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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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Larkin IE, Myers EA, Carstens BC, Barrow LN. Predictors of genomic diversity within North American squamates. J Hered 2023; 114:131-142. [PMID: 36638275 PMCID: PMC10078173 DOI: 10.1093/jhered/esad001] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/13/2023] [Indexed: 01/15/2023] Open
Abstract
Comparisons of intraspecific genetic diversity across species can reveal the roles of geography, ecology, and life history in shaping biodiversity. The wide availability of mitochondrial DNA (mtDNA) sequences in open-access databases makes this marker practical for conducting analyses across several species in a common framework, but patterns may not be representative of overall species diversity. Here, we gather new and existing mtDNA sequences and genome-wide nuclear data (genotyping-by-sequencing; GBS) for 30 North American squamate species sampled in the Southeastern and Southwestern United States. We estimated mtDNA nucleotide diversity for two mtDNA genes, COI (22 species alignments; average 16 sequences) and cytb (22 species; average 58 sequences), as well as nuclear heterozygosity and nucleotide diversity from GBS data for 118 individuals (30 species; four individuals and 6,820-44,309 loci per species). We showed that nuclear genomic diversity estimates were highly consistent across individuals for some species, while other species showed large differences depending on the locality sampled. Range size was positively correlated with both cytb diversity (Phylogenetically Independent Contrasts: R 2 = 0.31, p = 0.007) and GBS diversity (R 2 = 0.21; p = 0.006), while other predictors differed across the top models for each dataset. Mitochondrial and nuclear diversity estimates were not correlated within species, although sampling differences in the data available made these datasets difficult to compare. Further study of mtDNA and nuclear diversity sampled across species' ranges is needed to evaluate the roles of geography and life history in structuring diversity across a variety of taxonomic groups.
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Affiliation(s)
- Ivy E Larkin
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 318 W. 12th Ave, Columbus, OH
| | - Edward A Myers
- Department of Biological Sciences, Clemson University, Clemson, SC
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 318 W. 12th Ave, Columbus, OH
| | - Lisa N Barrow
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 318 W. 12th Ave, Columbus, OH.,Current Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque NM
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Steppan SJ, Meyer AA, Barrow LN, Alhajeri BH, S Y Al-Zaidan A, Gignac PM, Erickson GM. Phylogenetics And The Evolution Of Terrestriality In Mudskippers (Gobiidae: Oxudercinae). Mol Phylogenet Evol 2022; 169:107416. [PMID: 35032645 DOI: 10.1016/j.ympev.2022.107416] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 08/05/2020] [Revised: 11/30/2021] [Accepted: 12/08/2021] [Indexed: 01/23/2023]
Abstract
The initial vertebrate conquest of land by stegocephalians (Sarcopterygia) allowed access to new resources and exploitation of untapped niches precipitating a major phylogenetic diversification. However, a paucity of fossils has left considerable uncertainties about phylogenetic relationships and the eco-morphological stages in this key transition in Earth history. Among extant actinopterygians, three genera of mudskippers (Gobiidae: Oxudercinae), Boleophthalmus, Periophthalmus and Periophthalmodon are the most terrestrialized, with vertebral, appendicular, locomotory, respiratory, and epithelial specializations enabling overland excursions up to 14 hours. Unlike early stegocephalians, the ecologies and morphologies of the 45 species of oxudercines are well known, making them viable analogs for the initial vertebrate conquest of land. Nevertheless, they have received little phylogenetic attention. We compiled the largest molecular dataset to date, with 29 oxudercine species, and 5 nuclear and mitochondrial loci. Phylogenetic and comparative analyses revealed strong support for two independent terrestrial transitions, and a complex suit of ecomorphological forms in estuarine environments. Furthermore, neither Oxudercinae nor their presumed sister-group the eel gobies (Amblyopinae, a group of elongated gobies) were monophyletic with respect to each other, requiring a merging of these two subfamilies and revealing an expansion of phenotypic variation within the "mudskipper" clade. We did not find support for the expected linear model of ecomorphological and locomotory transition from fully aquatic, to mudswimming, to pectoral-aided mudswimming, to lobe-finned terrestrial locomotion proposed by earlier morphological studies. This high degree of convergent or parallel transitions to terrestriality, and apparent divergent directions of estuarine adaptation, promises even greater potential for this clade to illuminate the conquest of land. Future work should focus on these less-studied species with "transitional" and other mud-habitat specializations to fully resolve the dynamics of this diversification.
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Affiliation(s)
- Scott J Steppan
- Department of Biological Science, 327 Stadium Dr., Florida State University, Tallahassee Florida, 32306-4295, USA.
| | - Anna A Meyer
- Department of Biological Science, 327 Stadium Dr., Florida State University, Tallahassee Florida, 32306-4295, USA
| | - Lisa N Barrow
- Department of Biological Science, 327 Stadium Dr., Florida State University, Tallahassee Florida, 32306-4295, USA; Department of Biology, University of New Mexico, Albuquerque, NM 87131-0001, USA
| | - Bader H Alhajeri
- Department of Biological Sciences, Kuwait University, Safat, 13060, Kuwait
| | | | - Paul M Gignac
- Department of Anatomy and Cell Biology, Oklahoma State University Center for Health Sciences, Tulsa Oklahoma 74107-1898, USA
| | - Gregory M Erickson
- Department of Biological Science, 327 Stadium Dr., Florida State University, Tallahassee Florida, 32306-4295, USA
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Warwick AR, Barrow LN, Smith ML, Means DB, Lemmon AR, Lemmon EM. Signatures of north-eastern expansion and multiple refugia: genomic phylogeography of the Pine Barrens tree frog, Hyla andersonii (Anura: Hylidae). Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Range fragmentation poses challenges for species persistence over time and can be caused by both historical and contemporary processes. We combined genomic data, phylogeographical model testing and palaeoclimatic niche modelling to infer the evolutionary history of the Pine Barrens tree frog (Hyla andersonii), a seepage bog specialist, in eastern North America to gain a better understanding of the historical context of its fragmented distribution. We sampled H. andersonii populations across the three disjunct regions of the species range: Alabama/Florida (AF), the Carolinas (CL) and New Jersey (NJ). Phylogenetic relationships within H. andersonii were consistent between the nuclear species tree and mitochondrial analyses, indicating divergence between AF and CL/NJ (Atlantic clade) ~0.9 Mya and divergence of the NJ clade ~0.15 Mya. Several predictions of north-eastern expansion along the Atlantic coast were supported by phylogeographical analyses. Model testing using genome-wide single nucleotide polymorphism data and species distribution models both provided evidence for multiple disjunct refugia. This comprehensive phylogeographical study of H. andersonii demonstrates a long history of range fragmentation within an endemic coastal plain species and highlights the influence of historical climate change on the current distribution of species and their genetic diversity.
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Affiliation(s)
- Alexa R Warwick
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Lisa N Barrow
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Megan L Smith
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, IN, USA
| | - D Bruce Means
- Coastal Plains Institute and Land Conservancy, Tallahassee, FL, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, USA
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Barrow LN, Bauernfeind SM, Cruz PA, Williamson JL, Wiley DL, Ford JE, Baumann MJ, Brady SS, Chavez AN, Gadek CR, Galen SC, Johnson AB, Mapel XM, Marroquin-Flores RA, Martinez TE, McCullough JM, McLaughlin JE, Witt CC. Detecting turnover among complex communities using null models: a case study with sky-island haemosporidian parasites. Oecologia 2021; 195:435-451. [PMID: 33484348 DOI: 10.1007/s00442-021-04854-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 01/08/2021] [Indexed: 11/26/2022]
Abstract
Turnover in species composition between sites, or beta diversity, is a critical component of species diversity that is typically influenced by geography, environment, and biotic interactions. Quantifying turnover is particularly challenging, however, in multi-host, multi-parasite assemblages where undersampling is unavoidable, resulting in inflated estimates of turnover and uncertainty about its spatial scale. We developed and implemented a framework using null models to test for community turnover in avian haemosporidian communities of three sky islands in the southwestern United States. We screened 776 birds for haemosporidian parasites from three genera (Parahaemoproteus, Plasmodium, and Leucocytozoon) by amplifying and sequencing a mitochondrial DNA barcode. We detected infections in 280 birds (36.1%), sequenced 357 infections, and found a total of 99 parasite haplotypes. When compared to communities simulated from a regional pool, we observed more unique, single-mountain haplotypes and fewer haplotypes shared among three mountain ranges than expected, indicating that haemosporidian communities differ to some degree among adjacent mountain ranges. These results were robust even after pruning datasets to include only identical sets of host species, and they were consistent for two of the three haemosporidian genera. The two more distant mountain ranges were more similar to each other than the one located centrally, suggesting that the differences we detected were due to stochastic colonization-extirpation dynamics. These results demonstrate that avian haemosporidian communities of temperate-zone forests differ on relatively fine spatial scales between adjacent sky islands. Null models are essential tools for testing the spatial scale of turnover in complex, undersampled, and poorly known systems.
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Affiliation(s)
- Lisa N Barrow
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Selina M Bauernfeind
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Paxton A Cruz
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Jessie L Williamson
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Daniele L Wiley
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - John E Ford
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Matthew J Baumann
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Serina S Brady
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Andrea N Chavez
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
- Bureau of Land Management, Rio Puerco District Office, Albuquerque, NM, USA
- Cibola National Forest and National Grasslands, Albuquerque, NM, USA
| | - Chauncey R Gadek
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Spencer C Galen
- Department of Ornithology, Academy of Natural Sciences of Drexel University, Philadelphia, PA, USA
- Biology Department, University of Scranton, Scranton, PA, USA
| | - Andrew B Johnson
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Xena M Mapel
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Rosario A Marroquin-Flores
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
- School of Biological Sciences, Illinois State University, Normal, IL, USA
| | - Taylor E Martinez
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
- Department of Molecular Medicine and Pharmacology, University of South Florida, Tampa, FL, USA
| | - Jenna M McCullough
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Jade E McLaughlin
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Christopher C Witt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA.
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6
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Barrow LN, Masiero da Fonseca E, Thompson CEP, Carstens BC. Predicting amphibian intraspecific diversity with machine learning: Challenges and prospects for integrating traits, geography, and genetic data. Mol Ecol Resour 2020; 21:2818-2831. [PMID: 33249725 DOI: 10.1111/1755-0998.13303] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 11/11/2020] [Accepted: 11/24/2020] [Indexed: 12/19/2022]
Abstract
The growing availability of genetic data sets, in combination with machine learning frameworks, offers great potential to answer long-standing questions in ecology and evolution. One such question has intrigued population geneticists, biogeographers, and conservation biologists: What factors determine intraspecific genetic diversity? This question is challenging to answer because many factors may influence genetic variation, including life history traits, historical influences, and geography, and the relative importance of these factors varies across taxonomic and geographic scales. Furthermore, interpreting the influence of numerous, potentially correlated variables is difficult with traditional statistical approaches. To address these challenges, we analysed repurposed data using machine learning and investigated predictors of genetic diversity, focusing on Nearctic amphibians as a case study. We aggregated species traits, range characteristics, and >42,000 genetic sequences for 299 species using open-access scripts and various databases. After identifying important predictors of nucleotide diversity with random forest regression, we conducted follow-up analyses to examine the roles of phylogenetic history, geography, and demographic processes on intraspecific diversity. Although life history traits were not important predictors for this data set, we found significant phylogenetic signal in genetic diversity within amphibians. We also found that salamander species at northern latitudes contained low genetic diversity. Data repurposing and machine learning provide valuable tools for detecting patterns with relevance for conservation, but concerted efforts are needed to compile meaningful data sets with greater utility for understanding global biodiversity.
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Affiliation(s)
- Lisa N Barrow
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA.,Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | | | - Coleen E P Thompson
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
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7
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Mapel XM, Gyllenhaal EF, Modak TH, DeCicco LH, Naikatini A, Utzurrum RB, Seamon JO, Cibois A, Thibault JC, Sorenson MD, Moyle RG, Barrow LN, Andersen MJ. Inter- and intra-archipelago dynamics of population structure and gene flow in a Polynesian bird. Mol Phylogenet Evol 2020; 156:107034. [PMID: 33276120 DOI: 10.1016/j.ympev.2020.107034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 12/13/2022]
Abstract
Islands are separated by natural barriers that prevent gene flow between terrestrial populations and promote allopatric diversification. Birds in the South Pacific are an excellent model to explore the interplay between isolation and gene flow due to the region's numerous archipelagos and well-characterized avian communities. The wattled honeyeater complex (Foulehaio spp.) comprises three allopatric species that are widespread and common across Fiji, Tonga, Samoa, and Wallis and Futuna. Here, we explored patterns of diversification within and among these lineages using genomic and morphometric data. We found support for three clades of Foulehaio corresponding to three recognized species. Within F. carunculatus, population genetic analyses identified nine major lineages, most of which were composed of sub-lineages that aligned nearly perfectly to individual island populations. Despite genetic structure and great geographic distance between populations, we found low levels of gene flow between populations in adjacent archipelagos. Additionally, body size of F. carunculatus varied randomly with respect to evolutionary history (as Ernst Mayr predicted), but correlated negatively with island size, consistent with the island rule. Our findings support a hypothesis that widespread taxa can show population structure between immediately adjacent islands, and likely represent many independent lineages loosely connected by gene flow.
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Affiliation(s)
- Xena M Mapel
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA; Animal Genomics, ETH Zürich, Lindau, Switzerland.
| | - Ethan F Gyllenhaal
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| | - Tejashree H Modak
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA; Department of Biology, Boston University, Boston, MA, USA
| | - Lucas H DeCicco
- Biodiversity Institute and Natural History Museum, Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | - Alivereti Naikatini
- South Pacific Regional Herbarium, University of the South Pacific, Laucala Campus, Suva, Fiji
| | - Ruth B Utzurrum
- Department of Marine & Wildlife Resources, American Samoa Government, PO Box 3730, Pago Pago, AS 96799, USA
| | - Joshua O Seamon
- Department of Marine & Wildlife Resources, American Samoa Government, PO Box 3730, Pago Pago, AS 96799, USA
| | - Alice Cibois
- Natural History Museum of Geneva, CP 6434, CH 1211 Geneva, Switzerland
| | - Jean-Claude Thibault
- Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP50, F-75005 Paris, France
| | | | - Robert G Moyle
- Biodiversity Institute and Natural History Museum, Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | - Lisa N Barrow
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| | - Michael J Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
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8
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Miller SE, Barrow LN, Ehlman SM, Goodheart JA, Greiman SE, Lutz HL, Misiewicz TM, Smith SM, Tan M, Thawley CJ, Cook JA, Light JE. Building Natural History Collections for the Twenty-First Century and Beyond. Bioscience 2020. [DOI: 10.1093/biosci/biaa069] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Abstract
Natural history collections (NHCs) are important resources for a diverse array of scientific fields. Recent digitization initiatives have broadened the user base of NHCs, and new technological innovations are using materials generated from collections to address novel scientific questions. Simultaneously, NHCs are increasingly imperiled by reductions in funding and resources. Ensuring that NHCs continue to serve as a valuable resource for future generations will require the scientific community to increase their contribution to and acknowledgement of collections. We provide recommendations and guidelines for scientists to support NHCs, focusing particularly on new users that may be unfamiliar with collections. We hope that this perspective will motivate debate on the future of NHCs and the role of the scientific community in maintaining and improving biological collections.
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Affiliation(s)
- Sara E Miller
- Cornell University Department of Neurobiology and Behavior, Ithaca, New York
| | - Lisa N Barrow
- Museum of Southwestern Biology and with the Biology Department, University of New Mexico, Albuquerque
| | - Sean M Ehlman
- Ecology, Evolution, and Behavior Department, University of Minnesota—Twin Cities, Saint Paul
| | - Jessica A Goodheart
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, in Santa Barbara, California
- Scripps Institution of Oceanography, University of California San Diego, La Jolla
| | - Stephen E Greiman
- Department of Biology, Georgia Southern University, Statesboro Georgia
| | - Holly L Lutz
- Scripps Institution of Oceanography, University of California San Diego, La Jolla
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois
| | - Tracy M Misiewicz
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman
| | - Stephanie M Smith
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois
| | - Milton Tan
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Urbana–Champaign, Champaign
| | - Christopher J Thawley
- Department of Biological Sciences, University of Rhode Island, Kingston
- Department of Mathematics and Sciences, Neumann University, Aston, Pennsylvania
| | - Joseph A Cook
- Museum of Southwestern Biology and with the Biology Department, University of New Mexico, Albuquerque
| | - Jessica E Light
- Department of Ecology and Conservation Biology, Texas A&M University, College Station
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9
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Barrow LN, Allen JM, Huang X, Bensch S, Witt CC. Genomic sequence capture of haemosporidian parasites: Methods and prospects for enhanced study of host-parasite evolution. Mol Ecol Resour 2019; 19:400-410. [PMID: 30554480 DOI: 10.1111/1755-0998.12977] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 09/20/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 12/27/2022]
Abstract
Avian malaria and related haemosporidians (Plasmodium, [Para]Haemoproteus and Leucocytoozoon) represent an exciting multihost, multiparasite system in ecology and evolution. Global research in this field accelerated after the publication in 2000 of PCR protocols to sequence a haemosporidian mitochondrial (mtDNA) barcode and the development in 2009 of an open-access database to document the geographic and host ranges of parasite mtDNA haplotypes. Isolating haemosporidian nuclear DNA from bird hosts, however, has been technically challenging, slowing the transition to genomic-scale sequencing techniques. We extend a recently developed sequence capture method to obtain hundreds of haemosporidian nuclear loci from wild bird samples, which typically have low levels of infection, or parasitemia. We tested 51 infected birds from Peru and New Mexico and evaluated locus recovery in light of variation in parasitemia, divergence from reference sequences and pooling strategies. Our method was successful for samples with parasitemia as low as ~0.02% (2 of 10,000 blood cells infected) and mtDNA divergence as high as 15.9% (one Leucocytozoonsample), and using the most cost-effective pooling strategy tested. Phylogenetic relationships estimated with >300 nuclear loci were well resolved, providing substantial improvement over the mtDNA barcode. We provide protocols for sample preparation and sequence capture including custom probe sequences and describe our bioinformatics pipeline using atram 2.0, phyluce and custom Perl/Python scripts. This approach can be applied to thousands of avian samples that have already been found to have haemosporidian infections of at least moderate intensity, greatly improving our understanding of parasite speciation, biogeography and evolutionary dynamics.
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Affiliation(s)
- Lisa N Barrow
- Museum of Southwestern Biology and Department of Biology, MSC03 2020, 1 University of New Mexico, Albuquerque, New Mexico
| | - Julie M Allen
- Department of Biology, University of Nevada, Reno, Nevada
| | - Xi Huang
- Department of Biology, Molecular Ecology and Evolution Laboratory, Lund University, Lund, Sweden
| | - Staffan Bensch
- Department of Biology, Molecular Ecology and Evolution Laboratory, Lund University, Lund, Sweden
| | - Christopher C Witt
- Museum of Southwestern Biology and Department of Biology, MSC03 2020, 1 University of New Mexico, Albuquerque, New Mexico
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10
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Barrow LN, McNew SM, Mitchell N, Galen SC, Lutz HL, Skeen H, Valqui T, Weckstein JD, Witt CC. Deeply conserved susceptibility in a multi-host, multi-parasite system. Ecol Lett 2019; 22:987-998. [PMID: 30912262 DOI: 10.1111/ele.13263] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 01/24/2019] [Accepted: 02/20/2019] [Indexed: 01/06/2023]
Abstract
Variation in susceptibility is ubiquitous in multi-host, multi-parasite assemblages, and can have profound implications for ecology and evolution in these systems. The extent to which susceptibility to parasites is phylogenetically conserved among hosts can be revealed by analysing diverse regional communities. We screened for haemosporidian parasites in 3983 birds representing 40 families and 523 species, spanning ~ 4500 m elevation in the tropical Andes. To quantify the influence of host phylogeny on infection status, we applied Bayesian phylogenetic multilevel models that included a suite of environmental, spatial, temporal, life history and ecological predictors. We found evidence of deeply conserved susceptibility across the avian tree; host phylogeny explained substantial variation in infection status, and results were robust to phylogenetic uncertainty. Our study suggests that susceptibility is governed, in part, by conserved, latent aspects of anti-parasite defence. This demonstrates the importance of deep phylogeny for understanding present-day ecological interactions.
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Affiliation(s)
- Lisa N Barrow
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, 87131, USA.,Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Sabrina M McNew
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, 87131, USA.,Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA.,Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA
| | - Nora Mitchell
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Spencer C Galen
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, 87131, USA.,Sackler Institute for Comparative Genomics & Richard Gilder Graduate School, American Museum of Natural History, New York, NY, 10024, USA.,Department of Ornithology, Academy of Natural Sciences of Drexel University, Philadelphia, PA, 19103, USA.,Department of Biodiversity, Earth, and Environmental Sciences, Drexel University, Philadelphia, PA, 19103, USA
| | - Holly L Lutz
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA.,Integrative Research Center, The Field Museum, Chicago, IL, 60605, USA.,Department of Surgery, University of Chicago, Chicago, IL, 60637, USA
| | - Heather Skeen
- Integrative Research Center, The Field Museum, Chicago, IL, 60605, USA.,Committee on Evolutionary Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Thomas Valqui
- Centro de Ornitología y Biodiversidad (CORBIDI), Lima, Perú
| | - Jason D Weckstein
- Department of Ornithology, Academy of Natural Sciences of Drexel University, Philadelphia, PA, 19103, USA.,Department of Biodiversity, Earth, and Environmental Sciences, Drexel University, Philadelphia, PA, 19103, USA.,Integrative Research Center, The Field Museum, Chicago, IL, 60605, USA
| | - Christopher C Witt
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, 87131, USA.,Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
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11
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Kotze A, Ralph TM, Barrow LN, Tarrant J, du Preez L, Madisha MT, Dalton DL. Lack of phylogeographic structure in the endangered Pickersgill’s Reed Frog;Hyperolius pickersgilli(Raw, 1982). AFR J HERPETOL 2019. [DOI: 10.1080/21564574.2018.1462064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Antoinette Kotze
- National Zoological Garden, South African National Biodiversity Institute, PO Box 754, Pretoria, 0001, South Africa
- Genetics Department, University of the Free State, PO Box 339, Bloemfontein, 9300 South Africa
| | - Taryn M.C. Ralph
- Genetics Department, University of the Free State, PO Box 339, Bloemfontein, 9300 South Africa
| | - Lisa N. Barrow
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131-0001, USA
| | - Jeanne Tarrant
- Threatened Amphibian Programme, Endangered Wildlife Trust, Building K2, Pinelands Office Park, Ardeer Road, Modderfontein, 1609, South Africa
| | - Louis du Preez
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, 2520, South Africa
- South African Institute for Aquatic Biodiversity, Private Bag 1015, Grahamstown 6140
| | - M. Thabang Madisha
- National Zoological Garden, South African National Biodiversity Institute, PO Box 754, Pretoria, 0001, South Africa
| | - Desire L Dalton
- National Zoological Garden, South African National Biodiversity Institute, PO Box 754, Pretoria, 0001, South Africa
- Department of Zoology, University of Venda, Thohoyandou, South Africa
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12
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Vanwyk AM, Kotzé A, Paul Grobler J, Van Vuuren BJ, Barrow LN, Dalton DL. Isolation and characterization of species-specific microsatellite markers for blue and black wildebeest ( Connochaetes taurinus and C. gnou). J Genet 2018; 97:e101-e109. [PMID: 30574875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The bluewildebeest (Connochaetes taurinus) is distributed throughout southern and east Africa while the black wildebeest (Connochaetes gnou) is endemic to South Africa and was driven to near extinction in the early 1900s due to hunting pressure and disease outbreaks. Extensive translocation of both species throughout South Africa is threatening the genetic integrity of blue and blackwilde beest. To effectively manage these species, genetic tools that can be used to detect hybrid individuals, identify genetically unique subpopulations and determine the levels of genetic diversity are required. In this study, 11 microsatellite markers were developed for wildebeest through next-generation sequencing. The microsatellite loci displayed 2.00-4.14 alleles, unbiased heterozygosity values ranged from 0.32 to 0.60 and observed heterozygosity values ranged from 0.26 to 0.52. The comparatively high level of polymorphism observed in the microsatellite markers indicates that these markers can contribute significantly to our knowledge of population genetic structure, relatedness, genetic diversity and hybridization in these species.
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Affiliation(s)
- Anna M Vanwyk
- National Zoological Gardens, South African Biodiversity Institute, P.O. Box 754, Pretoria 0001, South Africa. ,
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13
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Barrow LN, Lemmon AR, Lemmon EM. Targeted Sampling and Target Capture: Assessing Phylogeographic Concordance with Genome-wide Data. Syst Biol 2018; 67:979-996. [DOI: 10.1093/sysbio/syy021] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 03/15/2018] [Indexed: 01/09/2023] Open
Affiliation(s)
- Lisa N Barrow
- Department of Biology, Museum of Southwestern Biology, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131-0001, USA
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4120, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, USA
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14
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Relyea RA, Stephens PR, Barrow LN, Blaustein AR, Bradley PW, Buck JC, Chang A, Collins JP, Crother B, Earl J, Gervasi SS, Hoverman JT, Hyman O, Lemmon EM, Luhring TM, Michelson M, Murray C, Price S, Semlitsch RD, Sih A, Stoler AB, VandenBroek N, Warwick A, Wengert G, Hammond JI. Phylogenetic patterns of trait and trait plasticity evolution: Insights from amphibian embryos. Evolution 2018; 72:663-678. [PMID: 29345312 PMCID: PMC6131697 DOI: 10.1111/evo.13428] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 12/27/2017] [Indexed: 12/25/2022]
Abstract
Environmental variation favors the evolution of phenotypic plasticity. For many species, we understand the costs and benefits of different phenotypes, but we lack a broad understanding of how plastic traits evolve across large clades. Using identical experiments conducted across North America, we examined prey responses to predator cues. We quantified five life-history traits and the magnitude of their plasticity for 23 amphibian species/populations (spanning three families and five genera) when exposed to no cues, crushed-egg cues, and predatory crayfish cues. Embryonic responses varied considerably among species and phylogenetic signal was common among the traits, whereas phylogenetic signal was rare for trait plasticities. Among trait-evolution models, the Ornstein-Uhlenbeck (OU) model provided the best fit or was essentially tied with Brownian motion. Using the best fitting model, evolutionary rates for plasticities were higher than traits for three life-history traits and lower for two. These data suggest that the evolution of life-history traits in amphibian embryos is more constrained by a species' position in the phylogeny than is the evolution of life history plasticities. The fact that an OU model of trait evolution was often a good fit to patterns of trait variation may indicate adaptive optima for traits and their plasticities.
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Affiliation(s)
- Rick A Relyea
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Darrin Fresh Water Institute, Troy, New York 12180
| | | | - Lisa N Barrow
- Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131
| | - Andrew R Blaustein
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon 97331
| | - Paul W Bradley
- Department of Biology, University of San Diego, San Diego, California 92110
| | - Julia C Buck
- Marine Science Institute, University of California, Santa Barbara, California 93106
| | - Ann Chang
- Museum of Vertebrate Zoology, University of California, Berkeley, California 94720
| | - James P Collins
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287
| | - Brian Crother
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, Louisiana 70402
| | - Julia Earl
- Department of Natural Resource Ecology and Management, Oklahoma State University, Stillwater, Oklahoma 74078
| | | | - Jason T Hoverman
- Department of Forestry & Natural Resources, Purdue University, West Lafayette, Indiana 47907
| | - Oliver Hyman
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287
| | | | - Thomas M Luhring
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588
| | - Moses Michelson
- Department of Biology, Florida State University, Tallahassee, Florida 32306
| | - Chris Murray
- Department of Biology, Tennessee Technological University, Cookeville, Tennessee 38505
| | - Steven Price
- Department of Forestry, University of Kentucky, Lexington, Kentucky 40546
| | - Raymond D Semlitsch
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
| | - Andrew Sih
- College of Biological Sciences, University of California-Davis, Davis, California 95616
| | - Aaron B Stoler
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Darrin Fresh Water Institute, Troy, New York 12180
| | - Nick VandenBroek
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, Louisiana 70402
| | - Alexa Warwick
- Department of Biology, Florida State University, Tallahassee, Florida 32306
| | - Greta Wengert
- College of Biological Sciences, University of California-Davis, Davis, California 95616
| | - John I Hammond
- Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131
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15
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Marroquin-Flores RA, Williamson JL, Chavez AN, Bauernfeind SM, Baumann MJ, Gadek CR, Johnson AB, McCullough JM, Witt CC, Barrow LN. Diversity, abundance, and host relationships of avian malaria and related haemosporidians in New Mexico pine forests. PeerJ 2017; 5:e3700. [PMID: 28828279 PMCID: PMC5563434 DOI: 10.7717/peerj.3700] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 05/29/2017] [Accepted: 07/26/2017] [Indexed: 01/28/2023] Open
Abstract
Avian malaria and related haemosporidian parasites (genera Haemoproteus, Plasmodium, and Leucocytozoon) affect bird demography, species range limits, and community structure, yet they remain unsurveyed in most bird communities and populations. We conducted a community-level survey of these vector-transmitted parasites in New Mexico, USA, to describe their diversity, abundance, and host associations. We focused on the breeding-bird community in the transition zone between piñon-juniper woodland and ponderosa pine forests (elevational range: 2,150–2,460 m). We screened 186 birds representing 49 species using both standard PCR and microscopy techniques to detect infections of all three avian haemosporidian genera. We detected infections in 68 out of 186 birds (36.6%), the highest proportion of which were infected with Haemoproteus (20.9%), followed by Leucocytozoon (13.4%), then Plasmodium (8.0%). We sequenced mtDNA for 77 infections representing 43 haplotypes (25 Haemoproteus, 12 Leucocytozoon, 6 Plasmodium). When compared to all previously known haplotypes in the MalAvi and GenBank databases, 63% (27) of the haplotypes we recovered were novel. We found evidence for host specificity at the avian clade and species level, but this specificity was variable among parasite genera, in that Haemoproteus and Leucocytozoon were each restricted to three avian groups (out of six), while Plasmodium occurred in all groups except non-passerines. We found striking variation in infection rate among host species, with nearly universal infection among vireos and no infection among nuthatches. Using rarefaction and extrapolation, we estimated the total avian haemosporidian diversity to be 70 haplotypes (95% CI [43–98]); thus, we may have already sampled ∼60% of the diversity of avian haemosporidians in New Mexico pine forests. It is possible that future studies will find higher diversity in microhabitats or host species that are under-sampled or unsampled in the present study. Fortunately, this study is fully extendable via voucher specimens, frozen tissues, blood smears, parasite images, and documentation provided in open-access databases (MalAvi, GenBank, and ARCTOS).
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Affiliation(s)
- Rosario A Marroquin-Flores
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, United States of America
| | - Jessie L Williamson
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, United States of America
| | - Andrea N Chavez
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, United States of America.,Bureau of Land Management Rio Puerco Field Office, Rio Puerco, NM, United States of America
| | - Selina M Bauernfeind
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, United States of America
| | - Matthew J Baumann
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, United States of America
| | - Chauncey R Gadek
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, United States of America
| | - Andrew B Johnson
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, United States of America
| | - Jenna M McCullough
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, United States of America
| | - Christopher C Witt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, United States of America
| | - Lisa N Barrow
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, United States of America
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16
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Engebretsen KN, Barrow LN, Rittmeyer EN, Brown JM, Moriarty Lemmon E. Quantifying the spatiotemporal dynamics in a chorus frog (Pseudacris) hybrid zone over 30 years. Ecol Evol 2016; 6:5013-31. [PMID: 27547330 PMCID: PMC4979724 DOI: 10.1002/ece3.2232] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 04/13/2016] [Revised: 05/11/2016] [Accepted: 05/16/2016] [Indexed: 12/14/2022] Open
Abstract
Although theory suggests that hybrid zones can move or change structure over time, studies supported by direct empirical evidence for these changes are relatively limited. We present a spatiotemporal genetic study of a hybrid zone between Pseudacris nigrita and P. fouquettei across the Pearl River between Louisiana and Mississippi. This hybrid zone was initially characterized in 1980 as a narrow and steep “tension zone,” in which hybrid populations were inferior to parentals and were maintained through a balance between selection and dispersal. We reanalyzed historical tissue samples and compared them to samples of recently collected individuals using microsatellites. Clinal analyses indicate that the cline has not shifted in roughly 30 years but has widened significantly. Anthropogenic and natural changes may have affected selective pressure or dispersal, and our results suggest that the zone may no longer best be described as a tension zone. To the best of our knowledge, this study provides the first evidence of significant widening of a hybrid cline but stasis of its center. Continued empirical study of dynamic hybrid zones will provide insight into the forces shaping their structure and the evolutionary potential they possess for the elimination or generation of species.
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Affiliation(s)
- Kristin N Engebretsen
- Department of Biological Science Florida State University 319 Stadium Drive Tallahassee Florida 32306
| | - Lisa N Barrow
- Department of Biological Science Florida State University 319 Stadium Drive Tallahassee Florida 32306
| | - Eric N Rittmeyer
- Department of Biological Sciences Museum of Natural Science Louisiana State University 202 Life Sciences Building Baton Rouge Louisiana 70803; Research School of Biology The Australian National University Gould Building 116 Canberra ACT 2601 Australia
| | - Jeremy M Brown
- Department of Biological Sciences Museum of Natural Science Louisiana State University 202 Life Sciences Building Baton Rouge Louisiana 70803
| | - Emily Moriarty Lemmon
- Department of Biological Science Florida State University 319 Stadium Drive Tallahassee Florida 32306
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Barrow LN, Bigelow AT, Phillips CA, Lemmon EM. Phylogeographic inference using Bayesian model comparison across a fragmented chorus frog species complex. Mol Ecol 2015; 24:4739-58. [DOI: 10.1111/mec.13343] [Citation(s) in RCA: 12] [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] [Received: 10/20/2014] [Revised: 07/24/2015] [Accepted: 08/08/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Lisa N. Barrow
- Department of Biological Science Florida State University 319 Stadium Drive, P.O. Box 3064340 Tallahassee FL 32306‐4340 USA
| | - Alyssa T. Bigelow
- Department of Biological Science Florida State University 319 Stadium Drive, P.O. Box 3064340 Tallahassee FL 32306‐4340 USA
| | - Christopher A. Phillips
- Illinois Natural History Survey Prairie Research Institute University of Illinois 185 Natural Resources Bldg, 607 E. Peabody Drive Champaign IL 61820 USA
| | - Emily Moriarty Lemmon
- Department of Biological Science Florida State University 319 Stadium Drive, P.O. Box 3064340 Tallahassee FL 32306‐4340 USA
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Barrow LN, Ralicki HF, Emme SA, Lemmon EM. Species tree estimation of North American chorus frogs (Hylidae: Pseudacris) with parallel tagged amplicon sequencing. Mol Phylogenet Evol 2014; 75:78-90. [DOI: 10.1016/j.ympev.2014.02.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 12/24/2013] [Accepted: 02/13/2014] [Indexed: 11/28/2022]
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Soto-Centeno JA, Barrow LN, Allen JM, Reed DL. Reevaluation of a classic phylogeographic barrier: new techniques reveal the influence of microgeographic climate variation on population divergence. Ecol Evol 2013; 3:1603-13. [PMID: 23789071 PMCID: PMC3686195 DOI: 10.1002/ece3.576] [Citation(s) in RCA: 13] [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: 12/13/2012] [Revised: 03/16/2013] [Accepted: 03/27/2013] [Indexed: 11/08/2022] Open
Abstract
We evaluated the mtDNA divergence and relationships within Geomys pinetis to assess the status of formerly recognized Geomys taxa. Additionally, we integrated new hypothesis-based tests in ecological niche models (ENM) to provide greater insight into causes for divergence and potential barriers to gene flow in Southeastern United States (Alabama, Florida, and Georgia). Our DNA sequence dataset confirmed and strongly supported two distinct lineages within G. pinetis occurring east and west of the ARD. Divergence date estimates showed that eastern and western lineages diverged about 1.37 Ma (1.9 Ma-830 ka). Predicted distributions from ENMs were consistent with molecular data and defined each population east and west of the ARD with little overlap. Niche identity and background similarity tests were statistically significant suggesting that ENMs from eastern and western lineages are not identical or more similar than expected based on random localities drawn from the environmental background. ENMs also support the hypothesis that the ARD represents a ribbon of unsuitable climate between more suitable areas where these populations are distributed. The estimated age of divergence between eastern and western lineages of G. pinetis suggests that the divergence was driven by climatic conditions during Pleistocene glacial-interglacial cycles. The ARD at the contact zone of eastern and western lineages of G. pinetis forms a significant barrier promoting microgeographic isolation that helps maintain ecological and genetic divergence.
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Affiliation(s)
- J Angel Soto-Centeno
- Department of Biology, University of Florida Gainesville, Florida, 32611 ; Florida Museum of Natural History, University of Florida Gainesville, Florida, 32611
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Barrow RE, Mlcak R, Barrow LN, Hawkins HK. Increased liver weights in severely burned children: comparison of ultrasound and autopsy measurements. Burns 2004; 30:565-8. [PMID: 15302422 DOI: 10.1016/j.burns.2004.01.027] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2004] [Indexed: 11/22/2022]
Abstract
Hepatomegaly is a common finding at autopsy in severely burned children surviving less than 6 months. This study validates a reliable ultrasound method which can be used to identify changes in liver size in severely burned children during acute hospitalization. Thirty-eight children, age 0.5-17 years with burns covering over 40% of their total surface area were studied at autopsy. Liver weight was measured at autopsy and compared to predicted liver weight for age and height. Eighteen had liver size measured by ultrasound within 10 days of death while five had ultrasound liver measures after death just prior to autopsy. All burned children who survived 7 days or more (n = 33) had liver weights at autopsy that were greater than predicted for age and height while all 23 livers measured by ultrasound were greater than predicted. Autopsy weights correlated well with weights estimated by ultrasound, R = 0.824. At autopsy, those who survived 7 days or more had enlarged livers ranging from 142 to 406% of their predicted normal age and height. Common histologic findings include large and small-droplet fat deposits, and cholestasis. The degree of these histologic abnormalities correlated with the increase in liver weight, R = 0.652. Ultrasound is a valid, noninvasive method for measuring liver weight changes in severely burned children during acute hospitalization. Ninety-five percent of the severely burned children from this institute had significant hepatomegaly identified at autopsy.
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Affiliation(s)
- R E Barrow
- Department of Surgery, The University of Texas Medical Branch, Galveston, TX 77550, USA
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Chrysopoulo MT, Barrow RE, Muller M, Rubin S, Barrow LN, Herndon DN. Chest radiographic appearances in severely burned adults. A comparison of early radiographic and extravascular lung thermal volume changes. J Burn Care Rehabil 2001; 22:104-10. [PMID: 11302596 DOI: 10.1097/00004630-200103000-00004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Chest radiographs (CXRs) have previously been used as a diagnostic tool to detect changes in lung water. In this study CXR changes in severely burned adults, in the absence of an inhalation injury, preceded detectable increases in extravascular lung thermal volume (ELTV) by 3 to 5 days. The hypothesis that early CXR density changes in burned patients have an infectious cause, not related to changes in ELTV, was tested. Blood cultures, CXRs, and ELTV were evaluated during the first 15 days after injury in severely burned adults who had no identified inhalation injury. Chest radiographs were scored daily on a 1 to 5 scale, with 1 = normal, 2 = peribronchial cuffing, 3 = mild interstitial infiltrates, 4 = severe interstitial infiltrates, and 5 = alveolar infiltrates. In all patients, except those who were septic, increases in their CXR density scores correlated well with increases in ELTV. The ELTV/CXR score ratios for septic burn patients on days 1 to 6 postburn was 1.7 +/- 0.2 compared with 4.2 +/- 0.4, (means +/- SEM) for nonseptic (P < .001), whereas the ELTV/CXR score ratios for septic and nonseptic patients, 7 to 15 days postburn, were 3.8 +/- 0.4 and 3.4 +/- 0.5, respectively. We suggest that before any measurable change in ELTV early increases in CXR density scores in burned patients without a concomitant inhalation injury are caused by intraalveolar pneumonitis or hyaline membrane atelectasis and not increased ELTV.
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Affiliation(s)
- M T Chrysopoulo
- Department of Surgery, University of Texas Medical Branch, Galveston, USA
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