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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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H Tomasco I, Giorello FM, Boullosa N, Feijoo M, Lanzone C, Lessa EP. The contribution of incomplete lineage sorting and introgression to the evolutionary history of the fast-evolving genus Ctenomys (Rodentia, Ctenomyidae). Mol Phylogenet Evol 2022; 176:107593. [PMID: 35905819 DOI: 10.1016/j.ympev.2022.107593] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 03/24/2022] [Revised: 06/28/2022] [Accepted: 07/21/2022] [Indexed: 10/31/2022]
Abstract
Incomplete lineage sorting and introgression have been increasingly recognized as important processes involved in biological differentiation. Both incomplete lineage sorting and introgression result in incongruences between gene trees and species trees, consequently causing difficulties in phylogenetic reconstruction. This is particularly the case for rapid radiations, as short internodal distances and incomplete reproductive isolation increase the likelihood of both ILS and introgression. Estimation of the relative frequency of these processes requires assessments across many genomic regions. We use transcriptomics to test for introgression and estimate the frequency of incomplete lineage sorting in a set of three closely related and geographically adjacent South American tuco-tucos species (Ctenomys), a genus comprising 64 species resulting from recent, rapid radiation. After cleaning and filtering, 5764 orthologous genes strongly support paraphyly of C. pearsoni relative to C. brasiliensis (putatively represented by the population of Villa Serrana). In line with earlier phylogenetic work, the C. pearsoni - C. brasiliensis pair is closely related to C. torquatus, whereas C. rionegrensis is more distantly related to these three nominal species. Classical Patterson's D-statistic shows significant signals of introgression from C. torquatus into C. brasiliensis. However, a 5-taxon test shows no significant results. Incomplete lineage sorting was estimated to have involved about 9% of the loci, suggesting it represents an important process in the incipient diversification of tuco-tucos.
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Affiliation(s)
- Ivanna H Tomasco
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República. Iguá 4225. Montevideo, 11400. Uruguay.
| | - Facundo M Giorello
- Facundo M. Giorello. PDU Espacio de Biología Vegetal del Noreste, Centro Universitario de Tacuarembó (CUT), Universidad de la República, Ruta 5 km 386,200, 45000, Tacuarembó, Uruguay
| | - Nicolás Boullosa
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República. Iguá 4225. Montevideo, 11400. Uruguay
| | - Matías Feijoo
- Matías Feijoo. Departamento de Sistemas Agrarios y Paisajes Culturales, Centro Universitario Regional Este (CURE). Universidad de la República. Ruta 8 Km 281, Treinta y Tres, Uruguay
| | - Cecilia Lanzone
- Cecilia Lanzone. Laboratorio de Genética Evolutiva, IBS (CONICET-UNaM), FCEQyN, Félix de Azara 1553, Posadas,3300. Misiones, Argentina
| | - Enrique P Lessa
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República. Iguá 4225. Montevideo, 11400. Uruguay
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Quiroga‑Carmona M, Abud C, Lessa EP, D’Elía G. Correction to: The Mitochondrial Genetic Diversity of the Olive Field Mouse Abrothrix olivacea (Cricetidae; Abrotrichini) is Latitudinally Structured Across Its Geographic Distribution. J MAMM EVOL 2022. [DOI: 10.1007/s10914-022-09610-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Quiroga-Carmona M, Abud C, Lessa EP, D’Elía G. The Mitochondrial Genetic Diversity of the Olive Field Mouse Abrothrix olivacea (Cricetidae; Abrotrichini) is Latitudinally Structured Across Its Geographic Distribution. J MAMM EVOL 2022. [DOI: 10.1007/s10914-021-09582-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Colella JP, Agwanda BR, Anwarali Khan FA, Bates J, Carrión Bonilla CA, de la Sancha NU, Dunnum JL, Ferguson AW, Greiman SE, Kiswele PK, Lessa EP, Soltis P, Thompson CW, Vanhove MPM, Webala PW, Weksler M, Cook JA. Build international biorepository capacity. Science 2020; 370:773-774. [PMID: 33184198 DOI: 10.1126/science.abe4813] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Jocelyn P Colella
- Biodiversity Institute, University of Kansas, Lawrence, KS 66045 USA
| | | | | | - John Bates
- Field Museum, Chicago, IL 60605, USA.,Natural Science Collections Alliance, Washington, DC 20005, USA
| | - Carlos A Carrión Bonilla
- Museo de Zoologiá, Escuela de Biología, Pontificia Universidad Catolica del Ecuador, Quito, Ecuador.,Museum of Southwestern Biology and Biology Department, University of New Mexico, Albuquerque, NM 87131, USA
| | - Noé U de la Sancha
- Field Museum, Chicago, IL 60605, USA.,Department of Biological Sciences, Chicago State University, Chicago, IL 60628, USA
| | - Jonathan L Dunnum
- Museum of Southwestern Biology and Biology Department, University of New Mexico, Albuquerque, NM 87131, USA
| | | | - Stephen E Greiman
- Department of Biology, Georgia Southern University, Statesboro, GA 30458, USA
| | | | - Enrique P Lessa
- Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Pamela Soltis
- Florida Museum of Natural History and the University of Florida Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
| | - Cody W Thompson
- Department of Ecology and Evolutionary Biology and the Museum of Zoology, University of Michigan, Ann Arbor, MI 48108, USA
| | - Maarten P M Vanhove
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.,Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Leuven, Belgium
| | - Paul W Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok, Kenya
| | - Marcelo Weksler
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Joseph A Cook
- Museum of Southwestern Biology and Biology Department, University of New Mexico, Albuquerque, NM 87131, USA.
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Affiliation(s)
- Guillermo D’Elía
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Pierre-Henri Fabre
- Institut des Sciences de l’Evolution (ISEM, UMR 5554 CNRS-UM2-IRD), Université Montpellier, Montpellier Cedex 5, France
| | - Enrique P Lessa
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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Sawyer YE, MacDonald SO, Lessa EP, Cook JA. Living on the edge: Exploring the role of coastal refugia in the Alexander Archipelago of Alaska. Ecol Evol 2019; 9:1777-1797. [PMID: 30847072 PMCID: PMC6392352 DOI: 10.1002/ece3.4861] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 11/19/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 12/14/2022] Open
Abstract
Although islands are of long-standing interest to biologists, only a handful of studies have investigated the role of climatic history in shaping evolutionary diversification in high-latitude archipelagos. In this study of the Alexander Archipelago (AA) of Southeast Alaska, we address the impact of glacial cycles on geographic genetic structure for three mammals co-distributed along the North Pacific Coast. We examined variation in mitochondrial and nuclear loci for long-tailed voles (Microtus longicaudus), northwestern deermice (Peromyscus keeni), and dusky shrews (Sorex monticola), and then tested hypotheses derived from Species Distribution Models, reconstructions of paleoshorelines, and island area and isolation. In all three species, we identified paleoendemic clades that likely originated in coastal refugia, a finding consistent with other paleoendemic lineages identified in the region such as ermine. Although there is spatial concordance at the regional level for endemism, finer scale spatial and temporal patterns are less clearly defined. Demographic expansion across the region for these distinctive clades is also evident and highlights the dynamic history of Late Quaternary contraction and expansion that characterizes high-latitude species.
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Affiliation(s)
- Yadéeh E. Sawyer
- Department of Biology and Museum of Southwestern BiologyUniversity of New MexicoAlbuquerqueNew Mexico
| | - Stephen O. MacDonald
- Department of Biology and Museum of Southwestern BiologyUniversity of New MexicoAlbuquerqueNew Mexico
| | - Enrique P. Lessa
- Departamento de Ecología y Evolución, Facultad de CienciasUniversidad de la RepúblicaMontevideoUruguay
| | - Joseph A. Cook
- Department of Biology and Museum of Southwestern BiologyUniversity of New MexicoAlbuquerqueNew Mexico
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Giorello FM, Feijoo M, D'Elía G, Naya DE, Valdez L, Opazo JC, Lessa EP. An association between differential expression and genetic divergence in the Patagonian olive mouse (Abrothrix olivacea). Mol Ecol 2018; 27:3274-3286. [PMID: 29940092 DOI: 10.1111/mec.14778] [Citation(s) in RCA: 24] [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: 06/13/2017] [Revised: 05/30/2018] [Accepted: 05/31/2018] [Indexed: 12/19/2022]
Abstract
Recent molecular studies have found striking differences between desert-adapted species and model mammals regarding water conservation. In particular, aquaporin 4, a classical gene involved in water regulation of model species, is absent or not expressed in the kidneys of desert-adapted species. To further understand the molecular response to water availability, we studied the Patagonian olive mouse Abrothrix olivacea, a species with an unusually broad ecological tolerance that exhibits a great urine concentration capability. The species is able to occupy both the arid Patagonian steppe and the Valdivian and Magellanic forests. We sampled 95 olive mouse specimens from four localities (two in the steppe and two in the forests) and analysed both phenotypic variables and transcriptomic data to investigate the response of this species to the contrasting environmental conditions. The relative size of the kidney and the ratio of urine to plasma concentrations were, as expected, negatively correlated with annual rainfall. Expression analyses uncovered nearly 3,000 genes that were differentially expressed between steppe and forest samples and indicated that this species resorts to the "classical" gene pathways for water regulation. Differential expression across biomes also involves genes that involved in immune and detoxification functions. Overall, genes that were differentially expressed showed a slight tendency to be more divergent and to display an excess of intermediate allele frequencies, relative to the remaining loci. Our results indicate that both differential expression in pathways involved in water conservation and geographical allelic variation are important in the occupation of contrasting habitats by the Patagonian olive mouse.
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Affiliation(s)
- Facundo M Giorello
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Espacio de Biología Vegetal del Noreste, Centro Universitario de Tacuarembó, Universidad de la República, Tacuarembó, Uruguay
| | - Matias Feijoo
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Guillermo D'Elía
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Daniel E Naya
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Lourdes Valdez
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Enrique P Lessa
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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9
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Tomasco IH, Boullosa N, Tandonnet S, Hoffmann FG, Lessa EP. Nucleotide sequence and results of test of adaptive evolution in the α-globin gene of octodontoid rodents. Data Brief 2017; 15:517-521. [PMID: 29085872 PMCID: PMC5650648 DOI: 10.1016/j.dib.2017.09.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/04/2017] [Accepted: 09/12/2017] [Indexed: 11/30/2022] Open
Abstract
The data presented in this article are related to the research article entitled “Molecular adaptive convergence in the α-globin gene in subterranean octodontid rodents” (Tomasco et al., 2017) [1]. This article shows the nucleotide sequences of α-globin subunit gene of hemoglobin of several South American caviomorph rodents, including subterranean and fossorial species. These sequences are deposited in Genbank, with accession numbers ranging from MF169881 to MF169898. Of a total of 429 nucleotides analyzed (143 codons), 100 variable sites and 43 amino acid replacements were reported. In this article we also show the results of TreeSaap (Woolley et al., 2003) [2] and MEME (Murrell et al., 2012) [3], that identified some replacement changes as interesting for future studies of adaptive evolution in this large rodent radiation.
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Affiliation(s)
- I H Tomasco
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - N Boullosa
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | | | - F G Hoffmann
- Department of Biochemistry and Molecular Biology, Mississippi State University, MS, USA.,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, MS, USA
| | - E P Lessa
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
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Tomasco IH, Boullosa N, Hoffmann FG, Lessa EP. Molecular adaptive convergence in the α-globin gene in subterranean octodontid rodents. Gene 2017; 628:275-280. [PMID: 28735726 DOI: 10.1016/j.gene.2017.07.057] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 06/21/2017] [Accepted: 07/19/2017] [Indexed: 10/19/2022]
Abstract
Tuco-tucos (Ctenomys) and related coruros (Spalacopus) are South American subterranean rodents. An energetically demanding lifestyle within the hypoxic/hypercapnic underground atmosphere may change the selective regime on genes involved in O2 transport in blood. In addition, some species of tuco-tucos may be found at high altitude, thus facing additional reductions in changes O2 availabily. We examined sequence variation in the alpha globin subunit gene of hemoglobine in these lineages, within a robust phylogenetic context. Using different approaches (classical and Bayesian maximum likelihood (PAML/Datamonkey) and alternatives methods (TreeSAAP)) we found at least 2 sites with evidence of positive selection in the basal branch of Octodontidae, but not in tuco-tucos. These results suggest some adaptive changes associated to fossoriality, but not strictly to life underground.
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Affiliation(s)
- Ivanna H Tomasco
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, 11400, Uruguay.
| | - Nicolás Boullosa
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, 11400, Uruguay.
| | - Federico G Hoffmann
- Department of Biochemistry and Molecular Biology, Mississippi State University, MS, USA; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, MS, USA.
| | - Enrique P Lessa
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, 11400, Uruguay.
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Cook JA, Lessa EP. ARE RATES OF DIVERSIFICATION IN SUBTERRANEAN SOUTH AMERICAN TUCO-TUCOS (GENUS CTENOMYS, RODENTIA: OCTODONTIDAE) UNUSUALLY HIGH? Evolution 2017; 52:1521-1527. [PMID: 28565377 DOI: 10.1111/j.1558-5646.1998.tb02035.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 11/17/1997] [Accepted: 05/26/1998] [Indexed: 11/26/2022]
Abstract
Subterranean rodents have been used frequently as examples of explosive speciation in mammals. We tested for differential rates of diversification by using information from molecular phylogenies to focus primarily on tuco-tucos (Rodentia: Octodontidae), the most speciose lineage of subterranean rodents. Tuco-tucos were not significantly more diverse than their sister taxon (octodontines); however, a lineages-through-time analysis suggests an increase in diversification at the base of the tuco-tuco clade.
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Affiliation(s)
- Joseph A Cook
- University of Alaska Museum and Institute of Arctic Biology, 907 Yukon Drive, Fairbanks, Alaska, 99775-6960
| | - Enrique P Lessa
- Laboratorio de Evolución, Facultad de Ciencias, Casilla de Correos 12106, Montevideo, 11300, Uruguay
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12
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Trovant B, Basso NG, Orensanz JM, Lessa EP, Dincao F, Ruzzante DE. Scorched mussels (Brachidontes spp., Bivalvia: Mytilidae) from the tropical and warm-temperate southwestern Atlantic: the role of the Amazon River in their speciation. Ecol Evol 2016; 6:1778-98. [PMID: 26929816 PMCID: PMC4758806 DOI: 10.1002/ece3.2016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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: 11/19/2015] [Revised: 01/21/2016] [Accepted: 01/27/2016] [Indexed: 11/16/2022] Open
Abstract
Antitropicality is a distribution pattern where closely related taxa are separated by an intertropical latitudinal gap. Two potential examples include Brachidontes darwinianus (south eastern Brazil to Uruguay), considered by some authors as a synonym of B. exustus (Gulf of Mexico and the Caribbean), and B. solisianus, distributed along the Brazilian coast with dubious records north of the intertropical zone. Using two nuclear (18S and 28S rDNA) and one mitochondrial gene (mtDNA COI), we aimed to elucidate the phylogeographic and phylogenetic relationships among the scorched mussels present in the warm-temperate region of the southwest Atlantic. We evaluated a divergence process mediated by the tropical zone over alternative phylogeographic hypotheses. Brachidontes solisianus was closely related to B. exustus I, a species with which it exhibits an antitropical distribution. Their divergence time was approximately 2.6 Ma, consistent with the intensification of Amazon River flow. Brachidontes darwinianus, an estuarine species is shown here not to be related to this B. exustus complex. We suspect ancestral forms may have dispersed from the Caribbean to the Atlantic coast via the Trans-Amazonian seaway (Miocene). The third species, B rodriguezii is presumed to have a long history in the region with related fossil forms going back to the Miocene. Although scorched mussels are very similar in appearance, their evolutionary histories are very different, involving major historical contingencies as the formation of the Amazon River, the Panama Isthmus, and the last marine transgression.
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Affiliation(s)
- Berenice Trovant
- Instituto de Diversidad y Evolución (IDEAus‐CONICET)Boulevard Brown 2915U9120ACFPuerto MadrynChubutArgentina
| | - Néstor G. Basso
- Instituto de Diversidad y Evolución (IDEAus‐CONICET)Boulevard Brown 2915U9120ACFPuerto MadrynChubutArgentina
| | - José María Orensanz
- Instituto de Diversidad y Evolución (IDEAus‐CONICET)Boulevard Brown 2915U9120ACFPuerto MadrynChubutArgentina
| | - Enrique P. Lessa
- Departamento de Ecología y EvoluciónFacultad de CienciasUniversidad de la RepúblicaIguá 4225C.P. 11400MontevideoUruguay
| | - Fernando Dincao
- Universidade Federal do Rio Grande – FURGAv. Itália km 8 Bairro Carreiros96203‐900Rio GrandeBrazil
| | - Daniel E. Ruzzante
- Department of BiologyDalhousie University1355 Oxford St.HalifaxNova ScotiaB3H 4R2Canada
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Naya DE, Naya H, Lessa EP. Brain size and thermoregulation during the evolution of the genus Homo. Comp Biochem Physiol A Mol Integr Physiol 2016; 191:66-73. [DOI: 10.1016/j.cbpa.2015.09.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 08/18/2015] [Accepted: 09/24/2015] [Indexed: 11/16/2022]
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Ceballos SG, Lessa EP, Licandeo R, Fernández DA. Genetic relationships between Atlantic and Pacific populations of the notothenioid fish Eleginops maclovinus: the footprints of Quaternary glaciations in Patagonia. Heredity (Edinb) 2015; 116:372-7. [PMID: 26696136 DOI: 10.1038/hdy.2015.106] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 10/14/2015] [Accepted: 10/19/2015] [Indexed: 11/09/2022] Open
Abstract
The genetic relationships between the Pacific and the Atlantic populations of marine coastal biota in Southern South America have been analyzed in few studies, most of them relying on a single mitochondrial locus. We analyzed 10 polymorphic microsatellite loci, isolated from a dinucleotide-enriched Eleginops maclovinus genomic library, in a total of 240 individuals (48 from each of 5 sampled sites: 2 Atlantic, 2 Pacific and 1 in Beagle Channel). The results were contrasted against a previous work on the same species with mitochondrial DNA (mtDNA). Observed heterozygosity within localities ranged from 0.85 to 0.88 with the highest overall number of alleles observed at the northernmost locality on the Pacific side (Concepción), but no clear geographic pattern arose from the data. On the other hand, the number of private alleles was negatively correlated with latitude (Spearman's rs test, P=0.017). Among-population variance was low but significant (1.35%; P<0.0001, analysis of molecular variance (AMOVA)) and low genetic differentiation between populations was observed (pairwise FST values ranged from 0 to 0.021). A Mantel test revealed a significant correlation between geographic distances and FST (r=0.56, P=0.047). This could be partially accounted by the Atlantic versus Pacific population differentiation detected in three different analyses (STRUCTURE, SAMOVA (Spatial Analysis of MOlecular VAriance) and a population phylogeny). The observed pattern is compatible with a history of separation into two glacial refugia that was better captured by the multilocus microsatellite data than by the mtDNA analysis.
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Affiliation(s)
- S G Ceballos
- Centro Austral de Investigaciones Científicas (CADIC), Ushuaia, Argentina.,Universidad Nacional de Tierra del Fuego (UNTDF), Ushuaia, Argentina
| | - E P Lessa
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - R Licandeo
- Institute for the Oceans and Fisheries University of British Columbia, Vancouver, British Columbia, Canada
| | - D A Fernández
- Centro Austral de Investigaciones Científicas (CADIC), Ushuaia, Argentina.,Universidad Nacional de Tierra del Fuego (UNTDF), Ushuaia, Argentina
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Naya DE, Feijoo M, Lessa EP, Pardiñas UFJ, Teta P, Tomasco IH, Valdez L, D'Elía G. Digestive morphology of two species ofAbrothrix(Rodentia, Cricetidae): comparison of populations from contrasting environments. J Mammal 2014. [DOI: 10.1644/13-mamm-a-261] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Cañón C, Mir D, Pardiñas UFJ, Lessa EP, D'Elía G. A multilocus perspective on the phylogenetic relationships and diversification of rodents of the tribe Abrotrichini (Cricetidae: Sigmodontinae). ZOOL SCR 2014. [DOI: 10.1111/zsc.12069] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Carola Cañón
- Departamento de Zoología; Facultad de Ciencias Naturales y Oceanográficas; Universidad de Concepción; Concepción Chile
| | - Daiana Mir
- Departamento de Ecología y Evolución; Facultad de Ciencias; Universidad de la República; Montevideo Uruguay
| | - Ulyses F. J. Pardiñas
- Unidad de Investigación Diversidad, Sistemática y Evolución; Centro Nacional Patagónico; Casilla de Correo 128 Puerto Madryn 9120 Chubut Argentina
| | - Enrique P. Lessa
- Departamento de Ecología y Evolución; Facultad de Ciencias; Universidad de la República; Montevideo Uruguay
| | - Guillermo D'Elía
- Instituto de Ciencias Ambientales y Evolutivas; Facultad de Ciencias; Universidad Austral de Chile; Campus Isla Teja s/n Valdivia Chile
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18
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Giorello FM, Feijoo M, D’Elía G, Valdez L, Opazo JC, Varas V, Naya DE, Lessa EP. Characterization of the kidney transcriptome of the South American olive mouse Abrothrix olivacea. BMC Genomics 2014; 15:446. [PMID: 24909751 PMCID: PMC4189146 DOI: 10.1186/1471-2164-15-446] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [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: 12/13/2013] [Accepted: 05/27/2014] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The olive mouse Abrothrix olivacea is a cricetid rodent of the subfamily Sigmodontinae that inhabits a wide range of contrasting environments in southern South America, from aridlands to temperate rainforests. Along its distribution, it presents different geographic forms that make the olive mouse a good focal case for the study of geographical variation in response to environmental variation. We chose to characterize the kidney transcriptome because this organ has been shown to be associated with multiple physiological processes, including water reabsorption. RESULTS Transcriptomes of thirteen kidneys from individuals from Argentina and Chile were sequenced using Illumina technology in order to obtain a kidney reference transcriptome. After combining the reads produced for each sample, we explored three assembly strategies to obtain the best reconstruction of transcripts, TrinityNorm and DigiNorm, which include its own normalization algorithms for redundant reads removal, and Multireads, which simply consist on the assembly of the joined reads. We found that Multireads strategy produces a less fragmented assembly than normalization algorithms but recovers fewer number of genes. In general, about 15000 genes were annotated, of which almost half had at least one coding sequence reconstructed at 99% of its length. We also built a list of highly expressed genes, of which several are involved in water conservation under laboratory conditions using mouse models. CONCLUSION Based on our assembly results, Trinity's in silico normalization is the best algorithm in terms of cost-benefit returns; however, our results also indicate that normalization should be avoided if complete or nearly complete coding sequences of genes are desired. Given that this work is the first to characterize the transcriptome of any member of Sigmodontinae, a subfamily of cricetid rodents with about 400 living species, it will provide valuable resources for future ecological and evolutionary genomic analyses.
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Affiliation(s)
- Facundo M Giorello
- />Departamento de Ecología y Evolución, Facultad de
Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Matias Feijoo
- />Departamento de Ecología y Evolución, Facultad de
Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Guillermo D’Elía
- />Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Lourdes Valdez
- />Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Juan C Opazo
- />Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Valeria Varas
- />Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Daniel E Naya
- />Departamento de Ecología y Evolución, Facultad de
Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Enrique P Lessa
- />Departamento de Ecología y Evolución, Facultad de
Ciencias, Universidad de la República, Montevideo, Uruguay
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Phillips CJ, Phillips CD, Goecks J, Lessa EP, Sotero-Caio CG, Tandler B, Gannon MR, Baker RJ. Dietary and flight energetic adaptations in a salivary gland transcriptome of an insectivorous bat. PLoS One 2014; 9:e83512. [PMID: 24454705 PMCID: PMC3891661 DOI: 10.1371/journal.pone.0083512] [Citation(s) in RCA: 10] [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: 08/08/2013] [Accepted: 11/04/2013] [Indexed: 12/12/2022] Open
Abstract
We hypothesized that evolution of salivary gland secretory proteome has been important in adaptation to insectivory, the most common dietary strategy among Chiroptera. A submandibular salivary gland (SMG) transcriptome was sequenced for the little brown bat, Myotis lucifugus. The likely secretory proteome of 23 genes included seven (RETNLB, PSAP, CLU, APOE, LCN2, C3, CEL) related to M. lucifugus insectivorous diet and metabolism. Six of the secretory proteins probably are endocrine, whereas one (CEL) most likely is exocrine. The encoded proteins are associated with lipid hydrolysis, regulation of lipid metabolism, lipid transport, and insulin resistance. They are capable of processing exogenous lipids for flight metabolism while foraging. Salivary carboxyl ester lipase (CEL) is thought to hydrolyze insect lipophorins, which probably are absorbed across the gastric mucosa during feeding. The other six proteins are predicted either to maintain these lipids at high blood concentrations or to facilitate transport and uptake by flight muscles. Expression of these seven genes and coordinated secretion from a single organ is novel to this insectivorous bat, and apparently has evolved through instances of gene duplication, gene recruitment, and nucleotide selection. Four of the recruited genes are single-copy in the Myotis genome, whereas three have undergone duplication(s) with two of these genes exhibiting evolutionary 'bursts' of duplication resulting in multiple paralogs. Evidence for episodic directional selection was found for six of seven genes, reinforcing the conclusion that the recruited genes have important roles in adaptation to insectivory and the metabolic demands of flight. Intragenic frequencies of mobile- element-like sequences differed from frequencies in the whole M. lucifugus genome. Differences among recruited genes imply separate evolutionary trajectories and that adaptation was not a single, coordinated event.
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Affiliation(s)
- Carleton J. Phillips
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
| | - Caleb D. Phillips
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
| | - Jeremy Goecks
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
- Department of Math and Computer Science, Emory University, Atlanta, Georgia, United States of America
| | - Enrique P. Lessa
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Cibele G. Sotero-Caio
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
| | - Bernard Tandler
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Michael R. Gannon
- Department of Biology, Pennsylvania State University, Altoona College, Altoona, Pennsylvania, United States of America
| | - Robert J. Baker
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
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Tomasco IH, Lessa EP. Two mitochondrial genes under episodic positive selection in subterranean octodontoid rodents. Gene 2014; 534:371-8. [DOI: 10.1016/j.gene.2013.09.097] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 08/28/2013] [Accepted: 09/26/2013] [Indexed: 11/27/2022]
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D'Anatro A, Naya DE, Lessa EP, Defeo O. Contrasting patterns of morphological variation with dietary preferences in Micropogonias furnieri: insights from stable-isotope and digestive-trait analyses. J Fish Biol 2013; 82:1641-1658. [PMID: 23639159 DOI: 10.1111/jfb.12103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 02/14/2013] [Indexed: 06/02/2023]
Abstract
The dietary preferences of populations of whitemouth croaker Micropogonias furnieri, which commonly inhabit estuarine and oceanic environments of the south-western Atlantic Ocean, were investigated using stable-isotope analysis and digestive traits, and compared with previous genetic and morphometric surveys of this species. Isotopic and C:N-derived data suggested that individuals from coastal lagoons are the most differentiated from the remaining localities surveyed. In contrast, the analysis of the digestive traits did not show the same differentiation pattern. The overall correlation between isotopic, molecular and morphological variations suggests that genetic and phenotypic differences among populations are accompanied by differential resource use, supporting the idea that selective forces could be playing an important role in population differentiation.
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Affiliation(s)
- A D'Anatro
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay.
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Mora MS, Cutrera AP, Lessa EP, Vassallo AI, D'Anatro A, Mapelli FJ. Phylogeography and population genetic structure of the Talas tuco-tuco (Ctenomys talarum): integrating demographic and habitat histories. J Mammal 2013. [DOI: 10.1644/11-mamm-a-242.1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Costa-Urrutia P, Abud C, Secchi ER, Lessa EP. Population genetic structure and social kin associations of franciscana dolphin, Pontoporia blainvillei. ACTA ACUST UNITED AC 2011; 103:92-102. [PMID: 22013080 DOI: 10.1093/jhered/esr103] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We investigated population and social structure of the franciscana dolphin, Pontoporia blainvillei, an endemic and the most endangered cetacean of the southwestern Atlantic Ocean. We analyzed samples from the Rio de la Plata estuary obtained in Uruguayan waters and from the Atlantic Ocean obtained in both Uruguayan and Brazilian waters. Mitochondrial and microsatellite DNA markers were used to study differentiation between the estuary and the ocean and the association between kinship and social group structure. Although multilocus analyses suggested that franciscanas are structured into 2 subpopulations (K = 2, divergence among clusters: F(ST) = 0.06, P = 0.002; R(ST) = 0.3, P = 0.001), mitochondrial markers did not support such divergence (F(ST) = 0.02, P = 0.12; Ф(ST) = 0.06, P =0.06). However, these units are not entirely segregated geographically. Regarding social structure, some groups are composed by first-order related individuals (R ≥ 0.5, P < 0.5). Overall, the data suggest that matrilines could be the social unit in this species. We argue that the divergence found could be associated to local adaptation and social structure, resulting from either feature leading to a recent divergence or reflecting equilibrium between local differentiation and gene flow. This evidence supports considering franciscanas from the Rio de la Plata estuary a discrete management unit.
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Affiliation(s)
- Paula Costa-Urrutia
- Departamento de Ecología y Evolución Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay.
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Tomasco IH, Lessa EP. The evolution of mitochondrial genomes in subterranean caviomorph rodents: Adaptation against a background of purifying selection. Mol Phylogenet Evol 2011; 61:64-70. [DOI: 10.1016/j.ympev.2011.06.014] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 06/08/2011] [Accepted: 06/16/2011] [Indexed: 11/17/2022]
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Parada A, D'Elía G, Bidau CJ, Lessa EP. Species groups and the evolutionary diversification of tuco-tucos, genusCtenomys(Rodentia: Ctenomyidae). J Mammal 2011. [DOI: 10.1644/10-mamm-a-121.1] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Cañón C, D'Elía G, Pardiñas UFJ, Lessa EP. Phylogeography of Loxodontomys micropus with comments on the alpha taxonomy of Loxodontomys (Cricetidae: Sigmodontinae). J Mammal 2010. [DOI: 10.1644/10-mamm-a-027.1] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Abstract
Species are impacted by climate change at both ecological and evolutionary time scales. Studies in northern continents have provided abundant evidence of dramatic shifts in distributions of species subsequent to the last glacial maximum (LGM), particularly at high latitudes. However, little is known about the history of southern continents, especially at high latitudes. South America is the only continent, other than Antarctica, that extends beyond 40 degrees S. Genetic studies of a few Patagonian species have provided seemingly conflicting results, indicating either postglacial colonization from restricted glacial refugia or persistence through glacial cycles and in situ differentiation. Using mitochondrial DNA sequences of 14 species of sigmodontine rodents, a major faunal ensemble of Patagonia and Tierra del Fuego, we show that at least nine of these species bear genetic footprints of demographic expansion from single restricted sources. However, timing of demographic expansion precedes the LGM in most of these species. Four species are fragmented phylogeographically within the region. Our results indicate that (i) demographic instability in response to historical climate change has been widespread in the Patagonian-Fueguian region, and is generally more pronounced at high latitudes in both southern and northern continents; (ii) colonization from lower latitudes is an important component of current Patagonian-Fueguian diversity; but (iii) in situ differentiation has also contributed to species diversity.
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Affiliation(s)
- Enrique P Lessa
- Laboratorio de Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.
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Feijoo M, D’Elía G, Pardiñas UF, Lessa EP. Systematics of the southern Patagonian-Fueguian endemic Abrothrix lanosus (Rodentia: Sigmodontinae): Phylogenetic position, karyotypic and morphological data. Mamm Biol 2010. [DOI: 10.1016/j.mambio.2008.10.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Mora MS, Mapelli FJ, Gaggiotti OE, Kittlein MJ, Lessa EP. Dispersal and population structure at different spatial scales in the subterranean rodent Ctenomys australis. BMC Genet 2010; 11:9. [PMID: 20109219 PMCID: PMC2828403 DOI: 10.1186/1471-2156-11-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Accepted: 01/28/2010] [Indexed: 11/24/2022] Open
Abstract
Background The population genetic structure of subterranean rodent species is strongly affected by demographic (e.g. rates of dispersal and social structure) and stochastic factors (e.g. random genetic drift among subpopulations and habitat fragmentation). In particular, gene flow estimates at different spatial scales are essential to understand genetic differentiation among populations of a species living in a highly fragmented landscape. Ctenomys australis (the sand dune tuco-tuco) is a territorial subterranean rodent that inhabits a relatively secure, permanently sealed burrow system, occurring in sand dune habitats on the coastal landscape in the south-east of Buenos Aires province, Argentina. Currently, this habitat is threatened by urban development and forestry and, therefore, the survival of this endemic species is at risk. Here, we assess population genetic structure and patterns of dispersal among individuals of this species at different spatial scales using 8 polymorphic microsatellite loci. Furthermore, we evaluate the relative importance of sex and habitat configuration in modulating the dispersal patterns at these geographical scales. Results Our results show that dispersal in C. australis is not restricted at regional spatial scales (~ 4 km). Assignment tests revealed significant population substructure within the study area, providing support for the presence of two subpopulations from three original sampling sites. Finally, male-biased dispersal was found in the Western side of our study area, but in the Eastern side no apparent philopatric pattern was found, suggesting that in a more continuous habitat males might move longer distances than females. Conclusions Overall, the assignment-based approaches were able to detect population substructure at fine geographical scales. Additionally, the maintenance of a significant genetic structure at regional (~ 4 km) and small (less than 1 km) spatial scales despite apparently moderate to high levels of gene flow between local sampling sites could not be explained simply by the linear distance among them. On the whole, our results support the hypothesis that males disperse more frequently than females; however they do not provide support for strict philopatry within females.
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Affiliation(s)
- Matías S Mora
- Laboratorio de Ecofisiología, Departamento de Biología, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Casilla de Correo 1245, Mar del Plata, Argentina.
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Mora MS, Lessa EP, Cutrera AP, Kittlein MJ, Vassallo AI. Phylogeographical structure in the subterranean tuco-tuco Ctenomys talarum (Rodentia: Ctenomyidae): contrasting the demographic consequences of regional and habitat-specific histories. Mol Ecol 2007; 16:3453-65. [PMID: 17688545 DOI: 10.1111/j.1365-294x.2007.03398.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
In this work we examined the phylogeography of the South American subterranean herbivorous rodent Ctenomys talarum (Talas tuco-tuco) using mitochondrial DNA (mtDNA) control region (D-loop) sequences, and we assessed the geographical genetic structure of this species in comparison with that of subterranean Ctenomys australis, which we have shown previously to be parapatric to C. talarum and to also live in a coastal sand dune habitat. A significant apportionment of the genetic variance among regional groups indicated that putative geographical barriers, such as rivers, substantially affected the pattern of genetic structure in C. talarum. Furthermore, genetic differentiation is consistent with a simple model of isolation by distance, possibly evidencing equilibrium between gene flow and local genetic drift. In contrast, C. australis showed limited hierarchical partitioning of genetic variation and departed from an isolation-by-distance pattern. Mismatch distributions and tests of neutrality suggest contrasting histories of these two species: C. talarum appears to be characterized by demographic stability and no significant departures from neutrality, whereas C. australis has undergone a recent demographic expansion and/or departures from strict neutrality in its mtDNA.
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Affiliation(s)
- Matías S Mora
- Laboratorio de Ecofisiología, Departamento de Biología, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata. CC1 245, 7600 Mar del Plata, Argentina.
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Dragoo JW, Lackey JA, Moore KE, Lessa EP, Cook JA, Yates TL. Phylogeography of the deer mouse (Peromyscus maniculatus) provides a predictive framework for research on hantaviruses. J Gen Virol 2006; 87:1997-2003. [PMID: 16760402 DOI: 10.1099/vir.0.81576-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phylogeographical partitioning of Sin Nombre and Monongahela viruses (hantaviruses) may reflect that of their primary rodent host, the deer mouse (Peromyscus maniculatus). Lack of a comprehensive assessment of phylogeographical variation of the host has precluded the possibility of predicting spatial limits of existing strains of these viruses or geographical regions where novel viral strains might emerge. The complete cytochrome b gene was sequenced for 206 deer mice collected from sites throughout North America to provide a foundation for future studies of spatial structure and evolution of this ubiquitous host. Bayesian analyses of these sequences partitioned deer mice into six largely allopatric lineages, some of which may represent unrecognized species. The geographical distributions of these lineages were probably shaped by Quaternary climatic events. Populations of mice were apparently restricted to refugia during glacial advances, where they experienced genetic divergence. Expansion of these populations, following climatic amelioration, brought genetically distinctive forms into contact. Occurrence of parallel changes in virus strains can now be explored in appropriate regions. In New Mexico, for example, near the location where Sin Nombre virus was first discovered, there are three genetically distinctive lineages of deer mice whose geographical ranges need to be delineated precisely. The phylogeography of P. maniculatus provides a framework for interpreting geographical variability, not only in hosts, but also in associated viral variants and disease transmission, and an opportunity to predict the potential geographical distribution of newly emerging viral strains.
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Affiliation(s)
- Jerry W Dragoo
- Department of Biology, Museum of Southwestern Biology (MSB), The University of New Mexico, Albuquerque, NM 87131, USA
| | - J Alden Lackey
- Department of Biological Sciences, Oswego State University, Oswego, NY 13126, USA
| | - Kathryn E Moore
- School of Medicine, The University of New Mexico, Albuquerque, NM 87131, USA
| | - Enrique P Lessa
- Laboratorio de Evolución, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Joseph A Cook
- Department of Biology, Museum of Southwestern Biology (MSB), The University of New Mexico, Albuquerque, NM 87131, USA
| | - Terry L Yates
- Department of Biology, Museum of Southwestern Biology (MSB), The University of New Mexico, Albuquerque, NM 87131, USA
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Abstract
Insulin is a conservative molecule among mammals, maintaining both its structure and function. Rodents that belong to the Suborder Hystricognathi represent an exception, having a very divergent molecule with unusual physiological properties. In this work, we analyzed the evolutionary pattern of the insulin gene in caviomorph rodents (South American hystricomorph rodents). We found that these rodents have higher rates of nonsynonymous:synonymous substitutions (d(N)/d(S)) than nonhystricomorph rodents and that values are heterogeneous inside the group. We estimated codons under positive selection, specifically the second binding site (A13 and B17) and others related with hexamerization (B18, B20, and B22). In the monomer structure, all selected sites formed a single patch around the second binding site. In the hexamer structure, these amino acids were grouped into three major patches. In this structure, contacts between B chains involved all selected sites (except B18), and between faces in the center of the molecule, all contacts were among selected sites. While there is no clear hypothesis regarding the cause of this drastic change, experimental evidence does show that this group of rodents has some peculiarities in growth function, and, whether coincidental or not, these changes appeared together with important changes in life-history traits.
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Affiliation(s)
- Juan C Opazo
- Center for Advanced Studies in Ecology and Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.
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Castillo AH, Cortinas MN, Lessa EP. RAPID DIVERSIFICATION OF SOUTH AMERICAN TUCO-TUCOS (CTENOMYS; RODENTIA, CTENOMYIDAE): CONTRASTING MITOCHONDRIAL AND NUCLEAR INTRON SEQUENCES. J Mammal 2005. [DOI: 10.1644/1545-1542(2005)086<0170:rdosat>2.0.co;2] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Eddingsaas AA, Jacobsen BK, Lessa EP, Cook JA. EVOLUTIONARY HISTORY OF THE ARCTIC GROUND SQUIRREL (SPERMOPHILUS PARRYII) IN NEARCTIC BERINGIA. J Mammal 2004. [DOI: 10.1644/brb-204] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Lessa EP, Cook JA, Patton JL. Genetic footprints of demographic expansion in North America, but not Amazonia, during the Late Quaternary. Proc Natl Acad Sci U S A 2003; 100:10331-4. [PMID: 12913123 PMCID: PMC193561 DOI: 10.1073/pnas.1730921100] [Citation(s) in RCA: 319] [Impact Index Per Article: 15.2] [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: 02/15/2003] [Indexed: 11/18/2022] Open
Abstract
The biotic consequences of climate change have attracted considerable attention. In particular, the "refugial debate" centers on the possible retraction of habitats to limited areas that may have served as refuges for many associated species, especially during glaciations of the Quaternary. One prediction of such scenarios is that populations must have experienced substantial growth accompanying climatic amelioration and the occupation of newly expanded habitats. We used coalescence theory to examine the genetic evidence, or lack thereof, for late Pleistocene refugia of boreal North American and tropical Amazonian mammals. We found substantial and concordant evidence of demographic expansion in North American mammals, particularly at higher latitudes. In contrast, small mammals from western Amazonia appear to have experienced limited or no demographic expansion after the Late Pleistocene. Thus, demographic responses to climate change can be tracked genetically and appear to vary substantially across the latitudinal gradient of biotic diversity.
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Affiliation(s)
- Enrique P Lessa
- Laboratorio de Evolución, Facultad de Ciencias, Casilla 12106, Montevideo 11300, Uruguay.
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Wlasiuk G, Garza JC, Lessa EP. Genetic and geographic differentiation in the Rio Negro tuco-tuco (Ctenomys rionegrensis): inferring the roles of migration and drift from multiple genetic markers. Evolution 2003; 57:913-26. [PMID: 12778560 DOI: 10.1111/j.0014-3820.2003.tb00302.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Among tuco-tucos, Ctenomys rionegrensis is especially amenable to the study of the forces driving population differentiation because of the restricted geographic range it occupies in Uruguay. Within this limited area, the Rio Negro tuco-tuco is limited to sandy soils. It nonetheless exhibits remarkable variation in pelage color, including melanic, agouti, and dark-backed individuals. Two hypotheses have been put forth to explain this pattern: (1) local differentiation and fixation of alternative pelage types by genetic drift under limited gene flow; or (2) fixation by natural selection that may take place even in the presence of gene flow. A previous allozyme study rejected the genetic drift hypothesis on the basis of high inferred levels of migration. New estimates of gene flow from microsatellites and mitochondrial cytochrome b sequences were obtained for C. rionegrensis populations to further test these hypotheses. Much lower levels of gene flow were estimated with these more sensitive markers. Microsatellite-based estimates of gene flow are close to zero and may come closest to estimating current levels of migration. A lack of equilibrium between migration and genetic drift is also strongly suggested by the absence of an isolation-by-distance pattern found in all three genetic datasets. The microsatellite genotype data show that the species is strongly structured geographically, with subpopulations constituting distinct genetic entities. If current levels of gene flow are very low, as indicated by the new data, the local fixation of alternative alleles, including those responsible for pelage color polymorphism, is possible by drift alone. A scenario is thus proposed in which the species expanded in the recent past from a more restricted geographic range and has subsequently differentiated in near isolation, with genetic drift possibly playing a primary role in overall genetic differentiation. The local fixation of pelage color types could also be due to drift, but selection on this trait cannot be ruled out without direct analysis.
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Affiliation(s)
- Gabriela Wlasiuk
- Laboratorio de Evolución, Facultad de Ciencias, Montevideo 11400, Uruguay.
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Wlasiuk G, Carlos Garza J, Lessa EP. GENETIC AND GEOGRAPHIC DIFFERENTIATION IN THE RIO NEGRO TUCO-TUCO (CTENOMYS RIONEGRENSIS): INFERRING THE ROLES OF MIGRATION AND DRIFT FROM MULTIPLE GENETIC MARKERS. Evolution 2003. [DOI: 10.1554/0014-3820(2003)057[0913:gagdit]2.0.co;2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Lessa EP. THE ADAPTATIONIST PROGRAM GOES UNDERGROUND. Evolution 2001. [DOI: 10.1111/j.0014-3820.2001.tb01330.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Cortinas MN, Lessa EP. Molecular evolution of Aldolase A pseudogenes in mice: multiple origins, subsequent duplications, and heterogeneity of evolutionary rates. Mol Biol Evol 2001; 18:1643-53. [PMID: 11504845 DOI: 10.1093/oxfordjournals.molbev.a003953] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Aldolase multigene family comprises three functional genes (A, B, and C) with tissue-specific expression regulated during ontogeny. DGGE analysis and nucleotide sequencing reveal a family of retropseudogenes of type A in species of MUS: Significant variation in rates of evolution of Aldolase A retropseudogenes is apparent. Our analyses demonstrate that (1) multiple events of retrotransposition are needed to account for the diversity of Aldolase A processed pseudogenes found in mice; (2) some of these sequences have undergone further duplication subsequent to the original retrotransposition event; (3) the patterns of nucleotide substitution are broadly comparable with previous estimates; and (4) estimates of rates of divergence for this array of sequences are up to four times higher than those reported in the literature.
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Affiliation(s)
- M N Cortinas
- Laboratorio de Evolución, Facultad de Ciencias, Montevideo, Uruguay.
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Slamovits CH, Cook JA, Lessa EP, Rossi MS. Recurrent amplifications and deletions of satellite DNA accompanied chromosomal diversification in South American tuco-tucos (genus Ctenomys, Rodentia: Octodontidae): a phylogenetic approach. Mol Biol Evol 2001; 18:1708-19. [PMID: 11504851 DOI: 10.1093/oxfordjournals.molbev.a003959] [Citation(s) in RCA: 86] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We investigated the relationship between satellite copy number and chromosomal evolution in tuco-tucos (genus Ctenomys), a karyotypically diverse clade of rodents. To explore phylogenetic relationships among 23 species and 5 undescribed forms, we sequenced the complete mitochondrial cytochrome b genes of 27 specimens and incorporated 27 previously published sequences. We then used quantitative dot-blot techniques to assess changes in the copy number of the major Ctenomys satellite DNA (satDNA), named RPCS. Our analysis of the relationship between variation in copy number of RPCS and chromosomal changes employed a maximum-likelihood approach to infer the copy number of the satellite RPCS in the ancestors of each clade. We found that amplifications and deletions of RPCS were associated with extensive chromosomal rearrangements even among closely related species. In contrast, RPCS copy number stability was observed within clades characterized by chromosomal stability. This example reinforces the suspected role of amplification, deletion, and intragenomic movement of satDNA in promoting extensive chromosomal evolution.
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Affiliation(s)
- C H Slamovits
- Laboratorio de Fisiología y Biología Molecular, Facultad de Ciencias Exactas y Naturales, Departamento de Ciencias Biológicas, Pabellón II, Buenos Aires, Argentina
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Cook JA, Lessa EP. Are Rates of Diversification in Subterranean South American Tuco-Tucos (Genus Ctenomys, Rodentia: Octodontidae) Unusually High? Evolution 1998. [DOI: 10.2307/2411323] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Abstract
Variation in the nucleotide sequence of the entire mitochondrial cytochrome b gene (1140 bp) was examined for 27 individuals representing 13 species of South American rodents of the genera Ctenomys, Octodontomys, Tympanoctomys, and Spalacopus. Representatives of the family Echimyidae, Euryzygomatomys and Mesomys, were used as outgroups to test the monophyly of the Octodontinae and Ctenomyinae. Relationships among species of tuco-tucos (genus Ctenomys) were also examined including representatives of the three described subgenera and the two sperm morphs. Reciprocal monophyly of the Octodontinae and Ctenomyinae is strongly supported. Several basal relationships among species of the genus Ctenomys are poorly resolved, suggesting the possibility of a hard polytomy due to a rapid and potentially simultaneous radiation early in the history of the genus. In other cases, clades within the Ctenomyinae previously identified on the basis of allozymes, chromosomes, parasites, or skull morphology were supported. Calibrations based on the fossil record suggest that the mitochondrial cytochrome b of these caviomorphs has evolved at a rapid rate, comparable to those proposed for Mus-Rattus, and three to four times higher than ungulate rates.
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Affiliation(s)
- E P Lessa
- Laboratorio de Evolución, Facultad de Ciencias, Montevideo, Uruguay
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Abstract
This article reviews four 'DNA screening techniques', namely heteroduplex analysis, single-strand conformational polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) as tools for the study of allelic variation in natural populations. The resolving power, advantages, and limitations of each technique are discussed and compared. We also provide some criteria for choosing among techniques and illustrate some practical issues with examples taken primarily from our own laboratory experience.
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Affiliation(s)
- E P Lessa
- Museum of Vertebrate Zoology, University of California, Berkeley 94720
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Affiliation(s)
- E P Lessa
- Laboratorio de Evolución, Instituto de Biologia, Montevideo, Uruguay
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Abstract
DNA sequencing can be costly and time consuming for population studies because of the relative rarity of variation along exons. These problems can be substantially reduced by the use of the polymerase chain reaction on introns using primers from the exon region. These problems can be further reduced by the use of denaturing gradient gel electrophoresis to identify those alleles in need of sequencing.
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Affiliation(s)
- E P Lessa
- Museum of Vertebrate Zoology, University of California, Berkeley 94720
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