51
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Tolley KA, Telford NS, Taft JM, Bates MF, Conradie W, Makhubo BG, Alexander GJ. Taxonomic inflation due to inadequate sampling: are girdled lizards (Cordylus minor species complex) from the Great Karoo one and the same? Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The Great Karoo and Namaqualand of South Africa are home to a species complex of morphologically conserved lizards that occur in allopatry (Karoo: Cordylus aridus, Cordylus cloetei, Cordylus minor; Namaqualand: Cordylus imkeae). However, there are negligible morphological differences and a lack of obvious physical or climatic barriers, particularly among the three Karoo species. We hypothesized that poor geographic coverage in previous studies and lack of an explicit species concept has caused taxonomic inflation. We therefore tested species boundaries by examining multiple criteria: multi-gene phylogenetics, niche distribution modelling and re-examination of diagnostic morphological features with a larger sample size. We found that C. aridus, C. cloetei and C. minor lack diagnosable differences for both genetics and morphology. Distribution modelling, ranging from present day to the last interglacial period, show connectivity has been maintained especially during cooler periods. Conversely, C. imkeae is morphologically diagnosable, genetically distinct and lacks connectivity with the other taxa. By evaluating multiple operational criteria, we conclude that the C. minor species complex comprises only two species, C. minor (with C. aridus and C. cloetei as junior synonyms) and C. imkeae, demonstrating that species defined from inadequate data and lack of an explicit species concept can lead to taxonomic inflation.
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Affiliation(s)
- Krystal A Tolley
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont 7735, South Africa
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicolas S Telford
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont 7735, South Africa
| | - Jody M Taft
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont 7735, South Africa
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michael F Bates
- Division of Herpetology, Department of Animal and Plant Systematics, National Museum, Bloemfontein, South Africa
- Department of Zoology & Entomology, University of the Free State, Bloemfontein, South Africa
| | - Werner Conradie
- Port Elizabeth Museum (Bayworld), Gqeberha, South Africa
- Department of Nature Conservation Management, Natural Resource Science and Management Cluster, Faculty of Science, George Campus, Nelson Mandela University, George, South Africa
| | - Buyisile G Makhubo
- Division of Herpetology, Department of Animal and Plant Systematics, National Museum, Bloemfontein, South Africa
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Graham J Alexander
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
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52
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Paulus E, Brix S, Siebert A, Martínez Arbizu P, Rossel S, Peters J, Svavarsson J, Schwentner M. Recent speciation and hybridization in Icelandic deep-sea isopods: An integrative approach using genomics and proteomics. Mol Ecol 2021; 31:313-330. [PMID: 34676606 DOI: 10.1111/mec.16234] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 02/06/2023]
Abstract
The crustacean marine isopod species Haploniscus bicuspis (Sars, 1877) shows circum-Icelandic distribution in a wide range of environmental conditions and along well-known geographic barriers, such as the Greenland-Iceland-Faroe (GIF) Ridge. We wanted to explore population genetics, phylogeography and cryptic speciation as well as investigate whether previously described, but unaccepted subspecies have any merit. Using the same set of specimens, we combined mitochondrial COI sequences, thousands of nuclear loci (ddRAD), and proteomic profiles, plus selected morphological characters using confocal laser scanning microscopy (CLSM). Five divergent genetic lineages were identified by COI and ddRAD, two south and three north of the GIF Ridge. Assignment of populations to the three northern lineages varied and detailed analyses revealed hybridization and gene flow between them, suggesting a single northern species with a complex phylogeographic history. No apparent hybridization was observed among lineages south of the GIF Ridge, inferring the existence of two more species. Differences in proteomic profiles between the three putative species were minimal, implying an ongoing or recent speciation process. Population differentiation was high, even among closely associated populations, and higher in mitochondrial COI than nuclear ddRAD loci. Gene flow is apparently male-biased, leading to hybrid zones and instances of complete exchange of the local nuclear genome through immigrating males. This study did not confirm the existence of subspecies defined by male characters, which probably instead refer to different male developmental stages.
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Affiliation(s)
- Eva Paulus
- University of Groningen, Groningen, The Netherlands.,Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Hamburg, Germany
| | - Saskia Brix
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Hamburg, Germany
| | - Annabelle Siebert
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Hamburg, Germany.,Center of Natural History (CeNak), Universität Hamburg, Hamburg, Germany
| | - Pedro Martínez Arbizu
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Wilhelmshaven, Germany
| | - Sven Rossel
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Wilhelmshaven, Germany
| | - Janna Peters
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Wilhelmshaven, Germany
| | - Jörundur Svavarsson
- Department of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Martin Schwentner
- Center of Natural History (CeNak), Universität Hamburg, Hamburg, Germany.,Naturhistorisches Museum Wien, Vienna, Austria
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53
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Taft JM, Maritz B, Tolley KA. Stable climate corridors promote gene flow in the Cape sand snake species complex (Psammophiidae). ZOOL SCR 2021. [DOI: 10.1111/zsc.12514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Jody M. Taft
- Department of Biodiversity and Conservation Biology University of the Western Cape Private Bag X17 Bellville South Africa
- Kirstenbosch Research Center South African National Biodiversity Institute Cape Town South Africa
| | - Bryan Maritz
- Department of Biodiversity and Conservation Biology University of the Western Cape Private Bag X17 Bellville South Africa
| | - Krystal A. Tolley
- Kirstenbosch Research Center South African National Biodiversity Institute Cape Town South Africa
- School of Animal, Plant and Environmental Sciences University of the Witwatersrand Johannesburg South Africa
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54
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Ellepola G, Herath J, Manamendra-Arachchi K, Wijayathilaka N, Senevirathne G, Pethiyagoda R, Meegaskumbura M. Molecular species delimitation of shrub frogs of the genus Pseudophilautus (Anura, Rhacophoridae). PLoS One 2021; 16:e0258594. [PMID: 34665841 PMCID: PMC8525734 DOI: 10.1371/journal.pone.0258594] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 09/30/2021] [Indexed: 11/17/2022] Open
Abstract
Sri Lanka is an amphibian hotspot of global significance. Its anuran fauna is dominated by the shrub frogs of the genus Pseudophilautus. Except for one small clade of four species in Peninsular India, these cool-wet adapted frogs, numbering some 59 extant species, are distributed mainly across the montane and lowland rain forests of the island. With species described primarily by morphological means, the diversification has never yet been subjected to a molecular species delimitation analysis, a procedure now routinely applied in taxonomy. Here we test the species boundaries of Pseudophilautus in the context of the phylogenetic species concept (PSC). We use all the putative species for which credible molecular data are available (nDNA-Rag-1; mt-DNA- 12S rRNA, 16S rRNA) to build a well resolved phylogeny, which is subjected to species delimitation analyses. The ABGD, bPTP, mPTP and bGMYC species delimitation methods applied to the 16S rRNA frog barcoding gene (for all species), 12S rRNA and Rag-1 nDNA grouped P. procax and P. abundus; P. hallidayi and P. fergusonianus; P. reticulatus and P. pappilosus; P. pleurotaenia and P. hoipolloi; P. hoffmani and P. asankai; P. silvaticus and P. limbus; P. dilmah and P. hankeni; P. fulvus and P. silus.. Surprisingly, all analyses recovered 14 unidentified potential new species as well. The geophylogeny affirms a distribution across the island's aseasonal 'wet zone' and its three principal hill ranges, suggestive of allopatric speciation playing a dominant role, especially between mountain masses. Among the species that are merged by the delimitation analyses, a pattern leading towards a model of parapatric speciation emerges-ongoing speciation in the presence of gene flow. This delimitation analysis reinforces the species hypotheses, paving the way to a reasonable understanding of Sri Lankan Pseudophilautus, enabling both deeper analyses and conservation efforts of this remarkable diversification. http://zoobank.org/urn:lsid:zoobank.org:pub:DA869B6B-870A-4ED3-BF5D-5AA3F69DDD27.
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Affiliation(s)
- Gajaba Ellepola
- College of Forestry, Guangxi Key Lab for Forest Ecology and Conservation, Guangxi University, Nanning, PR China
- Faculty of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - Jayampathi Herath
- College of Forestry, Guangxi Key Lab for Forest Ecology and Conservation, Guangxi University, Nanning, PR China
| | | | - Nayana Wijayathilaka
- Department of Zoology, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Gayani Senevirathne
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, United States of America
| | - Rohan Pethiyagoda
- Ichthyology Section, Australian Museum, Sydney, New South Wales, Australia
| | - Madhava Meegaskumbura
- College of Forestry, Guangxi Key Lab for Forest Ecology and Conservation, Guangxi University, Nanning, PR China
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55
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Hu Y, Li S, Liu H, Kim ST, Kurenshchikov DK, Hou Z. Ancient volcanos as species pumps: A case study of freshwater amphipods in Northeast Asia. Mol Ecol 2021; 31:343-355. [PMID: 34657344 DOI: 10.1111/mec.16223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 09/28/2021] [Accepted: 10/04/2021] [Indexed: 01/12/2023]
Abstract
Volcano-tectonic processes have been viewed as primary drivers in the formation of present-day diversity. Volcanos associated with mountain uplifts drive allopatric speciation through vicariance and may impact the surrounding areas like species pump or species attractor. However, the application of these hypotheses to aquatic fauna has rarely been tested explicitly. We tested these hypotheses in the Changbai Mountains (Mts), which are one of the most typical, active volcanic ranges in Northeast (NE) Asia with a long and turbulent geological history. The Gammarus nekkensis species complex of amphipod crustaceans, widely distributed throughout NE Asia with poor dispersal abilities and a long evolutionary history, is a suitable model for testing hypotheses of species pump or species attractor. Phylogenetic and ancestral range reconstructions demonstrated that the studied amphipod originated from the Changbai Mts ~27 Ma and diverged into eastern (Clade I) and western (Clade II) clades, which corresponds well with the initial volcanic eruption of the Changbai Mts in the Late Oligocene. The subsequent diversifications of subclades CI-3, CII-1a and CII-2a were probably driven by second and third eruptions of the Changbai Mts during the Miocene. In particular, the Changbai lineages had spread to the Russian Far East multiple times since the Early Miocene, and widely colonized the region during the Pleistocene. Our discoveries suggest that the ancient volcanos of the Changbai Mts act as species pumps in NE Asia, resulted in burst of diversification around the Changbai Mts and subsequent dispersals into adjacent regions.
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Affiliation(s)
- Yueyao Hu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shuqiang Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hongguang Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Seung-Tae Kim
- Life and Environment Research Institute, Konkuk University, Seoul, Republic of Korea
| | - Dmitry K Kurenshchikov
- Laboratory of the Animal Ecology, Institute of Water and Ecology Problems, Far East Branch of the Russian Academy of Sciences, Khabarovsk, Russia
| | - Zhonge Hou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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56
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Lampri PN, Bouranta C, Radea C, Parmakelis A. Hidden diversity revealed in the freshwater snails, Bythinella and Pseudamnicola, in the Island of Crete. Integr Zool 2021; 17:804-824. [PMID: 34599771 DOI: 10.1111/1749-4877.12594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Crete with its complex geomorphological history is the island with the highest number of endemism observed in animal and plant taxa throughout the Aegean archipelago. While other groups of organisms within Crete are well-studied, the freshwater gastropod fauna still remains poorly investigated. Bythinella and Pseudamnicola, are 2 genera of freshwater springsnails, both present on the island, inhabiting springs and other freshwater habitats. Here, we conduct a comprehensive study on the distribution of the different genetic lineages of the 2 gastropod genera in order to assess the mode of their differentiation on the island and infer the actual number of species present in the island. Towards these aims, sequence data from the mitochondrial gene were used and analyzed within a phylogenetic framework. For Bythinella, our results strongly support at least 5 delineated Bythinella spp. inhabiting Crete, which correspond to the already described species from previous studies with the addition of a new one. Bythinella analyses reveal an old time-frame of differentiation with vicariant phenomena being more likely the main drivers shaping the present-day distribution of the genus' genetic lineages. For Pseudamnicola, our data indicate the presence of at least 2 delineated Pseudamnicola spp. with a differentiation more consistent to an isolation-by-distance pattern of a relatively recent origin. Dispersion processes followed by isolation of the populations and/or recent speciation, seem to be the underlying process for the current distribution of Pseudamnicola lineages.
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Affiliation(s)
- Paraskevi Niki Lampri
- Section of Ecology and Taxonomy, Department of Biology, National and Kapodistrian University of Athens, Athens, Greece.,Institute of Marine Biological Resources and Inland Waters, Hellenic Centre for Marine Research, Anavyssos Attica, Greece
| | - Christina Bouranta
- Section of Ecology and Taxonomy, Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Canella Radea
- Section of Ecology and Taxonomy, Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Aristeidis Parmakelis
- Section of Ecology and Taxonomy, Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
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57
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Lagourgue L, Payri CE. Diversity and taxonomic revision of tribes Rhipileae and Rhipiliopsideae (Halimedaceae, Chlorophyta) based on molecular and morphological data. JOURNAL OF PHYCOLOGY 2021; 57:1450-1471. [PMID: 34003495 DOI: 10.1111/jpy.13186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
Genera and species of the tribes Rhipileae and Rhipiliopsideae are abundant in most coral reef ecosystems worldwide. However, the group has been largely overlooked, and very little genetic data is available to accurately assess its diversity, phylogenetic relationships, and geographic distribution. Our study provided an in-depth reassessment of tribes Rhipileae and Rhipiliopsideae based on a species-rich dataset and the combination of molecular species delimitation, multilocus phylogenetic analyses (tufA, rbcL, and 18S rDNA), and morpho-anatomic observations. Our results revealed an unexpected diversity of 38 morphologically validated species hypotheses, including 20 new species, two of which are described in this paper and one resurrected species (Rhipilia diaphana). Based on our phylogenetic results we proposed to redefine the genera Rhipilia and Rhipiliopsis and described two new genera, Kraftalia gen. nov. (Rhipileae) and Rhipiliospina gen. nov. (Rhipiliopsideae). Finally, we validated Rhipiliella Kraft and included it in the tribe Rhipileae. Although Rhipilia and Rhipiliopsis have a pantropical distribution, none of the species studied here appeared cosmopolitan; instead, they have restricted distributions.
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Affiliation(s)
- Laura Lagourgue
- Sorbonne Universités, UPMC Univ Paris 06, IFD, 4 Place Jussieu, Paris Cedex 05, 75252, France
- UMR ENTROPIE (IRD, UR, UNC, Ifremer, CNRS), Institut de Recherche pour le Développement, B.P. A5 Nouméa Cedex, Nouvelle-Calédonie, 98848, France
| | - Claude E Payri
- UMR ENTROPIE (IRD, UR, UNC, Ifremer, CNRS), Institut de Recherche pour le Développement, B.P. A5 Nouméa Cedex, Nouvelle-Calédonie, 98848, France
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58
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Blue mussels of the Mytilus edulis species complex from South America: The application of species delimitation models to DNA sequence variation. PLoS One 2021; 16:e0256961. [PMID: 34473778 PMCID: PMC8412288 DOI: 10.1371/journal.pone.0256961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/19/2021] [Indexed: 11/30/2022] Open
Abstract
Smooth-shelled blue mussels, Mytilus spp., have a worldwide antitropical distribution and are ecologically and economically important. Mussels of the Mytilus edulis species complex have been the focus of numerous taxonomic and biogeographical studies, in particular in the Northern hemisphere, but the taxonomic classification of mussels from South America remains unclear. The present study analysed 348 mussels from 20 sites in Argentina, Chile, Uruguay and the Falkland Islands on the Atlantic and Pacific coasts of South America. We sequenced two mitochondrial locus, Cytochrome c Oxidase subunit I (625 bp) and 16S rDNA (443 bp), and one nuclear gene, ribosomal 18S rDNA (1770 bp). Mitochondrial and nuclear loci were analysed separately and in combination using maximum likelihood and Bayesian inference methods to identify the combination of the most informative dataset and model. Species delimitation using five different models (GMYC single, bGMYC, PTP, bPTP and BPP) revealed that the Mytilus edulis complex in South America is represented by three species: native M. chilensis, M. edulis, and introduced Northern Hemisphere M. galloprovincialis. However, all models failed to delimit the putative species Mytilus platensis. In contrast, however, broad spatial scale genetic structure in South America using Geneland software to analyse COI sequence variation revealed a group of native mussels (putatively M. platensis) in central Argentina and the Falkland Islands. We discuss the scope of species delimitation methods and the use of nuclear and mitochondrial genetic data to the recognition of species within the Mytilus edulis complex at regional and global scales.
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59
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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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60
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Rainha RN, Martinez PA, Moraes LJCL, Castro KMSA, Réjaud A, Fouquet A, Leite RN, Rodrigues MT, Werneck FP. Subtle environmental variation affects phenotypic differentiation of shallow divergent treefrog lineages in Amazonia. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Abstract
Amazonia harbours a vast biotic and ecological diversity, enabling investigation of the effects of microevolutionary processes and environmental variation on species diversification. Integrative approaches combining phenotypic and genetic variation can improve our knowledge on diversification processes in megadiverse regions. Here, we investigate the influence of environmental and geographic variation on the genetic and morphological differentiation in the Amazonian Boana calcarata-fasciata (Anura: Hylidae) species complex. We analysed the variation of one mtDNA gene from individuals of different forest environments, and assessed their phylogenetic relationships and species limits to define the lineages to perform a phenotypic-environmental approach. We collected morphological data (head shape and size) using 3D models and investigated the phylogenetic signal, evolutionary model and influence of environmental variables on morphology. We verified associations between environmental and geographical distances with morphological and genetic variation using distance-based redundancy analyses and Mantel tests. We found an even higher cryptic diversity than already recognized within the species complex. Body size and head shape varied among specimens, but did not present phylogenetic signal, diverging under a selective evolutionary model. Our results show that diverse factors have influenced morphological and genetic variation, but environmental conditions such as vegetation cover, precipitation and climate change velocity influenced morphological diversification. Possible population-level mechanisms such as parallel morphological evolution or plastic responses to similar environments could account for such patterns in these typical Amazonian treefrogs.
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Affiliation(s)
- Raíssa N Rainha
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, Manaus, Amazonas, Brazil
| | - Pablo A Martinez
- Laboratorio de Pesquisas Integrativas em Biodiversidade, Departamento de Biologia, Universidade Federal de Sergipe, Avenida Marechal Rondon, Aracaju, Sergipe, Brazil
| | - Leandro J C L Moraes
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, Manaus, Amazonas, Brazil
| | - Kathleen M S A Castro
- Laboratorio de Pesquisas Integrativas em Biodiversidade, Departamento de Biologia, Universidade Federal de Sergipe, Avenida Marechal Rondon, Aracaju, Sergipe, Brazil
| | - Alexandre Réjaud
- Laboratoire Evolution et Diversité Biologique, UMR5174, Université Paul Sabatier, Bâtiment, CNRS, IRD, Toulouse, France
| | - Antoine Fouquet
- Laboratoire Evolution et Diversité Biologique, UMR5174, Université Paul Sabatier, Bâtiment, CNRS, IRD, Toulouse, France
| | - Rafael N Leite
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, Manaus, Amazonas, Brazil
| | - Miguel T Rodrigues
- Departamento de Zoologia, Universidade de São Paulo Instituto de Biociências, Rua do Matão, travessa, nº. São Paulo, São Paulo, Brazil
| | - Fernanda P Werneck
- Programa de Pós-Graduação em Ecologia, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, Manaus, Amazonas, Brazil
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, Manaus, Amazonas, Brazil
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61
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Collado GA, Torres-Díaz C, Valladares MA. Phylogeography and molecular species delimitation reveal cryptic diversity in Potamolithus (Caenogastropoda: Tateidae) of the southwest basin of the Andes. Sci Rep 2021; 11:15735. [PMID: 34344905 PMCID: PMC8333322 DOI: 10.1038/s41598-021-94900-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/21/2021] [Indexed: 02/07/2023] Open
Abstract
The species of the genus Potamolithus inhabiting the southwestern basin of the Andes are difficult to distinguish due to small size and similar shell morphology. Only Potamolithus australis and Potamolithus santiagensis have been traditionally recognized in this region, but the occurrence of several morphologically similar undescribed populations could increase the regional richness. Here we delimit described and potentially undescribed cryptic species of the genus using partial sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Network analysis and diversity indices inferred six highly differentiated haplogroups, many of them sympatric and widespread in the study area. Phylogeographic analyses suggest a scenario of recent diversification and the occurrence of multiple refuges during the successive Pleistocene glaciations. Phylogenetic analysis also recovered six major clades that showed no relationship with physiography. Species delimitation analyses consistently recognized three or four candidate species apart from P. australis and P. santiagensis. Divergence times indicate that speciation of Chilean Potamolithus began at the end of the Pliocene, probably driven by climatic rather than geographic events. Considering the high inter- and intra-basin genetic diversity, conservation efforts should be focused on protecting sympatric taxa in the basins with the highest species richness.
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Affiliation(s)
- Gonzalo A. Collado
- grid.440633.6Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío, Avenida Andrés Bello 720, Chillán, Chile ,grid.440633.6Grupo de Investigación en Biodiversidad y Cambio Global (GBCG), Universidad del Bío-Bío, Chillán, Chile
| | - Cristian Torres-Díaz
- grid.440633.6Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío, Avenida Andrés Bello 720, Chillán, Chile ,grid.440633.6Grupo de Investigación en Biodiversidad y Cambio Global (GBCG), Universidad del Bío-Bío, Chillán, Chile
| | - Moisés A. Valladares
- grid.440633.6Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío, Avenida Andrés Bello 720, Chillán, Chile ,grid.440633.6Grupo de Investigación en Biodiversidad y Cambio Global (GBCG), Universidad del Bío-Bío, Chillán, Chile
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Lukic D, Eberle J, Thormann J, Holzschuh C, Ahrens D. Excluding spatial sampling bias does not eliminate oversplitting in DNA-based species delimitation analyses. Ecol Evol 2021; 11:10327-10337. [PMID: 34367578 PMCID: PMC8328443 DOI: 10.1002/ece3.7836] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/05/2021] [Accepted: 06/07/2021] [Indexed: 01/02/2023] Open
Abstract
DNA barcoding and DNA-based species delimitation are major tools in DNA taxonomy. Sampling has been a central debate in this context, because the geographical composition of samples affects the accuracy and performance of DNA barcoding. Performance of complex DNA-based species delimitation is to be tested under simpler conditions in absence of geographic sampling bias. Here, we present an empirical dataset sampled from a single locality in a Southeast-Asian biodiversity hotspot (Laos: Phou Pan mountain). We investigate the performance of various species delimitation approaches on a megadiverse assemblage of herbivorous chafer beetles (Coleoptera: Scarabaeidae) to infer whether species delimitation suffers in the same way from exaggerate infraspecific variation despite the lack of geographic genetic variation that led to inconsistencies between entities from DNA-based and morphology-based species inference in previous studies. For this purpose, a 658 bp fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) was analyzed for a total of 186 individuals of 56 morphospecies. Tree-based and distance-based species delimitation methods were used. All approaches showed a rather limited match ratio (max. 77%) with morphospecies. Poisson tree process (PTP) and statistical parsimony network analysis (TCS) prevailingly over-splitted morphospecies, while 3% clustering and Automatic Barcode Gap Discovery (ABGD) also lumped several species into one entity. ABGD revealed the highest congruence between molecular operational taxonomic units (MOTUs) and morphospecies. Disagreements between morphospecies and MOTUs have to be explained by historically acquired geographic genetic differentiation, incomplete lineage sorting, and hybridization. The study once again highlights how important morphology still is in order to correctly interpret the results of molecular species delimitation.
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Affiliation(s)
- Daniel Lukic
- Zoologisches Forschungsmuseum Alexander KoenigZentrum für Taxonomie und EvolutionsforschungBonnGermany
| | - Jonas Eberle
- Zoologische EvolutionsbiologieParis‐Lodron‐UniversitätSalzburgAustria
| | - Jana Thormann
- Zoologisches Forschungsmuseum Alexander KoenigZentrum für Taxonomie und EvolutionsforschungBonnGermany
| | | | - Dirk Ahrens
- Zoologisches Forschungsmuseum Alexander KoenigZentrum für Taxonomie und EvolutionsforschungBonnGermany
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Marin IN, Palatov DM. The hidden diversity of the genus Lyurella Derzhavin, 1939 (Crustacea: Amphipoda: Crangonyctidae): four new species from the subterranean habitats of the northwestern Caucasus, Russia. Zootaxa 2021; 5006:127-168. [PMID: 34810579 DOI: 10.11646/zootaxa.5006.1.17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Indexed: 11/04/2022]
Abstract
Four new species of the Palaearctic crangonyctid amphipod genus Lyurella Derzhavin, 1939 (Crustacea: Amphipoda: Crangonyctidae), L. mikhailovi sp. n., L. fanagorica sp. n., L. fontinalis sp. n. and L. asheensis sp. n., are described based on an integrative approach from the subterranean habitats of the southwestern foothills of the Greater Caucasian Ridge (the north-eastern Black Sea coast). Despite the relative proximity of the habitats, the interspecific genetic divergence (by COI mtDNA gene marker) between the newly outlined Caucasian species of the genus varied from 11 to 21%, demonstrating a long-term isolation and lack of gene flow for at least 37Mya, starting from the Pliocene. The lowest genetic divergence between L. shepsiensis Sidorov, 2015 and L. asheensis sp. n., estimated as 4%, is also considered species-specific due to the presence of distinct morphological differences. We discuss the phylogeny, morphology, and distribution and provide a key for all known species of Lyurella. DNA barcoding data for all species, including the type species of the genus, Lyurella hyrcana Derzhavin, 1939, are presented for the first time.
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Affiliation(s)
- Ivan N Marin
- A.N. Severtsov Institute of Ecology and Evolution of RAS, Moscow 119071, Russia..
| | - Dmitry M Palatov
- A.N. Severtsov Institute of Ecology and Evolution of RAS, Moscow 119071, Russia..
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Multiple evolutionary lineages for the main vector of Leishmania guyanensis, Lutzomyia umbratilis (Diptera: Psychodidae), in the Brazilian Amazon. Sci Rep 2021; 11:15323. [PMID: 34321495 PMCID: PMC8319306 DOI: 10.1038/s41598-021-93072-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/21/2021] [Indexed: 02/07/2023] Open
Abstract
Lutzomyia umbratilis is the main vector of Leishmania guyanensis in the Brazilian Amazon and in neighboring countries. Previous biological and molecular investigations have revealed significant differences between L. umbratilis populations from the central Brazilian Amazon region. Here, a phylogeographic survey of L. umbratilis populations collected from nine localities in the Brazilian Amazon was conducted using two mitochondrial genes. Statistical analyses focused on population genetics, phylogenetic relationships and species delimitations. COI genetic diversity was very high, whereas Cytb diversity was moderate. COI genealogical haplotypes, population structure and phylogenetic analyses identified a deep genetic differentiation and three main genetic groups. Cytb showed a shallower genetic structure, two main haplogroups and poorly resolved phylogenetic trees. These findings, allied to absence of isolation by distance, support the hypothesis that the Amazon and Negro Rivers and interfluves are the main evolutionary forces driving L. umbratilis diversification. The main three genetic groups observed represent three evolutionary lineages, possibly species. The first lineage occurs north of the Amazon River and east of Negro River, where Le. guyanensis transmission is intense, implying that L. umbratilis is an important vector there. The second lineage is in the interfluve between north of Amazon River and west of Negro River, an area reported to be free of Le. guyanensis transmission. The third lineage, first recorded in this study, is in the interfluve between south of Amazonas River and west of Madeira River, and its involvement in the transmission of this parasite remains to be elucidated.
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65
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MacGuigan DJ, Hoagstrom CW, Domisch S, Hulsey CD, Near TJ. Integrative ichthyological species delimitation in the Greenthroat Darter complex (Percidae: Etheostomatinae). ZOOL SCR 2021. [DOI: 10.1111/zsc.12504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Sami Domisch
- Department of Ecosystem Research Leibniz‐Institute of Freshwater Ecology and Inland Fisheries Berlin Germany
| | - C. Darrin Hulsey
- Laboratory for Zoology and Evolutionary Biology Department of Biology University of Konstanz Konstanz Germany
| | - Thomas J. Near
- Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
- Peabody Museum of Natural History Yale University New Haven CT USA
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66
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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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Ribolli J, Zaniboni Filho E, Scaranto BMS, Shibatta OA, Machado CB. Cryptic diversity and diversification processes in three cis-Andean Rhamdia species (Siluriformes: Heptapteridae) revealed by DNA barcoding. Genet Mol Biol 2021; 44:e20200470. [PMID: 34254973 PMCID: PMC8276235 DOI: 10.1590/1678-4685-gmb-2020-0470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/07/2021] [Indexed: 12/02/2022] Open
Abstract
The wide distribution of the Neotropical freshwater catfish Rhamdia offers an excellent opportunity to investigate the historical processes responsible for modeling South America’s hydrogeological structure. We used sequences from cis-Andean and Mesoamerican Rhamdia species to reconstruct and estimate divergence times among cis-Andean lineages, correlating the results with known geological events. Species delimitation methods based on distance (DNA barcoding and BIN) and coalescence (GMYC) approaches identified nine well-supported lineages from the cis-Andean region from sequences available in the BOLD dataset. The cis-Andean Rhamdia lineages diversification process began in Eocene and represented the split between cis-Andean and Mesoamerican clades. The cis-Andean clade contains two principal groups: Northwest clade (MOTUs from Amazon, Essequibo, Paraguay, and Itapecuru basins) and Southeast clade (Eastern Brazilian shield basins (Paraná, Uruguay, Iguaçu, and São Francisco) plus eastern coastal basins). The diversification of the cis-Andean Rhamdia lineages results from vicariance and geodispersion events, which played a key role in the current intricate distribution pattern of the Rhamdia lineages. The wide geographical distribution and large size of the specimens make it attractive to cultivate in different countries of the Neotropical region. The lineages delimitation minimizes identification mistakes, unintentional crossings by aquaculture, and reduces natural stocks contamination.
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Affiliation(s)
- Josiane Ribolli
- Universidade Federal de Santa Catarina, Departamento de Aquicultura, Lagoa do Peri, Laboratório de Biologia e Cultivo de Peixes de Água Doce, Florianópolis, SC, Brazil
| | - Evoy Zaniboni Filho
- Universidade Federal de Santa Catarina, Departamento de Aquicultura, Lagoa do Peri, Laboratório de Biologia e Cultivo de Peixes de Água Doce, Florianópolis, SC, Brazil
| | - Bianca Maria Soares Scaranto
- Universidade Federal de Santa Catarina, Departamento de Aquicultura, Lagoa do Peri, Laboratório de Biologia e Cultivo de Peixes de Água Doce, Florianópolis, SC, Brazil
| | - Oscar Akio Shibatta
- Universidade Estadual de Londrina, Departamento de Biologia Animal e Vegetal, Centro de Ciências Biológicas, Londrina, PR, Brazil
| | - Carolina Barros Machado
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
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68
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A taxonomist's nightmare - Cryptic diversity in Caribbean intertidal arthropods (Arachnida, Acari, Oribatida). Mol Phylogenet Evol 2021; 163:107240. [PMID: 34197900 DOI: 10.1016/j.ympev.2021.107240] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/16/2021] [Accepted: 06/24/2021] [Indexed: 12/28/2022]
Abstract
There has been a long controversy about what defines a species and how to delimitate them which resulted in the existence of more than two dozen different species concepts. Recent research on so-called "cryptic species" heated up this debate as some scientists argue that these cryptic species are only a result of incompatible species concepts. While this may be true, we should keep in mind that all concepts are nothing more than human constructs and that the phenomenon of high phenotypic similarity despite reproductive isolation is real. To investigate and understand this phenomenon it is important to classify and name cryptic species as it allows to communicate them with other fields of science that use Linnaean binomials. To provide a common framework for the description of cryptic species, we propose a possible protocol of how to formally name and describe these taxa in practice. The most important point of this protocol is to explain which species concept was used to delimitate the cryptic taxon. As a model, we present the case of the allegedly widespread Caribbean intertidal mite Thalassozetes barbara, which in fact consists of seven phenotypically very similar but genetically distinct species. All species are island or short-range endemics with poor dispersal abilities that have evolved in geographic isolation. Stabilizing selection caused by the extreme conditions of the intertidal environment is suggested to be responsible for the morphological stasis of this cryptic species complex.
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Guimarães RR, Rocha RG, Loss AC, Mendes-Oliveira AC, Patterson BD, Costa LP. Morphological and molecular discordance in the taxonomic rearrangement of the Marmosops pinheiroi complex (Marsupialia: Didelphidae). SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1921877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Roger Rodrigues Guimarães
- Departamento de Ciências Biológicas, Centro de Ciências Humanas e Naturais, Universidade Federal do Espírito Santo (UFES), Av. Fernando Ferrari, 514, Vitória, 29075-910, ES, Brazil
| | - Rita Gomes Rocha
- Departamento de Ciências Biológicas, Centro de Ciências Humanas e Naturais, Universidade Federal do Espírito Santo (UFES), Av. Fernando Ferrari, 514, Vitória, 29075-910, ES, Brazil
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, 4485-661, Portugal
| | - Ana Carolina Loss
- Departamento de Ciências Biológicas, Centro de Ciências Humanas e Naturais, Universidade Federal do Espírito Santo (UFES), Av. Fernando Ferrari, 514, Vitória, 29075-910, ES, Brazil
- National Institute of the Atlantic Forest, Av. José Ruschi, 4, Santa Teresa, 29650-000, ES, Brazil
| | | | - Bruce D. Patterson
- Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, 60605, IL, USA
| | - Leonora Pires Costa
- Departamento de Ciências Biológicas, Centro de Ciências Humanas e Naturais, Universidade Federal do Espírito Santo (UFES), Av. Fernando Ferrari, 514, Vitória, 29075-910, ES, Brazil
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70
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Levicoy D, Rosenfeld S, Cárdenas L. Divergence time and species delimitation of microbivalves in the Southern Ocean: the case of Kidderia species. Polar Biol 2021; 44:1365-1377. [PMID: 34092908 PMCID: PMC8169414 DOI: 10.1007/s00300-021-02885-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 05/10/2021] [Accepted: 05/19/2021] [Indexed: 11/18/2022]
Abstract
The systematics of Subantarctic and Antarctic near-shore marine benthic invertebrates requires major revision and highlights the necessity to incorporate additional sources of information in the specimen identification chart in the Southern Ocean (SO). In this study, we aim to improve our understanding of the biodiversity of Kidderia (Dall 1876) through molecular and morphological comparisons of Antarctic and Subantarctic taxa. The microbivalves of the genus Kidderia are small brooding organisms that inhabit intertidal and shallow subtidal rocky ecosystems. This genus represents an interesting model to test the vicariance and dispersal hypothesis in the biogeography of the SO. However, the description of Kidderia species relies on a few morphological characters and biogeographic records that raise questions about the true diversity in the group. Here we will define the specimens collected with genetic tools, delimiting their respective boundaries across provinces of the SO, validating the presence of two species of Kidderia. Through the revision of taxonomic issues and species delimitation, it was possible to report that the Antarctic species is Kidderia subquadrata and the species recorded in the Subantarctic islands Diego Ramirez, South Georgia and the Kerguelen Archipelago is Kidderia minuta. The divergence time estimation suggests the origin and diversification of Kidderia lineages are related to historical vicariant processes probably associated with the separation of the continental landmasses close to the late Eocene.
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Affiliation(s)
- Daniela Levicoy
- Centro FONDAP- IDEAL, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,Instituto de Ciencias Ambientales & Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Independencia 641, P.O. Box 567, Valdivia, Chile
| | - Sebastián Rosenfeld
- Laboratorio de Ecología Molecular, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras #3425, Ñuñoa, Santiago Chile.,Laboratorio de Ecosistemas Marinos Antárticos y Subantárticos, Universidad de Magallanes, Avenida Bulnes 01890, Punta Arenas, Chile.,Instituto de Ecología y Biodiversidad, Las Palmeras 3425, Ñuñoa, Santiago Chile.,Centro de Investigación Gaia-Antártica, Universidad de Magallanes, Avenida Bulnes 01855, Punta Arenas, Chile
| | - Leyla Cárdenas
- Centro FONDAP- IDEAL, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,Instituto de Ciencias Ambientales & Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Independencia 641, P.O. Box 567, Valdivia, Chile
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71
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Sklenář F, Jurjević Ž, Houbraken J, Kolařík M, Arendrup M, Jørgensen K, Siqueira J, Gené J, Yaguchi T, Ezekiel C, Silva Pereira C, Hubka V. Re-examination of species limits in Aspergillus section Flavipedes using advanced species delimitation methods and description of four new species. Stud Mycol 2021; 99:100120. [PMID: 35003383 PMCID: PMC8688885 DOI: 10.1016/j.simyco.2021.100120] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Since the last revision in 2015, the taxonomy of section Flavipedes evolved rapidly along with the availability of new species delimitation techniques. This study aims to re-evaluate the species boundaries of section Flavipedes members using modern delimitation methods applied to an extended set of strains (n = 90) collected from various environments. The analysis used DNA sequences of three house-keeping genes (benA, CaM, RPB2) and consisted of two steps: application of several single-locus (GMYC, bGMYC, PTP, bPTP) and multi-locus (STACEY) species delimitation methods to sort the isolates into putative species, which were subsequently validated using DELINEATE software that was applied for the first time in fungal taxonomy. As a result, four new species are introduced, i.e. A. alboluteus, A. alboviridis, A. inusitatus and A. lanuginosus, and A. capensis is synonymized with A. iizukae. Phenotypic analyses were performed for the new species and their relatives, and the results showed that the growth parameters at different temperatures and colonies characteristics were useful for differentiation of these taxa. The revised section harbors 18 species, most of them are known from soil. However, the most common species from the section are ecologically diverse, occurring in the indoor environment (six species), clinical samples (five species), food and feed (four species), droppings (four species) and other less common substrates/environments. Due to the occurrence of section Flavipedes species in the clinical material/hospital environment, we also evaluated the susceptibility of 67 strains to six antifungals (amphotericin B, itraconazole, posaconazole, voriconazole, isavuconazole, terbinafine) using the reference EUCAST method. These results showed some potentially clinically relevant differences in susceptibility between species. For example, MICs higher than those observed for A. fumigatus wild-type were found for both triazoles and amphotericin B for A. ardalensis, A. iizukae, and A. spelaeus whereas A. lanuginosus, A. luppiae, A. movilensis, A. neoflavipes, A. olivimuriae and A. suttoniae were comparable to or more susceptible as A. fumigatus. Finally, terbinafine was in vitro active against all species except A. alboviridis.
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Affiliation(s)
- F. Sklenář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | | | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - M. Kolařík
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - M.C. Arendrup
- Unit of Mycology, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - K.M. Jørgensen
- Unit of Mycology, Statens Serum Institut, Copenhagen, Denmark
| | - J.P.Z. Siqueira
- Laboratório de Microbiologia, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, Brazil
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - J. Gené
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - T. Yaguchi
- Medical Mycology Research Center, Chiba University, Chuo-ku, Chiba, Japan
| | - C.N. Ezekiel
- Department of Microbiology, Babcock University, Ilishan Remo, Ogun State, Nigeria
| | - C. Silva Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - V. Hubka
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
- Medical Mycology Research Center, Chiba University, Chuo-ku, Chiba, Japan
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Fegies AC, Carmignotto AP, Perez MF, Guilardi MD, Lessinger AC. Molecular Phylogeny of Cryptonanus (Didelphidae: Thylamyini): Evidence for a recent and complex diversification in South American open biomes. Mol Phylogenet Evol 2021; 162:107213. [PMID: 34029717 DOI: 10.1016/j.ympev.2021.107213] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 05/07/2021] [Accepted: 05/19/2021] [Indexed: 11/30/2022]
Abstract
Systematic revisions of South American marsupials have contributed to our knowledge about genus and species diversity in the last decades, including studies of the most recently described genus Cryptonanus (Didelphidae), currently comprising four recognized species. Herein we provide the first phylogeny for these mouse opossums based on comprehensive sampling, including representatives from all nominal taxa, encompassing most of the geographic distribution of the genus while also extending its known range. The taxonomic status of Cryptonanus species was explored by analyses of multiple mitochondrial and nuclear DNA markers to assess phylogenetic relationships and to provide divergence time estimates, species delimitations and biogeographical hypotheses. Cryptonanus monophyly remained highly supported despite the inclusion of abundant new data from more than a hundred specimens, comprising 10 independent evolutionary lineages. Species-complexes within valid nominal taxa reveal higher species richness in the genus. Based on divergence estimates from a dated phylogeny, we suggest that Cryptonanus diversified along the Quaternary, with speciation events occurring well into the Pleistocene. The best supported biogeographical hypothesis endorses speciation by vicariance and subset speciation across open formations in shaping the evolutionary history of this didelphid genus, strongly associated with dry tropical landscapes of South America.
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Affiliation(s)
- Ana Cláudia Fegies
- Departamento de Engenharia Ambiental, Universidade Estadual Paulista (UNESP), Campus Sorocaba, Av. Três de Março 511, Sorocaba, São Paulo CEP 18087-180, Brazil
| | - Ana Paula Carmignotto
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Campus Sorocaba, Rodovia João Leme dos Santos km 110, Sorocaba, São Paulo CEP 18052-780, Brazil.
| | - Manolo Fernandez Perez
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luís km 235, São Carlos, São Paulo CEP 13565-905, Brazil
| | - Mariana Dias Guilardi
- Laboratório de Ecologia e Evolução, Instituto Butantan, Avenida Vital Brazil 1500, São Paulo, São Paulo CEP 05503-000, Brazil
| | - Ana Cláudia Lessinger
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Campus Sorocaba, Rodovia João Leme dos Santos km 110, Sorocaba, São Paulo CEP 18052-780, Brazil.
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Flury JM, Haas A, Brown RM, Das I, Pui YM, Boon-Hee K, Scheidt U, Iskandar DT, Jankowski A, Hertwig ST. Unexpectedly high levels of lineage diversity in Sundaland puddle frogs (Dicroglossidae: Occidozyga Kuhl and van Hasselt, 1822). Mol Phylogenet Evol 2021; 163:107210. [PMID: 34029720 DOI: 10.1016/j.ympev.2021.107210] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 05/12/2021] [Accepted: 05/19/2021] [Indexed: 01/04/2023]
Abstract
One of the most urgent contemporary tasks for taxonomists and evolutionary biologists is to estimate the number of species on earth. Recording alpha diversity is crucial for protecting biodiversity, especially in areas of elevated species richness, which coincide geographically with increased anthropogenic environmental pressures - the world's so-called biodiversity hotspots. Although the distribution of Puddle frogs of the genus Occidozyga in South and Southeast Asia includes five biodiversity hotspots, the available data on phylogeny, species diversity, and biogeography are surprisingly patchy. Samples analyzed in this study were collected throughout Southeast Asia, with a primary focus on Sundaland and the Philippines. A mitochondrial gene region comprising ~ 2000 bp of 12S and 16S rRNA with intervening tRNA Valine and three nuclear loci (BDNF, NTF3, POMC) were analyzed to obtain a robust, time-calibrated phylogenetic hypothesis. We found a surprisingly high level of genetic diversity within Occidozyga, based on uncorrected p-distance values corroborated by species delimitation analyses. This extensive genetic diversity revealed 29 evolutionary lineages, defined by the > 5% uncorrected p-distance criterion for the 16S rRNA gene, suggesting that species diversity in this clade of phenotypically homogeneous forms probably has been underestimated. The comparison with results of other anuran groups leads to the assumption that anuran species diversity could still be substantially underestimated in Southeast Asia in general. Many genetically divergent lineages of frogs are phenotypically similar, indicating a tendency towards extensive morphological conservatism. We present a biogeographic reconstruction of the colonization of Sundaland and nearby islands which, together with our temporal framework, suggests that lineage diversification centered on the landmasses of the northern Sunda Shelf. This remarkably genetically structured group of amphibians could represent an exceptional case for future studies of geographical structure and diversification in a widespread anuran clade spanning some of the most pronounced geographical barriers on the planet (e.g., Wallace's Line). Studies considering gene flow, morphology, ecological and bioacoustic data are needed to answer these questions and to test whether observed diversity of Puddle frog lineages warrants taxonomic recognition.
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Affiliation(s)
- Jana M Flury
- Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany; Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, 3005 Bern, Switzerland
| | - Alexander Haas
- Centrum für Naturkunde, Universität Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Rafe M Brown
- Department of Ecology and Evolutionary Biology, Biodiversity Institute, University of Kansas, 1345 Jayhawk Blvd, Dyche Hall, Lawrence, KS 66045, USA
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - Yong Min Pui
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - Kueh Boon-Hee
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Ulrich Scheidt
- Naturkundemuseum Erfurt, Große Arche 14, 99084 Erfurt, Germany
| | - Djoko T Iskandar
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jalan Ganesa 10, Bandung 40132, Indonesia
| | - André Jankowski
- Centrum für Naturkunde, Universität Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Stefan T Hertwig
- Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, 3005 Bern, Switzerland; University of Bern, Institute of Ecology and Evolution, Baltzerstrasse 6, 3006 Bern, Switzerland.
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74
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Zangl L, Glatzhofer E, Schmid R, Randolf S, Koblmüller S. DNA barcoding of Austrian snow scorpionflies (Mecoptera, Boreidae) reveals potential cryptic diversity in Boreus westwoodi. PeerJ 2021; 9:e11424. [PMID: 34040896 PMCID: PMC8127955 DOI: 10.7717/peerj.11424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/17/2021] [Indexed: 02/01/2023] Open
Abstract
Background Snow scorpionflies (genus Boreus) belong to a family of Mecoptera, Boreidae, that has been vastly neglected by entomological researchers due to their shift in seasonality to the winter months. Their activity during this time is regarded as a strategy for predator avoidance and regular sightings on snow fields suggest that this also facilitates dispersal. However, many aspects about snow scorpionflies, especially systematics, taxonomy, distribution of species, phylogenetics and phylogeography have remained fairly unexplored until today. In this study, we fill some of these gaps by generating a reference DNA barcode database for Austrian snow scorpionflies in the frame of the Austrian Barcode of Life initiative and by characterising morphological diversity in the study region. Methods Initial species assignment of all 67 specimens was based on male morphological characters previously reported to differ between Boreus species and, for females, the shape of the ovipositor. DNA barcoding of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene was carried out for all 67 samples and served as a basis for BIN assignment, genetic distance calculations, as well as alternative species delimitation analyses (ABGD, GMYC, bGMYC, bPTP) and a statistical parsimony network to infer phylogenetic relationships among individual samples/sampling sites. Results Morphological investigations suggested the presence of both Boreus hyemalis and Boreus westwoodi in Austria. DNA barcoding also separated the two species, but resulted in several divergent clades, the paraphyly of B. westwoodi in Austria, and high levels of phylogeographic structure on a small geographic scale. Even though the different molecular species delimitation methods disagreed on the exact number of species, they unequivocally suggested the presence of more than the traditionally recognized two Boreus species in Austria, thus indicating potential cryptic species within the genus Boreus in general and especially in B. westwoodi.
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Affiliation(s)
- Lukas Zangl
- Institute of Biology, University of Graz, Graz, Styria, Austria.,Universalmuseum Joanneum, Studienzentrum Naturkunde, Graz, Styria, Austria
| | | | - Raphael Schmid
- Institute of Biology, University of Graz, Graz, Styria, Austria
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75
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Garibian PG, Karabanov DP, Neretina AN, Taylor DJ, Kotov AA. Bosminopsis deitersi (Crustacea: Cladocera) as an ancient species group: a revision. PeerJ 2021; 9:e11310. [PMID: 33981506 PMCID: PMC8074845 DOI: 10.7717/peerj.11310] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/29/2021] [Indexed: 12/02/2022] Open
Abstract
Water fleas (Crustacea: Cladocera) of the Family Bosminidae have been studied since the founding of paleolimnology and freshwater ecology. However, one species, Bosminopsis deitersi, stands out for its exceptional multicontinental range and broad ecological requirements. Here we use an integrated morphological and multilocus genetic approach to address the species problem in B. deitersi. We analyzed 32 populations of B. deitersi s. lat. Two nuclear and two mitochondrial loci were used to carry out the bGMYC, mPTP and STACEY algorithms for species delimitation. Detailed morphological study was also carried out across continents. The evidence indicated a widely distributed cryptic species in the Old World (Bosminopsis zernowi) that is genetically divergent from B. deitersi s.str. We revised the taxonomy and redescribed the species in this complex. Our sampling indicated that B. zernowi had weak genetic differentiation across its range. A molecular clock and biogeographic analysis with fossil calibrations suggested a Mesozoic origin for the Bosminopsis deitersi group. Our evidence rejects the single species hypothesis for B. deitersi and is consistent with an ancient species group (potentially Mesozoic) that shows marked morphological conservation. The family Bosminidae, then, has examples of both rapid morphological evolution (Holocene Bosmina), and morphological stasis (Bosminopsis).
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Affiliation(s)
- Petr G. Garibian
- Laboratory of Aquatic Ecology and Invasions, A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
| | - Dmitry P. Karabanov
- Laboratory of Fish Ecology, I.D. Papanin Institute for Biology of Inland Waters of Russian Academy of Sciences, Borok, Yaroslavl Area, Russia
| | - Anna N. Neretina
- Laboratory of Aquatic Ecology and Invasions, A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
| | - Derek J. Taylor
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, New York, United States
| | - Alexey A. Kotov
- Laboratory of Aquatic Ecology and Invasions, A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia
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76
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Moraes SDS, Murillo‐Ramos L, Machado PA, Ghanavi HR, Magaldi LM, Silva‐Brandão KL, Kato MJ, Freitas AVL, Wahlberg N. A double‐edged sword: Unrecognized cryptic diversity and taxonomic impediment in
Eois
(Lepidoptera, Geometridae). ZOOL SCR 2021. [DOI: 10.1111/zsc.12488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Simeão de Souza Moraes
- Departamento de Biologia Animal and Museu de Zoologia Universidade Estadual de Campinas Campinas Brazil
- Department of Biology Lund University Lund Sweden
| | - Leidys Murillo‐Ramos
- Department of Biology Lund University Lund Sweden
- Departamento de Biología Universidad de Sucre Sincelejo Colombia
| | - Patrícia A. Machado
- Departamento de Biologia Animal and Museu de Zoologia Universidade Estadual de Campinas Campinas Brazil
| | | | - Luiza M. Magaldi
- Departamento de Biologia Animal and Museu de Zoologia Universidade Estadual de Campinas Campinas Brazil
| | | | - Massuo J. Kato
- Laboratório de Química de Produtos Naturais Instituto de Química Universidade de São Paulo São Paulo Brazil
| | - André V. L. Freitas
- Departamento de Biologia Animal and Museu de Zoologia Universidade Estadual de Campinas Campinas Brazil
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77
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Myers EA, Folly H, Ragalzi E, Feio RN, Santana DJ. Late Pliocene population divergence and persistence despite Pleistocene climatic fluctuations in the Rio Doce snouted Treefrog ( Ololygon carnevallii). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Edward A. Myers
- Department of Vertebrate Zoology National Museum of Natural HistorySmithsonian Institution Washington DC USA
| | - Henrique Folly
- Departamento de Biologia Animal Museu de Zoologia João MoojenUniverisdade Federal de Viçosa Viçosa MG Brazil
- Instituto de Biociências Laboratório de Zoologia Universidade Federal de Mato Grosso do Sul Campo Grande MS Brazil
| | - Eric Ragalzi
- Instituto de Biociências Laboratório de Zoologia Universidade Federal de Mato Grosso do Sul Campo Grande MS Brazil
| | - Renato Neves Feio
- Departamento de Biologia Animal Museu de Zoologia João MoojenUniverisdade Federal de Viçosa Viçosa MG Brazil
| | - Diego José Santana
- Instituto de Biociências Laboratório de Zoologia Universidade Federal de Mato Grosso do Sul Campo Grande MS Brazil
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78
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Brasero N, Ghisbain G, Lecocq T, Michez D, Valterová I, Biella P, Monfared A, Williams PH, Rasmont P, Martinet B. Resolving the species status of overlooked West‐Palaearctic bumblebees. ZOOL SCR 2021. [DOI: 10.1111/zsc.12486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Nicolas Brasero
- Laboratory of Zoology Research institute for Biosciences, University of Mons MonsBelgium
| | - Guillaume Ghisbain
- Laboratory of Zoology Research institute for Biosciences, University of Mons MonsBelgium
| | - Thomas Lecocq
- Laboratory of Zoology Research institute for Biosciences, University of Mons MonsBelgium
- Université de Lorraine, INRAE, URAFPA Nancy France
| | - Denis Michez
- Laboratory of Zoology Research institute for Biosciences, University of Mons MonsBelgium
| | - Irena Valterová
- Academy of Sciences of the Czech Republic Institute of Organic Chemistry and Biochemistry Prague Czech Republic
- Faculty of Tropical AgriSciences Czech University of Life Sciences Prague Czech Republic
| | - Paolo Biella
- Department of Biotechnology and Biosciences University of Milano‐Bicocca Milano Italy
| | - Alireza Monfared
- Department of Plant Protection, Faculty of Agriculture Yasouj University Yasouj Iran
| | | | - Pierre Rasmont
- Laboratory of Zoology Research institute for Biosciences, University of Mons MonsBelgium
| | - Baptiste Martinet
- Laboratory of Zoology Research institute for Biosciences, University of Mons MonsBelgium
- Evolutionary Biology & Ecology Université Libre de Bruxelles Bruxelles Belgium
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79
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Tougard C, Vukić J, Ahnelt H, Buj I, Kovačić M, Moro GA, Tutman P, Šanda R. Quaternary climatic cycles promoted (re)colonization and diversification events in Adriatic sand gobies. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Jasna Vukić
- Department of Ecology Faculty of Science Charles University Prague Czech Republic
| | - Harald Ahnelt
- Department of Evolutionary Biology Faculty of Life Sciences University of Vienna Vienna Austria
- First Zoological Department Natural History Museum in Vienna Vienna Austria
| | - Ivana Buj
- Department of Zoology Faculty of Science University of Zagreb Zagreb Croatia
| | | | | | - Pero Tutman
- Laboratory for Ichthyology and Coastal Fisheries Institute of Oceanography and Fisheries Split Croatia
| | - Radek Šanda
- Department of Zoology National Museum Prague Czech Republic
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80
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Klesser R, Husemann M, Schmitt T, Sousa P, Moussi A, Habel JC. Molecular biogeography of the Mediterranean Buthus species complex (Scorpiones: Buthidae) at its southern Palaearctic margin. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Neogene orogenesis and climatic cycles strongly influenced inter- and intraspecific differentiation and variability of taxa. In this study, we focused on the southern margin of the western Palaearctic, known to be a geographically complex region. We performed mitochondrial DNA analyses of Buthus scorpions from the Moroccan Atlas Mountains, from the Hoggar Mountains in Algeria and from Tunisia, Iberia and Israel. Molecular species delimitation suggests the existence of ≥ 24 molecular operational taxonomic units. The data confirm complex differentiation patterns across the Atlas Mountains of Morocco, but structures in Iberia, Algeria and Tunisia have considerably lower complexity. This identifies the Atlas Mountain region as the most important differentiation centre of Buthus scorpions. Samples from the Hoggar Mountains (southern Algeria) cluster with those from the southernmost parts of Morocco in the middle and upper parts of the Draa Valley. This reinforces a recent connection of these regions. Samples from Israel are genetically similar to individuals from eastern Algeria and Tunisia. This suggests a widespread group across major parts of North Africa. Divergence time estimates indicate that differentiation in the genus began during the late Miocene, a period characterized by strong tectonic activities in this region. Further differentiation could be linked to subsequent climatic changes that have occurred since the end of the Miocene, with an increasing aridification of the Moroccan area. This also produced many microrefugia in the mountains of the area during the Pleistocene climatic fluctuations.
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Affiliation(s)
- Robert Klesser
- Department of Invertebrates, Natural History Museum Leipzig, Leipzig, Germany
- Department of Entomology, Centrum für Naturkunde, Universität Hamburg, Hamburg, Germany
| | - Martin Husemann
- Department of Entomology, Centrum für Naturkunde, Universität Hamburg, Hamburg, Germany
| | - Thomas Schmitt
- Senckenberg German Entomological Institute, Müncheberg, Germany
- Zoology, Institute of Biology, Faculty Natural Sciences I, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Pedro Sousa
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Abdelhamid Moussi
- Laboratory Valorization and Conservation of Natural Resources, University of Biskra, Algeria
| | - Jan Christian Habel
- Evolutionary Zoology, Department of Biosciences, University of Salzburg, Salzburg, Austria
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81
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Dal Vechio F, Prates I, Grazziotin FG, Graboski R, Rodrigues MT. Molecular and phenotypic data reveal a new Amazonian species of pit vipers (Serpentes: Viperidae: Bothrops). J NAT HIST 2021. [DOI: 10.1080/00222933.2020.1845835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Francisco Dal Vechio
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Ivan Prates
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | | | | | - Miguel Trefaut Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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82
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Katoziyan A, Imani Fooladi AA, Taheri RA, Vatanpour S. Multi-drug resistance of Staphylococcus aureus Strains in Baqiyatallah hospital: a Primary Step Towards Digital Health Biomonitoring Systems. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2021; 19:321-328. [PMID: 33680033 PMCID: PMC7758007 DOI: 10.22037/ijpr.2020.112966.14042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The aim of the study was to evaluate the drug-resistance patterns of Staphylococcus aureus infections in Baqiyatallah hospital within 2010–2019 and to present a novel monitoring and detection system making use of molecular laboratory methods teamed with molecular delimitation analyses. This in turn is a primary step to establishment of a digital health system within Baqiyatallah hospital as a perfect pilot instance for other hospitals to follow upon. Totally, 100 patients of Baqiyatallah hospital suspicious of Staphylococcus aureus infections were sampled. Bacterial identity confirmations were done using routine biochemical test. Antibiograms were made for all the patients in this study. Consequently, bacterial total DNA was extracted and 16S rDNA gene amplified and sequenced for all patients. To uncover any cryptic strain grouping within the samples, a molecular delimitation method, i.e. automated barcode gap discovery (ABGD), was done. Our results showed Ceftaroline to be the most and Erythromycin and Oxacillin the least effective drugs. Delimitation uncovered 19 groups out of which group 19 seemed to have location-specific genetic signals in regards to susceptibility of Erythromycin and Oxacillin. Our results indicate the importance of genetic identification of bacteria with respect to their genetic patterns before antibiotic administration in order to both reduce unnecessary medicine use and to biomonitor the bacterial patterns in respect to their behavior towards general antibiotics.
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Affiliation(s)
- Ahmadreza Katoziyan
- Center of Excellence in Phylogeny of Living Organisms, School of Biology, University of Tehran, Iran.,Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Abbas Ali Imani Fooladi
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ramezan Ali Taheri
- Nanobiotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Saba Vatanpour
- Department of Biology, University of British Columbia, Vancouver, Canada
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83
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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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84
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de Oliveira FFR, Gehara M, Solé M, Lyra M, Haddad CFB, Silva DP, de Magalhães RF, Leite FSF, Burbrink FT. Quaternary climatic fluctuations influence the demographic history of two species of sky-island endemic amphibians in the Neotropics. Mol Phylogenet Evol 2021; 160:107113. [PMID: 33610648 DOI: 10.1016/j.ympev.2021.107113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 01/13/2021] [Accepted: 02/08/2021] [Indexed: 10/22/2022]
Abstract
We evaluated the role of Quaternary climatic fluctuations on the demographic history and population structure of amphibian species endemic to the 'campo rupestre' in the Neotropics, evaluating their distributional shifts, demographic changes, and lineage formation from the end of Pleistocene to present. We chose two anurans endemic to the high-elevation 'campo rupestre' in the Espinhaço Range (ER) in northeastern and southeastern Brazil (Bokermannohyla alvarengai and Bokermannohyla oxente), as models to test the role of Quaternary climatic fluctuations over their distribution range in this region. We collected tissue samples throughout their distribution range and used statistical phylogeography to examine processes of divergence and population demography. We generated spatial-temporal reconstructions using Bayesian inference in a coalescent framework in combination with hind-cast projections of species distribution models (SDMs). We also used the results and literature information to test alternative diversification scenarios via approximate Bayesian computation (ABC). Our results show that Quaternary climatic fluctuations influenced the geographic ranges of both species showing population expansion during the last glacial maximum (LGM) and range contraction during interglacial periods, as inferred from selected ABC models and from past projections of SDMs. We recovered Pleistocene diversification for both species occuring in distinctly unique periods for each taxon. An older and range-restricted lineage was recovered in a geographically isolated geological massif, deserving conservation and further taxonomic study. The diversification and distribution of these amphibian species endemic to the Neotropical 'campo rupestre' were influenced by Quaternary climatic fluctuations. The expansion of cold adapted species restricted to higher elevations during glacial periods and their concomitant retraction during interglacial periods may have been crucial for producing patterns of species richness and endemism along elevation gradients in tropical and subtropical domains. Such processes may influence the evolution of the biota distributed in heterogeneous landscapes with varied topography.
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Affiliation(s)
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University - Newark, USA
| | - Mirco Solé
- Programa de Pós-graduação em Ecologia e Conservação da Biodiversidade, Universidade Estadual de Santa Cruz, Bahia, Brazil; Herpetology Section, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Mariana Lyra
- Universidade Estadual Paulista (UNESP), Departamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Campus Rio Claro, 13506-900 Rio Claro, São Paulo, Brazil
| | - Célio Fernando Baptista Haddad
- Universidade Estadual Paulista (UNESP), Departamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Campus Rio Claro, 13506-900 Rio Claro, São Paulo, Brazil
| | - Daniel Paiva Silva
- Instituto Federal Goiano - IF Goiano, Departamento de Biologia, Urutaí, Goiás, Brazil
| | - Rafael Félix de Magalhães
- Departamento de Ciências Naturais, Campus Dom Bosco, Universidade Federal de São João del-Rei, São João del Rei, MG 36301-160, Brazil
| | - Felipe Sá Fortes Leite
- Laboratório Sagarana, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa - UFV, Florestal, Minas Gerais, Brazil
| | - Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, New York, NY, USA
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85
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Cadenillas R, D'Elía G. The number of species of degus (genus Octodon) is currently underestimated: An appraisal of species limits and their phylogenetic relationships (Rodentia: Hystricomorpha: Octodontidae). Mol Phylogenet Evol 2021; 159:107111. [PMID: 33607277 DOI: 10.1016/j.ympev.2021.107111] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/28/2021] [Accepted: 02/05/2021] [Indexed: 01/04/2023]
Abstract
As currently understood, the genus Octodon contains five species degus, lunatus, bridgesii, pacificus, and ricardojeda. Previous phylogenetic studies suggest that genus specific diversity is underestimated. In order to evaluate the taxonomic diversity of Octodon, we implemented unilocus (cytochrome-b) and multilocus (cytochrome-b + 4 nuclear genes) species delimitation methods. Octodon degus was recovered as a sister of the other species of the genus. The unilocus bGMYC and mPTP methods, based on cytochrome-b sequences, delimits 11 and 7 candidate species respectively, and both methods fail to recognize O. pacificus from O. ricardojeda. Results of the multilocus analysis (BPP) vary as a function of the dataset used. When the five genes are used 11 species are delimited, while eight species are delimited when only the nuclear genes are used. Octodon bridgesii is shown as comprising at least two species (one on the Pacific coast and the typical form found on the Andean slopes), while O. ricardojeda may comprise two species (one on the Chilean side of the Andes and the other in Argentina). Likewise, both multilocus matrices recover O. pacificus as a distinct species. This shows that species diversity of Octodon is underestimated. Remarkably, many of the delimited species based on genetic data are morphologically differentiated in cranio-dental characteristics. However, a pair of species has not achieved morphological differentiation, being cryptic species. Finally, the incongruence between mitochondrial and nuclear phylogenies suggests that processes such as incomplete lineage sorting and/or introgression have been present during the radiation of the genus.
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Affiliation(s)
- Richard Cadenillas
- Doctorado en Ciencias, Mención Ecología y Evolución, Universidad Austral de Chile, Campus Isla Teja s/n, Valdivia 5090000, Chile; Instituto de Paleontología, Universidad Nacional de Piura, Piura 20002, Peru.
| | - Guillermo D'Elía
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Campus Isla Teja s/n, Valdivia 5090000, Chile.
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86
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Amador L, Victoriano PF, D’Elía G. Molecular species delimitation reveals hidden specific diversity within a freshwater burrowing crayfish (Decapoda: Parastacidae) from southern Chile. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2020.1865471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Luis Amador
- Doctorado en Ciencias mención Ecología y Evolución, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile
- Universidad Laica Vicente Rocafuerte, Guayaquil, 090514, Ecuador
| | - Pedro F. Victoriano
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, 4030000, Chile
| | - Guillermo D’Elía
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile
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87
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Neretina AN, Karabanov DP, Sacherova V, Kotov AA. Unexpected mitochondrial lineage diversity within the genus Alonella Sars, 1862 (Crustacea: Cladocera) across the Northern Hemisphere. PeerJ 2021; 9:e10804. [PMID: 33585083 PMCID: PMC7860113 DOI: 10.7717/peerj.10804] [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: 09/11/2020] [Accepted: 12/30/2020] [Indexed: 02/05/2023] Open
Abstract
Representatives of the genus Alonella Sars (Crustacea: Cladocera: Chydorinae) belong to the smallest known water fleas. Although species of Alonella are widely distributed and often abundant in acidic and mountain water bodies, their diversity is poorly studied. Morphological and genetic approaches have been complicated by the minute size of these microcrustaceans. As a result, taxonomists have avoided revising these species. Here, we present genetic data on Alonella species diversity across the Northern Hemisphere with particular attention to the A. excisa species complex. We analyzed 82 16S rRNA sequences (all newly obtained), and 78 COI sequences (39 were newly obtained). The results revealed at least twelve divergent phylogenetic lineages, possible cryptic species, of Alonella, with different distribution patterns. As expected, the potential species diversity of this genus is significantly higher than traditionally accepted. The A. excisa complex is represented by nine divergent clades in the Northern Hemisphere, some of them have relatively broad distribution ranges and others are more locally distributed. Our results provide a genetic background for subsequent morphological analyses, formal descriptions of Alonella species and detailed phylogeographical studies.
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Affiliation(s)
- Anna N. Neretina
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry P. Karabanov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
- I.D. Papanin Institute for Biology of Inland Waters, Borok, Yaroslavl State, Russia
| | | | - Alexey A. Kotov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
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88
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Cryptic Clitellata: Molecular Species Delimitation of Clitellate Worms (Annelida): An Overview. DIVERSITY-BASEL 2021. [DOI: 10.3390/d13020036] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Methods for species delimitation using molecular data have developed greatly and have become a staple in systematic studies of clitellate worms. Here we give a historical overview of the data and methods used to delimit clitellates from the mid-1970s to today. We also discuss the taxonomical treatment of the cryptic species, including the recommendation that cryptic species, as far as possible, should be described and named. Finally, we discuss the prospects and further development of the field.
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89
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Sánchez KI, Avila LJ, Sites JW, Morando M. An integrative approach to address species limits in the southernmost members of the Liolaemus kingii group (Squamata: Liolaemini). Mol Phylogenet Evol 2021; 157:107046. [PMID: 33421613 DOI: 10.1016/j.ympev.2020.107046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 11/07/2020] [Accepted: 12/14/2020] [Indexed: 11/28/2022]
Abstract
Recent conceptual and methodological advances have enabled an increasing number of studies to address the problem of species delimitation in a comprehensive manner. This is of particular interest in cases of species whose divergence times are recent and/or effective population sizes are large, where the conclusions obtained from a single source of evidence may lead to erroneous estimations of true species numbers or incorrect assignment of individuals to species. Iguanian lizards of the Liolaemus kingii group (13 species) comprise an important component of the endemic fauna of Patagonia. The southernmost species of this group (namely L. baguali, L. escarchadosi, L. sarmientoi, and L. tari) show widely overlapping distributions across southern Patagonia, also, their phylogenetic relationships are ambiguous and species boundaries have not been explicitly tested. Here we use a comprehensive approach to assess species limits through the use of molecular and morphological information (mitochondrial cytb, nuclear sequences collected by ddRADseq, and linear, meristic and landmark-based morphometrics). We found support for the current taxonomy given that the different analyses recognized the nominal species (4 entities), also a candidate species was supported by mitochondrial and morphological data. In addition, we detected signs of admixture between some of the species. Our results indicate that the L. kingii group can serve as a model system in studies of diversification accompanied by hybridization in nature, which in turn might have been promoted by past climatic oscillations and generalist morphologies. We emphasize the importance of using multiple lines of evidence in order to solve evolutionary stories, and minimizing potential erroneous results that may arise when relying on a single source of information.
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Affiliation(s)
- Kevin I Sánchez
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Boulevard Almirante Brown 2915, Puerto Madryn, CT U9120ACD, Argentina.
| | - Luciano J Avila
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Boulevard Almirante Brown 2915, Puerto Madryn, CT U9120ACD, Argentina
| | - Jack W Sites
- Department of Biology and M.L. Bean Life Science Museum, Brigham Young University (BYU), Provo, UT 84602, USA
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Boulevard Almirante Brown 2915, Puerto Madryn, CT U9120ACD, Argentina
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90
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Carvalho TR, Seger KR, Magalhães FM, Lourenço LB, Haddad CFB. Systematics and cryptic diversification of
Leptodactylus
frogs in the Brazilian campo rupestre. ZOOL SCR 2020. [DOI: 10.1111/zsc.12470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thiago R. Carvalho
- Laboratório de Herpetologia Departamento de Biodiversidade e Centro de Aquicultura Instituto de Biociências Universidade Estadual Paulista Rio Claro Brazil
| | - Karin R. Seger
- Laboratório de Estudos Cromossômicos Departamento de Biologia Estrutural e Funcional Instituto de Biologia Universidade Estadual de Campinas Campinas Brazil
| | - Felipe M. Magalhães
- Programa de Pós‐Graduação em Ciências Biológicas Centro de Ciências Exatas e da Natureza Universidade Federal da Paraíba João Pessoa Brazil
| | - Luciana B. Lourenço
- Laboratório de Estudos Cromossômicos Departamento de Biologia Estrutural e Funcional Instituto de Biologia Universidade Estadual de Campinas Campinas Brazil
| | - Célio F. B. Haddad
- Laboratório de Herpetologia Departamento de Biodiversidade e Centro de Aquicultura Instituto de Biociências Universidade Estadual Paulista Rio Claro Brazil
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91
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Magalhães FDM, Lyra ML, de Carvalho TR, Baldo D, Brusquetti F, Burella P, Colli GR, Gehara MC, Giaretta AA, Haddad CF, Langone JA, López JA, Napoli MF, Santana DJ, de Sá RO, Garda AA. Taxonomic Review of South American Butter Frogs: Phylogeny, Geographic Patterns, and Species Delimitation in the Leptodactylus latrans Species Group (Anura: Leptodactylidae). HERPETOLOGICAL MONOGRAPHS 2020. [DOI: 10.1655/0733-1347-31.4.131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Felipe de M. Magalhães
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal da Paraíba (UFPB), Centro de Ciências Exatas e da Natureza, Cidade Universitária, CEP 58000-000, João Pessoa, Paraíba, Brazil
| | - Mariana L. Lyra
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Campus Rio Claro, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), CEP 13506-900, Rio Claro, São Paulo, Brazil
| | - Thiago R. de Carvalho
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Campus Rio Claro, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), CEP 13506-900, Rio Claro, São Paulo, Brazil
| | - Diego Baldo
- Instituto de Biología Subtropical (IBS, CONICET-UNaM), Laboratorio de Genética Evolutiva, Facultad de Ciencias Exactas, Universidad Nacional de Misiones, CP N3300LQF, Posadas, Misiones, Argentina
| | - Francisco Brusquetti
- Instituto de Investigación Biológica del Paraguay (IIBP), Del Escudo 1607, CP 1425 Asunción, Paraguay
| | - Pamela Burella
- Departamento de Ciencias Naturales, Facultad de Humanidades y Ciencias, Universidad Nacional del Litoral. Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
| | - Guarino R. Colli
- Departamento de Zoologia, Universidade de Brasília (UNB), CEP 70910-900, Brasília, Distrito Federal, Brazil
| | - Marcelo C. Gehara
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, 07102, USA
| | - Ariovaldo A. Giaretta
- Laboratório de Taxonomia e Sistemática de Anuros Neotropicais (LTSAN), Instituto de Ciências Exatas e Naturais do Pontal (ICENP), Universidade Federal de Uberlândia (UFU), Ituiutaba, Minas Gerais, Brazil
| | - Célio F.B. Haddad
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Campus Rio Claro, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), CEP 13506-900, Rio Claro, São Paulo, Brazil
| | - José A. Langone
- Departamento de Herpetología, Museo Nacional de Historia Natural, Casilla de Correo 399, CP 11.000, Montevideo, Uruguay
| | - Javier A. López
- Departamento de Ciencias Naturales, Facultad de Humanidades y Ciencias, Universidad Nacional del Litoral. Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
| | - Marcelo F. Napoli
- Laboratório de Taxonomia e História Natural de Anfíbios (AMPHIBIA), Museu de História Natural, Instituto de Biologia, Universidade Federal da Bahia (UFBA), CEP 40170–115, Salvador, Bahia, Brazil
| | - Diego J. Santana
- Mapinguari – Laboratório de Biogeografia e Sistemática de Anfíbios e Répteis, Universidade Federal de Mato Grosso do Sul (UFMS), CEP 79002-970 Campo Grande, Mato Grosso, Brazil
| | - Rafael O. de Sá
- Department of Biology, University of Richmond, Richmond, Virginia, 23173, USA
| | - Adrian A. Garda
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal da Paraíba (UFPB), Centro de Ciências Exatas e da Natureza, Cidade Universitária, CEP 58000-000, João Pessoa, Paraíba, Brazil
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92
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Pons J, Campión D, Chiozzi G, Ettwein A, Grangé J, Kajtoch Ł, Mazgajski TD, Rakovic M, Winkler H, Fuchs J. Phylogeography of a widespread Palaearctic forest bird species: The White‐backed Woodpecker (Aves, Picidae). ZOOL SCR 2020. [DOI: 10.1111/zsc.12466] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jean‐Marc Pons
- Institut de Systématique, Evolution, Biodiversité CNRS MNHN UPMC EPHE Sorbonne Universités Muséum National d’Histoire Naturelle, UMR 7205 Paris Cedex France
| | - David Campión
- Área de Biodiversidad, Biodibertsitate Arloa, Padre Adoain Pamplona‐Iruñea Spain
| | | | | | | | - Łukasz Kajtoch
- Institute of Systematics and Evolution of Animals Polish Academy of Sciences Kraków Poland
| | | | | | - Hans Winkler
- Department of Integrative Biology and Evolution Konrad Lorenz‐Institute of Ethology Vienna Austria
| | - Jérôme Fuchs
- Institut de Systématique, Evolution, Biodiversité CNRS MNHN UPMC EPHE Sorbonne Universités Muséum National d’Histoire Naturelle, UMR 7205 Paris Cedex France
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93
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Puillandre N, Brouillet S, Achaz G. ASAP: assemble species by automatic partitioning. Mol Ecol Resour 2020; 21:609-620. [PMID: 33058550 DOI: 10.1111/1755-0998.13281] [Citation(s) in RCA: 397] [Impact Index Per Article: 99.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 11/27/2022]
Abstract
Here, we describe Assemble Species by Automatic Partitioning (ASAP), a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets). ASAP is efficient enough to split data sets as large 104 sequences into putative species in several minutes. Although grounded in evolutionary theory, ASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. Importantly, ASAP proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity. ASAP is a stand-alone program that can be used either through a graphical web-interface or that can be downloaded and compiled for local usage. We have assessed its power along with three others programs (ABGD, PTP and GMYC) on 10 real COI barcode data sets representing various degrees of challenge (from small and easy cases to large and complicated data sets). We also used Monte-Carlo simulations of a multispecies coalescent framework to assess the strengths and weaknesses of ASAP and the other programs. Through these analyses, we demonstrate that ASAP has the potential to become a major tool for taxonomists as it proposes rapidly in a full graphical exploratory interface relevant species hypothesis as a first step of the integrative taxonomy process.
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Affiliation(s)
- Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Sophie Brouillet
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Guillaume Achaz
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,SMILE Group, CIRB, UMR 7241, Collège de France, CNRS, INSERM, Paris, France.,Éco-anthropologie, Muséum National d'Histoire Naturelle, CNRS UMR 7206, Université de Paris, Paris, France
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94
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Gauffre-Autelin P, Stelbrink B, von Rintelen T, Albrecht C. Miocene geologic dynamics of the Australian Sahul Shelf determined the biogeographic patterns of freshwater planorbid snails (Miratestinae) in the Indo-Australian Archipelago. Mol Phylogenet Evol 2020; 155:107004. [PMID: 33157207 DOI: 10.1016/j.ympev.2020.107004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 09/01/2020] [Accepted: 10/28/2020] [Indexed: 11/30/2022]
Abstract
The complex geological and climatic processes that have shaped the Indo-Australian Archipelago since the Cenozoic likely also gave rise to its species-rich biota. Strictly freshwater organisms might be particularly suitable for understanding the influence of these abiotic factors on their biogeography in such a insular setting as their distribution may reflect past abiotic events at large and small geographical scales. We here investigate the historical biogeography of the Miratestinae, a subfamily of Planorbidae. These freshwater gastropods are widely distributed in the eastern IAA from Australia, New Guinea, the Moluccas, and Sulawesi to the Philippines. The first comprehensive molecular phylogeny of the Miratestinae was inferred based on two mitochondrial and two nuclear genetic markers using maximum likelihood and Bayesian inference. Four species delimitation methods were applied to identify molecular operational taxonomic units (MOTUs). Divergence times were inferred using an uncorrelated lognormal relaxed-clock model by applying a taxon- and marker-specific substitution rate. Ancestral geographic ranges were estimated based on the dated phylogeny using BioGeoBEARS. The species delimitation revealed a total of 23 MOTUs, 16 of which might represent species new to science. The BioGeoBEARS analyses suggest an Australian origin for the Miratestinae at c. 22 Ma and identified jump dispersal to be the main process of colonization. The first colonization events from Australia to the IAA occurred in the Middle-Late Miocene (12-13 Ma), whereas intra-island diversification took mainly place since the Late Miocene-Pliocene. Colonization and diversification events remarkably coincide with major geologic events that shaped the geography of the region. The increasing availability of landmasses along the Sahul Shelf likely promoted stepping-stone dispersal to New Guinea, Sulawesi and the Philippines as early as the islands emerged. Major geological and climatic events such as the amalgamation of the island Sulawesi, the regional aridification in Australia or the uplift of massive mountain ranges in New Guinea likely played a considerable role for intra-island diversification.
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Affiliation(s)
- Pauline Gauffre-Autelin
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 (IFZ), 35392 Giessen, Germany.
| | - Björn Stelbrink
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 (IFZ), 35392 Giessen, Germany
| | - Thomas von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115 Berlin, Germany
| | - Christian Albrecht
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 (IFZ), 35392 Giessen, Germany
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95
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Recent Apareiodon species evolutionary divergence (Characiformes: Parodontidae) evidenced by chromosomal and molecular inference. ZOOL ANZ 2020. [DOI: 10.1016/j.jcz.2020.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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96
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Menezes L, Batalha‐Filho H, Garda AA, Napoli M. Tiny treefrogs in the Pleistocene: Phylogeography of
Dendropsophus oliveirai
in the Atlantic Forest and associated enclaves in northeastern Brazil. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Lucas Menezes
- Programa de Pós‐Graduação em Biodiversidade e Evolução Instituto de Biologia Universidade Federal da Bahia Salvador Brazil
| | - Henrique Batalha‐Filho
- Programa de Pós‐Graduação em Biodiversidade e Evolução Instituto de Biologia Universidade Federal da Bahia Salvador Brazil
- Museu de História Natural (“Museu de Zoologia”) Instituto de Biologia Universidade Federal da Bahia Salvador Bahia Brazil
| | - Adrian Antonio Garda
- Laboratório de Anfíbios e Répteis ‐ LAR Departamento de Botânica e Zoologia Universidade Federal do Rio Grande do Norte Natal Brazil
| | - Marcelo Napoli
- Programa de Pós‐Graduação em Biodiversidade e Evolução Instituto de Biologia Universidade Federal da Bahia Salvador Brazil
- Museu de História Natural (“Museu de Zoologia”) Instituto de Biologia Universidade Federal da Bahia Salvador Bahia Brazil
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97
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Alström P, van Linschooten J, Donald PF, Sundev G, Mohammadi Z, Ghorbani F, Shafaeipour A, van den Berg A, Robb M, Aliabadian M, Wei C, Lei F, Oxelman B, Olsson U. Multiple species delimitation approaches applied to the avian lark genus Alaudala. Mol Phylogenet Evol 2020; 154:106994. [PMID: 33250446 DOI: 10.1016/j.ympev.2020.106994] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 10/18/2020] [Accepted: 10/19/2020] [Indexed: 11/16/2022]
Abstract
Species delimitation has advanced from a purely phenotypic exercise to a branch of science that integrates multiple sources of data to identify independently evolving lineages that can be treated as species. We here test species limits in the avian Lesser Short-toed Lark Alaudala rufesens-Sand Lark A. raytal complex, which has an intricate taxonomic history, ranging from a single to three recognised species, with different inclusiveness in different treatments. Our integrative taxonomic approach is based on a combination of DNA sequences, plumage, biometrics, songs, song-flights, geographical distributions, habitat, and bioclimatic data, and using various methods including a species delimitation program (STACEY) based on the multispecies coalescent model. We propose that four species should be recognised: Lesser Short-toed Lark A. rufescens (sensu stricto), Heine's Short-toed Lark A. heinei, Asian Short-toed Lark A. cheleensis and Sand Lark A. raytal. There is also some evidence suggesting lineage separation within A. cheleensis and A. raytal, but additional data are required to evaluate this. The species delimitation based on STACEY agrees well with the non-genetic data. Although computer-based species delimitation programs can be useful in identifying independently evolving lineages, we stress that whenever possible, species hypotheses proposed by these programs should be tested by independent, non-genetic data. Our results highlight the difficulty and subjectivity of delimiting lineages and species, especially at early stages in the speciation process.
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Affiliation(s)
- Per Alström
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, SE-752 36 Uppsala, Sweden; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Jip van Linschooten
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, SE-752 36 Uppsala, Sweden
| | - Paul F Donald
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Gombobaatar Sundev
- National University of Mongolia and Mongolian Ornithological Society, P.O. Box 537, Ulaanbaatar 210646a, Ulaanbaatar, Mongolia
| | - Zeinolabedin Mohammadi
- Department of Biology and Research Department of Zoological Innovation, Institute of Applied Zoology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Fatemeh Ghorbani
- Department of Biology and Research Department of Zoological Innovation, Institute of Applied Zoology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Arya Shafaeipour
- Department of Biology, Faculty of Science, Yasouj University, Yasouj, Iran
| | - Arnoud van den Berg
- The Sound Approach, c/o Duinlustparkweg 98, 2082 EG Santpoort-Zuid, the Netherlands
| | - Magnus Robb
- The Sound Approach, c/o Rua Dr Pedro Almeida Lima 6, 2710-122 Sintra, Portugal
| | - Mansour Aliabadian
- Department of Biology and Research Department of Zoological Innovation, Institute of Applied Zoology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Chentao Wei
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Bengt Oxelman
- Systematics and Biodiversity, Department of Biology and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30 Göteborg, Sweden; Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden
| | - Urban Olsson
- Systematics and Biodiversity, Department of Biology and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30 Göteborg, Sweden; Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden
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Cryptic Diversity in the Monotypic Neotropical Micromoth Genus Angelabella (Lepidoptera: Gracillariidae) in the Peru-Chile Desert. INSECTS 2020; 11:insects11100677. [PMID: 33036122 PMCID: PMC7601689 DOI: 10.3390/insects11100677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/09/2020] [Accepted: 09/15/2020] [Indexed: 11/17/2022]
Abstract
Simple Summary The Neotropical Region harbors a highly diverse and poorly known fauna of leaf miners of the micromoth family Gracillariidae (Lepidoptera). Angelabella is a genus of Gracillariidae whose geographic range is restricted to a few valleys of the arid environments of the Peru-Chile desert. Only one species is currently included in this genus. The aims of this study were to explore the geographic range, determine the spatial distribution of mitochondrial lineages, and test lineage conspecificity hypotheses in Angelabella. The spatial distribution of genetic diversity indicated four spatial clusters, three of which are north of the previously known geographic range. These groups were defined as different species by four species delimitation methods. These results suggest that Angelabella harbors at least four morphologically cryptic species with restricted, not overlapping geographic ranges. This study shows that adequate single locus sequence analysis can be useful to discover surprising biodiversity patterns in underexplored environments, providing the base to plan further studies involving little-known organisms. Abstract Angelabella (Lepidoptera: Gracillariidae: Oecophyllembiinae) is considered a monotypic Neotropical genus of leaf miner micromoths known only from a few valleys of the arid environments of the Peru-Chile desert, particularly the southernmost part of Peru and northernmost part of Chile (type locality), where natural populations of its primary host plant occur. The geographic distribution of potential host plants provides a scenario for a wider range for this micromoth genus. The aims of this study were to explore the geographic range of Angelabella, determine the spatial distribution of mitochondrial lineages, and test lineage conspecificity hypotheses. The spatial distribution of genetic diversity indicated the presence of four spatial clusters, three of which are north of the previously known geographic range. Genetic distances were 0.2–0.8% and 3.6–8.3% (K2P) between haplotypes of the same and different spatial clusters, respectively. Phylogenetic relationships indicated reciprocal monophyly among the four spatial clusters, suggesting that allopatric differentiation processes have governed the recent history of Angelabella in these arid environments. These groups were defined as different species by four species delimitation methods, suggesting that Angelabella is not a monotypic genus, but harbors at least four morphologically cryptic allopatric species with restricted geographic ranges, including the type species and three candidate species.
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Machado L, Salvi D, James Harris D, Brito JC, Crochet PA, Geniez P, Ahmadzadeh F, Carranza S. Systematics, biogeography and evolution of the Saharo-Arabian naked-toed geckos genus Tropiocolotes. Mol Phylogenet Evol 2020; 155:106969. [PMID: 33031930 DOI: 10.1016/j.ympev.2020.106969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/02/2020] [Accepted: 09/28/2020] [Indexed: 11/18/2022]
Abstract
Plate tectonics constitute one of the main mechanisms of biological diversification on Earth, often being associated with cladogenetic events at different phylogenetic levels, as well as with exchange of faunas and floras across previously isolated biogeographic regions. North Africa and Arabia share a complex geological history that dates back to the break-up of the Arabian plate from the African plate ~30-25 Mya, followed by various geological events, such as the formation of the Red Sea or the connection between the African, Arabian and Eurasian plates. Species with Saharo-Arabian distributions have shown a close association between their evolutionary history and these geological events. In this study, we investigate the systematics, biogeography and evolution of the genus Tropiocolotes, a group of small ground-dwelling geckos, comprised by 12 species distributed from the Atlantic coast of North Africa to southwestern Iran. Species delimitation analyses uncovered the existence of high levels of undescribed diversity, with forms here considered at the species level including Tropiocolotes tripolitanus (Mauritania and southern Morocco), T. nattereri (southern Israel) and T. scorteccii (Yemen and Oman). Phylogenetic and biogeographic analyses recovered two main clades, an exclusively African clade and a Saharo-Arabian clade, that split ~25 Mya following the vicariant event mediated by the separation of the Arabian and African plates. The complex geological activity around the Red Sea is associated with the diversification within the Saharo-Arabian clade, including the colonization of North Africa from a second Tropiocolotes group. Results also provide new insights into the geographic distribution of Tropiocolotes nubicus, previously considered as exclusively associated to the Nile River valley, extending its known distribution further west, up to the Central Mountains of the Sahara. Accordingly, the Nile River seems to act as a major biogeographic barrier, separating Tropiocolotes nubicus and T. steudneri in their western and eastern margins, respectively.
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Affiliation(s)
- Luís Machado
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBio Laboratório Associado, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal; Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.
| | - Daniele Salvi
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBio Laboratório Associado, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Department of Health, Life and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - D James Harris
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBio Laboratório Associado, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - José C Brito
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBio Laboratório Associado, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Pierre-André Crochet
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Philippe Geniez
- CEFE, Univ Montpellier, CNRS, PSL-EPHE, IRD, Univ Paul Valéry Montpellier 3, Biogéographie et Ecologie des Vertébrés, Montpellier, France
| | - Faraham Ahmadzadeh
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran 1983963113, Iran
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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Gueuning M, Frey JE, Praz C. Ultraconserved yet informative for species delimitation: Ultraconserved elements resolve long-standing systematic enigma in Central European bees. Mol Ecol 2020; 29:4203-4220. [PMID: 32916006 DOI: 10.1111/mec.15629] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 12/21/2022]
Abstract
Accurate and testable species hypotheses are essential for measuring, surveying and managing biodiversity. Taxonomists often rely on mitochondrial DNA barcoding to complement morphological species delimitations. Although COI-barcoding has largely proven successful in assisting identifications for most animal taxa, there are nevertheless numerous cases where mitochondrial barcodes do not reflect species hypotheses. For instance, what is regarded as a single species can be associated with two distinct DNA barcodes, which can point either to cryptic diversity or to within-species mitochondrial divergences without reproductive isolation. In contrast, two or more species can share barcodes, for instance due to mitochondrial introgression. These intrinsic limitations of DNA barcoding are commonly addressed with nuclear genomic markers, which are expensive, may have low repeatability and often require high-quality DNA. To overcome these limitations, we examined the use of ultraconserved elements (UCEs) as a quick and robust genomic approach to address such problematic cases of species delimitation in bees. This genomic method was assessed using six different species complexes suspected to harbour cryptic diversity, mitochondrial introgression or mitochondrial paraphyly. The sequencing of UCEs recovered between 686 and 1,860 homologous nuclear loci and provided explicit species delimitation in all investigated species complexes. These results provide strong evidence for the suitability of UCEs as a fast method for species delimitation even in recently diverged lineages. Furthermore, we provide the first evidence for both mitochondrial introgression among distinct bee species, and mitochondrial paraphyly within a single bee species.
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Affiliation(s)
- Morgan Gueuning
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland.,Institute of Biology, University of Neuchatel, Neuchatel, Switzerland
| | - Juerg E Frey
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland
| | - Christophe Praz
- Institute of Biology, University of Neuchatel, Neuchatel, Switzerland
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