1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Schär S, Menchetti M, Schifani E, Hinojosa JC, Platania L, Dapporto L, Vila R. Integrative biodiversity inventory of ants from a Sicilian archipelago reveals high diversity on young volcanic islands (Hymenoptera: Formicidae). ORG DIVERS EVOL 2020. [DOI: 10.1007/s13127-020-00442-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Obertegger U, Cieplinski A, Fontaneto D, Papakostas S. Mitonuclear discordance as a confounding factor in the DNA taxonomy of monogonont rotifers. ZOOL SCR 2017. [DOI: 10.1111/zsc.12264] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ulrike Obertegger
- Research and Innovation Centre; Fondazione Edmund Mach (FEM); San Michele all'Adige Italy
| | - Adam Cieplinski
- Research and Innovation Centre; Fondazione Edmund Mach (FEM); San Michele all'Adige Italy
- Research Institute for Limnology; Mondsee University of Innsbruck; Mondsee Austria
| | - Diego Fontaneto
- Consiglio Nazionale delle Ricerche; Istituto per lo Studio degli Ecosistemi; Verbania Pallanza Italy
| | | |
Collapse
|
5
|
Ait Belkacem A, Gast O, Stuckas H, Canal D, LoValvo M, Giacalone G, Päckert M. North African hybrid sparrows (Passer domesticus, P. hispaniolensis) back from oblivion - ecological segregation and asymmetric mitochondrial introgression between parental species. Ecol Evol 2016; 6:5190-206. [PMID: 27551376 PMCID: PMC4984497 DOI: 10.1002/ece3.2274] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 05/31/2016] [Accepted: 06/03/2016] [Indexed: 01/23/2023] Open
Abstract
A stabilized hybrid form of the house sparrow (Passer domesticus) and the Spanish sparrow (P. hispaniolensis) is known as Passer italiae from the Italian Peninsula and a few Mediterranean islands. The growing attention for the Italian hybrid sparrow and increasing knowledge on its biology and genetic constitution greatly contrast the complete lack of knowledge of the long‐known phenotypical hybrid sparrow populations from North Africa. Our study provides new data on the breeding biology and variation of mitochondrial DNA in three Algerian populations of house sparrows, Spanish sparrows, and phenotypical hybrids. In two field seasons, the two species occupied different breeding habitats: Spanish sparrows were only found in rural areas outside the cities and bred in open‐cup nests built in large jujube bushes. In contrast, house sparrows bred only in the town centers and occupied nesting holes in walls of buildings. Phenotypical hybrids were always associated with house sparrow populations. House sparrows and phenotypical hybrids started breeding mid of March, and most pairs had three successive clutches, whereas Spanish sparrows started breeding almost one month later and had only two successive clutches. Mitochondrial introgression is strongly asymmetric because about 75% of the rural Spanish sparrow population carried house sparrow haplotypes. In contrast, populations of the Italian hybrid form, P. italiae, were genetically least diverse among all study populations and showed a near‐fixation of house sparrow haplotypes that elsewhere were extremely rare or that were even unique for the Italian Peninsula. Such differences between mitochondrial gene pools of Italian and North African hybrid sparrow populations provide first evidence that different demographic histories have shaped the extant genetic diversity observed on both continents.
Collapse
Affiliation(s)
- Abdelkrim Ait Belkacem
- Faculty of Sciences of nature and lifes Department of Agropastoralism University of Djelfa BP. 3117 17000 Djelfa Algeria
| | - Oliver Gast
- Senckenberg Naturhistorische Sammlungen Königsbrücker Landstraße 159D-01109 Dresden Germany; Institute of Vertebrate Biology Czech Academy of Sciences External Research Facility Studenec Studenec 122675 02 Koněšín Czech Republic
| | - Heiko Stuckas
- Senckenberg Naturhistorische Sammlungen Königsbrücker Landstraße 159 D-01109 Dresden Germany
| | - David Canal
- Department of Evolutionary Ecology Estación Biológica de Doñana - CSIC Avda. Américo Vespucio s/n 41092 Seville Spain
| | - Mario LoValvo
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche Via Archirafi 18 I-90123 Palermo Italy
| | | | - Martin Päckert
- Senckenberg Naturhistorische Sammlungen Königsbrücker Landstraße 159 D-01109 Dresden Germany
| |
Collapse
|
6
|
Genetic assessment of the threatened microendemic Pleurodeles poireti (Caudata, Salamandridae), with molecular evidence for hybridization with Pleurodeles nebulosus. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0875-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
7
|
Papakostas S, Michaloudi E, Proios K, Brehm M, Verhage L, Rota J, Peña C, Stamou G, Pritchard VL, Fontaneto D, Declerck SAJ. Integrative Taxonomy Recognizes Evolutionary Units Despite Widespread Mitonuclear Discordance: Evidence from a Rotifer Cryptic Species Complex. Syst Biol 2016; 65:508-24. [DOI: 10.1093/sysbio/syw016] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 02/09/2016] [Indexed: 01/23/2023] Open
|
8
|
Rato C, Harris DJ, Perera A, Carvalho SB, Carretero MA, Rödder D. A Combination of Divergence and Conservatism in the Niche Evolution of the Moorish Gecko, Tarentola mauritanica (Gekkota: Phyllodactylidae). PLoS One 2015; 10:e0127980. [PMID: 26000981 PMCID: PMC4441378 DOI: 10.1371/journal.pone.0127980] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 04/21/2015] [Indexed: 11/30/2022] Open
Abstract
The quantification of realized niche overlap and the integration of species distribution models (SDMs) with calibrated phylogenies to study niche evolution are becoming not only powerful tools to understand speciation events, but can also be used as proxies regarding the delimitation of cryptic species. We applied these techniques in order to unravel how the fundamental niche evolved during cladogenesis within the Tarentola mauritanica species-complex. Our results suggest that diversification within this complex, during the Miocene and Pleistocene, is associated with both niche divergence and niche conservatism, with a pattern that varies depending on whether the variables involved are related to the mean or seasonality of temperature and humidity. Moreover, climatic variables related to humidity and temperature seasonality were involved in the niche shift and genetic diversification of the European/North African clade during the Pleistocene and in its maintenance in a fundamental niche distinct from that of the remaining members of the group. This study further highlights the need for a taxonomic revision of the T. mauritanica species-complex.
Collapse
Affiliation(s)
- Catarina Rato
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, Vairão, Vila do Conde, Portugal
| | - David James Harris
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, Vairão, Vila do Conde, Portugal
| | - Ana Perera
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, Vairão, Vila do Conde, Portugal
| | - Silvia B. Carvalho
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, Vairão, Vila do Conde, Portugal
| | - Miguel A. Carretero
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, Vairão, Vila do Conde, Portugal
| | - Dennis Rödder
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| |
Collapse
|
9
|
Wielstra B, Arntzen JW, van der Gaag KJ, Pabijan M, Babik W. Data concatenation, Bayesian concordance and coalescent-based analyses of the species tree for the rapid radiation of Triturus newts. PLoS One 2014; 9:e111011. [PMID: 25337997 PMCID: PMC4206468 DOI: 10.1371/journal.pone.0111011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 09/22/2014] [Indexed: 11/18/2022] Open
Abstract
The phylogenetic relationships for rapid species radiations are difficult to disentangle. Here we study one such case, namely the genus Triturus, which is composed of the marbled and crested newts. We analyze data for 38 genetic markers, positioned in 3-prime untranslated regions of protein-coding genes, obtained with 454 sequencing. Our dataset includes twenty Triturus newts and represents all nine species. Bayesian analysis of population structure allocates all individuals to their respective species. The branching patterns obtained by data concatenation, Bayesian concordance analysis and coalescent-based estimations of the species tree differ from one another. The data concatenation based species tree shows high branch support but branching order is considerably affected by allele choice in the case of heterozygotes in the concatenation process. Bayesian concordance analysis expresses the conflict between individual gene trees for part of the Triturus species tree as low concordance factors. The coalescent-based species tree is relatively similar to a previously published species tree based upon morphology and full mtDNA and any conflicting internal branches are not highly supported. Our findings reflect high gene tree discordance due to incomplete lineage sorting (possibly aggravated by hybridization) in combination with low information content of the markers employed (as can be expected for relatively recent species radiations). This case study highlights the complexity of resolving rapid radiations and we acknowledge that to convincingly resolve the Triturus species tree even more genes will have to be consulted.
Collapse
Affiliation(s)
- Ben Wielstra
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- * E-mail:
| | | | | | - Maciej Pabijan
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
- Institute of Zoology, Jagiellonian University, Kraków, Poland
| | - Wieslaw Babik
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| |
Collapse
|
10
|
Wielstra B, Sillero N, Vörös J, Arntzen JW. The distribution of the crested and marbled newt species (Amphibia: Salamandridae: Triturus) – an addition to the New Atlas of Amphibians and Reptiles of Europe. AMPHIBIA-REPTILIA 2014. [DOI: 10.1163/15685381-00002960] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In the recently published New Atlas of Amphibians and Reptiles of Europe (Sillero et al., 2014a), the distribution of the newt genusTrituruswas not resolved at the level of the species. The main reason for this was the lack of high quality distribution data from in and around the parapatric contact zones between species, where interspecific hybridization occurs. We are working extensively onTriturusand the (particularly genetic) data we have accumulated allow us to map the individualTriturusspecies at the appropriate scale. We here provide a database composed of distribution data for the individual species, at generally high resolution, particularly from in and around contact zones. Based on this database we produce maps at the 50 × 50 km UTM grid resolution as used in the new atlas and highlight those grid cells in which more than oneTriturusspecies occurs.
Collapse
Affiliation(s)
- Ben Wielstra
- Department of Animal and Plant Sciences, University of Sheffield, S10 2TN Sheffield, UK
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
| | - Neftalí Sillero
- Centro de Investigação em Ciências Geo-Espaciais, Observatório Astronómico Prof. Manuel de Barros, Alameda do Monte da Virgem, 4430-146 Vila Nova de Gaia, Portugal
| | - Judit Vörös
- Department of Zoology, Hungarian Natural History Museum, 1088 Budapest, Hungary
| | - Jan W. Arntzen
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
| |
Collapse
|