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Shirali H, Hübner J, Both R, Raupach M, Reischl M, Schmidt S, Pylatiuk C. Image-based recognition of parasitoid wasps using advanced neural networks. INVERTEBR SYST 2024; 38:IS24011. [PMID: 38838190 DOI: 10.1071/is24011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/08/2024] [Indexed: 06/07/2024]
Abstract
Hymenoptera has some of the highest diversity and number of individuals among insects. Many of these species potentially play key roles as food sources, pest controllers and pollinators. However, little is known about the diversity and biology and ~80% of the species have not yet been described. Classical taxonomy based on morphology is a rather slow process but DNA barcoding has already brought considerable progress in identification. Innovative methods such as image-based identification and automation can further speed up the process. We present a proof of concept for image data recognition of a parasitic wasp family, the Diapriidae (Hymenoptera), obtained as part of the GBOL III project. These tiny (1.2-4.5mm) wasps were photographed and identified using DNA barcoding to provide a solid ground truth for training a neural network. Taxonomic identification was used down to the genus level. Subsequently, three different neural network architectures were trained, evaluated and optimised. As a result, 11 different genera of diaprids and one mixed group of 'other Hymenoptera' can be classified with an average accuracy of 96%. Additionally, the sex of the specimen can be classified automatically with an accuracy of >97%.
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Affiliation(s)
- Hossein Shirali
- Institute for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), D-76149 Karlsruhe, Germany
| | - Jeremy Hübner
- Zoologische Staatssammlung München, Münchhausenstraße 21, D-81247 Munich, Germany
| | - Robin Both
- Institute for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), D-76149 Karlsruhe, Germany
| | - Michael Raupach
- Zoologische Staatssammlung München, Münchhausenstraße 21, D-81247 Munich, Germany
| | - Markus Reischl
- Institute for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), D-76149 Karlsruhe, Germany
| | - Stefan Schmidt
- Deceased. Formerly at Zoologische Staatssammlung München, Münchhausenstraße 21, D-81247 Munich, Germany
| | - Christian Pylatiuk
- Institute for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), D-76149 Karlsruhe, Germany
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2
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Palandačić A, Chai MJ, Shandikov GA, Akkari N, Frade PR, Randolf S, Berg HM, Mikschi E, Bogutskaya NG. An annotated catalogue of selected historical type specimens, including genetic data, housed in the Natural History Museum Vienna. Zookeys 2024; 1203:253-323. [PMID: 38855791 PMCID: PMC11161686 DOI: 10.3897/zookeys.1203.117699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/08/2024] [Indexed: 06/11/2024] Open
Abstract
Museum collections are an important source for resolving taxonomic issues and species delimitation. Type specimens as name-bearing specimens, traditionally used in morphology-based taxonomy, are, due to the progress in historical DNA methodology, increasingly used in molecular taxonomic studies. Museum collections are subject to constant deterioration and major disasters. The digitisation of collections offers a partial solution to these problems and makes museum collections more accessible to the wider scientific community. The Extended Specimen Approach (ESA) is a method of digitisation that goes beyond the physical specimen to include the historical information stored in the collection. The collections of the Natural History Museum Vienna represent one of the largest non-university research centres in Europe and, due to their size and numerous type specimens, are frequently used for taxonomic studies by visiting and resident scientists. Recently, a version of ESA was presented in the common catalogue of the Fish and Evertebrata Varia collections and extended to include genetic information on type specimens in a case study of a torpedo ray. Here the case study was extended to a heterogeneous selection of historical type series from different collections with the type locality of Vienna. The goal was to apply the ESA, including genetic data on a selected set of type material: three parasitic worms, three myriapods, two insects, twelve fishes, and one bird species. Five hundred digital items (photographs, X-rays, scans) were produced, and genetic analysis was successful in eleven of the 21 type series. In one case a complete mitochondrial genome was assembled, and in another case ten short fragments (100-230 bp) of the cytochrome oxidase I gene were amplified and sequenced. For five type series, genetic analysis confirmed their taxonomic status as previously recognised synonyms, and for one the analysis supported its status as a distinct species. For two species, genetic information was provided for the first time. This catalogue thus demonstrates the usefulness of ESA in providing digitised data of types that can be easily made available to scientists worldwide for further study.
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Affiliation(s)
- Anja Palandačić
- Fish collection, First Zoological Department, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Min J. Chai
- Fish collection, First Zoological Department, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Gennadiy A. Shandikov
- Fish collection, First Zoological Department, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Nesrine Akkari
- Myriapoda collection, Third Zoological Department, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Pedro R. Frade
- Fish collection, First Zoological Department, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Susanne Randolf
- Fish collection, First Zoological Department, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Hans-Martin Berg
- Fish collection, First Zoological Department, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Ernst Mikschi
- Fish collection, First Zoological Department, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Nina G. Bogutskaya
- Fish collection, First Zoological Department, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
- Evertebrata Varia collection, Third Zoological Department, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
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3
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Miralles A, Puillandre N, Vences M. DNA Barcoding in Species Delimitation: From Genetic Distances to Integrative Taxonomy. Methods Mol Biol 2024; 2744:77-104. [PMID: 38683312 DOI: 10.1007/978-1-0716-3581-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Over the past two decades, DNA barcoding has become the most popular exploration approach in molecular taxonomy, whether for identification, discovery, delimitation, or description of species. The present contribution focuses on the utility of DNA barcoding for taxonomic research activities related to species delimitation, emphasizing the following aspects:(1) To what extent DNA barcoding can be a valuable ally for fundamental taxonomic research, (2) its methodological and theoretical limitations, (3) the conceptual background and practical use of pairwise distances between DNA barcode sequences in taxonomy, and (4) the different ways in which DNA barcoding can be combined with complementary means of investigation within a broader integrative framework. In this chapter, we recall and discuss the key conceptual advances that have led to the so-called renaissance of taxonomy, elaborate a detailed glossary for the terms specific to this discipline (see Glossary in Chap. 35 ), and propose a newly designed step-by-step species delimitation protocol starting from DNA barcode data that includes steps from the preliminary elaboration of an optimal sampling strategy to the final decision-making process which potentially leads to nomenclatural changes.
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Affiliation(s)
- Aurélien Miralles
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Miguel Vences
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany.
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4
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Vences M, Miralles A, DeSalle R. A Glossary of DNA Barcoding Terms. Methods Mol Biol 2024; 2744:561-572. [PMID: 38683343 DOI: 10.1007/978-1-0716-3581-0_35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
This chapter provides a reference glossary for the protocols in this volume. We have chosen only the very basic terms in the DNA barcode lexicon to include, and provide clear and concise definitions of these terms. We hope the reader finds this glossary useful.
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Affiliation(s)
- Miguel Vences
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Aurélien Miralles
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Robert DeSalle
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA.
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5
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Brower AVZ, DeSalle R. DNA Barcodes in Taxonomic Descriptions. Methods Mol Biol 2024; 2744:105-115. [PMID: 38683313 DOI: 10.1007/978-1-0716-3581-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
This chapter discusses methods for incorporating DNA barcode information into formal taxonomic descriptions. We first review what a formal description entails and then discuss previous attempts to incorporate barcode information into taxonomic descriptions. Several computer programs are listed that extract diagnostics from DNA barcode data. Finally, we examine a test case (Astraptes taxonomy).
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Affiliation(s)
- Andrew V Z Brower
- USDA APHIS PPQ Pest Exclusion and Import Programs, Riverdale, MD, USA
| | - Robert DeSalle
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA.
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6
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Puillandre N, Miralles A, Brouillet S, Fedosov A, Fischell F, Patmanidis S, Vences M. Species Delimitation and Exploration of Species Partitions with ASAP and LIMES. Methods Mol Biol 2024; 2744:313-334. [PMID: 38683328 DOI: 10.1007/978-1-0716-3581-0_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
DNA barcoding plays an important role in exploring undescribed biodiversity and is increasingly used to delimit lineages at the species level (see Chap. 4 by Miralles et al.). Although several approaches and programs have been developed to perform species delimitation from datasets of single-locus DNA sequences, such as DNA barcodes, most of these were not initially provided as user-friendly GUI-driven executables. In spite of their differences, most of these tools share the same goal, i.e., inferring de novo a partition of subsets, potentially each representing a distinct species. More recently, a proposed common exchange format for the resulting species partitions (SPART) has been implemented by several of these tools, paving the way toward developing an interoperable digital environment entirely dedicated to integrative and comparative species delimitation. In this chapter, we provide detailed protocols for the use of two bioinformatic tools, one for single locus molecular species delimitation (ASAP) and one for statistical comparison of species partitions resulting from any kind of species delimitation analyses (LIMES).
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Affiliation(s)
- Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Aurélien Miralles
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Sophie Brouillet
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Alexander Fedosov
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Frank Fischell
- Institute of Zoology, University of Cologne, Köln, Germany
| | - Stefanos Patmanidis
- School of Electrical and Computer Engineering, National Technical University of Athens, Athens, Greece
| | - Miguel Vences
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany.
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7
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Ahrens D. Species Diagnosis and DNA Taxonomy. Methods Mol Biol 2024; 2744:33-52. [PMID: 38683310 DOI: 10.1007/978-1-0716-3581-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
The use of DNA has helped to improve and speed up species identification and delimitation. However, it also provides new challenges to taxonomists. Incongruence of outcome from various markers and delimitation methods, bias from sampling and skewed species distribution, implemented models, and the choice of methods/priors may mislead results and also may, in conclusion, increase elements of subjectivity in species taxonomy. The lack of direct diagnostic outcome from most contemporary molecular delimitation approaches and the need for a reference to existing and best sampled trait reference systems reveal the need for refining the criteria of species diagnosis and diagnosability in the current framework of nomenclature codes and good practices to avoid nomenclatorial instability, parallel taxonomies, and consequently more and new taxonomic impediment.
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Affiliation(s)
- Dirk Ahrens
- Museum A. Koenig Bonn, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany.
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8
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Vences M, Patmanidis S, Fedosov A, Miralles A, Puillandre N. iTaxoTools 1.0: Improved DNA Barcode Exploration with TaxI2. Methods Mol Biol 2024; 2744:281-296. [PMID: 38683326 DOI: 10.1007/978-1-0716-3581-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
The overall availability of user-friendly software tools tailored to the analysis of DNA barcodes is limited. Several obvious functions such as detecting and visualizing the DNA barcode gap, the calculation of matrices of pairwise distances at the level of species, or the filtering and decontaminating of sets of sequences based on comparisons with reference databases can typically be carried out only by complex procedures that involve various programs and/or a substantial manual work of formatting. The iTaxoTools project aims at contributing user-friendly software solutions to improve the speed and quality of the workflow of alpha-taxonomy. In this chapter, we provide detailed protocols for the use of a substantially improved version of the tool TaxI2 for distance-based exploration of DNA barcodes. The program calculates genetic distances from prealigned data sets, or based on pairwise alignments, or with an alignment-free approach. Sequence and metadata input can be formatted as tab-delimited files and TaxI2 then computes tables, matrices and graphs of distances, and distance summary statistics within and between species and genera. TaxI2 also includes modes to compare a set of sequences against one or two reference data sets and output lists of best matches or filter data according to thresholds or reciprocal matches. Here, detailed step-by-step protocols are provided for the use of TaxI2, as well as for the interpretation of the program's output.
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Affiliation(s)
- Miguel Vences
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany.
| | - Stefanos Patmanidis
- School of Electrical and Computer Engineering, National Technical University of Athens, Athens, Greece
| | - Alexander Fedosov
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Aurélien Miralles
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
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9
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Dias de Oliveira L, Oliveira da Silva W, Rodrigues da Costa MJ, Carneiro JC, Sampaio I, da Silva JS, Rossi RV, Mendes-Oliveira AC, Pieczarka JC, Nagamachi CY. Genetic diversity analysis in the Brazilian Amazon reveals a new evolutionary lineage and new karyotype for the genus Mesomys (Rodentia, Echimyidae, Eumysopinae). PLoS One 2023; 18:e0291797. [PMID: 37792706 PMCID: PMC10550160 DOI: 10.1371/journal.pone.0291797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 09/06/2023] [Indexed: 10/06/2023] Open
Abstract
Morphological, molecular and chromosomal studies in the genera Lonchothrix and Mesomys have contributed to a better understanding of taxonomic design, phylogenetic relationships and karyotypic patterns. Recent molecular investigations have shown a yet undescribed diversity, suggesting that these taxa are even more diverse than previously assumed. Furthermore, some authors have questioned the limits of geographic distribution in the Amazon region for the species M. hispidus and M. stimulax. In this sense, the current study sought to understand the karyotypic evolution and geographic limits of the genus Mesomys, based on classical (G- and C-banding) and molecular cytogenetic analysis (FISH using rDNA 18S and telomeric probes) and through the sequencing of mitochondrial genes Cytochrome b (Cytb) and Cytochrome Oxidase-Subunit I (CO using phylogeny, species delimitation and time of divergence, from samples of different locations in the Brazilian Amazon. The species M. stimulax and Mesomys sp. presented 2n = 60/FN = 110, while M. hispidus presented 2n = 60/FN = 112, hitherto unpublished. Molecular dating showed that Mesomys diversification occurred during the Plio-Pleistocene period, with M. occultus diverging at around 5.1 Ma, followed by Mesomys sp. (4.1 Ma) and, more recently, the separation between M. hispidus and M. stimulax (3.5 Ma). The ABGD and ASAP species delimiters support the formation of 7 and 8 potential species of the genus Mesomys, respectively. Furthermore, in both analyzes Mesomys sp. was recovered as a valid species. Our multidisciplinary approach involving karyotypic, molecular and biogeographic analysis is the first performed in Mesomys, with the description of a new karyotype for M. hispidus, a new independent lineage for the genus and new distribution data for M. hispidus and M. stimulax.
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Affiliation(s)
- Leony Dias de Oliveira
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, ICB, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Willam Oliveira da Silva
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, ICB, Universidade Federal do Pará, Belém, Pará, Brazil
| | | | | | - Iracilda Sampaio
- Genômica e Biologia de Sistemas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Juliane Saldanha da Silva
- Laboratório de Mastozoologia, Instituto de Biociências, Universidade Federal do Mato Grosso, Cuiabá, Brazil
| | - Rogério Vieira Rossi
- Laboratório de Mastozoologia, Instituto de Biociências, Universidade Federal do Mato Grosso, Cuiabá, Brazil
| | | | - Julio Cesar Pieczarka
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, ICB, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Cleusa Yoshiko Nagamachi
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, ICB, Universidade Federal do Pará, Belém, Pará, Brazil
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10
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Amorim JA, de Oliveira TMP, de Sá ILR, da Silva TP, Sallum MAM. DNA Barcodes of Mansonia ( Mansonia) Blanchard, 1901 (Diptera, Culicidae). Genes (Basel) 2023; 14:1127. [PMID: 37372310 DOI: 10.3390/genes14061127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 05/17/2023] [Accepted: 05/21/2023] [Indexed: 06/29/2023] Open
Abstract
Females of the genus Mansonia feed on the blood of humans, livestock, and other vertebrates to develop their eggs. The females' biting behavior may cause severe disturbance to blood hosts, with a negative impact on public health and economics. Certain species have been identified as potential or effective disease vectors. The accurate species identification of field-collected specimens is of paramount importance for the success of monitoring and control strategies. Mansonia (Mansonia) morphological species boundaries are blurred by patterns of intraspecific heteromorphism and interspecific isomorphism. DNA barcodes can help to solve taxonomic controversies, especially if combined with other molecular tools. We used cytochrome c oxidase subunit I (COI) gene 5' end (DNA barcode) sequences to identify 327 field-collected specimens of Mansonia (Mansonia) spp. The sampling encompassed males and females collected from three Brazilian regions and previously assigned to species based on their morphological characteristics. Eleven GenBank and BOLD sequences were added to the DNA barcode analyses. Initial morphospecies assignments were mostly corroborated by the results of five clustering methods based on Kimura two-parameter distance and maximum likelihood phylogeny. Five to eight molecular operational taxonomic units may represent taxonomically unknown species. The first DNA barcode records for Mansonia fonsecai, Mansonia iguassuensis, and Mansonia pseudotitillans are presented.
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Affiliation(s)
- Jandui Almeida Amorim
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo 01246-904, SP, Brazil
- Departamento de Ciências e Matemática, Instituto Federal de Educação, Ciência e Tecnologia de São Paulo, São Paulo 01109-010, SP, Brazil
| | | | - Ivy Luizi Rodrigues de Sá
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo 01246-904, SP, Brazil
| | - Taires Peniche da Silva
- Laboratório de Entomologia Médica, Instituto de Pesquisas Científicas e Tecnológicas do Estado do Amapá, Macapá 68903-419, AP, Brazil
| | - Maria Anice Mureb Sallum
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo 01246-904, SP, Brazil
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11
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Kimura LT, Andrade ER, Nobre I, Nobre CA, de Medeiros BAS, Riaño-Pachón DM, Shiraishi FK, Carvalho TCMB, Simplicio MA. Amazon Biobank: a collaborative genetic database for bioeconomy development. Funct Integr Genomics 2023; 23:101. [PMID: 36964864 DOI: 10.1007/s10142-023-01015-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/12/2022] [Accepted: 03/06/2023] [Indexed: 03/26/2023]
Abstract
Biodiversity is proposed as a sustainable alternative for the economic development of high-biodiversity regions. Especially in the field of biodiversity genomics, the development of low-cost DNA sequencing opens an opportunity for new actors beyond academia to engage in genomic sequencing. However, it is challenging to adequately compensate non-academic actors such as local populations for their contribution to the innovation process, preventing better bioeconomy development. Although many repositories register genomic data to support biodiversity research, they do not facilitate the fair sharing of economic benefits. In this work, we propose the creation of the Amazon Biobank, a community-based genetic database. We employed blockchain to build a transparent and verifiable log of transactions involving genomic data, and we used smart contracts to implement an internal monetary system for all participants who collect, insert, process, store, and validate genomic data. We also used peer-to-peer solutions to allow users with commodity computers to collaborate with the storage and distribution of DNA files. By combining emerging technologies, Amazon Biobank provides adequate benefit-sharing among all participants that collaborate with data, knowledge, and computational resources. It also provides traceability and auditability, allowing easy association between biotechnological research and DNA data. In addition, the solution is highly scalable and less dependent on the trust deposited in any system player. Therefore, Amazon Biobank can become an important stepping stone to unlock the potential of bioeconomy in rich ecosystems such as the Amazon Rainforest.
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Affiliation(s)
| | - Ewerton R Andrade
- University of Sao Paulo, Sao Paulo, SP, Brazil
- Federal University of Rondonia, Porto Velho, RO, Brazil
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12
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Kantak M, Batra P, Shende P. Integration of DNA barcoding and nanotechnology in drug delivery. Int J Biol Macromol 2023; 230:123262. [PMID: 36646350 DOI: 10.1016/j.ijbiomac.2023.123262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/05/2023] [Accepted: 01/08/2023] [Indexed: 01/15/2023]
Abstract
In recent years' development in nanotechnology utilization of DNA barcodes with potential benefit of nanoparticulate system is a hallmark for novel advancement in healthcare, biomedical and research sector. Interplay of biological barcoding with nanodimensional system encompasses innovative technologies to offer unique advantages of ultra-sensitivity, error-free, accuracy with minimal label reagents, and less time consumption in comparison to conventional techniques like ELISA, PCR, culture media, electrophoresis. DNA barcoding systems used as universal novel tool for identification and multiplex structural detection of proteins, DNAs, toxins, allergens, and nucleic acids of humans, viruses, animals, bacteria, plants as well as personalized treatment in ovarian cancer, AIDS-related Kaposi sarcoma, breast cancer and cardiovascular diseases. Barcoding tools offer substantial attention in drug delivery, in-vivo screening, gene transport for theranostics, bioimaging, and nano-biosensors applications. This review article outlines the recent advances in nano-mediated DNA barcodes to explore various applications in detection of cancer markers, tumor cells, pathogens, allergens, as theranostics, biological sensors, and plant authentication. Furthermore, it summarizes the diverse newer technologies such as bio-barcode amplification (BBA), Profiling Relative Inhibition Simultaneously in Mixtures (PRISM) and CRISPR-Cas9 gene knockout and their applications as sensors for detections of antigens, allergens, and other specimens.
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Affiliation(s)
- Maithili Kantak
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, V. L. Mehta Road, Vile Parle (W), Mumbai, India
| | - Priyanka Batra
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, V. L. Mehta Road, Vile Parle (W), Mumbai, India
| | - Pravin Shende
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, V. L. Mehta Road, Vile Parle (W), Mumbai, India.
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13
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Kisekelwa T, Snoeks J, Decru E, Schedel FBD, Isumbisho M, Vreven E. A mismatch between morphological and molecular data in lineages of Enteromius (Cypriniformes: Cyprinidae) from the Lowa basin (East Democratic Republic of the Congo: DRC) with the description of a new species. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2135630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Tchalondawa Kisekelwa
- Centre of Research in Biodiversity, Ecology, Evolution and Conservation (CRBEC), DRC
- Département de Biologie-Chimie, Unité d’Enseignement et de Recherche en Hydrobiologie Appliquée, Institut Supérieur Pédagogique (ISP) of Bukavu, Bukavu, 854, DRC
- 3Vertebrates section, Ichthyology, Royal Museum for Central Africa (RMCA), Leuvensesteenweg 13, Tervuren, 3080, Belgium
- Biology Department, Fish Diversity and Conservation, KU Leuven, Charles Deberiotstraat 32, Leuven, B-3000, Belgium
| | - Jos Snoeks
- 3Vertebrates section, Ichthyology, Royal Museum for Central Africa (RMCA), Leuvensesteenweg 13, Tervuren, 3080, Belgium
- Biology Department, Fish Diversity and Conservation, KU Leuven, Charles Deberiotstraat 32, Leuven, B-3000, Belgium
| | - Eva Decru
- 3Vertebrates section, Ichthyology, Royal Museum for Central Africa (RMCA), Leuvensesteenweg 13, Tervuren, 3080, Belgium
- Biology Department, Fish Diversity and Conservation, KU Leuven, Charles Deberiotstraat 32, Leuven, B-3000, Belgium
| | - Frederic B. D. Schedel
- Zoological Institute, University of Basel, Vesalgasse 1, Basel, 4051, Switzerland
- Faculty of Biology, Division of Evolutionary Biology, LMU Munich, Großhaderner Straße 2, Planegg-Martinsried, 82152, Germany
| | - Mwapu Isumbisho
- Département de Biologie-Chimie, Unité d’Enseignement et de Recherche en Hydrobiologie Appliquée, Institut Supérieur Pédagogique (ISP) of Bukavu, Bukavu, 854, DRC
| | - Emmanuel Vreven
- 3Vertebrates section, Ichthyology, Royal Museum for Central Africa (RMCA), Leuvensesteenweg 13, Tervuren, 3080, Belgium
- Biology Department, Fish Diversity and Conservation, KU Leuven, Charles Deberiotstraat 32, Leuven, B-3000, Belgium
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14
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Guo B, Kong L. Comparing the Efficiency of Single-Locus Species Delimitation Methods within Trochoidea (Gastropoda: Vetigastropoda). Genes (Basel) 2022; 13:genes13122273. [PMID: 36553540 PMCID: PMC9778293 DOI: 10.3390/genes13122273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
In the context of diminishing global biodiversity, the validity and practicality of species delimitation methods for the identification of many neglected and undescribed biodiverse species have been paid increasing attention. DNA sequence-based species delimitation methods are mainly classified into two categories, namely, distance-based and tree-based methods, and have been widely adopted in many studies. In the present study, we performed three distance-based (ad hoc threshold, ABGD, and ASAP) and four tree-based (sGMYC, mGMYC, PTP, and mPTP) analyses based on Trochoidea COI data and analyzed the discordance between them. Moreover, we also observed the performance of these methods at different taxonomic ranks (the genus, subfamily, and family ranks). The results suggested that the distance-based approach is generally superior to the tree-based approach, with the ASAP method being the most efficient. In terms of phylogenetic methods, the single threshold version performed better than the multiple threshold version of GMYC, and PTP showed higher efficiency than mPTP in delimiting species. Additionally, GMYC was found to be significantly influenced by taxonomic rank, showing poorer efficiency in datasets at the genus level than at higher levels. Finally, our results highlighted that cryptic diversity within Trochoidea (Mollusca: Vetigastropoda) might be underestimated, which provides quantitative evidence for excavating the cryptic lineages of these species.
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Affiliation(s)
- Bingyu Guo
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
- Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
- Correspondence:
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15
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Barroso M, Moreira J, Capa M, Nygren A, Parapar J. A further step towards the characterisation of Terebellides (Annelida, Trichobranchidae) diversity in the Northeast Atlantic, with the description of a new species. Zookeys 2022; 1132:85-126. [PMID: 36760494 PMCID: PMC9836732 DOI: 10.3897/zookeys.1132.91244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/23/2022] [Indexed: 11/29/2022] Open
Abstract
Several new species of genus Terebellides Sars, 1835 (Annelida, Trichobranchidae) have been recently described from the Northeast Atlantic Ocean after the detection of a large complex of species based on DNA sequence data from previous research. Some of those species (belonging to the so-called Group A) have already been described elsewhere. In this paper, we revise several Terebellides clades belonging to Groups B, C and D resulting in the identification of five nominal species: Terebellidesgracilis Malm, 1874, Terebellidesatlantis Williams, 1984, Terebellideswilliamsae Jirkov, 1989, Terebellidesirinae Gagaev, 2009, and Terebellidesshetlandica Parapar, Moreira & O'Reilly, 2016, plus one new species described here as Terebellideslavesquei sp. nov. All these species are characterised by a combination of morphological features complemented with a nucleotide diagnostic approach (specific COI nucleotides in the alignment position). Morphological characters used to discriminate between taxa refer to the branchial shape, presence/absence of ciliated papillae dorsal to thoracic notopodia and the morphology of thoracic and abdominal uncinal teeth. An updated identification key to all described species of this genus in NE Atlantic waters is also included.
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Affiliation(s)
- María Barroso
- Departamento de Bioloxía, Universidade da Coruña, A Coruña, SpainUniversidade da CoruñaA CoruñaSpain
| | - Juan Moreira
- Departamento de Biología (Zoología) & Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, SpainUniversidad Autónoma de MadridMadridSpain
| | - María Capa
- Departament de Biologia, Universitat de les Illes Balears, Mallorca, SpainUniversitat de les Illes BalearsMallorcaSpain
| | - Arne Nygren
- Sjöfartmuseet Akvariet, Göteborg, SwedenSjöfartmuseet AkvarietGöteborgSweden,Institutionen för marina vetenskaper, Göteborgs Universitet, Göteborg, SwedenGöteborgs UniversitetGöteborgSweden
| | - Julio Parapar
- Departamento de Bioloxía, Universidade da Coruña, A Coruña, SpainUniversidade da CoruñaA CoruñaSpain
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16
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Bikashvili A, Kachlishvili N, Japoshvili B, Mumladze L. Species diversity and DNA barcode library of freshwater Molluscs of South Caucasus. Biodivers Data J 2022; 10:e84887. [PMID: 36761591 PMCID: PMC9848562 DOI: 10.3897/bdj.10.e84887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/29/2022] [Indexed: 11/12/2022] Open
Abstract
This study provides the first attempt to investigate the molecular diversity of South Caucasian freshwater molluscs (Mollusca, Gastropoda) and lay down the first bricks to build up a DNA-barcode library. In total, 289 COI barcode sequences were obtained from 33 morpho-species belonging to 24 molluscan genera and 10 families that represent nearly 30% of known freshwater molluscan diversity of the South Caucasus region. DNA barcodes were analysed by means of the Barcode Index Number (BIN) and the other tools available in BOLD Systems. Results showed that the knowledge of freshwater molluscs diversity in the South Caucasus is far from comprehensive. For the studied 33 morpho-species, 289 barcodes were clustered into 40 BINs, from which unique BINs were defined for 12 species and five species were characterised with more than a single BIN. From the studied taxa, 60% were characterised larger than 2.2% sequence divergence indicating high genetic variation or cryptic diversity. Within our limited taxonomic coverage, we found one new species for the Republic of Georgia (Galbaschirazensis) and at least three undescribed species belonging to the genera Stagnicola, Segmentina and Anisus. Uniqueness and high molecular diversity of the studied species emphasise the need for further intensive morphological and molecular investigations of the South Caucasian freshwater molluscan fauna.
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Affiliation(s)
- Ani Bikashvili
- Institute of Zoology, Ilia State University, Tbilisi, GeorgiaInstitute of Zoology, Ilia State UniversityTbilisiGeorgia
| | - Nino Kachlishvili
- Institute of Zoology, Ilia State University, Tbilisi, GeorgiaInstitute of Zoology, Ilia State UniversityTbilisiGeorgia
| | - Bella Japoshvili
- Institute of Zoology, Ilia State University, Tbilisi, GeorgiaInstitute of Zoology, Ilia State UniversityTbilisiGeorgia
| | - Levan Mumladze
- Institute of Zoology, Ilia State University, Tbilisi, GeorgiaInstitute of Zoology, Ilia State UniversityTbilisiGeorgia
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17
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Guo M, Yuan C, Tao L, Cai Y, Zhang W. Life barcoded by DNA barcodes. CONSERV GENET RESOUR 2022; 14:351-365. [PMID: 35991367 PMCID: PMC9377290 DOI: 10.1007/s12686-022-01291-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/05/2022] [Indexed: 11/15/2022]
Abstract
The modern concept of DNA-based barcoding for cataloguing biodiversity was proposed in 2003 by first adopting an approximately 600 bp fragment of the mitochondrial COI gene to compare via nucleotide alignments with known sequences from specimens previously identified by taxonomists. Other standardized regions meeting barcoding criteria then are also evolving as DNA barcodes for fast, reliable and inexpensive assessment of species composition across all forms of life, including animals, plants, fungi, bacteria and other microorganisms. Consequently, global DNA barcoding campaigns have resulted in the formation of many online workbenches and databases, such as BOLD system, as barcode references, and facilitated the development of mini-barcodes and metabarcoding strategies as important extensions of barcode techniques. Here we intend to give an overview of the characteristics and features of these barcode markers and major reference libraries existing for barcoding the planet’s life, as well as to address the limitations and opportunities of DNA barcodes to an increasingly broader community of science and society.
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18
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Toro-Delgado E, Hernández-Roldán J, Dincă V, Vicente JC, Shaw MR, Quicke DL, Vodă R, Albrecht M, Fernández-Triana J, Vidiella B, Valverde S, Dapporto L, Hebert PDN, Talavera G, Vila R. Butterfly–parasitoid–hostplant interactions in Western Palaearctic Hesperiidae: a DNA barcoding reference library. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The study of ecological interactions between plants, phytophagous insects and their natural enemies is an essential but challenging component for understanding ecosystem dynamics. Molecular methods such as DNA barcoding can help elucidate these interactions. In this study, we employed DNA barcoding to establish hostplant and parasitoid interactions with hesperiid butterflies, using a complete reference library for Hesperiidae of continental Europe and north-western Africa (53 species, 100% of those recorded) based on 2934 sequences from 38 countries. A total of 233 hostplant and parasitoid interactions are presented, some recovered by DNA barcoding larval remains or parasitoid cocoons. Combining DNA barcode results with other lines of evidence allowed 94% species-level identification for Hesperiidae, but success was lower for parasitoids, in part due to unresolved taxonomy. Potential cases of cryptic diversity, both in Hesperiidae and Microgastrinae, are discussed. We briefly analyse the resulting interaction networks. Future DNA barcoding initiatives in this region should focus attention on north-western Africa and on parasitoids, because in these cases barcode reference libraries and taxonomy are less well developed.
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Affiliation(s)
| | - Juan Hernández-Roldán
- Institut de Biologia Evolutiva (CSIC-UPF) , 03008 Barcelona , Spain
- Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid , c/ Darwin, 2, ES - 28049 Madrid , Spain
| | - Vlad Dincă
- Ecology and Genetics Research Unit, PO Box 3000, University of Oulu , 90014 Oulu , Finland
- Research Institute of the University of Bucharest (ICUB), University of Bucharest , Bucharest , Romania
| | | | - Mark R Shaw
- National Museums of Scotland , Edinburgh , UK
| | - Donald Lj Quicke
- Department of Biology, Faculty of Life Sciences, Chulalongkorn University , Bangkok , Thailand
| | | | | | | | - Blai Vidiella
- Centre de Recerca Matemàtica , Edifici C , Campus de Bellaterra, Barcelona , Spain
| | - Sergi Valverde
- Institut de Biologia Evolutiva (CSIC-UPF) , 03008 Barcelona , Spain
- European Centre for Living Technology , Venice , Italy
| | - Leonardo Dapporto
- Dipartimento di Biologia, University of Florence , 50019 Sesto Fiorentino , Italy
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph , Guelph, ON N1G 2W1 , Canada
| | - Gerard Talavera
- Institut Botànic de Barcelona (IBB), CSIC-Ajuntament de Barcelona , Passeig del Migdia s/n, 08038 Barcelona , Spain
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF) , 03008 Barcelona , Spain
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19
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Negrete L, Francavilla ML, Damborenea C, Brusa F. A new genus of land planarian (Platyhelminthes, Geoplanidae) for a new ‘blind’ species. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2046200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Lisandro Negrete
- División Zoología Invertebrados, Facultad de Ciencias Naturales y Museo, UNLP, Boulevard 120 & 61, La Plata, B1900CHX, Buenos Aires, Argentina
- CONICET – Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Buenos Aires, Argentina
| | - Marina Lenguas Francavilla
- División Zoología Invertebrados, Facultad de Ciencias Naturales y Museo, UNLP, Boulevard 120 & 61, La Plata, B1900CHX, Buenos Aires, Argentina
- CONICET – Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Buenos Aires, Argentina
| | - Cristina Damborenea
- División Zoología Invertebrados, Facultad de Ciencias Naturales y Museo, UNLP, Boulevard 120 & 61, La Plata, B1900CHX, Buenos Aires, Argentina
- CONICET – Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Buenos Aires, Argentina
| | - Francisco Brusa
- División Zoología Invertebrados, Facultad de Ciencias Naturales y Museo, UNLP, Boulevard 120 & 61, La Plata, B1900CHX, Buenos Aires, Argentina
- CONICET – Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Buenos Aires, Argentina
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20
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Ojeda AA, Novillo A, Lanzone C, Rodríguez D, Cuevas MF, Jayat JP, Teta P, Ojeda RA, Borisenko A. DNA barcodes highlight genetic diversity patterns in rodents from lowland desert and andean areas in argentina. Mol Ecol Resour 2022; 22:2349-2362. [PMID: 35201669 DOI: 10.1111/1755-0998.13603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 02/14/2022] [Indexed: 11/27/2022]
Abstract
Rodents are an important component of South America fauna. Their high diversity has motivated researchers to continually review their taxonomy, genetic diversity, species limits, and phylogenetic relationships. We apply DNA-barcodes for assessing the taxonomic and genetic diversity in the two major lineages of South American rodents: caviomorphs and sigmodontines. We analyzed 335 COI barcodes in 34 morphologically determined species from 39 localities along central Andes and arid lands of Argentina. Neighbor Joining and Maximum Likelihood reconstruction provided clear separation between species. The Barcode Index Number and Bayesian Poisson Tree Processes were used to confirm concordance between sequence clusters and species designations by taxonomy. We found deep divergence within the Phyllotis xanthopygus species complex, with distances up to 13.0% between geographically separated lineages. Minor divergences (3.30% and 2.52%) were found within Abrothrix hirta, and Tympanoctomys barrerae, respectively, with differentiation in their genetic lineages. Also, we documented geographically separated clusters for Akodon spegazzinii and A.oenos with up to 2.3% divergence, but clustering methods failed to distinguish them as different species. Sequence results show a clear barcode gap with a mean intraspecific divergence (0.56%) vs. a minimum nearest-neighbor distance averaging (10.1%). Distances between congeneric species varied from 4.1 to 14%, with the exception of two related forms within Euneomys and the sister species Akodon spegazzinii and A. oenos. This study constitutes a substantial contribution to the global barcode reference library. It provides insights into the complex phylogeographic patterns and speciation scenarios in rodents, while highlighting areas that require in-depth taxonomic and integrative research.
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Affiliation(s)
- Agustina A Ojeda
- Grupo de Investigaciones de la Biodiversidad. Instituto Argentino de Investigaciones de las Zonas Áridas, CONICET, Centro de Ciencia y Técnica Mendoza, Argentina
| | - Agustina Novillo
- Instituto de Biodiversidad Neotropical (IBN) CONICET-UNT. Facultad de Ciencias Naturales, Universidad Nacional de Tucumán, Argentina
| | - Cecilia Lanzone
- Laboratorio de Genética Evolutiva (FCEQyN, IBS, UNaM-CONICET). Posadas. Misiones, Argentina
| | - Daniela Rodríguez
- Witral-Red de Investigaciones en conservación y manejo de vida silvestre en sistemas socio-ecológicos, Instituto Argentino de Investigaciones de las Zonas Áridas, CONICET, Centro de Ciencia y Técnica Mendoza, Argentina
| | - M Fernanda Cuevas
- Grupo de Investigaciones de la Biodiversidad. Instituto Argentino de Investigaciones de las Zonas Áridas, CONICET, Centro de Ciencia y Técnica Mendoza, Argentina
| | - J Pablo Jayat
- Unidad Ejecutora Lillo (CONICET-Fundación M. Lillo). San Miguel de Tucumán. Tucumán, Argentina
| | - Pablo Teta
- División Mastozoología, Museo Argentino de Ciencias Naturales Bernardino Rivadavia. Buenos Aires, Argentina
| | - Ricardo A Ojeda
- Grupo de Investigaciones de la Biodiversidad. Instituto Argentino de Investigaciones de las Zonas Áridas, CONICET, Centro de Ciencia y Técnica Mendoza, Argentina
| | - Alex Borisenko
- Department of Integrative Biology. College of Biological Sciences, University of Guelph, Guelph, Ontario, Canada
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21
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Martínez-Borrego D, Arellano E, González-Cózatl FX, Castro-Arellano I, León-Paniagua L, Rogers DS. Molecular systematics of the Reithrodontomys tenuirostris group (Rodentia: Cricetidae) highlighting the Reithrodontomys microdon species complex. J Mammal 2022; 103:29-44. [PMID: 35087329 PMCID: PMC8789765 DOI: 10.1093/jmammal/gyab133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 10/23/2021] [Indexed: 11/13/2022] Open
Abstract
The Reithrodontomys tenuirostris species group is considered "the most specialized" within the genus Reithrodontomys from morphological and ecological perspectives. Previous studies based on molecular data recommended changes in the taxonomy of the group. In particular, R. microdon has been the most taxonomically questioned, with the suggestion that it constitutes a complex of cryptic species. We analyzed the phylogenetic relationships of the R. tenuirostris species group using DNA sequences from the mitochondrial Cytochrome b gene and Intron 7 of the nuclear beta fibrinogen gene. In addition, divergence times were estimated, and possible new taxa delimited with three widely used species delimitation methods. Finally, possible connectivity routes based on shared haplotypes were tested among the R. microdon populations. All species were recovered as monophyletic with the exception of R. microdon, whose individuals were grouped into four different haplogroups, one of which included specimens of R. bakeri. Diversification within the R. tenuirostris species group began about 3 Ma, in the Pleistocene. The bGMYC and STACEY delimitation methods were congruent with each other, delimiting at the species-level each haplogroup within R. microdon, while the mPTP suggested a greater number of species. Moreover, none of the haplogroups showed potential connectivity routes between them, evidencing lack of gene flow. Our results suggest the existence of a higher number of species in the R. tenuirostris group, because we show that there are four species within what is currently recognized as R. microdon.
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Affiliation(s)
- Daily Martínez-Borrego
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Avenida Universidad, Chamilpa, Cuernavaca, Morelos, México
| | - Elizabeth Arellano
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Avenida Universidad, Chamilpa, Cuernavaca, Morelos, México
| | - Francisco X González-Cózatl
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Avenida Universidad, Chamilpa, Cuernavaca, Morelos, México
| | | | - Livia León-Paniagua
- Colección de Mamíferos – Museo de Zoología “Alfonso L. Herrera”, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
| | - Duke S Rogers
- Department of Biology and Monte L Bean Life Science Museum, Brigham Young University, Provo, UT, USA
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22
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Molecular signature characters complement taxonomic diagnoses: a bioinformatic approach exemplified by ciliated protists (Ciliophora, Oligotrichea). Mol Phylogenet Evol 2022; 170:107433. [DOI: 10.1016/j.ympev.2022.107433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/13/2022] [Accepted: 01/20/2022] [Indexed: 11/21/2022]
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23
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Fedosov A, Achaz G, Gontchar A, Puillandre N. MOLD, a novel software to compile accurate and reliable DNA diagnoses for taxonomic descriptions. Mol Ecol Resour 2022; 22:2038-2053. [DOI: 10.1111/1755-0998.13590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Alexander Fedosov
- A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Leninsky prospect 33 119071 Moscow Russia
- Institut Systématique Evolution Biodiversité (ISYEB) Muséum national d'Histoire naturelle CNRS Sorbonne Université EPHE Université des Antilles 57 rue Cuvier, CP 26 75005 Paris France
| | - Guillaume Achaz
- Institut Systématique Evolution Biodiversité (ISYEB) Muséum national d'Histoire naturelle CNRS Sorbonne Université EPHE Université des Antilles 57 rue Cuvier, CP 26 75005 Paris France
- UMR7206 Eco‐Anthropologie Université de Paris‐CNRS‐MNHN Paris
- UMR7241 Centre Interdisciplinaire de Recherche en Biologie Collége de France‐CNRS‐INSERM Paris
| | - Andrey Gontchar
- Molecular Immunology Laboratory Dmitry Rogachev National Medical Research Center of Pediatric Hematology Oncology and Immunology Samory Mashela street 1 117997 Moscow Russia
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB) Muséum national d'Histoire naturelle CNRS Sorbonne Université EPHE Université des Antilles 57 rue Cuvier, CP 26 75005 Paris France
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24
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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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25
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Surveillance along the Rio Grande during the 2020 Vesicular Stomatitis Outbreak Reveals Spatio-Temporal Dynamics of and Viral RNA Detection in Black Flies. Pathogens 2021; 10:pathogens10101264. [PMID: 34684213 PMCID: PMC8541391 DOI: 10.3390/pathogens10101264] [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: 07/28/2021] [Revised: 09/24/2021] [Accepted: 09/24/2021] [Indexed: 11/26/2022] Open
Abstract
Vesicular stomatitis virus (VSV) emerges periodically from its focus of endemic transmission in southern Mexico to cause epizootics in livestock in the US. The ecology of VSV involves a diverse, but largely undefined, repertoire of potential reservoir hosts and invertebrate vectors. As part of a larger program to decipher VSV transmission, we conducted a study of the spatiotemporal dynamics of Simulium black flies, a known vector of VSV, along the Rio Grande in southern New Mexico, USA from March to December 2020. Serendipitously, the index case of VSV-Indiana (VSIV) in the USA in 2020 occurred at a central point of our study. Black flies appeared soon after the release of the Rio Grande’s water from an upstream dam in March 2020. Two-month and one-year lagged precipitation, maximum temperature, and vegetation greenness, measured as Normalized Difference Vegetation Index (NDVI), were associated with increased black fly abundance. We detected VSIV RNA in 11 pools comprising five black fly species using rRT-PCR; five pools yielded a VSIV sequence. To our knowledge, this is the first detection of VSV in the western US from vectors that were not collected on premises with infected domestic animals.
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26
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Lue CH, Buffington ML, Scheffer S, Lewis M, Elliott TA, Lindsey ARI, Driskell A, Jandova A, Kimura MT, Carton Y, Kula RR, Schlenke TA, Mateos M, Govind S, Varaldi J, Guerrieri E, Giorgini M, Wang X, Hoelmer K, Daane KM, Abram PK, Pardikes NA, Brown JJ, Thierry M, Poirié M, Goldstein P, Miller SE, Tracey WD, Davis JS, Jiggins FM, Wertheim B, Lewis OT, Leips J, Staniczenko PPA, Hrcek J. DROP: Molecular voucher database for identification of Drosophila parasitoids. Mol Ecol Resour 2021; 21:2437-2454. [PMID: 34051038 DOI: 10.1111/1755-0998.13435] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 01/03/2023]
Abstract
Molecular identification is increasingly used to speed up biodiversity surveys and laboratory experiments. However, many groups of organisms cannot be reliably identified using standard databases such as GenBank or BOLD due to lack of sequenced voucher specimens identified by experts. Sometimes a large number of sequences are available, but with too many errors to allow identification. Here, we address this problem for parasitoids of Drosophila by introducing a curated open-access molecular reference database, DROP (Drosophila parasitoids). Identifying Drosophila parasitoids is challenging and poses a major impediment to realize the full potential of this model system in studies ranging from molecular mechanisms to food webs, and in biological control of Drosophila suzukii. In DROP, genetic data are linked to voucher specimens and, where possible, the voucher specimens are identified by taxonomists and vetted through direct comparison with primary type material. To initiate DROP, we curated 154 laboratory strains, 856 vouchers, 554 DNA sequences, 16 genomes, 14 transcriptomes, and six proteomes drawn from a total of 183 operational taxonomic units (OTUs): 114 described Drosophila parasitoid species and 69 provisional species. We found species richness of Drosophila parasitoids to be heavily underestimated and provide an updated taxonomic catalogue for the community. DROP offers accurate molecular identification and improves cross-referencing between individual studies that we hope will catalyse research on this diverse and fascinating model system. Our effort should also serve as an example for researchers facing similar molecular identification problems in other groups of organisms.
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Affiliation(s)
- Chia-Hua Lue
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
- Department of Biology, Brooklyn College, City University of New York (CUNY), Brooklyn, NY, USA
| | - Matthew L Buffington
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Sonja Scheffer
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Matthew Lewis
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Tyler A Elliott
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Amy Driskell
- Laboratories of Analytical Biology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Anna Jandova
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
| | | | - Yves Carton
- "Évolution, Génomes, Comportement, Écologie", CNRS et Université Paris-Saclay, Paris, France
| | - Robert R Kula
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Todd A Schlenke
- Department of Entomology, University of Arizona, Tucson, AZ, USA
| | - Mariana Mateos
- Wildlife and Fisheries Sciences Department, Texas A&M University, College Station, TX, USA
| | - Shubha Govind
- The Graduate Center of the City University of New York, New York, NY, USA
| | - Julien Varaldi
- CNRS, Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université de Lyon, Université Lyon 1, Villeurbanne, France
| | - Emilio Guerrieri
- CNR-Institute for Sustainable Plant Protection (CNR-IPSP), National Research Council of Italy, Portici, Italy
| | - Massimo Giorgini
- CNR-Institute for Sustainable Plant Protection (CNR-IPSP), National Research Council of Italy, Portici, Italy
| | - Xingeng Wang
- United States Department of Agriculture, Agricultural Research Services, Beneficial Insects Introduction Research Unit, Newark, DE, USA
| | - Kim Hoelmer
- United States Department of Agriculture, Agricultural Research Services, Beneficial Insects Introduction Research Unit, Newark, DE, USA
| | - Kent M Daane
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Paul K Abram
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, Agassiz, BC, Canada
| | - Nicholas A Pardikes
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
| | - Joel J Brown
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branisovska 31, Czech Republic
| | - Melanie Thierry
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branisovska 31, Czech Republic
| | - Marylène Poirié
- INRAE, CNRS. and Evolution and Specificity of Multitrophic Interactions (ESIM) Sophia Agrobiotech Institute, Université "Côte d'Azur", Sophia Antipolis, France
| | - Paul Goldstein
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Scott E Miller
- Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - W Daniel Tracey
- Department of Biology, Indiana University Bloomington, Bloomington, IN, USA
- Gill Center for Biomolecular Science, Indiana University Bloomington, Bloomington, IN, USA
| | - Jeremy S Davis
- Department of Biology, Indiana University Bloomington, Bloomington, IN, USA
- Biology Department, University of Kentucky, Lexington, KY, USA
| | | | - Bregje Wertheim
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands
| | - Owen T Lewis
- Department of Zoology, University of Oxford, Oxford, UK
| | - Jeff Leips
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Phillip P A Staniczenko
- Department of Biology, Brooklyn College, City University of New York (CUNY), Brooklyn, NY, USA
| | - Jan Hrcek
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branisovska 31, Czech Republic
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27
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Lawley JW, Gamero-Mora E, Maronna MM, Chiaverano LM, Stampar SN, Hopcroft RR, Collins AG, Morandini AC. The importance of molecular characters when morphological variability hinders diagnosability: systematics of the moon jellyfish genus Aurelia (Cnidaria: Scyphozoa). PeerJ 2021; 9:e11954. [PMID: 34589293 PMCID: PMC8435205 DOI: 10.7717/peerj.11954] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/21/2021] [Indexed: 11/20/2022] Open
Abstract
Cryptic species have been detected across Metazoa, and while no apparent morphological features distinguish them, it should not impede taxonomists from formal descriptions. We accepted this challenge for the jellyfish genus Aurelia, which has a long and confusing taxonomic history. We demonstrate that morphological variability in Aurelia medusae overlaps across very distant geographic localities. Even though some morphological features seem responsible for most of the variation, regional geographic patterns of dissimilarities are lacking. This is further emphasized by morphological differences found when comparing lab-cultured Aurelia coerulea medusae with the diagnostic features in its recent redescription. Previous studies have also highlighted the difficulties in distinguishing Aurelia polyps and ephyrae, and their morphological plasticity. Therefore, mostly based on genetic data, we recognize 28 species of Aurelia, of which seven were already described, 10 are formally described herein, four are resurrected and seven remain undescribed. We present diagnostic genetic characters for all species and designate type materials for newly described and some resurrected species. Recognizing moon jellyfish diversity with formal names is vital for conservation efforts and other studies. This work clarifies the practical implications of molecular genetic data as diagnostic characters, and sheds light on the patterns and processes that generate crypsis.
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Affiliation(s)
- Jonathan W. Lawley
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
- School of Environment and Science, Coastal and Marine Research Centre, Australian Rivers Institute, Griffith University, Gold Coast, Queensland, Australia
| | - Edgar Gamero-Mora
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Maximiliano M. Maronna
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Luciano M. Chiaverano
- Instituto Nacional de Investigación y Desarrollo Pesquero, Mar del Plata, Buenos Aires, Argentina
| | - Sérgio N. Stampar
- Departamento de Ciências Biológicas, Faculdade de Ciências e Letras, Universidade Estadual Paulista, Assis, São Paulo, Brazil
| | - Russell R. Hopcroft
- College of Fisheries and Ocean Sciences, University of Alaska—Fairbanks, Fairbanks, Alaska, United States
| | - Allen G. Collins
- National Systematics Laboratory of the National Oceanic and Atmospheric Administration Fisheries Service, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States
| | - André C. Morandini
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil
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28
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Oliveira CMCA, Mantelatto FL, Terossi M. Systematics of the shrimp genus
Atya
(Decapoda, Atyidae) in the light of multigene‐based phylogenetic and species delimitation inference. ZOOL SCR 2021. [DOI: 10.1111/zsc.12503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Caio M. C. A. Oliveira
- Laboratory of Bioecology and Crustacean Systematics (LBSC) Department of Biology Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP) University of São Paulo (USP) Ribeirão Preto SP Brazil
| | - Fernando L. Mantelatto
- Laboratory of Bioecology and Crustacean Systematics (LBSC) Department of Biology Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP) University of São Paulo (USP) Ribeirão Preto SP Brazil
| | - Mariana Terossi
- Laboratory of Carcinology Department of Zoology Institute of Biosciences Federal University of Rio Grande do Sul (UFRGS) Porto Alegre RS Brazil
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Smart U, Cihlar JC, Budowle B. International Wildlife Trafficking: A perspective on the challenges and potential forensic genetics solutions. Forensic Sci Int Genet 2021; 54:102551. [PMID: 34134047 DOI: 10.1016/j.fsigen.2021.102551] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/29/2022]
Abstract
International wildlife trafficking (IWT) is a thriving and pervasive illegal enterprise that adversely affects modern societies. Yet, despite being globally recognized as a threat to biodiversity, national security, economy, and biosecurity, IWT remains largely unabated and is proliferating at an alarming rate. The increase in IWT is generally attributed to a lack of prioritization to curb wildlife crime through legal and scientific infrastructure. This review: (1) lays out the damaging scope and influence of IWT; (2) discusses the potential of DNA marker systems, barcodes, and emerging molecular technologies, such as long-read portable sequencing, to facilitate rapid, in situ identification of species and individuals; and (3) encourages initiatives that promote quality and innovation. Interdisciplinary collaboration promises to be one of the most effective ways forward to surmounting the complex scientific and legal challenges posed by IWT.
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Affiliation(s)
- Utpal Smart
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA.
| | - Jennifer Churchill Cihlar
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
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30
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Siriwut W, Jeratthitikul E, Panha S, Chanabun R, Ngor PB, Sutcharit C. Evidence of cryptic diversity in freshwater Macrobrachium prawns from Indochinese riverine systems revealed by DNA barcode, species delimitation and phylogenetic approaches. PLoS One 2021; 16:e0252546. [PMID: 34077477 PMCID: PMC8171930 DOI: 10.1371/journal.pone.0252546] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/18/2021] [Indexed: 12/04/2022] Open
Abstract
The diversity of Indochinese prawns in genus Macrobrachium is enormous due to the habitat diversification and broad tributary networks of two river basins: the Chao Phraya and the Mekong. Despite long-standing interest in SE-Asian decapod diversity, the subregional Macrobrachium fauna is still not yet comprehensively clarified in terms of taxonomic identification or genetic diversification. In this study, integrative taxonomic approaches including morphological examination, DNA barcoding, and molecular species delimitation were used to emphasize the broad scale systematics of Macrobrachium prawns in Indochina. Twenty-seven nominal species were successfully re-verified by traditional and molecular taxonomy. Barcode gap analysis supported broad overlapping of species boundaries. Taxonomic ambiguity of several deposited samples in the public database is related to inter- and intraspecific genetic divergence as indicated by BOLD discordance. Diagnostic nucleotide positions were found in six Macrobrachium species. Eighteen additional putative lineages are herein assigned using the consensus of species delimitation methods. Genetic divergence indicates the possible existence of cryptic species in four morphologically complex and wide-ranging species: M. lanchesteri, M. niphanae, M. sintangense, and some members of the M. pilimanus group. The geographical distribution of some species supports the connections and barriers attributed to paleo-historical events of SE-Asian rivers and land masses. Results of this study show explicitly the importance of freshwater ecosystems in Indochinese subregions, especially for the Mekong River Basin due to its high genetic diversity and species composition found throughout its tributaries.
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Affiliation(s)
- Warut Siriwut
- Animal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Ekgachai Jeratthitikul
- Animal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Somsak Panha
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Academy of Science, The Royal Society of Thailand, Dusit, Bangkok, Thailand
| | - Ratmanee Chanabun
- Program in Animal Science, Faculty of Agricultural Technology, Sakon Nakhon Rajabhat University, Sakon Nakhon, Thailand
| | - Peng Bun Ngor
- Inland Fisheries Research and Development Institute (IFReDI), Fisheries Administration, Phnom Penh, Cambodia
- Wonders of the Mekong Project, Phnom Penh, Cambodia
| | - Chirasak Sutcharit
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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31
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Papa Y, Le Bail PY, Covain R. Genetic landscape clustering of a large DNA barcoding data set reveals shared patterns of genetic divergence among freshwater fishes of the Maroni Basin. Mol Ecol Resour 2021; 21:2109-2124. [PMID: 33892518 DOI: 10.1111/1755-0998.13402] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 03/27/2021] [Accepted: 04/13/2021] [Indexed: 11/27/2022]
Abstract
The Maroni is one of the most speciose basins of the Guianas and hosts a megadiverse freshwater fish community. Although taxonomic references based on morphological identification exist for both the Surinamese and Guianese parts of the basin, there are still taxonomic uncertainties concerning the status of several species. We used COI sequences of 1284 fish in conjunction with morphological and biogeographical evidence to assist with species delineation and discovery in order to validate and standardize the current taxonomy. This resulted in a final DNA barcode data set of 199 fish species (125 genera, 36 families and eight orders; 68.86% of strictly freshwater fishes from the basin), among which 25 are new putative candidate species flagged as requiring taxonomic update. DNA barcoding delineation through Barcode Index Numbers (BINs) revealed further cryptic diversity (230 BINs in total). To explore global genetic patterns across the basin, genetic divergence landscapes were computed for 128 species, showing a global trend of high genetic divergence between the Surinamese southwest (Tapanahony and Paloemeu), the Guianese southeast (Marouini, Litany, Tampok, etc.), and the river outlet in the north. This could be explained by lower levels of connectivity between these three main areas and/or the exchange of individuals between these areas and the neighbouring basins. A new method of ordination of genetic landscapes successfully assigned species into cluster groups based on their respective pattern of genetic divergence across the Maroni Basin: genetically homogeneous species were effectively discriminated from species showing high spatial genetic fragmentation and possible lower capacity for dispersal.
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Affiliation(s)
- Yvan Papa
- Herpetology and Ichthyology, Museum of Natural History of Geneva, Geneva, Switzerland.,School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | | | - Raphaël Covain
- Herpetology and Ichthyology, Museum of Natural History of Geneva, Geneva, Switzerland
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32
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Lenguas Francavilla M, Negrete L, Martínez-Aquino A, Damborenea C, Brusa F. Two new freshwater planarian species (Platyhelminthes: Tricladida: Dugesiidae) partially sympatric in Argentinean Patagonia. CAN J ZOOL 2021. [DOI: 10.1139/cjz-2020-0169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Girardia Ball, 1974 is the most diverse and widely distributed genus of the family Dugesiidae (Platyhelminthes: Continenticola) in the Neotropical region. Seven out of the 52 species of the genus are known for Argentina. The Somuncurá Plateau is a region in northern Patagonia with several endemic flora and fauna, but little is known about the free-living Platyhelminthes. We describe two new species of Girardia partially inhabiting in sympatry in the Somuncurá Plateau: Girardia somuncura sp. nov. and Girardia tomasi sp. nov. The identification criteria that we followed was an integrative taxonomic approach based on morphological and molecular data. Thus, we used anatomical features focused on the reproductive system, together with a phylogenetic analysis, using a mitochondrial (COI barcode region) genetic marker. This study is the first phylogenetic analysis of the genus Girardia in which we include the southernmost representatives of America here described, thus making it possible to incorporate them in global phylogenies.
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Affiliation(s)
- M. Lenguas Francavilla
- División Zoología Invertebrados, Facultad de Ciencias Naturales y Museo (UNLP), Boulevard 120 & 61, B1902CHX, La Plata, Buenos Aires, Argentina
- CONICET - Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina
| | - L. Negrete
- División Zoología Invertebrados, Facultad de Ciencias Naturales y Museo (UNLP), Boulevard 120 & 61, B1902CHX, La Plata, Buenos Aires, Argentina
- CONICET - Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina
| | - A. Martínez-Aquino
- Facultad de Ciencias, Universidad Autónoma de Baja California, Carretera Transpeninsular 3917, Fraccionamiento Playitas, Ensenada, Baja California, 22860, México
| | - C. Damborenea
- División Zoología Invertebrados, Facultad de Ciencias Naturales y Museo (UNLP), Boulevard 120 & 61, B1902CHX, La Plata, Buenos Aires, Argentina
- CONICET - Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina
| | - F. Brusa
- División Zoología Invertebrados, Facultad de Ciencias Naturales y Museo (UNLP), Boulevard 120 & 61, B1902CHX, La Plata, Buenos Aires, Argentina
- CONICET - Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina
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Abstract
Annelida is a ubiquitous, common and diverse group of organisms, found in terrestrial, fresh waters and marine environments. Despite the large efforts put into resolving the evolutionary relationships of these and other Lophotrochozoa, and the delineation of the basal nodes within the group, these are still unanswered. Annelida holds an enormous diversity of forms and biological strategies alongside a large number of species, following Arthropoda, Mollusca, Vertebrata and perhaps Platyhelminthes, among the species most rich in phyla within Metazoa. The number of currently accepted annelid species changes rapidly when taxonomic groups are revised due to synonymies and descriptions of a new species. The group is also experiencing a recent increase in species numbers as a consequence of the use of molecular taxonomy methods, which allows the delineation of the entities within species complexes. This review aims at succinctly reviewing the state-of-the-art of annelid diversity and summarizing the main systematic revisions carried out in the group. Moreover, it should be considered as the introduction to the papers that form this Special Issue on Systematics and Biodiversity of Annelids.
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34
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Paz-Sedano S, Candás M, Gosliner TM, Pola M. Undressing Lophodoris danielsseni (Friele & Hansen, 1878) (Nudibranchia: Goniodorididae). ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-020-00470-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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35
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Brito PS, Guimarães EC, Guimarães KLA, Rodrigues LRR, Anjos MR, Katz AM, Carvalho-Costa LF, Ottoni FP. Cryptic speciation in populations of the genus Aphyocharax (Characiformes: Characidae) from eastern Amazon coastal river drainages and surroundings revealed by single locus species delimitation methods. NEOTROPICAL ICHTHYOLOGY 2021. [DOI: 10.1590/1982-0224-2021-0095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract Recent studies in eastern Amazon coastal drainages and their surroundings have revealed new fish species that sometimes exhibit little morphological differentiation (cryptic species). Thus, we used a DNA-based species delimitation approach to test if populations showing the morphotype and typical character states of the Aphyocharax avary holotype correspond either to A. avary or A. brevicaudatus, two known species from the region, or if they form independent lineages, indicating cryptic speciation. WP and GMYC analyses recovered five lineages (species) in the ingroup, while a bPTP analysis delimited three lineages. ABGD analyses produced two possible results: one corroborating the WP and GMYC methods and another corroborating the bPTP method. All methods indicate undescribed cryptic species in the region and show variation from at least 1 to 4 species in the ingroup, depending on the approach, corroborating previous studies, and revealing this region as a possible hotspot for discovering undescribed fish species.
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Affiliation(s)
- Pâmella S. Brito
- Universidade Federal do Maranhão, Brazil; Universidade Federal do Oeste do Pará, Brazil
| | - Erick C. Guimarães
- Universidade Federal do Maranhão, Brazil; Universidade Federal do Oeste do Pará, Brazil
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36
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Corrêa de Barros R, Moreira da Rocha R. Genetic analyses reveal cryptic diversity in the widely distributed Styela canopus (Ascidiacea:Styelidae). INVERTEBR SYST 2021. [DOI: 10.1071/is20058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The routine use of DNA sequencing techniques and phylogenetic analysis has resulted in the discovery of many cryptic species, especially in the oceans. The common, globally introduced species Styela canopus is suspected to be a complex of cryptic species because of its widespread distribution and variable external morphology. We tested this possibility using COI and ANT marker sequences to uncover the phylogenetic relationship among 19 populations, and to examine genetic variability as well as gene flow. We obtained 271 COI and 67 ANT sequences and found surprising diversity among the 19 populations (COI: π = 0.18, hd = 0.99; ANT: π = 0.13, hd = 0.95). Corresponding topologies were found using Bayesian inference and maximum likelihood for both simple locus (COI) and multilocus (COI + ANT) analyses and so the clades received strong support. We used simple (ABGD, bPTP, GMYC) and multiple (BSD) locus methods to delimit species. The simple locus methods indicated that the current Styela canopus comprises at least 15 species. The BSD method for concatenated data supported 7 of the 15 species. We suggest that S. canopus should be treated as the Styela canopus complex. The large number of cryptic species found, often with more than one clade found in sympatry, creates opportunities for better understanding reproductive isolation, hybridisation or speciation. As several lineages have already been introduced widely around the world, we must quickly understand their diversity and invasive abilities.
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37
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Pan J, Luo X, Bian J, Shao T, Li C, Zhao T, Zhang S, Zhou F, Wang G. Identification of Genomic Islands in Synechococcus sp. WH8102 Using Genomic Barcode and Whole-Genome Microarray Analysis. Curr Bioinform 2021. [DOI: 10.2174/1574893615666200121160615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Synechococcus sp. WH8102 is one of the most abundant photosynthetic organisms in many ocean regions.
Objective:
The aim of this study is to identify genomic islands (GIs) in Synechococcus sp. WH8102 with integrated methods.
Methods:
We have applied genomic barcode to identify the GIs in Synechococcus sp. WH8102, which could make genomic regions of different origins visually apparent. The gene expression data of the predicted GIs was analyzed through microarray data which was collected for functional analysis of the relevant genes.
Results:
Seven GIs were identified in Synechococcus sp. WH8102. Most of them are involved in cell surface modification, photosynthesis and drug resistance. In addition, our analysis also revealed the functions of these GIs, which could be used for in-depth study on the evolution of this strain.
Conclusion:
Genomic barcodes provide us with a comprehensive and intuitive view of the target genome. We can use it to understand the intrinsic characteristics of the whole genome and identify GIs or other similar elements.
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Affiliation(s)
- Jiahui Pan
- Department of Pathogenbiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, 130021,China
| | - Xizi Luo
- Department of Pathogenbiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, 130021,China
| | - Jiang Bian
- Jilin Provincial Center for Disease Control and Prevention, Changchun, 130062,China
| | - Tong Shao
- Department of Pathogenbiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, 130021,China
| | - Chaoying Li
- Department of Pathogenbiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, 130021,China
| | - Tingting Zhao
- Department of Pathogenbiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, 130021,China
| | - Shiwei Zhang
- Department of Pathogenbiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, 130021,China
| | - Fengfeng Zhou
- Department of Pathogenbiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, 130021,China
| | - Guoqing Wang
- Department of Pathogenbiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, 130021,China
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Nogueira AF, Oliveira C, Langeani F, Netto-Ferreira AL. Molecular species delimitation of the genera Anodus, Argonectes, Bivibranchia and Micromischodus (Ostariophysi: Characiformes). NEOTROPICAL ICHTHYOLOGY 2021. [DOI: 10.1590/1982-0224-2021-0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
ABSTRACT A good taxonomic assessment of specimens is an essential task to many biological studies and DNA data have provided additional sources of information to assist in the disentanglement of taxonomic problems among living organisms, as has been the case of some taxa of the megadiverse Neotropical ichthyofauna. Here we assessed all valid species in the Neotropical freshwater fish genera Anodus, Argonectes, Bivibranchia and Micromischodus of the family Hemiodontidae to establish molecular species boundaries among them. All species delimitation methods defined exactly only one MOTU for Anodus elongatus, Argonectes longiceps, A. robertsi, Bivibranchia bimaculata, B. notata, B. velox, and Micromischodus sugillatus, resulting in total congruence between nominal species and MOTUs for these seven taxa. The three species having discordant results across analyses: Anodus orinocensis, Bivibranchia fowleri, and Bivibranchia simulata, matched more than one MOTU per species in some methods, meaning that cryptic diversity may exist within these taxa. Overall, this great correspondence among morphological and molecular boundaries for thae species analysed seem to be indicative of a reasonably stable taxonomy within these Hemiodontidae genera.
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Affiliation(s)
- Acácio Freitas Nogueira
- Universidade Federal do Pará, Brazil; Universidade Estadual Paulista, Brazil; Universidade Federal do Rio Grande do Sul, Brazil
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Nogueira AF, Oliveira C, Langeani F, Netto‐Ferreira AL. Overlooked biodiversity of mitochondrial lineages in
Hemiodus
(Ostariophysi, Characiformes). ZOOL SCR 2020. [DOI: 10.1111/zsc.12469] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Acácio F. Nogueira
- Programa de Pós‐Graduação em Zoologia Instituto de Ciências Biológicas Universidade Federal do Pará and Museu Paraense Emílio Goeldi Belém Brazil
- Laboratório de Biologia e Genética de Peixes Departamento de Biologia Estrutural e Funcional Instituto de Biociências Universidade Estadual Paulista Botucatu Brazil
- Laboratório de Ictiologia Departamento de Zoologia Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
| | - Claudio Oliveira
- Laboratório de Biologia e Genética de Peixes Departamento de Biologia Estrutural e Funcional Instituto de Biociências Universidade Estadual Paulista Botucatu Brazil
| | - Francisco Langeani
- Departamento de Zoologia e Botânica Instituto de Biociências, Letras e Ciências Exatas Universidade Estadual Paulista São Jose do Rio Preto Brazil
| | - André L. Netto‐Ferreira
- Laboratório de Ictiologia Departamento de Zoologia Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
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40
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Alves PV, Chambrier A, Luque JL, Scholz T. Integrative taxonomy reveals hidden cestode diversity in
Pimelodus
catfishes in the Neotropics. ZOOL SCR 2020. [DOI: 10.1111/zsc.12465] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Philippe V. Alves
- Departamento de Parasitologia Instituto de Ciências Biológicas Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - Alain Chambrier
- Department of Invertebrates Natural History Museum Geneva Switzerland
| | - José L. Luque
- Departamento de Parasitologia Animal Universidade Federal Rural do Rio de Janeiro Seropédica Brazil
| | - Tomáš Scholz
- Institute of Parasitology Biology Centre of the Academy of Sciences of the Czech Republic České Budějovice Czech Republic
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41
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Walters AD, Cannizzaro AG, Trujillo DA, Berg DJ. Addressing the Linnean shortfall in a cryptic species complex. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Biodiversity is being lost at an alarming rate, but the rate of this loss is likely to be underestimated as a result of a deficit in taxonomic knowledge (i.e. the Linnean shortfall). This knowledge gap is more extensive for morphologically indistinct taxa. The advancement of molecular techniques and delimitation methods has facilitated the identification of such cryptic species, but a majority of these taxa remain undescribed. To investigate the effects of taxonomic uncertainty on understanding of biodiversity, we applied the general lineage concept of species to an amphipod species complex, the Gammaruslacustris lineage that occupies springs of the northern Chihuahuan Desert, which is emerging in contemporary times. We investigated species boundaries using a validation-based approach and examined genetic structure of the lineage using a suite of microsatellite markers to identify independently evolving metapopulations. Our results show that each spring contains a genetically distinct population that is geographically isolated from other springs, suggesting evolutionary independence and status as separate species. Additionally, we observed subtle interspecific morphological variation among the putative species. We used multiple lines of evidence to formally describe four new species (Gammarus langi sp. nov., G. percalacustris sp. nov., G. colei sp. nov. and G. malpaisensis sp. nov.) endemic to the northern Chihuahuan Desert. Cryptic speciation is likely to be high in other aquatic taxa within these ecosystems, and across arid landscapes throughout North America and elsewhere, suggesting that the magnitude of the Linnean shortfall is currently underestimated in desert springs worldwide.
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Affiliation(s)
| | | | | | - David J Berg
- Department of Biology, Miami University, Hamilton, OH USA
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Keita ML, Medkour H, Sambou M, Dahmana H, Mediannikov O. Tabanids as possible pathogen vectors in Senegal (West Africa). Parasit Vectors 2020; 13:500. [PMID: 33004069 PMCID: PMC7528383 DOI: 10.1186/s13071-020-04375-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 09/23/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Species of the Tabanidae are potent vectors of human and animal diseases, but they have not been thoroughly investigated to date. In Senegal (West Africa), little information is available on these dipterans. Our objective in this study was to investigate Senegalese tabanids and their diversity by using molecular and proteomics approaches, as well as their associated pathogens. METHODS A total of 171 female tabanids were collected, including 143 from Casamance and 28 from Niokolo-Koba. The samples were identified morphologically by PCR sequencing and by MALDI-TOF MS, and PCR analysis was employed for pathogen detection and blood-meal characterization. RESULTS The morphological identification revealed four species concordantly with the molecular identification: Atylotus fuscipes (79.5%), Tabanus guineensis (16.4%), Chrysops distinctipennis (3.5%) and Tabanus taeniola (0.6%) (not identified by PCR). The molecular investigation of pathogens revealed the presence of Trypanosoma theileri (6.6%), Leishmania donovani (6.6%), Setaria digitata (1.5%), Rickettsia spp. (5.1%) and Anaplasmataceae bacteria (0.7%) in A. fuscipes. Tabanus guineensis was positive for L. donovani (35.7%), S. digitata (3.6%) and Anaplasmataceae (17.8%). Leishmania donovani has been detected in 50% of C. distinctipennis specimens and the only T. taeniola specimen. No Piroplasmida, Mansonella spp. or Coxeilla burnetii DNA was detected. In addition to humans (96.43%), Chlorocebus sabeus, a non-human primate, has been identified as a host of (3.57%) analysed tabanids. MALDI-TOF MS enabled us to correctly identify all tabanid species that had good quality spectra and to create a database for future identification. CONCLUSIONS Tabanids in Senegal could be vectors of several pathogens threatening animal and public health. To fully characterize these dipterans, it is therefore necessary that researchers in entomology and infectiology employ molecular characterization and mass spectrometric techniques such as MALDI-TOF MS to analyse these dipterans in Senegal and West Africa.
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Affiliation(s)
- Mohamed Lamine Keita
- IHU Méditerranée Infection - Microbes, Evolution, Phylogeny and Infection (MEФI), Marseille, France
- UMR Aix-Marseille University, IRD, APHM -19-21, Bd Jean Moulin, 13385, Marseille Cedex 05, France
| | - Hacène Medkour
- IHU Méditerranée Infection - Microbes, Evolution, Phylogeny and Infection (MEФI), Marseille, France
- UMR Aix-Marseille University, IRD, APHM -19-21, Bd Jean Moulin, 13385, Marseille Cedex 05, France
| | - Masse Sambou
- IHU Méditerranée Infection - Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
- Vectors-Tropical and Mediterranean Infections (VITROME), Campus International, UCAD-IRD, Dakar, Sénégal
| | - Handi Dahmana
- IHU Méditerranée Infection - Microbes, Evolution, Phylogeny and Infection (MEФI), Marseille, France
- UMR Aix-Marseille University, IRD, APHM -19-21, Bd Jean Moulin, 13385, Marseille Cedex 05, France
| | - Oleg Mediannikov
- IHU Méditerranée Infection - Microbes, Evolution, Phylogeny and Infection (MEФI), Marseille, France.
- UMR Aix-Marseille University, IRD, APHM -19-21, Bd Jean Moulin, 13385, Marseille Cedex 05, France.
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43
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Martínez-Domínguez L, Nicolalde-Morejón F, Lorea-Hernández FG, Vergara-Silva F, Stevenson DW. A novelty in Ceratozamia (Zamiaceae, Cycadales) from the Sierra Madre del Sur, Mexico: biogeographic and morphological patterns, DNA barcoding and phenology. PHYTOKEYS 2020; 156:1-25. [PMID: 32943975 PMCID: PMC7471474 DOI: 10.3897/phytokeys.156.53502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/24/2020] [Indexed: 06/11/2023]
Abstract
Ceratozamia is a genus of cycads occurring in eastern Mexico and Central America. In this study, we describe a new species from the Pacific region of Mexico in Guerrero state. This locality represents the most northwestern Mexico distribution for the genus. We focus the comparison of this species with the most geographically proximate and phenotypically relevant lineages for this taxon. We followed an integrative taxonomy approach to evaluate the classification of these species, including geographic location, morphology, DNA barcoding and phenology as primary sources of systematic data. Within the morphological dataset, reproductive structures are described in detail and new characters are proposed for microsporophylls. The comparative morphology of these structures facilitated the elucidation of differences in forms and species for identification. The two chosen DNA barcoding markers - namely, the chloroplast genome coding region matK and the nuclear ribosomal internal transcribed spacer (ITS) region - had low divergence, allowing only 61% of species identification, suggesting slow molecular evolutionary rates. Besides employing these three basic sources of evidence, we introduced phenology as additional information for species circumscription. In addition, this work includes a brief review of the genus at the species-level. This is therefore the most recent review for Ceratozamia across its full geographic range (latitudinal and elevational). Overall, this work further contributes to a comprehensive framework for systematic studies in Mexican cycads.
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Affiliation(s)
- Lilí Martínez-Domínguez
- Posgrado en Ciencias Biológicas, Instituto de Biología, Universidad Nacional Autónoma de México, 3er. Circuito Exterior, Ciudad Universitaria, 04510, Coyoacán, CDMX, Mexico
- Laboratorio de Taxonomía Integrativa, Instituto de Investigaciones Biológicas, Universidad Veracruzana, Xalapa, 91190, Veracruz. Mexico
- Laboratorio de Sistemática Molecular (Jardín Botánico), Instituto de Biología, Universidad Nacional Autónoma de México, 3er. Circuito Exterior, Ciudad Universitaria, 04510, Coyoacán, CDMX. Mexico
| | - Fernando Nicolalde-Morejón
- Laboratorio de Taxonomía Integrativa, Instituto de Investigaciones Biológicas, Universidad Veracruzana, Xalapa, 91190, Veracruz. Mexico
| | | | - Francisco Vergara-Silva
- Laboratorio de Sistemática Molecular (Jardín Botánico), Instituto de Biología, Universidad Nacional Autónoma de México, 3er. Circuito Exterior, Ciudad Universitaria, 04510, Coyoacán, CDMX. Mexico
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44
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Zhao D, Kong LF, Sasaki T, Li Q. Molecular Species Delimitation of the Genus Reishia (Mollusca: Gastropoda) along the Coasts of China and Korea. Zoolog Sci 2020; 37:382-390. [PMID: 32729717 DOI: 10.2108/zs190153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/22/2020] [Indexed: 11/17/2022]
Abstract
Species of the predatory gastropod genus Reishia Kuroda and Habe, 1971 (Muricidae) inhabit intertidal rocky shores in East Asia. Due to their highly variable external shell morphology, the taxonomy of this genus at species-level is still in need of re-evaluation. Using DNA-based delimitation methods, we aimed to ascertain the number of species of Reishia along the coasts of China and adjacent Asian areas. Also, we looked for diagnostic traits using morphology-based statistical approaches. Our genetic data suggest that the studied individuals comprised two separate species of a Reishia complex in this region, in contrast to the previously proposed four or more taxa. This conclusion is further supported by statistical analyses of shell morphological characteristics. The morphospecies R. bronni (Dunker, 1860), R. jubilaea (Tan and Sigurdsson, 1990), and R. luteostoma (Holten, 1803) were assigned to a single taxon, indicating that they might be synonyms of the same species. The morphospecies R. clavigera (Küster, 1860) singly formed one group, suggesting that it is likely a valid name. The estimated divergence time of the two identified taxa indicates that speciation might have been associated with the sea level and temperature fluctuations during the Plio-Pleistocene period. Our study on Reishia species provides crucial information for further research on the ecology, evolutionary biology, and conservation of this genus.
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Affiliation(s)
- Dan Zhao
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China.,Fisheries College, Zhejiang Ocean University, Zhoushan 316022, China
| | - Ling-Feng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Takenori Sasaki
- The University Museum, The University of Tokyo, Tokyo 113-0033, Japan
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China,
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45
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Merckelbach LM, Borges LMS. Make every species count: fastachar software for rapid determination of molecular diagnostic characters to describe species. Mol Ecol Resour 2020; 20:1761-1768. [PMID: 32623815 DOI: 10.1111/1755-0998.13222] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 06/25/2020] [Accepted: 06/29/2020] [Indexed: 11/29/2022]
Abstract
Only a fraction of species found so far has been described, particularly cryptic species uncovered by molecular data. The latter might require the use of molecular data for its diagnosis, but it is important to make use of the diagnostic content of the molecular data itself. The molecular character-based model provides discrete molecular diagnostic characters within DNA sequences that can be used in species descriptions fulfilling the requirement of most codes of nomenclature for a character-based description of species. Here, we introduce fastachar, a software developed to extract molecular diagnostic characters from one or several taxonomically informative DNA markers of a selected taxon compared with those of other taxa in a single step. The input data consist of a single file with aligned sequences in the fasta format, which can be created using alignment software such as mega or geneious. fastachar is an easy-to-use software with a graphical interface. Thus, the software does not require the user to have any knowledge of the underlying programming environment (Python). We hope this software, based on the method proposed by Jörger and Schrödl (Frontiers in Zoology, 10, 59, 2013) to describe cryptic species, will encourage researchers to take the final step in taxonomy: the formal description of species. We propose the use of this method and fastachar also for the inclusion of molecular data in the description of any species. fastachar is released as open-source software under GNU General Public License V3 and is freely available for all major operating systems from https://github.com/smerckel/FastaChar.
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Affiliation(s)
- Lucas M Merckelbach
- Centre for Materials and Coastal Research, Helmholtz-Zentrum Geesthacht, Geesthacht, Germany
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46
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Salvi D, Berrilli E, D'Alessandro P, Biondi M. Sharpening the DNA barcoding tool through a posteriori taxonomic validation: The case of Longitarsus flea beetles (Coleoptera: Chrysomelidae). PLoS One 2020; 15:e0233573. [PMID: 32437469 PMCID: PMC7241800 DOI: 10.1371/journal.pone.0233573] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/07/2020] [Indexed: 11/30/2022] Open
Abstract
The accuracy of the DNA barcoding tool depends on the existence of a comprehensive archived library of sequences reliably determined at species level by expert taxonomists. However, misidentifications are not infrequent, especially following large-scale DNA barcoding campaigns on diverse and taxonomically complex groups. In this study we used the species-rich flea beetle genus Longitarsus, that requires a high level of expertise for morphological species identification, as a case study to assess the accuracy of the DNA barcoding tool following several optimization procedures. We built a cox1 reference database of 1502 sequences representing 78 Longitarsus species, among which 117 sequences (32 species) were newly generated using a non-invasive DNA extraction method that allows keeping reference voucher specimens. Within this dataset we identified 69 taxonomic inconsistencies using barcoding gap analysis and tree topology methods. Threshold optimisation and a posteriori taxonomic revision based on newly generated reference sequences and metadata allowed resolving 44 sequences with ambiguous and incorrect identification and provided a significant improvement of the DNA barcoding accuracy and identification efficacy. Unresolved taxonomic uncertainties, due to overlapping intra- and inter-specific levels of divergences, mainly regards the Longitarsus pratensis species complex and polyphyletic groups L. melanocephalus, L. nigrofasciatus and L. erro. Such type of errors indicates either poorly established taxonomy or any biological processes that make mtDNA groups poorly predictive of species boundaries (e.g. recent speciation or interspecific hybridisation), thus providing directions for further integrative taxonomic and evolutionary studies. Overall, this study underlines the importance of reference vouchers and high-quality metadata associated to sequences in reference databases and corroborates, once again, the key role of taxonomists in any step of the DNA barcoding pipeline in order to generate and maintain a correct and functional reference library.
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Affiliation(s)
- Daniele Salvi
- Department of Health, Life and Environmental Sciences, University of L'Aquila, Coppito, L'Aquila, Italy
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Emanuele Berrilli
- Department of Health, Life and Environmental Sciences, University of L'Aquila, Coppito, L'Aquila, Italy
| | - Paola D'Alessandro
- Department of Health, Life and Environmental Sciences, University of L'Aquila, Coppito, L'Aquila, Italy
| | - Maurizio Biondi
- Department of Health, Life and Environmental Sciences, University of L'Aquila, Coppito, L'Aquila, Italy
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Sabadini CP, Machado CB, Vilhena PDS, Garófalo CA, Del Lama MA. Species delimitation and phylogenetic relationships in the genusTrypoxylon(Hymenoptera: Crabronidae) using molecular markers: an alternative to taxonomic impediment. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1758824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Camila Pereira Sabadini
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235, São Carlos, 13565-905, SP, Brazil
| | - Carolina Barros Machado
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235, São Carlos, 13565-905, SP, Brazil
| | - Patrícia Dos Santos Vilhena
- Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes, 3900, Ribeirão Preto, 14040-900, SP, Brazil
| | - Carlos Alberto Garófalo
- Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes, 3900, Ribeirão Preto, 14040-900, SP, Brazil
| | - Marco Antonio Del Lama
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235, São Carlos, 13565-905, SP, Brazil
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Hütter T, Ganser MH, Kocher M, Halkic M, Agatha S, Augsten N. DeSignate: detecting signature characters in gene sequence alignments for taxon diagnoses. BMC Bioinformatics 2020; 21:151. [PMID: 32312224 PMCID: PMC7171811 DOI: 10.1186/s12859-020-3498-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Molecular characters have been added in integrative taxonomic approaches in recent years. Nevertheless, taxon diagnoses are still widely restricted to morphological characters. The inclusion of molecular characters into taxon diagnoses is not only hampered by problems, such as their definition and the designation of their positions in a reference alignment, but also by the technical effort. RESULTS DeSignate is a tool for character-based taxon diagnoses that includes a novel ranking scheme. It detects and classifies individual and combined signature characters (diagnostic molecular characters) based on so-called character state vectors. An intuitive web application guides the user through the analysis process and provides the results at a glance. Further, formal definitions and a uniform terminology of characters are introduced. CONCLUSIONS DeSignate facilitates the inclusion of diagnostic molecular characters and their positions to complement taxon diagnoses. Compared to previous solutions, the tool simplifies the workflow and improves reproducibility and traceability of the results. The tool is freely available as a web application at (https://designate.dbresearch.uni-salzburg.at/) and is open source (https://github.com/DatabaseGroup/DeSignate/).
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Affiliation(s)
- Thomas Hütter
- Department of Computer Sciences, University of Salzburg, Jakob-Haringer-Straße 2a, Salzburg, 5020, Austria.
| | - Maximilian H Ganser
- Department of Biosciences, University of Salzburg, Hellbrunnerstraße 34, Salzburg, 5020, Austria
| | - Manuel Kocher
- Department of Computer Sciences, University of Salzburg, Jakob-Haringer-Straße 2a, Salzburg, 5020, Austria
| | - Merima Halkic
- Department of Computer Sciences, University of Salzburg, Jakob-Haringer-Straße 2a, Salzburg, 5020, Austria
| | - Sabine Agatha
- Department of Biosciences, University of Salzburg, Hellbrunnerstraße 34, Salzburg, 5020, Austria
| | - Nikolaus Augsten
- Department of Computer Sciences, University of Salzburg, Jakob-Haringer-Straße 2a, Salzburg, 5020, Austria
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Bowser ML, Brassfield R, Dziergowski A, Eskelin T, Hester J, Magness DR, McInnis M, Melvin T, Morton JM, Stone J. Towards conserving natural diversity: A biotic inventory by observations, specimens, DNA barcoding and high-throughput sequencing methods. Biodivers Data J 2020; 8:e50124. [PMID: 32165853 PMCID: PMC7058680 DOI: 10.3897/bdj.8.e50124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 02/15/2020] [Indexed: 11/12/2022] Open
Abstract
The Kenai National Wildlife Refuge has been given a broad conservation mandate to conserve natural diversity. A prerequisite for fulfilling this purpose is to be able to identify the species and communities that make up that biodiversity. We tested a set of varied methods for inventory and monitoring of plants, birds and terrestrial invertebrates on a grid of 40 sites in a 938 ha study area in the Slikok Creek watershed, Kenai Peninsula, Alaska. We sampled plants and lichens through observation and specimen-based methods. We surveyed birds using bird call surveys on variable circular plots. We sampled terrestrial arthropods by sweep net sampling, processing samples with High Throughput Sequencing methods. We surveyed for earthworms, using the hot mustard extraction method and identified worm specimens by morphology and DNA barcoding. We examined community membership using clustering methods and Nonmetric Multidimensional Scaling. We documented a total of 4,764 occurrences of 984 species and molecular operational taxonomic units: 87 vascular plants, 51 mosses, 12 liverworts, 111 lichens, 43 vertebrates, 663 arthropods, 9 molluscs and 8 annelid worms. Amongst these records, 102 of the arthropod species appeared to be new records for Alaska. We found three non-native species: Deroceras agreste (Linnaeus, 1758) (Stylommatophora: Agriolimacidae), Dendrobaena octaedra (Savigny, 1826) (Crassiclitellata: Lumbricidae) and Heterarthrus nemoratus (Fallén, 1808) (Hymenoptera: Tenthredinidae). Both D. octaedra and H. nemoratus were found at sites distant from obvious human disturbance. The 40 sites were grouped into five community groups: upland mixed forest, black spruce forest, open deciduous forest, shrub-sedge bog and willow. We demonstrated that, at least for a subset of species that could be detected using these methods, we were able to document current species distributions and assemblages in a way that could be efficiently repeated for the purposes of biomonitoring. While our methods could be improved and additional methods and groups could be added, our combination of techniques yielded a substantial portion of the data necessary for fulfilling Kenai National Wildlife Refuge's broad conservation purposes.
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Affiliation(s)
- Matthew Lewis Bowser
- U.S. Fish & Wildlife Service, Kenai National Wildlife Refuge, Soldotna, Alaska, United States of AmericaU.S. Fish & Wildlife Service, Kenai National Wildlife RefugeSoldotna, AlaskaUnited States of America
| | - Rebekah Brassfield
- Salish Kootenai College, Pablo, Montana, United States of AmericaSalish Kootenai CollegePablo, MontanaUnited States of America
| | - Annie Dziergowski
- U.S. Fish & Wildlife Service, North Florida Ecological Services Office, Jacksonville, Florida, United States of AmericaU.S. Fish & Wildlife Service, North Florida Ecological Services OfficeJacksonville, FloridaUnited States of America
| | - Todd Eskelin
- U.S. Fish & Wildlife Service, Kenai National Wildlife Refuge, Soldotna, Alaska, United States of AmericaU.S. Fish & Wildlife Service, Kenai National Wildlife RefugeSoldotna, AlaskaUnited States of America
| | - Jennifer Hester
- City of Soldotna, Planning and Zoning Commision, Soldotna, Alaska, United States of AmericaCity of Soldotna, Planning and Zoning CommisionSoldotna, AlaskaUnited States of America
| | - Dawn Robin Magness
- U.S. Fish & Wildlife Service, Kenai National Wildlife Refuge, Soldotna, Alaska, United States of AmericaU.S. Fish & Wildlife Service, Kenai National Wildlife RefugeSoldotna, AlaskaUnited States of America
| | - Mariah McInnis
- Auburn University, School of Forestry & Wildlife Sciences, Auburn, Alabama, United States of AmericaAuburn University, School of Forestry & Wildlife SciencesAuburn, AlabamaUnited States of America
| | - Tracy Melvin
- Michigan State University, College of Agriculture & Natural Resources, Department of Fisheries and Wildlife, East Lansing, Michigan, United States of AmericaMichigan State University, College of Agriculture & Natural Resources, Department of Fisheries and WildlifeEast Lansing, MichiganUnited States of America
| | - John M. Morton
- U.S. Fish & Wildlife Service (retired), Soldotna, Alaska, United States of AmericaU.S. Fish & Wildlife Service (retired)Soldotna, AlaskaUnited States of America
| | - Joel Stone
- University of Alaska Fairbanks, Fairbanks, Alaska, United States of AmericaUniversity of Alaska FairbanksFairbanks, AlaskaUnited States of America
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A world review of reported myiases caused by flower flies (Diptera: Syrphidae), including the first case of human myiasis from Palpada scutellaris (Fabricius, 1805). Parasitol Res 2020; 119:815-840. [PMID: 32006229 DOI: 10.1007/s00436-020-06616-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 01/22/2020] [Indexed: 10/25/2022]
Abstract
Rat-tailed larvae of the syrphid species Palpada scutellaris (Fabricius, 1805) are documented causing an enteric human myiasis in Costa Rica. This is the first time that the genus Palpada is recorded as a human myiasis agent. We report a 68-year-old woman with intestinal pain and bloody diarrhea with several live Palpada larvae present in the stool. Using molecular techniques (DNA barcodes) and both electronic and optical microscopy to study the external morphology, the preimaginal stages of the fly were unambiguously identified. An identification key to all syrphid genera actually known as agents of human and animal myiases is provided for larvae, puparia, and adults. Moreover, a critical world review of more than 100 references of Syrphidae as myiasis agents is also given, with emphasis on the species with rat-tailed larvae.
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