101
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Posada-López L, Rodrigues BL, Velez ID, Uribe S. Improving the COI DNA barcoding library for Neotropical phlebotomine sand flies (Diptera: Psychodidae). Parasit Vectors 2023; 16:198. [PMID: 37308979 DOI: 10.1186/s13071-023-05807-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/10/2023] [Indexed: 06/14/2023] Open
Abstract
Sand fly species are traditionally identified using morphological traits, though this method is hampered by the presence of cryptic species. DNA barcoding is a widely used tool in the case of insects of medical importance, where it is necessary to know quickly which species are present in a transmission area. Here, we assess the usefulness of mitochondrial cytochrome c oxidase subunit I (COI) DNA barcoding as a practical tool for species identification, correct assignment of isomorphic females, and to evaluate the detection of cryptic diversity that occurs in the same species. A fragment of the COI gene was used to generate 156 new barcode sequences for sand flies from different countries of the Neotropical region, mainly Colombia, which had been identified morphologically as 43 species. The sequencing of the COI gene allowed the detection of cryptic diversity within species and correctly associated isomorphic females with males identified by morphology. The maximum intraspecific genetic distances ranged from 0 to 8.32% and 0 to 8.92% using uncorrected p distances and the Kimura 2-parameter (K2P) model, respectively. The minimum interspecific distance (nearest neighbor) for each species ranged from 1.5 to 14.14% and 1.51 to 15.7% using p and K2P distances, respectively. Three species had more than 3% maximum intraspecific distance: Psychodopygus panamensis, Micropygomyia cayennensis cayennensis, and Pintomyia evansi. They also were split into at least two molecular operational taxonomic units (MOTUs) each, using different species delimitation algorithms. Regarding interspecific genetic distances, the species of the genera Nyssomyia and Trichophoromyia generated values lower than 3% (except Nyssomyia ylephiletor and Ny. trapidoi). However, the maximum intraspecific distances did not exceed these values, indicating the presence of a barcode gap despite their proximity. Also, nine sand fly species were DNA barcoded for the first time: Evandromyia georgii, Lutzomyia sherlocki, Ny. ylephiletor, Ny. yuilli pajoti, Psathyromyia punctigeniculata, Sciopemyia preclara, Trichopygomyia triramula, Trichophoromyia howardi, and Th. velezbernali. The COI DNA barcode analysis enabled the correct delimitation of several Neotropical sand fly species from South and Central America and raised questions about the presence of cryptic species for some taxa, which should be further assessed.
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Affiliation(s)
- Laura Posada-López
- PECET (Programa de Estudio y Control de Enfermedades Tropicales), Universidad de Antioquia, Medellín, Colombia.
- Programa de Pós-graduação em Saúde Pública, Faculdade de Saúde Pública (FSP/USP), São Paulo, SP, Brasil.
| | - Bruno Leite Rodrigues
- Programa de Pós-graduação em Saúde Pública, Faculdade de Saúde Pública (FSP/USP), São Paulo, SP, Brasil
| | - Ivan Dario Velez
- PECET (Programa de Estudio y Control de Enfermedades Tropicales), Universidad de Antioquia, Medellín, Colombia
| | - Sandra Uribe
- Grupo de Investigación en Sistemática Molecular, Universidad Nacional de Colombia, Campus, Medellín, Colombia
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102
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Hebert PDN, Bock DG, Prosser SWJ. Interrogating 1000 insect genomes for NUMTs: A risk assessment for estimates of species richness. PLoS One 2023; 18:e0286620. [PMID: 37289794 PMCID: PMC10249859 DOI: 10.1371/journal.pone.0286620] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/22/2023] [Indexed: 06/10/2023] Open
Abstract
The nuclear genomes of most animal species include NUMTs, segments of the mitogenome incorporated into their chromosomes. Although NUMT counts are known to vary greatly among species, there has been no comprehensive study of their frequency/attributes in the most diverse group of terrestrial organisms, insects. This study examines NUMTs derived from a 658 bp 5' segment of the cytochrome c oxidase I (COI) gene, the barcode region for the animal kingdom. This assessment is important because unrecognized NUMTs can elevate estimates of species richness obtained through DNA barcoding and derived approaches (eDNA, metabarcoding). This investigation detected nearly 10,000 COI NUMTs ≥ 100 bp in the genomes of 1,002 insect species (range = 0-443). Variation in nuclear genome size explained 56% of the mitogenome-wide variation in NUMT counts. Although insect orders with the largest genome sizes possessed the highest NUMT counts, there was considerable variation among their component lineages. Two thirds of COI NUMTs possessed an IPSC (indel and/or premature stop codon) allowing their recognition and exclusion from downstream analyses. The remainder can elevate species richness as they showed 10.1% mean divergence from their mitochondrial homologue. The extent of exposure to "ghost species" is strongly impacted by the target amplicon's length. NUMTs can raise apparent species richness by up to 22% when a 658 bp COI amplicon is examined versus a doubling of apparent richness when 150 bp amplicons are targeted. Given these impacts, metabarcoding and eDNA studies should target the longest possible amplicons while also avoiding use of 12S/16S rDNA as they triple NUMT exposure because IPSC screens cannot be employed.
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Affiliation(s)
- Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Dan G. Bock
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Sean W. J. Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
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103
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Huemer P, Mayr T. A surprising new species of Exapate Hübner, 1825 (Lepidoptera, Tortricidae) from Armenia. Zootaxa 2023; 5296:75-82. [PMID: 37518455 DOI: 10.11646/zootaxa.5296.1.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Indexed: 08/01/2023]
Abstract
A new species of cold-season moths, Exapate aidasi sp. nov., is described from male specimens collected in Armenia. This is also the first record of the genus Exapate in Armenia and south of the Caucasus. The new species differs from the two previously known congeneric taxa both in phenotypic characteristics and in the structure of the male genitalia. In addition, DNA barcodes (cytochrome c-oxidase subunit 1) are clearly divergent from those of other species. Adult and male genitalia of all three species of Exapate are shown for comparison.
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Affiliation(s)
- Peter Huemer
- Tiroler Landesmuseen Betriebsges.m.b.H.; Natural History Collections; Krajnc-Str. 1; A-6060 Hall in Tirol; Austria Egelseestraße 21; A-6800 Feldkirch; Austria.
| | - Toni Mayr
- Tiroler Landesmuseen Betriebsges.m.b.H.; Natural History Collections; Krajnc-Str. 1; A-6060 Hall in Tirol; Austria Egelseestraße 21; A-6800 Feldkirch; Austria.
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104
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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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105
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Sheffield C. Agapostemonfasciatus Crawford (Hymenoptera, Halictidae), a valid North American bee species ranging into southern Canada. Biodivers Data J 2023; 11:e103982. [PMID: 37250957 PMCID: PMC10220499 DOI: 10.3897/bdj.11.e103982] [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: 03/23/2023] [Accepted: 05/12/2023] [Indexed: 05/31/2023] Open
Abstract
Background Sweat bees of the genus Agapostemon Guérin-Méneville, 1844 (Hymenoptera: Halictidae) are common and widespread in the Americas. Despite distinct morphological characters that were recognised in earlier taxonomic treatments, Agapostemonfasciatus Crawford, 1901 has been considered a variety of A.melliventris Cresson, 1874 since the 1930s and later placed into synonymy under A.melliventris in the early 1970s. New information A more detailed study of morphology (including examination of type materials), distribution and genetic data (i.e. DNA barcodes) of these two taxa suggests they are not conspecific. As such, A.fasciatus is resurrected as a valid North American bee species. Agapostemonfasciatus ranges further north in North America than A.mellivenrtis, reaching the southern Prairies Ecozone of Canada (Alberta, Saskatchewan), while most records of A.melliventris are from the south-western United States and northern Mexico. More accurate distributions for both species can be modelled as specimens in collections are identified using the diagnostic features provided. However, additional work is required on the A.melliventris species complex in the southern United States as genetic data suggest that multiple taxa could be present.
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Affiliation(s)
- Cory Sheffield
- Royal Saskatchewan Museum, Regina, CanadaRoyal Saskatchewan MuseumReginaCanada
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106
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Souza DDES, Sepúlveda TA, Monné MA, Marinoni L, Monné ML. Molecular and morphological approaches redefine the limits among polymorphic species in the Neotropical longhorn beetle genus, Myzomorphus Sallé (Coleoptera: Cerambycidae: Prioninae). Zootaxa 2023; 5285:252-270. [PMID: 37518707 DOI: 10.11646/zootaxa.5285.2.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Indexed: 08/01/2023]
Abstract
Myzomorphus Sallé is a charismatic genus of prionine longhorn beetles (Cerambycidae) composed of nine species. Myzomorphus species are found from Costa Rica to southern Brazil, but only two species have wide distributions across this range: M. scutellatus Sallé from Costa Rica to northern Brazil, and M. quadripunctatus (Gray) from Colombia to southern Brazil. These species are highly polymorphic and their limits are difficult to determine due to their strong morphological similarities--males are only distinguishable by subtle size variations and females by color patterns. Here, we used mitochondrial DNA (cox1 and 12S) to reconstruct the first phylogeny of Myzomorphus and, in combination with morphological data, assess the taxonomic limits between M. scutellatus and M. quadripunctatus. Our phylogenetic results confirm the monophyly of Myzomorphus and reveal a close relationship among M. birai, M. quadripunctatus and M. scutellatus. Using pairwise distance estimations, we found that the intraspecific variation of M. quadripunctatus is remarkably high (K2P: 0-11.7%; p-distances: 0-9.7%) and the interspecific distances of M. quadripunctatus in relation to M. birai and M. scutellatus (K2P: 14.8-20.1%; p-distances: 12-15%) are close to the intraspecific distances of M. quadripunctatus. We further analyzed the diagnostic characters of these species and found that their morphological intraspecific variations largely overlap. Altogether, our results demonstrate that the variability of M. birai, M. scutellatus and M. quadripunctatus represent polymorphisms of a single species. We thus argue for the synonymy of M. birai and M. scutellatus under M. quadripunctatus (syn. nov.) and highlight the need for multiple lines of evidence to solve the taxonomic problems in polymorphic species of Cerambycidae.
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Affiliation(s)
- Diego DE S Souza
- Department of Entomology; National Museum; Federal University of Rio de Janeiro; MNRJ; Quinta da Boa Vista; São Cristóvão; 20940-040; Rio de Janeiro; Rio de Janeiro; Brazil; Department of Zoology; Federal University of Paranaì; UFPR; Caixa Postal 19020; Centro Politeìcnico; Jardim das Ameìricas; 81531-990; Curitiba; Paranaì; Brazil.
| | - Tatiana A Sepúlveda
- Department of Zoology; Federal University of Paranaì; UFPR; Caixa Postal 19020; Centro Politeìcnico; Jardim das Ameìricas; 81531-990; Curitiba; Paranaì; Brazil.
| | - Miguel A Monné
- Department of Entomology; National Museum; Federal University of Rio de Janeiro; MNRJ; Quinta da Boa Vista; São Cristóvão; 20940-040; Rio de Janeiro; Rio de Janeiro; Brazil.
| | - Luciane Marinoni
- Department of Zoology; Federal University of Paranaì; UFPR; Caixa Postal 19020; Centro Politeìcnico; Jardim das Ameìricas; 81531-990; Curitiba; Paranaì; Brazil.
| | - Marcela L Monné
- Department of Entomology; National Museum; Federal University of Rio de Janeiro; MNRJ; Quinta da Boa Vista; São Cristóvão; 20940-040; Rio de Janeiro; Rio de Janeiro; Brazil.
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107
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Levesque-Beaudin V, Miller ME, Dikow T, Miller SE, Prosser SW, Zakharov EV, McKeown JT, Sones JE, Redmond NE, Coddington JA, Santos BF, Bird J, deWaard JR. A workflow for expanding DNA barcode reference libraries through 'museum harvesting' of natural history collections. Biodivers Data J 2023; 11:e100677. [PMID: 38327333 PMCID: PMC10848567 DOI: 10.3897/bdj.11.e100677] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/20/2023] [Indexed: 02/09/2024] Open
Abstract
Natural history collections are the physical repositories of our knowledge on species, the entities of biodiversity. Making this knowledge accessible to society - through, for example, digitisation or the construction of a validated, global DNA barcode library - is of crucial importance. To this end, we developed and streamlined a workflow for 'museum harvesting' of authoritatively identified Diptera specimens from the Smithsonian Institution's National Museum of Natural History. Our detailed workflow includes both on-site and off-site processing through specimen selection, labelling, imaging, tissue sampling, databasing and DNA barcoding. This approach was tested by harvesting and DNA barcoding 941 voucher specimens, representing 32 families, 819 genera and 695 identified species collected from 100 countries. We recovered 867 sequences (> 0 base pairs) with a sequencing success of 88.8% (727 of 819 sequenced genera gained a barcode > 300 base pairs). While Sanger-based methods were more effective for recently-collected specimens, the methods employing next-generation sequencing recovered barcodes for specimens over a century old. The utility of the newly-generated reference barcodes is demonstrated by the subsequent taxonomic assignment of nearly 5000 specimen records in the Barcode of Life Data Systems.
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Affiliation(s)
- Valerie Levesque-Beaudin
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Meredith E. Miller
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Torsten Dikow
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashington, DCUnited States of America
| | - Scott E. Miller
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashington, DCUnited States of America
| | - Sean W.J. Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Evgeny V. Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
- Department of Integrative Biology, University of Guelph, Guelph, CanadaDepartment of Integrative Biology, University of GuelphGuelphCanada
| | - Jaclyn T.A. McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Jayme E. Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Niamh E Redmond
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashington, DCUnited States of America
| | - Jonathan A. Coddington
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashington, DCUnited States of America
| | - Bernardo F. Santos
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashington, DCUnited States of America
| | - Jessica Bird
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashington, DCUnited States of America
| | - Jeremy R. deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of AmericaNational Museum of Natural History, Smithsonian InstitutionWashington, DCUnited States of America
- School of Environmental Sciences, University of Guelph, Guelph, CanadaSchool of Environmental Sciences, University of GuelphGuelphCanada
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108
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Shimbori EM, Giacomelli ADECS, Fernández-Triana JL, Watanabe IM, Santos EB, Santos JMD, Fazolin WX, Penteado-Dias AM. The Apanteles adelinamoralesae species group (Hymenoptera, Braconidae) from Brazil, with descriptions of three new species reared from fruit borers(Lepidoptera, Depressariidae). Zootaxa 2023; 5277:339-362. [PMID: 37518316 DOI: 10.11646/zootaxa.5277.2.5] [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: 05/01/2023] [Indexed: 08/01/2023]
Abstract
With more than 633 species, Apanteles is the largest genus within the subfamily Microgastrinae (Hymenoptera, Braconidae). We describe three new species reared from pests of commercial fruits, Apanteles ahuacatl Shimbori, Giacomelli & Fernández-Triana sp. n., A. aratiku Shimbori sp. n., and A. mayochinchipe Shimbori sp. n. They parasitize caterpillars in the subfamily Stenomatinae (Depressariidae): the soursop moth Cerconota anonella (Sepp), in fruits of sweetsop (Annona squamosa L.) and atemoya (Annona squamosa x Annona cherimola Mill.) (Annonaceae), the avocado borer Stenoma catenifer Walsingham, in fruits of avocado (Persea americana Mill.) (Lauraceae), and the cacao shoot borer Stenoma decora Zeller, in fruits and shoots of cacao (Theobroma cacao L.) (Malvaceae). The new Apanteles species are included in an expanded version of the key provided by Fernández-Triana et al. (2014) for the Apanteles adelinamoralesae species group. In addition, the previous record of Apanteles stenomae Muesebeck in Brazil is revised and considered to actually represent the species A. yolandarojasae Fernández-Triana.
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Affiliation(s)
- Eduardo Mitio Shimbori
- Departamento de Entomologia e Acarologia; Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ); Universidade de São Paulo (USP); Piracicaba; São Paulo; Brazil.
| | - Arthuro DE Castro Stolf Giacomelli
- Departamento de Entomologia e Acarologia; Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ); Universidade de São Paulo (USP); Piracicaba; São Paulo; Brazil.
| | - José L Fernández-Triana
- Canadian National Collection of Insects; Arachnids and Nematodes; 960 Carling Ave.; Ottawa; ON K1A 0C6 Canada.
| | - Isabela Midori Watanabe
- Departamento de Ecologia e Biologia Evolutiva; Universidade Federal de São Carlos (UFSCar); São Carlos; São Paulo; Brazil.
| | - Eliaber Barros Santos
- Departamento de Ciências Agrárias e Ambientais; Universidade Estadual de Santa Cruz; Rodovia Jorge Amado; km 16; Bairro Salobrinho; Ilhéus; Bahia; Brazil CEP 45662-900.
| | - Jakeline Maria Dos Santos
- AgroVerde Soluções Agrícolas Ltda; Rua Rivadavia Carnauba 91 Sala 04; Pinheiro; Maceió; Alagoas; Brazil; CEP 57057-260.
| | - Wilian Xavier Fazolin
- Departamento de Entomologia e Acarologia; Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ); Universidade de São Paulo (USP); Piracicaba; São Paulo; Brazil.
| | - Angélica Maria Penteado-Dias
- Departamento de Ecologia e Biologia Evolutiva; Universidade Federal de São Carlos (UFSCAR); Rodovia Washington Luiz; Km 235; CEP 13.565-905; São Carlos; SP; Brazil.
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109
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Vandromme M, Van de Sande E, Pinceel T, Vanhove W, Trekels H, Vanschoenwinkel B. Resolving the identity and breeding habitats of cryptic dipteran cacao flower visitors in a neotropical cacao agroforestry system. Basic Appl Ecol 2023. [DOI: 10.1016/j.baae.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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110
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Ortiz AS, Rubio RM, de Freina JJ, Guerrero JJ, Garre M, Yela JL. DNA barcoding and morphology reveal European and western Asian Arctiavillica (Linnaeus, 1758) as a complex of species (Lepidoptera, Erebidae, Arctiinae). Zookeys 2023; 1159:69-86. [PMID: 37234560 PMCID: PMC10208439 DOI: 10.3897/zookeys.1159.95225] [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: 09/22/2022] [Accepted: 02/23/2023] [Indexed: 05/28/2023] Open
Abstract
Currently, the genus Arctia Schrank, 1802 includes approximately 16 species in the Palaearctic region, depending on the taxonomic interpretation. Here, populations of the Arctiavillica (Linnaeus, 1758) morphospecies complex were studied from Europe to the Middle East (Turkey, northern Iran) by molecular methods. Morphological treatment has traditionally revealed the presence of five nominal taxa: A.villica (Linnaeus, 1758), A.angelica (Boisduval, 1829), A.konewkaii (Freyer, 1831), A.marchandi de Freina, 1983, and A.confluens Romanoff, 1884. The molecular approach tests whether they represent well-delimited species. Subsequently, this study corroborates the suitability of the mitochondrial cytochrome c oxidase subunit 1 (COI) marker sequence for species delimitation. In total, 55 barcodes of the Arctiavillica complex were compared, and two molecular species delimitation algorithms were applied to reveal the potential Molecular Operational Taxonomic Units (MOTUs), namely the distance-based Barcode Index Number (BIN) System, and the hierarchical clustering algorithm based on a pairwise genetic distances approach using the Assemble Species by Automatic Partitioning (ASAP). The applied ASAP distance-based species delimitation method for the analysed dataset revealed an interspecific threshold of 2.0-3.5% K2P distance as suitable for species identification purposes of the Iberian A.angelica and the Sicilian A.konewkaii and less than 2% for the three taxa of the A.villica clade: A.villica, A.confluens, and A.marchandi. This study contributes to a better understanding of the taxonomy of the genus Arctia and challenges future revision of this genus in Turkey, the Caucasus, Transcaucasia as well as northern Iran using standard molecular markers.
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Affiliation(s)
- Antonio S. Ortiz
- Department of Zoology and Physical Anthropology, University of Murcia, Campus de Espinardo, 30100 Murcia, SpainUniversity of MurciaMurciaSpain
| | - Rosa M. Rubio
- Department of Zoology and Physical Anthropology, University of Murcia, Campus de Espinardo, 30100 Murcia, SpainUniversity of MurciaMurciaSpain
| | - Josef J. de Freina
- Eduard Schmid-Str. 10, D-81541, München, GermanyUnaffiliatedMunichGermany
| | - Juan J. Guerrero
- Department of Zoology and Physical Anthropology, University of Murcia, Campus de Espinardo, 30100 Murcia, SpainUniversity of MurciaMurciaSpain
| | - Manuel Garre
- Department of Zoology and Physical Anthropology, University of Murcia, Campus de Espinardo, 30100 Murcia, SpainUniversity of MurciaMurciaSpain
| | - José Luis Yela
- Grupo DITEG, Área de Zoología, Facultad de Ciencias Ambientales, Universidad de Castilla-La Mancha, Avda, Carlos III, s.n., Campus Real Fábrica de Armas, E-45071, Toledo, SpainUniversidad de Castilla-La ManchaToledoSpain
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111
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Giantsis IA, Tokamani M, Triantaphyllidis G, Tzatzani S, Chatzinikolaou E, Toros A, Bouchorikou A, Chatzoglou E, Miliou H, Sarantopoulou J, Gkafas GA, Exadactylos A, Sandaltzopoulos R, Apostolidis AP. Development of Multiplex PCR and Melt-Curve Analysis for the Molecular Identification of Four Species of the Mullidae Family, Available in the Market. Genes (Basel) 2023; 14:genes14050960. [PMID: 37239320 DOI: 10.3390/genes14050960] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/13/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
The authentication of food products and the verification of their identity are of major importance for consumers. Food fraud through mislabeling is an illegal practice consisting of the substitution of an expensive food product by a relatively cheaper one, misleading false labelling of their origin and adulteration in processed or frozen products. This issue is particularly of high importance concerning fish and seafood, which are easily adulterated primarily due to difficult morphological identification. Fish species of the Mullidae family are considered among the most high-valued seafood products traded in Greece and Eastern Mediterranean in general, in terms of the price and demand. Specifically, the red mullet (Mullus barbatus) and the striped red mullet (Mullus surmuletus) are both indigenous in the Aegean (FAO Division 37.3.1) and the Ionian (FAO Division 37.2.2) Seas, with high levels of consumers' preferences. However, they could be easily adulterated or misidentified by the invasive Aegean Sea Lessepsian migrator goldband goatfish (Upeneus moluccensis) as well as by the imported West African goatfish (Pseudupeneus prayensis). Keeping this in mind, we designed two novel, time-saving and easy-to-apply multiplex PCR assays and one multiple Melt-Curve analysis real-time PCR for the identification of these four species. These methodologies are based on species-specific primers targeting single nucleotide polymorphisms (SNPs) detected via sequencing analysis of the mitochondrial cytochrome C oxidase subunit I (CO1) and of the cytochrome b (CYTB) genes in newly collected individuals, with additional comparison with congeneric and conspecific haplotypes obtained from the GenBank database. Both methodologies, targeting CO1 or CYTB, utilize one common and four diagnostic primers, producing amplicons of different length that are easily and reliably separated on agarose gel electrophoresis, yielding a single clear band of diagnostic size for each species or a certain Melt-Curve profile. The applicability of this cost-effective and fast methodology was tested in 328 collected specimens, including 10 cooked samples obtained from restaurants. In the vast majority (327 out of the 328) of the specimens tested, one single band was produced, in agreement with the expected products with a single exception a M. barbatus sample that was identified as M. surmuletus, the identity of which was confirmed using sequencing, indicating erroneous morphological identification. The developed methodologies are expected to contribute to the detection of commercial fraud in fish authentication.
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Affiliation(s)
- Ioannis A Giantsis
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100 Florina, Greece
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
- Laboratory of Fish & Fisheries, Department of Animal Production, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Maria Tokamani
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - George Triantaphyllidis
- Laboratory of Applied Hydrobiology, School of Animal Biosciences, Agricultural University of Athens, 11855 Athens, Greece
| | - Stella Tzatzani
- Laboratory of Fish & Fisheries, Department of Animal Production, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Emmanuella Chatzinikolaou
- Laboratory of Fish & Fisheries, Department of Animal Production, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Athanasios Toros
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Anastasia Bouchorikou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Evanthia Chatzoglou
- Laboratory of Applied Hydrobiology, School of Animal Biosciences, Agricultural University of Athens, 11855 Athens, Greece
| | - Helen Miliou
- Laboratory of Applied Hydrobiology, School of Animal Biosciences, Agricultural University of Athens, 11855 Athens, Greece
| | - Joanne Sarantopoulou
- Hydrobiology-Ichthyology Lab, Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
| | - Georgios A Gkafas
- Hydrobiology-Ichthyology Lab, Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
| | - Athanasios Exadactylos
- Hydrobiology-Ichthyology Lab, Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
| | - Raphael Sandaltzopoulos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Apostolos P Apostolidis
- Laboratory of Fish & Fisheries, Department of Animal Production, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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Anđelić Dmitrović B, Ivanković Tatalović L, Kos T, Crnčan P, Gajski D, Jelić M, Šerić Jelaska L. Mediterranean vineyards and olive groves in Croatia harbour some rare and endemic invertebrates. Biodivers Data J 2023; 11:e100963. [PMID: 38333190 PMCID: PMC10850877 DOI: 10.3897/bdj.11.e100963] [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: 01/24/2023] [Accepted: 03/05/2023] [Indexed: 02/10/2024] Open
Abstract
The Mediterranean is characterised by high biodiversity and numerous endemic species. These species are not only present in natural habitats, but also inhabit areas under human influence, such as agricultural lands. In the biodiversity assessment of Mediterranean vineyards and olive orchards within Zadar County, in Croatia, we identified eight endemic species with Mediterranean distribution, six with a Balkan Peninsula distribution, four with Dinaric Alps distribution and three species rare and endangered in Europe. Alongside these species, we have recorded five new species for Croatian fauna, many of those identified by combining morphological characteristics and the DNA barcoding tool. Araneae and Coleoptera contributed the highest number of endemic species and groups with new record were the following: Coleoptera, Diptera and Araneae. Compared to other sites, an olive orchard with ecological pest management (EPM), surrounded by natural ecosystems, had the highest ratio of endemic and rare species. Our findings emphasise that agricultural lands in the Mediterranean can be habitats for endemic and rare species and that future biodiversity research of these habitats is highly important, to monitor potential biodiversity changes and motivate future species and ecosystem conservation.
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Affiliation(s)
- Barbara Anđelić Dmitrović
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, Zagreb, CroatiaDepartment of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6ZagrebCroatia
| | - Lara Ivanković Tatalović
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, Zagreb, CroatiaDepartment of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6ZagrebCroatia
| | - Tomislav Kos
- Department for Ecology, Agronomy and Aquaculture, University of Zadar, Trg kneza Višeslava, Zadar, CroatiaDepartment for Ecology, Agronomy and Aquaculture, University of Zadar, Trg kneza VišeslavaZadarCroatia
| | - Petar Crnčan
- Croatian Natural History Museum, Demetrova 1, Zagreb, CroatiaCroatian Natural History Museum, Demetrova 1ZagrebCroatia
| | - Domagoj Gajski
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech RepublicDepartment of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2BrnoCzech Republic
| | - Mišel Jelić
- Varaždin City Museum, Šetalište Josipa Jurja Strossmayera 3, Varaždin, CroatiaVaraždin City Museum, Šetalište Josipa Jurja Strossmayera 3VaraždinCroatia
| | - Lucija Šerić Jelaska
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, Zagreb, CroatiaDepartment of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6ZagrebCroatia
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Cock MJW, Laguerre M, Buddie AG, Cafa G, Alston-Smith S, Morrall J, Gosula VS. Using DNA barcodes to test the association of sexes and morphs in Calodesma spp. (Lepidoptera, Erebidae, Arctiinae, Arctiini, Pericopina) of Trinidad, West Indies, with an overview of the genus, taxonomic changes and a new species. Zootaxa 2023; 5270:231-261. [PMID: 37518166 DOI: 10.11646/zootaxa.5270.2.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Indexed: 08/01/2023]
Abstract
Phalaena militta Stoll, [1781], currently in the combination Thyrgis militta, is transferred to the new combination Calodesma militta. Phalaena militta is the type species of Thyrgis Walker, 1854, and so Thyrgis is a junior synonym of Calodesma Hübner, [1820]. The reinstated genus Seileria Dognin, 1923 is the next available name for the genus previously known as Thyrgis, and the remaining eight species and their subspecies currently in Thyrgis are transferred to new combinations as species of Seileria: S. angustifascia (Hering, 1925), S. basipunctata (Hering, 1926), S. constrictifascia (Dognin, 1919), S. flavonigra (Dognin, 1910), S. investigatorum (Toulgoët, 1988), S. marginata (Butler, 1875), S. meres (Druce, 1911), S. phlegon (Druce, 1885), S. phlegon ruscia (Druce, 1895), S. tenuifascia (Hering, 1930) and S. tenuifascia daguana (Hering, 1930). Eucyanoides Toulgoët, 1988, currently a synonym of Thyrgis, is made a new subjective synonym of Seileria. Based on DNA barcodes, we recognise three very similar, sexually dimorphic and in two cases polymorphic South American species of Calodesma with some phenotypes in common but very similar male genitalia: C. militta (BOLD:AAK1660), C. sp. cf. collaris (BOLD:ABZ2392) and C. pseudocollaris Cock new species (BOLD:AEI2170). Calodesma militta is widespread in South America, with two male morphs (collaris and dioptis) and two female morphs with variable markings (white and orange morphs). Centronia plorator Kaye, [1923] and Thyrgis lacryma Dognin, 1919 are variants of the white female morph and are new synonyms of Calodesma militta. A third female morph with red markings was not sequenced and could not be allocated to a species. Calodesma sp. cf. collaris (BOLD:ABZ2392) occurs in southern South America with both male morphs but only a white female morph. Calodesma pseudocollaris new species (BOLD:AEI2170) is only known from Trinidad, with one male morph (collaris) and the white female morph. Although more than ten morphs relating to this complex have been described as species, they cannot be synonymised without more data on distribution of the different species or DNA barcodes from the type specimens. Collated life history information indicates species of this group are split between Malpighiaceae feeders and Bromeliaceae feeders, but more work is needed to define these differences. The morphism patterns observed are discussed in terms of Müllerian mimicry and mimicry rings, and we suggest that in Trinidad (and elsewhere) there is a loose mimicry ring of diurnal black species with white spots or transparent patches on the wings which are most conspicuous and frequently observed when feeding on white Asteraceae flowers.
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Affiliation(s)
| | | | | | - Giovanni Cafa
- Eurofins County Pathology Ltd.; 8 Huxley Road; Guildford; Surrey GU2 7RE; UK.
| | | | - John Morrall
- Upper Schoolfields; Blithbury Road; Hamstall Ridware; WS15 3RR; UK.
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BROWN JOHNW, AARVIK LEIF, TIMM ALICIA. Gibbalaria : A new genus of Olethreutini from the Afrotropical Region (Lepidoptera: Tortricidae: Olethreutinae), and a new combination in Cosmopoda Diakonoff. Zootaxa 2023; 5263:217-239. [PMID: 37044989 DOI: 10.11646/zootaxa.5263.2.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Indexed: 04/07/2023]
Abstract
Gibbalaria Brown and Aarvik, new genus, is described to accommodate the following species: G. divergana Brown and Aarvik, new species (TL: South Africa); G. occidentana Brown and Aarvik, new species (TL: South Africa); G. chiloanei Brown and Aarvik, new species (TL: South Africa); G. scabellana Zeller, 1852, new combination (TL: South Africa); G. mabalingwae Razowski, 2008, status revised, new combination (TL: South Africa); G. longiphallus Brown and Aarvik, new species (TL: South Africa); G. bagamoyo (Razowski & Wojtusiak, 2014), new combination (TL: Tanzania); and G. analcis (Razowski, 2015), new combination (TL: Republic of Cameroon). Gibbalaria sistrata (Meyrick, 1911), new combination (TL: South Africa), is synonymized with G. scabellana, new synonymy. Although the male genitalia of Gibbalaria form two moderately divergent groups, the two groups share extremely similar female genitalia, which feature a broad, somewhat cylindrical antrum, followed immediately anterad by a conspicuously elbowed region of the ductus bursae forming a weak diverticulum on the left side, and a signum in the form of a patch of small arrowhead-shaped sclerites, usually with a shallow pocket. Male genitalia morphology shows many similarities with the Neopotamia group (Olethreutini), Afroploce Aarvik in particular. The monophyly of Gibbalaria is supported by the raised, curled, opalescent scales on the forewing in both sexes, which occurs in a few other genera scattered through the subfamily (e.g., Thylacandra Diakonoff in Grapholitini; Astronauta Diakonoff and Cosmopoda Diakonoff in Olethreutini); the angled diverticulum in the ductus bursae in the female genitalia; the subrectangular flange from the lower margin of the valva immediately basal to the cucullus; and the setose, protruding ridge immediate above the basal cavity, which appears to be homologous with the subbasal process of the valva in many members of the Neopotamia group of genera. In addition, Diakonoffiana graziani Razowski, 2015 (TL: Republic of Cameroon) is transferred to Cosmopoda Diakonoff, resulting in C. graziani (Razowski), new combination.
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Korshunova T, Grøtan VV, Johnson KB, Bakken T, Picton BE, Martynov A. Similar Ones Are Not Related and Vice Versa—New Dendronotus Taxa (Nudibranchia: Dendronotidae) from the North Atlantic Ocean Provide a Platform for Discussion of Global Marine Biodiversity Patterns. DIVERSITY 2023. [DOI: 10.3390/d15040504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
One new species of the genus Dendronotus (Nudibranchia: Dendronotidae) is described from Norway and Northern Ireland, as well as from the adjacent North Sea, and one new subspecies of Dendronotus arcticus is described from Norway by applying a combination of fine-scale morphological and molecular phylogenetic data. The present case demonstrates multilevel morphological and molecular similarities and differences considering on the one hand a grouping of three similar looking sympatric taxa (D. yrjargul, D. arcticus gartensis n. subsp. and D. keatleyae n. sp.), and on the other hand two different looking apparently allopatric subspecies (D. arcticus arcticus and D. arcticus gartensis n. subsp.). The type species of the genus, D. frondosus, which is the commonest dendronotid in Norway and the United Kingdom, consistently demonstrates substantial molecular and fine-scale morphological differences from D. keatleyae n. sp. The present study, apart from providing purely taxonomic information, also provides new data for a broad discussion of global biodiversity patterns.
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Affiliation(s)
| | | | | | - Torkild Bakken
- NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Bernard E. Picton
- National Museums Northern Ireland, Holywood BT18 0EU, UK
- Marine Laboratory, Queen’s University Belfast, Belfast BT22 1PF, Northern Ireland, UK
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Carrington-Hoekstra P, Fernandez-Triana J, Dyer LA, Whitfield J. Larissimusnigricans sp. nov. (Hymenoptera, Braconidae), a new reared species of a rare neotropical genus recovered through biodiversity inventory in Ecuador. Zookeys 2023; 1156:15-24. [PMID: 37214269 PMCID: PMC10193278 DOI: 10.3897/zookeys.1156.101396] [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: 02/02/2023] [Accepted: 03/05/2023] [Indexed: 05/24/2023] Open
Abstract
A new species of the rarely collected neotropical microgastrine braconid wasp genus Larissimus Nixon, represented previously by only a single described species, L.cassander Nixon, was recovered by the Caterpillars and Parasitoids of the Eastern Andes in Ecuador inventory project. Larissimusnigricanssp. nov. was reared from an unidentified species of arctiine Erebidae feeding on the common bamboo species Chusqueascandens Kunth at the Yanayacu Biological Station near Cosanga, Napo Province, Ecuador. The new species is described and diagnosed from L.cassander using both morphological and DNA barcode data.
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Affiliation(s)
| | | | - Lee A. Dyer
- Department of Biology, University of Nevada, Reno, NV 89557 USA
| | - James Whitfield
- School of Integrative Biology, University of Illinois, Urbana, IL 61801 USA
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McLaughlin JF, Aguilar C, Bernstein JM, Navia-Gine WG, Cueto-Aparicio LE, Alarcon AC, Alarcon BD, Collier R, Takyar A, Vong SJ, López-Chong OG, Driver R, Loaiza JR, De León LF, Saltonstall K, Lipshutz SE, Arcila D, Brock KM, Miller MJ. Comparative phylogeography reveals widespread cryptic diversity driven by ecology in Panamanian birds. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023. [PMID: 36993716 DOI: 10.1101/2023.01.26.525769] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
UNLABELLED Widespread species often harbor unrecognized genetic diversity, and investigating the factors associated with such cryptic variation can help us better understand the forces driving diversification. Here, we identify potential cryptic species based on a comprehensive dataset of COI mitochondrial DNA barcodes from 2,333 individual Panamanian birds across 429 species, representing 391 (59%) of the 659 resident landbird species of the country, as well as opportunistically sampled waterbirds. We complement this dataset with additional publicly available mitochondrial loci, such as ND2 and cytochrome b, obtained from whole mitochondrial genomes from 20 taxa. Using barcode identification numbers (BINs), we find putative cryptic species in 19% of landbird species, highlighting hidden diversity in the relatively well-described avifauna of Panama. Whereas some of these mitochondrial divergence events corresponded with recognized geographic features that likely isolated populations, such as the Cordillera Central highlands, the majority (74%) of lowland splits were between eastern and western populations. The timing of these splits are not temporally coincident across taxa, suggesting that historical events, such as the formation of the Isthmus of Panama and Pleistocene climatic cycles, were not the primary drivers of cryptic diversification. Rather, we observed that forest species, understory species, insectivores, and strongly territorial species-all traits associated with lower dispersal ability-were all more likely to have multiple BINs in Panama, suggesting strong ecological associations with cryptic divergence. Additionally, hand-wing index, a proxy for dispersal capability, was significantly lower in species with multiple BINs, indicating that dispersal ability plays an important role in generating diversity in Neotropical birds. Together, these results underscore the need for evolutionary studies of tropical bird communities to consider ecological factors along with geographic explanations, and that even in areas with well-known avifauna, avian diversity may be substantially underestimated. LAY SUMMARY - What factors are common among bird species with cryptic diversity in Panama? What role do geography, ecology, phylogeographic history, and other factors play in generating bird diversity?- 19% of widely-sampled bird species form two or more distinct DNA barcode clades, suggesting widespread unrecognized diversity.- Traits associated with reduced dispersal ability, such as use of forest understory, high territoriality, low hand-wing index, and insectivory, were more common in taxa with cryptic diversity. Filogeografía comparada revela amplia diversidad críptica causada por la ecología en las aves de Panamá. RESUMEN Especies extendidas frecuentemente tiene diversidad genética no reconocida, y investigando los factores asociados con esta variación críptica puede ayudarnos a entender las fuerzas que impulsan la diversificación. Aquí, identificamos especies crípticas potenciales basadas en un conjunto de datos de códigos de barras de ADN mitocondrial de 2,333 individuos de aves de Panama en 429 especies, representando 391 (59%) de las 659 especies de aves terrestres residentes del país, además de algunas aves acuáticas muestreada de manera oportunista. Adicionalmente, complementamos estos datos con secuencias mitocondriales disponibles públicamente de otros loci, tal como ND2 o citocroma b, obtenidos de los genomas mitocondriales completos de 20 taxones. Utilizando los números de identificación de código de barras (en ingles: BINs), un sistema taxonómico numérico que proporcina una estimación imparcial de la diversidad potencial a nivel de especie, encontramos especies crípticas putativas en 19% de las especies de aves terrestres, lo que destaca la diversidad oculta en la avifauna bien descrita de Panamá. Aunque algunos de estos eventos de divergencia conciden con características geográficas que probablemente aislaron las poblaciones, la mayoría (74%) de la divergencia en las tierras bajas se encuentra entre las poblaciones orientales y occidentales. El tiempo de esta divergencia no coincidió entre los taxones, sugiriendo que eventos históricos tales como la formación del Istmo de Panamá y los ciclos climáticos del pleistoceno, no fueron los principales impulsores de la especiación. En cambio, observamos asociaciones fuertes entre las características ecológicas y la divergencia mitocondriale: las especies del bosque, sotobosque, con una dieta insectívora, y con territorialidad fuerte mostraton múltiple BINs probables. Adicionalmente, el índice mano-ala, que está asociado a la capacidad de dispersión, fue significativamente menor en las especies con BINs multiples, sugiriendo que la capacidad de dispersión tiene un rol importamente en la generación de la diversidad de las aves neotropicales. Estos resultos demonstran la necesidad de que estudios evolutivos de las comunidades de aves tropicales consideren los factores ecológicos en conjunto con las explicaciones geográficos. Palabras clave: biodiversidad tropical, biogeografía, códigos de barras, dispersión, especies crípticas.
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McLaughlin JF, Aguilar C, Bernstein JM, Navia-Gine WG, Cueto-Aparicio LE, Alarcon AC, Alarcon BD, Collier R, Takyar A, Vong SJ, López-Chong OG, Driver R, Loaiza JR, De León LF, Saltonstall K, Lipshutz SE, Arcila D, Brock KM, Miller MJ. Comparative phylogeography reveals widespread cryptic diversity driven by ecology in Panamanian birds. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.530646. [PMID: 36993716 PMCID: PMC10055050 DOI: 10.1101/2023.03.15.530646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Widespread species often harbor unrecognized genetic diversity, and investigating the factors associated with such cryptic variation can help us better understand the forces driving diversification. Here, we identify potential cryptic species based on a comprehensive dataset of COI mitochondrial DNA barcodes from 2,333 individual Panamanian birds across 429 species, representing 391 (59%) of the 659 resident landbird species of the country, as well as opportunistically sampled waterbirds. We complement this dataset with additional publicly available mitochondrial loci, such as ND2 and cytochrome b, obtained from whole mitochondrial genomes from 20 taxa. Using barcode identification numbers (BINs), we find putative cryptic species in 19% of landbird species, highlighting hidden diversity in the relatively well-described avifauna of Panama. Whereas some of these mitochondrial divergence events corresponded with recognized geographic features that likely isolated populations, such as the Cordillera Central highlands, the majority (74%) of lowland splits were between eastern and western populations. The timing of these splits are not temporally coincident across taxa, suggesting that historical events, such as the formation of the Isthmus of Panama and Pleistocene climatic cycles, were not the primary drivers of cryptic diversification. Rather, we observed that forest species, understory species, insectivores, and strongly territorial species-all traits associated with lower dispersal ability-were all more likely to have multiple BINs in Panama, suggesting strong ecological associations with cryptic divergence. Additionally, hand-wing index, a proxy for dispersal capability, was significantly lower in species with multiple BINs, indicating that dispersal ability plays an important role in generating diversity in Neotropical birds. Together, these results underscore the need for evolutionary studies of tropical bird communities to consider ecological factors along with geographic explanations, and that even in areas with well-known avifauna, avian diversity may be substantially underestimated.
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Affiliation(s)
- J. F. McLaughlin
- Department of Biology, University of Oklahoma, Norman, OK, USA
- Sam Noble Oklahoma Museum of Natural History Norman, OK, USA
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA
| | - Celestino Aguilar
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama
| | - Justin M. Bernstein
- Department of Biology, Villanova University, Villanova, PA, USA
- Center for Genomics, University of Kansas, Lawrence, KS, USA
| | - Wayra G. Navia-Gine
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
- Pacific Biosciences, 1305 O’Brien Dr, Menlo Park, CA, USA
| | | | | | | | - Rugger Collier
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Anshule Takyar
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Sidney J. Vong
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | | | - Robert Driver
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Jose R. Loaiza
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama
| | - Luis F. De León
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | | | | | - Dahiana Arcila
- Department of Biology, University of Oklahoma, Norman, OK, USA
- Sam Noble Oklahoma Museum of Natural History Norman, OK, USA
| | - Kinsey M. Brock
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, USA
| | - Matthew J. Miller
- Department of Biology, University of Oklahoma, Norman, OK, USA
- Sam Noble Oklahoma Museum of Natural History Norman, OK, USA
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
- Reneco International Wildlife Consultants, Abu Dhabi, UAE
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Liu WB, Wang Y, Zhao KZ, Wang CY, Zhang JY, Yan CC, Lin XL. New species, a new combination, and DNA barcodes of Parachironomus Lenz, 1921 (Diptera, Chironomidae). Zookeys 2023; 1153:121-140. [DOI: 10.3897/zookeys.1153.98542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
The genus Parachironomus has a cosmopolitan distribution including 85 valid described species worldwide. Species records and studies of the genus in the Tibetan Plateau are scarce. In this study, the genus Parachironomus from China is revised and two new species, Parachironomus wangi Liu & Lin, sp. nov. and Parachironomus nankaiensis Liu & Lin, sp. nov., are described based on adult morphology and molecular data. Paracladopelma demissum Yan, Wang & Bu is placed in the genus Parachironomus as a new combination. A neighbor-joining tree was reconstructed based on all known ParachironomusCOI DNA barcodes. A key to adult males of the genus Parachironomus from China is also provided.
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PCR-Based Method for Authentication of Meat and Processed Meat from Three Commercially Important Catfish Species. FOOD ANAL METHOD 2023. [DOI: 10.1007/s12161-023-02475-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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Csabai Z, Čiamporová-Zaťovičová Z, Boda P, Čiampor F. 50%, not great, not terrible: Pan-European gap-analysis shows the real status of the DNA barcode reference libraries in two aquatic invertebrate groups and points the way ahead. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160922. [PMID: 36539085 DOI: 10.1016/j.scitotenv.2022.160922] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
The essential key to routine molecular species identification (DNA barcoding/metabarcoding) is the existence of an error-free DNA barcode reference library providing full coverage of all species. Published studies generally state the need to produce more barcodes, and control their quality, but unfortunately, the number of barcoded species is still low. However, to initiate real progress, we need to know where the gaps lie, how big they are and why they persist. Our aims were to draw and understand the current state of knowledge regarding species diversity, distribution, and barcode coverage, and offer solutions for improvement. In this study, we used two groups of aquatic insects, beetles and true bugs. We have compiled and critically evaluated an essentially complete and up-to-date European list, containing 1527 species. The list served as a basis for the barcode gap analyses in the Barcode-of-Life-Data-System (BOLD) conducted in three subsequent years (2020-2022). The overall barcode coverage of the pan-European fauna was around 50 % in both groups. The lowest coverage was in the Mediterranean, the Balkans and South-eastern Europe. The coverage in each country depended significantly on the local diversity, the number of rare, endemic species and the similarity of its fauna to that of the most active barcoding European countries. Gap analyses showed a very small increase in species coverage (<1 % in European aquatic beetles) despite an ~25 % increase in the number of barcodes. Hence, it is clear that future barcoding campaigns must prioritise quality over quantity. To visibly improve reference libraries, we need to increase the involvement of taxonomic experts and focus on targeted studies and underexplored but biodiversity-rich areas.
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Affiliation(s)
- Zoltán Csabai
- University of Pécs, Faculty of Sciences, Department of Hydrobiology, Ifjúság útja 6, H7624 Pécs, Hungary; Masaryk University, Faculty of Sciences, Department of Zoology and Botany, Kotlářská 2, 62500 Brno, Czech Republic; Balaton Limnological Research Institute, Klebelsberg Kuno utca 3, 8237 Tihany, Hungary.
| | - Zuzana Čiamporová-Zaťovičová
- Slovak Academy of Sciences, Plant Science and Biodiversity Centre, Department of Biodiversity and Ecology, Dúbravská cesta 9, 84523 Bratislava, Slovakia; Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia.
| | - Pál Boda
- Centre for Ecological Research, Institute of Aquatic Ecology, Bem tér 18/c, H4026 Debrecen, Hungary.
| | - Fedor Čiampor
- Slovak Academy of Sciences, Plant Science and Biodiversity Centre, Department of Biodiversity and Ecology, Dúbravská cesta 9, 84523 Bratislava, Slovakia.
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Ouyang X, Fan Q, Chen A, Huang J. Effects of trunk injection with emamectin benzoate on arthropod diversity. PEST MANAGEMENT SCIENCE 2023; 79:935-946. [PMID: 36309931 DOI: 10.1002/ps.7264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 10/20/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Pine wood nematode is a major plant quarantine object in the world. Trunk injection is an effective method for controlling pests that cause disease. To evaluate the ecological safety of trunk injection with emamectin benzoates in forests of Pinus massoniana, the community diversity and community composition of soil arthropods and flying insects (Hymenoptera) were studied at different stages of trunk injection. RESULTS The dominant taxonomic groups of soil arthropods were Collembola (30.80%), Insecta (26.42%), and Arachnida (23.84%). The taxonomic groups of flying insects (Hymenoptera) were Ichneumonidae (48.94%), Formicidae (14.10%), and Braconidae (8.44%). Trunk injection with emamectin benzoate has no significant effect on the community diversity indices of total soil arthropods and flying insects (Hymenoptera). However, it has a significant effect on the community diversity indices of detritivores for soil arthropods. It changed the community composition of soil arthropods but did not impact the community composition of flying insects (Hymenoptera). Redundancy analysis of arthropod community structure and environmental variables showed that total potassium, residual of green leaf, and residual of litter leaf have a significant impact on the community structure of soil arthropods, and total phosphorus, total nitrogen, water content, organic matter, and total potassium have a significant impact on the community structure of flying insects (Hymenoptera). CONCLUSION Trunk injection with emamectin benzoate is safe for the ecological environment. This study provides a new insight into the field for the prevention and control of pine wood nematode disease, which is of great significance to forest management and pest control. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Xianheng Ouyang
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Qingbin Fan
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Anliang Chen
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Junhao Huang
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
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Tobisch C, Rojas-Botero S, Uhler J, Müller J, Kollmann J, Moning C, Brändle M, Gossner MM, Redlich S, Zhang J, Steffan-Dewenter I, Benjamin C, Englmeier J, Fricke U, Ganuza C, Haensel M, Riebl R, Uphus L, Ewald J. Plant species composition and local habitat conditions as primary determinants of terrestrial arthropod assemblages. Oecologia 2023; 201:813-825. [PMID: 36869183 PMCID: PMC10038969 DOI: 10.1007/s00442-023-05345-6] [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: 01/26/2022] [Accepted: 02/22/2023] [Indexed: 03/05/2023]
Abstract
Arthropods respond to vegetation in multiple ways since plants provide habitat and food resources and indicate local abiotic conditions. However, the relative importance of these factors for arthropod assemblages is less well understood. We aimed to disentangle the effects of plant species composition and environmental drivers on arthropod taxonomic composition and to assess which aspects of vegetation contribute to the relationships between plant and arthropod assemblages. In a multi-scale field study in Southern Germany, we sampled vascular plants and terrestrial arthropods in typical habitats of temperate landscapes. We compared independent and shared effects of vegetation and abiotic predictors on arthropod composition distinguishing between four large orders (Lepidoptera, Coleoptera, Hymenoptera, Diptera), and five functional groups (herbivores, pollinators, predators, parasitoids, detritivores). Across all investigated groups, plant species composition explained the major fraction of variation in arthropod composition, while land-cover composition was another important predictor. Moreover, the local habitat conditions depicted by the indicator values of the plant communities were more important for arthropod composition than trophic relationships between certain plant and arthropod species. Among trophic groups, predators showed the strongest response to plant species composition, while responses of herbivores and pollinators were stronger than those of parasitoids and detritivores. Our results highlight the relevance of plant community composition for terrestrial arthropod assemblages across multiple taxa and trophic levels and emphasize the value of plants as a proxy for characterizing habitat conditions that are hardly accessible to direct environmental measurements.
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Affiliation(s)
- Cynthia Tobisch
- Institute of Ecology and Landscape, Weihenstephan-Triesdorf University of Applied Sciences, Freising, Germany.
- Chair of Restoration Ecology, School of Life Sciences, Technical University of Munich, Freising, Germany.
| | - Sandra Rojas-Botero
- Chair of Restoration Ecology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Johannes Uhler
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Jörg Müller
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Julius-Maximilians-University Würzburg, Würzburg, Germany
- Bavarian Forest National Park, Grafenau, Germany
| | - Johannes Kollmann
- Chair of Restoration Ecology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Christoph Moning
- Institute of Ecology and Landscape, Weihenstephan-Triesdorf University of Applied Sciences, Freising, Germany
| | - Martin Brändle
- Division of Animal Ecology, Department of Ecology, Philipps-Universität Marburg, Marburg, Germany
| | - Martin M Gossner
- Forest Entomology, Swiss Federal Institute for Forest, Snow, and Landscape Research WSL, Birmensdorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zürich, Switzerland
| | - Sarah Redlich
- Department of Animal Ecology and Tropical Biology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Jie Zhang
- Department of Animal Ecology and Tropical Biology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Ingolf Steffan-Dewenter
- Department of Animal Ecology and Tropical Biology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Caryl Benjamin
- Ecoclimatology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Jana Englmeier
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Ute Fricke
- Department of Animal Ecology and Tropical Biology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Cristina Ganuza
- Department of Animal Ecology and Tropical Biology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Maria Haensel
- Professorship of Ecological Services, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Rebekka Riebl
- Professorship of Ecological Services, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Lars Uphus
- Ecoclimatology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Jörg Ewald
- Institute of Ecology and Landscape, Weihenstephan-Triesdorf University of Applied Sciences, Freising, Germany
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Song C, Wang L, Lei T, Qi X. New Color-Patterned Species of Microtendipes Kieffer, 1913 (Diptera: Chironomidae) and a Deep Intraspecific Divergence of Species by DNA Barcodes. INSECTS 2023; 14:227. [PMID: 36975912 PMCID: PMC10054112 DOI: 10.3390/insects14030227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
The genus Microtendipes Kieffer (Diptera: Chironomidae) has a nearly worldwide distribution, comprising more than 60 species, which are further divided into two species groups based on larval stage. However, species delimitation and identification among the adults of this genus are controversial and uncertain. For instance, previous studies have provided many synonymies based on conspecific color pattern variations in Microtendipes species. Here, we used DNA barcode data to address Microtendipes species delimitation as well as to test whether color pattern variations can be diagnostic characters for interspecific identification. The 151 DNA barcodes used, 51 of which were contributed by our laboratory, represent 21 morphospecies. Species with specific color patterns could be accurately separated based on DNA barcodes. Consequently, the color patterns of adult males could be important diagnostic characters. The average intraspecific and interspecific sequence divergences were 2.8% and 12.5%, respectively, and several species exhibited deep intraspecific divergences higher than 5%. Molecular operational taxonomic units (OTUs) ranged from 21 to 73, based on methods including phylogenetic trees, the assemble species by automatic partitioning method, the Poisson tree process (PTP), and the general mixed Yule-coalescent (GMYC) method. As a result of these analyses, five new species were recognized (M. baishanzuensis sp. nov., M. bimaculatus sp. nov., M. nigrithorax sp. nov., M. robustus sp. nov., and M. wuyiensis sp. nov.).
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Affiliation(s)
- Chao Song
- College of Life Sciences, Taizhou University, Taizhou 318000, China
- Institute of Soil and Waste Treatment and Biodiversity Protection, Taizhou University, Taizhou 318000, China
| | - Le Wang
- Nanjing Institute of Environmental Sciences under Ministry of Ecology and Environment of China, Nanjing 210042, China
| | - Teng Lei
- College of Life Sciences, Taizhou University, Taizhou 318000, China
- Institute of Soil and Waste Treatment and Biodiversity Protection, Taizhou University, Taizhou 318000, China
| | - Xin Qi
- College of Life Sciences, Taizhou University, Taizhou 318000, China
- Institute of Soil and Waste Treatment and Biodiversity Protection, Taizhou University, Taizhou 318000, China
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González C, Ballesteros-Mejia L, Díaz-Díaz J, Toro-Vargas DM, Amarillo-Suarez AR, Gey D, León C, Tovar E, Arias M, Rivera N, Buitrago LS, Pinto-Moraes RH, Sano Martins IS, Decaëns T, González MA, Kitching IJ, Rougerie R. Deadly and venomous Lonomia caterpillars are more than the two usual suspects. PLoS Negl Trop Dis 2023; 17:e0011063. [PMID: 36821543 PMCID: PMC9949635 DOI: 10.1371/journal.pntd.0011063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/28/2022] [Indexed: 02/24/2023] Open
Abstract
Caterpillars of the Neotropical genus Lonomia (Lepidoptera: Saturniidae) are responsible for some fatal envenomation of humans in South America inducing hemostatic disturbances in patients upon skin contact with the caterpillars' spines. Currently, only two species have been reported to cause hemorrhagic syndromes in humans: Lonomia achelous and Lonomia obliqua. However, species identifications have remained largely unchallenged despite improved knowledge of venom diversity and growing evidence that the taxonomy used over past decades misrepresents and underestimates species diversity. Here, we revisit the taxonomic diversity and distribution of Lonomia species using the most extensive dataset assembled to date, combining DNA barcodes, morphological comparisons, and geographical information. Considering new evidence for seven undescribed species as well as three newly proposed nomenclatural changes, our integrative approach leads to the recognition of 60 species, of which seven are known or strongly suspected to cause severe envenomation in humans. From a newly compiled synthesis of epidemiological data, we also examine the consequences of our results for understanding Lonomia envenomation risks and call for further investigations of other species' venom activities. This is required and necessary to improve alertness in areas at risk, and to define adequate treatment strategies for envenomed patients, including performing species identification and assessing the efficacy of anti-Lonomia serums against a broader diversity of species.
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Affiliation(s)
- Camila González
- Centro de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Facultad de Ciencias, Universidad de los Andes, Bogotá, Colombia, Bogotá, Colombia
- * E-mail: ;
| | - Liliana Ballesteros-Mejia
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, EPHE, Sorbonne Université, Université des Antilles, Paris, France
- CESAB, Centre de synthèse et d’Analyse sur la Biodiversité, Montpellier, France
| | - Juana Díaz-Díaz
- Centro de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Facultad de Ciencias, Universidad de los Andes, Bogotá, Colombia, Bogotá, Colombia
| | - Diana M. Toro-Vargas
- Centro de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Facultad de Ciencias, Universidad de los Andes, Bogotá, Colombia, Bogotá, Colombia
| | | | - Delphine Gey
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, EPHE, Sorbonne Université, Université des Antilles, Paris, France
| | - Cielo León
- Centro de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Facultad de Ciencias, Universidad de los Andes, Bogotá, Colombia, Bogotá, Colombia
| | - Eduardo Tovar
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogotá, Colombia
| | - Mónica Arias
- CIRAD, UMR PHIM, Montpellier, France
- PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Nazario Rivera
- Secretaría de Salud de Casanare. Area de Salud Pública, Yopal, Colombia
| | | | | | | | - Thibaud Decaëns
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Mailyn A. González
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogotá, Colombia
| | | | - Rodolphe Rougerie
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, EPHE, Sorbonne Université, Université des Antilles, Paris, France
- * E-mail: ;
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Bourret A, Nozères C, Parent E, Parent GJ. Maximizing the reliability and the number of species assignments in metabarcoding studies using a curated regional library and a public repository. METABARCODING AND METAGENOMICS 2023. [DOI: 10.3897/mbmg.7.98539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Biodiversity assessments relying on DNA have increased rapidly over the last decade. However, the reliability of taxonomic assignments in metabarcoding studies is variable and affected by the reference databases and the assignment methods used. Species level assignments are usually considered as reliable using regional libraries but unreliable using public repositories. In this study, we aimed to test this assumption for metazoan species detected in the Gulf of St. Lawrence in the Northwest Atlantic. We first created a regional library (GSL-rl) by data mining COI barcode sequences from BOLD, and included a reliability ranking system for species assignments. We then estimated 1) the accuracy and precision of the public repository NCBI-nt for species assignments using sequences from the regional library and 2) compared the detection and reliability of species assignments of a metabarcoding dataset using either NCBI-nt or the regional library and popular assignment methods. With NCBI-nt and sequences from the regional library, the BLAST-LCA (least common ancestor) method was the most precise method for species assignments, but the accuracy was higher with the BLAST-TopHit method (>80% over all taxa, between 70% and 90% amongst taxonomic groups). With the metabarcoding dataset, the reliability of species assignments was greater using GSL-rl compared to NCBI-nt. However, we also observed that the total number of reliable species assignments could be maximized using both GSL-rl and NCBI-nt with different optimized assignment methods. The use of a two-step approach for species assignments, i.e., using a regional library and a public repository, could improve the reliability and the number of detected species in metabarcoding studies.
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DNA Barcode Library of Megadiverse Lepidoptera in an Alpine Nature Park (Italy) Reveals Unexpected Species Diversity. DIVERSITY 2023. [DOI: 10.3390/d15020214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Species inventories are a prerequisite for biodiversity monitoring and conservation, particularly in protected areas. However, the possibilities of a standardized survey of species diversity using DNA barcoding have so far hardly been implemented, especially in species-rich groups. A first-time molecular-based and nearly complete inventory of the megadiverse insect order Lepidoptera in a protected area in the Alps (Cottian Alps, Italy) was intended to test the possibilities and reliability of DNA-based identifications. From voucher material collected between 2019 and 2022, we successfully sequenced 1213 morphospecies that grouped into 1204 BINs (barcode index numbers), whereas DNA barcoding failed for another 18 species. A total of 35 species shared a BIN with one or more taxa, but a majority of 19 species could still be discriminated by divergent sequences. A total of 12 morphospecies split into two BINs. These species and a further 22 taxa with unique BINs and barcode divergences >2% to the nearest neighbor require taxonomic re-assessment. Two additional cryptic species from the study area were described recently. Finally, 16 species are newly recorded for Italy. Our study, therefore, demonstrates the importance of DNA barcoding for both faunistics and the discovery of cryptic diversity, even in apparently well-studied protected areas.
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Najera‐Cortazar LA, Keen A, Kitching T, Stokes D, Goodman SJ. Phylogenetic analyses reveal bat communities in Northwestern Mexico harbor a high diversity of novel cryptic ectoparasite species. Ecol Evol 2023; 13:e9645. [PMID: 36744076 PMCID: PMC9889969 DOI: 10.1002/ece3.9645] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 02/04/2023] Open
Abstract
Parasites are integral parts of ecosystem function and important drivers of evolutionary processes. Characterizing ectoparasite diversity is fundamental to studies of host-parasite interactions, evolution, and conservation, and also for understanding emerging disease threats for some vector borne pathogens. With more than 1400 species, bats represent the second most speciose mammalian clade, but their ectoparasite fauna are poorly known for most species. We sequenced mitochondrial Cytochrome Oxidase C subunit I and nuclear 18S ribosomal gene fragments, and used Bayesian phylogenetic analyses to characterize ectoparasite taxon identity and diversity for 17 species of parasitized bats sampled along the Baja California peninsula and in Northwestern Mexico. The sequence data revealed multiple novel lineages of bat bugs (Cimicidae), flies (Nycteribiidae and Streblidae), and ticks (Argasidae). Within families, the new linages showed more than 10% sequence divergence, which is consistent with separation at least at the species level. Both families of bat flies showed host specificity, particularly on Myotis species. We also identified new records for the Baja peninsula of one tick (Carios kelleyi), and of five Streblid bat fly species. One Nycteribiid bat fly haplotype from Pallid bat (Antrozous pallidus) hosts was found throughout the peninsula, suggesting potential long distance co-dispersal with hosts. Different bat bug and tick communities were found in the north and south of the peninsula. This study is the first systematic survey of bat ectoparasites in the Baja California peninsula, revealing novel lineages that are highly genetically differentiated from other parts of North America. For some ectoparasite species, haplotype distributions may reflect patterns of bat migration. This work is a first step in characterizing ectoparasite diversity over the Baja California peninsula, and understanding how ecological and evolutionary interactions shape bat ectoparasite communities among host species in different parts of their ranges.
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Affiliation(s)
| | - Alex Keen
- School of BiologyUniversity of LeedsLeedsUK
| | - Thomas Kitching
- School of BiologyUniversity of LeedsLeedsUK
- Present address:
Vincent Wildlife Trust, Ledbury, HerefordshireUK
| | - Drew Stokes
- San Diego Natural History MuseumSan DiegoCaliforniaUSA
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Lira NL, Tonello S, Lui RL, Traldi JB, Brandão H, Oliveira C, Blanco DR. Identifying fish eggs and larvae: from classic methodologies to DNA metabarcoding. Mol Biol Rep 2023; 50:1713-1726. [PMID: 36418775 DOI: 10.1007/s11033-022-08091-9] [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] [Received: 05/25/2022] [Accepted: 11/04/2022] [Indexed: 11/25/2022]
Abstract
Studies involving fish eggs and larvae date back to the end of the nineteenth century. Since then, studies with ichthyoplankton have proved to be an essential tool, generating information for the knowledge of the ichthyofauna and the environmental inventory. Most of these studies reveal the difficulty of obtaining a precise taxonomic identification of the collected materials, making research with ichthyoplankton extremely challenging. With the advent of molecular biology, the use of markers such as COI enabled greater taxonomic precision, helping to understand events involving ichthyofauna. Now we can observe the evolution of the molecular identification tool for ichthyoplankton via DNA barcoding, which has been increasingly used over the last few decades. From 2000 to 2010, we found six publications; from 2011 to 2021, 75 papers were published, and in 2022 four studies. Our survey also showed the accuracy of molecular identification when compared to the taxonomic identification of these. In this review, we show the state of the art of studies that used barcode and DNA metabarcoding to identify fish eggs and larvae in different environments and discuss their importance as the best practice for working with these organisms.
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Affiliation(s)
- Natália Lima Lira
- Programa de Pós-Graduação em Recursos Naturais e Sustentabilidade, Universidade Tecnológica Federal do Paraná, Prolongamento da Rua Cerejeira, S/N, Santa Helena, PR, 85892-000, Brazil.
| | - Sandro Tonello
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936, Aleixo, Manaus, AM, 69080-971, Brazil
| | - Roberto Laridondo Lui
- Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná, R. Universitária, 1619, Cascavel, PR, 85819-170, Brazil
| | - Josiane Baccarin Traldi
- Instituto de Ciências Biológicas, Departamento de Genética, Universidade Federal do Amazonas, Av. General Rodrigo Octavio, 6200, Manaus, AM, 69080-900, Brazil
| | - Heleno Brandão
- Programa de Pós-Graduação em Recursos Naturais e Sustentabilidade, Universidade Tecnológica Federal do Paraná, Prolongamento da Rua Cerejeira, S/N, Santa Helena, PR, 85892-000, Brazil
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, R. Prof. Dr. Antônio C. W. Zanin, 250, Botucatu, SP, 18618-689, Brazil
| | - Daniel Rodrigues Blanco
- Programa de Pós-Graduação em Recursos Naturais e Sustentabilidade, Universidade Tecnológica Federal do Paraná, Prolongamento da Rua Cerejeira, S/N, Santa Helena, PR, 85892-000, Brazil
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DNA Barcoding of Fish Species Diversity in Guizhou, China. DIVERSITY 2023. [DOI: 10.3390/d15020203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Guizhou is an important ecological barrier in the upper reaches of the Yangtze River and the Pearl River basins with abundant fish species. However, fish from these regions are threatened by anthropogenic activities, including overfishing and habitat destruction. Here, we assessed the fish diversity including more than half of the species from the region using DNA barcoding (partial sequence of cytochrome c oxidase subunit I (COI) gene). We obtained 800 mitochondrial COI barcode sequences from 82 genera, 18 families and 8 orders of fishes. The average Kimura two-parameter (K2P) distances within species and genera were 0.35% and 5.44%, respectively. The average interspecific distance was 15.54 times higher than the mean intraspecific distance. Moreover, DNA barcodes revealed 175 operational taxonomic units (OTUs) based on consensus demarcation schemes. Barcoding gaps were detected in 94.81% of morphospecies. Three fish species (Schistura fasciolata, Vanmanenia pingchowensis, and Misgurnus dabryanus) have considerable intraspecific variability, and each was divided into multiple molecular operational taxonomic units (MOTUs) using molecular definition methods (Automatic Barcode Gap Discovery, Refined Single Linkage, General Mixed Yule Coalescent, and Poisson Tree Processes), possibly indicating the occurrence of cryptic species. Altogether, our study reveals the complex diversity of fish species in Guizhou Province, serving as a reference for the conservation and monitoring of fish species in this region.
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131
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Han W, Tang H, Wei L, Zhang E. The first DNA barcode library of Chironomidae from the Tibetan Plateau with an evaluation of the status of the public databases. Ecol Evol 2023; 13:e9849. [PMID: 36861023 PMCID: PMC9969238 DOI: 10.1002/ece3.9849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 03/03/2023] Open
Abstract
The main aim of this study was to curate a COI barcode library of Chironomidae from the Tibetan Plateau (TP) as an essential supplement to the public database. Another aim is to evaluate the current status of the public database of Chironomidae in aspects of taxonomic coverage, geographic representation, barcode quality, and efficiency for molecular identification, the Tibetan Plateau, China. In this study, 512 individuals of Chironomidae from the TP were identified based on morphological taxonomy and barcode analysis. The metadata of public records of Chironomidae were downloaded from the BOLD, and the quality of the public barcodes was ranked using the BAGS program. The reliability of the public library for molecular identification was evaluated with the newly curated library using the BLAST method. The newly curated library comprised 159 barcode species of 54 genera, of which 58.4% of species were likely new to science. There were great gaps in the taxonomic coverage and geographic representation in the public database, and only 29.18% of barcodes were identified at the species level. The quality of the public database was of concern, with only 20% of species being determined as concordant between BINs and morphological species. The accuracy of molecular identification using the public database was poor, and about 50% of matched barcodes could be correctly identified at the species level at the identity threshold of 97%. Based on these data, some recommendations are included here for improving barcoding studies on Chironomidae. The species richness of Chironomidae from the TP is much higher than ever recorded. Barcodes from more taxonomic groups and geographic regions are urgently needed to fill the great gap in the current public database of Chironomidae. Users should take caution when public databases are adopted as reference libraries for the taxonomic assignment.
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Affiliation(s)
- Wu Han
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and LimnologyChinese Academy of ScienceNanjingChina
- University of Chinese Academy of SciencesBeijing100039China
| | - Hongqu Tang
- Life Science and Technology CollegeJinan UniversityGuangzhouChina
| | - Lili Wei
- Life Science and Technology CollegeJinan UniversityGuangzhouChina
| | - Enlou Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and LimnologyChinese Academy of ScienceNanjingChina
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132
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Rodrigues BL, Galati EAB. Molecular taxonomy of phlebotomine sand flies (Diptera, Psychodidae) with emphasis on DNA barcoding: A review. Acta Trop 2023; 238:106778. [PMID: 36435214 DOI: 10.1016/j.actatropica.2022.106778] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022]
Abstract
The taxonomy and systematics of sand flies (Diptera, Psychodidae, Phlebotominae) are one of the pillars of research aimed to identifying vector populations and the agents transmitted by these insects. Traditionally, the use of morphological traits has been the main line of evidence for the definition of species, but the use of DNA sequences is useful as an integrative approach for their delimitation. Here, we discuss the current status of the molecular taxonomy of sand flies, including their most sequenced molecular markers and the main results. Only about 37% of all sand fly species have been processed for any molecular marker and are publicly available in the NCBI GenBank or BOLD Systems databases. The genera Phlebotomus, Nyssomyia, Psathyromyia and Psychodopygus are well-sampled, accounting for more than 56% of their sequenced species. However, less than 34% of the species of Sergentomyia, Lutzomyia, Trichopygomyia and Trichophoromyia have been sampled, representing a major gap in the knowledge of these groups. The most sequenced molecular markers are those within mtDNA, especially the DNA barcoding fragment of the cytochrome c oxidase subunit I (coi) gene, which has shown promising results in detecting cryptic diversity within species. Few sequences of conserved genes have been generated, which hampers higher-level phylogenetic inferences. We argue that sand fly species should be sequenced for at least the coi DNA barcoding marker, but multiple markers with different mutation rates should be assessed, whenever possible, to generate multilocus analysis.
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Affiliation(s)
- Bruno Leite Rodrigues
- Programa de Pós-Graduação em Saúde Pública, Faculdade de Saúde Pública da Universidade de São Paulo (FSP/USP). Av. Dr. Arnaldo, 715 - Cerqueira César, São Paulo SP, Brazil, 01246-904.
| | - Eunice Aparecida Bianchi Galati
- Programa de Pós-Graduação em Saúde Pública, Faculdade de Saúde Pública da Universidade de São Paulo (FSP/USP). Av. Dr. Arnaldo, 715 - Cerqueira César, São Paulo SP, Brazil, 01246-904
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133
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High Levels of Diversity in Anopheles Subgenus Kerteszia Revealed by Species Delimitation Analyses. Genes (Basel) 2023; 14:genes14020344. [PMID: 36833271 PMCID: PMC9956091 DOI: 10.3390/genes14020344] [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: 12/22/2022] [Revised: 01/21/2023] [Accepted: 01/24/2023] [Indexed: 02/03/2023] Open
Abstract
The Anopheles subgenus Kerteszia is a poorly understood group of mosquitoes that includes several species of medical importance. Although there are currently twelve recognized species in the subgenus, previous studies have shown that this is likely to be an underestimate of species diversity. Here, we undertake a baseline study of species delimitation using the barcode region of the mtDNA COI gene to explore species diversity among a geographically and taxonomically diverse range of Kerteszia specimens. Beginning with 10 of 12 morphologically identified Kerteszia species spanning eight countries, species delimitation analyses indicated a high degree of cryptic diversity. Overall, our analyses found support for at least 28 species clusters within the subgenus Kerteszia. The most diverse taxon was Anopheles neivai, a known malaria vector, with eight species clusters. Five other species taxa showed strong signatures of species complex structure, among them Anopheles bellator, which is also considered a malaria vector. There was some evidence for species structure within An. homunculus, although the results were equivocal across delimitation analyses. The current study, therefore, suggests that species diversity within the subgenus Kerteszia has been grossly underestimated. Further work will be required to build on this molecular characterization of species diversity and will rely on genomic level approaches and additional morphological data to test these species hypotheses.
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134
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Compilation, Revision, and Annotation of DNA Barcodes of Marine Invertebrate Non-Indigenous Species (NIS) Occurring in European Coastal Regions. DIVERSITY 2023. [DOI: 10.3390/d15020174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The introduction of non-indigenous species (NIS) is one of the major threats to the integrity of European coastal ecosystems. DNA-based assessments have been increasingly adopted for monitoring NIS. However, the accuracy of DNA-based taxonomic assignments is largely dependent on the completion and reliability of DNA barcode reference libraries. As such, we aimed to compile and audit a DNA barcode reference library for marine invertebrate NIS occurring in Europe. To do so, we compiled a list of NIS using three databases: the European Alien Species Information Network (EASIN), the Information System on Aquatic Non-indigenous and Cryptogenic Species (AquaNIS), and the World Register of Introduced Marine Species (WRiMS). For each species, we retrieved the available cytochrome c oxidase subunit I (COI) mitochondrial gene sequences from the Barcode of Life Data System (BOLD) and used the Barcode, Audit & Grade System (BAGS) to check congruence between morphospecies names and Barcode Index Numbers (BINs). From the 1249 species compiled, approximately 42% had records on BOLD, among which 56% were discordant. We further analyzed these cases to determine the causes of the discordances and attributed additional annotation tags. Of the 622 discordant BINs, after revision, 35% were successfully solved, which increased the number of NIS detected in metabarcoding datasets from 12 to 16. However, a fair number of BINs remained discordant. Reliability of reference barcode records is particularly critical in the case of NIS, where erroneous identification may trigger action or inaction when not required.
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135
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Phillips JD, Athey TB, McNicholas PD, Hanner RH. VLF: An R package for the analysis of very low frequency variants in DNA sequences. Biodivers Data J 2023; 11:e96480. [PMID: 38327328 PMCID: PMC10848336 DOI: 10.3897/bdj.11.e96480] [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: 10/18/2022] [Accepted: 11/30/2022] [Indexed: 01/27/2023] Open
Abstract
Here, we introduce VLF, an R package to determine the distribution of very low frequency variants (VLFs) in nucleotide and amino acid sequences for the analysis of errors in DNA sequence records. The package allows users to assess VLFs in aligned and trimmed protein-coding sequences by automatically calculating the frequency of nucleotides or amino acids in each sequence position and outputting those that occur under a user-specified frequency (default of p = 0.001). These results can then be used to explore fundamental population genetic and phylogeographic patterns, mechanisms and processes at the microevolutionary level, such as nucleotide and amino acid sequence conservation. Our package extends earlier work pertaining to an implementation of VLF analysis in Microsoft Excel, which was found to be both computationally slow and error prone. We compare those results to our own herein. Results between the two implementations are found to be highly consistent for a large DNA barcode dataset of bird species. Differences in results are readily explained by both manual human error and inadequate Linnean taxonomy (specifically, species synonymy). Here, VLF is also applied to a subset of avian barcodes to assess the extent of biological artifacts at the species level for Canada goose (Branta canadensis), as well as within a large dataset of DNA barcodes for fishes of forensic and regulatory importance. The novelty of VLF and its benefit over the previous implementation include its high level of automation, speed, scalability and ease-of-use, each desirable characteristics which will be extremely valuable as more sequence data are rapidly accumulated in popular reference databases, such as BOLD and GenBank.
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Affiliation(s)
- Jarrett D. Phillips
- School of Computer Science and Department of Integrative Biology, University of Guelph, Guelph, CanadaSchool of Computer Science and Department of Integrative Biology, University of GuelphGuelphCanada
| | - Taryn B.T. Athey
- Stollery Children's Hospital, Edmonton, CanadaStollery Children's HospitalEdmontonCanada
| | - Paul D. McNicholas
- Department of Mathematics and Statistics, McMaster University, Hamilton, CanadaDepartment of Mathematics and Statistics, McMaster UniversityHamiltonCanada
| | - Robert H. Hanner
- Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, CanadaBiodiversity Institute of Ontario and Department of Integrative Biology, University of GuelphGuelphCanada
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136
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DeSanctis ML, Soranno EA, Messner E, Wang Z, Turner EM, Falco R, Appiah-Madson HJ, Distel DL. Greater than pH 8: The pH dependence of EDTA as a preservative of high molecular weight DNA in biological samples. PLoS One 2023; 18:e0280807. [PMID: 36689492 PMCID: PMC9870144 DOI: 10.1371/journal.pone.0280807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 01/08/2023] [Indexed: 01/24/2023] Open
Abstract
Ethylenediaminetetraacetic acid (EDTA) is a divalent cation chelator and chemical preservative that has been shown to be the active ingredient of the popular DNA preservative DESS. EDTA may act to reduce DNA degradation during tissue storage by sequestering divalent cations that are required by nucleases naturally occurring in animal tissues. Although EDTA is typically used between pH 7.5 and 8 in preservative preparations, the capacity of EDTA to chelate divalent cations is known to increase with increasing pH. Therefore, increasing the pH of EDTA-containing preservative solutions may improve their effectiveness as DNA preservatives. To test this hypothesis, we stored tissues from five aquatic species in 0.25 M EDTA adjusted to pH 8, 9, and 10 for 12 months at room temperature before DNA isolation. For comparison, tissues from the same specimens were also stored in 95% ethanol. DNA extractions performed on tissues preserved in EDTA pH 9 or 10 resulted in as great or greater percent recovery of high molecular weight DNA than did extractions from tissues stored at pH 8. In all cases examined, percent recovery of high molecular weight DNA from tissues preserved in EDTA pH 10 was significantly better than that observed from tissues preserved in 95% ethanol. Our results support the conclusion that EDTA contributes to DNA preservation in tissues by chelating divalent cations and suggest that preservative performance can be improved by increasing the pH of EDTA-containing DNA preservative solutions.
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Affiliation(s)
- Mia L. DeSanctis
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Elizabeth A. Soranno
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Ella Messner
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Ziyu Wang
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Elena M. Turner
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Rosalia Falco
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Hannah J. Appiah-Madson
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Daniel L. Distel
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
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137
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Pauperio J, Gonzalez LM, Martinez J, González MA, Martins FMS, Veríssimo J, Puppo P, Pinto J, Chaves C, Pinho CJ, Grosso-Silva JM, Quaglietta L, Silva TLL, Sousa P, Alves PC, Fonseca N, Beja P, Ferreira S. The InBIO barcoding initiative database: DNA barcodes of Iberian Trichoptera, documenting biodiversity for freshwater biomonitoring in a Mediterranean hotspot. Biodivers Data J 2023; 11:e97484. [PMID: 38327295 PMCID: PMC10848855 DOI: 10.3897/bdj.11.e97484] [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: 11/12/2022] [Accepted: 12/28/2022] [Indexed: 01/20/2023] Open
Abstract
Background The Trichoptera are an important component of freshwater ecosystems. In the Iberian Peninsula, 380 taxa of caddisflies are known, with nearly 1/3 of the total species being endemic in the region. A reference collection of morphologically identified Trichoptera specimens, representing 142 Iberian taxa, was constructed. The InBIO Barcoding Initiative (IBI) Trichoptera 01 dataset contains records of 438 sequenced specimens. The species of this dataset correspond to about 37% of Iberian Trichoptera species diversity. Specimens were collected between 1975 and 2018 and are deposited in the IBI collection at the CIBIO (Research Center in Biodiversity and Genetic Resources, Portugal) or in the collection Marcos A. González at the University of Santiago de Compostela (Spain). New information Twenty-nine species, from nine different families, were new additions to the Barcode of Life Data System (BOLD). A success identification rate of over 80% was achieved when comparing morphological identifications and DNA barcodes for the species analysed. This encouraging step advances incorporation of informed Environmental DNA tools in biomonitoring schemes, given the shortcomings of morphological identifications of larvae and adult Caddisflies in such studies. DNA barcoding was not successful in identifying species in six Trichoptera genera: Hydropsyche (Hydropsychidae), Athripsodes (Leptoceridae), Wormaldia (Philopotamidae), Polycentropus (Polycentropodidae) Rhyacophila (Rhyacophilidae) and Sericostoma (Sericostomatidae). The high levels of intraspecific genetic variability found, combined with a lack of a barcode gap and a challenging morphological identification, rendered these species as needing additional studies to resolve their taxonomy.
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Affiliation(s)
- Joana Pauperio
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, United KingdomEuropean Molecular Biology Laboratory, European Bioinformatics InstituteHinxton, CambridgeUnited Kingdom
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
| | - Luis Martin Gonzalez
- Departamento de Zoología, Genética y Antropología Física, Facultad de Biología. Universidad de Santiago de Compostela, Santiago de Compostela, SpainDepartamento de Zoología, Genética y Antropología Física, Facultad de Biología. Universidad de Santiago de CompostelaSantiago de CompostelaSpain
| | - Jesus Martinez
- Departamento de Zoología, Genética y Antropología Física, Facultad de Biología. Universidad de Santiago de Compostela, Santiago de Compostela, SpainDepartamento de Zoología, Genética y Antropología Física, Facultad de Biología. Universidad de Santiago de CompostelaSantiago de CompostelaSpain
| | - Marcos A González
- Departamento de Zoología, Genética y Antropología Física, Facultad de Biología. Universidad de Santiago de Compostela, Santiago de Compostela, SpainDepartamento de Zoología, Genética y Antropología Física, Facultad de Biología. Universidad de Santiago de CompostelaSantiago de CompostelaSpain
| | - Filipa MS Martins
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
| | - Joana Veríssimo
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, PortugalDepartamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007PortoPortugal
| | - Pamela Puppo
- Marshall University, Department of Biological Sciences, Huntington, United States of AmericaMarshall University, Department of Biological SciencesHuntingtonUnited States of America
| | - Joana Pinto
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
| | - Cátia Chaves
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
| | - Catarina J. Pinho
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, PortugalDepartamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007PortoPortugal
| | - José Manuel Grosso-Silva
- Museu de História Natural e da Ciência da Universidade do Porto, Porto, PortugalMuseu de História Natural e da Ciência da Universidade do PortoPortoPortugal
| | - Lorenzo Quaglietta
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia, Universidade de LisboaLisboaPortugal
| | - Teresa Luísa L Silva
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
| | - Pedro Sousa
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
| | - Paulo Celio Alves
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
- EBM, Estação Biológica de Mértola, Praça Luís de Camões, Mértola, PortugalEBM, Estação Biológica de Mértola, Praça Luís de CamõesMértolaPortugal
| | - Nuno Fonseca
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
| | - Pedro Beja
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia, Universidade de LisboaLisboaPortugal
| | - Sónia Ferreira
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
- EBM, Estação Biológica de Mértola, Praça Luís de Camões, Mértola, PortugalEBM, Estação Biológica de Mértola, Praça Luís de CamõesMértolaPortugal
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138
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Revealing the diversity of the green Eulalia (Annelida, Phyllodocidae) species complex along the European coast, with description of three new species. ORG DIVERS EVOL 2023. [DOI: 10.1007/s13127-022-00597-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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139
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Schubert HC, Duda M, Eschner A, Weigand E, Kruckenhauser L. DNA barcoding as a tool to monitor the diversity of endangered spring snails in an Austrian National Park. Biodivers Data J 2023; 11:e91496. [PMID: 36761079 PMCID: PMC9850253 DOI: 10.3897/bdj.11.e91496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/22/2022] [Indexed: 01/13/2023] Open
Abstract
The Kalkalpen National Park is situated in Upper Austria and contains more than 800 springs. The international importance of this Park is, from the perspective of nature conservation directives, highly significant (European Nature Reserve Natura 2000, recognised wetland of the Ramsar convention). In the current study, the hydrobioid fauna ('spring snails') of the Kalkalpen National Park was evaluated. These tiny snails are difficult to determine; however, their investigation is especially desirable, as several species are threatened and as they are important for water quality assessment. Snails collected in 39 selected springs were examined with classical morphological methods (shell and genital anatomy) and, subsequently, by DNA analysis. For this task, the DNA barcode, a partial sequence of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene (length of the sequence 658-682 bp), was PCR amplified and sequenced. From 107 specimens, the DNA barcoding sequence could be obtained and compared with already existing DNA sequences. The (sub)endemic species Bythinellaconica, Hauffeniakerschneri, Hauffeniawienerwaldensis and Belgrandiellaaulaei could be clearly identified. For Bythiospeumnocki, despite the ambitious collecting effort, only empty shells were found in four springs (including the locus typicus spring) in the Park and its surroundings. The genus Bythinella was detected in 36 springs. From 25 of these localities, DNA barcodes could be created, which matches those of Bythinellaconica (comparison data from ABOL). It is, therefore, concluded that the species occurs widely in the Kalkalpen National Park. The genus Hauffenia was sampled from 16 springs. From one, the haplotype of Hauffeniawienerwaldensis could be identified (spring is 5 km outside the Park) and from six, the haplotype of Hauffeniakerschneri. Belgrandiellaaulaei was found in three springs, which all lie outside the boundaries and are, therefore, not included in the protection measures of the National Park. The data and analyses obtained contribute to the assessment of the taxonomic status of the species studied. The present study gives a good baseline for further monitoring of the hydrobioids in the Kalkalpen National Park, which is important to evaluate current as well as to decide on future protection measures for this group.
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Affiliation(s)
- Hannah C Schubert
- Central Research Laboratories, Natural History Museum, Vienna, AustriaCentral Research Laboratories, Natural History MuseumViennaAustria,Department of Evolutionary Biology, University of Vienna, Vienna, AustriaDepartment of Evolutionary Biology, University of ViennaViennaAustria
| | - Michael Duda
- Central Research Laboratories, Natural History Museum, Vienna, AustriaCentral Research Laboratories, Natural History MuseumViennaAustria,3rd Zoological Department, Natural History Museum Vienna, Vienna, Austria3rd Zoological Department, Natural History Museum ViennaViennaAustria
| | - Anita Eschner
- 3rd Zoological Department, Natural History Museum Vienna, Vienna, Austria3rd Zoological Department, Natural History Museum ViennaViennaAustria
| | - Erich Weigand
- Nationalpark OÖ Kalkalpen Ges.m.b.H., Molln, AustriaNationalpark OÖ Kalkalpen Ges.m.b.H.MollnAustria
| | - Luise Kruckenhauser
- Central Research Laboratories, Natural History Museum, Vienna, AustriaCentral Research Laboratories, Natural History MuseumViennaAustria,Department of Evolutionary Biology, University of Vienna, Vienna, AustriaDepartment of Evolutionary Biology, University of ViennaViennaAustria
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140
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Berman TS, Inbar M. Molecular identification of individual and seasonal variation in incidental ingestion of arthropods by free-ranging goats. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.1070088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The extent of direct interactions between large mammalian herbivores (LMH) and plant-dwelling arthropods (PDA), i.e., the ingestion of PDA by LMH, remains largely unexplored. Grazing LMH may ingest a variety of PDA, yet, it is unknown how different foraging strategies (i.e., browsing, grazing, etc.) influence the ingestion of PDA or whether individual variation within herds affects it. Here we examine how individual variation within a herd of browsing LMH impacts PDA ingestion. This was done using a DNA metabarcoding analysis on feces collected monthly from marked individuals within a herd of free-ranging goats. We found that goats frequently ingest PDA while feeding (all samples contains PDA), including a complex food-chain of herbivores, predators and parasites, which differed over the season and among individual goats. In total, 63 families of insects and 9 families of arachnids from 15 orders were ingested by the goats. Most ingested PDA were herbivores with reduced mobility, such as immature or sessile species. Highly mobile and noxious PDA were rarely detected. We show for the first time that ingestion of PDA by LMH is influenced by seasonal and individual variation within the herd and that it is common among LMH, regardless of feeding strategy or habitat.
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141
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Hlebec D, Podnar M, Kučinić M, Harms D. Molecular analyses of pseudoscorpions in a subterranean biodiversity hotspot reveal cryptic diversity and microendemism. Sci Rep 2023; 13:430. [PMID: 36624298 PMCID: PMC9829860 DOI: 10.1038/s41598-022-26298-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/13/2022] [Indexed: 01/11/2023] Open
Abstract
Nested within the Mediterranean biodiversity hotspot, the Dinaric Karst of the western Balkans is one of the world's most heterogeneous subterranean ecosystems and renowned for its highly diverse and mostly endemic fauna. The evolutionary processes leading to both endemism and diversity remain insufficiently understood, and large-scale analyses on taxa that are abundant in both subterranean and surface habitats remain infrequent. Here, we provide the first comprehensive molecular study on Croatian pseudoscorpions, a lineage of arachnids that is common and diverse in both habitats. Phylogenetic reconstructions using 499 COI sequences derived from 128 morphospecies collected across the Dinaric Karst show that: (i) occurrence in karstic microhabitats boosters speciation and endemism in the most diverse genera Chthonius C.L. Koch, 1843 (37 morphospecies) and Neobisium Chamberlin, 1930 (34 morphospecies), (ii) evidence for ongoing diversification is found in many species and species complexes through low optimal thresholds (OTs) and species delineation analyses, and (iii) landscape features, such as mountain ranges, correlate with patterns of genetic diversity in the diverse genus Neobisium. We present two synonymies: Protoneobisium Ćurčić, 1988 = Neobisium, syn. nov., and Archaeoroncus Ćurčić and Rađa, 2012 = Roncus L. Koch, 1873, syn. nov. Overall, our study suggests that karstic microhabitats promote diversification in soil- and cave-dwelling arthropods at all taxonomic levels, but also provide important refugia for invertebrates in past and present periods of environmental change.
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Affiliation(s)
- Dora Hlebec
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia. .,Section of Arachnology, Department of Invertebrates, Museum of Nature Hamburg - Zoology, Leibniz Institute for the Analysis of Biodiversity Change, Hamburg, Germany. .,Croatian Biospeleological Society, Zagreb, Croatia.
| | - Martina Podnar
- grid.452330.30000 0001 2230 9365Croatian Natural History Museum, Zagreb, Croatia
| | - Mladen Kučinić
- grid.4808.40000 0001 0657 4636Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Danilo Harms
- grid.517093.90000 0005 0294 9006Section of Arachnology, Department of Invertebrates, Museum of Nature Hamburg - Zoology, Leibniz Institute for the Analysis of Biodiversity Change, Hamburg, Germany
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142
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Burks GR, Yao L, Kalutantirige FC, Gray KJ, Bello E, Rajagopalan S, Bialik SB, Barrick JE, Alleyne M, Chen Q, Schroeder CM. Electron Tomography and Machine Learning for Understanding the Highly Ordered Structure of Leafhopper Brochosomes. Biomacromolecules 2023; 24:190-200. [PMID: 36516996 DOI: 10.1021/acs.biomac.2c01035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Insects known as leafhoppers (Hemiptera: Cicadellidae) produce hierarchically structured nanoparticles known as brochosomes that are exuded and applied to the insect cuticle, thereby providing camouflage and anti-wetting properties to aid insect survival. Although the physical properties of brochosomes are thought to depend on the leafhopper species, the structure-function relationships governing brochosome behavior are not fully understood. Brochosomes have complex hierarchical structures and morphological heterogeneity across species, due to which a multimodal characterization approach is required to effectively elucidate their nanoscale structure and properties. In this work, we study the structural and mechanical properties of brochosomes using a combination of atomic force microscopy (AFM), electron microscopy (EM), electron tomography, and machine learning (ML)-based quantification of large and complex scanning electron microscopy (SEM) image data sets. This suite of techniques allows for the characterization of internal and external brochosome structures, and ML-based image analysis methods of large data sets reveal correlations in the structure across several leafhopper species. Our results show that brochosomes are relatively rigid hollow spheres with characteristic dimensions and morphologies that depend on leafhopper species. Nanomechanical mapping AFM is used to determine a characteristic compression modulus for brochosomes on the order of 1-3 GPa, which is consistent with crystalline proteins. Overall, this work provides an improved understanding of the structural and mechanical properties of leafhopper brochosomes using a new set of ML-based image classification tools that can be broadly applied to nanostructured biological materials.
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Affiliation(s)
- Gabriel R Burks
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States
| | - Lehan Yao
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States
| | - Falon C Kalutantirige
- Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States
| | - Kyle J Gray
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States
| | - Elizabeth Bello
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States.,Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States
| | - Shreyas Rajagopalan
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States.,Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States
| | - Sarah B Bialik
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jeffrey E Barrick
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Marianne Alleyne
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States.,Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States.,Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States
| | - Qian Chen
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States
| | - Charles M Schroeder
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States
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143
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Laporta GZ, Potter AM, Oliveira JFA, Bourke BP, Pecor DB, Linton YM. Global Distribution of Aedes aegypti and Aedes albopictus in a Climate Change Scenario of Regional Rivalry. INSECTS 2023; 14:49. [PMID: 36661976 PMCID: PMC9860750 DOI: 10.3390/insects14010049] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/17/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Arboviral mosquito vectors are key targets for the surveillance and control of vector-borne diseases worldwide. In recent years, changes to the global distributions of these species have been a major research focus, aimed at predicting outbreaks of arboviral diseases. In this study, we analyzed a global scenario of climate change under regional rivalry to predict changes to these species' distributions over the next century. Using occurrence data from VectorMap and environmental variables (temperature and precipitation) from WorldClim v. 2.1, we first built fundamental niche models for both species with the boosted regression tree modelling approach. A scenario of climate change on their fundamental niche was then analyzed. The shared socioeconomic pathway scenario 3 (regional rivalry) and the global climate model Geophysical Fluid Dynamics Laboratory Earth System Model v. 4.1 (GFDL-ESM4.1; gfdl.noaa.gov) were utilized for all analyses, in the following time periods: 2021-2040, 2041-2060, 2061-2080, and 2081-2100. Outcomes from these analyses showed that future climate change will affect Ae. aegypti and Ae. albopictus distributions in different ways across the globe. The Northern Hemisphere will have extended Ae. aegypti and Ae. albopictus distributions in future climate change scenarios, whereas the Southern Hemisphere will have the opposite outcomes. Europe will become more suitable for both species and their related vector-borne diseases. Loss of suitability in the Brazilian Amazon region further indicated that this tropical rainforest biome will have lower levels of precipitation to support these species in the future. Our models provide possible future scenarios to help identify locations for resource allocation and surveillance efforts before a significant threat to human health emerges.
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Affiliation(s)
- Gabriel Z. Laporta
- Graduate Research and Innovation Program, Centro Universitario FMABC, Santo André 09060-870, SP, Brazil
| | - Alexander M. Potter
- One Health Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Walter Reed Biosystematics Unit, Smithsonian Museum Support Center, Suitland, MD 20746, USA
- Department of Entomology, Smithsonian Institution—National Museum of Natural History (NMNH), Washington, DC 20560, USA
| | - Janeide F. A. Oliveira
- Graduate Research and Innovation Program, Centro Universitario FMABC, Santo André 09060-870, SP, Brazil
- Department of Civil Engineering, School of Engineering, Campus Crajubar, Universidade Regional do Cariri, Crato 63105-010, CE, Brazil
| | - Brian P. Bourke
- One Health Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Walter Reed Biosystematics Unit, Smithsonian Museum Support Center, Suitland, MD 20746, USA
- Department of Entomology, Smithsonian Institution—National Museum of Natural History (NMNH), Washington, DC 20560, USA
| | - David B. Pecor
- One Health Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Walter Reed Biosystematics Unit, Smithsonian Museum Support Center, Suitland, MD 20746, USA
- Department of Entomology, Smithsonian Institution—National Museum of Natural History (NMNH), Washington, DC 20560, USA
| | - Yvonne-Marie Linton
- One Health Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Walter Reed Biosystematics Unit, Smithsonian Museum Support Center, Suitland, MD 20746, USA
- Department of Entomology, Smithsonian Institution—National Museum of Natural History (NMNH), Washington, DC 20560, USA
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144
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In support of morphology: Molecular analysis successfully delineates the Afrotropical genus Atylotus (Diptera: Tabanidae) into species. Acta Trop 2023; 237:106725. [DOI: 10.1016/j.actatropica.2022.106725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]
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145
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Baena-Bejarano N, Reina C, Martínez-Revelo DE, Medina CA, Tovar E, Uribe-Soto S, Neita-Moreno JC, Gonzalez MA. Taxonomic identification accuracy from BOLD and GenBank databases using over a thousand insect DNA barcodes from Colombia. PLoS One 2023; 18:e0277379. [PMID: 37093820 PMCID: PMC10124890 DOI: 10.1371/journal.pone.0277379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/10/2023] [Indexed: 04/25/2023] Open
Abstract
Recent declines of insect populations at high rates have resulted in the need to develop a quick method to determine their diversity and to process massive data for the identification of species of highly diverse groups. A short sequence of DNA from COI is widely used for insect identification by comparing it against sequences of known species. Repositories of sequences are available online with tools that facilitate matching of the sequences of interest to a known individual. However, the performance of these tools can differ. Here we aim to assess the accuracy in identification of insect taxonomic categories from two repositories, BOLD Systems and GenBank. This was done by comparing the sequence matches between the taxonomist identification and the suggested identification from the platforms. We used 1,160 COI sequences representing eight orders of insects from Colombia. After the comparison, we reanalyzed the results from a representative subset of the data from the subfamily Scarabaeinae (Coleoptera). Overall, BOLD systems outperformed GenBank, and the performance of both engines differed by orders and other taxonomic categories (species, genus and family). Higher rates of accurate identification were obtained at family and genus levels. The accuracy was higher in BOLD for the order Coleoptera at family level, for Coleoptera and Lepidoptera at genus and species level. Other orders performed similarly in both repositories. Moreover, the Scarabaeinae subset showed that species were correctly identified only when BOLD match percentage was above 93.4% and a total of 85% of the samples were correctly assigned to a taxonomic category. These results accentuate the great potential of the identification engines to place insects accurately into their respective taxonomic categories based on DNA barcodes and highlight the reliability of BOLD Systems for insect identification in the absence of a large reference database for a highly diverse country.
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Affiliation(s)
| | - Catalina Reina
- ICA-Instituto Colombiano Agropecuario, Soledad, Atlántico, Colombia
| | - Diego Esteban Martínez-Revelo
- Asociación GAICA, Pasto, Nariño, Colombia
- Grupo de Investigación en Sistemática Molecular, Universidad Nacional de Colombia, Sede Medellín, Medellín, Antioquia, Colombia
| | - Claudia A Medina
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogotá, Colombia
| | - Eduardo Tovar
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogotá, Colombia
| | - Sandra Uribe-Soto
- Grupo de Investigación en Sistemática Molecular, Universidad Nacional de Colombia, Sede Medellín, Medellín, Antioquia, Colombia
| | | | - Mailyn A Gonzalez
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogotá, Colombia
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146
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Liu C, Ashfaq M, Yin Y, Zhu Y, Wang Z, Cheng H, Hebert P. Using DNA metabarcoding to assess insect diversity in citrus orchards. PeerJ 2023; 11:e15338. [PMID: 37168534 PMCID: PMC10166080 DOI: 10.7717/peerj.15338] [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: 09/23/2022] [Accepted: 04/11/2023] [Indexed: 05/13/2023] Open
Abstract
Background DNA metabarcoding is rapidly emerging as a cost-effective approach for large-scale biodiversity assessment and pest monitoring. The current study employed metabarcoding to assess insect diversity in citrus orchards in Ganzhou City, Jiangxi, China in both 2018 and 2019. Insects were sampled using Malaise traps deployed in three citrus orchards producing a total of 43 pooled monthly samples. Methods The Malaise trap samples were sequenced following DNA metabarcoding workflow. Generated sequences were curated and analyzed using two cloud databases and analytical platforms, the barcode of life data system (BOLD) and multiplex barcode research and visualization environment (mBRAVE). Results These platforms assigned the sequences to 2,141 barcode index numbers (BINs), a species proxy. Most (63%) of the BINs were shared among the three sampling sites while BIN sharing between any two sites did not exceed 71%. Shannon diversity index (H') showed a similar pattern of BIN assortment at the three sampling sites. Beta diversity analysis by Jaccard similarity coefficient (J) and Bray-Curtis distance matrix (BC) revealed a high level of BIN similarity among the three sites (J = 0.67-0.68; BC = 0.19-0.20). Comparison of BIN records against all those on BOLD made it possible to identify 40% of the BINs to a species, 57% to a genus, 97% to a family and 99% to an order. BINs which received a species match on BOLD were placed in one of four categories based on this assignment: pest, parasitoid, predator, or pollinator. As this study provides the first baseline data on insect biodiversity in Chinese citrus plantations, it is a valuable resource for research in a broad range of areas such as pest management and monitoring beneficial insects in citrus gardens.
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Affiliation(s)
- Chenxi Liu
- Sino-American Biological Control Laboratory, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Ashfaq
- Centre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Yanfang Yin
- Sino-American Biological Control Laboratory, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanjuan Zhu
- Sino-American Biological Control Laboratory, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhen Wang
- Sino-American Biological Control Laboratory, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongmei Cheng
- Sino-American Biological Control Laboratory, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Paul Hebert
- Centre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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147
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Preti A, Stohs SM, DiNardo GT, Saavedra C, MacKenzie K, Noble LR, Jones CS, Pierce GJ. Feeding ecology of broadbill swordfish (Xiphias gladius) in the California current. PLoS One 2023; 18:e0258011. [PMID: 36795680 PMCID: PMC9934375 DOI: 10.1371/journal.pone.0258011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/17/2022] [Indexed: 02/17/2023] Open
Abstract
The feeding ecology of broadbill swordfish (Xiphias gladius) in the California Current was described based on analysis of stomach contents collected by fishery observers aboard commercial drift gillnet boats from 2007 to 2014. Prey were identified to the lowest taxonomic level and diet composition was analyzed using univariate and multivariate methods. Of 299 swordfish sampled (74 to 245 cm eye-to-fork length), 292 non-empty stomachs contained remains from 60 prey taxa. Genetic analyses were used to identify prey that could not be identified visually. Diet consisted mainly of cephalopods but also included epipelagic and mesopelagic teleosts. Jumbo squid (Dosidicus gigas) and Gonatopsis borealis were the most important prey based on the geometric index of importance. Swordfish diet varied with body size, location and year. Jumbo squid, Gonatus spp. and Pacific hake (Merluccius productus) were more important for larger swordfish, reflecting the ability of larger specimens to catch large prey. Jumbo squid, Gonatus spp. and market squid (Doryteuthis opalescens) were more important in inshore waters, while G. borealis and Pacific hake predominated offshore. Jumbo squid was more important in 2007-2010 than in 2011-2014, with Pacific hake being the most important prey item in the latter period. Diet variation by area and year probably reflects differences in swordfish preference, prey availability, prey distribution, and prey abundance. The range expansion of jumbo squid that occurred during the first decade of this century may particularly explain their prominence in swordfish diet during 2007-2010. Some factors (swordfish size, area, time period, sea surface temperature) that may influence dietary variation in swordfish were identified. Standardizing methods could make future studies more comparable for conservation monitoring purposes.
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Affiliation(s)
- Antonella Preti
- Institute of Marine Studies, University of California Santa Cruz, Santa Cruz, California, United States of America
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
- NOAA Fisheries, Southwest Fisheries Science Center, La Jolla, California, United States of America
- * E-mail:
| | - Stephen M. Stohs
- NOAA Fisheries, Southwest Fisheries Science Center, La Jolla, California, United States of America
| | - Gerard T. DiNardo
- SCS Global Services, Emeryville, California, United States of America
| | - Camilo Saavedra
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, Vigo, Spain
| | - Ken MacKenzie
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Leslie R. Noble
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Catherine S. Jones
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Graham J. Pierce
- Instituto de Investigaciones Marinas, Vigo, Spain
- Oceanlab, University of Aberdeen, Newburgh, Aberdeenshire, Scotland, United Kingdom
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Teixeira MAL, Bakken T, Vieira PE, Langeneck J, Sampieri BR, Kasapidis P, Ravara A, Nygren A, Costa FO. The curious and intricate case of the European Hediste diversicolor (Annelida, Nereididae) species complex, with description of two new species. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2116124] [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)
- Marcos A. L. Teixeira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
| | - Torkild Bakken
- Norwegian University of Science and Technology, NTNU University Museum, Trondheim, NO-7491, Norway
| | - Pedro E. Vieira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
| | - Joachim Langeneck
- Dipartimento di Biologia, Università di Pisa, via Derna 1, Pisa, I-56126, Italy
| | - Bruno R. Sampieri
- Museu de Zoologia, Instituto de Biologia, Universidade Estadual de Campinas – IB/UNICAMP, Rua Charles Darwin, Bloco N, Cidade Universitária, Campinas, SP, Brasil
| | - Panagiotis Kasapidis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Anávyssos, Greece
| | - AscensÃO Ravara
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, 3810-193, Portugal
| | - Arne Nygren
- Institutionen for marina vetenskaper, Göteborgs Universitet, Tjärnö, Strömstad, Sweden
| | - Filipe O. Costa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, Braga, 4710-057, Portugal
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149
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Morhun H, Son MO, Rewicz T, Kazanavičiūtė E, Copilas-Ciocianu D. The first records of Niphargus hrabei and N. potamophilus in Ukraine and Bulgaria significantly enlarge the ranges of these species. THE EUROPEAN ZOOLOGICAL JOURNAL 2022. [DOI: 10.1080/24750263.2022.2126534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- H. Morhun
- Department of Water Quality, Institute of Marine Biology of National Academy of Sciences of Ukraine, Odesa, Ukraine
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
| | - M. O. Son
- Department of Water Quality, Institute of Marine Biology of National Academy of Sciences of Ukraine, Odesa, Ukraine
| | - T. Rewicz
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
| | - E. Kazanavičiūtė
- Laboratory of Evolutionary Ecology of Hydrobionts, Nature Research Centre, Vilnius, Lithuania
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - D. Copilas-Ciocianu
- Laboratory of Evolutionary Ecology of Hydrobionts, Nature Research Centre, Vilnius, Lithuania
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150
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Deady RJ, Delaney MA, Jones E, Chandler PJ. Further interceptions of the Neotropical fungus gnat Sciophilafractinervis Edwards, 1940 (Diptera, Mycetophilidae) in Britain with comments and observations on its biology and spread. Biodivers Data J 2022; 10:e94812. [PMID: 36761592 PMCID: PMC9836520 DOI: 10.3897/bdj.10.e94812] [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: 09/16/2022] [Accepted: 12/01/2022] [Indexed: 12/15/2022] Open
Abstract
From 2020 onwards, several specimens of the Neotropical fungus gnat Sciophilafractinervis (Edwards, 1940) have been intercepted by Fera Science Ltd. on or near plant material in the United Kingdom originating from nurseries and glasshouses at four separate locations: Preston, Lancashire; Chichester, West Sussex; East Riding of Yorkshire; and Middlesbrough, North Yorkshire, as well as a single interception from the Netherlands. Gnat interceptions were associated with a wide range of plant species: Ficusbenjamina, Ficuselastica, Dracaenareflexavar.angustifolia, Origanumvulgare, Rosmarinusofficinalis, Thymusvulgaris, Impatienshawkeri (Impatiens New Guinea hybrids), Chrysanthemum, as well as Fragariavesca (var. Lusa). The species does not appear to be doing any damage to affected plants with growing conditions likely promoting multiplication under protection. The larvae likely feed on spores (generally saprophytic) adhering to webs they erect on the soil and around the base of plants with spores likely originating from the growing medium and plants. Their spread is likely facilitated by movement of the growing medium or plant material where pupae are suspended in the lower stem or leaf axils. An account of the various interceptions is provided, as well as images of the different life-stages with a brief discussion of Sciophilacincticornis Edwards, 1940, its relationship with Sciophilafractinervis and further evidence of instability in vein R2+3 in the Sciophila genus.
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Affiliation(s)
- Rob J. Deady
- Fera Science Ltd, York Biotech Campus, York, United KingdomFera Science Ltd, York Biotech CampusYorkUnited Kingdom
| | - Mark A. Delaney
- Fera Science Ltd, York Biotech Campus, York, United KingdomFera Science Ltd, York Biotech CampusYorkUnited Kingdom
| | - Eleanor Jones
- Fera Science Ltd, York Biotech Campus, York, United KingdomFera Science Ltd, York Biotech CampusYorkUnited Kingdom
| | - Peter J. Chandler
- 606B Berryfield Lane, Melksham, Wilts SN12 6EL, United Kingdom606B Berryfield Lane, MelkshamWilts SN12 6ELUnited Kingdom
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