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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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Holmes IA, Monagan IV, Westphal MF, Johnson PJ, Rabosky ARD. Parsing variance by marker type: Testing biogeographic hypotheses and differential contribution of historical processes to population structure in a desert lizard. Mol Ecol 2023; 32:4880-4897. [PMID: 37466017 PMCID: PMC10530499 DOI: 10.1111/mec.17076] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 06/19/2023] [Accepted: 07/04/2023] [Indexed: 07/20/2023]
Abstract
A fundamental goal of population genetic studies is to identify historical biogeographic patterns and understand the processes that generate them. However, localized demographic events can skew population genetic inference. Assessing populations with multiple types of genetic markers, each with unique mutation rates and responses to changes in population size, can help to identify potentially confounding population-specific demographic processes. Here, we compared population structure and connectivity inferred from microsatellites and restriction site-associated DNA loci among 17 populations of an arid-specialist lizard, the desert night lizard, Xantusia vigilis, in central California to test among historical processes structuring population genetic diversity. We found that both marker types yielded generally concordant insights into population genetic structure including a major phylogenetic break maintained between two populations separated by less than 10 km, suggesting that either marker type could be used to understand generalized demographic patterns across the region for management purposes. However, we also found that the effects of demography on marker discordance could be used to elucidate population histories and distinguish among competing biogeographic hypotheses. Our results suggest that comparisons of within-population diversity across marker types provide powerful opportunities for leveraging marker discordance, particularly for understanding the creation and maintenance of contact zones among clades.
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Affiliation(s)
- Iris A. Holmes
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI USA
- Cornell Institute of Host Microbe Interactions and Disease and Department of Microbiology, Cornell University, Ithaca, NY 14853 USA
| | - Ivan V. Monagan
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI USA
- Department of Ecology, Evolution, and Environmental Biology, Columbia University and American Museum of Natural History, NY, USA
| | | | | | - Alison R. Davis Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI USA
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA USA
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3
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Srodawa K, Cerda PA, Davis Rabosky AR, Crowe-Riddell JM. Evolution of Three-Finger Toxin Genes in Neotropical Colubrine Snakes (Colubridae). Toxins (Basel) 2023; 15:523. [PMID: 37755949 PMCID: PMC10534312 DOI: 10.3390/toxins15090523] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/16/2023] [Accepted: 08/23/2023] [Indexed: 09/28/2023] Open
Abstract
Snake venom research has historically focused on front-fanged species (Viperidae and Elapidae), limiting our knowledge of venom evolution in rear-fanged snakes across their ecologically diverse phylogeny. Three-finger toxins (3FTxs) are a known neurotoxic component in the venoms of some rear-fanged snakes (Colubridae: Colubrinae), but it is unclear how prevalent 3FTxs are both in expression within venom glands and more broadly among colubrine species. Here, we used a transcriptomic approach to characterize the venom expression profiles of four species of colubrine snakes from the Neotropics that were dominated by 3FTx expression (in the genera Chironius, Oxybelis, Rhinobothryum, and Spilotes). By reconstructing the gene trees of 3FTxs, we found evidence of putative novel heterodimers in the sequences of Chironius multiventris and Oxybelis aeneus, revealing an instance of parallel evolution of this structural change in 3FTxs among rear-fanged colubrine snakes. We also found positive selection at sites within structural loops or "fingers" of 3FTxs, indicating these areas may be key binding sites that interact with prey target molecules. Overall, our results highlight the importance of exploring the venoms of understudied species in reconstructing the full evolutionary history of toxins across the tree of life.
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Affiliation(s)
- Kristy Srodawa
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA; (K.S.); (A.R.D.R.); (J.M.C.-R.)
- Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter A. Cerda
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA; (K.S.); (A.R.D.R.); (J.M.C.-R.)
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48108, USA
| | - Alison R. Davis Rabosky
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA; (K.S.); (A.R.D.R.); (J.M.C.-R.)
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48108, USA
| | - Jenna M. Crowe-Riddell
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA; (K.S.); (A.R.D.R.); (J.M.C.-R.)
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48108, USA
- School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC 3086, Australia
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Sanders NJ, Cooper N, Davis Rabosky AR, Gibson DJ. Leveraging natural history collections to understand the impacts of global change. J Anim Ecol 2023; 92:232-236. [PMID: 36751040 DOI: 10.1111/1365-2656.13882] [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: 12/22/2022] [Accepted: 01/06/2023] [Indexed: 02/09/2023]
Abstract
This joint Special Feature focuses on the contributions and potential of natural history collections to address global change questions.
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Affiliation(s)
- Nathan J Sanders
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Natalie Cooper
- Science Group, Natural History Museum London, London, UK
| | - Alison R Davis Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, Michigan, USA
| | - David J Gibson
- School of Biological Sciences, Southern Illinois University, Carbondale, Illinois, USA
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5
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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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6
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Larson JG, Crowell HL, Walsh LL, Davis Rabosky AR. The Batrachian Barf Bowl: An authentic research experience using ecological data from frog diets. Ecol Evol 2022; 12:e9095. [PMID: 35866014 PMCID: PMC9288929 DOI: 10.1002/ece3.9095] [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: 02/17/2022] [Revised: 05/17/2022] [Accepted: 06/22/2022] [Indexed: 11/22/2022] Open
Abstract
Authentic research experiences (AREs) are a powerful strategy for inspiring and retaining students in science, technology, engineering, and math (STEM) fields. However, recent demand for virtual learning has emphasized the need for remote AREs that also foster a sense of community and interpersonal connections among participants. Here, we describe an ARE activity that leverages digitized diet data from natural history collections to provide students with collaborative research experience across any learning environment. Using magnified photographs of frog stomach contents collected in the Peruvian Amazon, we designed an open‐source “bowl game” competition that challenges students to identify, measure, and compare diet items across vouchered frog specimens (“Batrachian Barf Bowl”). To demonstrate learning outcomes, we ran this activity with 39 herpetology class students from the University of Notre Dame and the University of Michigan. We used pre‐ and post‐activity assessments to evaluate effectiveness, scientific accuracy of results, and impact on student well‐being. With minimal preparation and training in invertebrate identification, students were successful in identifying hundreds of frog diet items to taxonomic order, although accuracy varied among clades (global accuracy ~70%). While we found no difference in science identity, community, or self‐efficacy between the two institutions at either time point (pre‐ and post‐activity), we found that well‐being was significantly higher for both sets of students after the activity. Overall, this approach offers a model for combining active learning with museum collections to provide experiential research opportunities that highlight the power of scientific collaboration.
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Affiliation(s)
- Joanna G Larson
- Department of Ecology and Evolutionary Biology and Museum of Zoology University of Michigan Ann Arbor Michigan USA
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana USA
| | - Hayley L Crowell
- Department of Ecology and Evolutionary Biology and Museum of Zoology University of Michigan Ann Arbor Michigan USA
| | - Lisa L Walsh
- Education Research & Outreach Donald Danforth Plant Science Center St. Louis Missouri USA
| | - Alison R Davis Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology University of Michigan Ann Arbor Michigan USA
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Curlis JD, Renney T, Rabosky ARD, Moore TY. Batch-Mask: Automated image segmentation for organisms with limbless or non-standard body forms. Integr Comp Biol 2022; 62:1111-1120. [PMID: 35575628 PMCID: PMC9617216 DOI: 10.1093/icb/icac036] [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: 01/31/2022] [Revised: 04/28/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
Efficient comparisons of biological color patterns are critical for understanding the mechanisms by which organisms evolve in nature, including sexual selection, predator–prey interactions, and thermoregulation. However, limbless, elongate, or spiral-shaped organisms do not conform to the standard orientation and photographic techniques required for many automated analyses. Currently, large-scale color analysis of elongate animals requires time-consuming manual landmarking, which reduces their representation in coloration research despite their ecological importance. We present Batch-Mask: an automated, customizable workflow to automatically analyze large photographic datasets to isolate non-standard biological organisms from the background. Batch-Mask is completely open-source and does not depend on any proprietary software. We also present a user guide for fine-tuning weights to a custom dataset and incorporating existing manual visual analysis tools (e.g., micaToolbox) into a single automated workflow for comparing color patterns across images. Batch-Mask was 60x faster than manual landmarking and produced masks that correctly identified 96% of all snake pixels. To validate our approach, we used micaToolbox to compare pattern energy in a sample set of snake photographs segmented by Batch-Mask and humans and found no significant difference in the output results. The fine-tuned weights, user guide, and automated workflow substantially decrease the amount of time and attention required to quantitatively analyze non-standard biological subjects. With these tools, biologists can compare color, pattern, and shape differences in large datasets that include significant morphological variation in elongate body forms. This advance is especially valuable for comparative analyses of natural history collections across a broad range of morphologies. Through landmark-free automation, Batch-Mask can greatly expand the scale of space, time, or taxonomic breadth across which color variation can be quantitatively examined.
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Affiliation(s)
- John David Curlis
- Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, 1105 N University Ave, 48109, Michigan, USA
| | - Timothy Renney
- Computer Science, University of Michigan, Street, Postcode, Michigan, USA
| | - Alison R Davis Rabosky
- Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, 1105 N University Ave, 48109, Michigan, USA
| | - Talia Y Moore
- Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, 1105 N University Ave, 48109, Michigan, USA.,Mechanical Engineering and Robotics Institute, University of Michigan, 2505 Hayward St, Ann Arbor, 48109, Michigan, USA
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8
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Callahan S, Crowe‐Riddell JM, Nagesan RS, Gray JA, Davis Rabosky AR. A guide for optimal iodine staining and high-throughput diceCT scanning in snakes. Ecol Evol 2021; 11:11587-11603. [PMID: 34522326 PMCID: PMC8427571 DOI: 10.1002/ece3.7467] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 01/05/2021] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 01/10/2023] Open
Abstract
Diffusible iodine-based contrast-enhanced computed tomography (diceCT) visualizes soft tissue from micro-CT (µCT) scans of specimens to uncover internal features and natural history information without incurring physical damage via dissection. Unlike hard-tissue imaging, taxonomic sampling within diceCT datasets is currently limited. To initiate best practices for diceCT in a nonmodel group, we outline a guide for staining and high-throughput µCT scanning in snakes. We scanned the entire body and one region of interest (i.e., head) for 23 specimens representing 23 species from the clades Aniliidae, Dipsadinae, Colubrinae, Elapidae, Lamprophiidae, and Viperidae. We generated 82 scans that include 1.25% Lugol's iodine stained (soft tissue) and unstained (skeletal) data for each specimen. We found that duration of optimal staining time increased linearly with body size; head radius was the best indicator. Postreconstruction of scans, optimal staining was evident by evenly distributed grayscale values and clear differentiation among soft-tissue anatomy. Under and over stained specimens produced poor contrast among soft tissues, which was often exacerbated by user bias during "digital dissections" (i.e., segmentation). Regardless, all scans produced usable data from which we assessed a range of downstream analytical applications within ecology and evolution (e.g., predator-prey interactions, life history, and morphological evolution). Ethanol destaining reversed the known effects of iodine on the exterior appearance of physical specimens, but required substantially more time than reported for other destaining methods. We discuss the feasibility of implementing diceCT techniques for a new user, including approximate financial and temporal commitments, required facilities, and potential effects of staining on specimens. We present the first high-throughput workflow for full-body skeletal and diceCT scanning in snakes, which can be generalized to any elongate vertebrates, and increases publicly available diceCT scans for reptiles by an order of magnitude.
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Affiliation(s)
- Sean Callahan
- Museum of ZoologyUniversity of MichiganAnn ArborMIUSA
- Department of BiologyEastern Michigan UniversityYpsilantiMIUSA
| | - Jenna M. Crowe‐Riddell
- Museum of ZoologyUniversity of MichiganAnn ArborMIUSA
- Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMIUSA
| | | | - Jaimi A. Gray
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFLUSA
| | - Alison R. Davis Rabosky
- Museum of ZoologyUniversity of MichiganAnn ArborMIUSA
- Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMIUSA
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9
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Cox CL, Chung AK, Blackwell C, Davis MM, Gulsby M, Islam H, Miller N, Lambert C, Lewis O, Rector IV, Walsh M, Yamamoto AD, Davis Rabosky AR. Tactile stimuli induce deimatic antipredator displays in ringneck snakes. Ethology 2021. [DOI: 10.1111/eth.13152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Christian L. Cox
- Department of Biological Sciences Florida International University Miami FL USA
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
| | - Albert K. Chung
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
- Department of Ecology and Evolutionary Biology University of California Los Angeles Los Angeles CA USA
| | | | - Maura M. Davis
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
| | - Miranda Gulsby
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
- Department of Biology Kennesaw State University Kennesaw GA USA
| | - Hasib Islam
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
| | - Nathan Miller
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
- James Madison University Harrisonburg VA USA
| | - Carson Lambert
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
| | - Olivia Lewis
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
| | - Ian V. Rector
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
| | - Marleigh Walsh
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
| | - Alannah D. Yamamoto
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
- University of Maryland College Park MD USA
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10
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Curlis JD, Davis Rabosky AR, Holmes IA, Renney TJ, Cox CL. Genetic mechanisms and correlational selection structure trait variation in a coral snake mimic. Proc Biol Sci 2021; 288:20210003. [PMID: 33726595 PMCID: PMC8059570 DOI: 10.1098/rspb.2021.0003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Covariation among traits shapes both phenotypic evolution and ecological interactions across space and time. However, rampant geographical variation in the strength and direction of such correlations can be particularly difficult to explain through generalized mechanisms. By integrating population genomics, surveys of natural history collections and spatially explicit analyses, we tested multiple drivers of trait correlations in a coral snake mimic that exhibits remarkable polymorphism in mimetic and non-mimetic colour traits. We found that although such traits co-occur extensively across space, correlations were best explained by a mixture of genetic architecture and correlational selection, rather than by any single mechanism. Our findings suggest that spatially complex trait distributions may be driven more by the simple interaction between multiple processes than by complex variation in one mechanism alone. These interactions are particularly important in mimicry systems, which frequently generate striking geographical variation and genetic correlations among colour pattern traits.
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Affiliation(s)
- John David Curlis
- Department of Biology, Georgia Southern University, Statesboro, GA, USA,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA,University of Michigan Museum of Zoology, Ann Arbor, MI, USA
| | - Alison R. Davis Rabosky
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA,University of Michigan Museum of Zoology, Ann Arbor, MI, USA
| | - Iris A. Holmes
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA,University of Michigan Museum of Zoology, Ann Arbor, MI, USA,Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY, USA
| | - Timothy J. Renney
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Christian L. Cox
- Department of Biology, Georgia Southern University, Statesboro, GA, USA,Department of Biological Sciences and Institute of Environment, Florida International University, Miami, FL, USA
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11
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Davis Rabosky AR, Moore TY, Sánchez-Paredes CM, Westeen EP, Larson JG, Sealey BA, Balinski BA. Convergence and divergence in anti-predator displays: a novel approach to quantitative behavioural comparison in snakes. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa222] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Abstract
Animals in nature use many strategies to evade or deter their predators. Within venomous snake mimicry, stereotyped anti-predator behaviours are hypothesized to be effective warning signals under strong selection for independent convergence across species. However, no studies have systematically quantified snake anti-predator displays across taxonomically broad clades to examine how these behaviours evolve within a comparative methods framework. Here we describe a new high-throughput approach for collecting and quantifying anti-predator displays in snakes that demonstrates both low observer bias and infinite extension. Then, we show this method’s utility by comparing 20 species spanning six taxonomic families from Peru. We found that a simple experimental set-up varying simulated predator cues was successful in eliciting displays across species and that high-speed videography captured a great diversity of anti-predator responses. Although display components show complicated patterns of covariance, we found support for behavioural convergence in anti-predator displays among elapid coral snakes and their distantly related mimics. Our approach provides new analytical opportunities for both behaviour and kinematics, especially macroevolutionary analyses across clades with similar difficulty in observing or comparing trait diversity.
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Affiliation(s)
- Alison R Davis Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology (UMMZ), University of Michigan, Ann Arbor, Michigan, USA
| | - Talia Y Moore
- Department of Ecology and Evolutionary Biology and Museum of Zoology (UMMZ), University of Michigan, Ann Arbor, Michigan, USA
- Department of Mechanical Engineering and Robotics Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Ciara M Sánchez-Paredes
- Department of Ecology and Evolutionary Biology and Museum of Zoology (UMMZ), University of Michigan, Ann Arbor, Michigan, USA
- Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
- Department of Environment and Geography, University of York, Heslington, York, UK
| | - Erin P Westeen
- Department of Ecology and Evolutionary Biology and Museum of Zoology (UMMZ), University of Michigan, Ann Arbor, Michigan, USA
- Department of Environmental Science, Policy, and Management and Museum of Vertebrate Zoology, University of California, Berkeley, California, USA
| | - Joanna G Larson
- Department of Ecology and Evolutionary Biology and Museum of Zoology (UMMZ), University of Michigan, Ann Arbor, Michigan, USA
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Briana A Sealey
- Department of Ecology and Evolutionary Biology and Museum of Zoology (UMMZ), University of Michigan, Ann Arbor, Michigan, USA
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Bailey A Balinski
- Department of Ecology and Evolutionary Biology and Museum of Zoology (UMMZ), University of Michigan, Ann Arbor, Michigan, USA
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12
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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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13
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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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14
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Myers EA, Xue AT, Gehara M, Cox CL, Davis Rabosky AR, Lemos‐Espinal J, Martínez‐Gómez JE, Burbrink FT. Environmental heterogeneity and not vicariant biogeographic barriers generate community‐wide population structure in desert‐adapted snakes. Mol Ecol 2019; 28:4535-4548. [DOI: 10.1111/mec.15182] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/23/2019] [Accepted: 07/08/2019] [Indexed: 01/04/2023]
Affiliation(s)
- Edward A. Myers
- Department of Vertebrate Zoology Smithsonian Institution National Museum of Natural History Washington DC USA
- Department of Herpetology The American Museum of Natural History New York NY USA
| | | | - Marcelo Gehara
- Department of Herpetology The American Museum of Natural History New York NY USA
| | - Christian L. Cox
- Department of Biology Georgia Southern University Statesboro GA USA
| | - Alison R. Davis Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology University of Michigan Ann Arbor MI USA
| | - Julio Lemos‐Espinal
- Laboratorio de Ecología, UBIPRO, FES Iztacala Universidad Nacional Autónoma de México Tlalnepantla Mexico
| | | | - Frank T. Burbrink
- Department of Herpetology The American Museum of Natural History New York NY USA
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15
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Holmes I, Davis Rabosky AR. Natural history bycatch: a pipeline for identifying metagenomic sequences in RADseq data. PeerJ 2018; 6:e4662. [PMID: 29682427 PMCID: PMC5907781 DOI: 10.7717/peerj.4662] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 04/03/2018] [Indexed: 01/04/2023] Open
Abstract
Background Reduced representation genomic datasets are increasingly becoming available from a variety of organisms. These datasets do not target specific genes, and so may contain sequences from parasites and other organisms present in the target tissue sample. In this paper, we demonstrate that (1) RADseq datasets can be used for exploratory analysis of tissue-specific metagenomes, and (2) tissue collections house complete metagenomic communities, which can be investigated and quantified by a variety of techniques. Methods We present an exploratory method for mining metagenomic “bycatch” sequences from a range of host tissue types. We use a combination of the pyRAD assembly pipeline, NCBI’s blastn software, and custom R scripts to isolate metagenomic sequences from RADseq type datasets. Results When we focus on sequences that align with existing references in NCBI’s GenBank, we find that between three and five percent of identifiable double-digest restriction site associated DNA (ddRAD) sequences from host tissue samples are from phyla to contain known blood parasites. In addition to tissue samples, we examine ddRAD sequences from metagenomic DNA extracted snake and lizard hind-gut samples. We find that the sequences recovered from these samples match with expected bacterial and eukaryotic gut microbiome phyla. Discussion Our results suggest that (1) museum tissue banks originally collected for host DNA archiving are also preserving valuable parasite and microbiome communities, (2) that publicly available RADseq datasets may include metagenomic sequences that could be explored, and (3) that restriction site approaches are a useful exploratory technique to identify microbiome lineages that could be missed by primer-based approaches.
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Affiliation(s)
- Iris Holmes
- Department of Ecology and Evolutionary Biology, University of Michigan Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - Alison R Davis Rabosky
- Department of Ecology and Evolutionary Biology, University of Michigan Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
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16
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Cox CL, Davis Rabosky AR, Holmes IA, Reyes-Velasco J, Roelke CE, Smith EN, Flores-Villela O, McGuire JA, Campbell JA. Synopsis and taxonomic revision of three genera in the snake tribe Sonorini. J NAT HIST 2018. [DOI: 10.1080/00222933.2018.1449912] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Christian L. Cox
- Department of Biology, Georgia Southern University, Statesboro, Georgia, USA
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas-Arlington, Arlington, TX, USA
| | - Alison R. Davis Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Iris A. Holmes
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - Jacobo Reyes-Velasco
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas-Arlington, Arlington, TX, USA
- Evolutionary Genomics Laboratory, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Corey E. Roelke
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas-Arlington, Arlington, TX, USA
| | - Eric N. Smith
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas-Arlington, Arlington, TX, USA
| | | | - Jimmy A. McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Jonathan A. Campbell
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas-Arlington, Arlington, TX, USA
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17
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Abstract
Color polymorphism in natural populations can manifest as a striking patchwork of phenotypes in space, with neighboring populations characterized by dramatic differences in morph composition. These geographic mosaics can be challenging to explain in the absence of localized selection because they are unlikely to result from simple isolation-by-distance or clinal variation in selective regimes. To identify processes that can lead to the formation of geographic mosaics, we developed a simulation-based model to explore the influence of predator perspective, selection, migration, and genetic linkage of color loci on allele frequencies in polymorphic populations over space and time. Using simulated populations inspired by the biology of Heliconius longwing butterflies, Cepaea land snails, Oophaga poison frogs, and Sonora ground snakes, we found that the relative sizes of predator and prey home ranges can produce large differences in morph composition between neighboring populations under both positive and negative frequency-dependent selection. We also demonstrated the importance of the interaction of predator perspective with the type of frequency dependence and localized directional selection across migration and selection intensities. Our results show that regional-scale predation can promote the formation of phenotypic mosaics in prey species, without the need to invoke spatial variation in selective regimes. We suggest that predator behavior can play an important and underappreciated role in the formation and maintenance of geographic mosaics in polymorphic species.
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18
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Monagan IV, Morris JR, Davis Rabosky AR, Perfecto I, Vandermeer J. Anolis lizards as biocontrol agents in mainland and island agroecosystems. Ecol Evol 2017; 7:2193-2203. [PMID: 28405283 PMCID: PMC5383488 DOI: 10.1002/ece3.2806] [Citation(s) in RCA: 11] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 10/25/2016] [Accepted: 01/14/2017] [Indexed: 11/19/2022] Open
Abstract
Our knowledge of ecological interactions that bolster ecosystem function and productivity has broad applications to the management of agricultural systems. Studies suggest that the presence of generalist predators in agricultural landscapes leads to a decrease in the abundance of herbivorous pests, but our understanding of how these interactions vary across taxa and along gradients of management intensity and eco‐geographic space remains incomplete. In this study, we assessed the functional response and biocontrol potential of a highly ubiquitous insectivore (lizards in the genus Anolis) on the world's most important coffee pest, the coffee berry borer (Hypothalemus hampei). We conducted field surveys and laboratory experiments to examine the impact of land‐use intensification on species richness and abundance of anoles and the capacity of anoles to reduce berry borer infestations in mainland and island coffee systems. Our results show that anoles significantly reduce coffee infestation rates in laboratory settings (Mexico, p = .03, F = 5.13 df = 1, 35; Puerto Rico, p = .014, F = 8.82, df = 1, 10) and are capable of consuming coffee berry borers in high abundance. Additionally, diversified agroecosystems bolster anole abundance, while high‐intensity practices, including the reduction of vegetation complexity and the application of agrochemicals were associated with reduced anole abundance. The results of this study provide supporting evidence of the positive impact of generalist predators on the control of crop pests in agricultural landscapes, and the role of diversified agroecosystems in sustaining both functionally diverse communities and crop production in tropical agroecosystems.
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Affiliation(s)
- Ivan V Monagan
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI USA; Museum of Zoology University of Michigan Ann Arbor MI USA
| | - Jonathan R Morris
- School of Natural Resources and the Environment University of Michigan Ann Arbor MI USA
| | - Alison R Davis Rabosky
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI USA; Museum of Zoology University of Michigan Ann Arbor MI USA
| | - Ivette Perfecto
- School of Natural Resources and the Environment University of Michigan Ann Arbor MI USA
| | - John Vandermeer
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI USA
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Holmes IA, Mautz WJ, Davis Rabosky AR. Historical Environment Is Reflected in Modern Population Genetics and Biogeography of an Island Endemic Lizard (Xantusia riversiana reticulata). PLoS One 2016; 11:e0163738. [PMID: 27828958 PMCID: PMC5102444 DOI: 10.1371/journal.pone.0163738] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [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: 03/02/2016] [Accepted: 09/13/2016] [Indexed: 11/29/2022] Open
Abstract
The restricted distribution and isolation of island endemics often produces unique genetic and phenotypic diversity of conservation interest to management agencies. However, these isolated species, especially those with sensitive life history traits, are at high risk for the adverse effects of genetic drift and habitat degradation by non-native wildlife. Here, we study the population genetic diversity, structure, and stability of a classic “island giant” (Xantusia riversiana, the Island Night Lizard) on San Clemente Island, California following the removal of feral goats. Using DNA microsatellites, we found that this population is reasonably genetically robust despite historical grazing, with similar effective population sizes and genetic diversity metrics across all sampling locations irrespective of habitat type and degree of degradation. However, we also found strong site-specific patterns of genetic variation and low genetic diversity compared to mainland congeners, warranting continued special management as an island endemic. We identify both high and low elevation areas that remain valuable repositories of genetic diversity and provide a case study for other low-dispersal coastal organisms in the face of future climate change.
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Affiliation(s)
- Iris A. Holmes
- Department of Ecology and Evolutionary Biology, University of Michigan, 1109 Geddes Ave, Ann Arbor, MI, 48103, United States of America
| | - William J. Mautz
- Department of Biology, University of Hawaii at Hilo, Hilo, HI, 96720, United States of America
| | - Alison R. Davis Rabosky
- Department of Ecology and Evolutionary Biology, University of Michigan, 1109 Geddes Ave, Ann Arbor, MI, 48103, United States of America
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 1156 High St., Santa Cruz, CA, 95064, United States of America
- * E-mail:
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21
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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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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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Castoe TA, Braun EL, Bronikowski AM, Cox CL, Rabosky ARD, Jason de Koning AP, Dobry J, Fujita MK, Giorgianni MW, Hargreaves A, Henkel CV, Mackessy SP, O'Meally D, Rokyta DR, Secor SM, Streicher JW, Wray KP, Yokoyama KD, Pollock DD. Report from the first snake genomics and integrative biology meeting. Stand Genomic Sci 2012; 7:150-2. [PMID: 23451292 PMCID: PMC3570801 DOI: 10.4056/sigs.3106480] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This report summarizes the proceedings of the 1st Snake Genomics and Integrative Biology Meeting held in Vail, CO USA, 5-8 October 2011. The meeting had over twenty registered participants, and was conducted as a single session of presentations. Goals of the meeting included coordination of genomic data collection and fostering collaborative interactions among researchers using snakes as model systems.
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Affiliation(s)
- Todd A Castoe
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
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Rabosky ARD, Corl A, Liwanag HEM, Surget-Groba Y, Sinervo B. Direct fitness correlates and thermal consequences of facultative aggregation in a desert lizard. PLoS One 2012; 7:e40866. [PMID: 22844413 PMCID: PMC3402482 DOI: 10.1371/journal.pone.0040866] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [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: 09/13/2011] [Accepted: 06/18/2012] [Indexed: 11/18/2022] Open
Abstract
Social aggregation is a common behavioral phenomenon thought to evolve through adaptive benefits to group living. Comparing fitness differences between aggregated and solitary individuals in nature--necessary to infer an evolutionary benefit to living in groups--has proven difficult because communally-living species tend to be obligately social and behaviorally complex. However, these differences and the mechanisms driving them are critical to understanding how solitary individuals transition to group living, as well as how and why nascent social systems change over time. Here we demonstrate that facultative aggregation in a reptile (the Desert Night Lizard, Xantusia vigilis) confers direct reproductive success and survival advantages and that thermal benefits of winter huddling disproportionately benefit small juveniles, which can favor delayed dispersal of offspring and the formation of kin groups. Using climate projection models, however, we estimate that future aggregation in night lizards could decline more than 50% due to warmer temperatures. Our results support the theory that transitions to group living arise from direct benefits to social individuals and offer a clear mechanism for the origin of kin groups through juvenile philopatry. The temperature dependence of aggregation in this and other taxa suggests that environmental variation may be a powerful but underappreciated force in the rapid transition between social and solitary behavior.
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Affiliation(s)
- Alison R Davis Rabosky
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America.
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Cox CL, Davis Rabosky AR, Reyes-Velasco J, Ponce-Campos P, Smith EN, Flores-Villela O, Campbell JA. Molecular systematics of the genusSonora(Squamata: Colubridae) in central and western Mexico. SYST BIODIVERS 2012. [DOI: 10.1080/14772000.2012.666293] [Citation(s) in RCA: 7] [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] [Indexed: 10/28/2022]
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