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Oswald CB, de Magalhães RF, Garcia PC, Santos FR, Neckel-Oliveira S. Integrative species delimitation helps to find the hidden diversity of the leaf-litter frog Ischnocnema manezinho (Garcia, 1996) (Anura, Brachycephalidae), endemic to the southern Atlantic Forest. PeerJ 2023; 11:e15393. [PMID: 37250715 PMCID: PMC10225124 DOI: 10.7717/peerj.15393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 04/20/2023] [Indexed: 05/31/2023] Open
Abstract
Background The delimitation of cryptic species is a challenge for biodiversity conservation. Anurans show high cryptic diversity levels, and molecular species delimitation methods could help identify putative new species. Additionally, species delimitation approaches can provide important results for cryptic species conservation, with integrative methods adding robustness to results. Ischnocnema manezinho was described from Santa Catarina Island (SCI), southern Brazil. More recently, some inventories indicated continental populations supposedly similar in morphology to it. If these records are confirmed as I. manezinho, it would likely change its endangered status on National Red List, removing the species from conservation agendas. We investigated the threatened frog Ischnocnema manezinho, to evaluate if the continental populations belong to this species or if they form an undescribed species complex. Methods We used coalescent, distance, and allele-sharing-based species delimitation methods and integrative analyses of morphometric and bioacoustics traits to test evolutionary independence between I. manezinho from SCI, Arvoredo Island, and continental populations. Results Ischnocnema manezinho is restricted to Santa Catarina Island, while the five remaining lineages should be further investigated through a taxonomic review. Our results point to a small geographic range of Ischnocnema manezinho. Additionally, the species occurs in isolated fragments of forest in SCI surrounded by expanding urban areas, confirming its status as Endangered. Thus, the protection and monitoring of I. manezinho and the taxonomic description of the continental and Arvoredo Island candidate species should be priorities.
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Affiliation(s)
- Caroline Batistim Oswald
- Programa de Pós-Graduação em Zoologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rafael Félix de Magalhães
- Programa de Pós-Graduação em Zoologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Departamento de Ciências Naturais, Universidade Federal de São João del-Rei, São João del-Rei, Brazil
| | - Paulo C.A. Garcia
- Programa de Pós-Graduação em Zoologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Departamento de Ecologia e Zoologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Fabrício R. Santos
- Programa de Pós-Graduação em Zoologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Selvino Neckel-Oliveira
- Programa de Pós-Graduação em Zoologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Departamento de Ecologia e Zoologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
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2
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Brandt S, Sole C, Lyle R. The phylogenetic structure and coalescent species delimitation of an endemic trapdoor spider genus, Stasimopus (Araneae, Mygalomorphae, Stasimopidae) in the Karoo region of South Africa. Mol Phylogenet Evol 2023; 184:107798. [PMID: 37094612 DOI: 10.1016/j.ympev.2023.107798] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 03/30/2023] [Accepted: 04/18/2023] [Indexed: 04/26/2023]
Abstract
The Karoo region of South Africa is a unique and sensitive ecosystem which is facing pressure for development due to economic incentives such as mining, farming and shale gas exploration. The species diversity of many taxa in the area is largely unknown. A phylogenetic analysis of the cork-lid trapdoor spider genus, Stasimopus (Stasimopidae) was undertaken in order to gain insight into the relationships between the species that may be present in the area. The species within Stasimopus are challenging to identify and define using traditional morphological methods due to a high degree of morphological conservatism within the genus. For this reason, multiple coalescent based species delimitation methods were used to attempt to determine the species present for Stasimopus in the region which was tested against the morphological identifications and genetic clades (based on CO1, 16S and EF-1ɣ). We tested single-locus methods Automatic Barcode Gap Discovery (ABGD), Bayesian implementation of Poisson Tree Processes (bPTP) and General Mixed Yule- Coalescent (GMYC), as well as multi-locus Brownie. The phylogenetic analysis of Stasimopus in the Karoo showed that there is a high degree of genetic diversity within the genus. The species delimitation results proved unfruitful for the genus, as they appear to delimit population structure rather than species for most methods. Alternative methods should be investigated to aid in the identification of the species in order truly understand the species diversity of the genus.
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Affiliation(s)
- Shannon Brandt
- Department of Zoology and Entomology, University of Pretoria, Hatfield, Pretoria, South Africa.
| | - Catherine Sole
- Department of Zoology and Entomology, University of Pretoria, Hatfield, Pretoria, South Africa.
| | - Robin Lyle
- Agricultural Research Council - Plant Health and Protection, Biosystematics, Roodeplaat, Pretoria, South Africa
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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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Leaché AD, Davis HR, Singhal S, Fujita MK, Lahti ME, Zamudio KR. Phylogenomic Assessment of Biodiversity Using a Reference-Based Taxonomy: An Example With Horned Lizards (Phrynosoma). Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.678110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Phylogenomic investigations of biodiversity facilitate the detection of fine-scale population genetic structure and the demographic histories of species and populations. However, determining whether or not the genetic divergence measured among populations reflects species-level differentiation remains a central challenge in species delimitation. One potential solution is to compare genetic divergence between putative new species with other closely related species, sometimes referred to as a reference-based taxonomy. To be described as a new species, a population should be at least as divergent as other species. Here, we develop a reference-based taxonomy for Horned Lizards (Phrynosoma; 17 species) using phylogenomic data (ddRADseq data) to provide a framework for delimiting species in the Greater Short-horned Lizard species complex (P. hernandesi). Previous species delimitation studies of this species complex have produced conflicting results, with morphological data suggesting that P. hernandesi consists of five species, whereas mitochondrial DNA support anywhere from 1 to 10 + species. To help address this conflict, we first estimated a time-calibrated species tree for P. hernandesi and close relatives using SNP data. These results support the paraphyly of P. hernandesi; we recommend the recognition of two species to promote a taxonomy that is consistent with species monophyly. There is strong evidence for three populations within P. hernandesi, and demographic modeling and admixture analyses suggest that these populations are not reproductively isolated, which is consistent with previous morphological analyses that suggest hybridization could be common. Finally, we characterize the population-species boundary by quantifying levels of genetic divergence for all 18 Phrynosoma species. Genetic divergence measures for western and southern populations of P. hernandesi failed to exceed those of other Phrynosoma species, but the relatively small population size estimated for the northern population causes it to appear as a relatively divergent species. These comparisons underscore the difficulties associated with putting a reference-based approach to species delimitation into practice. Nevertheless, the reference-based approach offers a promising framework for the consistent assessment of biodiversity within clades of organisms with similar life histories and ecological traits.
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5
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Mason NA, Fletcher NK, Gill BA, Funk WC, Zamudio KR. Coalescent-based species delimitation is sensitive to geographic sampling and isolation by distance. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1730475] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Nicholas A. Mason
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, New York 14853, USA
| | - Nicholas K. Fletcher
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, New York 14853, USA
| | - Brian A. Gill
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - W. Chris Funk
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Kelly R. Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, New York 14853, USA
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Pie MR, Bornschein MR, Ribeiro LF, Faircloth BC, McCormack JE. Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest. Mol Phylogenet Evol 2019; 141:106627. [PMID: 31539606 DOI: 10.1016/j.ympev.2019.106627] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 08/17/2019] [Accepted: 09/17/2019] [Indexed: 10/26/2022]
Abstract
The advent of next-generation sequencing allows researchers to use large-scale datasets for species delimitation analyses, yet one can envision an inflection point where the added accuracy of including more loci does not offset the increased computational burden. One alternative to including all loci could be to prioritize the analysis of loci for which there is an expectation of high informativeness. Here, we explore the issue of species delimitation and locus selection with montane species from two anuran genera that have been isolated in sky islands across the southern Brazilian Atlantic Forest: Melanophryniscus (Bufonidae) and Brachycephalus (Brachycephalidae). To delimit species, we obtained genetic data using target enrichment of ultraconserved elements from 32 populations (13 for Melanophryniscus and 19 for Brachycephalus), and we were able to create datasets that included over 800 loci with no missing data. We ranked loci according to their number of parsimony-informative sites, and we performed species delimitation analyses using BPP with the most informative 10, 20, 40, 80, 160, 320, and 640 loci. We identified three types of phylogenetic node: nodes with either consistently high or low support regardless of the number of loci or their informativeness and nodes that were initially poorly supported where support became stronger as we included more data. When viewed across all sensitivity analyses, our results suggest that the current species richness in both genera is likely underestimated. In addition, our results show the effects of different sampling strategies on species delimitation using phylogenomic datasets.
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Affiliation(s)
- Marcio R Pie
- Departamento de Zoologia, Universidade Federal do Paraná, CEP 81531-980 Curitiba, Paraná, Brazil; Mater Natura - Instituto de Estudos Ambientais, CEP 80250-020 Curitiba, Paraná, Brazil.
| | - Marcos R Bornschein
- Mater Natura - Instituto de Estudos Ambientais, CEP 80250-020 Curitiba, Paraná, Brazil; Instituto de Biociências, Universidade Estadual Paulista, Praça Infante Dom Henrique s/no, Parque Bitaru, CEP 11330-900 São Vicente, São Paulo, Brazil
| | - Luiz F Ribeiro
- Mater Natura - Instituto de Estudos Ambientais, CEP 80250-020 Curitiba, Paraná, Brazil; Escola de Ciências da Vida, Pontifícia Universidade Católica do Paraná, CEP 80215-901 Curitiba, Paraná, Brazil
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - John E McCormack
- Moore Laboratory of Zoology, Occidental College, 1600 Campus Road, Los Angeles, CA 90041, USA
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8
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Coalescent-based species delimitation in the sand lizards of the Liolaemus wiegmannii complex (Squamata: Liolaemidae). Mol Phylogenet Evol 2019; 138:89-101. [DOI: 10.1016/j.ympev.2019.05.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/21/2019] [Accepted: 05/21/2019] [Indexed: 12/20/2022]
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9
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Different species or genetically divergent populations? Integrative species delimitation of the Primulina hochiensis complex from isolated karst habitats. Mol Phylogenet Evol 2019; 132:219-231. [DOI: 10.1016/j.ympev.2018.12.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 12/09/2018] [Accepted: 12/09/2018] [Indexed: 12/15/2022]
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10
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Johnson NA, Smith CH, Pfeiffer JM, Randklev CR, Williams JD, Austin JD. Integrative taxonomy resolves taxonomic uncertainty for freshwater mussels being considered for protection under the U.S. Endangered Species Act. Sci Rep 2018; 8:15892. [PMID: 30367102 PMCID: PMC6203750 DOI: 10.1038/s41598-018-33806-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 10/07/2018] [Indexed: 11/30/2022] Open
Abstract
Objectively delimiting species boundaries remains an important challenge in systematics and becomes urgent when unresolved taxonomy complicates conservation and recovery efforts. We examined species boundaries in the imperiled freshwater mussel genus Cyclonaias (Bivalvia: Unionidae) using morphometrics, molecular phylogenetics, and multispecies coalescent models to help guide pending conservation assessments and legislative decisions. Congruence across multiple lines of evidence indicated that current taxonomy overestimates diversity in the C. pustulosa species complex. The only genetically and morphologically diagnosable species in the C. pustulosa species complex were C. pustulosa and C. succissa and we consider C. aurea, C. houstonensis, C. mortoni, and C. refulgens to be synonyms of C. pustulosa. In contrast, all three species in the C. nodulata complex (C. necki, C. nodulata, and C. petrina) were genetically, geographically, and morphologically diagnosable. Our findings have important conservation and management implications, as three nominal species (C. aurea, C. houstonensis, and C. petrina) are being considered for protection under the Endangered Species Act.
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Affiliation(s)
- Nathan A Johnson
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, 32653, USA.
| | - Chase H Smith
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, 32653, USA.,Baylor University, Biology Department, Waco, TX, 76798, USA
| | - John M Pfeiffer
- University of Florida, Florida Museum, Gainesville, FL, 32611, USA
| | - Charles R Randklev
- Texas A&M Natural Resources Institute and AgriLife Research Center, Dallas, TX, 75252, USA
| | - James D Williams
- University of Florida, Florida Museum, Gainesville, FL, 32611, USA
| | - James D Austin
- Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, 32601, USA
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11
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Lagourgue L, Puillandre N, Payri CE. Exploring the Udoteaceae diversity (Bryopsidales, Chlorophyta) in the Caribbean region based on molecular and morphological data. Mol Phylogenet Evol 2018; 127:758-769. [DOI: 10.1016/j.ympev.2018.06.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 06/03/2018] [Accepted: 06/11/2018] [Indexed: 11/26/2022]
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12
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Reyes-Velasco J, Manthey JD, Bourgeois Y, Freilich X, Boissinot S. Revisiting the phylogeography, demography and taxonomy of the frog genus Ptychadena in the Ethiopian highlands with the use of genome-wide SNP data. PLoS One 2018; 13:e0190440. [PMID: 29389966 PMCID: PMC5794058 DOI: 10.1371/journal.pone.0190440] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 12/14/2017] [Indexed: 11/18/2022] Open
Abstract
Understanding the diversification of biological lineages is central to evolutionary studies. To properly study the process of speciation, it is necessary to link micro-evolutionary studies with macro-evolutionary mechanisms. Micro-evolutionary studies require proper sampling across a taxon's range to adequately infer genetic diversity. Here we use the grass frogs of the genus Ptychadena from the Ethiopian highlands as a model to study the process of lineage diversification in this unique biodiversity hotspot. We used thousands of genome-wide SNPs obtained from double digest restriction site associated DNA sequencing (ddRAD-seq) in populations of the Ptychadena neumanni species complex from the Ethiopian highlands in order to infer their phylogenetic relationships and genetic structure, as well as to study their demographic history. Our genome-wide phylogenetic study supports the existence of approximately 13 lineages clustered into 3 species groups. Our phylogenetic and phylogeographic reconstructions suggest that those endemic lineages diversified in allopatry, and subsequently specialized to different habitats and elevations. Demographic analyses point to a continuous decrease in the population size across the majority of lineages and populations during the Pleistocene, which is consistent with a continuous period of aridification that East Africa experienced since the Pliocene. We discuss the taxonomic implications of our analyses and, in particular, we warn against the recent practice to solely use Bayesian species delimitation methods when proposing taxonomic changes.
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Affiliation(s)
| | - Joseph D. Manthey
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Yann Bourgeois
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Xenia Freilich
- Department of Biology, Queens College, City University of New York, Flushing, New York, United States of America
| | - Stéphane Boissinot
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
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13
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Molecular systematics, species delimitation and diversification patterns of the Phyllodactylus lanei complex (Gekkota: Phyllodactylidae) in Mexico. Mol Phylogenet Evol 2017; 115:82-94. [PMID: 28739370 DOI: 10.1016/j.ympev.2017.07.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 07/10/2017] [Accepted: 07/13/2017] [Indexed: 11/21/2022]
Abstract
The description of cryptic gecko species worldwide has revealed both that many putative species are, in fact, conformed by a complex of morphologically conserved species that are genetically distinct and highly divergent, and that gecko species diversity could be underestimated. The taxonomy and species delimitation of geckos belonging to the genus Phyllodactylus is still controversial, 16 of which are distributed in Mexico and 13 are endemic. Although the large morphological variation shown by the Phyllodactylus species from Mexico has been amply documented, little is known about their genetic diversity and evolutionary relationships, and much less regarding cryptic speciation. Here, we included the most comprehensive sampling of populations and species of the Phyllodactylus lanei complex distributed in Mexico, and applied an analytical approach that included probabilistic phylogenetic analyses, jointly with species delimitation methods and Bayesian putative species validation analysis. Our results suggest the existence of 10 lineages within the complex, supporting the existence of cryptic species, and in great contrast with the current taxonomic proposal that includes only four subspecies. The most recent common ancestor (MRCA) for the P. lanei clade originated on the Early Eocene (∼54Mya), along the southern coasts of Mexico, followed by the highest diversification of the complex MRCA during the Eocene (34-56Mya). Lineages subsequently dispersed and diversified towards the northwest, and the diversification process ended with the most recent lineages inhabiting two islands on the coasts of Nayarit (Miocene; 5.5-23Mya). Our results highlight three vicariant events associated with the evolution of the lineages, two of them intimately related to the formation of the Sierra Madre del Sur and the Transmexican Volcanic Belt mountain ranges, main geographic barriers that isolated and facilitated the divergence and speciation in this group of geckos. Finally, we propose that there are 10 species in the P. lanei complex, from which four represent taxonomic changes and six are new species and require a formal description. We acknowledge that more analyses, including a detailed evaluation of morphological characters and use of more unlinked nuclear loci with enough variability, are needed to further support their taxonomic description.
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Díaz-Cárdenas B, Ruiz-Sanchez E, Castro-Felix P, Castañeda-Gaytán G, Ruiz-Santana S, Gadsden H. Species delimitation of the blue-spotted spiny lizard within a multilocus, multispecies coalescent framework, results in the recognition of a new Sceloporus species. Mol Phylogenet Evol 2017; 111:185-195. [PMID: 28392486 DOI: 10.1016/j.ympev.2017.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 02/03/2017] [Accepted: 04/04/2017] [Indexed: 11/29/2022]
Abstract
Species delimitation is a major topic in systematics. Species delimitation methods based on molecular data have become more common since this approach provides insights about species identification via levels of gene flow, the degree of hybridization and phylogenetic relationships. Also, combining multilocus mitochondrial and nuclear DNA leads to more reliable conclusions about species limits. Coalescent-based species delimitation methods explicitly reveal separately evolving lineages using probabilistic approaches and testing the delimitation hypotheses for several species. Within a multispecies, multilocus, coalescent framework, we were able to clarify taxonomic uncertainties within S. cyanostictus, an endangered lizard that inhabits a narrow strip of the Chihuahuan Desert in Mexico. We included, for the first time in a phylogenetic analysis, lizards from the three populations of S. cyanostictus recognized so far (East Coahuila, West Coahuila and Nuevo León). Phylogenetic analysis corroborates the hypothesis of two separately evolving lineages, i.e. the East and West Coahuila populations, as proposed in a previous study. We also found a distant phylogenetic relationship between the lizards from Nuevo León and those of East and West Coahuila. Finally, based on the species delimitation results, we propose and describe a new species of Sceloporus: S. gadsdeni sp. nov.
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Affiliation(s)
- Brenda Díaz-Cárdenas
- Instituto de Ecología, A. C., Carretera antigua a Coatepec 351, El Haya, C.P. 91070 Xalapa Enríquez, Veracruz, Mexico
| | - Eduardo Ruiz-Sanchez
- Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ing. Ramón Padilla Sánchez 2100, Nextipac, Zapopán, Jalisco 45510, Mexico.
| | - Patricia Castro-Felix
- Departamento de Biología Celular y Molecular, Universidad de Guadalajara, Centro Universitario de Ciencias Biológicas y Agropecuarias, Camino Ing. Ramón Padilla Sánchez 2100, Nextipac, C.P. 45510 Zapopan, Jalisco, Mexico
| | - Gamaliel Castañeda-Gaytán
- Universidad Juárez del Estado de Durango, Facultad de Ciencias Biológicas, Av. Universidad S/N col. Filadelfia, C.P. 35010 Gómez Palacio, Durango, Mexico
| | - Sergio Ruiz-Santana
- Instituto de Ecología, A. C., Carretera antigua a Coatepec 351, El Haya, C.P. 91070 Xalapa Enríquez, Veracruz, Mexico
| | - Héctor Gadsden
- Instituto de Ecología, A. C., Centro Regional de Bajío, Av. Lázaro Cárdenas 253, 61600 Pátzcuaro, Michoacán, Mexico
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Willis SC. One species or four? Yes!...and, no. Or, arbitrary assignment of lineages to species obscures the diversification processes of Neotropical fishes. PLoS One 2017; 12:e0172349. [PMID: 28235096 PMCID: PMC5325279 DOI: 10.1371/journal.pone.0172349] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 02/03/2017] [Indexed: 11/18/2022] Open
Abstract
Species are fundamental units in many biological disciplines, but there is continuing disagreement as to what species are, how to define them, and even whether the concept is useful. While some of this debate can be attributed to inadequate data and insufficient statistical frameworks in alpha taxonomy, an equal part results from the ambiguity over what species are expected to represent by the many who use them. Here, mtDNA data, microsatellite data, and sequence data from 17 nuclear loci are used in an integrated and quantitative manner to resolve the presence of evolutionary lineages, their contemporary and historical structure, and their correspondence to species, in a species complex of Amazonian peacock "bass" cichlids (Cichla pinima sensu lato). Results suggest that the historical narrative for these populations is more complex than can be portrayed by recognizing them as one, two, or four species: their history and contemporary dynamics cannot be unambiguously rendered as discrete units (taxa) at any level without both choosing the supremacy of one delimitation criterion and obscuring the very information that provides insight into the diversification process. This calls into question the utility of species as a rank, term, or concept, and suggests that while biologists may have a reasonable grasp of the structure of evolution, our methods of conveying these insights need updating. The lack of correspondence between evolutionary phenomena and discrete species should serve as a null hypothesis, and researchers should focus on quantifying the diversity in nature at whatever hierarchical level it occurs.
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Affiliation(s)
- Stuart C. Willis
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, Texas, United States of America
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Rocha S, Perera A, Bunbury N, Kaiser-Bunbury CN, Harris DJ. Speciation history and species-delimitation within the Seychelles Bronze geckos,Ailuronyxspp.: molecular and morphological evidence. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Sara Rocha
- Department of Biochemistry, Genetics and Immunology; University of Vigo; Campus Lagoas-Marcosende; 36310 Vigo Spain
| | - Ana Perera
- CIBIO-InBIO; Research Center in Biodiversity and Genetic Resources; Campus Agrário de Vairão; Rua Padre Armando Quintas; 4485-661 Vairão Portugal
| | - Nancy Bunbury
- Seychelles Islands Foundation; La Ciotat Building; Mont Fleuri PO Box 853 Victoria, Mahé Seychelles
| | | | - David J. Harris
- CIBIO-InBIO; Research Center in Biodiversity and Genetic Resources; Campus Agrário de Vairão; Rua Padre Armando Quintas; 4485-661 Vairão Portugal
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Liu F, Wang M, Damm U, Crous PW, Cai L. Species boundaries in plant pathogenic fungi: a Colletotrichum case study. BMC Evol Biol 2016; 16:81. [PMID: 27080690 PMCID: PMC4832473 DOI: 10.1186/s12862-016-0649-5] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 03/31/2016] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Accurate delimitation of plant pathogenic fungi is critical for the establishment of quarantine regulations, screening for genetic resistance to plant pathogens, and the study of ecosystem function. Concatenation analysis of multi-locus DNA sequence data represents a powerful and commonly used approach to recognizing evolutionary independent lineages in fungi. It is however possible to mask the discordance between individual gene trees, thus the speciation events might be erroneously estimated if one simply recognizes well supported clades as distinct species without implementing a careful examination of species boundary. To investigate this phenomenon, we studied Colletotrichum siamense s. lat., which is a cosmopolitan pathogen causing serious diseases on many economically important plant hosts. Presently there are significant disagreements among mycologists as to what constitutes a species in C. siamense s. lat., with the number of accepted species ranging from one to seven. RESULTS In this study, multiple approaches were used to test the null hypothesis "C. siamense is a species complex", using a global strain collection. Results of molecular analyses based on the Genealogical Concordance Phylogenetic Species Recognition (GCPSR) and coalescent methods (e.g. Generalized Mixed Yule-coalescent and Poisson Tree Processes) do not support the recognition of any independent evolutionary lineages within C. siamense s. lat. as distinct species, thus rejecting the null hypothesis. This conclusion is reinforced by the recognition of genetic recombination, cross fertility, and the comparison of ecological and morphological characters. Our results indicate that reproductive isolation, geographic and host plant barriers to gene flow are absent in C. siamense s. lat. CONCLUSIONS This discovery emphasized the importance of a polyphasic approach when describing novel species in morphologically conserved genera of plant pathogenic fungi.
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Affiliation(s)
- Fang Liu
- />State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- />Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Mei Wang
- />State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Ulrike Damm
- />Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany
| | - Pedro W. Crous
- />Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- />CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- />Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002 South Africa
| | - Lei Cai
- />State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
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18
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Pyron RA, Hsieh FW, Lemmon AR, Lemmon EM, Hendry CR. Integrating phylogenomic and morphological data to assess candidate species-delimitation models in brown and red-bellied snakes (Storeria). Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12392] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- R. Alexander Pyron
- Department of Biological Sciences; The George Washington University; 2023 G St. NW Washington DC 20052 USA
| | - Felisa W. Hsieh
- Department of Biological Sciences; The George Washington University; 2023 G St. NW Washington DC 20052 USA
| | - Alan R. Lemmon
- Department of Scientific Computing; Florida State University; Tallahassee FL 32306-4120 USA
| | - Emily M. Lemmon
- Department of Biological Science; Florida State University; Tallahassee FL 32306-4295 USA
| | - Catriona R. Hendry
- Department of Biological Sciences; The George Washington University; 2023 G St. NW Washington DC 20052 USA
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19
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Phiri EE, Daniels SR. Multilocus coalescent species delimitation reveals widespread cryptic differentiation among Drakensberg mountain-living freshwater crabs (Decapoda : Potamonautes). INVERTEBR SYST 2016. [DOI: 10.1071/is15035] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Cryptic lineages present major challenges for evolutionary and conservation studies, particularly where these lineages remain undiscovered. Freshwater crabs are known to harbour cryptic diversity, in most cases with limited morphological differences. During the present study, we used a multilocus (12S rRNA, 16S rRNA, COI, 28S rRNA, DecapANT and PEPCK) Bayesian species delimitation to examine cryptic diversity within a freshwater crab species complex (Potamonautes clarus/P. depressus). We sampled 25 highland rivers in the Tugela and uMkomazi River drainage systems of the Drakensberg Mountain range, in the KwaZulu–Natal province of South Africa. Our results showed there to be at least eight lineages: six novel potamonautid freshwater crabs, and two described taxa P. clarus and P. depressus. Divergence from the most recent common ancestor occurred between the mid- and late Miocene (12.1 Mya), while divergence within the species complex occurred ~10.3 Mya up until the Holocene (0.11 Mya). The discovery of six novel lineages of freshwater crabs from a seemingly restricted distribution range has conservation implications, but to date most conservation planning strategies have focussed on freshwater vertebrates. By conducting a fine-scale phylogenetic survey using invertebrates, this study provides a platform for the inclusion of freshwater invertebrates in future conservation assessments.
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20
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Comparative molecular species delimitation in the charismatic Nawab butterflies (Nymphalidae, Charaxinae, Polyura). Mol Phylogenet Evol 2015; 91:194-209. [DOI: 10.1016/j.ympev.2015.05.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 04/28/2015] [Accepted: 05/19/2015] [Indexed: 11/15/2022]
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21
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Blair C, Méndez de la Cruz FR, Law C, Murphy RW. Molecular phylogenetics and species delimitation of leaf-toed geckos (Phyllodactylidae: Phyllodactylus) throughout the Mexican tropical dry forest. Mol Phylogenet Evol 2015; 84:254-65. [DOI: 10.1016/j.ympev.2015.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 01/07/2015] [Accepted: 01/09/2015] [Indexed: 10/24/2022]
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22
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Díaz-Rodríguez J, Gonçalves H, Sequeira F, Sousa-Neves T, Tejedo M, Ferrand N, Martínez-Solano I. Molecular evidence for cryptic candidate species in Iberian Pelodytes (Anura, Pelodytidae). Mol Phylogenet Evol 2015; 83:224-41. [DOI: 10.1016/j.ympev.2014.12.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 12/03/2014] [Accepted: 12/14/2014] [Indexed: 11/16/2022]
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23
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Hedin M. High-stakes species delimitation in eyeless cave spiders (Cicurina, Dictynidae, Araneae) from central Texas. Mol Ecol 2015; 24:346-61. [PMID: 25492722 DOI: 10.1111/mec.13036] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/03/2014] [Accepted: 12/03/2014] [Indexed: 01/26/2023]
Abstract
A remarkable radiation of completely eyeless, cave-obligate spider species (Cicurina) has been described from limestone caves of Texas. This radiation includes over 50 described species, with a large number of hypothesized single-cave endemics, and four species listed as US Federally Endangered. Because of this conservation importance, species delimitation in the group is 'high-stakes'- it is imperative that species hypotheses are data rich, objective, and robust. This study focuses on a complex of four cave-dwelling Cicurina distributed on the northwestern edge of Austin, Texas. Several of the existing species hypotheses in this complex are weak, based on morphological comparisons of small samples of adult female specimens; one species description (for C. wartoni) is based on a single adult specimen. Species limits in this group were newly assessed using morphological, mitochondrial and nuclear DNA sequence data evidence, analysed using a variety of approaches. All data support a clear lineage separation between C. buwata versus the C. travisae complex (including C. travisae, C. wartoni and C. reddelli). Observed congruence across multiple analyses indicate that the C. travisae complex represents a single species, and the formal species synonymy presented here has important conservation implications. The integrative framework utilized in this study serves as a potential model for other Texas cave Cicurina, including US Federally Endangered species. More generally, this study illustrates how and why taxon-focused conservation efforts must prioritize modern species delimitation research (if the existing taxonomy is weak), before devoting precious downstream resources to conservation efforts. The study also highlights the issue of taxonomic type II error that diversity biologists increasingly face as species delimitation moves into the genomics era.
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Affiliation(s)
- Marshal Hedin
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
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24
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Meyer-Wachsmuth I, Curini Galletti M, Jondelius U. Hyper-cryptic marine meiofauna: species complexes in Nemertodermatida. PLoS One 2014; 9:e107688. [PMID: 25225981 PMCID: PMC4166464 DOI: 10.1371/journal.pone.0107688] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 08/08/2014] [Indexed: 01/30/2023] Open
Abstract
Nemertodermatida are microscopically small, benthic marine worms. Specimens of two nominal species, Sterreria psammicola and Nemertinoides elongatus from 33 locations worldwide were sequenced for three molecular markers. Species delimitation and validation was done using gene trees, haplotype networks and multilocus Bayesian analysis. We found 20 supported species of which nine: Nemertinoides glandulosum n.sp., N. wolfgangi n.sp., Sterreria boucheti n.sp., S. lundini n.sp., S. martindalei n.sp., S. monolithes n.sp., S. papuensis n.sp., S. variabilis n.sp. and S. ylvae n.sp., are described including nucleotide-based diagnoses. The distribution patterns indicate transoceanic dispersal in some of the species. Sympatric species were found in many cases. The high level of cryptic diversity in this meiofauna group implies that marine diversity may be higher than previously estimated.
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Affiliation(s)
- Inga Meyer-Wachsmuth
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Marco Curini Galletti
- Dipartimento di Scienze della Natura e del Territorio, Università di Sassari, Sassari, Italy
| | - Ulf Jondelius
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
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25
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Zhang C, Rannala B, Yang Z. Bayesian species delimitation can be robust to guide-tree inference errors. Syst Biol 2014; 63:993-1004. [PMID: 25096853 PMCID: PMC4195854 DOI: 10.1093/sysbio/syu052] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Chi Zhang
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden; Genome Center and Section of Evolution and Ecology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA; Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK; and Center for Computational Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bruce Rannala
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden; Genome Center and Section of Evolution and Ecology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA; Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK; and Center for Computational Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ziheng Yang
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden; Genome Center and Section of Evolution and Ecology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA; Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK; and Center for Computational Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden; Genome Center and Section of Evolution and Ecology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA; Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK; and Center for Computational Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
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26
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Leaché AD, Fujita MK, Minin VN, Bouckaert RR. Species delimitation using genome-wide SNP data. Syst Biol 2014; 63:534-42. [PMID: 24627183 DOI: 10.1093/sysbio/syu018] [Citation(s) in RCA: 271] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The multispecies coalescent has provided important progress for evolutionary inferences, including increasing the statistical rigor and objectivity of comparisons among competing species delimitation models. However, Bayesian species delimitation methods typically require brute force integration over gene trees via Markov chain Monte Carlo (MCMC), which introduces a large computation burden and precludes their application to genomic-scale data. Here we combine a recently introduced dynamic programming algorithm for estimating species trees that bypasses MCMC integration over gene trees with sophisticated methods for estimating marginal likelihoods, needed for Bayesian model selection, to provide a rigorous and computationally tractable technique for genome-wide species delimitation. We provide a critical yet simple correction that brings the likelihoods of different species trees, and more importantly their corresponding marginal likelihoods, to the same common denominator, which enables direct and accurate comparisons of competing species delimitation models using Bayes factors. We test this approach, which we call Bayes factor delimitation (*with genomic data; BFD*), using common species delimitation scenarios with computer simulations. Varying the numbers of loci and the number of samples suggest that the approach can distinguish the true model even with few loci and limited samples per species. Misspecification of the prior for population size θ has little impact on support for the true model. We apply the approach to West African forest geckos (Hemidactylus fasciatus complex) using genome-wide SNP data. This new Bayesian method for species delimitation builds on a growing trend for objective species delimitation methods with explicit model assumptions that are easily tested. [Bayes factor; model testing; phylogeography; RADseq; simulation; speciation.].
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Affiliation(s)
- Adam D Leaché
- Department of Biology, University of Washington, Seattle, WA 98195, USA;Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98195, USA;
| | - Matthew K Fujita
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Vladimir N Minin
- Department of Biology, University of Washington, Seattle, WA 98195, USA;Department of Statistics, University of Washington, Seattle, WA 98195, USA
| | - Remco R Bouckaert
- Computational Evolution Group, University of Auckland, Auckland, New Zealand
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27
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McKay BD, Mays HL, Wu Y, Li H, Yao CT, Nishiumi I, Zou F. An empirical comparison of character-based and coalescent-based approaches to species delimitation in a young avian complex. Mol Ecol 2014; 22:4943-57. [PMID: 24073650 DOI: 10.1111/mec.12446] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 06/26/2013] [Accepted: 07/02/2013] [Indexed: 11/30/2022]
Abstract
The process of discovering species is a fundamental responsibility of systematics. Recently, there has been a growing interest in coalescent-based methods of species delimitation aimed at objectively identifying species early in the divergence process. However, few empirical studies have compared these new methods with character-based approaches for discovering species. In this study, we applied both a character-based and a coalescent-based approaches to delimit species in a closely related avian complex, the light-vented/Taiwan bulbul (Pycnonotus sinensis/Pycnonotus taivanus). Population aggregation analyses of plumage, mitochondrial and 13 nuclear intron character data sets produced conflicting species hypotheses with plumage data suggesting three species, mitochondrial data suggesting two species, and nuclear intron data suggesting one species. Such conflict is expected among recently diverged species, and by integrating all sources of data, we delimited three species verified with independently congruent character evidence as well as a more weakly supported fourth species identified by a single character. Attempts to validate species hypothesis using Bayesian Phylogenetics and Phylogeography (BPP), a coalescent-based method of species delimitation, revealed several issues that can seemingly affect statistical support for species recognition. We found that θ priors had a dramatic impact on speciation probabilities, with lower values consistently favouring splitting and higher values consistently favouring lumping. More resolved guide trees also resulted in overall higher speciation probabilities. Finally, we found suggestive evidence that BPP is sensitive to the divergent effects of nonrandom mating caused by intraspecific processes such as isolation-with-distance, and therefore, BPP may not be a conservative method for delimiting independently evolving population lineages. Based on these concerns, we questioned the reliability of BPP results and based our conclusions about species limits exclusively on character data.
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Affiliation(s)
- Bailey D McKay
- Bell Museum of Natural History, Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, 55108, USA
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28
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Edwards DL, Knowles LL. Species detection and individual assignment in species delimitation: can integrative data increase efficacy? Proc Biol Sci 2014; 281:20132765. [PMID: 24403337 PMCID: PMC3896021 DOI: 10.1098/rspb.2013.2765] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 12/02/2013] [Indexed: 11/12/2022] Open
Abstract
Statistical species delimitation usually relies on singular data, primarily genetic, for detecting putative species and individual assignment to putative species. Given the variety of speciation mechanisms, singular data may not adequately represent the genetic, morphological and ecological diversity relevant to species delimitation. We describe a methodological framework combining multivariate and clustering techniques that uses genetic, morphological and ecological data to detect and assign individuals to putative species. Our approach recovers a similar number of species recognized using traditional, qualitative taxonomic approaches that are not detected when using purely genetic methods. Furthermore, our approach detects groupings that traditional, qualitative taxonomic approaches do not. This empirical test suggests that our approach to detecting and assigning individuals to putative species could be useful in species delimitation despite varying levels of differentiation across genetic, phenotypic and ecological axes. This work highlights a critical, and often overlooked, aspect of the process of statistical species delimitation-species detection and individual assignment. Irrespective of the species delimitation approach used, all downstream processing relies on how individuals are initially assigned, and the practices and statistical issues surrounding individual assignment warrant careful consideration.
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Affiliation(s)
- Danielle L. Edwards
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven CT 06520, USA
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, The University of Michigan, Ann Arbor, MI 48109, USA
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29
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Jörger KM, Schrödl M. How to describe a cryptic species? Practical challenges of molecular taxonomy. Front Zool 2013; 10:59. [PMID: 24073641 PMCID: PMC4015967 DOI: 10.1186/1742-9994-10-59] [Citation(s) in RCA: 180] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 09/03/2013] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Molecular methods of species delineation are rapidly developing and widely considered as fast and efficient means to discover species and face the 'taxonomic impediment' in times of biodiversity crisis. So far, however, this form of DNA taxonomy frequently remains incomplete, lacking the final step of formal species description, thus enhancing rather than reducing impediments in taxonomy. DNA sequence information contributes valuable diagnostic characters and -at least for cryptic species - could even serve as the backbone of a taxonomic description. To this end solutions for a number of practical problems must be found, including a way in which molecular data can be presented to fulfill the formal requirements every description must meet. Multi-gene barcoding and a combined molecular species delineation approach recently revealed a radiation of at least 12 more or less cryptic species in the marine meiofaunal slug genus Pontohedyle (Acochlidia, Heterobranchia). All identified candidate species are well delimited by a consensus across different methods based on mitochondrial and nuclear markers. RESULTS The detailed microanatomical redescription of Pontohedyle verrucosa provided in the present paper does not reveal reliable characters for diagnosing even the two major clades identified within the genus on molecular data. We thus characterize three previously valid Pontohedyle species based on four genetic markers (mitochondrial cytochrome c oxidase subunit I, 16S rRNA, nuclear 28S and 18S rRNA) and formally describe nine cryptic new species (P. kepii sp. nov., P. joni sp. nov., P. neridae sp. nov., P. liliae sp. nov., P. wiggi sp. nov., P. wenzli sp. nov., P. peteryalli sp. nov., P. martynovi sp. nov., P. yurihookeri sp. nov.) applying molecular taxonomy, based on diagnostic nucleotides in DNA sequences of the four markers. Due to the minute size of the animals, entire specimens were used for extraction, consequently the holotype is a voucher of extracted DNA ('DNA-type'). We used the Character Attribute Organization System (CAOS) to determine diagnostic nucleotides, explore the dependence on input data and data processing, and aim for maximum traceability in our diagnoses for future research. Challenges, pitfalls and necessary considerations for applied DNA taxonomy are critically evaluated. CONCLUSIONS To describe cryptic species traditional lines of evidence in taxonomy need to be modified. DNA sequence information, for example, could even serve as the backbone of a taxonomic description. The present contribution demonstrates that few adaptations are needed to integrate into traditional taxonomy novel diagnoses based on molecular data. The taxonomic community is encouraged to join the discussion and develop a quality standard for molecular taxonomy, ideally in the form of an automated final step in molecular species delineation procedures.
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Affiliation(s)
- Katharina M Jörger
- Mollusca Section, SNSB-Bavarian State Collection of Zoology, Münchhausenstr 21, 81247 München, Germany
- Department Biology II, Ludwig-Maximilians-University, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - Michael Schrödl
- Mollusca Section, SNSB-Bavarian State Collection of Zoology, Münchhausenstr 21, 81247 München, Germany
- Department Biology II, Ludwig-Maximilians-University, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
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Barley AJ, White J, Diesmos AC, Brown RM. THE CHALLENGE OF SPECIES DELIMITATION AT THE EXTREMES: DIVERSIFICATION WITHOUT MORPHOLOGICAL CHANGE IN PHILIPPINE SUN SKINKS. Evolution 2013; 67:3556-72. [DOI: 10.1111/evo.12219] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 07/08/2013] [Indexed: 12/01/2022]
Affiliation(s)
- Anthony J. Barley
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence Kansas 66045
| | - Jordan White
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence Kansas 66045
| | | | - Rafe M. Brown
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence Kansas 66045
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31
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Miralles A, Vences M. New metrics for comparison of taxonomies reveal striking discrepancies among species delimitation methods in Madascincus lizards. PLoS One 2013; 8:e68242. [PMID: 23874561 PMCID: PMC3710018 DOI: 10.1371/journal.pone.0068242] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 05/24/2013] [Indexed: 01/17/2023] Open
Abstract
Delimiting and describing species is fundamental to numerous biological disciplines such as evolution, macroecology, and conservation. Delimiting species as independent evolutionary lineages may and often does yield different outcomes depending on the species criteria applied, but methods should be chosen that minimize the inference of objectively erroneous species limits. Several protocols exploit single-gene or multi-gene coalescence statistics, assignment tests or other rationales related to nuclear DNA (nDNA) allele sharing to automatically delimit species. We apply seven different species delimitation protocols to a taxonomically confusing group of Malagasy lizards (Madascincus), and compare the resulting taxonomies with two newly developed metrics: the Taxonomic index of congruence C tax which quantifies the congruence between two taxonomies, and the Relative taxonomic resolving power index R tax which quantifies the potential of an approach to capture a high number of species boundaries. The protocols differed in the total number of species proposed, between 9 and 34, and were also highly incongruent in placing species boundaries. The Generalized Mixed Yule-Coalescent approach captured the highest number of potential species boundaries but many of these were clearly contradicted by extensive nDNA admixture between sympatric mitochondrial DNA (mtDNA) haplotype lineages. Delimiting species as phenotypically diagnosable mtDNA clades failed to detect two cryptic species that are unambiguous due to a lack of nDNA gene flow despite sympatry. We also consider the high number of species boundaries and their placement by multi-gene Bayesian species delimitation as poorly reliable whereas the Bayesian assignment test approach provided a species delimitation highly congruent with integrative taxonomic practice. The present study illustrates the trade-off in taxonomy between reliability (favored by conservative approaches) and resolving power (favored by inflationist approaches). Quantifying excessive splitting is more difficult than quantifying excessive lumping, suggesting a priority for conservative taxonomies in which errors are more liable to be detected and corrected by subsequent studies.
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Affiliation(s)
- Aurélien Miralles
- Division of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany.
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32
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Sistrom M, Donnellan SC, Hutchinson MN. Delimiting species in recent radiations with low levels of morphological divergence: A case study in Australian Gehyra geckos. Mol Phylogenet Evol 2013; 68:135-43. [DOI: 10.1016/j.ympev.2013.03.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 01/05/2013] [Accepted: 03/08/2013] [Indexed: 11/29/2022]
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33
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Satler JD, Carstens BC, Hedin M. Multilocus species delimitation in a complex of morphologically conserved trapdoor spiders (mygalomorphae, antrodiaetidae, aliatypus). Syst Biol 2013; 62:805-23. [PMID: 23771888 DOI: 10.1093/sysbio/syt041] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Species are a fundamental unit for biological studies, yet no uniform guidelines exist for determining species limits in an objective manner. Given the large number of species concepts available, defining species can be both highly subjective and biased. Although morphology has been commonly used to determine species boundaries, the availability and prevalence of genetic data has allowed researchers to use such data to make inferences regarding species limits. Genetic data also have been used in the detection of cryptic species, where other lines of evidence (morphology in particular) may underestimate species diversity. In this study, we investigate species limits in a complex of morphologically conserved trapdoor spiders (Mygalomorphae, Antrodiaetidae, Aliatypus) from California. Multiple approaches were used to determine species boundaries in this highly genetically fragmented group, including both multilocus discovery and validation approaches (plus a chimeric approach). Additionally, we introduce a novel tree-based discovery approach using species trees. Results suggest that this complex includes multiple cryptic species, with two groupings consistently recovered across analyses. Due to incongruence across analyses for the remaining samples, we take a conservative approach and recognize a three species complex, and formally describe two new species (Aliatypus roxxiae, sp. nov. and Aliatypus starretti, sp. nov.). This study helps to clarify species limits in a genetically fragmented group and provides a framework for identifying and defining the cryptic lineage diversity that prevails in many organismal groups.
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Affiliation(s)
- Jordan D Satler
- Department of Evolution, Ecology and Organismal Biology, The Ohio University, Columbus, OH 43210, USA and Department of Biology, San Diego University, San Diego, CA 92182, USA
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Leavitt S, Fernández-Mendoza F, Pérez-Ortega S, Sohrabi M, Divakar P, Lumbsch T, St. Clair L. DNA barcode identification of lichen-forming fungal species in the Rhizoplaca melanophthalma species-complex (Lecanorales, Lecanoraceae), including five new species. MycoKeys 2013. [DOI: 10.3897/mycokeys.7.4508] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Rasoloarison RM, Weisrock DW, Yoder AD, Rakotondravony D, Kappeler PM. Two New Species of Mouse Lemurs (Cheirogaleidae: Microcebus) from Eastern Madagascar. INT J PRIMATOL 2013. [DOI: 10.1007/s10764-013-9672-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Coalescent-based species delimitation in an integrative taxonomy. Trends Ecol Evol 2012; 27:480-8. [PMID: 22633974 DOI: 10.1016/j.tree.2012.04.012] [Citation(s) in RCA: 500] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 04/09/2012] [Accepted: 04/24/2012] [Indexed: 11/21/2022]
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Camargo A, Morando M, Avila LJ, Sites JW. SPECIES DELIMITATION WITH ABC AND OTHER COALESCENT-BASED METHODS: A TEST OF ACCURACY WITH SIMULATIONS AND AN EMPIRICAL EXAMPLE WITH LIZARDS OF THE LIOLAEMUS DARWINII COMPLEX (SQUAMATA: LIOLAEMIDAE). Evolution 2012; 66:2834-49. [PMID: 22946806 DOI: 10.1111/j.1558-5646.2012.01640.x] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Arley Camargo
- Department of Biology & Monte L Bean Museum, Brigham Young University, Provo, Utah 84602, USA.
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Leavitt SD, Johnson LA, Goward T, St. Clair LL. Species delimitation in taxonomically difficult lichen-forming fungi: An example from morphologically and chemically diverse Xanthoparmelia (Parmeliaceae) in North America. Mol Phylogenet Evol 2011; 60:317-32. [DOI: 10.1016/j.ympev.2011.05.012] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 05/13/2011] [Accepted: 05/16/2011] [Indexed: 01/03/2023]
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Zhang C, Zhang DX, Zhu T, Yang Z. Evaluation of a Bayesian Coalescent Method of Species Delimitation. Syst Biol 2011; 60:747-61. [PMID: 21876212 DOI: 10.1093/sysbio/syr071] [Citation(s) in RCA: 214] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Chi Zhang
- Center for Computational and Evolutionary Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - De-Xing Zhang
- Center for Computational and Evolutionary Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tianqi Zhu
- School of Mathematical Sciences, Peking University, Beijing 100871, China
| | - Ziheng Yang
- Center for Computational and Evolutionary Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
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Falk BG, Mahler DL, Perkins SL. Tree-based delimitation of morphologically ambiguous taxa: a study of the lizard malaria parasites on the Caribbean island of Hispaniola. Int J Parasitol 2011; 41:967-80. [PMID: 21718698 DOI: 10.1016/j.ijpara.2011.05.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Revised: 05/01/2011] [Accepted: 05/05/2011] [Indexed: 11/29/2022]
Abstract
Malaria parasites in the genus Plasmodium have been classified primarily on the basis of differences in morphology. These single-celled organisms often lack distinguishing morphological features, and this can encumber both species delimitation and identification. Six saurian malaria parasites have been described from the Caribbean island of Hispaniola. All six infect lizards in the genus Anolis, but only two of these parasites can be distinguished using morphology. The remaining four species overlap in morphology and geography, and cannot be consistently identified using traditional methods. We compared a morphological approach with a molecular phylogenetic approach for assessing the taxonomy of these parasites. We surveyed for blood parasites from 677 Anolis lizards, representing 26 Anolis spp. from a total of 52 sites across Hispaniola. Fifty-five of these lizards were infected with Plasmodium spp., representing several new host records, but only 24 of these infections could be matched to previously described species using traditional morphological criteria. We then estimated the phylogeny of these parasites using both mitochondrial (cytb and coxI) and nuclear (EF2) genes, and included carefully selected GenBank sequences to confirm identities for certain species. Our molecular results unambiguously corroborated our morphology-based species identifications for only the two species previously judged to be morphologically distinctive. The remaining infections fell into two well-supported and reciprocally monophyletic clades, which contained the morphological variation previously reported for all four of the morphologically ambiguous species. One of these clades was identified as Plasmodium floridense and the other as Plasmodium fairchildi hispaniolae. We elevate the latter to Plasmodium hispaniolae comb. nov. because it is polyphyletic with the mainland species Plasmodium fairchildifairchildi and we contribute additional morphological and molecular characters for future species delimitation. Our phylogenetic hypotheses indicate that two currently recognised taxa, Plasmodium minasense anolisi and Plasmodium tropiduri caribbense, are not valid on Hispaniola. These results illustrate that molecular data can improve taxonomic hypotheses in Plasmodium when reliable morphological characters are lacking.
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Affiliation(s)
- Bryan G Falk
- Richard Gilder Graduate School, Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA.
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