351
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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352
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353
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Pimvichai P, Panha S, Backeljau T. Combining mitochondrial DNA and morphological data to delineate four new millipede species and provisional assignment to the genus Apeuthes Hoffman & Keeton (Diplopoda : Spirobolida : Pachybolidae : Trigoniulinae). INVERTEBR SYST 2022. [DOI: 10.1071/is21038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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354
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Dutra GM, Vita G, Gentile PV, Ochoa LE, Netto-Ferreira AL. Integrative taxonomy reveals a new species of Cyphocharax (Characiformes: Curimatidae) from the Upper Paraíba do Sul River basin, Brazil. NEOTROPICAL ICHTHYOLOGY 2022. [DOI: 10.1590/1982-0224-2022-0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract A new species of Cyphocharax is described from the Upper Paraíba do Sul River basin, São Paulo, Brazil based on integrated morphological and molecular delimitation criteria. It is morphologically distinguished from its congeners by the presence of a round, dark blotch at the midlength of the caudal peduncle not extending to the proximal portions of the median caudal-fin rays, 19–20 circumpeduncular scales, 34–41 perforated lateral-line scales, 6–7 longitudinal scale rows above and below the lateral line, greatest body depth corresponding to 34.7–39.9% of standard length (SL), and the caudal peduncle depth corresponding to 13.3–15.2% of SL. The lowest genetic distances between the new species and other congeners are: 2.5% from C. gilbert, followed by 3.0% from C. santacatarinae, and 3.2% from C. aff. gilbert. All species delimitation criteria employed herein corroborated the recognition of the new species. In addition, comments on its conservation status are provided.
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Affiliation(s)
| | - George Vita
- Museu de Zoologia da Universidade de São Paulo, Brazil
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355
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Novaes RLM, Cláudio VC, Carrión-Bonilla C, Abreu EF, Wilson DE, Maldonado JE, Weksler M. Variation in the Myotis keaysi complex (Chiroptera, Vespertilionidae), with description of a new species from Ecuador. J Mammal 2021. [DOI: 10.1093/jmammal/gyab139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
The genus Myotis comprises a diverse group of vespertilionid bats with worldwide distribution. Twenty-eight Neotropical species are currently recognized. In this study, we evaluate molecular and morphological variation in the M. keaysi complex, a high elevation clade of Neotropical myotine bats characterized by complex taxonomy and high morphological variation. A phylogeny inferred with cytochrome-b sequences recovered two clades composed of samples traditionally assigned to M. keaysi, with 9% of genetic divergence between them. These clades were also suggested as putative distinct species by molecular species delimitation methods. Qualitative and quantitative morphological analyses indicated a phenotypic discontinuity between specimens from central Andes (including the holotype of M. keaysi) and western lowlands of Ecuador, showing strong congruence between molecular and morphological approaches. We therefore describe a new species for the Tumbes-Choco-Magdalena region, documenting their external and cranial diagnostic characters by comparing them with other Neotropical species. In addition, we provide an emended diagnosis for our new concept of M. keaysi.
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Affiliation(s)
- Roberto Leonan M Novaes
- Fundação Oswaldo Cruz, Fiocruz Mata Atlântica, Rio de Janeiro, RJ 22713-375, Brazil
- Universidade Federal do Rio de Janeiro, Programa de Pós-Graduação em Biodiversidade e Biologia Evolutiva, Rio de Janeiro, RJ 21941-902, Brazil
| | - Vinícius C Cláudio
- Universidade Federal do Rio de Janeiro, Programa de Pós-Graduação em Biodiversidade e Biologia Evolutiva, Rio de Janeiro, RJ 21941-902, Brazil
| | - Carlos Carrión-Bonilla
- University of New Mexico, Department of Biology, Albuquerque, NM 87131, USA
- Pontificia Universidad Católica del Ecuador, Escuela de Biología, Museo de Zoología, Quito 17-01-2184, Ecuador
| | - Edson F Abreu
- Universidade de São Paulo, Escola Superior de Agricultura Luiz de Queiroz, Laboratório de Mamíferos, Piracicaba, SP 13418-900, Brazil
- National Zoological Park, Smithsonian Conservation Biology Institute, Center for Conservation Genomics, Washington, DC 20013, USA
| | - Don E Wilson
- Smithsonian Institution, National Museum of Natural History, Division of Mammals, Washington, DC 20560, USA
| | - Jesús E Maldonado
- National Zoological Park, Smithsonian Conservation Biology Institute, Center for Conservation Genomics, Washington, DC 20013, USA
| | - Marcelo Weksler
- Museu Nacional, Universidade Federal do Rio de Janeiro, Departamento de Vertebrados, Rio de Janeiro 20940-040, Brazil
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356
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Matsvay A, Dyachkova M, Mikhaylov I, Kiselev D, Say A, Burskaia V, Artyushin I, Khafizov K, Shipulin G. Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Novel Tern Atadenovirus. Microorganisms 2021; 10:31. [PMID: 35056480 PMCID: PMC8781740 DOI: 10.3390/microorganisms10010031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 01/03/2023] Open
Abstract
Discovery and study of viruses carried by migratory birds are tasks of high importance due to the host's ability to spread infectious diseases over significant distances. With this paper, we present and characterize the first complete genome sequence of atadenovirus from a tern bird (common tern, Sterna hirundo) preliminarily named tern atadenovirus 1 (TeAdV-1). TeAdV-1 genome is a linear double-stranded DNA molecule, 31,334 base pairs which contain 30 methionine-initiated open reading frames with gene structure typical for Atadenovirus genus, and the shortest known inverted terminal repeats (ITRs) within the Atadenovirus genus consisted of 25 bases. The nucleotide composition of the genome is characterized by a low G + C content (33.86%), which is the most AT-rich genome of known avian adenoviruses within Atadenovirus genus. The nucleotide sequence of the TeAdV-1 genome shows high divergence compared to known representatives of the Atadenovirus genus with the highest similarity to the duck atadenovirus 1 (53.7%). Phylogenetic analysis of the protein sequences of core genes confirms the taxonomic affiliation of the new representative to the genus Atadenovirus with the degree of divergence from the known representatives exceeding the interspecies distance within the genus. Thereby we proposed a novel TeAdV-1 to be considered as a separate species.
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Affiliation(s)
- Alina Matsvay
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
- Moscow Institute of Physics and Technology, National Research University, 115184 Moscow, Russia
| | - Marina Dyachkova
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Ivan Mikhaylov
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Daniil Kiselev
- Institute for Neurosciences of Montpellier, University of Montpellier, INSERM, 34091 Montpellier, France
| | - Anna Say
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | | | - Ilya Artyushin
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Kamil Khafizov
- Moscow Institute of Physics and Technology, National Research University, 115184 Moscow, Russia
| | - German Shipulin
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
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357
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Cannizzaro AG, Daniels JD, Berg DJ. Phylogenetic analyses of a new freshwater amphipod reveal polyphyly within the Holarctic family Crangonyctidae, with revision of the genus Synurella. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
A new genus and species of crangonyctid amphipod, Sicifera cahawba gen. & sp. nov., is described from Dallas County, AL, USA, based on both morphological and molecular comparison with similar crangonyctids. These data, with the application of four species delimitation models, identify the taxon as distinct when compared with related species. Nearctic members of the crangonyctid genus Synurella form a separate, well-supported monophyletic lineage when compared with Palaearctic members, which differ considerably in both molecular and morphological markers. Nearctic members, with the exception of the enigmatic Synurella (Eosynurella) johanseni, are placed in the newly erected Sicifera. The separation of these two genera implies that Palaearctic and Nearctic crangonyctid lineages might not be as closely related as once thought, and their evolutionary and biogeographical history requires further review. In addition, a key to Nearctic members of the genera Eosynurella/Sicifera is presented to aid in future identification.
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Affiliation(s)
| | - James D Daniels
- Department of Biology and Cell Biology, Huntingdon College, Montgomery, AL, Alabama, USA
| | - David J Berg
- Department of Biology, Miami University, Hamilton, OH, Ohio, USA
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358
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Silva-do-Nascimento TF, Sánchez-Ribas J, Oliveira TMP, Bourke BP, Oliveira-Ferreira J, Rosa-Freitas MG, Lourenço-de-Oliveira R, Marinho-e-Silva M, Neves MSAS, Conn JE, Sallum MAM. Molecular Analysis Reveals a High Diversity of Anopheline Mosquitoes in Yanomami Lands and the Pantanal Region of Brazil. Genes (Basel) 2021; 12:1995. [PMID: 34946944 PMCID: PMC8701885 DOI: 10.3390/genes12121995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/06/2021] [Accepted: 12/10/2021] [Indexed: 11/16/2022] Open
Abstract
Identifying the species of the subfamily Anophelinae that are Plasmodium vectors is important to vector and malaria control. Despite the increase in cases, vector mosquitoes remain poorly known in Brazilian indigenous communities. This study explores Anophelinae mosquito diversity in the following areas: (1) a Yanomami reserve in the northwestern Amazon Brazil biome and (2) the Pantanal biome in southwestern Brazil. This is carried out by analyzing cytochrome c oxidase (COI) gene data using Refined Single Linkage (RESL), Assemble Species by Automatic Partitioning (ASAP), and tree-based multi-rate Poisson tree processes (mPTP) as species delimitation approaches. A total of 216 specimens collected from the Yanomami and Pantanal regions were sequenced and combined with 547 reference sequences for species delimitation analyses. The mPTP analysis for all sequences resulted in the delimitation of 45 species groups, while the ASAP analysis provided the partition of 48 groups. RESL analysis resulted in 63 operational taxonomic units (OTUs). This study expands our scant knowledge of anopheline species in the Yanomami and Pantanal regions. At least 18 species of Anophelinae mosquitoes were found in these study areas. Additional studies are now required to determine the species that transmit Plasmodium spp. in these regions.
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Affiliation(s)
- Teresa Fernandes Silva-do-Nascimento
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil; (T.F.S.-d.-N.); (J.S.-R.); (J.O.-F.); (M.G.R.-F.); (R.L.-d.-O.); (M.M.-e.-S.); (M.S.A.S.N.)
| | - Jordi Sánchez-Ribas
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil; (T.F.S.-d.-N.); (J.S.-R.); (J.O.-F.); (M.G.R.-F.); (R.L.-d.-O.); (M.M.-e.-S.); (M.S.A.S.N.)
- Laboratório de Imunoparasitologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
- Distrito Sanitário Especial Indígena Yanomami, Roraima 69301-080, Brazil
| | - Tatiane M. P. Oliveira
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo 01246-904, Brazil;
| | - Brian Patrick Bourke
- Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, 4210 Silver Hill Rd., Suitland, MD 20746, USA;
- Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
- Department of Entomology, Smithsonian Institution—National Museum of Natural History, 10th St. NE & Constitution Ave. NE, Washington, DC 20002, USA
| | - Joseli Oliveira-Ferreira
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil; (T.F.S.-d.-N.); (J.S.-R.); (J.O.-F.); (M.G.R.-F.); (R.L.-d.-O.); (M.M.-e.-S.); (M.S.A.S.N.)
| | - Maria Goreti Rosa-Freitas
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil; (T.F.S.-d.-N.); (J.S.-R.); (J.O.-F.); (M.G.R.-F.); (R.L.-d.-O.); (M.M.-e.-S.); (M.S.A.S.N.)
- Geniac Ltd., São Paulo 01031-902, Brazil
| | - Ricardo Lourenço-de-Oliveira
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil; (T.F.S.-d.-N.); (J.S.-R.); (J.O.-F.); (M.G.R.-F.); (R.L.-d.-O.); (M.M.-e.-S.); (M.S.A.S.N.)
| | - Mariana Marinho-e-Silva
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil; (T.F.S.-d.-N.); (J.S.-R.); (J.O.-F.); (M.G.R.-F.); (R.L.-d.-O.); (M.M.-e.-S.); (M.S.A.S.N.)
- Instituto Nacional da Propriedade Industrial, Rio de Janeiro 20090-910, Brazil
| | - Maycon Sebastião Alberto Santos Neves
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil; (T.F.S.-d.-N.); (J.S.-R.); (J.O.-F.); (M.G.R.-F.); (R.L.-d.-O.); (M.M.-e.-S.); (M.S.A.S.N.)
| | - Jan E. Conn
- Wadsworth Center, New York State Department of Health, Albany, NY 12159, USA;
- Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, NY 12222, USA
| | - Maria Anice Mureb Sallum
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo 01246-904, Brazil;
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359
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DNA barcodes evidence the contact zone of eastern and western caddisfly lineages in the Western Carpathians. Sci Rep 2021; 11:24020. [PMID: 34912013 PMCID: PMC8674257 DOI: 10.1038/s41598-021-03411-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/02/2021] [Indexed: 11/28/2022] Open
Abstract
The region of the Western Carpathians is, among other aspects, very important for survival and diversity of European freshwater fauna due to the presence of a large number of (sub)mountain springs and streams. However, these ecologically and faunistically diversified habitats are still understudied in the context of genetic diversity and population structure of their inhabitants. This study focuses on genetic diversity and distribution patterns of the caddisfly Rhyacophila tristis, common and widespread representative of mountain freshwater fauna. Analysis of the COI mitochondrial marker revealed presence of the western and eastern lineages, with samples from both lineages being grouped in BOLD (Barcode of Life Data System) into separate BINs (Barcode Index Numbers). Our data indicates that eastern lineage (BIN_E) is more closely related to the Balkan populations than to co-occurring western lineage (BIN_W), and that the contact zone of the lineages passes through the W Carpathians. The study revealed phylogeographic and demographic differences between lineages, supporting hypothesis of their evolutionary independence and specific ecological preferences. The obtained genetic data of the R. tristis population from W Carpathians improved our knowledge about population genetics of this aquatic species and can contribute to understanding the state and evolution of biodiversity of freshwater ecosystems in Europe.
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360
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Oumarou Farikou P, Christophe P, Paul Bertrand SN, Serge Hubert ZT. Distribution of Stenasellidae in Africa and description of a new species of Metastenasellus from Cameroonian groundwaters. SUBTERRANEAN BIOLOGY 2021. [DOI: 10.3897/subtbiol.40.76301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
During recent investigations of the groundwater fauna of Cameroon, specimens of a new species of the stygobitic genus Metastenasellus, M. boutini sp. nov. were collected in wells of the city of Douala. The new species can be easily distinguished from the other species of the genus by its relatively large size (up to 11 mm), pleonite 1 and 2 half the length of pereonite 7, the shape of pleopod 2 in males (presence of an external lobe on the protopodite, distal part of the spermatic duct slightly protruding out of the second article, lack of a distal seta on the exopodite), and uropod half the length of the pleotelson. Ecological data and a key to Metastenasellus species are provided. We also performed an exhaustive analysis of the literature on Stenasellidae in Africa to study the geographical distribution of the family in this continent and discuss some hypotheses about the origin of African species.
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361
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Bhaskar R, Das MK, Sharon EA, Kumar RR, R. G. C. Genetic identification of marine eels (Anguilliformes: Congroidei) through DNA barcoding from Kasimedu fishing harbour. Mitochondrial DNA B Resour 2021; 6:3354-3361. [PMID: 34790868 PMCID: PMC8592592 DOI: 10.1080/23802359.2021.1996291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Along with the mysteries of their body's shape like snakes, marine eels have fascinated biologists for centuries. Information on the molecular taxonomy of marine eels is scarce from the Southeast Indian region and hence, the present study aimed to barcode marine eels collected from Kasimedu fishing harbor, Chennai, Tamil Nadu. A total of 44 specimens were collected and DNA barcoding was done with a COI marker. The evolutionary history was inferred using the BA method. We observed 17 species, 10 genera, 4 families from the suborder Congroidei of which the genus Ariosoma and Conger were found to be predominant. The species of the family Muraenesocidae and Congridae are highly variable. The average Kimura two-parameter (K2P) distances within species, genera, and families were 3.08%, 6.80%, 13.80%, respectively. Maximum genetic distance (0.307) was observed between the species Muraenesox cinereus and Ariosoma sp.1. BA tree topology revealed distinct clusters in concurrence with the taxonomic status of the species. A deeper split was observed in Uroconger lepturus. We sequenced for the first-time barcode of Sauromuraenesox vorax and a new species Ophichthus chennaiensis is the gap-filling in identifying this taxon in the Indian context. We found a correct match between morphological and genetic identification of the species analyzed, depending on the cluster analysis performed (BINs and ASAP). This demonstrates that the COI gene sequence is suitable for phylogenetic analysis and species identification.
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Affiliation(s)
- Ranjana Bhaskar
- Zoological Survey of India, Southern Regional Centre, Chennai, India
| | - Mrinal Kumar Das
- Zoological Survey of India, Marine Biology Regional Centre, Chennai, India
| | - E. Agnita Sharon
- Zoological Survey of India, Southern Regional Centre, Chennai, India
| | | | - Chandika R. G.
- Zoological Survey of India, Southern Regional Centre, Chennai, India
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362
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Jorna J, Linde JB, Searle PC, Jackson AC, Nielsen M, Nate MS, Saxton NA, Grewe F, Herrera‐Campos MDLA, Spjut RW, Wu H, Ho B, Lumbsch HT, Leavitt SD. Species boundaries in the messy middle-A genome-scale validation of species delimitation in a recently diverged lineage of coastal fog desert lichen fungi. Ecol Evol 2021; 11:18615-18632. [PMID: 35003697 PMCID: PMC8717302 DOI: 10.1002/ece3.8467] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 11/01/2021] [Accepted: 11/16/2021] [Indexed: 12/05/2022] Open
Abstract
Species delimitation among closely related species is challenging because traditional phenotype-based approaches, for example, using morphology, ecological, or chemical characteristics, may not coincide with natural groupings. With the advent of high-throughput sequencing, it has become increasingly cost-effective to acquire genome-scale data which can resolve previously ambiguous species boundaries. As the availability of genome-scale data has increased, numerous species delimitation analyses, such as BPP and SNAPP+Bayes factor delimitation (BFD*), have been developed to delimit species boundaries. However, even empirical molecular species delimitation approaches can be biased by confounding evolutionary factors, for example, hybridization/introgression and incomplete lineage sorting, and computational limitations. Here, we investigate species boundaries and the potential for micro-endemism in a lineage of lichen-forming fungi, Niebla Rundel & Bowler, in the family Ramalinaceae by analyzing single-locus and genome-scale data consisting of (a) single-locus species delimitation analysis using ASAP, (b) maximum likelihood-based phylogenetic tree inference, (c) genome-scale species delimitation models, e.g., BPP and SNAPP+BFD, and (d) species validation using the genealogical divergence index (gdi). We specifically use these methods to cross-validate results between genome-scale and single-locus datasets, differently sampled subsets of genomic data and to control for population-level genetic divergence. Our species delimitation models tend to support more speciose groupings that were inconsistent with traditional taxonomy, supporting a hypothesis of micro-endemism, which may include morphologically cryptic species. However, the models did not converge on robust, consistent species delimitations. While the results of our analysis are somewhat ambiguous in terms of species boundaries, they provide a valuable perspective on how to use these empirical species delimitation methods in a nonmodel system. This study thus highlights the challenges inherent in delimiting species, particularly in groups such as Niebla, with complex, relatively recent phylogeographic histories.
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Affiliation(s)
- Jesse Jorna
- Department of BiologyBrigham Young UniversityProvoUtahUSA
| | | | | | | | | | | | | | - Felix Grewe
- Science & EducationThe Grainger Bioinformatics CenterThe Field MuseumChicagoIllinoisUSA
| | | | | | - Huini Wu
- Science & EducationThe Grainger Bioinformatics CenterThe Field MuseumChicagoIllinoisUSA
| | - Brian Ho
- Science & EducationThe Grainger Bioinformatics CenterThe Field MuseumChicagoIllinoisUSA
| | - H. Thorsten Lumbsch
- Science & EducationThe Grainger Bioinformatics CenterThe Field MuseumChicagoIllinoisUSA
| | - Steven D. Leavitt
- Department of BiologyBrigham Young UniversityProvoUtahUSA
- Monte L. Bean Life Science MuseumBrigham Young UniversityProvoUtahUSA
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363
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Gippner S, Travers SL, Scherz MD, Colston TJ, Lyra ML, Mohan AV, Multzsch M, Nielsen SV, Rancilhac L, Glaw F, Bauer AM, Vences M. A comprehensive phylogeny of dwarf geckos of the genus Lygodactylus, with insights into their systematics and morphological variation. Mol Phylogenet Evol 2021; 165:107311. [PMID: 34530117 DOI: 10.1016/j.ympev.2021.107311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 08/22/2021] [Accepted: 09/09/2021] [Indexed: 11/27/2022]
Abstract
The 71 currently known species of dwarf geckos of the genus Lygodactylus are a clade of biogeographic interest due to their occurrence in continental Africa, Madagascar, and South America. Furthermore, because many species are morphologically cryptic, our knowledge of species-level diversity within this genus is incomplete, as indicated by numerous unnamed genetic lineages revealed in previous molecular studies. Here we provide an extensive multigene phylogeny covering 56 of the named Lygodactylus species, four named subspecies, and 34 candidate species of which 19 are newly identified in this study. Phylogenetic analyses, based on ∼10.1 kbp concatenated sequences of eight nuclear-encoded and five mitochondrial gene fragments, confirm the monophyly of 14 Lygodactylus species groups, arranged in four major clades. We recover two clades splitting from basal nodes, one comprising exclusively Malagasy species groups, and the other containing three clades. In the latter, there is a clade with only Madagascar species, which is followed by a clade containing three African and one South American species groups, and its sister clade containing six African and two Malagasy species groups. Relationships among species groups within these latter clades remain weakly supported. We reconstruct a Lygodactylus timetree based on a novel fossil-dated phylotranscriptomic tree of squamates, in which we included data from two newly sequenced Lygodactylus transcriptomes. We estimate the crown diversification of Lygodactylus started at 46 mya, and the dispersal of Lygodactylus among the main landmasses in the Oligocene and Miocene, 35-22 mya, but emphasize the wide confidence intervals of these estimates. The phylogeny suggests an initial out-of-Madagascar dispersal as most parsimonious, but accounting for poorly resolved nodes, an out-of-Africa scenario may only require one extra dispersal step. More accurate inferences into the biogeographic history of these geckos will likely require broader sampling of related genera and phylogenomic approaches to provide better topological support. A survey of morphological characters revealed that most of the major clades and species groups within Lygodactylus cannot be unambiguously characterized by external morphology alone, neither by unique character states nor by a diagnostic combination of character states. Thus, any future taxonomic work will likely benefit from integrative, phylogenomic approaches.
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Affiliation(s)
- Sven Gippner
- Zoological Institute, Technical University of Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany; State Natural History Museum of Braunschweig, Pockelsstr. 10, 38106 Braunschweig, Germany
| | - Scott L Travers
- Department of Biological Sciences, Rutgers University-Newark, 195 University Avenue, Newark, NJ 07102, USA
| | - Mark D Scherz
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Timothy J Colston
- Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL 32611, USA
| | - Mariana L Lyra
- Departamento de Biodiversidade, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Campus Rio Claro, Avenida 24A, N 1515 Bela Vista, Rio Claro, SP CEP13506-900, Brazil
| | - Ashwini V Mohan
- Zoological Institute, Technical University of Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Malte Multzsch
- Zoological Institute, Technical University of Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Stuart V Nielsen
- Santa Fe College, 3000 NW 83rd St., Gainesville, FL 32606, USA; Florida Museum of Natural History, Division of Herpetology, 1659 Museum Road - Dickinson Hall, Gainesville, FL 32611, USA
| | - Loïs Rancilhac
- Zoological Institute, Technical University of Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Frank Glaw
- Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstraße 21, 81247 München, Germany
| | - Aaron M Bauer
- Department of Biology and Center for Biodiversity and Ecosystem Stewardship, Villanova University, 800 Lancaster Avenue, Villanova, PA 19085, USA
| | - Miguel Vences
- Zoological Institute, Technical University of Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany
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364
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Gąsiorek P, Vončina K, Nelson DR, Michalczyk Ł. The importance of being integrative: a remarkable case of synonymy in the genus Viridiscus (Heterotardigrada: Echiniscidae). ZOOLOGICAL LETTERS 2021; 7:13. [PMID: 34801080 PMCID: PMC8605589 DOI: 10.1186/s40851-021-00181-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
There are two predominant sources of taxonomically useful morphological variability in the diverse tardigrade family Echiniscidae: the internal structure and surface sculpture of the cuticular plates covering the dorsum (sculpturing) and the arrangement and morphology of the trunk appendages (chaetotaxy). However, since the appendages often exhibit intraspecific variation (they can be reduced or can develop asymmetrically), sculpturing has been considered more stable at the species level and descriptions of new echiniscid species based solely on morphology are still being published. Here, we present a case study in which a detailed analysis of the morphology and multiple genetic markers of several species of the genus Viridiscus shows that cuticular sculpture may also exhibit considerable intraspecific variation and lead to false taxonomic conclusions. In a population collected from the eastern Nearctic, in the type locality of the recently described species V. miraviridis, individuals with transitional morphotypes between those reported for V. viridissimus and V. miraviridis were found. Importantly, all morphotypes within the viridissimus-miraviridis spectrum were grouped in a single monospecific clade according to rapidly evolving markers (ITS-1, ITS-2 and COI). Given the morphological and genetic evidence, we establish V. miraviridis as a junior synonym of V. viridissimus. This study explicitly demonstrates that a lack of DNA data associated with morphological descriptions of new taxa jeopardizes the efforts to unclutter tardigrade systematics. Additionally, V. perviridis and V. viridissimus are reported from Lâm Đồng Province in southern Vietnam, which considerably broadens their known geographic ranges.
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Affiliation(s)
- Piotr Gąsiorek
- Department of Invertebrate Evolution, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Gronostajowa 9, 30-387, Kraków, Poland.
| | - Katarzyna Vončina
- Department of Invertebrate Evolution, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Gronostajowa 9, 30-387, Kraków, Poland
| | - Diane R Nelson
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37614, USA
| | - Łukasz Michalczyk
- Department of Invertebrate Evolution, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Gronostajowa 9, 30-387, Kraków, Poland
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365
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Hedenäs L. Incipient speciation in Scandinavian Distichium capillaceum (Distichiaceae, Bryophyta). LINDBERGIA 2021. [DOI: 10.25227/linbg.01144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Lars Hedenäs
- L. Hedenäs (https://orcid.org/0000-0003-1763-1696) ✉ , Dept of Botany, Swedish Museum of Natural History, Stockholm, Sweden
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366
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Lai Y, Liu Y, Liu X. Elevational Diversity Patterns of Green Lacewings (Neuroptera: Chrysopidae) Uncovered With DNA Barcoding in a Biodiversity Hotspot of Southwest China. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.778686] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Elevational diversity patterns can reflect the responses of biodiversity to climate change spatially. We investigate the species diversity patterns of green lacewings (an important predatory group of insects) along the gradient of elevation from the Shaluli Mountains (Mts. Shaluli), which belong to the Hengduan Mountains in southwestern China, one of the important hotspots of global biodiversity. We combined multiple approaches, including Automatic Barcode Gap Discovery (ABGD), Assemble Species by Automatic Partitioning analysis (ASAP), General Mixed Yule Coalescent (GMYC), Poisson tree processes (bPTP), multi-rate Poisson tree processes (mPTP), to delimit the green lacewings species based on the standard barcoding region of cytochrome c oxidase subunit I (COI). The α-diversity and β-diversity patterns of green lacewings from the Mts. Shaluli along the gradient of elevation were analyzed, with further exploration on how the temperature effect elevational-diversity pattern on broad-scale (county scale) elevational gradients. The DNA barcoding reference library consisted of 40 green lacewing species from the Mts. Shaluli. The α-diversity of green lacewings decreased with the increasing elevation. The temperature was found to have a significant effect on the abundance and Shannon-Wiener diversity index but not on the species richness. Nestedness replaced turnover as the main component of Sørensen’s dissimilarity with the increasing elevation, and greater nestedness occurred at low temperature areas. The combination of a reliable DNA barcoding database could improve the accuracy and efficiency to investigate the species diversity patterns of green lacewings. Temperature, resource, and resultant interspecific competitions may have important roles in explaining the species diversity patterns of green lacewings from the Mts. Shaluli. Priority of conservation should be given to the species at low elevation, middle elevation, and relatively high temperature regions under the background of global climate warming.
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367
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Macher JN, Wideman JG, Girard EB, Langerak A, Duijm E, Jompa J, Sadekov A, Vos R, Wissels R, Renema W. First report of mitochondrial COI in foraminifera and implications for DNA barcoding. Sci Rep 2021; 11:22165. [PMID: 34772985 PMCID: PMC8589990 DOI: 10.1038/s41598-021-01589-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/28/2021] [Indexed: 01/04/2023] Open
Abstract
Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in many marine environments and play a major role in global carbon cycling. Species recognition in Foraminifera is mainly based on morphological characters and nuclear 18S ribosomal RNA barcoding. The 18S rRNA contains variable sequence regions that allow for the identification of most foraminiferal species. Still, some species show limited variability, while others contain high levels of intragenomic polymorphisms, thereby complicating species identification. The use of additional, easily obtainable molecular markers other than 18S rRNA will enable more detailed investigation of evolutionary history, population genetics and speciation in Foraminifera. Here we present the first mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences ("barcodes") of Foraminifera. We applied shotgun sequencing to single foraminiferal specimens, assembled COI, and developed primers that allow amplification of COI in a wide range of foraminiferal species. We obtained COI sequences of 49 specimens from 17 species from the orders Rotaliida and Miliolida. Phylogenetic analysis showed that the COI tree is largely congruent with previously published 18S rRNA phylogenies. Furthermore, species delimitation with ASAP and ABGD algorithms showed that foraminiferal species can be identified based on COI barcodes.
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Affiliation(s)
- Jan-Niklas Macher
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands.
| | - Jeremy G Wideman
- Biodesign Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Elsa B Girard
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
- Department of Ecosystem and Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Anouk Langerak
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
| | - Elza Duijm
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
| | | | - Aleksey Sadekov
- ARC Centre of Excellence for Coral Reef Studies, Ocean Graduate School, The University of Western Australia, Crawley, Australia
| | - Rutger Vos
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Richard Wissels
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
| | - Willem Renema
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
- Department of Ecosystem and Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
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368
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Young MK, Smith R, Pilgrim KL, Schwartz MK. Molecular species delimitation refines the taxonomy of native and nonnative physinine snails in North America. Sci Rep 2021; 11:21739. [PMID: 34741094 PMCID: PMC8571305 DOI: 10.1038/s41598-021-01197-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/15/2021] [Indexed: 11/21/2022] Open
Abstract
Being able to associate an organism with a scientific name is fundamental to our understanding of its conservation status, ecology, and evolutionary history. Gastropods in the subfamily Physinae have been especially troublesome to identify because morphological variation can be unrelated to interspecific differences and there have been widespread introductions of an unknown number of species, which has led to a speculative taxonomy. To resolve uncertainty about species diversity in North America, we targeted an array of single-locus species delimitation methods at publically available specimens and new specimens collected from the Snake River basin, USA to generate species hypotheses, corroborated using nuclear analyses of the newly collected specimens. A total-evidence approach delineated 18 candidate species, revealing cryptic diversity within recognized taxa and a lack of support for other named taxa. Hypotheses regarding certain local endemics were confirmed, as were widespread introductions, including of an undescribed taxon likely belonging to a separate genus in southeastern Idaho for which the closest relatives are in southeast Asia. Overall, single-locus species delimitation was an effective first step toward understanding the diversity and distribution of species in Physinae and to guiding future investigation sampling and analyses of species hypotheses.
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Affiliation(s)
- Michael K. Young
- grid.497401.f0000 0001 2286 5230USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802 USA
| | - Rebecca Smith
- grid.497401.f0000 0001 2286 5230USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802 USA ,grid.411461.70000 0001 2315 1184Present Address: Department of Ecology & Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, TN 37996 USA
| | - Kristine L. Pilgrim
- grid.497401.f0000 0001 2286 5230USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802 USA
| | - Michael K. Schwartz
- grid.497401.f0000 0001 2286 5230USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59802 USA
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369
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Mamos T, Jażdżewski K, Čiamporová-Zaťovičová Z, Čiampor F, Grabowski M. Fuzzy species borders of glacial survivalists in the Carpathian biodiversity hotspot revealed using a multimarker approach. Sci Rep 2021; 11:21629. [PMID: 34732763 PMCID: PMC8566499 DOI: 10.1038/s41598-021-00320-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/08/2021] [Indexed: 11/21/2022] Open
Abstract
The Carpathians are one of the key biodiversity hotspots in Europe. The mountain chain uplifted during Alpine orogenesis and is characterised by a complex geological history. Its current biodiversity was highly influenced by Pleistocene glaciations. The goal of the current study was to examine the phylogenetic and demographic history of Gammarus balcanicus species complex in the Carpathians using multiple markers as well as to delimit, using an integrative approach, and describe new species hidden so far under the name G. balcanicus. Results showed that divergence of the studied lineages reaches back to the Miocene, which supports the hypothesis of their survival in multiple micro refugia. Moreover, the increase of their diversification rate in the Pleistocene suggests that glaciation was the driving force of their speciation. The climatic changes during and after the Pleistocene also played a major role in the demography of the local Carpathian lineages. Comparison of diversity patterns and phylogenetic relationships of both, the mitochondrial and nuclear markers, provide evidence of putative hybridisation and retention of ancient polymorphism (i.e., incomplete lineage sorting). The morphological examination supported the existence of two morphological types; one we describe as a G. stasiuki sp. nov. and another we redescribe as a G. tatrensis (S. Karaman, 1931).
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Affiliation(s)
- Tomasz Mamos
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237, Lodz, Poland.
| | - Krzysztof Jażdżewski
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237, Lodz, Poland
| | - Zuzana Čiamporová-Zaťovičová
- ZooLab, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23, Bratislava, Slovakia
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Fedor Čiampor
- ZooLab, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23, Bratislava, Slovakia
| | - Michał Grabowski
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237, Lodz, Poland
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370
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Torres L, Pante E, González‐Solís J, Viricel A, Ribout C, Zino F, MacKin W, Precheur C, Tourmetz J, Calabrese L, Militão T, Zango L, Shirihai H, Bretagnolle V. Sea surface temperature, rather than land mass or geographic distance, may drive genetic differentiation in a species complex of highly dispersive seabirds. Ecol Evol 2021; 11:14960-14976. [PMID: 34765153 PMCID: PMC8571584 DOI: 10.1002/ece3.8180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 06/27/2021] [Accepted: 07/19/2021] [Indexed: 11/09/2022] Open
Abstract
Seabirds, particularly Procellariiformes, are highly mobile organisms with a great capacity for long dispersal, though simultaneously showing high philopatry, two conflicting life-history traits that may lead to contrasted patterns of genetic population structure. Landmasses were suggested to explain differentiation patterns observed in seabirds, but philopatry, isolation by distance, segregation between breeding and nonbreeding zones, and oceanographic conditions (sea surface temperatures) may also contribute to differentiation patterns. To our knowledge, no study has simultaneously contrasted the multiple factors contributing to the diversification of seabird species, especially in the gray zone of speciation. We conducted a multilocus phylogeographic study on a widespread seabird species complex, the little shearwater complex, showing highly homogeneous morphology, which led to considerable taxonomic debate. We sequenced three mitochondrial and six nuclear markers on all extant populations from the Atlantic (lherminieri) and Indian Oceans (bailloni), that is, five nominal lineages from 13 populations, along with one population from the eastern Pacific Ocean (representing the dichrous lineage). We found sharp differentiation among populations separated by the African continent with both mitochondrial and nuclear markers, while only mitochondrial markers allowed characterizing the five nominal lineages. No differentiation could be detected within these five lineages, questioning the strong level of philopatry showed by these shearwaters. Finally, we propose that Atlantic populations likely originated from the Indian Ocean. Within the Atlantic, a stepping-stone process accounts for the current distribution. Based on our divergence time estimates, we suggest that the observed pattern of differentiation mostly resulted from historical and current variation in sea surface temperatures.
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Affiliation(s)
- Lucas Torres
- Centre d'Etudes Biologiques de ChizéUMR 7372CNRS ‐ La Rochelle UniversitéBeauvoir sur NiortFrance
- Laboratoire LIENSsUMR 7266CNRS ‐ La Rochelle UniversitéLa RochelleFrance
| | - Eric Pante
- Laboratoire LIENSsUMR 7266CNRS ‐ La Rochelle UniversitéLa RochelleFrance
| | - Jacob González‐Solís
- Department de Biologia Evolutiva, Ecologia i Ciències Ambientals (BEECA)Institut de Recerca de la Biodiversitat (IRBio)Universitat de BarcelonaBarcelonaSpain
| | - Amélia Viricel
- Laboratoire LIENSsUMR 7266CNRS ‐ La Rochelle UniversitéLa RochelleFrance
| | - Cécile Ribout
- Centre d'Etudes Biologiques de ChizéUMR 7372CNRS ‐ La Rochelle UniversitéBeauvoir sur NiortFrance
| | | | - Will MacKin
- 3913 Sterling Ridge LnDurhamNorth CarolinaUSA
| | | | - Julie Tourmetz
- Société d'Etudes Ornithologiques de La RéunionSaint AndréFrance
| | - Licia Calabrese
- Island Conservation SocietyMahéSeychelles
- Faculty of Business & Sustainable DevelopmentIsland Biodiversity & Conservation CenterUniversity of SeychellesMahéSeychelles
| | - Teresa Militão
- Department de Biologia Evolutiva, Ecologia i Ciències Ambientals (BEECA)Institut de Recerca de la Biodiversitat (IRBio)Universitat de BarcelonaBarcelonaSpain
| | - Laura Zango
- Department de Biologia Evolutiva, Ecologia i Ciències Ambientals (BEECA)Institut de Recerca de la Biodiversitat (IRBio)Universitat de BarcelonaBarcelonaSpain
| | | | - Vincent Bretagnolle
- Centre d'Etudes Biologiques de ChizéUMR 7372CNRS ‐ La Rochelle UniversitéBeauvoir sur NiortFrance
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371
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Shchepin O, Novozhilov Y, Woyzichovski J, Bog M, Prikhodko I, Fedorova N, Gmoshinskiy V, Borg Dahl M, Dagamac NHA, Yajima Y, Schnittler M. Genetic structure of the protist Physarum albescens (Amoebozoa) revealed by multiple markers and genotyping by sequencing. Mol Ecol 2021; 31:372-390. [PMID: 34676941 DOI: 10.1111/mec.16239] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/26/2021] [Accepted: 10/08/2021] [Indexed: 01/05/2023]
Abstract
Myxomycetes are terrestrial protists with many presumably cosmopolitan species dispersing via airborne spores. A truly cosmopolitan species would suffer from outbreeding depression hampering local adaptation, while locally adapted species with limited distribution would be at a higher risk of extinction in changing environments. Here, we investigate intraspecific genetic diversity and phylogeography of Physarum albescens over the entire Northern Hemisphere. We sequenced 324 field collections of fruit bodies for 1-3 genetic markers (SSU, EF1A, COI) and analysed 98 specimens with genotyping by sequencing. The structure of the three-gene phylogeny, SNP-based phylogeny, phylogenetic networks, and the observed recombination pattern of three independently inherited gene markers can be best explained by the presence of at least 18 reproductively isolated groups, which can be seen as cryptic species. In all intensively sampled regions and in many localities, members of several phylogroups coexisted. Some phylogroups were found to be abundant in only one region and completely absent in other well-studied regions, and thus may represent regional endemics. Our results demonstrate that the widely distributed myxomycete species Ph. albescens represents a complex of at least 18 cryptic species, and some of these seem to have a limited geographical distribution. In addition, the presence of groups of presumably clonal specimens suggests that sexual and asexual reproduction coexist in natural populations of myxomycetes.
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Affiliation(s)
- Oleg Shchepin
- Laboratory of Systematics and Geography of Fungi, Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia.,General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Yuri Novozhilov
- Laboratory of Systematics and Geography of Fungi, Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Jan Woyzichovski
- General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Manuela Bog
- General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Ilya Prikhodko
- Laboratory of Systematics and Geography of Fungi, Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Nadezhda Fedorova
- Laboratory of Systematics and Geography of Fungi, Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia.,Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Vladimir Gmoshinskiy
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Polistovsky National Nature Reserve, Pskov Region, Russia
| | - Mathilde Borg Dahl
- General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany.,Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Nikki H A Dagamac
- General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany.,Department of Biological Sciences and Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Yuka Yajima
- Muroran Institute of Technology, Muroran, Japan
| | - Martin Schnittler
- General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
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372
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Kiourtsoglou A, Kaliontzopoulou A, Poursanidis D, Jablonski D, Lymberakis P, Poulakakis N. Evidence of cryptic diversity in
Podarcis peloponnesiacus
and re‐evaluation of its current taxonomy; insights from genetic, morphological, and ecological data. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Athina Kiourtsoglou
- Department of Biology School of Sciences and Engineering University of Crete Heraklion Greece
- Natural History Museum of Crete School of Sciences and Engineering University of Crete Heraklion Greece
| | - Antigoni Kaliontzopoulou
- CIBIO‐InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal
| | - Dimitris Poursanidis
- Institute of Applied and Computational Mathematics Foundation for Research and Technology ‐ Hellas Heraklion Greece
| | - Daniel Jablonski
- Department of Zoology Comenius University in Bratislava Bratislava Slovakia
| | - Petros Lymberakis
- Natural History Museum of Crete School of Sciences and Engineering University of Crete Heraklion Greece
| | - Nikos Poulakakis
- Department of Biology School of Sciences and Engineering University of Crete Heraklion Greece
- Natural History Museum of Crete School of Sciences and Engineering University of Crete Heraklion Greece
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373
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Jovanović M, Haring E, Sattmann H, Grosser C, Pesic V. DNA barcoding for species delimitation of the freshwater leech genus Glossiphonia from the Western Balkan (Hirudinea, Glossiphoniidae). Biodivers Data J 2021; 9:e66347. [PMID: 34616211 PMCID: PMC8458266 DOI: 10.3897/bdj.9.e66347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 08/20/2021] [Indexed: 11/12/2022] Open
Abstract
Glossiphoniid leeches are a diverse group and sometimes abundant elements of the aquatic fauna inhabiting various types of freshwater habitats. In this study, we sampled leeches of the genus Glossiphonia from the Western Balkan in order to test the suitability of the mitochondrial cytochrome c oxidase subunit 1 (COI) marker sequence for species delimitation. Morphological analysis revealed the presence of four taxa, G.complanata with two subspecies, G.c.complanata and G.c.maculosa, the latter an endemic of Ohrid Lake, G.nebulosa and endemic G.balcanica. In total, 29 new barcodes of Glossiphonia were sequenced in the course of this study and compared with the available molecular dataset of the latter genus from GenBank/BOLD databases. The applied ASAP distance-based species delimitation method for the analysed dataset revealed an interspecific threshold between 4-8% K2P distance as suitable for species identification purposes of the Western Balkan Glossiphonia species. Our study revealed that morphologically identified taxa as G.nebulosa and G.concolor each consists of more than one clearly different phylogenetic clade. This study contributes to a better knowledge of the taxonomy of glossiphoniid leeches and emphasises future work on the revision of this genus using a standard molecular COI marker in species identification.
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Affiliation(s)
- Milica Jovanović
- Department of Biology, Faculty of Natural Science and Mathematics, University of Montenegro, Džordža Vašingtona bb, 81000, Podgorica, Montenegro Department of Biology, Faculty of Natural Science and Mathematics, University of Montenegro, Džordža Vašingtona bb, 81000 Podgorica Montenegro
| | - Elisabeth Haring
- Department of Evolutionary Biology, University of Vienna, Althanstraße 14, 1090, Vienna, Austria Department of Evolutionary Biology, University of Vienna, Althanstraße 14, 1090 Vienna Austria.,Central Research Laboratories, Natural History Museum Vienna, Burgring 7, 1010, Vienna, Austria Central Research Laboratories, Natural History Museum Vienna, Burgring 7, 1010 Vienna Austria
| | - Helmut Sattmann
- 3rd Zoological Department, Natural History Museum Vienna, Burgring 7, Vienna, Austria 3rd Zoological Department, Natural History Museum Vienna, Burgring 7 Vienna Austria
| | - Clemens Grosser
- 4 Bernd-Blindow-Schule Leipzig, Comeniusstraße 17, 04315, Leipzig, Germany 4 Bernd-Blindow-Schule Leipzig, Comeniusstraße 17, 04315 Leipzig Germany
| | - Vladimir Pesic
- Department of Biology, Faculty of Natural Science and Mathematics, University of Montenegro, Džordža Vašingtona bb, 81000, Podgorica, Montenegro Department of Biology, Faculty of Natural Science and Mathematics, University of Montenegro, Džordža Vašingtona bb, 81000 Podgorica Montenegro
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374
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Muster C, Spelda J, Rulik B, Thormann J, von der Mark L, Astrin JJ. The dark side of pseudoscorpion diversity: The German Barcode of Life campaign reveals high levels of undocumented diversity in European false scorpions. Ecol Evol 2021; 11:13815-13829. [PMID: 34707820 PMCID: PMC8525104 DOI: 10.1002/ece3.8088] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 11/12/2022] Open
Abstract
DNA barcoding is particularly useful for identification and species delimitation in taxa with conserved morphology. Pseudoscorpions are arachnids with high prevalence of morphological crypsis. Here, we present the first comprehensive DNA barcode library for Central European Pseudoscorpiones, covering 70% of the German pseudoscorpion fauna (35 out of 50 species). For 21 species, we provide the first publicly available COI barcodes, including the rare Anthrenochernes stellae Lohmander, a species protected by the FFH Habitats Directive. The pattern of intraspecific COI variation and interspecific COI variation (i.e., presence of a barcode gap) generally allows application of the DNA barcoding approach, but revision of current taxonomic designations is indicated in several taxa. Sequences of 36 morphospecies were assigned to 74 BINs (barcode index numbers). This unusually high number of intraspecific BINs can be explained by the presence of overlooked cryptic species and by the accelerated substitution rate in the mitochondrial genome of pseudoscorpions, as known from previous studies. Therefore, BINs may not be an appropriate proxy for species numbers in pseudoscorpions, while partitions built with the ASAP algorithm (Assemble Species by Automatic Partitioning) correspond well with putative species. ASAP delineated 51 taxonomic units from our data, an increase of 42% compared with the present taxonomy. The Neobisium carcionoides complex, currently considered a polymorphic species, represents an outstanding example of cryptic diversity: 154 sequences from our dataset were allocated to 23 BINs and 12 ASAP units.
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Affiliation(s)
- Christoph Muster
- Zoologisches Institut und MuseumUniversität GreifswaldGreifswaldGermany
| | - Jörg Spelda
- SNSB‐Zoologische Staatssammlung MünchenMunichGermany
| | - Björn Rulik
- Zoologisches Forschungsmuseum A. KoenigZFMKBonnGermany
| | - Jana Thormann
- Zoologisches Forschungsmuseum A. KoenigZFMKBonnGermany
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375
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Tu F, Zhai X, Zhao W, Wang J. New Mitogenome of the Hainan Mole Mogera hainana and Taxonomic Implications Based on Molecular Data. MAMMAL STUDY 2021. [DOI: 10.3106/ms2021-0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Feiyun Tu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, 571158, Haikou, Hainan Province, China
| | - Xiaofei Zhai
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, 571158, Haikou, Hainan Province, China
| | - Wenjing Zhao
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, 571158, Haikou, Hainan Province, China
| | - Jichao Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, 571158, Haikou, Hainan Province, China
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376
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Meier R, Blaimer BB, Buenaventura E, Hartop E, von Rintelen T, Srivathsan A, Yeo D. A re-analysis of the data in Sharkey et al.'s (2021) minimalist revision reveals that BINs do not deserve names, but BOLD Systems needs a stronger commitment to open science. Cladistics 2021; 38:264-275. [PMID: 34487362 DOI: 10.1111/cla.12489] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2021] [Indexed: 11/30/2022] Open
Abstract
Halting biodiversity decline is one of the most critical challenges for humanity, but monitoring biodiversity is hampered by taxonomic impediments. One impediment is the large number of undescribed species (here called "dark taxon impediment") whereas another is caused by the large number of superficial species descriptions, that can only be resolved by consulting type specimens ("superficial description impediment"). Recently, Sharkey et al. (2021) proposed to address the dark taxon impediment for Costa Rican braconid wasps by describing 403 species based on COI barcode clusters ("BINs") computed by BOLD Systems. More than 99% of the BINs (387 of 390) were converted into species by assigning binominal names (e.g. BIN "BOLD:ACM9419" becomes Bracon federicomatarritai) and adding a minimal diagnosis (consisting only of a consensus barcode for most species). We here show that many of Sharkey et al.'s species are unstable when the underlying data are analyzed using different species delimitation algorithms. Add the insufficiently informative diagnoses, and many of these species will become the next "superficial description impediment" for braconid taxonomy because they will have to be tested and redescribed after obtaining sufficient evidence for confidently delimiting species. We furthermore show that Sharkey et al.'s approach of using consensus barcodes as diagnoses is not functional because it cannot be applied consistently. Lastly, we reiterate that COI alone is not suitable for delimiting and describing species, and voice concerns over Sharkey et al.'s uncritical use of BINs because they are calculated by a proprietary algorithm (RESL) that uses a mixture of public and private data. We urge authors, reviewers and editors to maintain high standards in taxonomy by only publishing new species that are rigorously delimited with open-access tools and supported by publicly available evidence.
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Affiliation(s)
- Rudolf Meier
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore.,Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany
| | - Bonnie B Blaimer
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany
| | - Eliana Buenaventura
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany
| | - Emily Hartop
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany
| | - Thomas von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany
| | - Amrita Srivathsan
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
| | - Darren Yeo
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
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377
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Jabłońska A, Navarro N, Laffont R, Wattier R, Pešić V, Zawal A, Vukić J, Grabowski M. An integrative approach challenges species hypotheses and provides hints for evolutionary history of two Mediterranean freshwater palaemonid shrimps (Decapoda: Caridea). THE EUROPEAN ZOOLOGICAL JOURNAL 2021. [DOI: 10.1080/24750263.2021.1953624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- A. Jabłońska
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
| | - N. Navarro
- EPHE, PSL University, Paris, France
- Biogéosciences, UMR 6282, CNRS, University of Burgundy, Dijon, France
| | - R. Laffont
- Biogéosciences, UMR 6282, CNRS, University of Burgundy, Dijon, France
| | - R. Wattier
- Biogéosciences, UMR 6282, CNRS, University of Burgundy, Dijon, France
| | - V. Pešić
- Department of Biology, University of Montenegro, Podgorica, Montenegro
| | - A. Zawal
- Department of Invertebrate Zoology and Limnology, Center of Molecular Biology and Biotechnology, University of Szczecin, Szczecin, Poland
| | - J. Vukić
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - M. Grabowski
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
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378
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Martins LF, Choueri EL, Oliveira AFS, Domingos FMCB, Caetano GHO, Cavalcante VHGL, Leite RN, Fouquet A, Rodrigues MT, Carnaval AC, Colli GR, Werneck FP. Whiptail lizard lineage delimitation and population expansion as windows into the history of Amazonian open ecosystems. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1953185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Lidia F. Martins
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | - Erik L. Choueri
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | - Alan F. S. Oliveira
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | | | - Gabriel H. O. Caetano
- Mitrani Department of Desert Ecology, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 849900 Midreshet Ben-Gurion, Israel
| | | | - Rafael N. Leite
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | - Antoine Fouquet
- Laboratoire Evolution et Diversité Biologique (EDB), UMR5174, Bâtiment 4R1, 118 Route de Narbonne 31077, Toulouse, France
| | - Miguel T. Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ana C. Carnaval
- City College of New York and Biology Ph.D. Program, The Graduate Center City University of New York, New York, NY 10031, USA
| | - Guarino R. Colli
- Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Fernanda P. Werneck
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
- Programa de Coleções Científicas Biológicas, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
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379
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Leavitt SD, Hollinger J, Summerhays S, Munger I, Allen J, Smith B. Alpine lichen diversity in an isolated sky island in the Colorado Plateau, USA-Insight from an integrative biodiversity inventory. Ecol Evol 2021; 11:11090-11101. [PMID: 34429905 PMCID: PMC8366874 DOI: 10.1002/ece3.7896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 11/12/2022] Open
Abstract
Lichens are major components of high altitude/latitude ecosystems. However, accurately characterizing their biodiversity is challenging because these regions and habitats are often underexplored, there are numerous poorly known taxonomic groups, and morphological variation in extreme environments can yield conflicting interpretations. Using an iterative taxonomic approach based on over 800 specimens and incorporating both traditional morphology-based identifications and information from the standard fungal DNA barcoding marker, we compiled a voucher-based inventory of biodiversity of lichen-forming fungi in a geographically limited and vulnerable alpine community in an isolated sky island in the Colorado Plateau, USA-the La Sal Mountains. We used the newly proposed Assemble Species by Automatic Partitioning (ASAP) approach to empirically delimit candidate species-level lineages from family-level multiple sequence alignments. Specimens comprising DNA-based candidate species were evaluated using traditional taxonomically diagnostic phenotypic characters to identify specimens to integrative species hypotheses and link these, where possible, to currently described species. Despite the limited alpine habitat (ca. 3,250 ha), we document the most diverse alpine lichen community known to date from the southern Rocky Mountains, with up to 240 candidate species/species-level lineages of lichen-forming fungi. 139 species were inferred using integrative taxonomy, plus an additional 52 candidate species within 29 different putative species complexes. Over 68% of sequences could not be assigned to species-level rank with statistical confidence, corroborating the limited utility of current sequence repositories for species-level DNA barcoding of lichen-forming fungi. By integrating vouchered specimens, DNA sequence data, and photographic documentation, we provide an important baseline of lichen-forming fungal diversity for the limited alpine habitat in the Colorado Plateau. These data provide an important resource for subsequent research in the ecology and evolution of lichens alpine habitats, including DNA barcodes for most putative species/species-level lineages occurring in the La Sal Mountains, and vouchered collections representing any potentially undescribed species that can be used for future taxonomic studies.
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Affiliation(s)
- Steven D. Leavitt
- M.L. Bean Life Science Museum & Department of BiologyBrigham Young UniversityProvoUtahUSA
| | - Jason Hollinger
- HerbariumDepartment of BiologyWestern Carolina UniversityCullowheeNorth CarolinaUSA
| | | | - Isaac Munger
- Department of BiologyBrigham Young UniversityProvoUtahUSA
| | - Jonah Allen
- Department of BiologyBrigham Young UniversityProvoUtahUSA
| | - Barb Smith
- Wildlife Biologist/Botanist, Moab DistrictManti–La Sal National ForestMoabUtahUSA
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380
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Miralles A, Ducasse J, Brouillet S, Flouri T, Fujisawa T, Kapli P, Knowles LL, Kumari S, Stamatakis A, Sukumaran J, Lutteropp S, Vences M, Puillandre N. SPART: A versatile and standardized data exchange format for species partition information. Mol Ecol Resour 2021; 22:430-438. [PMID: 34288531 DOI: 10.1111/1755-0998.13470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/25/2021] [Accepted: 07/12/2021] [Indexed: 11/28/2022]
Abstract
A wide range of data types can be used to delimit species and various computer-based tools dedicated to this task are now available. Although these formalized approaches have significantly contributed to increase the objectivity of species delimitation (SD) under different assumptions, they are not routinely used by alpha-taxonomists. One obvious shortcoming is the lack of interoperability among the various independently developed SD programs. Given the frequent incongruences between species partitions inferred by different SD approaches, researchers applying these methods often seek to compare these alternative species partitions to evaluate the robustness of the species boundaries. This procedure is excessively time consuming at present, and the lack of a standard format for species partitions is a major obstacle. Here, we propose a standardized format, SPART, to enable compatibility between different SD tools exporting or importing partitions. This format reports the partitions and describes, for each of them, the assignment of individuals to the "inferred species". The syntax also allows support values to be optionally reported, as well as original trees and the full command lines used in the respective SD analyses. Two variants of this format are proposed, overall using the same terminology but presenting the data either optimized for human readability (matricial SPART) or in a format in which each partition forms a separate block (SPART.XML). ABGD, DELINEATE, GMYC, PTP and TR2 have already been adapted to output SPART files and a new version of LIMES has been developed to import, export, merge and split them.
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Affiliation(s)
- Aurélien Miralles
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | | | - Sophie Brouillet
- Department of Genetics, Evolution and Environment, Centre for Life's Origins and Evolution, University College London, London, UK
| | - Tomas Flouri
- Department of Genetics, Evolution and Environment, Centre for Life's Origins and Evolution, University College London, London, UK
| | - Tomochika Fujisawa
- Center for Data Science Education and Research, Shiga University, Shiga, Japan
| | - Paschalia Kapli
- Department of Genetics, Evolution and Environment, Centre for Life's Origins and Evolution, University College London, London, UK
| | - L Lacey Knowles
- Department of Ecology and Evolution, University of Michigan, Ann Arbor, MI, USA
| | - Sangeeta Kumari
- Braunschweig University of Technology, Zoological Institute, Braunschweig, Germany
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.,Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Jeet Sukumaran
- Biology Department, LS 262, San Diego State University, San Diego, CA, USA
| | - Sarah Lutteropp
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Miguel Vences
- Braunschweig University of Technology, Zoological Institute, Braunschweig, Germany
| | - Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
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381
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Maggioni D, Garese A, Huang D, Hoeksema BW, Arrigoni R, Seveso D, Galli P, Berumen ML, Montalbetti E, Pica D, Torsani F, Montano S. Diversity, host specificity and biogeography in the Cladocorynidae (Hydrozoa, Capitata), with description of a new genus. Cladistics 2021; 38:13-37. [DOI: 10.1111/cla.12480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2021] [Indexed: 11/28/2022] Open
Affiliation(s)
- Davide Maggioni
- Department of Earth and Environmental Sciences (DISAT) University of Milano‐Bicocca Piazza della Scienza Milano 20126 Italy
- Marine Research and High Education (MaRHE) Center University of Milano‐Bicocca Faafu Magoodhoo Island 12030 Republic of Maldives
| | - Agustín Garese
- Instituto de Investigaciones Marinas y Costeras (IIMyC) Facultad de Ciencias Exactas y Naturales Universidad Nacional de Mar del Plata (UNMDP) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Mar del Plata 7600 Argentina
| | - Danwei Huang
- Department of Biological Sciences Tropical Marine Science Institute and Centre for Nature‐based Climate Solutions National University of Singapore Singapore 117558 Singapore
| | - Bert W. Hoeksema
- Taxonomy, Systematics and Geodiversity Group Naturalis Biodiversity Center Leiden 2300 RA The Netherlands
- Groningen Institute for Evolutionary Life Sciences University of Groningen Groningen 9700 CC The Netherlands
| | - Roberto Arrigoni
- Department of Biology and Evolution of Marine Organisms (BEOM) Stazione Zoologica Anton Dohrn Villa Comunale Napoli 80121 Italy
| | - Davide Seveso
- Department of Earth and Environmental Sciences (DISAT) University of Milano‐Bicocca Piazza della Scienza Milano 20126 Italy
- Marine Research and High Education (MaRHE) Center University of Milano‐Bicocca Faafu Magoodhoo Island 12030 Republic of Maldives
| | - Paolo Galli
- Department of Earth and Environmental Sciences (DISAT) University of Milano‐Bicocca Piazza della Scienza Milano 20126 Italy
- Marine Research and High Education (MaRHE) Center University of Milano‐Bicocca Faafu Magoodhoo Island 12030 Republic of Maldives
| | - Michael L. Berumen
- Red Sea Research Center Division of Biological and Environmental Science and Engineering King Abdullah University of Science and Technology (KAUST) Thuwal 23955‐6900 Saudi Arabia
| | - Enrico Montalbetti
- Department of Earth and Environmental Sciences (DISAT) University of Milano‐Bicocca Piazza della Scienza Milano 20126 Italy
- Marine Research and High Education (MaRHE) Center University of Milano‐Bicocca Faafu Magoodhoo Island 12030 Republic of Maldives
| | - Daniela Pica
- Department of Biological and Environmental Sciences and Technologies University of Salento Lecce 73100 Italy
- CoNISMa – Consorzio Nazionale Interuniversitario per le Scienze del Mare Roma 00196 Italy
| | - Fabrizio Torsani
- Department of Life and Environmental Sciences Polytechnic University of Marche Ancona 60131 Italy
| | - Simone Montano
- Department of Earth and Environmental Sciences (DISAT) University of Milano‐Bicocca Piazza della Scienza Milano 20126 Italy
- Marine Research and High Education (MaRHE) Center University of Milano‐Bicocca Faafu Magoodhoo Island 12030 Republic of Maldives
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382
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Benítez ÁJ, Ricardo-Caldera D, Atencia-Pineda M, Ballesteros-Correa J, Chacón-Pacheco J, Hoyos-López R. DNA barcoding of bats (Chiroptera) from the Colombian northern region. MAMMALIA 2021. [DOI: 10.1515/mammalia-2020-0138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Bats are mammals of great ecological and medical importance, which have associations with different pathogenic microorganisms. DNA barcoding is a tool that can expedite species identification using short DNA sequences. In this study, we assess the DNA barcoding methodology in bats from the Colombian Northern region, specifically in the Córdoba department. Cytochrome oxidase subunit I (COI) gene sequences of nine bat species were typified, and their comparison with other Neotropic samples revealed that this marker is suitable for individual species identification, with ranges of intra-species variation from 0.1 to 0.9%. Bat species clusters are well supported and differentiated, showing average genetic distances ranging from 3% between Artibeus lituratus and Artibeus planirostris, up to 27% between Carollia castanea and Molossus molossus. C. castanea and Glossophaga soricina show geographical structuring in the Neotropic. The findings reported in this study confirm DNA barcoding usefulness for fast species identification of bats in the region.
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Affiliation(s)
- Álvaro J. Benítez
- Facultad de Ciencias de la Salud, Grupo de investigación en Enfermedades Tropicales y Resistencia Bacteriana , Universidad del Sinú , Calle 38 Cra. 1 W, Barrio Juan XXIII , 230001 Montería , Córdoba , Colombia
- Grupo de Investigación Biodiversidad Unicórdoba , Universidad de Córdoba , 230002 Montería , Córdoba , Colombia
| | - Dina Ricardo-Caldera
- Facultad de Ciencias de la Salud, Grupo de investigación en Enfermedades Tropicales y Resistencia Bacteriana , Universidad del Sinú , Calle 38 Cra. 1 W, Barrio Juan XXIII , 230001 Montería , Córdoba , Colombia
| | - María Atencia-Pineda
- Facultad de Ciencias de la Salud, Grupo de investigación en Enfermedades Tropicales y Resistencia Bacteriana , Universidad del Sinú , Calle 38 Cra. 1 W, Barrio Juan XXIII , 230001 Montería , Córdoba , Colombia
| | - Jesús Ballesteros-Correa
- Grupo de Investigación Biodiversidad Unicórdoba , Universidad de Córdoba , 230002 Montería , Córdoba , Colombia
| | - Julio Chacón-Pacheco
- Grupo de Investigación Biodiversidad Unicórdoba , Universidad de Córdoba , 230002 Montería , Córdoba , Colombia
| | - Richard Hoyos-López
- Facultad de Ciencias de la Salud, Grupo de investigación en Enfermedades Tropicales y Resistencia Bacteriana , Universidad del Sinú , Calle 38 Cra. 1 W, Barrio Juan XXIII , 230001 Montería , Córdoba , Colombia
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383
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Abstract
The estimation of phylogenetic trees for individual genes or multi-locus datasets is a basic part of considerable biological research. In order to enable large trees to be computed, Disjoint Tree Mergers (DTMs) have been developed; these methods operate by dividing the input sequence dataset into disjoint sets, constructing trees on each subset, and then combining the subset trees (using auxiliary information) into a tree on the full dataset. DTMs have been used to advantage for multi-locus species tree estimation, enabling highly accurate species trees at reduced computational effort, compared to leading species tree estimation methods. Here, we evaluate the feasibility of using DTMs to improve the scalability of maximum likelihood (ML) gene tree estimation to large numbers of input sequences. Our study shows distinct differences between the three selected ML codes—RAxML-NG, IQ-TREE 2, and FastTree 2—and shows that good DTM pipeline design can provide advantages over these ML codes on large datasets.
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384
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DNA Barcoding of Marine Mollusks Associated with Corallina officinalis Turfs in Southern Istria (Adriatic Sea). DIVERSITY 2021. [DOI: 10.3390/d13050196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Presence of mollusk assemblages was studied within red coralligenous algae Corallina officinalis L. along the southern Istrian coast. C. officinalis turfs can be considered a biodiversity reservoir, as they shelter numerous invertebrate species. The aim of this study was to identify mollusk species within these settlements using DNA barcoding as a method for detailed identification of mollusks. Nine locations and 18 localities with algal coverage range above 90% were chosen at four research areas. From 54 collected samples of C. officinalis turfs, a total of 46 mollusk species were identified. Molecular methods helped identify 16 gastropod, 14 bivalve and one polyplacophoran species. COI sequences for two bivalve species (Musculus cf. costulatus (Risso, 1826) and Gregariella semigranata (Reeve, 1858)) and seven gastropod species (Megastomia winfriedi Peñas & Rolán, 1999, Eatonina sp. Thiele, 1912, Eatonina cossurae (Calcara, 1841), Crisilla cf. maculata (Monterosato, 1869), Alvania cf. carinata (da Costa, 1778), Vitreolina antiflexa (Monterosato, 1884) and Odostomia plicata (Montagu, 1803)) represent new BINs in BOLD database. This study contributes to new findings related to the high biodiversity of mollusks associated with widespread C. officinalis settlements along the southern coastal area of Istria.
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385
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Maggioni D, Assandri G, Ramazzotti F, Magnani D, Pellegrino I, Valsecchi E, Galimberti A. Differential genetic variability at two mtDNA COI regions does not imply mismatches in Odonata molecular identification performances. THE EUROPEAN ZOOLOGICAL JOURNAL 2021. [DOI: 10.1080/24750263.2021.1896795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- D. Maggioni
- Department of Environmental and Earth Sciences (DISAT), University of Milano - Bicocca, Milan, Italy
- Marine Research and High Education (MaRHE) Center, University of Milano - Bicocca, Faafu Magoodhoo, Maldives
| | - G. Assandri
- Area Avifauna Migratrice, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia, Italy
| | - F. Ramazzotti
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano - Bicocca, Milan, Italy
| | - D. Magnani
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano - Bicocca, Milan, Italy
| | - I. Pellegrino
- Department of Sciences and Technological Innovation (DISIT), University of Eastern Piedmont, Alessandria, Italy
| | - E. Valsecchi
- Department of Environmental and Earth Sciences (DISAT), University of Milano - Bicocca, Milan, Italy
| | - A. Galimberti
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano - Bicocca, Milan, Italy
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386
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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: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [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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387
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Criscione F, Hallan A, Puillandre N, Fedosov A. Snails in depth: integrative taxonomy of Famelica, Glaciotomella and Rimosodaphnella (Conoidea: Raphitomidae) from the deep sea of temperate Australia. INVERTEBR SYST 2021. [DOI: 10.1071/is21008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The deep sea of temperate south-eastern Australia appears to be a ‘hotspot’ for diversity and endemism of conoidean neogastropods of the family Raphitomidae. Following a series of expeditions in the region, a considerable amount of relevant DNA-suitable material has become available. A molecular phylogeny based on this material has facilitated the identification of diagnostic morphological characters, allowing the circumscription of monophyletic genera and the introduction of several new genus-level taxa. Both named and new genera are presently being investigated through integrative taxonomy, with the discovery of a significant number of undescribed species. As part of this ongoing investigation, our study focuses on the genera Famelica Bouchet & Warén, 1980, Glaciotomella Criscione, Hallan, Fedosov & Puillandre, 2020 and Rimosodaphnella Cossmann, 1914. We subjected a comprehensive mitochondrial DNA dataset of representative deep-sea raphitomids to the species delimitation methods ABGD and ASAP that recognised 18 and 15 primary species hypotheses (PSHs) respectively. Following additional evaluation of shell and radular features, and examination of geographic and bathymetric ranges, nine of these PSHs were converted to secondary species hypotheses (SSHs). Four SSHs (two in Famelica and two in Rimosodaphnella) were recognised as new, and formal descriptions are provided herein.
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