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Lehmann Albornoz P, Bartzen CS, Malabarba LR. The barcode trap-Description of a new species of Microglanis, with a review of the status of Microglanis cibelae (Siluriformes: Pseudopimelodidae). J Fish Biol 2024. [PMID: 38646664 DOI: 10.1111/jfb.15764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 03/27/2024] [Accepted: 04/02/2024] [Indexed: 04/23/2024]
Abstract
In a recent study based on the generalized mixed Yule coalescent method for delimiting species, a threshold of 2% genetic distance using cytochrome c oxidase subunit I sequences was used to delimit the species of Microglanis. That action resulted in assembling several populations of Microglanis from Atlantic coastal rivers between Rio Grande do Sul and São Paulo states as a single species, Microglanis cottoides, including Microglanis cibelae as a junior synonym. We reexamined these populations and found three species diagnosed by their morphology and that constitute separate mtDNA lineages, including a new species. The synonym of M. cibelae and M. cottoides is reviewed and refuted based on morphological and molecular evidence. M. cibelae and the new species are sympatric and occasionally syntopic in the Tramandaí, Mampituba, and Araranguá river basins. The new species is distinguished from M. cibelae and M. cottoides by the anterior margin of the posttemporosupracleitrum narrow articulated with the epioccipital, the short mental and maxillary barbels, and depressed head and body.
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Affiliation(s)
| | - César Sá Bartzen
- Universidade do Vale do Rio dos Sinos (Unisinos), São Leopoldo, Brazil
| | - Luiz R Malabarba
- Departamento de Zoologia, IB, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Hubert N, Phillips JD, Hanner RH. Delimiting Species with Single-Locus DNA Sequences. Methods Mol Biol 2024; 2744:53-76. [PMID: 38683311 DOI: 10.1007/978-1-0716-3581-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
DNA sequences are increasingly used for large-scale biodiversity inventories. Because these genetic data avoid the time-consuming initial sorting of specimens based on their phenotypic attributes, they have been recently incorporated into taxonomic workflows for overlooked and diverse taxa. Major statistical developments have accompanied this new practice, and several models have been proposed to delimit species with single-locus DNA sequences. However, proposed approaches to date make different assumptions regarding taxon lineage history, leading to strong discordance whenever comparisons are made among methods. Distance-based methods, such as Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP), rely on the detection of a barcode gap (i.e., the lack of overlap in the distributions of intraspecific and interspecific genetic distances) and the associated threshold in genetic distances. Network-based methods, as exemplified by the REfined Single Linkage (RESL) algorithm for the generation of Barcode Index Numbers (BINs), use connectivity statistics to hierarchically cluster-related haplotypes into molecular operational taxonomic units (MOTUs) which serve as species proxies. Tree-based methods, including Poisson Tree Processes (PTP) and the General Mixed Yule Coalescent (GMYC), fit statistical models to phylogenetic trees by maximum likelihood or Bayesian frameworks.Multiple webservers and stand-alone versions of these methods are now available, complicating decision-making regarding the most appropriate approach to use for a given taxon of interest. For instance, tree-based methods require an initial phylogenetic reconstruction, and multiple options are now available for this purpose such as RAxML and BEAST. Across all examined species delimitation methods, judicious parameter setting is paramount, as different model parameterizations can lead to differing conclusions. The objective of this chapter is to guide users step-by-step through all the procedures involved for each of these methods, while aggregating all necessary information required to conduct these analyses. The "Materials" section details how to prepare and format input files, including options to align sequences and conduct tree reconstruction with Maximum Likelihood and Bayesian inference. The Methods section presents the procedure and options available to conduct species delimitation analyses, including distance-, network-, and tree-based models. Finally, limits and future developments are discussed in the Notes section. Most importantly, species delimitation methods discussed herein are categorized based on five indicators: reliability, availability, scalability, understandability, and usability, all of which are fundamental properties needed for any approach to gain unanimous adoption within the DNA barcoding community moving forward.
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Affiliation(s)
- Nicolas Hubert
- UMR ISEM (IRD, UM, CNRS), Université de Montpellier, Montpellier, France.
| | - Jarrett D Phillips
- School of Computer Science, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Robert H Hanner
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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3
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Ramirez JL, Valdivia P, Rosas-Puchuri U, Valdivia NL. SPdel: A pipeline to compare and visualize species delimitation methods for single-locus datasets. Mol Ecol Resour 2023; 23:1959-1965. [PMID: 37702121 DOI: 10.1111/1755-0998.13864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/28/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023]
Abstract
An accurate species delimitation is critical for biological studies. In this context, the use of molecular techniques along with species delimitation methods would help to a rapid and accurate biodiversity assessment. The species delimitation methods cluster data sets of orthologous sequences in molecular operational taxonomic units (MOTU). In particular, the methods based on a single gene are easily integrated with the widely used DNA barcoding approach. We developed SPdel a user-friendly pipeline to integrate different single-gene species delimitation methods. SPdel is designed to calculate and compare MOTUs obtained by different species delimitation approaches. SPdel also outputs diverse ready-to-publish quality figures, that facilitate the interpretation of results. SPdel aims to help researchers use species delimitation methods that would improve biodiversity studies.
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Affiliation(s)
- Jorge L Ramirez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Paola Valdivia
- Department of Biology, The University of Oklahoma, Norman, Oklahoma, USA
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Franco ADODR, Ashworth MP, Odebrecht C. Comparison between p-distance and single-locus species delimitation models for delineating reproductively tested strains of pennate diatoms (Bacillariophyceae) using cox1, rbcL and ITS. J Eukaryot Microbiol 2023; 70:e12986. [PMID: 37243408 DOI: 10.1111/jeu.12986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/18/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023]
Abstract
Several automated molecular methods have emerged for distinguishing eukaryote species based on DNA sequence data. However, there are knowledge gaps around which of these single-locus methods is more accurate for the identification of microalgal species, such as the highly diverse and ecologically relevant diatoms. We applied genetic divergence, Automatic Barcode Gap Discovery for primary species delimitation (ABGD), Assemble Species by Automatic Partitioning (ASAP), Statistical Parsimony Network Analysis (SPNA), Generalized Mixed Yule Coalescent (GMYC) and Poisson Tree Processes (PTP) using partial cox1, rbcL, 5.8S + ITS2, ITS1 + 5.8S + ITS2 markers to delineate species and compare to published polyphasic identification data (morphological features, phylogeny and sexual reproductive isolation) to test the resolution of these methods. ASAP, ABGD, SPNA and PTP models resolved species of Eunotia, Seminavis, Nitzschia, Sellaphora and Pseudo-nitzschia corresponding to previous polyphasic identification, including reproductive isolation studies. In most cases, these models identified diatom species in similar ways, regardless of sequence fragment length. GMYC model presented smallest number of results that agreed with previous published identification. Following the recommendations for proper use of each model presented in the present study, these models can be useful tools to identify cryptic or closely related species of diatoms, even when the datasets have relatively few sequences.
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Affiliation(s)
| | - Matt P Ashworth
- Department of Molecular Biosciences, UTEX Culture Collection of Algae, University of Texas at Austin, Austin, Texas, USA
| | - Clarisse Odebrecht
- Institute of Oceanography, Federal University of Rio Grande - FURG, Rio Grande, Brazil
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Guo B, Kong L. Comparing the Efficiency of Single-Locus Species Delimitation Methods within Trochoidea (Gastropoda: Vetigastropoda). Genes (Basel) 2022; 13:genes13122273. [PMID: 36553540 PMCID: PMC9778293 DOI: 10.3390/genes13122273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
In the context of diminishing global biodiversity, the validity and practicality of species delimitation methods for the identification of many neglected and undescribed biodiverse species have been paid increasing attention. DNA sequence-based species delimitation methods are mainly classified into two categories, namely, distance-based and tree-based methods, and have been widely adopted in many studies. In the present study, we performed three distance-based (ad hoc threshold, ABGD, and ASAP) and four tree-based (sGMYC, mGMYC, PTP, and mPTP) analyses based on Trochoidea COI data and analyzed the discordance between them. Moreover, we also observed the performance of these methods at different taxonomic ranks (the genus, subfamily, and family ranks). The results suggested that the distance-based approach is generally superior to the tree-based approach, with the ASAP method being the most efficient. In terms of phylogenetic methods, the single threshold version performed better than the multiple threshold version of GMYC, and PTP showed higher efficiency than mPTP in delimiting species. Additionally, GMYC was found to be significantly influenced by taxonomic rank, showing poorer efficiency in datasets at the genus level than at higher levels. Finally, our results highlighted that cryptic diversity within Trochoidea (Mollusca: Vetigastropoda) might be underestimated, which provides quantitative evidence for excavating the cryptic lineages of these species.
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Affiliation(s)
- Bingyu Guo
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
- Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
- Correspondence:
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Mendoza‐Ramírez BH, Páiz‐Medina L, Salvatierra‐Suárez T, Hernández N, Huete‐Pérez JA. A survey of aquatic macroinvertebrates in a river from the dry corridor of Nicaragua using biological indices and DNA barcoding. Ecol Evol 2022; 12:e9487. [PMID: 36349251 PMCID: PMC9636505 DOI: 10.1002/ece3.9487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/31/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022] Open
Abstract
Aquatic macroinvertebrates are widely used as indicators for water quality assessment around the world. Modern strategies for environmental assessment implement molecular analysis to delimitate species of aquatic macroinvertebrates. Delimitation methods have been established to determine boundaries between species units using sequencing data from DNA barcodes and serve as first exploratory tools for taxonomic revisions. This is useful in regions such as the neotropics where aquatic macroinvertebrate habitats are threatened by human interference and DNA databases remain understudied. We asked whether the biodiversity of aquatic macroinvertebrates in a stream in Nicaragua, within the Central American Dry Corridor, could be characterized with biological indices and DNA barcoding. In this study, we combined regional biological indices (BMWP-CR, IBF-SV-2010) along with distance-based (ASAP, BIN) and tree-based (GMYC, bPTP) delimitation methods, as well as nucleotide BLAST in public barcode databases. We collected samples from the upper, middle, and low reaches of the Petaquilla river. The three sites presented excellent water quality with the BMWP-CR index, but evidence of high organic pollution was found in the middle reach with the IBF-SV-2010 index. We report a total of 219 COI sequences successfully generated from 18 families and 8 orders. Operational taxonomic units (OTUs) designation ranged from 69 to 73 using the four methods, with a congruency of 92% for barcode assignation. Nucleotide BLAST identified 14 species (27.4% of barcodes) and 33 genera (39.3% of barcodes) from query sequences in GenBank and BOLD system databases. This small number of identified OTUs may be explained by the paucity of molecular data from the Neotropical region. Our study provides valuable information about the characterization of macroinvertebrate families that are important biological indicators for the assessment of water quality in Nicaragua. The application of molecular approaches will allow the study of local diversity and further improve the application of molecular techniques for biomonitoring.
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Affiliation(s)
| | - Lucía Páiz‐Medina
- Molecular Biology CenterUniversity of Central America, UCAManaguaNicaragua
| | | | - Nelvia Hernández
- Institute of Interdisciplinary Research in Natural SciencesUniversity of Central America, UCAManaguaNicaragua
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Montes J, Peláez P, Moreno‐Letelier A, Gernandt DS. Coalescent-based species delimitation in North American pinyon pines using low-copy nuclear genes and plastomes. Am J Bot 2022; 109:706-726. [PMID: 35526278 PMCID: PMC9321694 DOI: 10.1002/ajb2.1847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
PREMISE Accurate species delimitation is essential for evolutionary biology, conservation, and biodiversity management. We studied species delimitation in North American pinyon pines, Pinus subsection Cembroides, a natural group with high levels of incomplete lineage sorting. METHODS We used coalescent-based methods and multivariate analyses of low-copy number nuclear genes and nearly complete high-copy number plastomes generated with the Hyb-Seq method. The three coalescent-based species delimitation methods evaluated were the Generalized Mixed Yule Coalescent (GMYC), Poisson Tree Process (PTP), and Trinomial Distribution of Triplets (Tr2). We also measured admixture in populations with possible introgression. RESULTS Our results show inconsistencies among GMYC, PTP, and Tr2. The single-locus based GMYC analysis of plastid DNA recovered a higher number of species (up to 24 entities, including singleton lineages and clusters) than PTP and the multi-locus coalescent approach. The PTP analysis identified 10 species whereas Tr2 recovered 13, which agreed closely with taxonomic treatments. CONCLUSIONS We found that PTP and GMYC identified species with low levels of ILS and high morphological divergence (P. maximartinezii, P. pinceana, and P. rzedowskii). However, GMYC method oversplit species by identification of more divergent samples as singletons. Moreover, both PTP and GMYC were incapable of identifying some species that are readily identified morphologically. We suggest that the divergence times between lineages within North American pinyon pines are so disparate that GMYC results are unreliable. Results of the Tr2 method coincided well with previous delimitations based on morphology, DNA, geography, and secondary chemistry.
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Affiliation(s)
- José‐Rubén Montes
- Posgrado en Ciencias Biológicas, Instituto de BiologíaUniversidad Nacional Autónoma de México04510Ciudad de MéxicoMexico
| | - Pablo Peláez
- Centro de Ciencias GenómicasUniversidad Nacional Autónoma de México62210CuernavacaMorelosMexico
| | - Alejandra Moreno‐Letelier
- Jardín Botánico, Instituto de BiologíaUniversidad Nacional Autónoma de México04510Ciudad de MéxicoMexico
| | - David S. Gernandt
- Departamento de Botánica, Instituto de BiologíaUniversidad Nacional Autónoma de México04510Ciudad de MéxicoMexico
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Peres PHF, Luduvério DJ, Bernegossi AM, Galindo DJ, Nascimento GB, Oliveira ML, Sandoval EDP, Vozdova M, Kubickova S, Cernohorska H, Duarte JMB. Revalidation of Mazama rufa (Illiger 1815) (Artiodactyla: Cervidae) as a Distinct Species out of the Complex Mazama americana (Erxleben 1777). Front Genet 2022; 12:742870. [PMID: 34970296 PMCID: PMC8712859 DOI: 10.3389/fgene.2021.742870] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
The red brocket deer Mazama americana Erxleben, 1777 is considered a polyphyletic complex of cryptic species with wide chromosomal divergence. Evidence indicates that the observed chromosomal divergences result in reproductive isolation. The description of a neotype for M. americana allowed its genetic characterization and represented a comparative basis to resolve the taxonomic uncertainties of the group. Thus, we designated a neotype for the synonym Mazama rufa Illiger, 1815 and tested its recognition as a distinct species from the M. americana complex with the analysis of morphological, cytogenetic and molecular data. We also evaluated its distribution by sampling fecal DNA in the wild. Morphological data from craniometry and body biometry indicated an overlap of quantitative measurements between M. rufa and the entire M. americana complex. The phylogenetic hypothesis obtained through mtDNA confirmed the reciprocal monophyly relationship between M. americana and M. rufa, and both were identified as distinct molecular operational taxonomic units by the General Mixed Yule Coalescent species delimitation analysis. Finally, classic cytogenetic data and fluorescence in situ hybridization with whole chromosome painting probes showed M. rufa with a karyotype of 2n = 52, FN = 56. Comparative analysis indicate that at least fifteen rearrangements separate M. rufa and M. americana (sensu stricto) karyotypes, which confirmed their substantial chromosomal divergence. This divergence should represent an important reproductive barrier and allow its characterization as a distinct and valid species. Genetic analysis of fecal samples demonstrated a wide distribution of M. rufa in the South American continent through the Atlantic Forest, Cerrado and south region of Amazon. Thus, we conclude for the revalidation of M. rufa as a distinct species under the concept of biological isolation, with its karyotype as the main diagnostic character. The present work serves as a basis for the taxonomic review of the M. americana complex, which should be mainly based on cytogenetic characterization and directed towards a better sampling of the Amazon region, the evaluation of available names in the species synonymy and a multi-locus phylogenetic analysis.
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Affiliation(s)
- Pedro H F Peres
- Deer Research and Conservation Center (NUPECCE), São Paulo State University (UNESP), Jaboticabal, Brazil
| | - Douglas J Luduvério
- Deer Research and Conservation Center (NUPECCE), São Paulo State University (UNESP), Jaboticabal, Brazil
| | - Agda Maria Bernegossi
- Deer Research and Conservation Center (NUPECCE), São Paulo State University (UNESP), Jaboticabal, Brazil
| | - David J Galindo
- Faculty of Veterinary Medicine, National University of San Marcos (UNMSM), Lima, Peru
| | | | - Márcio L Oliveira
- Deer Research and Conservation Center (NUPECCE), São Paulo State University (UNESP), Jaboticabal, Brazil
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He JJ, Jin DT, Wang YS, Che YL, Wang ZQ. Species delimitation of Margattea cockroaches from China, with seven new species (Blattodea, Ectobiidae, Pseudophyllodromiinae). Zookeys 2021; 1036:121-151. [PMID: 34040483 PMCID: PMC8128847 DOI: 10.3897/zookeys.1036.63232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 04/01/2021] [Indexed: 11/19/2022] Open
Abstract
Nearly 450 Margattea specimens were collected from 27 locations in China and their morphology was examined. Then 68 Margattea COI sequences were obtained and used to carry out phylogenetic analyses as well as species delimitation analyses using General Mixed Yule Coalescent (GMYC), Automatic Barcode Gap Discovery (ABGD), and Poisson Tree Processes (bPTP). GMYC analysis resulted in 21 molecular operational taxonomic units (MOTUs) (confidence interval: 20–22), which was completely consistent with the result of the bPTP. There were 15 MOTUs using the ABGD method. The number of MOTUs was slightly different from the assigned morphospecies (16). As to the incongruence between molecular and morphological results, we checked the specimens again and made sure that most morphological differences were determined to be intraspecific differences (except the difference between M.angusta and M.mckittrickae), although a large genetic distance existed. Finally, 16 Margattea species from China were defined in this study, of which, seven new species are established, i.e. Margatteadeltodonta J-J He & Z-Q Wang, sp. nov., Margatteacuspidata J-J He & Z-Q Wang, sp. nov., Margatteacaudata J-J He & Z-Q Wang, sp. nov., Margatteaparatransversa J-J He & Z-Q Wang, sp. nov., Margatteadisparilis J-J He & Z-Q Wang, sp. nov., Margatteatransversa J-J He & Z-Q Wang, sp. nov., and Margatteabicruris J-J He & Z-Q Wang, sp. nov.
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Affiliation(s)
- Jia-Jun He
- College of Plant Protection, Southwest University, Beibei, Chongqing 400715, China Southwest University Chongqing China
| | - Du-Ting Jin
- College of Plant Protection, Southwest University, Beibei, Chongqing 400715, China Southwest University Chongqing China
| | - Yi-Shu Wang
- College of Plant Protection, Southwest University, Beibei, Chongqing 400715, China Southwest University Chongqing China
| | - Yan-Li Che
- College of Plant Protection, Southwest University, Beibei, Chongqing 400715, China Southwest University Chongqing China
| | - Zong-Qing Wang
- College of Plant Protection, Southwest University, Beibei, Chongqing 400715, China Southwest University Chongqing China
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Magoga G, Fontaneto D, Montagna M. Factors affecting the efficiency of molecular species delimitation in a species-rich insect family. Mol Ecol Resour 2021; 21:1475-1489. [PMID: 33565247 DOI: 10.1111/1755-0998.13352] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/19/2021] [Accepted: 02/03/2021] [Indexed: 11/28/2022]
Abstract
In the context of global biodiversity loss, molecular species delimitation approaches can be very useful for accelerating species discovery through DNA taxonomy and inventory through DNA metabarcoding. In this study, the effect of some intrinsic factors on the efficiency of various single-marker species delimitation methods (fixed and variable nucleotide distance thresholds, ABGD, ASAP, GMYC, mPTP) was tested on more than 90 empirical data sets, derived from a set of 7,237 COI sequences attributed to 542 leaf beetles species (Coleoptera: Chrysomelidae). The considered factors were: (i) the number of haplotypes per species (as a proxy for genetic diversity), (ii) the geographic distance among conspecific collection localities (as a proxy of sampling width), (iii) the difficulty related to morphological identification of species, and (iv) the taxonomic rank. Distance-based methods, with on average more than 70% of match with morphological identification, outperformed those relying on phylogenetic trees, with less than 59%. A high number of haplotypes per species was found to have a negative effect on delimitation efficiency, whereas large geographic distances within species had a positive effect. All methods delimitations (except for GMYC) were significantly affected by the presence of species that are difficult to be identified, decreasing their efficiency. Finally, the only method influenced by the taxonomic rank of the data set was GMYC, showing lower efficiency in data sets at the genus than at higher levels. The observed biases we highlighted affecting efficiency could be accounted for when developing input data sets for species delimitation analyses to obtain a more reliable representation of biological diversity.
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Affiliation(s)
- Giulia Magoga
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Diego Fontaneto
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Ricerca Sulle Acque (IRSA), Molecular Ecology Group (MEG), Verbania, Italy
| | - Matteo Montagna
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milano, Italy.,BAT Center - Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Napoli "Federico II", Portici, Italy
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Marín MA, López-Rubio A, Clavijo A, Pyrcz TW, Freitas AVL, Uribe SI, Álvarez CF. Use of species delimitation approaches to tackle the cryptic diversity of an assemblage of high Andean butterflies (Lepidoptera: Papilionoidea). Genome 2021; 64:937-949. [PMID: 33596120 DOI: 10.1139/gen-2020-0100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cryptic biological diversity has generated ambiguity in taxonomic and evolutionary studies. Single-locus methods and other approaches for species delimitation are useful for addressing this challenge, enabling the practical processing of large numbers of samples for identification and inventory purposes. This study analyzed an assemblage of high Andean butterflies using DNA barcoding and compared the identifications based on the current morphological taxonomy with three methods of species delimitation (automatic barcode gap discovery, generalized mixed Yule coalescent model, and Poisson tree processes). Sixteen potential cryptic species were recognized using these three methods, representing a net richness increase of 11.3% in the assemblage. A well-studied taxon of the genus Vanessa, which has a wide geographical distribution, appeared with the potential cryptic species that had a higher genetic differentiation at the local level than at the continental level. The analyses were useful for identifying the potential cryptic species in Pedaliodes and Forsterinaria complexes, which also show differentiation along altitudinal and latitudinal gradients. This genetic assessment of an entire assemblage of high Andean butterflies (Papilionoidea) provides baseline information for future research in a region characterized by high rates of endemism and population isolation.
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Affiliation(s)
- Mario Alejandro Marín
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, São Paulo (SP), Brazil.,Grupo de Investigación en Sistemática Molecular, Universidad Nacional de Colombia, Medellín, Antioquia, Colombia
| | - Andrés López-Rubio
- Grupo de Investigación en Sistemática Molecular, Universidad Nacional de Colombia, Medellín, Antioquia, Colombia
| | - Alejandra Clavijo
- Grupo de Investigación en Sistemática Molecular, Universidad Nacional de Colombia, Medellín, Antioquia, Colombia
| | - Tomasz Wilhelm Pyrcz
- Department of Invertebrate Evolution, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa, Kraków, Poland.,Nature Education Centre, Jagiellonian University, Gronostajowa, Kraków, Poland
| | - André Victor Lucci Freitas
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, São Paulo (SP), Brazil.,Museu de Diversidade Biológica, Instituto de Biologia, Universidade Estadual de Campinas, São Paulo, Brazil
| | - Sandra Inés Uribe
- Grupo de Investigación en Sistemática Molecular, Universidad Nacional de Colombia, Medellín, Antioquia, Colombia
| | - Carlos Federico Álvarez
- Grupo de Investigación en Sistemática Molecular, Universidad Nacional de Colombia, Medellín, Antioquia, Colombia
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Abstract
Delimitation of species boundaries within the fungal genus Diaporthe has been challenging, but the analyses of combined multilocus DNA sequences has become an important tool to infer phylogenetic relationships and to circumscribe species. However, analyses of congruence between individual gene genealogies and the application of the genealogical concordance principle have been somehow overlooked. We noted that a group of species including D. amygdali, D. garethjonesii, D. sterilis, D. kadsurae, D. ternstroemia, D. ovoicicola, D. fusicola, D. chongqingensis and D. mediterranea, commonly known as D. amygdali complex, occupy a monophyletic clade in Diaporthe phylogenies but the limits of all species within the complex are not entirely clear. To assess the boundaries of species within this complex we employed the Genealogical Concordance Phylogenetic Species Recognition principle (GCPSR) and coalescence-based models: General Mixed Yule-Coalescent (GMYC) and Poisson Tree Processes (PTP). The incongruence detected between individual gene phylogenies, as well as the results of coalescent methods do not support the recognition of lineages within the complex as distinct species. Moreover, results support the absence of reproductive isolation and barriers to gene flow in this complex, thus providing further evidence that the D. amygdali species complex constitutes a single species. This study highlights the relevance of the application of the GCPSR principle, showing that concatenation analysis of multilocus DNA sequences, although being a powerful tool, might lead to an erroneous definition of species limits. Additionally, it further shows that coalescent methods are useful tools to assist in a more robust delimitation of species boundaries in the genus Diaporthe.
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Affiliation(s)
- Sandra Hilário
- Departamento de Biologia, CESAM (Centro de Estudos do Ambiente e do Mar), Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - Liliana Santos
- Departamento de Biologia, CESAM (Centro de Estudos do Ambiente e do Mar), Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - Artur Alves
- Departamento de Biologia, CESAM (Centro de Estudos do Ambiente e do Mar), Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
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13
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Menchetti M, Talavera G, Cini A, Salvati V, Dincă V, Platania L, Bonelli S, Balletto E, Vila R, Dapporto L. Two ways to be endemic. Alps and Apennines are different functional refugia during climatic cycles. Mol Ecol 2021; 30:1297-1310. [PMID: 33421216 DOI: 10.1111/mec.15795] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/21/2020] [Accepted: 01/04/2021] [Indexed: 01/03/2023]
Abstract
Endemics co-occur because they evolved in situ and persist regionally or because they evolved ex situ and later dispersed to shared habitats, generating evolutionary or ecological endemicity centres, respectively. We investigate whether different endemicity centres can intertwine in the region ranging from Alps to Sicily, by studying their butterfly fauna. We gathered an extensive occurrence data set for butterflies of the study area (27,123 records, 269 species, in cells of 0.5 × 0.5 degrees of latitude-longitude). We applied molecular-based delimitation methods (GMYC model) to 26,557 cytochrome c oxidase subunit 1 (COI) sequences of Western Palearctic butterflies. We identified entities based on molecular delimitations and/or the checklist of European butterflies and objectively attributed occurrences to their most probable entity. We obtained a zoogeographic regionalisation based on the 69 endemics of the area. Using phylogenetic ANOVA we tested if endemics from different centres differ from each other and from nonendemics for key ecological traits and divergence time. Endemicity showed high incidence in the Alps and Southern Italy. The regionalisation separated the Alps from the Italian Peninsula and Sicily. The endemics of different centres showed a high turnover and differed in phylogenetic distances, phenology and distribution traits. Endemics are on average younger than nonendemics and the Peninsula-Sicily endemics also have lower variance in divergence than those from the Alps. The observed variation identifies Alpine endemics as paleoendemics, now occupying an ecological centre, and the Peninsula-Sicily ones as neoendemics, that diverged in the region since the Pleistocene. The results challenge the common view of the Alpine-Apennine area as a single "Italian refugium".
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Affiliation(s)
- Mattia Menchetti
- ZEN Laboratory, Dipartimento di Biologia, Università degli Studi di Firenze, Sesto Fiorentino, Italy.,Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Gerard Talavera
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain
| | - Alessandro Cini
- ZEN Laboratory, Dipartimento di Biologia, Università degli Studi di Firenze, Sesto Fiorentino, Italy.,Centre for Biodiversity & Environment Research, University College London, London, UK
| | - Vania Salvati
- ZEN Laboratory, Dipartimento di Biologia, Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Vlad Dincă
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Leonardo Platania
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Simona Bonelli
- ZOOLAB, Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, Turin, Italy
| | - Emilio Balletto
- ZOOLAB, Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, Turin, Italy
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Leonardo Dapporto
- ZEN Laboratory, Dipartimento di Biologia, Università degli Studi di Firenze, Sesto Fiorentino, Italy
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14
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Pozzi L, Penna A, Bearder SK, Karlsson J, Perkin A, Disotell TR. Cryptic diversity and species boundaries within the Paragalago zanzibaricus species complex. Mol Phylogenet Evol 2020; 150:106887. [PMID: 32534184 DOI: 10.1016/j.ympev.2020.106887] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 05/04/2020] [Accepted: 06/03/2020] [Indexed: 11/17/2022]
Abstract
The recently described genus Paragalago is a complex of several nocturnal and morphologically cryptic species distributed in the forests of eastern Africa. Species diversity within this genus has been mainly described using species-specific differences in their loud calls. However, molecular data are still lacking for this group and species boundaries remain unclear. In this study, we explore species diversity within the zanzibaricus-complex using a combination of mitochondrial and nuclear data and comparing multiple species delimitation methods. Our results consistently support the existence of three independent lineages, P. cocos, P. zanzibaricus, and P. granti, confirming previous hypotheses based on vocal data. We conclude that these three lineages represent valid cryptic species and we hypothesize that speciation within this complex was characterized by cycles of forest expansion and contraction in the Plio-Pleistocene.
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Affiliation(s)
- Luca Pozzi
- Department of Anthropology, University of Texas at San Antonio, San Antonio, TX, USA.
| | - Anna Penna
- Department of Anthropology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Simon K Bearder
- Nocturnal Primate Research Group, Oxford Brookes University, Oxford, UK
| | - Johan Karlsson
- Nocturnal Primate Research Group, Oxford Brookes University, Oxford, UK
| | - Andrew Perkin
- Nocturnal Primate Research Group, Oxford Brookes University, Oxford, UK
| | - Todd R Disotell
- Department of Anthropology, New York University, New York, NY, USA; Department of Anthropology, University of Massachusetts, Amherst, MA, USA
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15
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Abstract
Gasteruptiidae Ashmead is an easily recognised family of wasps with ∼589 described species worldwide. Although well characterised by traditional taxonomy, multiple authors have commented on the extreme morphological uniformity of the group, making species-level identification difficult. This problem is enhanced by the lack of molecular data and molecular phylogenetic research for the group. We used 187 cytochrome c oxidase subunit I (COI) barcodes to explore the efficiency of sequence data to delimitate species in Gasteruptiidae. We undertook a graphical and discussion-based comparison of six methods for species delimitation, with the success of methods judged based on known species boundaries and morphology. Both distance-based (ABGD and jMOTU threshold analysis) and tree-based (GMYC and PTP) methods compared across multiple parameters recovered variable molecular operational taxonomic units (MOTUs), ranging from 55 to 123 MOTUs. Tree-based methods tended to split known morphological species less than distance-based methods, with the single-threshold GMYC method the most concordant with known morphospecies. Our results suggest that the incorporation of molecular species delimitation techniques provides a powerful tool to assist in the interpretation of species and help direct informed decisions with taxonomic uncertainty in the family.
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Affiliation(s)
- Ben A Parslow
- Biological Sciences, College of Science and Engineering, Flinders University, Adelaide, SA 5001, Australia.,Biological and Earth Sciences, South Australian Museum, SA 5000, Australia
| | - Michael P Schwarz
- Biological Sciences, College of Science and Engineering, Flinders University, Adelaide, SA 5001, Australia
| | - Mark I Stevens
- Biological and Earth Sciences, South Australian Museum, SA 5000, Australia.,University of South Australia, Clinical and Health Sciences, SA 5000, Australia
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16
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Hashimoto S, Py-Daniel LHR, Batista JS. A molecular assessment of species diversity in Tympanopleura and Ageneiosus catfishes (Auchenipteridae: Siluriformes). J Fish Biol 2020; 96:14-22. [PMID: 31631341 DOI: 10.1111/jfb.14173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
In order to test the congruence of genetic data to the morphologically defined Neotropical catfish genera Tympanopleura and Ageneiosus and explore species diversity, we generated 17 DNA barcodes from five of six species of Tympanopleura and 12 of 13 species of Ageneiosus. To discriminate limits between species, an automatic barcode gap discovery (ABGD), a generalised mixed yule-coalescent model (GYMC) and fixed distance thresholds Kimura two-parameter (K2P; 3%) were used to discriminate putative species limits from the DNA barcodes. The ABGD, GMYC and K2P methods agreed by each generating 13 clusters: six in Tympanopleura (five nominal plus one undescribed species) and seven in Ageneiosus. These clusters corresponded broadly to the described species, except in the case of the Ageneiosus ucayalensis group (A. akamai, A. dentatus, A. intrusus, A. ucayalensis, A. uranophthalmus and A. vittatus). Haplotype sharing and low divergences may have prevented molecular methods from distinguishing these species. We hypothesise that this is the result of a recent radiation of a sympatric species group distributed throughout the Amazon Basin. One putative new species of Tympanopleura was also supported by the molecular data. These results taken together highlight the utility of molecular methods such as DNA barcoding in understanding patterns of diversification across large geographic areas and in recognising overlooked diversity.
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Affiliation(s)
- Shizuka Hashimoto
- Instituto Nacional de Pesquisas da Amazônia, Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Manaus, Amazonas, Brazil
- Instituto Nacional de Pesquisas da Amazônia, Coleção de Peixes, Programa de Coleções Científicas, Manaus, Amazonas, Brazil
| | - Lúcia H Rapp Py-Daniel
- Instituto Nacional de Pesquisas da Amazônia, Coleção de Peixes, Programa de Coleções Científicas, Manaus, Amazonas, Brazil
| | - Jacqueline S Batista
- Instituto Nacional de Pesquisas da Amazônia, Laboratório Temático de Biologia Molecular, Manaus, Amazonas, Brazil
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17
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Ranarilalatiana T, Raveloson Ravaomanarivo LH, Bergsten J. Taxonomic revision of the genus Copelatus of Madagascar (Coleoptera, Dytiscidae, Copelatinae): the non- erichsonii group species. Zookeys 2019; 869:19-90. [PMID: 31413659 PMCID: PMC6690892 DOI: 10.3897/zookeys.869.33997] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/30/2019] [Indexed: 12/04/2022] Open
Abstract
The genus Copelatus Erichson, 1832 (Coleoptera, Dytiscidae, Copelatinae) of Madagascar is revised in two parts. This review is restricted to the Copelatus species that have fewer than ten elytral + one submarginal stria, including all species except those of the erichsonii species group. Both morphological and molecular (mitochondrial COI) data are used in an integrative taxonomic approach. Thirteen species are recognised, of which five are described as new: Copelatusankaratrasp. nov., Copelatuskelysp. nov., Copelatuspseudostriatussp. nov., Copelatussafiotrasp. nov. and Copelatusvokokasp. nov.Copelatusunguicularis Régimbart, 1903 and Copelatusapicalis Fairmaire, 1898 are both transferred to the genus Madaglymbus Shaverdo & Balke, 2008 (comb. nov.). CopelatusmimetesGuignot 1957 is a junior synonym of the widespread Afrotropical–Arabian Copelatuspulchellus (Klug, 1834) (syn. nov.). Copelatusmarginipennis (Laporte, 1835) is reinstated (stat. nov.) as a valid species with Copelatusaldabricus Balfour-Browne, 1950 and Copelatusaldabricusvar.simplex Guignot, 1952 as junior synonyms (syn. nov.). We designate lectotypes for Colymbetesmarginipennis Laporte, 1835 and Copelatusobtusus Boheman, 1848. Copelatusperidinus Guignot, 1955 is recorded for Madagascar for the first time and Copelatusnodieri Régimbart, 1895 is rejected as a species present in Madagascar.
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Affiliation(s)
- Tolotra Ranarilalatiana
- Department of Entomology, Faculty of Sciences, Box 906, Antananarivo University, 101 Antananarivo, Madagascar Antananarivo University Antananarivo Madagascar
| | - Lala Harivelo Raveloson Ravaomanarivo
- Department of Entomology, Faculty of Sciences, Box 906, Antananarivo University, 101 Antananarivo, Madagascar Antananarivo University Antananarivo Madagascar
| | - Johannes Bergsten
- Department of Zoology, Swedish Museum of Natural History, Box 50007, SE-10405 Stockholm, Sweden Swedish Museum of Natural History Stockholm Sweden
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18
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Yang R, Wang Z, Zhou Y, Wang Z, Che Y. Establishment of six new Rhabdoblatta species (Blattodea, Blaberidae, Epilamprinae) from China. Zookeys 2019; 851:27-69. [PMID: 31205442 PMCID: PMC6557905 DOI: 10.3897/zookeys.851.31403] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 04/02/2019] [Indexed: 11/23/2022] Open
Abstract
This study examined 504 Rhabdoblatta specimens sampled from China, of which, 86 Rhabdoblatta specimens were used for COI sequencing. A phylogenetic analysis using the ML method and MOTUs estimations by ABGD and GMYC based on COI sequences was performed. Eighteen Rhabdoblatta species were identified when these data were combined with morphological data. Six new species were established among these samples, i.e., Rh.similsinuatasp. n., Rh.densimaculatasp. n., Rh.gyroflexasp. n., Rh.chaulformissp. n., Rh.maculatasp. n., and Rh.ecarinatasp. n. For the first time, females including female genitalia of 14 known Rhabdoblatta species are described worldwide. Our study shows that combining molecular species delimitation methods with morphological data helps to delimit species and understand cockroach biodiversity.
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Affiliation(s)
- Rong Yang
- Institute of Entomology, College of Plant Protection, Southwest University Beibei China
| | - Zhenzhen Wang
- Institute of Entomology, College of Plant Protection, Southwest University Beibei China
| | - Yanshuang Zhou
- Institute of Entomology, College of Plant Protection, Southwest University Beibei China
| | - Zongqing Wang
- Institute of Entomology, College of Plant Protection, Southwest University Beibei China
| | - Yanli Che
- Institute of Entomology, College of Plant Protection, Southwest University Beibei China
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19
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Hofmann EP, Nicholson KE, Luque-Montes IR, Köhler G, Cerrato-Mendoza CA, Medina-Flores M, Wilson LD, Townsend JH. Cryptic Diversity, but to What Extent? Discordance Between Single-Locus Species Delimitation Methods Within Mainland Anoles (Squamata: Dactyloidae) of Northern Central America. Front Genet 2019; 10:11. [PMID: 30804976 PMCID: PMC6378269 DOI: 10.3389/fgene.2019.00011] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 01/11/2019] [Indexed: 01/10/2023] Open
Abstract
Single-locus molecular barcoding is a useful method for identifying overlooked and undescribed biodiversity, providing the groundwork for further systematic study and taxonomic investigation. A variety of methods for delimiting species from barcoding libraries have been developed and applied, allowing for rapid estimates of species diversity in a broad range of taxa. However, tree-based and distance-based analyses can infer different group assignments, potentially over- or underestimating the number of putative species groups. Here, we explore diversity of mainland species of anole lizards from the Chortís Block biogeographical province of northern Central America using a DNA barcoding approach, generating and analyzing cytochrome oxidase subunit I (COI) sequences for over 400 samples assignable to 33 of 38 (86.8%) native and one introduced mainland species. We subsequently tested the effects different models of nucleotide substitution, different species-delimitation algorithms, and reducing our dataset had on species delimitation estimates. We performed of two distance-based (ABGD, RESL) and three tree-based (bPTP, mPTP, GMYC) analyses on both the full dataset and a dataset consisting only of unique halotypes. From 34 nominal taxa, analyses of the full dataset recovered between 34 and 64 operational taxonomic units (OTUs), while analyses of the reduced dataset inferred between 36 and 59. Reassigning individuals to either mPTP-inferred or ABGD clustered (7.2% threshold) groups improved the detection of a barcoding gap across three different models of nucleotide substitution, removing overlap between intra- and interspecific distances. Our results highlight the underestimated diversity of mainland Chortís Block anoles, but the lack of congruence between analyses demonstrates the importance of considering multiple analytical methods when dealing with single-locus datasets. We recommend future studies consider the effects of different models of nucleotide substitution on proposed barcoding gaps, as well as the effect reducing a dataset to unique haplotypes may have on proposed diversity estimates.
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Affiliation(s)
- Erich P. Hofmann
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA, United States
- Department of Biological Sciences, Clemson University, Clemson, SC, United States
| | - Kirsten E. Nicholson
- Department of Biology, Central Michigan University, Mount Pleasant, MI, United States
| | | | - Gunther Köhler
- Senckenberg Forschungsinstitut und Naturmuseum, Frankfurt, Germany
| | - César A. Cerrato-Mendoza
- Federación Hondureña de Deportes de Montaña Y Escalada, Departamento de Francisco Morazán, Tegucigalpa, Honduras
| | - Melissa Medina-Flores
- Federación Hondureña de Deportes de Montaña Y Escalada, Departamento de Francisco Morazán, Tegucigalpa, Honduras
| | - Larry David Wilson
- Centro Zamorano de Biodiversidad, Escuela Agrícola Panamericana Zamorano, Departamento de Francisco Morazán, Tegucigalpa, Honduras
| | - Josiah H. Townsend
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA, United States
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20
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Amador L, Parada A, D'Elía G, Guayasamin JM. Uncovering hidden specific diversity of Andean glassfrogs of the Centrolene buckleyi species complex (Anura: Centrolenidae). PeerJ 2018; 6:e5856. [PMID: 30402351 PMCID: PMC6215445 DOI: 10.7717/peerj.5856] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 10/02/2018] [Indexed: 11/20/2022] Open
Abstract
The glassfrog Centrolene buckleyi has been recognized as a species complex. Herein, using coalescence-based species delimitation methods, we evaluate the specific diversity within this taxon. Four coalescence approaches (generalized mixed Yule coalescents, Bayesian general mixed Yule-coalescent, Poisson tree processes, and Bayesian Poisson tree processes) were consistent with the delimitation results, identifying four lineages within what is currently recognized as C. buckleyi. We propose three new candidate species that should be tested with nuclear markers, morphological, and behavioral data. In the meantime, for conservation purposes, candidate species should be considered evolutionary significant units, in light of observed population crashes in the C. buckleyi species complex. Finally, our results support the validity of C. venezuelense, formerly considered as a subspecies of C. buckleyi.
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Affiliation(s)
- Luis Amador
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.,Departamento de Investigación Científica, Universidad Laica Vicente Rocafuerte de Guayaquil, Guayaquil, Ecuador
| | - Andrés Parada
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Guillermo D'Elía
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Juan M Guayasamin
- Instituto BIÓSFERA-USFQ, Laboratorio de Biología Evolutiva, Colegio de Ciencias Biológicas y Ambientales COCIBA, Universidad San Francisco de Quito, Quito, Ecuador.,Centro de Investigación de la Biodiversidad y Cambio Climático, Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias del Medio Ambiente, Universidad Tecnológica Indoamérica, Quito, Ecuador
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21
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Galen SC, Nunes R, Sweet PR, Perkins SL. Integrating coalescent species delimitation with analysis of host specificity reveals extensive cryptic diversity despite minimal mitochondrial divergence in the malaria parasite genus Leucocytozoon. BMC Evol Biol 2018; 18:128. [PMID: 30165810 PMCID: PMC6117968 DOI: 10.1186/s12862-018-1242-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 08/15/2018] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Coalescent methods that use multi-locus sequence data are powerful tools for identifying putatively reproductively isolated lineages, though this approach has rarely been used for the study of microbial groups that are likely to harbor many unrecognized species. Among microbial symbionts, integrating genetic species delimitation methods with trait data that could indicate reproductive isolation, such as host specificity data, has rarely been used despite its potential to inform species limits. Here we test the ability of an integrative approach combining genetic and host specificity data to delimit species within the avian malaria parasite genus Leucocytozoon in central Alaska. RESULTS We sequenced seven nuclear loci for 69 Leucocytozoon samples and used multiple species delimitation methods (GMYC and BPP models), tested for differences in host infection patterns among putative species based on 406 individual infections, and characterized parasite morphology. We found that cryptic morphology has masked a highly diverse Leucocytozoon assemblage, with most species delimitation methods recovering support for at least 21 separate species that occur sympatrically and have divergent host infection patterns. Reproductive isolation among putative species appears to have evolved despite low mtDNA divergence, and in one instance two Leucocytozoon cytb haplotypes that differed by a single base pair (~ 0.2% divergence) were supported as separate species. However, there was no consistent association between mtDNA divergence and species limits. Among cytb haplotypes that differed by one to three base pairs we observed idiosyncratic patterns of nuclear and ecological divergence, with cytb haplotype pairs found to be either conspecific, reproductively isolated with no divergence in host specificity, or reproductively isolated with divergent patterns of host specialization. CONCLUSION Integrating multi-locus genetic species delimitation methods and non-traditional ecological data types such as host specificity provide a novel view of the diversity of avian malaria parasites that has been missed previously using morphology and mtDNA barcodes. Species delimitation methods show that Leucocytozoon is highly species-rich in Alaska, and the genus is likely to harbor extraordinary species-level diversity worldwide. Integrating genetic and ecological data will be an important approach for understanding the diversity and evolutionary history of microbial symbionts moving forward.
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Affiliation(s)
- Spencer C. Galen
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024 USA
- Richard Gilder Graduate School, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024 USA
| | - Renato Nunes
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024 USA
| | - Paul R. Sweet
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024 USA
| | - Susan L. Perkins
- 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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22
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Hjalmarsson AE, Graf W, Jähnig SC, Vitecek S, Pauls SU. Molecular association and morphological characterisation of Himalopsyche larval types (Trichoptera, Rhyacophilidae). Zookeys 2018; 773:79-108. [PMID: 30026662 PMCID: PMC6048183 DOI: 10.3897/zookeys.773.24319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 05/23/2018] [Indexed: 12/22/2022] Open
Abstract
Himalopsyche Banks, 1940 (Trichoptera, Rhyacophilidae) is a genus of caddisflies inhabiting mountain and alpine environments in Central and East Asia and the Nearctic. Of 53 known species, only five species have been described previously in the aquatic larval stage. We perform life stage association using three strategies (GMYC, PTP, and reciprocal monophyly) based on fragments of two molecular markers: the nuclear CAD, and the mitochondrial COI gene. A total of 525 individuals from across the range of Himalopsyche (Himalayas, Hengduan Shan, Tian Shan, South East Asia, Japan, and western North America) was analysed and 32 operational taxonomic units (OTUs) in our dataset delimited. Four distinct larval types of Himalopsyche are uncovered, and these are defined as the phryganea type, japonica type, tibetana type, and gigantea type and a comparative morphological characterisation of the larval types is presented. The larval types differ in a number of traits, most prominently in their gill configuration, as well as in other features such as setal configuration of the pronotum and presence/absence of accessory hooks of the anal prolegs.
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Affiliation(s)
- Anna E Hjalmarsson
- Goethe-University Frankfurt, 60323 Frankfurt am Main, Germany. Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 63025 Frankfurt am Main, Germany
| | - Wolfram Graf
- Institute of Hydrobiology and Aquatic Ecology Management, University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33/DG, 1180 Vienna, Austria
| | - Sonja C Jähnig
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Ecosystem Research, Justus-von-Liebig-Str. 7, 12489 Berlin, Germany
| | - Simon Vitecek
- Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 63025 Frankfurt am Main, Germany
| | - Steffen U Pauls
- Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 63025 Frankfurt am Main, Germany
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Chakona A, Kadye WT, Bere T, Mazungula DN, Vreven E. Evidence of hidden diversity and taxonomic conflicts in five stream fishes from the Eastern Zimbabwe Highlands freshwater ecoregion. Zookeys 2018:69-95. [PMID: 29955212 PMCID: PMC6019476 DOI: 10.3897/zookeys.768.21944] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 04/25/2018] [Indexed: 11/25/2022] Open
Abstract
Stream fishes of the Eastern Afromontane region are among the least studied vertebrates in this region, despite the potential for harbouring cryptic diversity. The present study examined mitochondrial cytochrome oxidase subunit I (COI) sequence divergence in 153 specimens of stream fishes belonging to four genera and three families, [(Amphilius and Zaireichthys (Amphiliidae); Chiloglanis (Mochokidae); and Hippopotamyrus (Mormyridae)], in the Eastern Zimbabwe Highlands (EZH) freshwater ecoregion to explore the extent to which the current taxonomy conceals the ichthyofaunal diversity in the region. The General Mixed Yule Coalescent (GMYC) species delineation method identified 14 clusters within five currently recognised ‘species’ from the EZH ecoregion. Only one of these clusters represents a named species, while 13 of them represent candidate or undescribed species. Our results revealed that effective conservation of this region’s unique biota is limited by the incomplete knowledge of taxonomic diversity and inaccurate mapping of species distribution ranges.
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Affiliation(s)
- Albert Chakona
- South African Institute for Aquatic Biodiversity, Private Bag 1015, Grahamstown, South Africa, 6140.,Department of Ichthyology and Fisheries Science, Rhodes University, P.O. Box 94, Grahamstown, South Africa, 6140
| | - Wilbert T Kadye
- Department of Ichthyology and Fisheries Science, Rhodes University, P.O. Box 94, Grahamstown, South Africa, 6140
| | - Taurai Bere
- School of Wildlife, Ecology and Conservation, Chinhoyi University of Technology, P. Bag 7724, Chinhoyi, Zimbabwe
| | - Daniel N Mazungula
- South African Institute for Aquatic Biodiversity, Private Bag 1015, Grahamstown, South Africa, 6140.,Department of Ichthyology and Fisheries Science, Rhodes University, P.O. Box 94, Grahamstown, South Africa, 6140
| | - Emmanuel Vreven
- Royal Museum for Central Africa, Section of Vertebrates, Ichthyology, Leuvensesteenweg 13, 3080, Tervuren, Belgium.,KU Leuven, Department of Biology, Laboratory of Biodiversity and Evolutionary Genomics, Deberiotstraat 32, 3000 Leuven, Belgium
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24
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Lorén JG, Farfán M, Fusté MC. Species Delimitation, Phylogenetic Relationships, and Temporal Divergence Model in the Genus Aeromonas. Front Microbiol 2018; 9:770. [PMID: 29731747 PMCID: PMC5920023 DOI: 10.3389/fmicb.2018.00770] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/05/2018] [Indexed: 11/16/2022] Open
Abstract
The definition of species boundaries constitutes an important challenge in biodiversity studies. In this work we applied the Generalized Mixed Yule Coalescent (GMYC) method, which determines a divergence threshold to delimit species in a phylogenetic tree. Based on the tree branching pattern, the analysis fixes the transition threshold between speciation and the coalescent process associated with the intra-species diversification. This approach has been widely used to delineate eukaryote species and establish their diversification process from sequence data. Nevertheless, there are few examples in which this analysis has been applied to a bacterial population. Although the GMYC method was originally designed to assume a constant (Yule) model of diversification at between-species level, it was later evaluated simulating other conditions. Our aim was therefore to determine the species delineation in Aeromonas using the GMYC method and asses which model best explains the speciation process in this bacterial genus. The application of the GMYC method allowed us to clearly delineate the Aeromonas species boundaries, even in the controversial groups, such as the A. veronii or A. media species complexes.
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Affiliation(s)
- J G Lorén
- Departament de Biologia, Sanitat i Medi Ambient, Secció de Microbiologia, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Spain
| | - Maribel Farfán
- Departament de Biologia, Sanitat i Medi Ambient, Secció de Microbiologia, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - M C Fusté
- Departament de Biologia, Sanitat i Medi Ambient, Secció de Microbiologia, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
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25
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da Silva R, Peloso PLV, Sturaro MJ, Veneza I, Sampaio I, Schneider H, Gomes G. Comparative analyses of species delimitation methods with molecular data in snappers (Perciformes: Lutjaninae). Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:1108-1114. [PMID: 29216781 DOI: 10.1080/24701394.2017.1413364] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The integration of approaches that allow the incorporation of stochasticity of gene histories with phylogenetic methods resulted in new approaches for the old issue of species delimitation. Nevertheless, coalescent methods seem problematic for taxa with large effective population size and shallow temporal diversification (like marine fishes). Here, we investigate the performance of single-locus (cytochrome oxidase 1, commonly used in DNA barcoding initiatives) methods for molecular species delimitation in snappers of Lutjaninae from the Western Atlantic and Pacific Eastern. Our results show incongruences among methods. ABGD, PTP and mPTP trend towards a lower number of estimated species. Phylogenetic-coalescent methods with single threshold were majority congruent for a same number of lineages. On the other hand, algorithms with multiple thresholds tend to estimate a higher number of potential species. We do not endorse the use of single-locus for species delimitation, but we do reinforce that single-locus data is sufficient to flag many problems.
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Affiliation(s)
- Raimundo da Silva
- a Laboratório de Genética Aplicada, Universidade Federal do Pará , Bragança , Brazil
| | - Pedro L V Peloso
- b Coordenação de Zoologia, Museu Paraense Emílio Goeldi , Belém , Brazil
| | | | - Ivana Veneza
- a Laboratório de Genética Aplicada, Universidade Federal do Pará , Bragança , Brazil
| | - Iracilda Sampaio
- d Laboratório de Genética e Biologia Molecular, Universidade Federal do Pará , Bragança , Brazil
| | - Horacio Schneider
- d Laboratório de Genética e Biologia Molecular, Universidade Federal do Pará , Bragança , Brazil
| | - Grazielle Gomes
- a Laboratório de Genética Aplicada, Universidade Federal do Pará , Bragança , Brazil
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26
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Bergsten J, Weingartner E, Hájek J. Species delimitation of the Hyphydrus ovatus complex in western Palaearctic with an update of species distributions (Coleoptera, Dytiscidae). Zookeys 2017:73-96. [PMID: 28769697 PMCID: PMC5523363 DOI: 10.3897/zookeys.678.12886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 05/10/2017] [Indexed: 11/12/2022] Open
Abstract
The species status of Hyphydrusanatolicus Guignot, 1957 and H.sanctus Sharp, 1882, previously often confused with the widespread H.ovatus (Linnaeus, 1760), are tested with molecular and morphological characters. Cytochrome c oxidase subunit 1 (CO1) was sequenced for 32 specimens of all three species. Gene-trees were inferred with parsimony, time-free bayesian and strict clock bayesian analyses. The GMYC model was used to estimate species limits. All three species were reciprocally monophyletic with CO1 and highly supported. The GMYC species delimitation analysis unequivocally delimited the three species with no other than the three species solution included in the confidence interval. A likelihood ratio test rejected the one-species null model. Important morphological characters distinguishing the species are provided and illustrated. New distributional data are given for the following species: Hyphydrusanatolicus from Slovakia and Ukraine, and H.aubei Ganglbauer, 1891, and H.sanctus from Turkey.
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Affiliation(s)
- Johannes Bergsten
- Department of Zoology, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | | | - Jiří Hájek
- Department of Entomology, National Museum, Cirkusová 1740, CZ-193 00 Praha 9 - Horní Počernice, Czech Republic
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27
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Abstract
Macalpinomyces was established in 1977, with the type species M. eriachnes described from a specimen collected in northern Australia on the grass Eriachne sp. in 1855. Subsequently, M. eriachnes has been reported on more than 21 species of Eriachne in northern Australia. In this study, a polyphasic approach was employed to determine whether M. eriachnes masked cryptic diversity. On the basis of morphology, multilocus phylogeny, and coalescent methods of generalized mixed Yule-coalescent (GMYC) and Poisson tree processes (PTP) models, 26 specimens of Macalpinomyces on 13 species of Eriachne held in Australian herbaria were studied. Consequently, 10 new species of Macalpinomyces that satisfied the phylogenetic species recognition criteria are described.
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Affiliation(s)
- Ying-Ming Li
- a State Key Laboratory of Mycology, Institute of Microbiology , Chinese Academy of Sciences , Beijing 100101 , China.,b College of Life Sciences , University of Chinese Academy of Sciences , Beijing , 100049 , China
| | - Roger G Shivas
- c Plant Pathology Herbarium , Department of Agriculture and Fisheries , Dutton Park , Queensland 4102 , Australia
| | - Alistair R McTaggart
- d Department of Microbiology and Plant Pathology, Tree Protection Co-operative Programme (TPCP), Forestry and Agricultural Biotechnology Institute (FABI) , University of Pretoria , Private Bag X20, Pretoria 0028 , South Africa
| | - Peng Zhao
- a State Key Laboratory of Mycology, Institute of Microbiology , Chinese Academy of Sciences , Beijing 100101 , China.,b College of Life Sciences , University of Chinese Academy of Sciences , Beijing , 100049 , China
| | - Lei Cai
- a State Key Laboratory of Mycology, Institute of Microbiology , Chinese Academy of Sciences , Beijing 100101 , China.,b College of Life Sciences , University of Chinese Academy of Sciences , Beijing , 100049 , China
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28
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Tomioka S, Kondoh T, Sato-Okoshi W, Ito K, Kakui K, Kajihara H. Cosmopolitan or Cryptic Species? A Case Study of Capitella teleta (Annelida: Capitellidae). Zoolog Sci 2017; 33:545-554. [PMID: 27715419 DOI: 10.2108/zs160059] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Capitella teleta Blake et al., 2009 is an opportunistic capitellid originally described from Massachusetts (USA), but also reported from the Mediterranean, NW Atlantic, and North Pacific, including Japan. This putatively wide distribution had not been tested with DNA sequence data; intraspecific variation in morphological characters diagnostic for the species had not been assessed with specimens from non-type localities, and the species status of the Japanese population(s) was uncertain. We examined the morphology and mitochondrial COI (cytochrome c oxidase subunit I) gene sequences of Capitella specimens from two localities (Ainan and Gamo) in Japan. Specimens from Ainan and Gamo differed from C. teleta from Massachusetts in methyl-green staining pattern, shape of the genital spines, and shape of the capillary chaetae; we concluded that these characters vary intraspecifically. Species delimitation analyses of COI sequences suggested that worms from Ainan and Massachusetts represent C. teleta; these populations share a COI haplotype. The specimens from Gamo may represent a distinct species and comprise a sister group to C. teleta s. str.; we refer to the Gamo population as Capitella aff. teleta. The average Kimura 2-parameter (K2P) distance between C. teleta s. str. and C. aff. teleta was 3.7%. The COI data indicate that C. teleta actually occurs in both the NW Atlantic and NW Pacific. Given the short planktonic larval duration of C. teleta, this broad distribution may have resulted from anthropogenic dispersal.
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Affiliation(s)
- Shinri Tomioka
- 1 Department of Natural History Sciences, Graduate School of Science, Hokkaido University,N10 W8, Sapporo 060-0810, Japan
| | - Tomohiko Kondoh
- 2 Laboratory of Biological Oceanography, Graduate School of Agricultural Science,Tohoku University, Sendai 981-8555, Japan
| | - Waka Sato-Okoshi
- 2 Laboratory of Biological Oceanography, Graduate School of Agricultural Science,Tohoku University, Sendai 981-8555, Japan
| | - Katsutoshi Ito
- 3 National Research Institute of Fisheries and Environment of Inland Sea, FisheriesResearch Agency, Maruishi 2-17-5, Hatsukaichi 739-0452, Japan
| | - Keiichi Kakui
- 1 Department of Natural History Sciences, Graduate School of Science, Hokkaido University,N10 W8, Sapporo 060-0810, Japan
| | - Hiroshi Kajihara
- 1 Department of Natural History Sciences, Graduate School of Science, Hokkaido University,N10 W8, Sapporo 060-0810, Japan
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29
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Gélin P, Postaire B, Fauvelot C, Magalon H. Reevaluating species number, distribution and endemism of the coral genus Pocillopora Lamarck, 1816 using species delimitation methods and microsatellites. Mol Phylogenet Evol 2017; 109:430-446. [PMID: 28219759 DOI: 10.1016/j.ympev.2017.01.018] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 01/25/2017] [Accepted: 01/30/2017] [Indexed: 01/06/2023]
Abstract
Species delimitation methods based on genetic information, notably using single locus data, have been proposed as means of increasing the rate of biodiversity description, but can also be used to clarify complex taxonomies. In this study, we explore the species diversity within the cnidarian genus Pocillopora, widely distributed in the tropical belt of the Indo-Pacific Ocean. From 943 Pocillopora colonies sampled in the Western Indian Ocean, the Tropical Southwestern Pacific and Southeast Polynesia, representing a huge variety of morphotypes, we delineated Primary Species Hypotheses (PSH) applying the Automatic Barcode Gap Discovery method, the Poisson Tree Processes algorithm and the Generalized mixed Yule-coalescent model on two mitochondrial markers (Open Reading Frame and Dloop) and reconstructing a haploweb using one nuclear marker (Internal Transcribed Spacer 2). Then, we confronted identified PSHs to the results of clustering analyses using 13 microsatellites to determine Secondary Species Hypotheses (SSH). Based on the congruence of all methods used and adding sequences from the literature, we defined at least 18 Secondary Species Hypotheses among 14 morphotypes, confirming the high phenotypic plasticity in Pocillopora species and the presence of cryptic lineages. We also identified three new genetic lineages never found to date, which could represent three new putative species. Moreover, the biogeographical ranges of several SSHs were re-assessed in the light of genetic data, which may have direct implications in conservation policies. Indeed, the cryptic diversity within this genus should be taken into account seriously, as neglecting its importance is source of confusion in our understanding of ecosystem functioning. Next generation sequencing, combined with other parameters (i.e. microstructure, zooxanthellae identification, ecology even at a micro-scale, resistance and resilience ability to bleaching) will be the next step towards an integrative framework of Pocillopora taxonomy, which will have profound implications for ecological studies, such as studying biodiversity, response to global warming and symbiosis.
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Affiliation(s)
- P Gélin
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS), Laboratoire d'excellence-CORAIL, Faculté des Sciences et Technologies, 15 Bd René Cassin, CS 92003, 97744 St Denis Cedex 09, La Réunion, France
| | - B Postaire
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS), Laboratoire d'excellence-CORAIL, Faculté des Sciences et Technologies, 15 Bd René Cassin, CS 92003, 97744 St Denis Cedex 09, La Réunion, France
| | - C Fauvelot
- UMR ENTROPIE (IRD, Université de La Réunion, CNRS), Laboratoire d'excellence-CORAIL, Centre IRD de Nouméa, 101 Promenade Roger Laroque, BP A5, 98848 Nouméa cedex, New Caledonia
| | - H Magalon
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS), Laboratoire d'excellence-CORAIL, Faculté des Sciences et Technologies, 15 Bd René Cassin, CS 92003, 97744 St Denis Cedex 09, La Réunion, France.
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30
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Arrigoni R, Berumen ML, Chen CA, Terraneo TI, Baird AH, Payri C, Benzoni F. Species delimitation in the reef coral genera Echinophyllia and Oxypora (Scleractinia, Lobophylliidae) with a description of two new species. Mol Phylogenet Evol 2016; 105:146-159. [PMID: 27593164 DOI: 10.1016/j.ympev.2016.08.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/26/2016] [Accepted: 08/31/2016] [Indexed: 10/21/2022]
Abstract
Scleractinian corals are affected by environment-induced phenotypic plasticity and intraspecific morphological variation caused by genotype. In an effort to identify new strategies for resolving this taxonomic issue, we applied a molecular approach for species evaluation to two closely related genera, Echinophyllia and Oxypora, for which few molecular data are available. A robust multi-locus phylogeny using DNA sequence data across four loci of both mitochondrial (COI, ATP6-NAD4) and nuclear (histone H3, ITS region) origin from 109 coral colonies was coupled with three independent putative species delimitation methods based on barcoding threshold (ABGD) and coalescence theory (PTP, GMYC). Observed overall congruence across multiple genetic analyses distinguished two traditional species (E. echinoporoides and O. convoluta), a species complex composed of E. aspera, E. orpheensis, E. tarae, and O. glabra, whereas O. lacera and E. echinata were indistinguishable with the sequenced loci. The combination of molecular species delimitation approaches and skeletal character observations allowed the description of two new reef coral species, E. bulbosa sp. n. from the Red Sea and E. gallii sp. n. from the Maldives and Mayotte. This work demonstrated the efficiency of multi-locus phylogenetic analyses and recently developed molecular species delimitation approaches as valuable tools to disentangle taxonomic issues caused by morphological ambiguities and to re-assess the diversity of scleractinian corals.
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Affiliation(s)
- Roberto Arrigoni
- Red Sea Research Center, Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
| | - Michael L Berumen
- Red Sea Research Center, Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Chaolun Allen Chen
- Biodiversity Research Centre, Academia Sinica, Nangang, Taipei 115, Taiwan; Institute of Oceanography, National Taiwan University, Taipei 106, Taiwan
| | - Tullia I Terraneo
- Red Sea Research Center, Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Andrew H Baird
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville 4811, Australia
| | - Claude Payri
- UMR ENTROPIE (IRD, Université de La Réunion, CNRS), Laboratoire d'excellence-CORAIL, centre IRD de Nouméa, 101 Promenade Roger Laroque, BP A5, 98848 Noumea Cedex, New Caledonia
| | - Francesca Benzoni
- UMR ENTROPIE (IRD, Université de La Réunion, CNRS), Laboratoire d'excellence-CORAIL, centre IRD de Nouméa, 101 Promenade Roger Laroque, BP A5, 98848 Noumea Cedex, New Caledonia; Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
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31
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Mateussi NTB, Pavanelli CS, Oliveira C. Molecular identification of cryptic diversity in species of cis-Andean Mylossoma (Characiformes: Serrasalmidae). Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:778-780. [PMID: 27159585 DOI: 10.1080/24701394.2016.1180515] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Mylossoma is a Serrasalmidae genus with only two current valid species in the cis-Andean region but with several available names, today considered as junior synonymous. Morphological information combined with single-locus DNA sequences of cytochrome c oxidase I gene analysed by Barcode Index Number and General Mixed Yule Coalescent model were used in the present study to help the recognition of Operational Taxonomic Units (OTUs) in cis-Andean Mylossoma and discuss species boundaries within the genus. Five OTUs were recognized based on both morphological and molecular approaches. The analysis using the Barcode Index Number resulted in five OTUs, with M. duriventre being split in one unity in the Amazon, one in the Orinoco, one in Paraná-Paraguay and one in Tocantins-Araguaia which is coherent with our morphological results.
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Affiliation(s)
- Nadayca T B Mateussi
- a Coleção Ictiológica, Núcleo De Pesquisas Em Limnologia, Ictiologia E Aquicultura , Universidade Estadual De Maringá , Maringá , Brazil.,b Laboratório De Biologia E Genética De Peixes, Departamento De Morfologia , Universidade Estadual Paulista, Distrito De Rubião Junior , Botucatu , Brazil.,c Programa De Pós-Graduação Em Ecologia De Ambientes Aquáticos Continentais , Universidade Estadual De Maringá , Maringá , Brazil
| | - Carla Simone Pavanelli
- a Coleção Ictiológica, Núcleo De Pesquisas Em Limnologia, Ictiologia E Aquicultura , Universidade Estadual De Maringá , Maringá , Brazil.,c Programa De Pós-Graduação Em Ecologia De Ambientes Aquáticos Continentais , Universidade Estadual De Maringá , Maringá , Brazil
| | - Claudio Oliveira
- b Laboratório De Biologia E Genética De Peixes, Departamento De Morfologia , Universidade Estadual Paulista, Distrito De Rubião Junior , Botucatu , Brazil
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32
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Fossen EI, Ekrem T, Nilsson AN, Bergsten J. Species delimitation in northern European water scavenger beetles of the genus Hydrobius (Coleoptera, Hydrophilidae). Zookeys 2016; 564:71-120. [PMID: 27081333 PMCID: PMC4820092 DOI: 10.3897/zookeys.564.6558] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 12/23/2015] [Indexed: 12/18/2022] Open
Abstract
The chiefly Holarctic Hydrobius species complex (Coleoptera, Hydrophilidae) currently consists of Hydrobius arcticus Kuwert, 1890, and three morphological variants of Hydrobius fuscipes (Linnaeus, 1758): var. fuscipes, var. rottenbergii and var. subrotundus in northern Europe. Here molecular and morphological data are used to test the species boundaries in this species complex. Three gene segments (COI, H3 and ITS2) were sequenced and analyzed with Bayesian methods to infer phylogenetic relationships. The Generalized Mixed Yule Coalescent (GMYC) model and two versions of the Bayesian species delimitation method BPP, with or without an a priori defined guide tree (v2.2 & v3.0), were used to evaluate species limits. External and male genital characters of primarily Fennoscandian specimens were measured and statistically analyzed to test for significant differences in quantitative morphological characters. The four morphotypes formed separate genetic clusters on gene trees and were delimited as separate species by GMYC and by both versions of BPP, despite specimens of Hydrobius fuscipes var. fuscipes and Hydrobius fuscipes var. subrotundus being sympatric. Hydrobius arcticus and Hydrobius fuscipes var. rottenbergii could only be separated genetically with ITS2, and were delimited statistically with GMYC on ITS2 and with BPP on the combined data. In addition, six or seven potentially cryptic species of the Hydrobius fuscipes complex from regions outside northern Europe were delimited genetically. Although some overlap was found, the mean values of six male genital characters were significantly different between the morphotypes (p < 0.001). Morphological characters previously presumed to be diagnostic were less reliable to separate Hydrobius fuscipes var. fuscipes from Hydrobius fuscipes var. subrotundus, but characters in the literature for Hydrobius arcticus and Hydrobius fuscipes var. rottenbergii were diagnostic. Overall, morphological and molecular evidence strongly suggest that Hydrobius arcticus and the three morphological variants of Hydrobius fuscipes are separate species and Hydrobius rottenbergii Gerhardt, 1872, stat. n. and Hydrobius subrotundus Stephens, 1829, stat. n. are elevated to valid species. An identification key to northern European species of Hydrobius is provided.
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Affiliation(s)
- Erlend I. Fossen
- Department of Biology, Centre for Biodiversity Dynamics, NTNU Norwegian University of Science and Technology, 7491 Trondheim, Norway
- Department of Natural History, NTNU University Museum, 7491 Trondheim, Norway
| | - Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, 7491 Trondheim, Norway
| | - Anders N. Nilsson
- Department of Ecology and Environmental Science, University of Umeå, S-901 87 Umeå, Sweden
| | - Johannes Bergsten
- Department of Zoology, Swedish Museum of Natural History, Box 50007, SE-10405 Stockholm, Sweden
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33
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Schwarzfeld MD, Sperling FAH. Comparison of five methods for delimitating species in Ophion Fabricius, a diverse genus of parasitoid wasps (Hymenoptera, Ichneumonidae). Mol Phylogenet Evol 2015; 93:234-48. [PMID: 26265257 DOI: 10.1016/j.ympev.2015.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 07/31/2015] [Accepted: 08/04/2015] [Indexed: 10/23/2022]
Abstract
DNA taxonomy has been proposed as a method to quickly assess diversity and species limits in highly diverse, understudied taxa. Here we use five methods for species delimitation and two genetic markers (COI and ITS2) to assess species diversity within the parasitoid genus, Ophion. We searched for compensatory base changes (CBC's) in ITS2, and determined that they are too rare to be of practical use in delimiting species in this genus. The other four methods used both COI and ITS2, and included distance-based (threshold analysis and ABGD) and tree-based (GMYC and PTP) models. We compared the results of these analyses to each other under various parameters and tested their performance with respect to 11 Nearctic species/morphospecies and 15 described Palearctic species. We also computed barcode accumulation curves of COI sequences to assess the completeness of sampling. The species count was highly variable depending on the method and parameters used, ranging from 47 to 168 species, with more conservative estimates of 89-121 species. Despite this range, many of the Nearctic test species were fairly robust with respect to method. We concluded that while there was often good congruence between methods, GMYC and PTP were less reliant on arbitrary parameters than the other two methods and more easily applied to genetic markers other than COI. However, PTP was less successful at delimiting test species than was GMYC. All methods, as well as the barcode accumulation curves, indicate that several Palearctic species remain undescribed and that we have scarcely begun to appreciate the Nearctic diversity within this genus.
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Affiliation(s)
- Marla D Schwarzfeld
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada.
| | - Felix A H Sperling
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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Mutanen M, Kekkonen M, Prosser SWJ, Hebert PDN, Kaila L. One species in eight: DNA barcodes from type specimens resolve a taxonomic quagmire. Mol Ecol Resour 2015; 15:967-84. [PMID: 25524367 PMCID: PMC4964951 DOI: 10.1111/1755-0998.12361] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 12/04/2014] [Accepted: 12/08/2014] [Indexed: 11/26/2022]
Abstract
Each holotype specimen provides the only objective link to a particular Linnean binomen. Sequence information from them is increasingly valuable due to the growing usage of DNA barcodes in taxonomy. As type specimens are often old, it may only be possible to recover fragmentary sequence information from them. We tested the efficacy of short sequences from type specimens in the resolution of a challenging taxonomic puzzle: the Elachista dispunctella complex which includes 64 described species with minuscule morphological differences. We applied a multistep procedure to resolve the taxonomy of this species complex. First, we sequenced a large number of newly collected specimens and as many holotypes as possible. Second, we used all >400 bp examine species boundaries. We employed three unsupervised methods (BIN, ABGD, GMYC) with specified criteria on how to handle discordant results and examined diagnostic bases from each delineated putative species (operational taxonomic units, OTUs). Third, we evaluated the morphological characters of each OTU. Finally, we associated short barcodes from types with the delineated OTUs. In this step, we employed various supervised methods, including distance‐based, tree‐based and character‐based. We recovered 658 bp barcode sequences from 194 of 215 fresh specimens and recovered an average of 141 bp from 33 of 42 holotypes. We observed strong congruence among all methods and good correspondence with morphology. We demonstrate potential pitfalls with tree‐, distance‐ and character‐based approaches when associating sequences of varied length. Our results suggest that sequences as short as 56 bp can often provide valuable taxonomic information. The results support significant taxonomic oversplitting of species in the Elachista dispunctella complex.
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Affiliation(s)
- Marko Mutanen
- Biodiversity Unit, Department of Biology, University of Oulu, P.O. Box 3000, FI-90014, Oulu, Finland
| | - Mari Kekkonen
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 17, FI-00014, Helsinki, Finland.,Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Sean W J Prosser
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Paul D N Hebert
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Lauri Kaila
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 17, FI-00014, Helsinki, Finland
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Vieira C, D'hondt S, De Clerck O, Payri CE. Toward an inordinate fondness for stars, beetles and Lobophora? Species diversity of the genus Lobophora (Dictyotales, Phaeophyceae) in New Caledonia. J Phycol 2014; 50:1101-1119. [PMID: 26988791 DOI: 10.1111/jpy.12243] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 07/27/2014] [Indexed: 06/05/2023]
Abstract
Until the recent use of molecular markers, species diversity of Lobophora, an ecologically important brown algal genus with a worldwide distribution in temperate and tropical seas, has been critically underestimated. Using a DNA-based taxonomic approach, we re-examined diversity of the genus from New Caledonia in the Southwest Pacific Ocean. First, species were delineated using general mixed Yule coalescent-based and barcoding gap approaches applied to a mitochondrial cox3 data set. Results were subsequently confirmed using chloroplast psbA and rbcL data sets. Species delimitation analyses agreed well across markers and delimitation algorithms, with the barcoding gap approach being slightly more conservative. Analyses of the cox3 data set resulted in 31-39 molecular operational taxonomic units (MOTUs), four of which are previously described species (L. asiatica, L. crassa, L. nigrescens s.l., L. pachyventera). Of the remaining MOTUs for which we obtained a representative number of sequences and results are corroborated across analyses and genes, we described 10 species de novo: L. abaculusa, L. abscondita, L. densa, L. dimorpha, L. gibbera, L. hederacea, L. monticola, L. petila, L. rosacea, and L. undulata. Our study presents an excellent case of how a traditional morphology-based taxonomy fails to provide accurate estimates of algal diversity. Furthermore, the level of Lobophora diversity unveiled from a single locality in the Pacific Ocean raises important questions with respect to the global diversity of the genus, the distributions and range sizes of the individual species, as well as the mechanisms facilitating coexistence.
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Affiliation(s)
- Christophe Vieira
- CoRéUs, LabEx-CORAIL, U227 "Biocomplexité des écosystèmes coralliens", Institut de Recherche pour le Développement, B.P. A5, 98848 Nouméa Cedex, Nouvelle-Calédonie, France
- Sorbonne Universités, UPMC Univ Paris 06, IFD, 4 Place Jussieu, 75252, Paris Cedex 05, France
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281 (S8), Ghent, B-9000, Belgium
| | - Sofie D'hondt
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281 (S8), Ghent, B-9000, Belgium
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281 (S8), Ghent, B-9000, Belgium
| | - Claude E Payri
- CoRéUs, LabEx-CORAIL, U227 "Biocomplexité des écosystèmes coralliens", Institut de Recherche pour le Développement, B.P. A5, 98848 Nouméa Cedex, Nouvelle-Calédonie, France
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36
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Tang CQ, Humphreys AM, Fontaneto D, Barraclough TG, Paradis E. Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data. Methods Ecol Evol 2014; 5:1086-1094. [PMID: 25821577 PMCID: PMC4374709 DOI: 10.1111/2041-210x.12246] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 08/13/2014] [Indexed: 11/27/2022]
Abstract
Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The generalised mixed Yule coalescent (GMYC) and the Poisson tree process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such as DNA barcodes.
Here, we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothing methods. We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2000 separate species delimitation analyses across 16 empirical data sets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods.
The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification.
Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model-based gene tree (e.g. RAxML) and GMYC approaches with BEAST trees for obtaining species hypotheses.
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Affiliation(s)
- Cuong Q Tang
- Department of Life Sciences, Imperial College London Ascot, Berkshire, SL5 7PY, UK
| | - Aelys M Humphreys
- Department of Life Sciences, Imperial College London Ascot, Berkshire, SL5 7PY, UK ; Department of Ecology, Environment and Plant Sciences, Stockholm University 10691, Stockholm, Sweden
| | - Diego Fontaneto
- National Research Council, Institute of Ecosystem Study 28922, Verbania Pallanza, Italy
| | | | - Emmanuel Paradis
- Department of Life Sciences, Imperial College London Ascot, Berkshire, SL5 7PY, UK
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Tang CQ, Obertegger U, Fontaneto D, Barraclough TG. Sexual species are separated by larger genetic gaps than asexual species in rotifers. Evolution 2014; 68:2901-16. [PMID: 24975991 PMCID: PMC4262011 DOI: 10.1111/evo.12483] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 06/13/2014] [Indexed: 12/17/2022]
Abstract
Why organisms diversify into discrete species instead of showing a continuum of genotypic and phenotypic forms is an important yet rarely studied question in speciation biology. Does species discreteness come from adaptation to fill discrete niches or from interspecific gaps generated by reproductive isolation? We investigate the importance of reproductive isolation by comparing genetic discreteness, in terms of intra- and interspecific variation, between facultatively sexual monogonont rotifers and obligately asexual bdelloid rotifers. We calculated the age (phylogenetic distance) and average pairwise genetic distance (raw distance) within and among evolutionarily significant units of diversity in six bdelloid clades and seven monogonont clades sampled for 4211 individuals in total. We find that monogonont species are more discrete than bdelloid species with respect to divergence between species but exhibit similar levels of intraspecific variation (species cohesiveness). This pattern arises because bdelloids have diversified into discrete genetic clusters at a faster net rate than monogononts. Although sampling biases or differences in ecology that are independent of sexuality might also affect these patterns, the results are consistent with the hypothesis that bdelloids diversified at a faster rate into less discrete species because their diversification does not depend on the evolution of reproductive isolation.
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Affiliation(s)
- Cuong Q Tang
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, SL5 7PY, United Kingdom.
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Millanes AM, Truong C, Westberg M, Diederich P, Wedin M. Host switching promotes diversity in host-specialized mycoparasitic fungi: uncoupled evolution in the Biatoropsis-usnea system. Evolution 2014; 68:1576-93. [PMID: 24495034 DOI: 10.1111/evo.12374] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 01/24/2014] [Indexed: 12/15/2022]
Abstract
Fungal mycoparasitism-fungi parasitizing other fungi-is a common lifestyle in some basal lineages of the basidiomycetes, particularly within the Tremellales. Relatively nonaggressive mycoparasitic fungi of this group are in general highly host specific, suggesting cospeciation as a plausible speciation mode in these associations. Species delimitation in the Tremellales is often challenging because morphological characters are scant. Host specificity is therefore a great aid to discriminate between species but appropriate species delimitation methods that account for actual diversity are needed to identify both specialist and generalist taxa and avoid inflating or underestimating diversity. We use the Biatoropsis-Usnea system to study factors inducing parasite diversification. We employ morphological, ecological, and molecular data-methods including genealogical concordance phylogenetic species recognition (GCPSR) and the general mixed Yule-coalescent (GMYC) model-to assess the diversity of fungi currently assigned to Biatoropsis usnearum. The degree of cospeciation in this association is assessed with two cophylogeny analysis tools (ParaFit and Jane 4.0). Biatoropsis constitutes a species complex formed by at least seven different independent lineages and host switching is a prominent force driving speciation, particularly in host specialists. Combining ITS and nLSU is recommended as barcode system in tremellalean fungi.
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Affiliation(s)
- Ana M Millanes
- Departamento de Biología y Geología, Universidad Rey Juan Carlos, E-28933 Móstoles, Spain.
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Belton GS, van Reine WFP, Huisman JM, Draisma SGA, D Gurgel CF. Resolving phenotypic plasticity and species designation in the morphologically challenging Caulerpa racemosa-peltata complex (Chlorophyta, Caulerpaceae). J Phycol 2014; 50:32-54. [PMID: 26988007 DOI: 10.1111/jpy.12132] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 09/07/2013] [Indexed: 06/05/2023]
Abstract
Although recent molecular studies have indicated the presence of a number of distinct species within the Caulerpa racemosa-peltata complex, due to the difficulties presented by high levels of phenotypic plasticity and the large number of synonyms, infra-specific taxa, and names of uncertain affinity, taxonomic proposals are yet to be made. In this study, we aimed to resolve the taxonomy of the complex and provide an example of how historical nomenclature can best be integrated into molecular based taxonomies. We accomplished this by first determining the number of genetic species within our globally sampled data set through a combination of phylogenetic and species-delimitation approaches of partial elongation factor TU and RUBISCO large subunit gene sequences. Guided by these results, comparative morphological examinations were then undertaken to gauge the extent of phenotypic plasticity within each species, as well as any morphological overlap between them. Our results revealed the presence of 11 distinct species within the complex, five of which showed high levels of phenotypic plasticity and partial overlap with other species. On the basis of observations of a large number of specimens, including type specimens/descriptions, and geographic inferences, we were able to confidently designate names for the lineages. Caulerpa peltata, C. imbricata and C. racemosa vars. laetevirens, occidentalis and turbinata were found to represent environmentally induced forms of a single species, for which the earlier-described C. chemnitzia, previously regarded as a synonym of C. racemosa var. turbinata, is reinstated. C. cylindracea, C. lamourouxii, C. macrodisca, C. nummularia and C. oligophylla are also reinstated and two new species, C. macra stat. nov. and C. megadisca sp. nov., are proposed.
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Affiliation(s)
- Gareth S Belton
- School of Earth and Environmental Sciences, The University of Adelaide, North Terrace, Adelaide, South Australia, 5005, Australia
| | | | - John M Huisman
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, 6150, Australia
- Western Australian Herbarium, Science Division, Department of Parks and Wildlife, Bentley Delivery Centre, Locked Bag 104, Bentley, Western Australia, 6983, Australia
| | - Stefano G A Draisma
- Institute of Ocean & Earth Sciences, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | - Carlos Frederico D Gurgel
- School of Earth and Environmental Sciences, The University of Adelaide, North Terrace, Adelaide, South Australia, 5005, Australia
- Department of Environment, Water & Natural Resources, South Australian State Herbarium, GPO Box 1047, Adelaide, South Australia, 5001, Australia
- Aquatic Sciences, South Australian Research and Development Institute, P.O. Box 120, Henley Beach, South Australia, 5022, Australia
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40
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Hjalmarsson AE, Bukontaite R, Ranarilalatiana T, Randriamihaja JH, Bergsten J. Taxonomic revision of Madagascan Rhantus (Coleoptera, Dytiscidae, Colymbetinae) with an emphasis on Manjakatompo as a conservation priority. Zookeys 2013:21-45. [PMID: 24294082 PMCID: PMC3837497 DOI: 10.3897/zookeys.350.6127] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 10/24/2013] [Indexed: 11/13/2022] Open
Abstract
We review the diving-beetle genus Rhantus Dejean of Madagascar (Coleoptera, Dytiscidae, Colymbetinae) based on museum collection holdings and recently collected expedition material. Both morphology and DNA is used to test species boundaries, in particular whether newly collected material from the Tsaratanana mountains in the north represent a new species or are conspecific with Rhantus manjakatompo Pederzani and Rocchi 2009, described based on a single male specimen from the central Ankaratra mountains. DNA of the holotype of R. manjakatompo was successfully extracted in a non-destructive way and sequenced. The general mixed Yule coalescent model applied to an ultrametric tree constructed from mitochondrial cytochrome c oxidase subunit I (COI) sequence data delimited three species. Morphological characters supported the same species unambiguously. We therefore recognise three species of Rhantus to occur in Madagascar: R. latus (Fairmaire, 1869), R. bouvieri Régimbart, 1900 and R. manjakatompo Pederzani and Rocchi, 2009. All three species are endemic to Madagascar and restricted to the highlands of the island. Rhantusstenonychus Régimbart, 1895, syn. n., is considered a junior synonym of R. latus. We designate lectotypes for R. bouvieri and R. goudoti Sharp, 1882, the latter a junior synonym of R. latus. We provide descriptions, a determination key, SEM-images of fine pronotal and elytral structures, distribution maps, habitus photos, and illustrations of male genitalia and pro- and mesotarsal claws. We discuss the role of the Manjakatompo forest as a refugium for Madagascan Rhantus diversity and other endemics of the montane central high plateau.
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Affiliation(s)
- Anna Emilia Hjalmarsson
- Department of Entomology, Swedish Museum of Natural History, Box 50007, SE-10405 Stockholm, Sweden ; Biodiversity and Climate Research Centre (BiK-F), Georg-Viogt-Straße 14-16, D-60325 Frankfurt am Main, Germany
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Abstract
Species delimitation directly impacts on global biosecurity. It is a critical element in the decisions made by national governments in regard to the flow of trade and to the biosecurity measures imposed to protect countries from the threat of invasive species. Here we outline a novel approach to species delimitation, “tip to root”, for two highly invasive insect pests, Bemisia tabaci (sweetpotato whitefly) and Lymantria dispar (Asian gypsy moth). Both species are of concern to biosecurity, but illustrate the extremes of phylogenetic resolution that present the most complex delimitation issues for biosecurity; B. tabaci having extremely high intra-specific genetic variability and L. dispar composed of relatively indistinct subspecies. This study tests a series of analytical options to determine their applicability as tools to provide more rigorous species delimitation measures and consequently more defensible species assignments and identification of unknowns for biosecurity. Data from established DNA barcode datasets (COI), which are becoming increasingly considered for adoption in biosecurity, were used here as an example. The analytical approaches included the commonly used Kimura two-parameter (K2P) inter-species distance plus four more stringent measures of taxon distinctiveness, (1) Rosenberg’s reciprocal monophyly, (P(AB)),1 (2) Rodrigo’s (P(randomly distinct)),2 (3) genealogical sorting index, (gsi),3 and (4) General mixed Yule-coalescent (GMYC).4,5 For both insect datasets, a comparative analysis of the methods revealed that the K2P distance method does not capture the same level of species distinctiveness revealed by the other three measures; in B. tabaci there are more distinct groups than previously identified using the K2P distances and for L. dipsar far less variation is apparent within the predefined subspecies. A consensus for the results from P(AB), P(randomly distinct) and gsi offers greater statistical confidence as to where genetic limits might be drawn. In the species cases here, the results clearly indicate that there is a need for more gene sampling to substantiate either the new cohort of species indicated for B. tabaci or to detect the established subspecies taxonomy of L. dispar. Given the ease of use through the Geneious species delimitation plugins, similar analysis of such multi-gene datasets would be easily accommodated. Overall, the tip to root approach described here is recommended where careful consideration of species delimitation is required to support crucial biosecurity decisions based on accurate species identification.
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Affiliation(s)
- Laura M Boykin
- Bio-Protection Research Centre, PO Box 84, Lincoln University, Lincoln 7647, New Zealand
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