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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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A new bunting species in South China revealed by an integrative taxonomic investigation of the Emberiza godlewskii complex (Aves, Emberidae). Mol Phylogenet Evol 2023; 180:107697. [PMID: 36586546 DOI: 10.1016/j.ympev.2022.107697] [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: 01/27/2022] [Revised: 12/23/2022] [Accepted: 12/26/2022] [Indexed: 12/30/2022]
Abstract
Species boundaries of birds across the Euro-Asian continent, especially the widely distributed passerines with multiple subspecies, are not completely resolved. The Rock Bunting complex, Emberiza cia and E. godlewskii, is subject to ongoing debate due to geographic variation in its morphology, and deep genetic splits. In this study, the phylogenetic relationships of the E. cia/godlewskii complex were evaluated based on multilocus coalescence methods combined with analyses of plumage color and morphological variation. Although the northern and southern populations of E. godlewski formed reciprocally monophyletic groups, the northern E. godlewskii clade is the sister group to E. cia, rendering E. godlewskii as currently defined paraphyletic. The significant differences in morphometry and plumage color reflectance are complementary and support the phenotypic validity of northern and southern E. godlewskii. Thus, we recommend the following taxonomic revisions: the northern and southern E. godlewskii subspecies should be recognized as different full species, such as E. godlewskii and E. yunnanensis, respectively. This resolves the issue that E. godlewskii, as currently defined, is paraphyletic. Our research provides direct evidence of cryptic species in old world buntings and highlights the underestimation of species diversity in birds in East Asia.
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3
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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4
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Stopiglia R, Barbosa W, Ferreira M, Raposo MA, Dubois A, Harvey MG, Kirwan GM, Forcato G, Bockmann FA, Ribas CC. Taxonomic challenges posed by discordant evolutionary scenarios supported by molecular and morphological data in the Amazonian Synallaxis rutilans group (Aves: Furnariidae). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Alpha taxonomy endeavours to propose a coherent vision of existing species and, simultaneously, to individualize the natural entities useful to understand evolutionary processes. This ideal is especially difficult when available data lack congruence. Here we address the polytypic species Synallaxis rutilans (ruddy spinetail), a suboscine passerine widely distributed in the Amazon Basin and whose taxonomy could, potentially, aid our understanding of processes shaping its biodiversity. Combining genetic [genomic ultraconserved elements (UCE) and mtDNA] and morphological data, we demonstrate that while delimitation of genetic lineages and their phylogenetic relationships are strongly associated with classic Amazonian geographic barriers, such as rivers, different coloration patterns appear to be more associated with local selection processes for phenotype. Employing an evolutionary approach, whereby the species is considered a taxonomic category, rather than a nomenclatural rank, we propose to recognize five species: S. amazonica, S. caquetensis, S. dissors, S. omissa and S. rutilans. The taxonomic arrangement proposed here permits better understanding of the similarities and differences among taxa from different areas of endemism, and represents patterns of genetic and morphological diversity resulting from distinct processes acting across certain time frames. This arrangement draws attention to the importance of understanding the evolutionary processes operating in the complex and constantly changing Amazonian landscape.
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Affiliation(s)
- Renata Stopiglia
- Museu de História Natural do Ceará Prof. Dias da Rocha, CCS, Universidade Estadual do Ceará, Av. Dr. Silas Munguba, 1700, Fortaleza, CE, 60714–903, Brazil
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, s/n, São Cristóvão, 20940-040, Rio de Janeiro, RJ, Brazil
- Laboratório de Ictiologia de Ribeirão Preto, FFCLRP, Universidade de São Paulo, Av. Bandeirantes, 3900, Ribeirão Preto, SP, Brazil
- Institut de Systématique, Évolution, Biodiversité, Muséum National d’Histoire Naturelle, Sorbonne Universités, 25 rue Cuvier, 75005, Paris, France
| | - Waleska Barbosa
- Programa de Pós-Graduação em Ecologia, INPA, Manaus, AM, Brazil
| | - Mateus Ferreira
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, INPA, Manaus, AM, Brazil
- Centro de Estudos da Biodiversidade, Universidade Federal de Roraima, Boa Vista, RR, 69310-000, Brazil
| | - Marcos A Raposo
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, s/n, São Cristóvão, 20940-040, Rio de Janeiro, RJ, Brazil
| | - Alain Dubois
- Institut de Systématique, Évolution, Biodiversité, Muséum National d’Histoire Naturelle, Sorbonne Universités, 25 rue Cuvier, 75005, Paris, France
| | - Michael G Harvey
- Department of Biological Sciences and Biodiversity Collections, The University of Texas at El Paso, 304 Biology Building, 500 West University Ave., El Paso, Texas 79968, USA
| | - Guy M Kirwan
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, s/n, São Cristóvão, 20940-040, Rio de Janeiro, RJ, Brazil
- Bird Group, Department of Life Sciences, Natural History Museum, Tring, Herts, UK
| | - Giovanna Forcato
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, s/n, São Cristóvão, 20940-040, Rio de Janeiro, RJ, Brazil
| | - Flavio A Bockmann
- Laboratório de Ictiologia de Ribeirão Preto, FFCLRP, Universidade de São Paulo, Av. Bandeirantes, 3900, Ribeirão Preto, SP, Brazil
- Programa de Pós-Graduação em Biologia Comparada, FFCLRP-USP, Ribeirão Preto, SP, Brazil
| | - Camila C Ribas
- Biodiversity Section and Zoological Collections, Instituto Nacional de Pesquisas da Amazônia, 69067–375, Manaus, AM, Brazil
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Esquerré D, Donnellan SC, Pavón-Vázquez CJ, Fenker J, Keogh JS. Phylogeography, historical demography and systematics of the world's smallest pythons (Pythonidae, Antaresia). Mol Phylogenet Evol 2021; 161:107181. [PMID: 33892100 DOI: 10.1016/j.ympev.2021.107181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 04/06/2021] [Accepted: 04/15/2021] [Indexed: 11/18/2022]
Abstract
Advances from empirical studies in phylogeography, systematics and species delimitation highlight the importance of integrative approaches for quantifying taxonomic diversity. Genomic data have greatly improved our ability to discern both systematic diversity and evolutionary history. Here we combine analyses of mitochondrial DNA sequences, thousands of genome-wide SNPs and linear and geometric morphometrics on Antaresia, a clade of four currently recognised dwarf pythons from Australia and New Guinea (Antaresia childreni, A. stimsoni, A. maculosa and A. perthensis). Our integrative analyses of phylogenetics, population structure, species delimitation, historical demography and morphometrics revealed that the true evolutionary diversity is not well reflected in the current appraisal of the diversity of the group. We find that Antaresia childreni and A. stimsoni comprise a widespread network of populations connected by gene flow and without evidence of species-level divergence among them. However, A. maculosa shows considerable genetic structuring which leads us to recognise two subspecies in northeastern Australia and a new species in Torres Strait and New Guinea. These two contrasting cases of over and under estimation of diversity, respectively, illustrate the power of thorough integrative approaches into understanding evolution of biodiversity. Furthermore, our analyses of historical demographic patterns highlight the importance of the Kimberley, Pilbara and Cape York as origins of biodiversity in Australia.
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Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia.
| | | | - Carlos J Pavón-Vázquez
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Jéssica Fenker
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
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6
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Vázquez-López M, Morrone JJ, Ramírez-Barrera SM, López-López A, Robles-Bello SM, Hernández-Baños BE. Multilocus, phenotypic, behavioral, and ecological niche analyses provide evidence for two species within Euphonia affinis (Aves, Fringillidae). Zookeys 2020; 952:129-157. [PMID: 32774114 PMCID: PMC7394775 DOI: 10.3897/zookeys.952.51785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/02/2020] [Indexed: 11/26/2022] Open
Abstract
The integration of genetic, morphological, behavioral, and ecological information in the analysis of species boundaries has increased, allowing integrative systematics that better reflect the evolutionary history of biological groups. In this context, the goal of this study was to recognize independent evolutionary lineages within Euphonia affinis at the genetic, morphological, and ecological levels. Three subspecies have been described: E. affinis godmani, distributed in the Pacific slope from southern Sonora to Guerrero; E. affinis affinis, from Oaxaca, Chiapas and the Yucatan Peninsula to Costa Rica; and E. affinis olmecorum from Tamaulipas and San Luis Potosi east to northern Chiapas (not recognized by some authors). A multilocus analysis was performed using mitochondrial and nuclear genes. These analyses suggest two genetic lineages: E. godmani and E. affinis, which diverged between 1.34 and 4.3 My, a period in which the ice ages and global cooling fragmented the tropical forests throughout the Neotropics. To analyze morphometric variations, six morphometric measurements were taken, and the Wilcoxon Test was applied to look for sexual dimorphism and differences between the lineages. Behavioral information was included, by performing vocalization analysis which showed significant differences in the temporal characteristics of calls. Finally, Ecological Niche Models were estimated with MaxEnt, and then compared using the method of Broennimann. These analyses showed that the lineage distributed in western Mexico (E. godmani) has a more restricted niche than the eastern lineage (E. affinis) and thus we rejected the hypotheses of niche equivalence and similarity. Based on the combined evidence from genetic, morphological, behavioral, and ecological data, it is concluded that E. affinis (with E. olmecorum as its synonym) and E. godmani represent two independent evolutionary lineages.
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Affiliation(s)
- Melisa Vázquez-López
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 70-399. 04510 Mexico City, MexicoUniversidad Nacional Autónoma de MéxicoMexicoMexico
| | - Juan J. Morrone
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 70-399. 04510 Mexico City, MexicoUniversidad Nacional Autónoma de MéxicoMexicoMexico
| | - Sandra M. Ramírez-Barrera
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 70-399. 04510 Mexico City, MexicoUniversidad Nacional Autónoma de MéxicoMexicoMexico
| | - Anuar López-López
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 70-399. 04510 Mexico City, MexicoUniversidad Nacional Autónoma de MéxicoMexicoMexico
| | - Sahid M. Robles-Bello
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 70-399. 04510 Mexico City, MexicoUniversidad Nacional Autónoma de MéxicoMexicoMexico
| | - Blanca E. Hernández-Baños
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 70-399. 04510 Mexico City, MexicoUniversidad Nacional Autónoma de MéxicoMexicoMexico
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7
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Chaplin K, Sumner J, Hipsley CA, Melville J. An Integrative Approach Using Phylogenomics and High-Resolution X-Ray Computed Tomography for Species Delimitation in Cryptic Taxa. Syst Biol 2020; 69:294-307. [PMID: 31372642 DOI: 10.1093/sysbio/syz048] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 06/18/2019] [Accepted: 07/12/2019] [Indexed: 11/14/2022] Open
Abstract
Morphologically cryptic taxa have proved to be a long-standing challenge for taxonomists. Lineages that show strong genomic structuring across the landscape but are phenotypically similar pose a conundrum, with traditional morphological analyses of these cryptic lineages struggling to keep up with species delimitation advances. Micro X-ray computed tomography (CT) combined with geometric morphometric analyses provides a promising avenue for identification of morphologically cryptic taxa, given its ability to detect subtle differences in anatomical structures. However, this approach has yet to be used in combination with genomic data in a comparative analytical framework to distinguish cryptic taxa. We present an integrative approach incorporating genomic and geometric morphometric evidence to assess the species delimitation of grassland earless dragons (Tympanocryptis spp.) in north-eastern Australia. Using mitochondrial and nuclear genes (ND2 and RAG1, respectively), along with $>$8500 SNPs (nuclear single nucleotide polymorphisms), we assess the evolutionary independence of target lineages and several closely related species. We then integrate phylogenomic data with osteological cranial variation between lineages using landmark-based analyses of three-dimensional CT models. High levels of genomic differentiation between the three target lineages were uncovered, also supported by significant osteological differences. By incorporating multiple lines of evidence, we provide strong support for three undescribed cryptic lineages of Tympanocryptis in north-eastern Australia that warrant taxonomic review. Our approach demonstrates the successful application of CT with integrative taxonomic approaches for cryptic species delimitation, which is broadly applicable across vertebrates containing morphologically similar yet genetically distinct lineages. Additionally, we provide a review of recent integrative taxonomic approaches for cryptic species delimitation and an assessment of how our approach can value-add to taxonomic research.
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Affiliation(s)
- Kirilee Chaplin
- Department of Sciences, Museums Victoria, GPO Box 666, Melbourne, Victoria 3001, Australia.,School of BioSciences The University of Melbourne Parkville Campus Victoria 3010, Australia
| | - Joanna Sumner
- Department of Sciences, Museums Victoria, GPO Box 666, Melbourne, Victoria 3001, Australia
| | - Christy A Hipsley
- Department of Sciences, Museums Victoria, GPO Box 666, Melbourne, Victoria 3001, Australia.,School of BioSciences The University of Melbourne Parkville Campus Victoria 3010, Australia
| | - Jane Melville
- Department of Sciences, Museums Victoria, GPO Box 666, Melbourne, Victoria 3001, Australia
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Brasero N, Martinet B, Michez D, Lecocq T, Valterova I, Rasmont P. Taxonomic revision of the Sylvarum group of bumblebees using an integrative approach. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1737843] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Nicolas Brasero
- Research Institute of Biosciences, Laboratory of Zoology, University of Mons, Place du Parc 20, Mons, 7000, Belgium
| | - Baptiste Martinet
- Research Institute of Biosciences, Laboratory of Zoology, University of Mons, Place du Parc 20, Mons, 7000, Belgium
| | - Denis Michez
- Research Institute of Biosciences, Laboratory of Zoology, University of Mons, Place du Parc 20, Mons, 7000, Belgium
| | - Thomas Lecocq
- Research Institute of Biosciences, Laboratory of Zoology, University of Mons, Place du Parc 20, Mons, 7000, Belgium
- INRAe, URAFPA, University of Lorraine, Nancy, F-54000, France
| | - Irena Valterova
- Academy of Sciences of the Czech Republic, Institute of Organic Chemistry and Biochemistry, Flemingovo nám 2, Prague, CZ-166 10, Czech Republic
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Kamýcká 129, Prague, CZ-165 21, Czech Republic
| | - Pierre Rasmont
- Research Institute of Biosciences, Laboratory of Zoology, University of Mons, Place du Parc 20, Mons, 7000, Belgium
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Mângia S, Oliveira EF, Santana DJ, Koroiva R, Paiva F, Garda AA. Revising the taxonomy of
Proceratophrys
Miranda‐Ribeiro, 1920 (Anura: Odontophrynidae) from the Brazilian semiarid Caatinga: Morphology, calls and molecules support a single widespread species. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12365] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sarah Mângia
- Departamento de Sistemática e Ecologia Programa de Pós‐Graduação em Ciências Biológicas (Zoologia) Universidade Federal da Paraı́ba João Pessoa Brazil
| | - Eliana Faria Oliveira
- Instituto de Biociências Universidade Federal de Mato Grosso do Sul Cidade Universitária Campo Grande Brazil
| | - Diego José Santana
- Instituto de Biociências Universidade Federal de Mato Grosso do Sul Cidade Universitária Campo Grande Brazil
| | - Ricardo Koroiva
- Laboratório de Citotaxonomia e Insetos Aquáticos Instituto Nacional de Pesquisas da Amazônia Manaus Brazil
| | - Fernando Paiva
- Instituto de Biociências Universidade Federal de Mato Grosso do Sul Cidade Universitária Campo Grande Brazil
| | - Adrian Antonio Garda
- Departamento de Botânica e Zoologia Universidade Federal do Rio Grande do Norte Natal Brazil
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Wollenberg Valero KC, Marshall JC, Bastiaans E, Caccone A, Camargo A, Morando M, Niemiller ML, Pabijan M, Russello MA, Sinervo B, Werneck FP, Sites JW, Wiens JJ, Steinfartz S. Patterns, Mechanisms and Genetics of Speciation in Reptiles and Amphibians. Genes (Basel) 2019; 10:genes10090646. [PMID: 31455040 PMCID: PMC6769790 DOI: 10.3390/genes10090646] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/21/2019] [Accepted: 08/05/2019] [Indexed: 12/22/2022] Open
Abstract
In this contribution, the aspects of reptile and amphibian speciation that emerged from research performed over the past decade are reviewed. First, this study assesses how patterns and processes of speciation depend on knowing the taxonomy of the group in question, and discuss how integrative taxonomy has contributed to speciation research in these groups. This study then reviews the research on different aspects of speciation in reptiles and amphibians, including biogeography and climatic niches, ecological speciation, the relationship between speciation rates and phenotypic traits, and genetics and genomics. Further, several case studies of speciation in reptiles and amphibians that exemplify many of these themes are discussed. These include studies of integrative taxonomy and biogeography in South American lizards, ecological speciation in European salamanders, speciation and phenotypic evolution in frogs and lizards. The final case study combines genomics and biogeography in tortoises. The field of amphibian and reptile speciation research has steadily moved forward from the assessment of geographic and ecological aspects, to incorporating other dimensions of speciation, such as genetic mechanisms and evolutionary forces. A higher degree of integration among all these dimensions emerges as a goal for future research.
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Affiliation(s)
| | - Jonathon C Marshall
- Department of Zoology, Weber State University, 1415 Edvalson Street, Dept. 2505, Ogden, UT 84401, USA
| | - Elizabeth Bastiaans
- Department of Biology, State University of New York, College at Oneonta, Oneonta, NY 13820, USA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Arley Camargo
- Centro Universitario de Rivera, Universidad de la República, Ituzaingó 667, Rivera 40000, Uruguay
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC, CENPAT-CONICET) Bv. Brown 2915, Puerto Madryn U9120ACD, Argentina
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Maciej Pabijan
- Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, ul. Gronostajowa 9, 30-387 Kraków, Poland
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC V1V 1V7, Canada
| | - Barry Sinervo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Coastal Biology Building, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Fernanda P Werneck
- Programa de Coleções Científicas Biológicas, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus 69060-000, Brazil
| | - Jack W Sites
- Department of Biological and Marine Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, UK
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Sebastian Steinfartz
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, 04103 Leipzig, Germany
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11
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Christodoulou MD, Battey NH, Culham A. Can you make morphometrics work when you know the right answer? Pick and mix approaches for apple identification. PLoS One 2018; 13:e0205357. [PMID: 30321222 PMCID: PMC6188776 DOI: 10.1371/journal.pone.0205357] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 09/24/2018] [Indexed: 11/19/2022] Open
Abstract
Morphological classification of living things has challenged science for several centuries and has led to a wide range of objective morphometric approaches in data gathering and analysis. In this paper we explore those methods using apple cultivars, a model biological system in which discrete groups are pre-defined but in which there is a high level of overall morphological similarity. The effectiveness of morphometric techniques in discovering the groups is evaluated using statistical learning tools. No one technique proved optimal in classification on every occasion, linear morphometric techniques slightly out-performing geometric (72.6% accuracy on test set versus 66.7%). The combined use of these techniques with post-hoc knowledge of their individual successes with particular cultivars achieves a notably higher classification accuracy (77.8%). From this we conclude that even with pre-determined discrete categories, a range of approaches is needed where those categories are intrinsically similar to each other, and we raise the question of whether in studies where potentially continuous natural variation is being categorised the level of match between categories is routinely set too high.
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Affiliation(s)
- Maria D. Christodoulou
- University of Reading Herbarium, Harborne Building, School of Biological Sciences, University of Reading, Whiteknights, Reading, United Kingdom
| | - Nicholas Hugh Battey
- School of Biological Sciences, University of Reading, Whiteknights Reading, United Kingdom
| | - Alastair Culham
- University of Reading Herbarium, Harborne Building, School of Biological Sciences, University of Reading, Whiteknights, Reading, United Kingdom
- * E-mail:
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12
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Cadena CD, Zapata F, Jiménez I. Issues and Perspectives in Species Delimitation using Phenotypic Data: Atlantean Evolution in Darwin's Finches. Syst Biol 2018; 67:181-194. [PMID: 28945876 DOI: 10.1093/sysbio/syx071] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/30/2017] [Indexed: 11/13/2022] Open
Abstract
Progress in the development and use of methods for species delimitation employing phenotypic data lags behind conceptual and practical advances in molecular genetic approaches. The basic evolutionary model underlying the use of phenotypic data to delimit species assumes random mating and quantitative polygenic traits, so that phenotypic distributions within a species should be approximately normal for individuals of the same sex and age. Accordingly, two or more distinct normal distributions of phenotypic traits suggest the existence of multiple species. In light of this model, we show that analytical approaches employed in taxonomic studies using phenotypic data are often compromised by three issues: 1) reliance on graphical analyses that convey little information on phenotype frequencies; 2) exclusion of characters potentially important for species delimitation following reduction of data dimensionality; and 3) use of measures of central tendency to evaluate phenotypic distinctiveness. We outline approaches to overcome these issues based on statistical developments related to normal mixture models (NMMs) and illustrate them empirically with a reanalysis of morphological data recently used to claim that there are no morphologically distinct species of Darwin's ground-finches (Geospiza). We found negligible support for this claim relative to taxonomic hypotheses recognizing multiple species. Although species limits among ground-finches merit further assessments using additional sources of information, our results bear implications for other areas of inquiry including speciation research: because ground-finches have likely speciated and are not trapped in a process of "Sisyphean" evolution as recently argued, they remain useful models to understand the evolutionary forces involved in speciation. Our work underscores the importance of statistical approaches grounded on appropriate evolutionary models for species delimitation. We discuss how NMMs offer new perspectives in the kind of inferences available to systematists, with significant repercussions on ideas about the phenotypic structure of biodiversity.
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Affiliation(s)
| | - Felipe Zapata
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Iván Jiménez
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St. Louis, MO, USA
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Dai C, Hao Y, He Y, Lei F. The absence of reproductive isolation between non-sister and deeply diverged mitochondrial lineages of the black-throated tit (Aegithalos concinnus) revealed by a multilocus genetic analysis in a contact zone. BMC Evol Biol 2017; 17:266. [PMID: 29262786 PMCID: PMC5738821 DOI: 10.1186/s12862-017-1114-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 12/11/2017] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND A deep divergence of mitochondrial DNA is common in species delimitated by morphological traits. Several hypotheses can explain such variations, such as cryptic species, introgression, allopatric divergence and ancestral lineage. The black-throated tit harbors several deeply divergent mitochondrial lineages. Two lineages with 5% divergence, but having a high level of gene flow, have been detected in its subspecies, A. C. concinnus and A. c. talifuenses. In this study, we conducted a genetic analysis at a contact zone of these two lineages to identify whether these lineages either reflect a high level of intraspecific variation in mitochondrial loci or represent incipient speciation. Mitochondrial ND2 and 11 microsatellite loci were used to conduct phylogenetic and population structure analyses. RESULTS ND2 haplotypes actually diverged into two groups within subspecies A. c. talifuenses; however, they formed a non-sister relationship when including all available GenBank ND2 sequences. Analyses of microsatellite data indicated no existing population structure and showed a pattern of isolation by distance. Individuals sampled at the contact zone were almost identified as F2 hybrids. CONCLUSIONS Isolation for 2.4 Ma, as suggested by a previous study, appeared to be insufficient to develop robust reproductive barriers. Reproductive barriers were weak, or even absent between the divergent lineages, highlighting that incipient speciation was unlikely to be the case. Considering the results from previous studies, the divergent lineages may be better explained by secondary contact after allopatric isolation because of Pleistocene climate changes, but other hypotheses cannot be definitively ruled out because of the lack of representative samples from the other distribution region and its relatives. Considering that divergence in morphology was hardly observed and the particular split in genetics, the two subspecies might be better merged. The current findings also highlight the likely contribution of male-biased dispersal to male-biased gene flow among mitochondrial lineages; more efforts are needed to illustrate the evolutionary history of the black-throated tit.
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Affiliation(s)
- Chuanyin Dai
- School of Chemistry and Life Sciences, Guizhou Normal College, Gaoxin Road 115, Guiyang, Guizhou 550018 China
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beichen Xi Road 1, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yong He
- School of Chemistry and Life Sciences, Guizhou Normal College, Gaoxin Road 115, Guiyang, Guizhou 550018 China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beichen Xi Road 1, Beijing, 100101 China
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Dupuis JR, Mcdonald CM, Acorn JH, Sperling FAH. Genomics-informed species delimitation to support morphological identification of anglewing butterflies (Lepidoptera: Nymphalidae: Polygonia). Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Julian R Dupuis
- Department of Plant and Environmental Protection Sciences, University of Hawai’i at Mānoa, Honolulu, HI, USA
- Department of Biological Sciences, CW 405 Biosciences Centre, University of Alberta, Edmonton, AB, Canada
| | - Christianne M Mcdonald
- Department of Biological Sciences, CW 405 Biosciences Centre, University of Alberta, Edmonton, AB, Canada
| | - John H Acorn
- Department of Renewable Resources, University of Alberta, Edmonton, AB, Canada
| | - Felix A H Sperling
- Department of Biological Sciences, CW 405 Biosciences Centre, University of Alberta, Edmonton, AB, Canada
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Time to Spread Your Wings: A Review of the Avian Ancient DNA Field. Genes (Basel) 2017; 8:genes8070184. [PMID: 28718817 PMCID: PMC5541317 DOI: 10.3390/genes8070184] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/27/2017] [Accepted: 07/10/2017] [Indexed: 01/16/2023] Open
Abstract
Ancient DNA (aDNA) has the ability to inform the evolutionary history of both extant and extinct taxa; however, the use of aDNA in the study of avian evolution is lacking in comparison to other vertebrates, despite birds being one of the most species-rich vertebrate classes. Here, we review the field of “avian ancient DNA” by summarising the past three decades of literature on this topic. Most studies over this time have used avian aDNA to reconstruct phylogenetic relationships and clarify taxonomy based on the sequencing of a few mitochondrial loci, but recent studies are moving toward using a comparative genomics approach to address developmental and functional questions. Applying aDNA analysis with more practical outcomes in mind (such as managing conservation) is another increasingly popular trend among studies that utilise avian aDNA, but the majority of these have yet to influence management policy. We find that while there have been advances in extracting aDNA from a variety of avian substrates including eggshell, feathers, and coprolites, there is a bias in the temporal focus; the majority of the ca. 150 studies reviewed here obtained aDNA from late Holocene (100–1000 yBP) material, with few studies investigating Pleistocene-aged material. In addition, we identify and discuss several other issues within the field that require future attention. With more than one quarter of Holocene bird extinctions occurring in the last several hundred years, it is more important than ever to understand the mechanisms driving the evolution and extinction of bird species through the use of aDNA.
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Olave M, Avila LJ, Sites JW, Morando M. Hidden diversity within the lizard genus Liolaemus: Genetic vs morphological divergence in the L. rothi complex (Squamata:Liolaeminae). Mol Phylogenet Evol 2017; 107:56-63. [DOI: 10.1016/j.ympev.2016.09.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 07/25/2016] [Accepted: 09/12/2016] [Indexed: 11/29/2022]
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17
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Huang Y, Hu J, Wang B, Song Z, Zhou C, Jiang J. Integrative taxonomy helps to reveal the mask of the genus Gynandropaa (Amphibia: Anura: Dicroglossidae). Integr Zool 2016; 11:134-50. [PMID: 26531851 DOI: 10.1111/1749-4877.12169] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Species of the genus Gynandropaa within the family Dicroglossidae are typical spiny frogs whose taxonomic status has long been in doubt. We used integrative methods, involving morphological and molecular analyses, to elucidate the phylogenetic relationships, and to determine identities and the geographic distribution of each valid species. We obtained DNA sequence data of 5 species of Gynandropaa (complete sequences of the mitochondrial NADH dehydrogenase subunit 2 [ND2] gene, and 890 bp of 12S rRNA and 16S rRNA partial sequences) from 37 localities (including the topotypes of 5 described species) and constructed Bayesian and maximum-likelihood trees to examine the patterns of phylogeography. A total of 28 morphological variables were taken on 624 specimens. Three clades with clear geographic patterns were recognized: clade C (from south-western Sichuan Province and central Yunnan Province), clade E (western Guizhou Province and eastern to central Yunnan Province) and clade W (western to southern Yunnan Province). Integrating morphological characteristics and distribution information, the clades W, E and C represent Gynandropaa yunnanensis, G. phrynoides and G. sichuanensis, respectively. We draw the following conclusions: (i) the taxon G. phrynoides, formerly evaluated as a junior synonym of G. yunnanensis, is revalidated herein at the rank of species; (ii) G. liui is a junior synonym of G. sichuanensis; and (iii) G. yunnanensis is a valid species while G. bourreti is probably a subspecies of G. yunnanensis, with the distribution range from Vietnam to southern Yunnan Province. This study clears up the taxonomic status of Gynandropaa and provides important information for understanding the evolution and conservation of these spiny frogs.
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Affiliation(s)
- Yan Huang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,College of Life Science, Sichuan University, Chengdu, China.,University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Southwest China Wildlife Resources Conservation, China West Normal University, Ministry of Education, Nanchong, China
| | - Junhua Hu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Bin Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zhaobin Song
- College of Life Science, Sichuan University, Chengdu, China
| | - Caiquan Zhou
- Key Laboratory of Southwest China Wildlife Resources Conservation, China West Normal University, Ministry of Education, Nanchong, China
| | - Jianping Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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Aguilar C, Wood PL, Belk MC, Duff MH, Sites JW. Different roads lead to Rome: Integrative taxonomic approaches lead to the discovery of two new lizard lineages in theLiolaemus montanusgroup (Squamata: Liolaemidae). Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12890] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Cesar Aguilar
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University (BYU); Provo UT 84602 USA
- Departamento de Herpetologia; Museo de Historia Natural de San Marcos (MUSM); Av. Arenales 1256, Jesus Maria Lima Peru
- Facultad de Ciencias Biologicas; Instituto de Ciencias Biologicas Antonio Raimondi; Universidad Nacional Mayor de San Marcos; Lima Peru
| | - Perry L. Wood
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University (BYU); Provo UT 84602 USA
| | - Mark C. Belk
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University (BYU); Provo UT 84602 USA
| | - Mike H. Duff
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University (BYU); Provo UT 84602 USA
| | - Jack W. Sites
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University (BYU); Provo UT 84602 USA
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Breitman MF, Bonino MF, Sites JW, Avila LJ, Morando M. Morphological Variation, Niche Divergence, and Phylogeography of Lizards of the Liolaemus lineomaculatus Section (Liolaemini) from Southern Patagonia. HERPETOLOGICAL MONOGRAPHS 2015. [DOI: 10.1655/herpmonographs-d-14-00003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- M. Florencia Breitman
- CENPAT–Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Patagónico para el Estudio de Ecosistemas Continentales, Boulevard Almirante Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina
| | - Marcelo F. Bonino
- INIBIOMA (CONICET-UNCOMA), Laboratorio de Fotobiología, Centro Regional Universitario Bariloche, Quintral 1250, 8400, Bariloche, Río Negro, Argentina
| | - Jack W. Sites
- Brigham Young University, Life Sciences Building, Biology Department, Provo, UT 84602, USA
| | - Luciano J. Avila
- CENPAT–Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Patagónico para el Estudio de Ecosistemas Continentales, Boulevard Almirante Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina
| | - Mariana Morando
- CENPAT–Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Patagónico para el Estudio de Ecosistemas Continentales, Boulevard Almirante Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina
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Saitoh T, Sugita N, Someya S, Iwami Y, Kobayashi S, Kamigaichi H, Higuchi A, Asai S, Yamamoto Y, Nishiumi I. DNA barcoding reveals 24 distinct lineages as cryptic bird species candidates in and around the Japanese Archipelago. Mol Ecol Resour 2014; 15:177-86. [PMID: 24835119 DOI: 10.1111/1755-0998.12282] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 05/01/2014] [Accepted: 05/05/2014] [Indexed: 11/29/2022]
Abstract
DNA barcoding using a partial region (648 bp) of the cytochrome c oxidase I (COI) gene is a powerful tool for species identification and has revealed many cryptic species in various animal taxa. In birds, cryptic species are likely to occur in insular regions like the Japanese Archipelago due to the prevention of gene flow by sea barriers. Using COI sequences of 234 of the 251 Japanese-breeding bird species, we established a DNA barcoding library for species identification and estimated the number of cryptic species candidates. A total of 226 species (96.6%) had unique COI sequences with large genetic divergence among the closest species based on neighbour-joining clusters, genetic distance criterion and diagnostic substitutions. Eleven cryptic species candidates were detected, with distinct intraspecific deep genetic divergences, nine lineages of which were geographically separated by islands and straits within the Japanese Archipelago. To identify Japan-specific cryptic species from trans-Paleartic birds, we investigated the genetic structure of 142 shared species over an extended region covering Japan and Eurasia; 19 of these species formed two or more clades with high bootstrap values. Excluding six duplicated species from the total of 11 species within the Japanese Archipelago and 19 trans-Paleartic species, we identified 24 species that were cryptic species candidates within and surrounding the Japanese Archipelago. Repeated sea level changes during the glacial and interglacial periods may be responsible for the deep genetic divergences of Japanese birds in this insular region, which has led to inconsistencies in traditional taxonomies based on morphology.
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Affiliation(s)
- Takema Saitoh
- Division of Natural History, Yamashina Institute for Ornithology, 115 Konoyama, Abiko, Chiba, 270-1145, Japan
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