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Miralles A, Puillandre N, Vences M. DNA Barcoding in Species Delimitation: From Genetic Distances to Integrative Taxonomy. Methods Mol Biol 2024; 2744:77-104. [PMID: 38683312 DOI: 10.1007/978-1-0716-3581-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Over the past two decades, DNA barcoding has become the most popular exploration approach in molecular taxonomy, whether for identification, discovery, delimitation, or description of species. The present contribution focuses on the utility of DNA barcoding for taxonomic research activities related to species delimitation, emphasizing the following aspects:(1) To what extent DNA barcoding can be a valuable ally for fundamental taxonomic research, (2) its methodological and theoretical limitations, (3) the conceptual background and practical use of pairwise distances between DNA barcode sequences in taxonomy, and (4) the different ways in which DNA barcoding can be combined with complementary means of investigation within a broader integrative framework. In this chapter, we recall and discuss the key conceptual advances that have led to the so-called renaissance of taxonomy, elaborate a detailed glossary for the terms specific to this discipline (see Glossary in Chap. 35 ), and propose a newly designed step-by-step species delimitation protocol starting from DNA barcode data that includes steps from the preliminary elaboration of an optimal sampling strategy to the final decision-making process which potentially leads to nomenclatural changes.
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Affiliation(s)
- Aurélien Miralles
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Miguel Vences
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany.
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2
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Myers EA, Mulcahy DG, Falk B, Johnson K, Carbi M, de Queiroz K. Interspecific Gene Flow and Mitochondrial Genome Capture During the Radiation of Jamaican Anolis Lizards (Squamata; Iguanidae). Syst Biol 2021; 71:501-511. [PMID: 34735007 DOI: 10.1093/sysbio/syab089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 11/12/2022] Open
Abstract
Gene flow and reticulation are increasingly recognized as important processes in the diversification of many taxonomic groups. With the increasing ease of collecting genomic data and the development of multispecies coalescent network approaches, such reticulations can be accounted for when inferring phylogeny and diversification. Caribbean Anolis lizards are a classic example of an adaptive radiation in which species have independently radiated on the islands of the Greater Antilles into the same ecomorph classes. Within the Jamaican radiation at least one species, A. opalinus, has been documented to be polyphyletic in its mitochondrial DNA, which could be the result of an ancient reticulation event or incomplete lineage sorting. Here we generate mtDNA and genotyping-by-sequencing (GBS) data and implement gene-tree, species-tree, and multispecies coalescent network methods to infer the diversification of this group. Our mtDNA gene-tree recovers the same relationships previously inferred for this group, which is strikingly different from the species-tree inferred from our GBS data. Posterior predictive simulations suggest that our genomic data violate commonly adopted assumptions of the multispecies coalescent model, so we use network approaches to infer phylogenetic relationships. The inferred network topology contains a reticulation event but does not explain the mtDNA polyphyly observed in this group, however coalescent simulations suggest that the observed mtDNA topology is likely the result of past introgression. How common a signature of gene flow and reticulation is across the radiation of Anolis is unknown; however, the reticulation events that we demonstrate here may have allowed for adaptive evolution, as has been suggested in other, more recent adaptive radiations.
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Affiliation(s)
- Edward A Myers
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Herpetology, The American Museum of Natural History, New York, NY, USA
| | - Daniel G Mulcahy
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Bryan Falk
- Division of Invertebrate Zoology, Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Kiyomi Johnson
- Science Research Mentoring Program, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - Marina Carbi
- Science Research Mentoring Program, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - Kevin de Queiroz
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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3
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Burbrink FT, Ruane S. Contemporary Philosophy and Methods for Studying Speciation and Delimiting Species. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/h2020073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Frank T. Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024; . Send reprint requests to this address
| | - Sara Ruane
- Earth and Environmental Sciences: Ecology and Evolution, Rutgers University–Newark, 195 University Avenue, Newark, New Jersey 07102
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4
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Myers EA. Genome-wide data reveal extensive gene flow during the diversification of the western rattlesnakes (Viperidae: Crotalinae: Crotalus). Mol Phylogenet Evol 2021; 165:107313. [PMID: 34537323 DOI: 10.1016/j.ympev.2021.107313] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 08/28/2021] [Accepted: 09/14/2021] [Indexed: 11/15/2022]
Abstract
Hybridization and introgression are important, but often overlooked processes when inferring phylogenies. When these processes are not accounted for and a strictly diverging phylogenetic model is applied to groups with a history of hybridization, phylogenetic inference and parameter estimation can be inaccurate. Recent developments in phylogenetic network approaches coupled with the increasing availability of genomic data allow inferences of reticulate evolutionary histories across the tree of life. The western rattlesnake species group (C. viridis species complex, C. mitchellii species complex, C. scutulutas, and C. tigris) is an iconic snake lineage that is widespread across western North America. This group is composed of several species complexes with unclear species limits, likely the result of ongoing gene flow among nascent lineages. Here I generate reduced representation genomic data and test for a history of reticulation within this group. I demonstrate that all species have undergone hybridization with at least one other lineage, suggesting introgression is widespread in this group. Topologies differ between phylogenies estimated under the multispecies coalescent and multispecies network coalescent methods, indicating that gene flow has obscured phylogenetic relationships within this group. These past introgression events are predominantly restricted to species that co-occur geographically. However, within species that have a history of introgression, this signature is detected regardless of specimen sampling across geography. Overall, my results suggest the accumulation of reproductive isolating barriers occurs slowly in rattlesnakes which likely leads to the difficulty in delimiting species, furthermore, the results of this study have implications for trait evolution in this group.
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Affiliation(s)
- Edward A Myers
- Department of Herpetology, American Museum of Natural History, New York, NY, USA; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
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5
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Laver RJ, Daza JD, Ellis RJ, Stanley EL, Bauer AM. Underground Down Under: Skull anatomy of the southern blind snake Anilios australis Gray, 1845 (Typhlopidae: Serpentes: Squamata). Anat Rec (Hoboken) 2021; 304:2215-2242. [PMID: 34167172 DOI: 10.1002/ar.24696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/30/2021] [Accepted: 05/14/2021] [Indexed: 11/09/2022]
Abstract
The cranial anatomy of blindsnakes has been markedly understudied, with the small size and relative rarity of encountering these subterranean reptiles being significant limiting factors. In this article, we re-visit the skull anatomy of the Australian southern blind snake Anilios australis Gray, 1845 using microCT data, and produce the first complete atlas for the cranial anatomy of a representative of this speciose typhlopid genus. The skull is formed by 18 paired and four unpaired elements. We here produce a bone-by-bone description of each element as well as an inner ear endocast for each of two specimens differing in skull size. This approach has revealed the presence of a highly perforated dorsal plate on the septomaxilla-a structure convergent with the cribriform plate of the mammalian ethmoid bone-and a feature previously unknown for typhlopid snakes. This detailed anatomical study will facilitate ongoing taxonomic and systematic studies in the genus Anilios as well as provide comparative data for future studies on blindsnake anatomy more broadly.
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Affiliation(s)
- Rebecca J Laver
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Juan D Daza
- Department of Biological Sciences, Sam Houston State University, Huntsville, Texas, USA
| | - Ryan J Ellis
- Biologic Environmental Survey, East Perth, Western Australia, Australia.,Collections and Research, Western Australian Museum, Welshpool, Western Australia, Australia
| | - Edward L Stanley
- Department of Natural History, Florida Museum of Natural History, Gainesville, Florida, USA
| | - Aaron M Bauer
- Department of Biology and Center for Biodiversity and Ecosystem Stewardship, Villanova University, Villanova, Pennsylvania, USA
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6
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Wikramanayake SA, Wikramanayake ED, Pallewatta N, Leaché AD. Integration of genetic structure into conservation of an endangered, endemic lizard,
Ceratophora aspera
: A case study from Sri Lanka. Biotropica 2021. [DOI: 10.1111/btp.12970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Shanelle A. Wikramanayake
- Department of Biology & Burke Museum of Natural History and Culture University of Washington Washington, Seattle WA USA
| | | | - Nirmalie Pallewatta
- Department of Zoology and Environment Science Faculty of Science University of Colombo Colombo Sri Lanka
| | - Adam D. Leaché
- Department of Biology & Burke Museum of Natural History and Culture University of Washington Washington, Seattle WA USA
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7
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Melville J, Chapple DG, Keogh JS, Sumner J, Amey A, Bowles P, Brennan IG, Couper P, Donnellan SC, Doughty P, Edwards DL, Ellis RJ, Esquerré D, Fenker J, Gardner MG, Georges A, Haines ML, Hoskin CJ, Hutchinson M, Moritz C, Nankivell J, Oliver P, Pavón-Vázquez CJ, Pepper M, Rabosky DL, Sanders K, Shea G, Singhal S, Worthington Wilmer J, Tingley R. A return-on-investment approach for prioritization of rigorous taxonomic research needed to inform responses to the biodiversity crisis. PLoS Biol 2021; 19:e3001210. [PMID: 34061821 PMCID: PMC8168848 DOI: 10.1371/journal.pbio.3001210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/29/2021] [Indexed: 11/19/2022] Open
Abstract
Global biodiversity loss is a profound consequence of human activity. Disturbingly, biodiversity loss is greater than realized because of the unknown number of undocumented species. Conservation fundamentally relies on taxonomic recognition of species, but only a fraction of biodiversity is described. Here, we provide a new quantitative approach for prioritizing rigorous taxonomic research for conservation. We implement this approach in a highly diverse vertebrate group-Australian lizards and snakes. Of 870 species assessed, we identified 282 (32.4%) with taxonomic uncertainty, of which 17.6% likely comprise undescribed species of conservation concern. We identify 24 species in need of immediate taxonomic attention to facilitate conservation. Using a broadly applicable return-on-investment framework, we demonstrate the importance of prioritizing the fundamental work of identifying species before they are lost.
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Affiliation(s)
- Jane Melville
- Department of Sciences, Museums Victoria, Melbourne, Australia
- Department of Biology, Washington University, St. Louis, MI, United States of America
- School of Biological Sciences, Monash University, Clayton, Australia
| | - David G. Chapple
- School of Biological Sciences, Monash University, Clayton, Australia
| | - J. Scott Keogh
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Joanna Sumner
- Department of Sciences, Museums Victoria, Melbourne, Australia
| | - Andrew Amey
- Biodiversity & Geosciences Program, Queensland Museum, Brisbane, Australia
| | - Phil Bowles
- Snake & Lizard Red List Authority, CI-IUCN Biodiversity Assessment Unit, IUCN North America Office, Washington, DC, United States of America
| | - Ian G. Brennan
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Patrick Couper
- Biodiversity & Geosciences Program, Queensland Museum, Brisbane, Australia
| | | | - Paul Doughty
- Collections & Research, Western Australian Museum, Welshpool, Australia
| | - Danielle L. Edwards
- Department of Life & Environmental Sciences, University of California, Merced, Merced, CA, United States of America
| | - Ryan J. Ellis
- Collections & Research, Western Australian Museum, Welshpool, Australia
- Biologic Environmental Survey, East Perth, Australia
| | - Damien Esquerré
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Jéssica Fenker
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Michael G. Gardner
- South Australian Museum, North Terrace, Adelaide, Australia
- College of Science & Engineering, Flinders University, Adelaide, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | | | - Conrad J. Hoskin
- College of Science & Engineering, James Cook University, Townsville, Australia
| | | | - Craig Moritz
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - James Nankivell
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Paul Oliver
- Biodiversity & Geosciences Program, Queensland Museum, Brisbane, Australia
- Environmental Futures Research Institute, Griffith University, Australia
| | - Carlos J. Pavón-Vázquez
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Mitzy Pepper
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Daniel L. Rabosky
- Museum of Zoology & Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Kate Sanders
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Glenn Shea
- School of Veterinary Science, University of Sydney, Sydney, Australia
- Australian Museum Research Institute, The Australian Museum, Sydney, Australia
| | - Sonal Singhal
- Department of Biology, California State University, Dominguez Hills, Carson, CA, United States of America
| | | | - Reid Tingley
- School of Biological Sciences, Monash University, Clayton, Australia
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8
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Hipsley CA, Aguilar R, Black JR, Hocknull SA. High-throughput microCT scanning of small specimens: preparation, packing, parameters and post-processing. Sci Rep 2020; 10:13863. [PMID: 32807929 PMCID: PMC7431592 DOI: 10.1038/s41598-020-70970-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 08/04/2020] [Indexed: 12/17/2022] Open
Abstract
High-resolution X-ray microcomputed tomography, or microCT (μCT), enables the digital imaging of whole objects in three dimensions. The power of μCT to visualize internal features without disarticulation makes it particularly valuable for the study of museum collections, which house millions of physical specimens documenting the spatio-temporal patterns of life. Despite the potential for comparative analyses, most μCT studies include limited numbers of museum specimens, due to the challenges of digitizing numerous individuals within a project scope. Here we describe a method for high-throughput μCT scanning of hundreds of small (< 2 cm) specimens in a single container, followed by individual labelling and archival storage. We also explore the effects of various packing materials and multiple specimens per capsule to minimize sample movement that can degrade image quality, and hence μCT investment. We demonstrate this protocol on vertebrate fossils from Queensland Museum, Australia, as part of an effort to track community responses to climate change over evolutionary time. This system can be easily modified for other types of wet and dry material amenable to X-ray attenuation, including geological, botanical and zoological samples, providing greater access to large-scale phenotypic data and adding value to global collections.
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Affiliation(s)
- Christy A Hipsley
- School of BioSciences, University of Melbourne, BioSciences 4, Building 147, Parkville, VIC, 3010, Australia. .,Museums Victoria, GPO Box 666, Melbourne, VIC, 3001, Australia.
| | - Rocio Aguilar
- School of BioSciences, University of Melbourne, BioSciences 4, Building 147, Parkville, VIC, 3010, Australia.,Museums Victoria, GPO Box 666, Melbourne, VIC, 3001, Australia.,School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Jay R Black
- School of Earth Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Scott A Hocknull
- School of BioSciences, University of Melbourne, BioSciences 4, Building 147, Parkville, VIC, 3010, Australia.,Queensland Museum, Geosciences, 122 Gerler Rd., Hendra, QLD, 4011, Australia
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