contributing to spectacular radiations of these organisms in tropical and subtropical biomes worldwide.
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Affiliation(s)
- Erin P Westeen
- Department of Environmental Science, Policy, and Management & Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA.
- Department of Ecology and Evolutionary Biology & Museum of Zoology, University of Michigan, Ann Arbor, MI, USA.
| | - Andrew M Durso
- Department of Biological Sciences, Florida Gulf Coast University, Ft. Myers, FL, USA
| | - Michael C Grundler
- Department of Ecology and Evolutionary Biology & Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology & Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - Alison R Davis Rabosky
- Department of Ecology and Evolutionary Biology & Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
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21
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Grundler M, Rabosky DL. Complex Ecological Phenotypes on Phylogenetic Trees: A Markov Process Model for Comparative Analysis of Multivariate Count Data. Syst Biol 2020; 69:1200-1211. [DOI: 10.1093/sysbio/syaa031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 04/02/2020] [Accepted: 04/07/2020] [Indexed: 12/26/2022] Open
Abstract
AbstractThe evolutionary dynamics of complex ecological traits—including multistate representations of diet, habitat, and behavior—remain poorly understood. Reconstructing the tempo, mode, and historical sequence of transitions involving such traits poses many challenges for comparative biologists, owing to their multidimensional nature. Continuous-time Markov chains are commonly used to model ecological niche evolution on phylogenetic trees but are limited by the assumption that taxa are monomorphic and that states are univariate categorical variables. A necessary first step in the analysis of many complex traits is therefore to categorize species into a predetermined number of univariate ecological states, but this procedure can lead to distortion and loss of information. This approach also confounds interpretation of state assignments with effects of sampling variation because it does not directly incorporate empirical observations for individual species into the statistical inference model. In this study, we develop a Dirichlet-multinomial framework to model resource use evolution on phylogenetic trees. Our approach is expressly designed to model ecological traits that are multidimensional and to account for uncertainty in state assignments of terminal taxa arising from effects of sampling variation. The method uses multivariate count data across a set of discrete resource categories sampled for individual species to simultaneously infer the number of ecological states, the proportional utilization of different resources by different states, and the phylogenetic distribution of ecological states among living species and their ancestors. The method is general and may be applied to any data expressible as a set of observational counts from different categories. [Comparative methods; Dirichlet multinomial; ecological niche evolution; macroevolution; Markov model.]
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Affiliation(s)
- Michael Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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22
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Abstract
Studies of speciation typically investigate the evolution of reproductive isolation between populations, but several other processes can serve as key steps limiting the formation of species. In particular, the probability of successful speciation can be influenced by factors that affect the frequency with which population isolates form as well as their persistence through time. We suggest that population isolation and persistence have an inherently spatial dimension that can be profitably studied using a conceptual framework drawn from metapopulation ecology. We discuss models of speciation that incorporate demographic processes and highlight the need for a broader application of phylogenetic comparative approaches to evaluate the general importance of population isolation, persistence, and reproductive isolation in speciation. We review diverse and nontraditional data sources that can be leveraged to study isolation and persistence in a comparative framework. This incorporation of spatial demographic information facilitates the integration of perspectives on speciation across disciplines and timescales.
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Affiliation(s)
- Michael G. Harvey
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Sonal Singhal
- Department of Biology, California State University, Dominguez Hills, Carson, California 90747, USA
| | - Daniel L. Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
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23
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Holmes IA, Monagan IV, Rabosky DL, Davis Rabosky AR. Metabolically similar cohorts of bacteria exhibit strong cooccurrence patterns with diet items and eukaryotic microbes in lizard guts. Ecol Evol 2019; 9:12471-12481. [PMID: 31788191 PMCID: PMC6875663 DOI: 10.1002/ece3.5691] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/23/2019] [Accepted: 09/03/2019] [Indexed: 01/05/2023] Open
Abstract
Gut microbiomes perform essential services for their hosts, including helping them to digest food and manage pathogens and parasites. Performing these services requires a diverse and constantly changing set of metabolic functions from the bacteria in the microbiome. The metabolic repertoire of the microbiome is ultimately dependent on the outcomes of the ecological interactions of its member microbes, as these interactions in part determine the taxonomic composition of the microbiome. The ecological processes that underpin the microbiome's ability to handle a variety of metabolic challenges might involve rapid turnover of the gut microbiome in response to new metabolic challenges, or it might entail maintaining sufficient diversity in the microbiome that any new metabolic demands can be met from an existing set of bacteria. To differentiate between these scenarios, we examine the gut bacteria and resident eukaryotes of two generalist-insectivore lizards, while simultaneously identifying the arthropod prey each lizard was digesting at the time of sampling. We find that the cohorts of bacteria that occur significantly more or less often than expected with arthropod diet items or eukaryotes include bacterial species that are highly similar to each other metabolically. This pattern in the bacterial microbiome could represent an early step in the taxonomic shifts in bacterial microbiome that occur when host lineages change their diet niche over evolutionary timescales.
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Affiliation(s)
- Iris A. Holmes
- Museum of Zoology & Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMIUSA
| | - Ivan V. Monagan
- Museum of Zoology & Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMIUSA
- Division of HerpetologyAmerican Museum of Natural HistoryNew YorkNYUSA
- Department of Ecology, Evolution, and Environmental BiologyColumbia UniversityNew YorkNYUSA
| | - Daniel L. Rabosky
- Museum of Zoology & Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMIUSA
| | - Alison R. Davis Rabosky
- Museum of Zoology & Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMIUSA
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24
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von May R, Catenazzi A, Santa-Cruz R, Gutierrez AS, Moritz C, Rabosky DL. Thermal physiological traits in tropical lowland amphibians: Vulnerability to climate warming and cooling. PLoS One 2019; 14:e0219759. [PMID: 31369565 PMCID: PMC6675106 DOI: 10.1371/journal.pone.0219759] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 07/02/2019] [Indexed: 11/22/2022] Open
Abstract
Climate change is affecting biodiversity and ecosystem function worldwide, and the lowland tropics are of special concern because organisms living in this region experience temperatures that are close to their upper thermal limits. However, it remains unclear how and whether tropical lowland species will be able to cope with the predicted pace of climate warming. Additionally, there is growing interest in examining how quickly thermal physiological traits have evolved across taxa, and whether thermal physiological traits are evolutionarily conserved or labile. We measured critical thermal maximum (CTmax) and minimum (CTmin) in 56 species of lowland Amazonian frogs to determine the extent of phylogenetic conservatism in tolerance to heat and cold, and to predict species' vulnerability to climate change. The species we studied live in sympatry and represent ~65% of the known alpha diversity at our study site. Given that critical thermal limits may have evolved differently in response to different temperature constraints, we tested whether CTmax and CTmin exhibit different rates of evolutionary change. Measuring both critical thermal traits allowed us to estimate species' thermal breadth and infer their potential to respond to abrupt changes in temperature (warming and cooling). Additionally, we assessed the contribution of life history traits and found that both critical thermal traits were correlated with species' body size and microhabitat use. Specifically, small direct-developing frogs in the Strabomantidae family appear to be at highest risk of thermal stress while tree frogs (Hylidae) and narrow mouthed frogs (Microhylidae) tolerate higher temperatures. While CTmax and CTmin had considerable variation within and among families, both critical thermal traits exhibited similar rates of evolutionary change. Our results suggest that 4% of lowland rainforest frogs assessed will experience temperatures exceeding their CTmax, 25% might be moderately affected and 70% are unlikely to experience pronounced heat stress under a hypothetical 3°C temperature increase.
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Affiliation(s)
- Rudolf von May
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI, United States of America
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States of America
| | - Alessandro Catenazzi
- Department of Biological Sciences, Florida International University, Miami, FL, United States of America
| | - Roy Santa-Cruz
- Área de Herpetología, Museo de Historia Natural de la Universidad Nacional de San Agustín (MUSA), Arequipa, Perú
| | - Andrea S. Gutierrez
- Facultad de Ciencias Biológicas, Universidad Nacional Agraria La Molina, Lima, Perú
| | - Craig Moritz
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States of America
- Centre for Biodiversity Analysis and Research School of Biology, The Australian National University, Canberra, Australia
| | - Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI, United States of America
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25
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Chang J, Rabosky DL, Smith SA, Alfaro ME. An
r
package and online resource for macroevolutionary studies using the ray‐finned fish tree of life. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13182] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Jonathan Chang
- School of Biological Sciences Monash University Clayton VIC Australia
| | - Daniel L. Rabosky
- Museum of Zoology Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI
| | - Stephen A. Smith
- Museum of Zoology Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI
| | - Michael E. Alfaro
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaLos AngelesCA
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26
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Grundler MR, Singhal S, Cowan MA, Rabosky DL. Is genomic diversity a useful proxy for census population size? Evidence from a species-rich community of desert lizards. Mol Ecol 2019; 28:1664-1674. [PMID: 30739375 DOI: 10.1111/mec.15042] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/30/2019] [Accepted: 01/30/2019] [Indexed: 01/01/2023]
Abstract
Species abundance data are critical for testing ecological theory, but obtaining accurate empirical estimates for many taxa is challenging. Proxies for species abundance can help researchers circumvent time and cost constraints that are prohibitive for long-term sampling. Under simple demographic models, genetic diversity is expected to correlate with census size, such that genome-wide heterozygosity may provide a surrogate measure of species abundance. We tested whether nucleotide diversity is correlated with long-term estimates of abundance, occupancy and degree of ecological specialization in a diverse lizard community from arid Australia. Using targeted sequence capture, we obtained estimates of genomic diversity from 30 species of lizards, recovering an average of 5,066 loci covering 3.6 Mb of DNA sequence per individual. We compared measures of individual heterozygosity to a metric of habitat specialization to investigate whether ecological preference exerts a measurable effect on genetic diversity. We find that heterozygosity is significantly correlated with species abundance and occupancy, but not habitat specialization. Demonstrating the power of genomic sampling, the correlation between heterozygosity and abundance/occupancy emerged from considering just one or two individuals per species. However, genetic diversity does no better at predicting abundance than a single day of traditional sampling in this community. We conclude that genetic diversity is a useful proxy for regional-scale species abundance and occupancy, but a large amount of unexplained variation in heterozygosity suggests additional constraints or a failure of ecological sampling to adequately capture variation in true population size.
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Affiliation(s)
- Maggie R Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan.,Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, California
| | - Sonal Singhal
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan.,Department of Biology, CSU Dominguez Hills, Carson, California
| | - Mark A Cowan
- Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
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27
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Affiliation(s)
- Pascal O. Title
- Department of Ecology and Evolutionary Biology and Museum of ZoologyUniversity of Michigan Ann Arbor Michigan
- Environmental Resilience InstituteIndiana University Bloomington Indiana
| | - Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology and Museum of ZoologyUniversity of Michigan Ann Arbor Michigan
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28
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Mitchell JS, Etienne RS, Rabosky DL. Inferring Diversification Rate Variation From Phylogenies With Fossils. Syst Biol 2018; 68:1-18. [PMID: 29788398 DOI: 10.1093/sysbio/syy035] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/09/2018] [Indexed: 12/18/2022] Open
Abstract
Time-calibrated phylogenies of living species have been widely used to study the tempo and mode of species diversification. However, it is increasingly clear that inferences about species diversification-extinction rates in particular-can be unreliable in the absence of paleontological data. We introduce a general framework based on the fossilized birth-death process for studying speciation-extinction dynamics on phylogenies of extant and extinct species. The model assumes that phylogenies can be modeled as a mixture of distinct evolutionary rate regimes and that a hierarchical Poisson process governs the number of such rate regimes across a tree. We implemented the model in BAMM, a computational framework that uses reversible jump Markov chain Monte Carlo to simulate a posterior distribution of macroevolutionary rate regimes conditional on the branching times and topology of a phylogeny. The implementation, we describe can be applied to paleontological phylogenies, neontological phylogenies, and to phylogenies that include both extant and extinct taxa. We evaluate performance of the model on data sets simulated under a range of diversification scenarios. We find that speciation rates are reliably inferred in the absence of paleontological data. However, the inclusion of fossil observations substantially increases the accuracy of extinction rate estimates. We demonstrate that inferences are relatively robust to at least some violations of model assumptions, including heterogeneity in preservation rates and misspecification of the number of occurrences in paleontological data sets.
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Affiliation(s)
- Jonathan S Mitchell
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Avenue, Ann Arbor, Michigan 48109 USA
- Department of Biology, West Virginia University Institute of Technology, 410 Neville Street, Beckley, WV 25801, USA
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC Groningen, The Netherlands
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Avenue, Ann Arbor, Michigan 48109 USA
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29
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Rabosky DL. Phylogenies and Diversification Rates: Variance Cannot Be Ignored. Syst Biol 2018; 68:538-550. [DOI: 10.1093/sysbio/syy079] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 11/16/2018] [Accepted: 11/17/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, Biological Sciences Building, 1105 North University Avenue, University of Michigan, Ann Arbor, MI 48109, USA
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30
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Singhal S, Huang H, Grundler MR, Marchán-Rivadeneira MR, Holmes I, Title PO, Donnellan SC, Rabosky DL. Does Population Structure Predict the Rate of Speciation? A Comparative Test across Australia’s Most Diverse Vertebrate Radiation. Am Nat 2018; 192:432-447. [DOI: 10.1086/699515] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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31
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Rabosky DL. BAMM at the court of false equivalency: A response to Meyer and Wiens. Evolution 2018; 72:2246-2256. [DOI: 10.1111/evo.13566] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 03/14/2018] [Indexed: 01/16/2023]
Affiliation(s)
- Daniel L. Rabosky
- Museum of ZoologyUniversity of Michigan Ann Arbor MI 48109‐1079
- Department of Ecology and Evolutionary BiologyUniversity of Michigan Ann Arbor MI 48109‐1079
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32
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Rabosky DL. Phylogenetic tests for evolutionary innovation: the problematic link between key innovations and exceptional diversification. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0417. [PMID: 29061890 DOI: 10.1098/rstb.2016.0417] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2017] [Indexed: 11/12/2022] Open
Abstract
Evolutionary innovation contributes to the spectacular diversity of species and phenotypes across the tree of life. 'Key innovations' are widely operationalized within evolutionary biology as traits that facilitate increased diversification rates, such that lineages bearing the traits ultimately contain more species than closely related lineages lacking the focal trait. In this article, I briefly review the inference, analysis and interpretation of evolutionary innovation on phylogenetic trees. I argue that differential rates of lineage diversification should not be used as the basis for key innovation tests, despite the statistical tractability of such approaches. Under traditional interpretations of the macroevolutionary 'adaptive zone', we should not necessarily expect key innovations to confer faster diversification rates upon lineages that possess them relative to their extant sister clades. I suggest that a key innovation is a trait that allows a lineage to interact with the environment in a fundamentally different way and which, as a result, increases the total diversification-but not necessarily the diversification rate-of the parent clade. Considered alone, branching patterns in phylogenetic trees are poorly suited to the inference of evolutionary innovation due to their inherently low information content with respect to the processes that produce them. However, phylogenies may be important for identifying transformational shifts in ecological and morphological space that are characteristic of innovation at the macroevolutionary scale.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'.
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Affiliation(s)
- Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1079, USA
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33
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von May R, Lehr E, Rabosky DL. Evolutionary radiation of earless frogs in the Andes: molecular phylogenetics and habitat shifts in high-elevation terrestrial breeding frogs. PeerJ 2018; 6:e4313. [PMID: 29492332 PMCID: PMC5825883 DOI: 10.7717/peerj.4313] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/11/2018] [Indexed: 11/20/2022] Open
Abstract
The loss of hearing structures and loss of advertisement calls in many terrestrial breeding frogs (Strabomantidae) living at high elevations in South America are common and intriguing phenomena. The Andean frog genus Phrynopus Peters, 1873 has undergone an evolutionary radiation in which most species lack the tympanic membrane and tympanic annulus, yet the phylogenetic relationships among species in this group remain largely unknown. Here, we present an expanded molecular phylogeny of Phrynopus that includes 24 nominal species. Our phylogeny includes Phrynopus peruanus, the type species of the genus, and 10 other species for which genetic data were previously unavailable. We found strong support for monophyly of Phrynopus, and that two nominal species-Phrynopus curator and Phrynopus nicoleae-are junior synonyms of Phrynopus tribulosus. Using X-ray computed tomography (CT) imaging, we demonstrate that the absence of external hearing structures is associated with complete loss of the auditory skeletal elements (columella) in at least one member of the genus. We mapped the tympanum condition on to a species tree to infer whether the loss of hearing structures took place once or multiple times. We also assessed whether tympanum condition, body size, and body shape are associated with the elevational distribution and habitat use. We identified a single evolutionary transition that involved the loss of both the tympanic membrane and tympanic annulus, which in turn is correlated with the absence of advertisement calls. We also identified several species pairs where one species inhabits the Andean grassland and the other montane forest. When accounting for phylogenetic relatedness among species, we detected a significant pattern of increasing body size with increasing elevation. Additionally, species at higher elevations tend to develop shorter limbs, shorter head, and shorter snout than species living at lower elevations. Our findings strongly suggest a link between ecological divergence and morphological diversity of terrestrial breeding frogs living in montane gradients.
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Affiliation(s)
- Rudolf von May
- Museum of Zoology & Department of Ecology and Evolutionary Biology, University of Michigan-Ann Arbor, Ann Arbor, MI, United States of America.,Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States of America
| | - Edgar Lehr
- Department of Biology, Illinois Wesleyan University, Bloomington, IL, United States of America
| | - Daniel L Rabosky
- Museum of Zoology & Department of Ecology and Evolutionary Biology, University of Michigan-Ann Arbor, Ann Arbor, MI, United States of America
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Rosauer DF, Byrne M, Blom MPK, Coates DJ, Donnellan S, Doughty P, Keogh JS, Kinloch J, Laver RJ, Myers C, Oliver PM, Potter S, Rabosky DL, Afonso Silva AC, Smith J, Moritz C. Real‐world conservation planning for evolutionary diversity in the Kimberley, Australia, sidesteps uncertain taxonomy. Conserv Lett 2018. [DOI: 10.1111/conl.12438] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Dan F. Rosauer
- Division of Ecology & Evolution, Research School of Biology Australian National University Acton ACT Australia
- Centre for Biodiversity Analysis Canberra, ACT Australia
| | - Margaret Byrne
- Science and Conservation Department of Biodiversity Conservation and Attractions Kensington WA Australia
| | - Mozes P. K. Blom
- Division of Ecology & Evolution, Research School of Biology Australian National University Acton ACT Australia
- Centre for Biodiversity Analysis Canberra, ACT Australia
| | - David J. Coates
- Science and Conservation Department of Biodiversity Conservation and Attractions Kensington WA Australia
| | - Stephen Donnellan
- South Australian Museum North Terrace Adelaide SA Australia
- School of Biological Sciences University of Adelaide Adelaide SA Australia
| | - Paul Doughty
- Department of Terrestrial Zoology Western Australian Museum Welshpool WA Australia
| | - J. Scott Keogh
- Division of Ecology & Evolution, Research School of Biology Australian National University Acton ACT Australia
| | - Janine Kinloch
- Science and Conservation Department of Biodiversity Conservation and Attractions Kensington WA Australia
| | - Rebecca J. Laver
- Division of Ecology & Evolution, Research School of Biology Australian National University Acton ACT Australia
- Centre for Biodiversity Analysis Canberra, ACT Australia
- Department of Biosciences University of Melbourne Parkville VIC Australia
| | - Cecilia Myers
- Dunkeld Pastoral Company Pty Ltd. Dunkeld VIC Australia
| | - Paul M. Oliver
- Division of Ecology & Evolution, Research School of Biology Australian National University Acton ACT Australia
- Centre for Biodiversity Analysis Canberra, ACT Australia
| | - Sally Potter
- Division of Ecology & Evolution, Research School of Biology Australian National University Acton ACT Australia
- Centre for Biodiversity Analysis Canberra, ACT Australia
- Australian Museum Research Institute Australian Museum Sydney NSW Australia
| | - Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology University of Michigan Ann Arbor MI USA
| | - Ana Catarina Afonso Silva
- Division of Ecology & Evolution, Research School of Biology Australian National University Acton ACT Australia
- Centre for Biodiversity Analysis Canberra, ACT Australia
- Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências Universidade de Lisboa Lisboa Portugal
| | - James Smith
- Australian Wildlife Conservancy Mornington Sanctuary Derby WA Australia
- Research Institute for the Environment and Livelihoods Charles Darwin University Darwin NT Australia
| | - Craig Moritz
- Division of Ecology & Evolution, Research School of Biology Australian National University Acton ACT Australia
- Centre for Biodiversity Analysis Canberra, ACT Australia
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35
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Singhal S, Huang H, Title PO, Donnellan SC, Holmes I, Rabosky DL. Genetic diversity is largely unpredictable but scales with museum occurrences in a species-rich clade of Australian lizards. Proc Biol Sci 2018; 284:rspb.2016.2588. [PMID: 28469025 DOI: 10.1098/rspb.2016.2588] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 04/03/2017] [Indexed: 12/14/2022] Open
Abstract
Genetic diversity is a fundamental characteristic of species and is affected by many factors, including mutation rate, population size, life history and demography. To better understand the processes that influence levels of genetic diversity across taxa, we collected genome-wide restriction-associated DNA data from more than 500 individuals spanning 76 nominal species of Australian scincid lizards in the genus Ctenotus To avoid potential biases associated with variation in taxonomic practice across the group, we used coalescent-based species delimitation to delineate 83 species-level lineages within the genus for downstream analyses. We then used these genetic data to infer levels of within-population genetic diversity. Using a phylogenetically informed approach, we tested whether variation in genetic diversity could be explained by population size, environmental heterogeneity or historical demography. We find that the strongest predictor of genetic diversity is a novel proxy for census population size: the number of vouchered occurrences in museum databases. However, museum occurrences only explain a limited proportion of the variance in genetic diversity, suggesting that genetic diversity might be difficult to predict at shallower phylogenetic scales.
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Affiliation(s)
- Sonal Singhal
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Huateng Huang
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pascal O Title
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Stephen C Donnellan
- South Australian Museum, North Terrace, Adelaide 5000, Australia.,Australian Centre for Evolutionary Biology and Biodiversity, University of Adelaide, Adelaide 5005, Australia
| | - Iris Holmes
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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Title PO, Rabosky DL. Do Macrophylogenies Yield Stable Macroevolutionary Inferences? An Example from Squamate Reptiles. Syst Biol 2018; 66:843-856. [PMID: 27821703 DOI: 10.1093/sysbio/syw102] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 10/27/2016] [Indexed: 01/03/2023] Open
Abstract
Advances in the generation, retrieval, and analysis of phylogenetic data have enabled researchers to create phylogenies that contain many thousands of taxa. These "macrophylogenies"-large trees that typically derive from megaphylogeny, supermatrix, or supertree approaches-provide researchers with an unprecedented ability to conduct evolutionary analyses across broad phylogenetic scales. Many studies have now used these phylogenies to explore the dynamics of speciation, extinction, and phenotypic evolution across large swaths of the tree of life. These trees are characterized by substantial phylogenetic uncertainty on multiple levels, and the stability of macroevolutionary inferences from these data sets has not been rigorously explored. As a case study, we tested whether five recently published phylogenies for squamate reptiles-each consisting of more than 4000 species-yield congruent inferences about the processes that underlie variation in species richness across replicate evolutionary radiations of Australian snakes and lizards. We find discordance across the five focal phylogenies with respect to clade age and several diversification rate metrics, and in the effects of clade age on species richness. We also find that crown clade ages reported in the literature on these Australian groups are in conflict with all of the large phylogenies examined. Macrophylogenies offer an unprecedented opportunity to address evolutionary and ecological questions at broad phylogenetic scales, but accurately representing the uncertainty that is inherent to such analyses remains a critical challenge to our field. [Australia; macroevolution; macrophylogeny; squamates; time calibration.].
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Affiliation(s)
- Pascal O Title
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
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Rabosky DL, Mitchell JS, Chang J. Is BAMM Flawed? Theoretical and Practical Concerns in the Analysis of Multi-Rate Diversification Models. Syst Biol 2018; 66:477-498. [PMID: 28334223 PMCID: PMC5790138 DOI: 10.1093/sysbio/syx037] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 02/14/2017] [Indexed: 11/13/2022] Open
Abstract
Bayesian analysis of macroevolutionary mixtures (BAMM) is a statistical framework that uses reversible jump Markov chain Monte Carlo to infer complex macroevolutionary dynamics of diversification and phenotypic evolution on phylogenetic trees. A recent article by Moore et al. (MEA) reported a number of theoretical and practical concerns with BAMM. Major claims from MEA are that (i) BAMM’s likelihood function is incorrect, because it does not account for unobserved rate shifts; (ii) the posterior distribution on the number of rate shifts is overly sensitive to the prior; and (iii) diversification rate estimates from BAMM are unreliable. Here, we show that these and other conclusions from MEA are generally incorrect or unjustified. We first demonstrate that MEA’s numerical assessment of the BAMM likelihood is compromised by their use of an invalid likelihood function. We then show that “unobserved rate shifts” appear to be irrelevant for biologically plausible parameterizations of the diversification process. We find that the purportedly extreme prior sensitivity reported by MEA cannot be replicated with standard usage of BAMM v2.5, or with any other version when conventional Bayesian model selection is performed. Finally, we demonstrate that BAMM performs very well at estimating diversification rate variation across the \documentclass[12pt]{minimal}
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}{}${\sim}$\end{document}20% of simulated trees in MEA’s data set for which it is theoretically possible to infer rate shifts with confidence. Due to ascertainment bias, the remaining 80% of their purportedly variable-rate phylogenies are statistically indistinguishable from those produced by a constant-rate birth–death process and were thus poorly suited for the summary statistics used in their performance assessment. We demonstrate that inferences about diversification rates have been accurate and consistent across all major previous releases of the BAMM software. We recognize an acute need to address the theoretical foundations of rate-shift models for phylogenetic trees, and we expect BAMM and other modeling frameworks to improve in response to mathematical and computational innovations. However, we remain optimistic that that the imperfect tools currently available to comparative biologists have provided and will continue to provide important insights into the diversification of life on Earth.
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Affiliation(s)
- Daniel L Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jonathan S Mitchell
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jonathan Chang
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
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38
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Affiliation(s)
- Michael G. Harvey
- Department of Ecology and Evolutionary Biology and Museum of Zoology University of Michigan Ann Arbor MI USA
| | - Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology University of Michigan Ann Arbor MI USA
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Abstract
Rates of species origination and extinction can vary over time during evolutionary radiations, and it is possible to reconstruct the history of diversification using molecular phylogenies of extant taxa only. Maximum likelihood methods provide a useful framework for inferring temporal variation in diversification rates. LASER is a package for the R programming environment that implements maximum likelihood methods based on the birth-death process to test whether diversification rates have changed over time. LASER contrasts the likelihood of phylogenetic data under models where diversification rates have changed over time to alternative models where rates have remained constant over time. Major strengths of the package include the ability to detect temporal increases in diversification rates and the inference of diversification parameters under multiple rate-variable models of diversification. The program and associated documentation are freely available from the R package archive at http://cran.r-project.org.
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Affiliation(s)
- Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853-2701, U.S.A
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40
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Lavoué S, Arnegard ME, Rabosky DL, McIntyre PB, Arcila D, Vari RP, Nishida M. Trophic evolution in African citharinoid fishes (Teleostei: Characiformes) and the origin of intraordinal pterygophagy. Mol Phylogenet Evol 2017; 113:23-32. [DOI: 10.1016/j.ympev.2017.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 04/29/2017] [Accepted: 05/01/2017] [Indexed: 11/25/2022]
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41
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Harvey MG, Seeholzer GF, Smith BT, Rabosky DL, Cuervo AM, Brumfield RT. Positive association between population genetic differentiation and speciation rates in New World birds. Proc Natl Acad Sci U S A 2017; 114:6328-6333. [PMID: 28559330 PMCID: PMC5474768 DOI: 10.1073/pnas.1617397114] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
An implicit assumption of speciation biology is that population differentiation is an important stage of evolutionary diversification, but its significance as a rate-limiting control on phylogenetic speciation dynamics remains largely untested. If population differentiation within a species is related to its speciation rate over evolutionary time, the causes of differentiation could also be driving dynamics of organismal diversity across time and space. Alternatively, geographic variants might be short-lived entities with rates of formation that are unlinked to speciation rates, in which case the causes of differentiation would have only ephemeral impacts. By pairing population genetics datasets from 173 New World bird species (>17,000 individuals) with phylogenetic estimates of speciation rate, we show that the population differentiation rates within species are positively correlated with their speciation rates over long timescales. Although population differentiation rate explains relatively little of the variation in speciation rate among lineages, the positive relationship between differentiation rate and speciation rate is robust to species-delimitation schemes and to alternative measures of both rates. Population differentiation occurs at least three times faster than speciation, which suggests that most populations are ephemeral. Speciation and population differentiation rates are more tightly linked in tropical species than in temperate species, consistent with a history of more stable diversification dynamics through time in the Tropics. Overall, our results suggest that the processes responsible for population differentiation are tied to those that underlie broad-scale patterns of diversity.
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Affiliation(s)
- Michael G Harvey
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803;
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48109
| | - Glenn F Seeholzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803
| | - Brian Tilston Smith
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803
- Department of Ornithology, American Museum of Natural History, New York, NY 10024
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48109
| | - Andrés M Cuervo
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118
| | - Robb T Brumfield
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803
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42
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Singhal S, Grundler M, Colli G, Rabosky DL. Squamate Conserved Loci (SqCL): A unified set of conserved loci for phylogenomics and population genetics of squamate reptiles. Mol Ecol Resour 2017; 17:e12-e24. [PMID: 28417603 DOI: 10.1111/1755-0998.12681] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 03/05/2017] [Accepted: 04/03/2017] [Indexed: 11/28/2022]
Abstract
The identification of conserved loci across genomes, along with advances in target capture methods and high-throughput sequencing, has helped spur a phylogenomics revolution by enabling researchers to gather large numbers of homologous loci across clades of interest with minimal upfront investment in locus design. Target capture for vertebrate animals is currently dominated by two approaches-anchored hybrid enrichment (AHE) and ultraconserved elements (UCE)-and both approaches have proven useful for addressing questions in phylogenomics, phylogeography and population genomics. However, these two sets of loci have minimal overlap with each other; moreover, they do not include many traditional loci that that have been used for phylogenetics. Here, we combine across UCE, AHE and traditional phylogenetic gene locus sets to generate the Squamate Conserved Loci set, a single integrated probe set that can generate high-quality and highly complete data across all three loci types. We use these probes to generate data for 44 phylogenetically disparate taxa that collectively span approximately 33% of terrestrial vertebrate diversity. Our results generated an average of 4.29 Mb across 4709 loci per individual, of which an average of 2.99 Mb was sequenced to high enough coverage (≥10×) to use for population genetic analyses. We validate the utility of these loci for both phylogenomic and population genomic questions, provide a comparison among these locus sets of their relative usefulness and suggest areas for future improvement.
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Affiliation(s)
- Sonal Singhal
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Maggie Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Guarino Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Brazil
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
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Rabosky DL, Goldberg EE. FiSSE: A simple nonparametric test for the effects of a binary character on lineage diversification rates. Evolution 2017; 71:1432-1442. [DOI: 10.1111/evo.13227] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 03/06/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology University of Michigan Ann Arbor Michigan 48103
| | - Emma E. Goldberg
- Department of Ecology, Evolution, and Behavior University of Minnesota Saint Paul Minnesota 55108
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44
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Grundler MR, Pianka ER, Pelegrin N, Cowan MA, Rabosky DL. Stable isotope ecology of a hyper-diverse community of scincid lizards from arid Australia. PLoS One 2017; 12:e0172879. [PMID: 28245270 PMCID: PMC5330509 DOI: 10.1371/journal.pone.0172879] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 02/11/2017] [Indexed: 11/19/2022] Open
Abstract
We assessed the utility of stable isotope analysis as a tool for understanding community ecological structure in a species-rich clade of scincid lizards from one of the world's most diverse lizard communities. Using a phylogenetic comparative framework, we tested whether δ15N and δ13C isotopic composition from individual lizards was correlated with species-specific estimates of diet and habitat use. We find that species are highly divergent in isotopic composition with significant correlations to habitat use, but this relationship shows no phylogenetic signal. Isotopic composition corresponds to empirical observations of diet for some species but much variation remains unexplained. We demonstrate the importance of using a multianalytical approach to questions of long-term dietary preference, and suggest that the use of stable isotopes in combination with stomach content analysis and empirical data on habitat use can potentially reveal patterns in ecological traits at finer scales with important implications for community structuring.
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Affiliation(s)
- Maggie R. Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
| | - Eric R. Pianka
- Department of Integrative Biology C0930, University of Texas at Austin, One University Station, Austin, Texas, United States of America
| | - Nicolás Pelegrin
- Laboratorio de Ecología y Conservación de la Herpetofauna, Instituto de Diversidad y Ecología Animal, (IDEA, CONICET-UNC), and Centro de Zoología Aplicada (UNC), Córdoba, Argentina
| | - Mark A. Cowan
- Department of Parks and Wildlife, Wanneroo, Western Australia, Australia
| | - Daniel L. Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
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Mitchell JS, Rabosky DL. Bayesian model selection with BAMM: effects of the model prior on the inferred number of diversification shifts. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12626] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jonathan S. Mitchell
- Department of Ecology and Evolutionary Biology Museum of Zoology University of Michigan Ann Arbor MI 48109 USA
| | - Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology Museum of Zoology University of Michigan Ann Arbor MI 48109 USA
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46
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Davis Rabosky AR, Cox CL, Rabosky DL, Title PO, Holmes IA, Feldman A, McGuire JA. Coral snakes predict the evolution of mimicry across New World snakes. Nat Commun 2016; 7:11484. [PMID: 27146100 PMCID: PMC4858746 DOI: 10.1038/ncomms11484] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 04/01/2016] [Indexed: 11/09/2022] Open
Abstract
Batesian mimicry, in which harmless species (mimics) deter predators by deceitfully imitating the warning signals of noxious species (models), generates striking cases of phenotypic convergence that are classic examples of evolution by natural selection. However, mimicry of venomous coral snakes has remained controversial because of unresolved conflict between the predictions of mimicry theory and empirical patterns in the distribution and abundance of snakes. Here we integrate distributional, phenotypic and phylogenetic data across all New World snake species to demonstrate that shifts to mimetic coloration in nonvenomous snakes are highly correlated with coral snakes in both space and time, providing overwhelming support for Batesian mimicry. We also find that bidirectional transitions between mimetic and cryptic coloration are unexpectedly frequent over both long- and short-time scales, challenging traditional views of mimicry as a stable evolutionary 'end point' and suggesting that insect and snake mimicry may have different evolutionary dynamics.
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Affiliation(s)
- Alison R. Davis Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, Michigan 48109, USA
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, 3101 Valley Life Sciences, Berkeley, California 94720, USA
| | - Christian L. Cox
- Department of Biology, Georgia Southern University, PO Box 8042, Statesboro, Georgia 30460, USA
- Department of Biology, The University of Texas, Arlington, Texas 76019, USA
| | - Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, Michigan 48109, USA
| | - Pascal O. Title
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, Michigan 48109, USA
| | - Iris A. Holmes
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, Michigan 48109, USA
| | - Anat Feldman
- Department of Zoology, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jimmy A. McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, 3101 Valley Life Sciences, Berkeley, California 94720, USA
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47
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Davis Rabosky AR, Cox CL, Rabosky DL. Unlinked Mendelian inheritance of red and black pigmentation in snakes: Implications for Batesian mimicry. Evolution 2016; 70:944-53. [PMID: 26959901 DOI: 10.1111/evo.12902] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/24/2016] [Accepted: 02/22/2016] [Indexed: 11/28/2022]
Abstract
Identifying the genetic basis of mimetic signals is critical to understanding both the origin and dynamics of mimicry over time. For species not amenable to large laboratory breeding studies, widespread color polymorphism across natural populations offers a powerful way to assess the relative likelihood of different genetic systems given observed phenotypic frequencies. We classified color phenotype for 2175 ground snakes (Sonora semiannulata) across the continental United States to analyze morph ratios and test among competing hypotheses about the genetic architecture underlying red and black coloration in coral snake mimics. We found strong support for a two-locus model under simple Mendelian inheritance, with red and black pigmentation being controlled by separate loci. We found no evidence of either linkage disequilibrium between loci or sex linkage. In contrast to Batesian mimicry systems such as butterflies in which all color signal components are linked into a single "supergene," our results suggest that the mimetic signal in colubrid snakes can be disrupted through simple recombination and that color evolution is likely to involve discrete gains and losses of each signal component. Both outcomes are likely to contribute to the exponential increase in rates of color evolution seen in snake mimicry systems over insect systems.
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Affiliation(s)
- Alison R Davis Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, Michigan, 48109. .,Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California, 94720.
| | - Christian L Cox
- Department of Biology, Georgia Southern University, PO Box 8042, Statesboro, Georgia 30460
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, Michigan, 48109
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Abstract
The tropics contain far greater numbers of species than temperate regions, suggesting that rates of species formation might differ systematically between tropical and non-tropical areas. We tested this hypothesis by reconstructing the history of speciation in New World (NW) land birds using BAMM, a Bayesian framework for modelling complex evolutionary dynamics on phylogenetic trees. We estimated marginal distributions of present-day speciation rates for each of 2571 species of birds. The present-day rate of speciation varies approximately 30-fold across NW birds, but there is no difference in the rate distributions for tropical and temperate taxa. Using macroevolutionary cohort analysis, we demonstrate that clades with high tropical membership do not produce species more rapidly than temperate clades. For nearly any value of present-day speciation rate, there are far more species in the tropics than the temperate zone. Any effects of latitude on speciation rate are marginal in comparison to the dramatic variation in rates among clades.
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Affiliation(s)
- Daniel L Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pascal O Title
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Huateng Huang
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
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Affiliation(s)
- Daniel L. Rabosky
- Museum of Zoology & Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor MI 48109 USA
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Rabosky DL. No substitute for real data: A cautionary note on the use of phylogenies from birth-death polytomy resolvers for downstream comparative analyses. Evolution 2015; 69:3207-16. [DOI: 10.1111/evo.12817] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 10/30/2015] [Accepted: 11/02/2015] [Indexed: 11/26/2022]
Affiliation(s)
- Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology; University of Michigan; Ann Arbor Michigan 48103
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