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Jain K, Panigrahi M, Nayak SS, Rajawat D, Sharma A, Sahoo SP, Bhushan B, Dutt T. The evolution of contemporary livestock species: Insights from mitochondrial genome. Gene 2024; 927:148728. [PMID: 38944163 DOI: 10.1016/j.gene.2024.148728] [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: 04/16/2024] [Revised: 06/05/2024] [Accepted: 06/24/2024] [Indexed: 07/01/2024]
Abstract
The domestication of animals marks a pivotal moment in human history, profoundly influencing our demographic and cultural progress. This process has led to significant genetic, behavioral, and physical changes in livestock species compared to their wild ancestors. Understanding the evolutionary history and genetic diversity of livestock species is crucial, and mitochondrial DNA (mtDNA) has emerged as a robust marker for investigating molecular diversity in animals. Its highly conserved gene content across animal species, minimal duplications, absence of introns, and short intergenic regions make mtDNA analysis ideal for such studies. Mitochondrial DNA analysis has uncovered distinct cattle domestication events dating back to 8000 years BC in Southwestern Asia. The sequencing of water buffalo mtDNA in 2004 provided important insights into their domestication history. Caprine mtDNA analysis identified three haplogroups, indicating varied maternal origins. Sheep, domesticated 12,000 years ago, exhibit diverse mtDNA lineages, suggesting multiple domestication events. Ovine mtDNA studies revealed clades A, B, C, and a fourth lineage, group D. The origins of domestic pigs were traced to separate European and Asian events followed by interbreeding. In camels, mtDNA elucidated the phylogeographic structure and genetic differentiation between wild and domesticated species. Horses, domesticated around 3500 BC, show significant mtDNA variability, highlighting their diverse origins. Yaks exhibit unique adaptations for high-altitude environments, with mtDNA analysis providing insights into their adaptation. Chicken mtDNA studies supported a monophyletic origin from Southeast Asia's red jungle fowl, with evidence of multiple origins. This review explores livestock evolution and diversity through mtDNA studies, focusing on cattle, water buffalo, goat, sheep, pig, camel, horse, yak and chicken. It highlights mtDNA's significance in unraveling maternal lineages, genetic diversity, and domestication histories, concluding with insights into its potential application in improving livestock production and reproduction dynamics.
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Affiliation(s)
- Karan Jain
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | | | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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Jeunen GJ, Mills S, Mariani S, Treece J, Ferreira S, Stanton JAL, Durán-Vinet B, Duffy GA, Gemmell NJ, Lamare M. Streamlining large-scale oceanic biomonitoring using passive eDNA samplers integrated into vessel's continuous pump underway seawater systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174354. [PMID: 38955269 DOI: 10.1016/j.scitotenv.2024.174354] [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: 04/28/2024] [Revised: 06/13/2024] [Accepted: 06/26/2024] [Indexed: 07/04/2024]
Abstract
Passive samplers are enabling the scaling of environmental DNA (eDNA) biomonitoring in our oceans, by circumventing the time-consuming process of water filtration. Designing a novel passive sampler that does not require extensive sample handling time and can be connected to ocean-going vessels without impeding normal underway activities has potential to rapidly upscale global biomonitoring efforts onboard the world's oceanic fleet. Here, we demonstrate the utility of an artificial sponge sampler connected to the continuous pump underway seawater system as a means to enable oceanic biomonitoring. We compared the performance of this passive sampling protocol with standard water filtration at six locations during a research voyage from New Zealand to Antarctica in early 2023. Eukaryote metabarcoding of the mitochondrial COI gene revealed no significant difference in phylogenetic α-diversity between sampling methods and both methods delineated a progressive reduction in number of Zero-Radius Operational Taxonomic Units (ZOTUs) with increased latitudes. While both sampling methods revealed comparable trends in geographical community compositions, distinct clusters were identified for passive samplers and water filtration at each location. Additionally, greater variability between replicates was observed for passive samplers, resulting in an increased estimated level of replication needed to recover 90 % of the biodiversity. Furthermore, traditional water filtration failed to detect three phyla observed by passive samplers and extrapolation analysis estimated passive samplers recover a larger number of ZOTUs compared to water filtration for all six locations. Our results demonstrate the potential of this passive eDNA sampler protocol and highlight areas where this emerging technology could be improved, thereby enabling large-scale offshore marine eDNA biomonitoring by leveraging the world's oceanic fleet without interfering with onboard activities.
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Affiliation(s)
- Gert-Jan Jeunen
- Department of Marine Science, University of Otago, Dunedin 9016, New Zealand.
| | - Sadie Mills
- National Institute of Water and Atmospheric Research, Wellington 6021, New Zealand
| | - Stefano Mariani
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK
| | - Jackson Treece
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand
| | - Sara Ferreira
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand
| | - Jo-Ann L Stanton
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand
| | - Benjamín Durán-Vinet
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand
| | - Grant A Duffy
- Department of Marine Science, University of Otago, Dunedin 9016, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand
| | - Miles Lamare
- Department of Marine Science, University of Otago, Dunedin 9016, New Zealand
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Bessa MH, Gottschalk MS, Robe LJ. Whole genome phylogenomics helps to resolve the phylogenetic position of the Zygothrica genus group (Diptera, Drosophilidae) and the causes of previous incongruences. Mol Phylogenet Evol 2024; 199:108158. [PMID: 39025321 DOI: 10.1016/j.ympev.2024.108158] [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: 04/04/2024] [Revised: 06/28/2024] [Accepted: 07/14/2024] [Indexed: 07/20/2024]
Abstract
Incomplete Lineage Sorting (ILS) and introgression are among the two main factors causing incongruence between gene and species trees. Advances in phylogenomic studies have allowed us to overcome most of these issues, providing reliable phylogenetic hypotheses while revealing the underlying evolutionary scenario. Across the last century, many incongruent phylogenetic reconstructions were recovered for Drosophilidae, employing a limited sampling of genetic markers or species. In these studies, the monophyly and the phylogenetic positioning of the Zygothrica genus group stood out as one of the most controversial questions. Thus, here, we addressed these issues using a phylogenomic approach, while accessing the influence of ILS and introgressions on the diversification of these species and addressing the spatio-temporal scenario associated with their evolution. For this task, the genomes of nine specimens from six Neotropical species belonging to the Zygothrica genus group were sequenced and evaluated in a phylogenetic framework encompassing other 39 species of Drosophilidae. Nucleotide and amino acid sequences recovered for a set of 2,534 single-copy genes by BUSCO were employed to reconstruct maximum likelihood (ML) concatenated and multi-species coalescent (MSC) trees. Likelihood mapping, quartet sampling, and reticulation tests were employed to infer the level and causes of incongruence. Lastly, a penalized-likelihood molecular clock strategy with fossil calibrations was performed to infer divergence times. Taken together, our results recovered the subdivision of Drosophila into six different lineages, one of which clusters species of the Zygothrica genus group (except for H. duncani). The divergence of this lineage was dated to Oligocene ∼ 31 Mya and seems to have occurred in the same timeframe as other key diversification within Drosophila. According to the concatenated and MSC strategies, this lineage is sister to the clade joining Drosophila (Siphlodora) with the Hawaiian Drosophila and Scaptomyza. Likelihood mapping, quartet sampling, reticulation reconstructions as well as introgression tests revealed that this lineage was the target of several hybridization events involving the ancestors of different Drosophila lineages. Thus, our results generally show introgression as a major source of previous incongruence. Nevertheless, the similar diversification times recovered for several of the Neotropical Drosophila lineages also support the scenario of multiple and simultaneous diversifications taking place at the base of Drosophilidae phylogeny, at least in the Neotropics.
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Affiliation(s)
- Maiara Hartwig Bessa
- Programa de Pós-Graduação em Biodiversidade Animal (PPGBA), Universidade Federal de Santa Maria (UFSM), Brazil
| | - Marco Silva Gottschalk
- Programa de Pós-Graduação em Biodiversidade Animal (PPGBDiv), Instituto de Biologia, Universidade Federal de Pelotas (UFPel), Brazil
| | - Lizandra Jaqueline Robe
- Programa de Pós-Graduação em Biodiversidade Animal (PPGBA), Universidade Federal de Santa Maria (UFSM), Brazil.
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Lavrador AS, Amaral FG, Moutinho J, Vieira PE, Costa FO, Duarte S. Comprehensive DNA metabarcoding-based detection of non-indigenous invertebrates in recreational marinas through a multi-substrate approach. MARINE ENVIRONMENTAL RESEARCH 2024; 200:106660. [PMID: 39088889 DOI: 10.1016/j.marenvres.2024.106660] [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: 05/23/2024] [Revised: 07/15/2024] [Accepted: 07/29/2024] [Indexed: 08/03/2024]
Abstract
eDNA metabarcoding has been increasingly employed in the monitoring of marine invertebrate non-indigenous species (NIS), in particular using filtered seawater. However, comprehensive detection of all NIS may require a diversity of sampling substrates. To assess the effectiveness of 5 sample types (hard and artificial substrates, water, zooplankton) on the recovery of invertebrates' diversity, two marinas were monitored over three time points, using COI and 18S rRNA genes as DNA metabarcoding markers. We detected a total of 628 species and 23 NIS, with only up to 9% species and 17% of NIS detected by all sample types. Hard and artificial substrates were similar to each other but displayed the most significant difference in invertebrate recovery when compared to water eDNA and zooplankton. Five NIS are potential first records for Portugal. No NIS were detected in all sample types and seasons, highlighting the need for varied sampling approaches, and consideration of temporal variation for comprehensive marine NIS surveillance.
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Affiliation(s)
- Ana S Lavrador
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
| | - Fábio G Amaral
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Jorge Moutinho
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Pedro E Vieira
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Filipe O Costa
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Sofia Duarte
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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Nikolaeva OV, Rusin LY, Mikhailov KV, Aleoshin VV, De Ley P. Both-strand gene coding in a plastome-like mitogenome of an enoplid nematode. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024; 342:419-424. [PMID: 38318934 DOI: 10.1002/jez.b.23241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 12/18/2023] [Accepted: 01/17/2024] [Indexed: 02/07/2024]
Abstract
The phylum Nematoda remains very poorly sampled for mtDNA, with a strong bias toward parasitic, economically important or model species of the Chromadoria lineage. Most chromadorian mitogenomes share a specific order of genes encoded on one mtDNA strand. However, the few sequenced representatives of the Dorylaimia lineage exhibit a variable order of mtDNA genes encoded on both strands. While the ancestral arrangement of nematode mitogenome remains undefined, no evidence has been reported for Enoplia, the phylum's third early divergent major lineage. We describe the first mitogenome of an enoplian nematode, Campydora demonstrans, and contend that the complete 37-gene repertoire and both-strand gene encoding are ancestral states preserved in Enoplia and Dorylaimia versus the derived mitogenome arrangement in some Chromadoria. The C. demonstrans mitogenome is 17,018 bp in size and contains a noncoding perfect inverted repeat with 2013 bp-long arms, subdividing the mitogenome into two coding regions. This mtDNA arrangement is very rare among animals and instead resembles that of chloroplast genomes in land plants. Our report broadens mtDNA taxonomic sampling of the phylum Nematoda and adds support to the applicability of cox1 gene as a phylogenetic marker for establishing nematode relationships within higher taxa.
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Affiliation(s)
- Olga V Nikolaeva
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Leonid Yu Rusin
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
| | - Kirill V Mikhailov
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
| | - Vladimir V Aleoshin
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
| | - Paul De Ley
- Department of Entomology, Plant Pathology & Weed Science, New Mexico State University, Las Cruces, New Mexico, USA
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Tischer M, Bleidorn C. Further evidence of low infection frequencies of Wolbachia in soil arthropod communities. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105641. [PMID: 39004260 DOI: 10.1016/j.meegid.2024.105641] [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: 02/23/2024] [Revised: 06/22/2024] [Accepted: 07/11/2024] [Indexed: 07/16/2024]
Abstract
Endosymbiotic Alphaproteobacteria of the genus Wolbachia are exclusively transferred maternally from mother to offspring, but horizontal transfer across species boundaries seems to be frequent as well. However, the (ecological) mechanisms of how these bacteria are transferred between distantly related arthropod hosts remain unclear. Based on the observation that species that are part of the same ecological community often also share similar Wolbachia strains, host ecology has been hypothesized as an important factor enabling transmission and a key factor in explaining the global distribution of Wolbachia lineages. In this study, we focus on the diversity and abundance of Wolbachia strains in soil arthropods, a so far rather neglected community. We screened 82 arthropod morphotypes collected in the beech forest (dominated by Fagus sp.) soil in the area of Göttingen in central Germany for the presence of Wolbachia. By performing a PCR screen with Wolbachia-MLST markers (coxA, dnaA, fbpA, ftsZ, gatB, and hcpA), we found a rather low infection frequency of 12,2%. Additionally, we performed metagenomic screening of pooled individuals from the same sampling site and could not find evidence that this low infection frequency is an artefact due to PCR-primer bias. Phylogenetic analyses of the recovered Wolbachia strains grouped them in three known supergroups (A, B, and E), with the first report of Wolbachia in Protura (Hexapoda). Moreover, Wolbachia sequences from the pseudoscorpion Neobisium carcinoides cluster outside the currently known supergroup diversity. Our screening supports results from previous studies that the prevalence of Wolbachia infections seems to be lower in soil habitats than in above-ground terrestrial habitats. The reasons for this pattern are not completely understood but might stem from the low opportunity of physical contact and the prevalence of supergroups that are less suited for horizontal transfer.
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Affiliation(s)
- Marta Tischer
- Department for Animal Evolution and Biodiversity, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Georg-August-Universität Göttingen, Untere Karspüle 2, 37073 Göttingen, Germany.
| | - Christoph Bleidorn
- Department for Animal Evolution and Biodiversity, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Georg-August-Universität Göttingen, Untere Karspüle 2, 37073 Göttingen, Germany.
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Ferreira AO, Azevedo OM, Barroso C, Duarte S, Egas C, Fontes JT, Ré P, Santos AMP, Costa FO. Multi-marker DNA metabarcoding for precise species identification in ichthyoplankton samples. Sci Rep 2024; 14:19772. [PMID: 39187534 PMCID: PMC11347574 DOI: 10.1038/s41598-024-69963-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 08/12/2024] [Indexed: 08/28/2024] Open
Abstract
Ichthyoplankton monitoring is crucial for stock assessments, offering insights into spawning grounds, stock size, seasons, recruitment, and changes in regional ichthyofauna. This study evaluates the efficiency of multi-marker DNA metabarcoding using mitochondrial cytochrome c oxidase subunit I (COI), 12S rRNA and 16S rRNA gene markers, in comparison to morphology-based methods for fish species identification in ichthyoplankton samples. Two transects with four coastal distance categories were sampled along the southern coast of Portugal, being each sample divided for molecular and morphological analyses. A total of 76 fish species were identified by both approaches, with DNA metabarcoding overperforming morphology-75 versus 11 species-level identifications. Linking species-level DNA identifications with higher taxonomic morphological identifications resolved several uncertainties associated with traditional methods. Multi-marker DNA metabarcoding improved fish species detection by 20-36% compared to using a single marker/amplicon, and identified 38 species in common, reinforcing the validity of our results. PERMANOVA analysis revealed significant differences in species communities based on the primer set employed, transect location, and distance from the coast. Our findings underscore the potential of DNA metabarcoding to assess ichthyoplankton diversity and suggest that its integration into routine surveys could enhance the accuracy and comprehensiveness of fish stock assessments.
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Affiliation(s)
- André O Ferreira
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network Associated Laboratory, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
| | - Olga M Azevedo
- Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139, Faro, Portugal
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Cristina Barroso
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504, Coimbra, Portugal
- Biocant-Transfer Technology Association, 3060-197, Cantanhede, Portugal
| | - Sofia Duarte
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network Associated Laboratory, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Conceição Egas
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504, Coimbra, Portugal
- Biocant-Transfer Technology Association, 3060-197, Cantanhede, Portugal
| | - João T Fontes
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network Associated Laboratory, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Pedro Ré
- MARE-Marine and Environmental Sciences Centre and ARNET-Aquatic Research Network Associated Laboratory, Faculdade de Ciências da Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - A Miguel P Santos
- Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139, Faro, Portugal
- Portuguese Institute for the Sea and the Atmosphere (IPMA), 1749-077, Lisboa, Portugal
| | - Filipe O Costa
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network Associated Laboratory, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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8
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Cavalcante KS, Rodrigues BL, Posada-López L, Peniche T, Saraiva JF, Galardo AKR, Galati EAB. Description of Trichophoromyia jariensis, a new species of phlebotomine sand fly (Diptera: Psychodidae) from the eastern Amazon. JOURNAL OF MEDICAL ENTOMOLOGY 2024:tjae095. [PMID: 39159937 DOI: 10.1093/jme/tjae095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/26/2024] [Accepted: 07/18/2024] [Indexed: 08/21/2024]
Abstract
A new sand fly species, Trichophoromyia jariensis n. sp. Cavalcante, Rodrigues, & Galati, from the state of Amapá, Brazil, is described based on both male and female morphology and cytochrome c oxidase subunit I DNA barcodes. The DNA barcoding analysis clearly associated males and females of this new species.
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Affiliation(s)
- Keison S Cavalcante
- Laboratório de Entomologia Médica (LABENMED), Instituto de Pesquisas Científicas e Tecnológicas do Amapá (IEPA), Macapá, Brazil
- Faculdade de Saúde Pública, Programa de Pós-graduação em Saúde Pública, Universidade de São Paulo, São Paulo, Brazil
| | - Bruno L Rodrigues
- Faculdade de Saúde Pública, Programa de Pós-graduação em Saúde Pública, Universidade de São Paulo, São Paulo, Brazil
| | - Laura Posada-López
- Faculdade de Saúde Pública, Programa de Pós-graduação em Saúde Pública, Universidade de São Paulo, São Paulo, Brazil
- PECET (Programa de Estudio y Control de Enfermedades Tropicales), Facultad de Medicina, Universidad de Antioquia UdeA, Calle, Medellín, Colombia
| | - Taires Peniche
- Laboratório de Entomologia Médica (LABENMED), Instituto de Pesquisas Científicas e Tecnológicas do Amapá (IEPA), Macapá, Brazil
- Faculdade de Saúde Pública, Programa de Pós-graduação em Saúde Pública, Universidade de São Paulo, São Paulo, Brazil
| | - José F Saraiva
- Laboratório de Entomologia Médica (LABENMED), Instituto de Pesquisas Científicas e Tecnológicas do Amapá (IEPA), Macapá, Brazil
| | - Allan Kardec R Galardo
- Laboratório de Entomologia Médica (LABENMED), Instituto de Pesquisas Científicas e Tecnológicas do Amapá (IEPA), Macapá, Brazil
| | - Eunice A B Galati
- Departamento de Epidemiologia, Universidade de São Paulo São Paulo, Brazil
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Romão JA, Dias ÊR, Nolasco M, Boccardo L, Tomé LMR, Góes Neto A, Vieira IJC, Braz-Filho R, Branco A. Orthoporus fuscipes (PORAT, 1888) (Juliformia; Spirostreptidae): population structure and defensive secretion chemical analysis. AN ACAD BRAS CIENC 2024; 96:e20230493. [PMID: 39166616 DOI: 10.1590/0001-3765202420230493] [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: 04/30/2023] [Accepted: 10/11/2023] [Indexed: 08/23/2024] Open
Abstract
Diplopods are terrestrial arthropods important for the dynamics of terrestrial ecosystems. One of the reasons for that can be their low predation rate due to their defensive secretion. Thus, Orthoporus fuscipes, a species belonging to this group and endemic to northeastern Brazil, was investigated as to its population structure and chemical constituents of defensive secretion. The population structure showed that females are larger and have greater mass than do males, along with negative allometric growth between males and females. The defensive secretion hexane extract was submitted to fractionation using SiO2 open-column chromatography and the gas chromatographic coupled to mass spectrometric analysis was applied in the fraction possibilities to identify major fatty acid methyl esthers, along with minor alkanes, alkenes and fatty acids derivatives and the known quinoids 2-methoxy-3-methylhydroquinone, 2-methoxy-3-methyl-1,4-benzoquinone, 2,3-dimethoxy-1,4-benzoquinone and 2,3-dimethoxyhydroquinone. In addition, the cytochrome oxidase I sequence for the species was deposited for the first time.
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Affiliation(s)
- Julia A Romão
- Universidade Estadual de Feira de Santana, Departamento de Saúde, Laboratório de Fitoquímica, Rodovia Transnordestina, s/n, 44036-900 Feira de Santana, BA, Brazil
| | - Êuder R Dias
- Universidade Estadual de Feira de Santana, Departamento de Saúde, Laboratório de Fitoquímica, Rodovia Transnordestina, s/n, 44036-900 Feira de Santana, BA, Brazil
| | - Matheus Nolasco
- Universidade Estadual de Feira de Santana, Departamento de Saúde, Laboratório de Fitoquímica, Rodovia Transnordestina, s/n, 44036-900 Feira de Santana, BA, Brazil
| | - Lilian Boccardo
- Universidade Estadual do Sudoeste da Bahia, Departamento de Ciências Biológicas, Laboratório de Zoologia, Rua José Moreira Sobrinho, s/n, Jequiezinho, 45200-000 Jequié, BA, Brazil
| | - Luiz Marcelo R Tomé
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas (ICB), Av. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte MG, Brazil
| | - Aristóteles Góes Neto
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas (ICB), Av. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte MG, Brazil
| | - Ivo José C Vieira
- Universidade Estadual do Norte Fluminense Darcy Ribeiro, Departamento de Química, Av. Alberto Lamego, 2000, Parque Califórnia, 28013-600 Campos dos Goytacazes, RJ, Brazil
| | - Raimundo Braz-Filho
- Universidade Estadual do Norte Fluminense Darcy Ribeiro, Departamento de Química, Av. Alberto Lamego, 2000, Parque Califórnia, 28013-600 Campos dos Goytacazes, RJ, Brazil
- Universidade Federal Rural do Rio de Janeiro, Departamento de Química Orgânica, BR-465, Km 7, 23897-000 Seropédica, RJ, Brazil
| | - Alexsandro Branco
- Universidade Estadual de Feira de Santana, Departamento de Saúde, Laboratório de Fitoquímica, Rodovia Transnordestina, s/n, 44036-900 Feira de Santana, BA, Brazil
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10
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Landers E, Claridge B, Kuhn W, Seymour V, Peek H, Fluet S, Ramgren J, Phelps J, Paulk B, Cordner L, Blaschke J. Using DNA barcoding to identify high-priority taxa (Hymenoptera: Ichneumonidae) from Great Smoky Mountains National Park. ENVIRONMENTAL ENTOMOLOGY 2024; 53:730-739. [PMID: 38853372 DOI: 10.1093/ee/nvae058] [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: 03/20/2024] [Revised: 05/08/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024]
Abstract
The All Taxa Biodiversity Inventory (ATBI) in Great Smoky Mountains National Park (GSMNP) seeks to document every species of living thing in the park. The ATBI is decades in progress, yet some taxa remain virtually untouched by taxonomists. Such "high priority" taxa include the hyper-diverse parasitoid wasp family Ichneumonidae. Despite the positive and multifaceted effects ichneumonids have on their environment, only a small percentage of those collected in the park have been identified as species, mostly to their complex morphology and overwhelming diversity. Recently, DNA barcoding has transformed biodiversity inventories, streamlining the process to be more rapid and efficient. To test the effectiveness of barcoding 20 + year-old specimens of Ichneumonidae and catalog new records for GSMNP, COI was amplified from 95 ichneumonid morphospecies collected from Andrew's Bald, NC. Species identifications were confirmed morphologically. Eighty-one ichneumonids generated sequence data, representing 16 subfamilies and 44 genera. The subfamily Oxytorinae is newly recorded from GSMNP, along with 10 newly recorded genera and 23 newly recorded species across Ichneumonidae. These results contribute significantly to the ATBI by adding new park records for a high-priority taxon and demonstrate the effectiveness of applying DNA barcoding to samples in long-term storage or those lacking immediate taxonomic expertise.
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Affiliation(s)
- Emerie Landers
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
| | - Brandon Claridge
- Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT, 84322, USA
| | - Will Kuhn
- Discover Life in America, 1316 Cherokee Orchard Road, Gatlinburg, TN, 37738, USA
| | - Victoria Seymour
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
| | - Hettie Peek
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
| | - Scout Fluet
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
| | - Jake Ramgren
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
| | - Jake Phelps
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
| | - Brayden Paulk
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
| | - Lydia Cordner
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
| | - Jeremy Blaschke
- Department of Biology, Union University, 1050 Union University, Jackson, TN, 38305, USA
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11
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Knorrn AH, Beuck L, Barros-García D, Fernández-Peralta L, Freiwald A. Gaidropsarus mauritanicus (Gadiformes, Gaidropsaridae) a new three-bearded rockling from a deep-water coral ecosystem with a genetically verified biogeographical distribution of the genus and notes to its ecology and behavior. JOURNAL OF FISH BIOLOGY 2024. [PMID: 39150971 DOI: 10.1111/jfb.15859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 08/18/2024]
Abstract
Gaidropsarus mauritanicus sp. nov. is described from one specimen collected using a grab sample from the Tanoûdêrt Canyon (ca. 20° N) off Mauritania at a depth of 595 m. The new species was further observed during eight remotely operated vehicle (ROV) dives along the Mauritanian slope southwards down to the Tiguent Coral Mound Complex (~17° N) in a bathymetric range between 613 and 416 m. It can be distinguished from congeners by a combination of characteristics, including large eyes (38.1% head length [HL]), large head (25.8% standard length [SL]), elongated pelvic fins (35.7% SL), low number of vertebrae (44), and coloration (pinkish with a dorsal darker brownish hue and bright blotches along the dorsal-fin base). A species-delimitation analysis performed with available cytochrome c oxidase subunit 1 (COI) sequences affiliated to the genus Gaidropsarus additionally supported the validity of the new species. Video analyses showed a deep-water coral-associated and protection-seeking behavior, which may explain why the species has remained undescribed until now. Additional ROV footage from separate deep-water coral sites in the North Atlantic and Mediterranean Sea further highlights the ecological behavior and hidden diversity of bathyal three-bearded rocklings. Here, we additionally discuss the biogeographical distribution of all genetically verified Gaidropsarus spp. in combination with genetic data and morphological characters. G. mauritanicus sp. nov. is closely related to a species from Tasmania (43° S), a geographical point furthest among the studied samples, which may hint to an important influence of (paleo-) oceanography on the distributions of Gaidropsarus species.
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Affiliation(s)
- Alexander H Knorrn
- Senckenberg am Meer, Marine Research Department, Wilhelmshaven, Germany
- MARUM, University of Bremen, Bremen, Germany
| | - Lydia Beuck
- Senckenberg am Meer, Marine Research Department, Wilhelmshaven, Germany
| | - David Barros-García
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Matosinhos, Portugal
| | - Lourdes Fernández-Peralta
- Instituto Español de Oceanografía (IEO), Fuengirola, Spain
- Department of Animal Biology, Faculty of Science, University of Málaga, Málaga, Spain
| | - André Freiwald
- Senckenberg am Meer, Marine Research Department, Wilhelmshaven, Germany
- MARUM, University of Bremen, Bremen, Germany
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12
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Kazak M, Valavičiūtė-Pocienė K, Kondrotaitė S, Duc M, Bukauskaitė D, Hernández-Lara C, Bernotienė R, Chagas CRF. Culicoides biting midges feeding behaviour as a key for understanding avian Haemoproteus transmission in Lithuania. MEDICAL AND VETERINARY ENTOMOLOGY 2024. [PMID: 39150734 DOI: 10.1111/mve.12752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 07/26/2024] [Indexed: 08/17/2024]
Abstract
Investigations of host feeding behaviour in haematophagous insects are critical to assess transmission routes of vector-borne diseases. Understanding if a certain species has ornithophilic or mammalophilic feeding behaviour can facilitate future studies focused on pathogens transmission to and from certain host species. Culicoides Latreille (Diptera: Ceratopogonidae) are vectors of several pathogens, which include arboviruses, bacteria and parasites to a considerable diversity of vertebrate hosts. However, most of the studies focused on feeding habits target Culicoides species that could transmit the Bluetongue virus, consequently with a mammalophilic feeding behaviour, leaving aside the Culicoides species that are involved in the transmission of vector-borne parasites to birds, such as Haemoproteus Kruse (Haemosporida: Haemoproteidae). This study aimed to investigate the source of blood meals of wild-caught Culicoides using molecular-based methods and to correlate our findings with the reports of Haemoproteus parasites in Culicoides species. Engorged Culicoides females were collected using ultraviolet (UV)-light traps at seven different localities in Lithuania in 2021-2023. Biting midges were dissected, and the abdomens of engorged females were used for molecular investigation of the blood meal source. A polymerase chain reaction (PCR) protocol that amplifies a fragment of the Cytochrome B gene of vertebrates was used. Obtained sequences were compared to available information in GenBank database to confirm the source of the blood meal. In total, 258 engorged Culicoides females, representing nine different species, were analysed. The source of blood meal was identified in 29.1% of them with most of the insects having fed on birds (74.7%) and the remaining on mammals (25.3%). Culicoides segnis Campbell, Pelham-Clinton was the only species to feed exclusively on birds; Culicoides from the Obsoletus group, C. pallidicornis Kieffer and C. punctatus Latreille were found to feed exclusively on mammals; C. festivipennis Kieffer, C. kibunensis Tokunaga and C. pictipennis Staeger had an opportunistic feeding behaviour, with the first two preferably feeding on birds. Due to their feeding behaviour and the presence of Haemoproteus parasites reported in the literature, C. festivipennis, C. kibunensis, C. pictipennis, and C. segnis play an important role in the transmission of those avian vector-borne parasite in the wild. These Culicoides species were already confirmed as being able to support the development of several Haemoproteus species and lineages. Future studies focused on understanding the epidemiology of avian pathogens transmitted by Culicoides should target these species.
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Affiliation(s)
- Margarita Kazak
- Laboratory of Entomology, Nature Research Centre, Vilnius, Lithuania
| | | | | | - Mélanie Duc
- P. B. Šivickis Laboratory of Parasitology, Nature Research Centre, Vilnius, Lithuania
| | - Dovilė Bukauskaitė
- P. B. Šivickis Laboratory of Parasitology, Nature Research Centre, Vilnius, Lithuania
| | | | - Rasa Bernotienė
- Laboratory of Entomology, Nature Research Centre, Vilnius, Lithuania
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13
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Yamamoto T, Tachihara K, Toda M. Examination of sequence variations in partial mitochondrial 12S gene amongst damselfish species as references for DNA barcoding. Biodivers Data J 2024; 12:e126744. [PMID: 39184369 PMCID: PMC11342385 DOI: 10.3897/bdj.12.e126744] [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: 05/07/2024] [Accepted: 07/26/2024] [Indexed: 08/27/2024] Open
Abstract
Accurate species identification, based on DNA barcoding, can be achieved when sufficient sequence variations are present amongst species in the sampled marker. In general, the ability to discriminate species decreases with shorter sequences; however, shorter regions have a merit in amplification success by the polymerase chain reaction. In either case, it is important to investigate sequence variations amongst species before barcoding to understand its reliability and limitations. In this study, we investigate how accurately short, but hypervariable portion of the mitochondrial 12S ribosomal RNA (12S) gene (MiFish region with approximately 180 bp) is used to identify each species in diversified pomacentrid fishes compared with the longer region of the same gene (approximately 750 bp). We prepared three datasets with 301 sequences of the MiFish region for 150 species, the same 301 of sequences of the longer 12S region and 476 sequences of the MiFish region for 183 species. Neighbour-joining (NJ) analyses and genetic distance analyses revealed several indistinguishable pairs of species in these DNA regions. Although the number of such pairs was larger in the MiFish region, 83.6% (153 of 183) of species possessed respective unique sequences even in the MiFish region (versus 96.0% [144 of 150 species] in the longer 12S region). A part of indistinguishable pairs of species might have caused by mitochondrial DNA introgressions and taxonomically unresolved problems. Our analysis clarified the effectiveness and limitations of species identification using DNA barcoding for Pomacentridae and the sequences we provided here contribute to the expansion of references for pomacentrid mitochondrial 12S sequences.
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Affiliation(s)
- Takumi Yamamoto
- Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, JapanGraduate School of Engineering and Science, University of the RyukyusNishihara, OkinawaJapan
| | - Katsunori Tachihara
- Laboratory of Fisheries Biology and Coral Reef Studies, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, JapanLaboratory of Fisheries Biology and Coral Reef Studies, Faculty of Science, University of the RyukyusNishihara, OkinawaJapan
| | - Mamoru Toda
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, JapanTropical Biosphere Research Center, University of the RyukyusNishihara, OkinawaJapan
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14
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Vargovčík O, Čiamporová-Zaťovičová Z, Beracko P, Kopáček J, Macko P, Tuhrinová K, Čiampor F. Environmental gradients and optimal fixation time revealed with DNA metabarcoding of benthic sample fixative. Sci Rep 2024; 14:18396. [PMID: 39117754 PMCID: PMC11310421 DOI: 10.1038/s41598-024-68939-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 07/30/2024] [Indexed: 08/10/2024] Open
Abstract
Assessments of biodiversity and ecosystem status can benefit from DNA metabarcoding as a means to streamline sample processing and specimen identification. Moreover, processing the fixation medium instead of the precious material introduces straightforward protocols that allow subsequent focus on certain organisms detected among the preserved specimens. In this study, we present a proof of concept via the analysis of freshwater invertebrate samples from the Tatra Mountain lakes (Slovakia). Besides highlighting a match between the lake-specific environmental conditions and the results of our fixative DNA metabarcoding, we observed an option to fine-tune the fixation time: to prefer two weeks over a day or a month. This effect emerged from the presence/absence of individual taxa rather than from coarse per-sample records of taxonomic richness, demonstrating that metabarcoding studies-and efforts to optimize their protocols-can use the robust metrics to explore even subtle trends. We also provide evidence that fixative DNA might better capture large freshwater species than terrestrial or meiofauna.
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Affiliation(s)
- Ondrej Vargovčík
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, 842 15, Slovakia
- Department of Biodiversity and Ecology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, 845 23, Slovakia
| | - Zuzana Čiamporová-Zaťovičová
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, 842 15, Slovakia.
- Department of Biodiversity and Ecology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, 845 23, Slovakia.
| | - Pavel Beracko
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, 842 15, Slovakia
| | - Jiří Kopáček
- Institute of Hydrobiology, Biology Centre CAS, České Budějovice, 370 05, Czech Republic
| | - Patrik Macko
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, 842 15, Slovakia
| | - Kornélia Tuhrinová
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, 842 15, Slovakia
- Department of Biodiversity and Ecology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, 845 23, Slovakia
| | - Fedor Čiampor
- Department of Biodiversity and Ecology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, 845 23, Slovakia
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15
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Vanin S, Tuccia F, Pradelli J, Carta G, Giordani G. Identification of Diptera Puparia in Forensic and Archeo-Funerary Contexts. INSECTS 2024; 15:599. [PMID: 39194804 DOI: 10.3390/insects15080599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 07/28/2024] [Accepted: 07/31/2024] [Indexed: 08/29/2024]
Abstract
Diptera identification is fundamental in forensic entomology as well as in funerary archeoentomology, where the challenge is exacerbated by the presence of immature stages such as larvae and puparia. In these two developmental stages, specimens possess a very limited number of diagnostic features, and for puparia, there is also a lack of identification tools such as descriptions and identification keys. Morphological analysis, DNA-based techniques, and cuticular chemical analyses all show good potential for species identification; however, they also have some limitations. DNA-based identification is primarily hindered by the incompleteness of genetic databases and the presence of PCR inhibitors often co-extracted from the puparial cuticle. Chemical analysis of the cuticle is showing promising results, but this approach is also limited by the insufficient profile database and requires specific, expensive equipment, as well as trained personnel. Additionally, to ensure the repeatability of the analysis-a critical aspect in forensic investigations-and to preserve precious and unique specimens from museum collections, non-invasive protocols and techniques must be prioritized for species identification.
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Affiliation(s)
- Stefano Vanin
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, 16132 Genoa, Italy
- National Research Council, Institute for the Study of Anthropic Impact and Sustainability in the Marine Environment (CNR-IAS), 16149 Genova, Italy
| | - Fabiola Tuccia
- School of applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, UK
| | - Jennifer Pradelli
- School of applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, UK
| | - Giuseppina Carta
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, 16132 Genoa, Italy
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16
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(SOSA) SOSA, Brandt A, Chen C, Engel L, Esquete P, Horton T, Jażdżewska AM, Johannsen N, Kaiser S, Kihara TC, Knauber H, Kniesz K, Landschoff J, Lörz AN, Machado FM, Martínez-Muñoz CA, Riehl T, Serpell-Stevens A, Sigwart JD, Tandberg AHS, Tato R, Tsuda M, Vončina K, Watanabe HK, Wenz C, Williams JD. Ocean Species Discoveries 1-12 - A primer for accelerating marine invertebrate taxonomy. Biodivers Data J 2024; 12:e128431. [PMID: 39171079 PMCID: PMC11336395 DOI: 10.3897/bdj.12.e128431] [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: 05/27/2024] [Accepted: 07/05/2024] [Indexed: 08/23/2024] Open
Abstract
Background Discoveries of new species often depend on one or a few specimens, leading to delays as researchers wait for additional context, sometimes for decades. There is currently little professional incentive for a single expert to publish a stand-alone species description. Additionally, while many journals accept taxonomic descriptions, even specialist journals expect insights beyond the descriptive work itself. The combination of these factors exacerbates the issue that only a small fraction of marine species are known and new discoveries are described at a slow pace, while they face increasing threats from accelerating global change. To tackle this challenge, this first compilation of Ocean Species Discoveries (OSD) presents a new collaborative framework to accelerate the description and naming of marine invertebrate taxa that can be extended across all phyla. Through a mode of publication that can be speedy, taxonomy-focused and generate higher citation rates, OSD aims to create an attractive home for single species descriptions. This Senckenberg Ocean Species Alliance (SOSA) approach emphasises thorough, but compact species descriptions and diagnoses, with supporting illustrations and with molecular data when available. Even basic species descriptions carry key data for distributions and ecological interactions (e.g., host-parasite relationships) besides universally valid species names; these are essential for downstream uses, such as conservation assessments and communicating biodiversity to the broader public. New information This paper presents thirteen marine invertebrate taxa, comprising one new genus, eleven new species and one re-description and reinstatement, covering wide taxonomic, geographic, bathymetric and ecological ranges. The taxa addressed herein span three phyla (Mollusca, Arthropoda, Echinodermata), five classes, eight orders and twelve families. Apart from the new genus, an updated generic diagnosis is provided for four other genera. The newly-described species of the phylum Mollusca are Placiphorellamethanophila Vončina, sp. nov. (Polyplacophora, Mopaliidae), Lepetodrilusmarianae Chen, Watanabe & Tsuda, sp. nov. (Gastropoda, Lepetodrilidae), Shinkailepasgigas Chen, Watanabe & Tsuda, sp. nov. (Gastropoda, Phenacolepadidae) and Lyonsiellaillaesa Machado & Sigwart, sp. nov. (Bivalvia, Lyonsiellidae). The new taxa of the phylum Arthropoda are all members of the subphylum Crustacea: Lepechinellanaces Lörz & Engel, sp. nov. (Amphipoda, Lepechinellidae), Cuniculomaeragrata Tandberg & Jażdżewska, gen. et sp. nov. (Amphipoda, Maeridae), Pseudionellapumulaensis Williams & Landschoff, sp. nov. (Isopoda, Bopyridae), Mastigoniscusminimus Wenz, Knauber & Riehl, sp. nov. (Isopoda, Haploniscidae), Macrostylispapandreas Jonannsen, Riehl & Brandt, sp. nov. (Isopoda, Macrostylidae), Austroniscusindobathyasellus Kaiser, Kniesz & Kihara, sp. nov. (Isopoda, Nannoniscidae) and Apseudopsisdaria Esquete & Tato, sp. nov. (Tanaidacea, Apseudidae). In the phylum Echinodermata, the reinstated species is Psychropotesbuglossa E. Perrier, 1886 (Holothuroidea, Psychropotidae).The study areas span the North and Central Atlantic Ocean, the Indian Ocean and the North, East and West Pacific Ocean and depths from 5.2 m to 7081 m. Specimens of eleven free-living and one parasite species were collected from habitats ranging from an estuary to deep-sea trenches. The species were illustrated with photographs, line drawings, micro-computed tomography, confocal laser scanning microscopy and scanning electron microscopy images. Molecular data are included for nine species and four species include a molecular diagnosis in addition to their morphological diagnosis.The five new geographic and bathymetric distribution records comprise Lepechinellanaces Lörz & Engel, sp. nov., Cuniculomaeragrata Tandberg & Jażdżewska, sp. nov., Pseudionellapumulaensis Williams & Landschoff, sp. nov., Austroniscusindobathyasellus Kaiser, Kniesz & Kihara, sp. nov. and Psychropotesbuglossa E. Perrier, 1886, with the novelty spanning from the species to the family level. The new parasite record is Pseudionellapumulaensis Williams & Landschoff, sp. nov., found in association with the hermit crab Pagurusfraserorum Landschoff & Komai, 2018.
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Affiliation(s)
- Senckenberg Ocean Species Alliance (SOSA)
- Senckenberg Research Institute and Natural History Museum Frankfurt, Department of Marine Zoology, Senckenberganlage 25, 60325, Frankfurt am Main, GermanySenckenberg Research Institute and Natural History Museum Frankfurt, Department of Marine Zoology, Senckenberganlage 25, 60325Frankfurt am MainGermany
| | - Angelika Brandt
- Senckenberg Research Institute and Natural History Museum Frankfurt, Department of Marine Zoology, Senckenberganlage 25, 60325, Frankfurt am Main, GermanySenckenberg Research Institute and Natural History Museum Frankfurt, Department of Marine Zoology, Senckenberganlage 25, 60325Frankfurt am MainGermany
- Johann Wolfgang Goethe University Frankfurt, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, GermanyJohann Wolfgang Goethe University Frankfurt, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, 60438Frankfurt am MainGermany
| | - Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, 237-0061, Yokosuka, Kanagawa, JapanX-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, 237-0061Yokosuka, KanagawaJapan
| | - Laura Engel
- Institute of Marine Ecosystem and Fishery Science (IMF) Center for Earth System Research and Sustainability (CEN) University of Hamburg, Große Elbstraße 133, 22767, Hamburg, GermanyInstitute of Marine Ecosystem and Fishery Science (IMF) Center for Earth System Research and Sustainability (CEN) University of Hamburg, Große Elbstraße 133, 22767HamburgGermany
| | - Patricia Esquete
- Departamento de Biologia & CESAM (Centro de estudos do Ambiente e do Mar), Universidade de Aveiro, Aveiro, PortugalDepartamento de Biologia & CESAM (Centro de estudos do Ambiente e do Mar), Universidade de AveiroAveiroPortugal
| | - Tammy Horton
- National Oceanography Centre, Southampton, United KingdomNational Oceanography CentreSouthamptonUnited Kingdom
| | - Anna M. Jażdżewska
- University of Lodz, Faculty of Biology and Environmental Protection, Department of Invertebrate Zoology and Hydrobiology, Banacha 12/16, 90-237, Łódź, PolandUniversity of Lodz, Faculty of Biology and Environmental Protection, Department of Invertebrate Zoology and Hydrobiology, Banacha 12/16, 90-237ŁódźPoland
| | - Nele Johannsen
- Scharnhorststraße 44, 21335, Lüneburg, GermanyScharnhorststraße 44, 21335LüneburgGermany
| | - Stefanie Kaiser
- Senckenberg Research Institute and Natural History Museum Frankfurt, Department of Marine Zoology, Senckenberganlage 25, 60325, Frankfurt am Main, GermanySenckenberg Research Institute and Natural History Museum Frankfurt, Department of Marine Zoology, Senckenberganlage 25, 60325Frankfurt am MainGermany
| | - Terue C. Kihara
- Integrated Environmental Solutions UG—INES, c/o DZMB, Südstrand 44, 26382, Wilhelmshaven, GermanyIntegrated Environmental Solutions UG—INES, c/o DZMB, Südstrand 44, 26382WilhelmshavenGermany
| | - Henry Knauber
- Senckenberg Research Institute and Natural History Museum Frankfurt, Department of Marine Zoology, Senckenberganlage 25, 60325, Frankfurt am Main, GermanySenckenberg Research Institute and Natural History Museum Frankfurt, Department of Marine Zoology, Senckenberganlage 25, 60325Frankfurt am MainGermany
- Johann Wolfgang Goethe University Frankfurt, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, GermanyJohann Wolfgang Goethe University Frankfurt, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, 60438Frankfurt am MainGermany
| | - Katharina Kniesz
- Leibniz Institute for Baltic Sea Research Warnemünde, Seestraße 15, 18119, Rostock, GermanyLeibniz Institute for Baltic Sea Research Warnemünde, Seestraße 15, 18119RostockGermany
- German Centre for Marine Biodiversity Research (DZMB), Senckenberg am Meer, Südstrand 44, 26382, Wilhelmshaven, GermanyGerman Centre for Marine Biodiversity Research (DZMB), Senckenberg am Meer, Südstrand 44, 26382WilhelmshavenGermany
| | - Jannes Landschoff
- Sea Change Trust, Cape Town, Western Cape, South AfricaSea Change TrustCape Town, Western CapeSouth Africa
- Department of Botany and Zoology, Department of Botany and Zoology, Stellenbosch University, Private Bag X1, 7602, Matieland, South AfricaDepartment of Botany and Zoology, Department of Botany and Zoology, Stellenbosch University, Private Bag X1, 7602MatielandSouth Africa
| | - Anne-Nina Lörz
- Institute of Marine Ecosystem and Fishery Science (IMF) Center for Earth System Research and Sustainability (CEN) University of Hamburg, Große Elbstraße 133, 22767, Hamburg, GermanyInstitute of Marine Ecosystem and Fishery Science (IMF) Center for Earth System Research and Sustainability (CEN) University of Hamburg, Große Elbstraße 133, 22767HamburgGermany
| | - Fabrizio M. Machado
- Institute of Biology, Universidade Estadual de Campinas, 13083-970, Campinas, São Paulo, BrazilInstitute of Biology, Universidade Estadual de Campinas, 13083-970Campinas, São PauloBrazil
| | - Carlos A. Martínez-Muñoz
- Senckenberg Research Institute and Natural History Museum Frankfurt, Department of Marine Zoology, Senckenberganlage 25, 60325, Frankfurt am Main, GermanySenckenberg Research Institute and Natural History Museum Frankfurt, Department of Marine Zoology, Senckenberganlage 25, 60325Frankfurt am MainGermany
| | - Torben Riehl
- Senckenberg Research Institute and Natural History Museum Frankfurt, Department of Marine Zoology, Senckenberganlage 25, 60325, Frankfurt am Main, GermanySenckenberg Research Institute and Natural History Museum Frankfurt, Department of Marine Zoology, Senckenberganlage 25, 60325Frankfurt am MainGermany
- Johann Wolfgang Goethe University Frankfurt, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, GermanyJohann Wolfgang Goethe University Frankfurt, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, 60438Frankfurt am MainGermany
| | - Amanda Serpell-Stevens
- National Oceanography Centre, Southampton, United KingdomNational Oceanography CentreSouthamptonUnited Kingdom
| | - Julia D. Sigwart
- Senckenberg Research Institute and Natural History Museum Frankfurt, Department of Marine Zoology, Senckenberganlage 25, 60325, Frankfurt am Main, GermanySenckenberg Research Institute and Natural History Museum Frankfurt, Department of Marine Zoology, Senckenberganlage 25, 60325Frankfurt am MainGermany
- Johann Wolfgang Goethe University Frankfurt, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, GermanyJohann Wolfgang Goethe University Frankfurt, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, 60438Frankfurt am MainGermany
| | - Anne Helene S. Tandberg
- Senckenberg Research Institute and Natural History Museum Frankfurt, Department of Marine Zoology, Senckenberganlage 25, 60325, Frankfurt am Main, GermanySenckenberg Research Institute and Natural History Museum Frankfurt, Department of Marine Zoology, Senckenberganlage 25, 60325Frankfurt am MainGermany
- University Museum of Bergen, University of Bergen, Bergen, NorwayUniversity Museum of Bergen, University of BergenBergenNorway
| | - Ramiro Tato
- Estación de Bioloxía Mariña de A Graña, Universidade de Santiago de Compostela, A Coruña, SpainEstación de Bioloxía Mariña de A Graña, Universidade de Santiago de CompostelaA CoruñaSpain
| | - Miwako Tsuda
- Project Team for Development of New-Generation Research Protocol for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, 237-0061, Yokosuka, Kanagawa, JapanProject Team for Development of New-Generation Research Protocol for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, 237-0061Yokosuka, KanagawaJapan
| | - Katarzyna Vončina
- Senckenberg Research Institute and Natural History Museum Frankfurt, Department of Marine Zoology, Senckenberganlage 25, 60325, Frankfurt am Main, GermanySenckenberg Research Institute and Natural History Museum Frankfurt, Department of Marine Zoology, Senckenberganlage 25, 60325Frankfurt am MainGermany
- Johann Wolfgang Goethe University Frankfurt, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, GermanyJohann Wolfgang Goethe University Frankfurt, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, 60438Frankfurt am MainGermany
| | - Hiromi K. Watanabe
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, 237-0061, Yokosuka, Kanagawa, JapanX-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, 237-0061Yokosuka, KanagawaJapan
| | - Christian Wenz
- Senckenberg Research Institute and Natural History Museum Frankfurt, Department of Marine Zoology, Senckenberganlage 25, 60325, Frankfurt am Main, GermanySenckenberg Research Institute and Natural History Museum Frankfurt, Department of Marine Zoology, Senckenberganlage 25, 60325Frankfurt am MainGermany
- Johann Wolfgang Goethe University Frankfurt, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, GermanyJohann Wolfgang Goethe University Frankfurt, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, 60438Frankfurt am MainGermany
| | - Jason D. Williams
- Department of Biology, Hofstra University, 11549-1140, Hempstead, New York, United States of AmericaDepartment of Biology, Hofstra University, 11549-1140Hempstead, New YorkUnited States of America
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17
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Pinna M, Zangaro F, Specchia V. Assessing benthic macroinvertebrate communities' spatial heterogeneity in Mediterranean transitional waters through eDNA metabarcoding. Sci Rep 2024; 14:17890. [PMID: 39095544 PMCID: PMC11297313 DOI: 10.1038/s41598-024-69043-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024] Open
Abstract
Transitional waters are important habitats both for biodiversity and ecological functions, providing valuable natural resources and relevant ecosystem services. However, they are highly susceptible to climate changes and anthropogenic pressures responsible for biodiversity losses and require specific biomonitoring programs. Benthic macroinvertebrates are suitable as ecological indicators of transitional waters, being affected by biological, chemical, and physical conditions of the ecosystems about their life cycles and space-use behaviour. The advent of high-throughput sequencing technologies has allowed biodiversity investigations, at the molecular level, in multiple ecosystems and for different ecological guilds. Benthic macroinvertebrate communities' composition has been investigated, at the molecular level, mainly through DNA extracted from sediments in marine and riverine ecosystems. In this work, benthic macroinvertebrate communities are explored through eDNA metabarcoding from water samples in a Mediterranean transitional water ecosystem. This research highlighted the validity of eDNA metabarcoding as an efficient tool for the assessment of benthic macroinvertebrate community structure in transitional waters, unveiling the spatial heterogeneity of benthic macroinvertebrate communities correlated to the measured environmental gradients. The results suggest that peculiar features of transitional water ecosystems, such as shallow waters and limited currents, facilitate the assessment of benthic macroinvertebrate communities through environmental DNA analysis from surface water samples, opening for more rapid and accurate monitoring programs for these valuable ecosystems.
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Affiliation(s)
- Maurizio Pinna
- Department of Biological and Environmental Sciences and Technologies, DiSTeBA, University of Salento, Via Monteroni 165, 73100, Lecce, Italy
- NBFC, National Biodiversity Future Center, 90133, Palermo, Italy
- Research Centre for Fisheries and Aquaculture of Acquatina di Frigole, DiSTeBA, University of Salento, 73100, Lecce, Italy
| | - Francesco Zangaro
- Department of Biological and Environmental Sciences and Technologies, DiSTeBA, University of Salento, Via Monteroni 165, 73100, Lecce, Italy
| | - Valeria Specchia
- Department of Biological and Environmental Sciences and Technologies, DiSTeBA, University of Salento, Via Monteroni 165, 73100, Lecce, Italy.
- NBFC, National Biodiversity Future Center, 90133, Palermo, Italy.
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18
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Bernauer OM, Branstetter MG, Cook JM, Tierney SM. Functional trait mismatch between native and introduced bee pollinators servicing a global fruit crop. BMC Ecol Evol 2024; 24:104. [PMID: 39095704 PMCID: PMC11295329 DOI: 10.1186/s12862-024-02293-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Understanding connections between biodiversity and ecosystem services can be enhanced by shifting focus from species richness to functional trait-based approaches, that when paired with comparative phylogenetic methods can provide even deeper insights. We investigated the functional ecology and phylogenetic diversity of pollination services provided by hymenopteran insects visiting apple flowers in orchards surrounded by either 'natural' or 'disturbed' landscapes in New South Wales, Australia. We assessed whether morphological and behavioural traits (hairiness, body size, glossa length, pollen load purity, and probability of loose pollen) exhibited non-random phylogenetic patterns. Then, explored whether bees, the primary pollinators in this system, filled unique or overlapping functional entities (FEs). For each landscape, we calculated phylogenetic diversity and used FEs to assess functional richness, evenness, and diversion. RESULTS A phylogenomic matrix based on ultraconserved elements (UCEs; 1,382,620 bp from 1,969 loci) was used to infer a fully-resolved and well-supported maximum likelihood phylogeny for 48 hymenopteran morphospecies. There was no significant difference in species richness between landscape categories. Pollinator communities at natural sites had higher phylogenetic complexity (X = 2.37) and functional divergence (x̄ = 0.74 ± 0.02 s.e.) than disturbed sites (X = 1.65 and x̄ = 0.6 ± 0.01 s.e.). Hairiness showed significant phylogenetic clustering (K = 0.94), whereas body size, glossa length, and loose pollen showed weaker non-random phylogenetic patterns (K between 0.3-0.5). Pollen load purity showed no association with phylogeny. The assemblage of 17 bee morphospecies comprised nine FEs: eight FEs consisted of native bees with three containing 65% of all native bee taxa. The introduced honey bee (Apis mellifera) occupied a unique FE, likely due to its different evolutionary history. Both landscape types supported six FEs each with three overlapping: two native bee FEs and the honey bee FE. CONCLUSIONS Bee hairiness was the only functional trait to exhibit demonstrable phylogenetic signal. Despite differences in species richness, and functional and phylogenetic diversity between orchard landscape types, both maintained equal bee FE numbers. While no native bee taxon was analogous to the honey bee FE, four native bee FEs shared the same hairiness level as honey bees. Health threats to honey bee populations in Australia will likely disrupt pollination services to apple, and other pollination-dependent food crops, given the low level of functional redundancy within the investigated pollinator assemblages.
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Affiliation(s)
- Olivia M Bernauer
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia.
- Department of Entomology, University of Wisconsin-Madison, 1630 Linden Dr. Madison, Madison, WI, 53706, USA.
| | - Michael G Branstetter
- U.S. Department of Agriculture, Agricultural Research Service, Pollinating Insects Research Unit, Utah State University, 5310 Old Main Hill, Logan, UT, 84322, USA
| | - James M Cook
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Simon M Tierney
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
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19
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Li XL, Zhang JQ, Shen XJ, Zhang Y, Guo DA. Overview and limitations of database in global traditional medicines: A narrative review. Acta Pharmacol Sin 2024:10.1038/s41401-024-01353-1. [PMID: 39095509 DOI: 10.1038/s41401-024-01353-1] [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: 07/27/2023] [Accepted: 07/02/2024] [Indexed: 08/04/2024] Open
Abstract
The study of traditional medicine has garnered significant interest, resulting in various research areas including chemical composition analysis, pharmacological research, clinical application, and quality control. The abundance of available data has made databases increasingly essential for researchers to manage the vast amount of information and explore new drugs. In this article we provide a comprehensive overview and summary of 182 databases that are relevant to traditional medicine research, including 73 databases for chemical component analysis, 70 for pharmacology research, and 39 for clinical application and quality control from published literature (2000-2023). The review categorizes the databases by functionality, offering detailed information on websites and capacities to facilitate easier access. Moreover, this article outlines the primary function of each database, supplemented by case studies to aid in database selection. A practical test was conducted on 68 frequently used databases using keywords and functionalities, resulting in the identification of highlighted databases. This review serves as a reference for traditional medicine researchers to choose appropriate databases and also provides insights and considerations for the function and content design of future databases.
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Affiliation(s)
- Xiao-Lan Li
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian-Qing Zhang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xuan-Jing Shen
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Zhang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De-An Guo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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20
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Wolff JO, Kennedy SR, Houghton M, Pascoe P, Gajski D, Derkarabetian S, Fraser C, Krehenwinkel H, Renault D. Infrequent Long-Range Dispersal and Evolution of a Top Terrestrial Arthropod Predator in the Sub-Antarctic. Am Nat 2024; 204:191-199. [PMID: 39008836 DOI: 10.1086/730827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
AbstractThe sub-Antarctic terrestrial ecosystems survive on isolated oceanic islands in the path of circumpolar currents and winds that have raged for more than 30 million years and are shaped by climatic cycles that surpass the tolerance limits of many species. Surprisingly little is known about how these ecosystems assembled their native terrestrial fauna and how such processes have changed over time. Here, we demonstrate the patterns and timing of colonization and speciation in the largest and dominant arthropod predators in the eastern sub-Antarctic: spiders of the genus Myro. Our results indicate that this lineage originated from Australia before the Plio-Pleistocenic glacial cycles and underwent an adaptive radiation on the Crozet archipelago, from where one native species colonized multiple remote archipelagos via the Antarctic circumpolar current across thousands of kilometers. The results indicate limited natural connectivity between terrestrial macroinvertebrate faunas in the eastern sub-Antarctic and partial survival of repeated glaciations in the Plio-Pleistocene. Furthermore, our findings highlight that by integrating arthropod taxa from multiple continents, the climatically more stable volcanic Crozet archipelago played a critical role in the evolution and distribution of arthropod life in the sub-Antarctic.
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21
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Canals O, Lanzén A, Mendibil I, Bachiller E, Corrales X, Andonegi E, Cotano U, Rodríguez-Ezpeleta N. Increasing marine trophic web knowledge through DNA analyses of fish stomach content: a step towards an ecosystem-based approach to fisheries research. JOURNAL OF FISH BIOLOGY 2024; 105:431-443. [PMID: 38726501 DOI: 10.1111/jfb.15754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/12/2024] [Accepted: 03/28/2024] [Indexed: 08/20/2024]
Abstract
Multispecies and ecosystem models, which are key for the implementation of ecosystem-based approaches to fisheries management, require extensive data on the trophic interactions between marine organisms, including changes over time. DNA metabarcoding, by allowing the simultaneous taxonomic identification of the community present in hundreds of samples, could be used for speeding up large-scale stomach content data collection. Yet, for DNA metabarcoding to be routinely implemented, technical challenges should be addressed, such as the potentially complicated sampling logistics, the detection of a high proportion of predator DNA, and the inability to provide reliable abundance estimations. Here, we present a DNA metabarcoding assay developed to examine the diet of five commercially important fish, which can be feasibly incorporated into routinary samplings. The method is devised to speed up the analysis process by avoiding the stomach dissection and content extraction steps, while preventing the amplification of predator DNA by using blocking primers. Tested in mock samples and in real stomach samples, the method has proven effective and shows great effectiveness discerning diet variations due to predator ecology or prey availability. Additionally, by applying our protocol to mackerel stomachs previously analyzed by visual inspection, we showcase how DNA metabarcoding could complement visually based data by detecting overlooked prey by the visual approach. We finally discuss how DNA metabarcoding-based data can contribute to trophic data collection. Our work reinforces the potential of DNA metabarcoding for the study and monitoring of fish trophic interactions and provides a basis for its incorporation into routine monitoring programs, which will be critical for the implementation of ecosystem-based approaches to fisheries management.
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Affiliation(s)
- Oriol Canals
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Anders Lanzén
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
- IKERBASQUE - Basque Foundation for Science, Bilbao, Spain
| | - Iñaki Mendibil
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Eneko Bachiller
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Xavier Corrales
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Eider Andonegi
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Unai Cotano
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
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22
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Canelo T, Marquina D, Chozas S, Bergsten J, Gaytán Á, Pérez-Izquierdo C, Bonal R. Effects of livestock on arthropod biodiversity in Iberian holm oak savannas revealed by metabarcoding. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 365:121619. [PMID: 38963962 DOI: 10.1016/j.jenvman.2024.121619] [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: 04/24/2024] [Revised: 06/12/2024] [Accepted: 06/24/2024] [Indexed: 07/06/2024]
Abstract
Increasing food production while avoiding negative impacts on biodiversity constitutes one of the main challenges of our time. Traditional silvopastoral systems like Iberian oak savannas ("dehesas") set an example, where free-range livestock has been reared for centuries while preserving a high natural value. Nevertheless, factors decreasing productivity need to be addressed, one being acorn losses provoked by pest insects. An increased and focalized grazing by livestock on infested acorns would kill the larvae inside and decrease pest numbers, but increased livestock densities could have undesired side effects on ground arthropod communities as a whole. We designed an experimental setup including areas under trees with livestock exclosures of different ages (short-term: 1-year exclusion, long-term: 10-year exclusion), along with controls (continuous grazing), using DNA metabarcoding (mitochondrial markers COI and 16S) to rapidly assess arthropod communities' composition. Livestock removal quickly increased grass cover and arthropod taxonomic richness and diversity, which was already higher in short-term (1-year exclosures) than beneath the canopies of control trees. Interestingly, arthropod diversity was not highest at long-term exclosures (≥10 years), although their community composition was the most distinct. Also, regardless of treatment, we found that functional diversity strongly correlated with the vegetation structure, being higher at trees beneath which there was higher grass cover and taller herbs. Overall, the taxonomic diversity peak at short term exclosures would support the intermediate disturbance hypothesis, which relates it with the higher microhabitat heterogeneity at moderately disturbed areas. Thus, we propose a rotatory livestock management in dehesas: plots with increased grazing should co-exist with temporal short-term exclosures. Ideally, a few long-term excluded areas should be also kept for the singularity of their arthropod communities. This strategy would make possible the combination of biological pest control and arthropod conservation in Iberian dehesas.
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Affiliation(s)
- Tara Canelo
- Dpto. Ingeniería del Medio Agronómico y Forestal. Grupo de Investigación Forestal, INDEHESA, Centro Universitario de Plasencia, Universidad de Extremadura, Avda. Virgen del Puerto 2, 10600, Plasencia, Cáceres, Spain; Centro de Ecologia Aplicada "Prof. Baeta Neves" (CEABN), Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisboa, Portugal.
| | - Daniel Marquina
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden; Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Sergio Chozas
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute. FCUL: Sciences Faculty of the University of Lisbon Campo Grande, Portugal
| | - Johannes Bergsten
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Álvaro Gaytán
- Instituto de Recursos Naturales y Agrobiología de Sevilla, Consejo Superior de Investigaciones Científicas (IRNAS-CSIC), Sevilla, Spain
| | - Carlos Pérez-Izquierdo
- Dpto. Ingeniería del Medio Agronómico y Forestal. Grupo de Investigación Forestal, INDEHESA, Centro Universitario de Plasencia, Universidad de Extremadura, Avda. Virgen del Puerto 2, 10600, Plasencia, Cáceres, Spain
| | - Raúl Bonal
- Dpto. Ingeniería del Medio Agronómico y Forestal. Grupo de Investigación Forestal, INDEHESA, Centro Universitario de Plasencia, Universidad de Extremadura, Avda. Virgen del Puerto 2, 10600, Plasencia, Cáceres, Spain; Department of Biodiversity, Ecology and Evolution. Complutense University of Madrid, Spain
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23
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Jarman S, Alexander JB, Dawkins KL, Lukehurst SS, Nester GM, Wilkinson S, Marnane MJ, McDonald JI, Elsdon TS, Harvey ES. Marine eDNA sampling from submerged surfaces with paint rollers. Mar Genomics 2024; 76:101127. [PMID: 38905943 DOI: 10.1016/j.margen.2024.101127] [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: 02/16/2024] [Revised: 06/13/2024] [Accepted: 06/16/2024] [Indexed: 06/23/2024]
Abstract
Environmental DNA (eDNA) analyses of species present in marine environments is the most effective biological diversity measurement tool currently available. eDNA sampling methods are an intrinsically important part of the eDNA biodiversity analysis process. Identification and development of eDNA sampling methods that are as rapid, affordable, versatile and practical as possible will improve rates of detection of marine species. Optimal outcomes of eDNA biodiversity surveys come from studies employing high levels of sampling replication, so any methods that make sampling faster and cheaper will improve scientific outcomes. eDNA sampling methods that can be applied more widely will also enable sampling from a greater range of marine surface micro-habitats, resulting in detection of a wider range of organisms. In this study, we compared diversity detection by several methods for sampling eDNA from submerged marine surfaces: polyurethane foam, nylon swabs, microfibre paint rollers, and sediment scoops. All of the methods produced a diverse range of species identifications, with >250 multicellular species represented by eDNA at the study site. We found that widely-available small paint rollers were an effective, readily available and affordable method for sampling eDNA from underwater marine surfaces. This approach enables the sampling of marine eDNA using extended poles, or potentially by remotely operated vehicles, where surface sampling by hand is impractical.
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Affiliation(s)
- Simon Jarman
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; eDNA Frontiers, Curtin University, Bentley, WA, Australia.
| | - Jason B Alexander
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | | | | | - Georgia M Nester
- Minderoo-UWA Deep Sea Research Centre, University of Western Australia, Crawley, WA, Australia
| | - Shaun Wilkinson
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Wilderlab, Miramar, Wellington, New Zealand
| | - Michael J Marnane
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Chevron Technical Center, Perth, Western Australia, Australia
| | - Justin I McDonald
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Sustainability and Biosecurity, Department of Primary Industries and Regional Development (DPIRD), Hillarys, 6025, Western Australia, Australia
| | - Travis S Elsdon
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Chevron Technical Center, Perth, Western Australia, Australia
| | - Euan S Harvey
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
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24
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Fueyo Á, Sánchez O, Carleos C, Escudero A, Cordón J, Granero‐Castro J, Borrell YJ. Unlocking rivers' hidden diversity and ecological status using DNA metabarcoding in Northwest Spain. Ecol Evol 2024; 14:e70110. [PMID: 39100209 PMCID: PMC11294579 DOI: 10.1002/ece3.70110] [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: 04/09/2024] [Revised: 07/05/2024] [Accepted: 07/18/2024] [Indexed: 08/06/2024] Open
Abstract
Rivers are crucial ecosystems supporting biodiversity and human well-being, yet they face increasing degradation globally. Traditional river biomonitoring methods based on morphological identification of macroinvertebrates present challenges in terms of taxonomic resolution and scalability. This study explores the application of DNA metabarcoding analysis in both bulk and environmental DNA (eDNA) samples for comprehensive assessment of macrozoobenthic biodiversity, detection of invasive and endangered species, and evaluation of river ecological status in northwestern Spain. DNA metabarcoding of homogenized bulk samples and water eDNA revealed a mean of 100 and 87 macrozoobenthos species per sample respectively. However, the specific composition was significantly different with only 27.3% of the total species being shared. It was not possible to identify all the OTUs to species level; only 17.43% and 49.4% of the OTUs generated could be identified to species level in the bulk and eDNA samples, respectively. Additionally, a total of 11 exotic species (two first records for the Iberian Peninsula and another three first records for Asturias region) and one endangered species were detected by molecular tools. Molecular methods showed significant correlations with morphological identification for EQR values (Ecological Quality Ratio) of IBMWP index, yet differences in inferred river ecological status were noted, with bulk samples tending to indicate higher status. Overall, DNA metabarcoding offers a promising approach for river biomonitoring, providing insights into biodiversity, invasive species, and ecological status within a single analysis. Further optimization and intercalibration are required for its implementation in routine biomonitoring programmes, but its scalability and multi-tasking capabilities position it as a valuable tool for integrated monitoring of river ecosystems.
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Affiliation(s)
- Álvaro Fueyo
- Environment and Sustainability Area, Taxus Medio AmbienteOviedoSpain
- Department of Functional Biology, GeneticsUniversity of OviedoOviedoSpain
| | - Omar Sánchez
- Environment and Sustainability Area, Taxus Medio AmbienteOviedoSpain
- Department of Organisms and Systems Biology, ZoologyUniversity of OviedoOviedoSpain
| | - Carlos Carleos
- Department of Statistics and Operations Research and Mathematics DidacticsUniversity of OviedoOviedoSpain
| | - Amando Escudero
- Environment and Sustainability Area, Taxus Medio AmbienteOviedoSpain
| | - Javier Cordón
- Environment and Sustainability Area, Taxus Medio AmbienteOviedoSpain
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25
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Macher JN, Martínez A, Çakir S, Cholley PE, Christoforou E, Curini Galletti M, van Galen L, García-Cobo M, Jondelius U, de Jong D, Leasi F, Lemke M, Rubio Lopez I, Sánchez N, Sørensen MV, Todaro MA, Renema W, Fontaneto D. Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: A case study on beach meiofauna. Mol Ecol Resour 2024:e13997. [PMID: 39086104 DOI: 10.1111/1755-0998.13997] [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: 03/01/2024] [Revised: 07/03/2024] [Accepted: 07/15/2024] [Indexed: 08/02/2024]
Abstract
Molecular techniques like metabarcoding, while promising for exploring diversity of communities, are often impeded by the lack of reference DNA sequences available for taxonomic annotation. Our study explores the benefits of combining targeted DNA barcoding and morphological taxonomy to improve metabarcoding efficiency, using beach meiofauna as a case study. Beaches are globally important ecosystems and are inhabited by meiofauna, microscopic animals living in the interstitial space between the sand grains, which play a key role in coastal biodiversity and ecosystem dynamics. However, research on meiofauna faces challenges due to limited taxonomic expertise and sparse sampling. We generated 775 new cytochrome c oxidase I DNA barcodes from meiofauna specimens collected along the Netherlands' west coast and combined them with the NCBI GenBank database. We analysed alpha and beta diversity in 561 metabarcoding samples from 24 North Sea beaches, a region extensively studied for meiofauna, using both the enriched reference database and the NCBI database without the additional reference barcodes. Our results show a 2.5-fold increase in sequence annotation and a doubling of species-level Operational Taxonomic Units (OTUs) identification when annotating the metabarcoding data with the enhanced database. Additionally, our analyses revealed a bell-shaped curve of OTU richness across the intertidal zone, aligning more closely with morphological analysis patterns, and more defined community dissimilarity patterns between supralittoral and intertidal sites. Our research highlights the importance of expanding molecular reference databases and combining morphological taxonomy with molecular techniques for biodiversity assessments, ultimately improving our understanding of coastal ecosystems.
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Affiliation(s)
- Jan-Niklas Macher
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
- Department of Environmental Biology, Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands
| | - Alejandro Martínez
- National Research Council of Italy (CNR), Water Research Institute (IRSA), Verbania Pallanza, Italy
| | - Sude Çakir
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
| | | | - Eleni Christoforou
- Cyprus Marine and Maritime Institute, CMMI House, Larnaca, Cyprus
- Department of Chemical Engineering, Cyprus University of Technology, Limassol, Cyprus
| | - Marco Curini Galletti
- Dipartimento di Medicina Veterinaria, Università di Sassari, Sassari, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Lotte van Galen
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
| | - Marta García-Cobo
- Department of Biodiversity, Ecology and Evolution, Universidad Complutense de Madrid, Madrid, Spain
| | - Ulf Jondelius
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Daphne de Jong
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
| | - Francesca Leasi
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, Tennessee, USA
| | - Michael Lemke
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
| | - Iñigo Rubio Lopez
- National Research Council of Italy (CNR), Water Research Institute (IRSA), Verbania Pallanza, Italy
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Prague 2, Czech Republic
| | - Nuria Sánchez
- Department of Biodiversity, Ecology and Evolution, Universidad Complutense de Madrid, Madrid, Spain
| | | | - M Antonio Todaro
- National Biodiversity Future Center (NBFC), Palermo, Italy
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Willem Renema
- Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Diego Fontaneto
- National Research Council of Italy (CNR), Water Research Institute (IRSA), Verbania Pallanza, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
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Thomas LJ, Kirse A, Raus H, Langen K, Nümann B, Tschan GF, Gemeinholzer B, Wägele JW, Bourlat SJ. Synchronised monitoring of plant and insect diversity: a case study using automated Malaise traps and DNA-based methods. Biodivers Data J 2024; 12:e127669. [PMID: 39114129 PMCID: PMC11303846 DOI: 10.3897/bdj.12.e127669] [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: 05/16/2024] [Accepted: 07/04/2024] [Indexed: 08/10/2024] Open
Abstract
The occurrence and distribution of insects and their possible associations with plant species are largely unknown in Germany and baseline data to monitor future trends are urgently needed. Using newly-designed automated Malaise trap multi-samplers, the occurrence of insect species and their potential associations with plants was monitored synchronously at two contrasting field sites in Germany: an urban botanical garden and a forest research station. Taxa were identified by metabarcoding of the insects and the plant traces present in the preservative ethanol of the Malaise trap samples. For comparison, a botanical survey was conducted in the vicinity of the traps. Across both sites, we identified a total of 1290 exact sequence variants (ESVs) assigned to Insecta, of which 205 are known to be pollinators. In the botanical garden, we detected the occurrence of 128 plant taxa, of which 41 also had one of their known insect pollinator species detected. Insect species richness was highest in May, mainly attributed to an increase in Diptera. These results present a case study of the applicability of automated sampling and DNA-based methods to monitor the timings of flowering and corresponding activity of plant-visiting insects.
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Affiliation(s)
- Leighton J Thomas
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, GermanyLeibniz Institute for the Analysis of Biodiversity Change, Museum KoenigBonnGermany
| | - Ameli Kirse
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, GermanyLeibniz Institute for the Analysis of Biodiversity Change, Museum KoenigBonnGermany
| | - Hanna Raus
- University of Kassel, Kassel, GermanyUniversity of KasselKasselGermany
| | - Kathrin Langen
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, GermanyLeibniz Institute for the Analysis of Biodiversity Change, Museum KoenigBonnGermany
| | - Björn Nümann
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, GermanyLeibniz Institute for the Analysis of Biodiversity Change, Museum KoenigBonnGermany
| | - Georg F. Tschan
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, GermanyLeibniz Institute for the Analysis of Biodiversity Change, Museum KoenigBonnGermany
| | | | - J. Wolfgang Wägele
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, GermanyLeibniz Institute for the Analysis of Biodiversity Change, Museum KoenigBonnGermany
| | - Sarah J Bourlat
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, GermanyLeibniz Institute for the Analysis of Biodiversity Change, Museum KoenigBonnGermany
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27
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Sánchez Reyes LL, McTavish EJ, O’Meara B. DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life. Syst Biol 2024; 73:470-485. [PMID: 38507308 PMCID: PMC11282365 DOI: 10.1093/sysbio/syae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 03/09/2024] [Accepted: 03/18/2024] [Indexed: 03/22/2024] Open
Abstract
Chronograms-phylogenies with branch lengths proportional to time-represent key data on timing of evolutionary events, allowing us to study natural processes in many areas of biological research. Chronograms also provide valuable information that can be used for education, science communication, and conservation policy decisions. Yet, achieving a high-quality reconstruction of a chronogram is a difficult and resource-consuming task. Here we present DateLife, a phylogenetic software implemented as an R package and an R Shiny web application available at www.datelife.org, that provides services for efficient and easy discovery, summary, reuse, and reanalysis of node age data mined from a curated database of expert, peer-reviewed, and openly available chronograms. The main DateLife workflow starts with one or more scientific taxon names provided by a user. Names are processed and standardized to a unified taxonomy, allowing DateLife to run a name match across its local chronogram database that is curated from Open Tree of Life's phylogenetic repository, and extract all chronograms that contain at least two queried taxon names, along with their metadata. Finally, node ages from matching chronograms are mapped using the congruification algorithm to corresponding nodes on a tree topology, either extracted from Open Tree of Life's synthetic phylogeny or one provided by the user. Congruified node ages are used as secondary calibrations to date the chosen topology, with or without initial branch lengths, using different phylogenetic dating methods such as BLADJ, treePL, PATHd8, and MrBayes. We performed a cross-validation test to compare node ages resulting from a DateLife analysis (i.e, phylogenetic dating using secondary calibrations) to those from the original chronograms (i.e, obtained with primary calibrations), and found that DateLife's node age estimates are consistent with the age estimates from the original chronograms, with the largest variation in ages occurring around topologically deeper nodes. Because the results from any software for scientific analysis can only be as good as the data used as input, we highlight the importance of considering the results of a DateLife analysis in the context of the input chronograms. DateLife can help to increase awareness of the existing disparities among alternative hypotheses of dates for the same diversification events, and to support exploration of the effect of alternative chronogram hypotheses on downstream analyses, providing a framework for a more informed interpretation of evolutionary results.
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Affiliation(s)
- Luna L Sánchez Reyes
- Department of Life and Environmental Sciences, University of California, Merced, CA 95343, USA
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, 446 Hesler Biology Building, Knoxville, TN 37996, USA
| | - Emily Jane McTavish
- Department of Life and Environmental Sciences, University of California, Merced, CA 95343, USA
| | - Brian O’Meara
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, 446 Hesler Biology Building, Knoxville, TN 37996, USA
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Pozzobon APB, Ready JS, Di Dario F, Nunes-da-Fonseca R. Identification of pre-flexion fish larvae from the western South Atlantic using DNA barcoding and morphological characters. PeerJ 2024; 12:e17791. [PMID: 39071121 PMCID: PMC11283777 DOI: 10.7717/peerj.17791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 07/01/2024] [Indexed: 07/30/2024] Open
Abstract
Knowledge on species composition is the first step necessary for the proper conservation and management of biological resources and ecologically relevant species. High species diversity and a lack of diagnostic characters for some groups can impose difficulties for taxonomic identification through traditional methodologies, and ichthyoplankton (fish larvae and eggs) are a good example of such a scenario. With more than 35.000 valid species of fishes worldwide and overall similar anatomies in early developmental stages in closely related groups, fish larvae are often hard to be identified at the species or even more encompassing taxonomic levels. To overcome this situation, molecular techniques have been applied, with different markers tested over the years. Cytochrome c oxidase I (COI) is the most commonly used marker and now has the broadest public reference libraries, providing consistent results for species identification in different metazoan studies. Here we sequenced the mitochondrial COI-5P fragment of 89 fish larvae collected in the Campos Basin, coastal southeastern Brazil, and compared these sequences with references deposited in public databases to obtain taxonomic identifications. Most specimens identified are species of the Blenniiformes, with Parablennius and Labrisomus the most frequently identified genera. Parablennius included two species (P. marmoreus and P. pilicornis), while Labrisomus included three species (L. cricota, L. conditus and L. nuchipinnis). Anatomy of these molecularly identified specimens were then analyzed with the intention of finding anatomical characters that might be diagnostically informative amongst the early development stage (pre-flexion) larvae. Ventral pigmentation patterns are proposed as useful markers to identify Labrisomus species. However, additional specimens are needed to confirm if the character holds stability through the geographic distribution of the species.
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Affiliation(s)
- Allan Pierre Bonetti Pozzobon
- Instituto de Biodiversidade e Sustentabilidade (NUPEM), Universidade Federal do Rio de Janeiro (UFRJ), Macaé, Rio de Janeiro, Brazil
- Programa de Pós-Graduação em Ciências Ambientais e Conservação (PPG-CiAC), Instituto de Biodiversidade e Sustentabilidade (NUPEM), Universidade Federal do Rio de Janeiro (UFRJ), Macaé, Rio de Janeiro, Brazil
| | - Jonathan Stuart Ready
- Group for Integrated Biological Investigations, Center for Advanced Biodiversity Studies, Federal University of Pará (UFPA), Belém, Pará, Brazil
| | - Fabio Di Dario
- Instituto de Biodiversidade e Sustentabilidade (NUPEM), Universidade Federal do Rio de Janeiro (UFRJ), Macaé, Rio de Janeiro, Brazil
- Programa de Pós-Graduação em Ciências Ambientais e Conservação (PPG-CiAC), Instituto de Biodiversidade e Sustentabilidade (NUPEM), Universidade Federal do Rio de Janeiro (UFRJ), Macaé, Rio de Janeiro, Brazil
| | - Rodrigo Nunes-da-Fonseca
- Instituto de Biodiversidade e Sustentabilidade (NUPEM), Universidade Federal do Rio de Janeiro (UFRJ), Macaé, Rio de Janeiro, Brazil
- Programa de Pós-Graduação em Ciências Ambientais e Conservação (PPG-CiAC), Instituto de Biodiversidade e Sustentabilidade (NUPEM), Universidade Federal do Rio de Janeiro (UFRJ), Macaé, Rio de Janeiro, Brazil
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29
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Hübner J, Chemyreva V, Macek J, Kolyada V. A review of the genus Zygota (Hymenoptera, Diapriidae) in Germany with taxonomic notes on this genus and its distinction from Pantoclis. Zookeys 2024; 1207:325-353. [PMID: 39091449 PMCID: PMC11292123 DOI: 10.3897/zookeys.1207.121725] [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: 02/29/2024] [Accepted: 05/16/2024] [Indexed: 08/04/2024] Open
Abstract
This study provides a comprehensive overview of the genus Zygota Förster combining DNA barcoding and current morphology. Nineteen species of Zygota were found throughout Germany, including the newly described species Zygotawalli sp. nov. First species records for Germany are: Zygotabalteata Macek, 1997; Z.comitans Macek, 1997; Z.spinosipes (Kieffer, 1908); Z.sordida Macek, 1997; Z.angularis Macek, 1997 and Z.vigil Nixon, 1957. We also clarify diagnoses for the two related genera, Pantoclis Förster and Zygota to designate the boundaries of the Zygota genus and propose new synonymies: Zygotacaligula Buhl, 1997 is a junior synonym of Z.congener (Zetterstedt, 1840); Z.reticulata Kozlov, 1978 is a junior synonym of Z.ruficornis (Curtis, 1831). Thirteen species of Zygota sensu Nixon (1957) are transferred to the genus Pantoclis with the following new combinations proposed: Zygotabrevinervis (Kieffer, 1908) (= Pantoclisbrevinervis (Kieffer, 1909), comb. nov.); Z.brevipennis (Kieffer, 1908) (= P.brevipennis (Kieffer, 1908), comb. nov.); Z.caecutiens (Kieffer, 1908) (= P.caecutiens (Kieffer, 1908), comb. nov.); Z.cursor (Kieffer, 1908) (= P.cursor (Kieffer, 1908), comb. nov.); Z.fossulata (Thomson, 1858) (=P.fossulata (Thomson, 1858), comb. nov.); Z.fuscata (Thomson, 1858) (= P.fuscata (Thomson, 1858), comb. nov.); Z.hemiptera (Thomson, 1858) (= P.hemiptera (Thomson, 1858), comb. nov.); Z.microtoma (Kieffer, 1909) (= P.microtoma (Kieffer, 1909), comb. nov.); Z.soluta (Kieffer, 1907) (= P.soluta (Kieffer, 1907), comb. nov.); Z.striata (Kieffer, 1909) (= P.striata (Kieffer, 1909), comb. nov.); Z.subaptera (Thomson, 1858) (= P.subaptera (Thomson, 1858), comb. nov.); Z.sulciventris (Kieffer, 1909) (= P.sulciventris (Kieffer, 1909), comb. nov.), and Z.unicolor (Kieffer, 1908) (= P.unicolor (Kieffer, 1908), comb. nov.).
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Affiliation(s)
- Jeremy Hübner
- Bavarian State Collection of Zoology, Munich, Münchhausenstr. 21, 81247 Munich, GermanyBavarian State Collection of ZoologyMunichGermany
| | - Vasilisa Chemyreva
- Zoological Institute, Russian Academy of Sciences, 1 Universitetskaya Emb., St Petersburg 199034, RussiaZoological Institute, Russian Academy of SciencesSt. PetersburgRussia
| | - Jan Macek
- National Museum, Department of Entomology, Praha, Czech RepublicNational MuseumPragueCzech Republic
| | - Victor Kolyada
- Palaeontological Institute, Russian Academy of Sciences, Moscow 117997, RussiaPalaeontological Institute, Russian Academy of SciencesMoscowRussia
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Miller ML, Rota C, Welsh A. Transforming gastrointestinal helminth parasite identification in vertebrate hosts with metabarcoding: a systematic review. Parasit Vectors 2024; 17:311. [PMID: 39030625 PMCID: PMC11265005 DOI: 10.1186/s13071-024-06388-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 07/03/2024] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND Gastrointestinal helminths are a very widespread group of intestinal parasites that can cause major health issues in their hosts, including severe illness or death. Traditional methods of helminth parasite identification using microscopy are time-consuming and poor in terms of taxonomic resolution, and require skilled observers. DNA metabarcoding has emerged as a powerful alternative for assessing community composition in a variety of sample types over the last few decades. While metabarcoding approaches have been reviewed for use in other research areas, the use of metabarcoding for parasites has only recently become widespread. As such, there is a need to synthesize parasite metabarcoding methodology and highlight the considerations to be taken into account when developing a protocol. METHODS We reviewed published literature that utilized DNA metabarcoding to identify gastrointestinal helminth parasites in vertebrate hosts. We extracted information from 62 peer-reviewed papers published between 2014 and 2023 and created a stepwise guide to the metabarcoding process. RESULTS We found that studies in our review varied in technique and methodology, such as the sample type utilized, genetic marker regions targeted and bioinformatic databases used. The main limitations of metabarcoding are that parasite abundance data may not be reliably attained from sequence read numbers, metabarcoding data may not be representative of the species present in the host and the cost and bioinformatic expertise required to utilize this method may be prohibitive to some groups. CONCLUSIONS Overall, using metabarcoding to assess gastrointestinal parasite communities is preferable to traditional methods, yielding higher taxonomic resolution, higher throughput and increased versatility due to its utility in any geographical location, with a variety of sample types, and with virtually any vertebrate host species. Additionally, metabarcoding has the potential for exciting new discoveries regarding host and parasite evolution.
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Affiliation(s)
- Madison L Miller
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA.
| | - Christopher Rota
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA
| | - Amy Welsh
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, USA
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31
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Esayas E, Assefa M, Bennett A, Thomsen E, Gowelo S, Vajda E, Getachew A, Ashine T, Yeshaneh A, Kassa FA, Demisse M, Ntuku H, Dinka H, Golassa L, Lobo NF, Gadisa E. Bionomic characterization of Anopheles mosquitoes in the Ethiopian highlands and lowlands. Parasit Vectors 2024; 17:306. [PMID: 39014474 PMCID: PMC11251230 DOI: 10.1186/s13071-024-06378-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 06/26/2024] [Indexed: 07/18/2024] Open
Abstract
BACKGROUND The protective effectiveness of vector control in malaria relies on how the implemented tools overlap with mosquito species-specific compositions and bionomic traits. In Ethiopia, targeted entomological data enabling strategic decision-making are lacking around high-risk migrant worker camps in the lowlands and resident communities in the highlands-resulting in suboptimal malaria control strategies for both populations. This study investigates spatial and temporal mosquito behavior, generating baseline evidence that will improve malaria control for both migrant workers in the lowlands and their home communities in the highlands. METHODS Hourly Centers for Disease Control and Prevention (CDC) light trap collections were performed indoors and outdoors during the peak (October to December 2022) and minor (March to May 2023) malaria transmission seasons. These seasons coincide with the post-long rain and post-short rain seasons, respectively. Eight resident households were sampled from each of four villages in the highlands and eight households/farm structures on and near farms in four villages in the lowlands. The sampling occurred between 18:00 and 06:00. Spatiotemporal vector behaviors and hourly indoor and outdoor mosquito capture rates, used as a proxy for human biting rates, were calculated for overall catches and for individual species. Adult mosquitoes were identified using morphological keys, and a subset of samples were confirmed to species by sequencing ribosomal DNA internal transcribed spacer region 2 (ITS2) and/or mitochondrial DNA cytochrome c oxidase subunit 1 (Cox1). RESULTS In the highlands, 4697 Anopheles mosquitoes belonging to 13 morphologically identified species were collected. The predominant species of Anopheles identified in the highlands was An. gambiae sensu lato (s.l.) (n = 1970, 41.9%), followed by An. demeilloni (n = 1133, 24.1%) and An. cinereus (n = 520, 11.0%). In the lowland villages, 3220 mosquitoes belonging to 18 morphological species were collected. Anopheles gambiae s.l. (n = 1190, 36.9%), An. pretoriensis (n = 899, 27.9%), and An. demeilloni (n = 564, 17.5%) were the predominant species. A total of 20 species were identified molecularly, of which three could not be identified to species through comparison with published sequences. In highland villages, the indoor Anopheles mosquito capture rate was much greater than the outdoor rate. This trend reversed in the lowlands, where the rate of outdoor captures was greater than the indoor rate. In both highlands and lowlands, Anopheles mosquitoes showed early biting activities in the evening, which peaked between 18:00 and 21:00, for both indoor and outdoor locations. CONCLUSIONS The high diversity of Anopheles vectors and their variable behaviors result in a dynamic and resilient transmission system impacting both exposure to infectious bites and intervention effectiveness. This creates gaps in protection allowing malaria transmission to persist. To achieve optimal control, one-size-fits-all strategies must be abandoned, and interventions should be tailored to the diverse spatiotemporal behaviors of different mosquito populations.
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Affiliation(s)
- Endashaw Esayas
- Malaria and Neglected Tropical Diseases Research Division, Armauer Hansen Research Institute, Addis Ababa, Ethiopia.
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia.
| | - Muluken Assefa
- Malaria and Neglected Tropical Diseases Research Division, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Adam Bennett
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Seattle, USA
| | - Edward Thomsen
- Malaria Elimination Initiative, University of California San Francisco, San Francisco, USA
| | - Steven Gowelo
- Malaria Elimination Initiative, University of California San Francisco, San Francisco, USA
| | - Elodie Vajda
- Malaria Elimination Initiative, University of California San Francisco, San Francisco, USA
| | - Asefaw Getachew
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Addis Ababa, Ethiopia
| | - Temesgen Ashine
- Malaria and Neglected Tropical Diseases Research Division, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Abebaw Yeshaneh
- West Gondar Zone Health Department, Amhara Regional Health Bureau, Metema, Ethiopia
| | - Fikregabrail Aberra Kassa
- Malaria and Neglected Tropical Diseases Research Division, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Mulugeta Demisse
- Malaria and Neglected Tropical Diseases Research Division, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Henry Ntuku
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Seattle, USA
| | - Hunduma Dinka
- Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Neil F Lobo
- Malaria Elimination Initiative, University of California San Francisco, San Francisco, USA
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Endalamaw Gadisa
- Malaria and Neglected Tropical Diseases Research Division, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
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Steinke D, McKeown JTA, Zyba A, McLeod J, Feng C, Hebert PDN. Low-cost, high-volume imaging for entomological digitization. Zookeys 2024; 1206:315-326. [PMID: 39034988 PMCID: PMC11258454 DOI: 10.3897/zookeys.1206.123670] [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: 03/26/2024] [Accepted: 05/10/2024] [Indexed: 07/23/2024] Open
Abstract
Large-scale digitization of natural history collections requires automation of image acquisition and processing. Reflecting this fact, various approaches, some highly sophisticated, have been developed to support imaging of museum specimens. However, most of these systems are complex and expensive, restricting their deployment. Here we describe a simple, inexpensive technique for imaging arthropods larger than 5 mm. By mounting a digital SLR camera on a CNC (computer numerical control) motor-drive rig, we created a system that captures high-resolution z-axis stacked images (6960 × 4640 pixels) of 95 specimens in 30 minutes. This system can be assembled inexpensively ($1000 USD without a camera) and it is easy to set-up and maintain. By coupling low cost with high production capacity, it represents a solution for digitizing any natural history collection.
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Affiliation(s)
- Dirk Steinke
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, CanadaUniversity of GuelphGuelphCanada
| | - Jaclyn T. A. McKeown
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, CanadaUniversity of GuelphGuelphCanada
| | - Allison Zyba
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, CanadaUniversity of GuelphGuelphCanada
| | - Joschka McLeod
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, CanadaUniversity of GuelphGuelphCanada
| | - Corey Feng
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, CanadaUniversity of GuelphGuelphCanada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, CanadaUniversity of GuelphGuelphCanada
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Kremenetskaia A, Alvestad T, Penney HD, Hamel JF, de Moura Neves B, Côté D, Mercier A. A new species of holothuroid from the Labrador Sea (eastern Canada): Pseudothyonelabradorensis sp. nov. (Echinodermata, Holothuroidea, Dendrochirotida, Sclerodactylidae). Zookeys 2024; 1206:191-206. [PMID: 39015530 PMCID: PMC11249843 DOI: 10.3897/zookeys.1206.123364] [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: 03/19/2024] [Accepted: 06/13/2024] [Indexed: 07/18/2024] Open
Abstract
A new species of holothuroid, Pseudothyonelabradorensis sp. nov. (order Dendrochirotida and family Sclerodactylidae), was discovered off the coast of Labrador (eastern Canada) at a depth of 740-969 m. Two specimens were described based on morphological and genetic parameters. Distinctive characters included pinkish body colour, presence of tube feet on a 'tail', supporting rod-shaped ossicles in the tube feet, and rod-shaped ossicles in the tentacles. To investigate its phylogenetic relationships, partial sequences of COI were obtained for the new species as well as for the type species P.raphanus and another North Atlantic species P.serrifera. According to the phylogenetic analysis, P.labradorensis sp. nov. appeared in a well-supported clade with P.raphanus and P.serrifera. Molecular data also suggest polyphyly of the genus, showing the Northeast Pacific species Pseudothyonebelli recovered outside of the clade containing the type species. Pseudothyonelabradorensis sp. nov. is the first species of the genus from the Northwest Atlantic. A key to the North Atlantic Pseudothyone is provided.
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Affiliation(s)
- Antonina Kremenetskaia
- Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow, RussiaShirshov Institute of Oceanology, Russian Academy of SciencesMoscowRussia
| | - Tom Alvestad
- Department of Natural History, University Museum of Bergen, University of Bergen, Bergen, NorwayUniversity Museum of BergenBergenNorway
| | - Heather D. Penney
- Department of Ocean Sciences, Memorial University, St. John’s, Newfoundland and Labrador, CanadaMemorial UniversitySt. John’sCanada
- Aquatic Resources Program, St. Francis Xavier University, Antigonish, Nova Scotia, CanadaSt. Francis Xavier UniversityAntigonishCanada
| | - Jean-François Hamel
- Society for the Exploration and Valuing of the Environment (SEVE), St. Philips, Newfoundland and Labrador, CanadaSociety for the Exploration and Valuing of the EnvironmentSt. PhilipsCanada
| | - Bárbara de Moura Neves
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John’s, Newfoundland and Labrador, CanadaNorthwest Atlantic Fisheries Centre, Fisheries and Oceans CanadaSt. John’sCanada
| | - David Côté
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John’s, Newfoundland and Labrador, CanadaNorthwest Atlantic Fisheries Centre, Fisheries and Oceans CanadaSt. John’sCanada
| | - Annie Mercier
- Department of Ocean Sciences, Memorial University, St. John’s, Newfoundland and Labrador, CanadaMemorial UniversitySt. John’sCanada
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Chaumeau V, Piarroux M, Kulabkeeree T, Sawasdichai S, Inta A, Watthanaworawit W, Nosten F, Piarroux R, Nabet C. Identification of Southeast Asian Anopheles mosquito species using MALDI-TOF mass spectrometry. PLoS One 2024; 19:e0305167. [PMID: 38968228 PMCID: PMC11226003 DOI: 10.1371/journal.pone.0305167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/24/2024] [Indexed: 07/07/2024] Open
Abstract
Malaria elimination in Southeast Asia remains a challenge, underscoring the importance of accurately identifying malaria mosquitoes to understand transmission dynamics and improve vector control. Traditional methods such as morphological identification require extensive training and cannot distinguish between sibling species, while molecular approaches are costly for extensive screening. Matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid and cost-effective tool for Anopheles species identification, yet its current use is limited to few specialized laboratories. This study aimed to develop and validate an online reference database for MALDI-TOF MS identification of Southeast Asian Anopheles species. The database, constructed using the in-house data analysis pipeline MSI2 (Sorbonne University), comprised 2046 head mass spectra from 209 specimens collected at the Thailand-Myanmar border. Molecular identification via COI and ITS2 DNA barcodes enabled the identification of 20 sensu stricto species and 5 sibling species complexes. The high quality of the mass spectra was demonstrated by a MSI2 median score (min-max) of 61.62 (15.94-77.55) for correct answers, using the best result of four technical replicates of a test panel. Applying an identification threshold of 45, 93.9% (201/214) of the specimens were identified, with 98.5% (198/201) consistency with the molecular taxonomic assignment. In conclusion, MALDI-TOF MS holds promise for malaria mosquito identification and can be scaled up for entomological surveillance in Southeast Asia. The free online sharing of our database on the MSI2 platform (https://msi.happy-dev.fr/) represents an important step towards the broader use of MALDI-TOF MS in malaria vector surveillance.
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Affiliation(s)
- Victor Chaumeau
- Faculty of Tropical Medicine, Shoklo Malaria Research Unit, Mahidol-Oxford Research Unit, Mahidol University, Mae Ramat, Thailand
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Martine Piarroux
- Institut Pierre-Louis d’Epidémiologie et de Santé Publique, Inserm, IPLESP, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie-Mycologie, Sorbonne Université, Paris, France
| | - Thithiworada Kulabkeeree
- Faculty of Tropical Medicine, Shoklo Malaria Research Unit, Mahidol-Oxford Research Unit, Mahidol University, Mae Ramat, Thailand
| | - Sunisa Sawasdichai
- Faculty of Tropical Medicine, Shoklo Malaria Research Unit, Mahidol-Oxford Research Unit, Mahidol University, Mae Ramat, Thailand
| | - Aritsara Inta
- Faculty of Tropical Medicine, Shoklo Malaria Research Unit, Mahidol-Oxford Research Unit, Mahidol University, Mae Ramat, Thailand
| | - Wanitda Watthanaworawit
- Faculty of Tropical Medicine, Shoklo Malaria Research Unit, Mahidol-Oxford Research Unit, Mahidol University, Mae Ramat, Thailand
| | - François Nosten
- Faculty of Tropical Medicine, Shoklo Malaria Research Unit, Mahidol-Oxford Research Unit, Mahidol University, Mae Ramat, Thailand
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Renaud Piarroux
- Institut Pierre-Louis d’Epidémiologie et de Santé Publique, Inserm, IPLESP, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie-Mycologie, Sorbonne Université, Paris, France
| | - Cécile Nabet
- Institut Pierre-Louis d’Epidémiologie et de Santé Publique, Inserm, IPLESP, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie-Mycologie, Sorbonne Université, Paris, France
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Walt HK, King JG, Towles TB, Ahn SJ, Hoffmann FG. Comparative Genomics and the Salivary Transcriptome of the Redbanded Stink Bug Shed Light on Its High Damage Potential to Soybean. Genome Biol Evol 2024; 16:evae121. [PMID: 38864488 PMCID: PMC11226756 DOI: 10.1093/gbe/evae121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 05/28/2024] [Accepted: 06/05/2024] [Indexed: 06/13/2024] Open
Abstract
The redbanded stink bug, Piezodorus guildinii (Westwood) (Hemiptera: Pentatomidae), is a significant soybean pest in the Americas, which inflicts more physical damage on soybean than other native stink bugs. Studies suggest that its heightened impact is attributed to the aggressive digestive properties of its saliva. Despite its agricultural importance, the factors driving its greater ability to degrade plant tissues have remained unexplored in a genomic evolutionary context. In this study, we hypothesized that lineage-specific gene family expansions have increased the copy number of digestive genes expressed in the salivary glands. To investigate this, we annotated a previously published genome assembly of the redbanded stink bug, performed a comparative genomic analysis on 11 hemipteran species, and reconstructed patterns of gene duplication, gain, and loss in the redbanded stink bug. We also performed RNA-seq on the redbanded stink bug's salivary tissues, along with the rest of the body without salivary glands. We identified hundreds of differentially expressed salivary genes, including a subset lost in other stink bug lineages, but retained and expressed in the redbanded stink bug's salivary glands. These genes were significantly enriched with protein families involved in proteolysis, potentially explaining the redbanded stink bug's heightened damage to soybeans. Contrary to our hypothesis, we found no support for an enrichment of duplicated digestive genes that are also differentially expressed in the salivary glands of the redbanded stink bug. Nonetheless, these results provide insight into the evolution of this important crop pest, establishing a link between its genomic history and its agriculturally important physiology.
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Affiliation(s)
- Hunter K Walt
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Jonas G King
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Tyler B Towles
- Macon Ridge Research Station, Louisiana State University, Winnsboro, LA 71295, USA
| | - Seung-Joon Ahn
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
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Knoll A, Langová L, Přidal A, Urban T. Haplotype Diversity in mtDNA of Honeybee in the Czech Republic Confirms Complete Replacement of Autochthonous Population with the C Lineage. INSECTS 2024; 15:495. [PMID: 39057228 PMCID: PMC11276638 DOI: 10.3390/insects15070495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/28/2024] [Accepted: 06/29/2024] [Indexed: 07/28/2024]
Abstract
The study aimed to analyze the genetic diversity in the Czech population of Apis mellifera using mitochondrial DNA markers, tRNAleu-cox2 intergenic region and cox1 gene. A total of 308 samples of bees were collected from the entire Czech Republic (from colonies and flowers in 13 different regions). Following sequencing, several polymorphisms and haplotypes were identified. Analysis of tRNAleu-cox2 sequences revealed three DraI haplotypes (C, A1, and A4). The tRNAleu-cox2 region yielded 10 C lineage haplotypes, one of which is a newly described variant. Three A lineage haplotypes were identified, two of which were novel. A similar analysis of cox1 sequences yielded 16 distinct haplotypes (7 new) within the population. The most prevalent tRNAleu-cox2 haplotype identified was C1a, followed by C2a, C2c, C2l, and C2d. For the cox1 locus, the most frequent haplotypes were HpB02, HpB01, HpB03, and HpB04. The haplotype and nucleotide diversity indices were high in both loci, in tRNAleu-cox2 with values of 0.682 and 0.00172, respectively, and in cox1 0.789 and 0.00203, respectively. The Tajima's D values were negative and lower in tRNAleu-cox2 than in cox1. The most frequent haplotypes were uniformly distributed across all regions of the Czech Republic. No haplotype of the indigenous M lineage was identified. High diversity and the occurrence of rare haplotypes indicate population expansion and continuous import of tribal material of the C lineage.
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Affiliation(s)
- Aleš Knoll
- Department of Animal Morphology, Physiology and Genetics, Faculty of AgriSciences, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic
| | - Lucie Langová
- Department of Animal Morphology, Physiology and Genetics, Faculty of AgriSciences, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic
| | - Antonín Přidal
- Department of Zoology, Fishery, Hydrobiology and Apidology, Faculty of AgriSciences, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic
| | - Tomáš Urban
- Department of Animal Morphology, Physiology and Genetics, Faculty of AgriSciences, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic
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Charrier E, Chen R, Thundathil N, Gilleard JS. A set of nematode rRNA cistron databases and a primer assessment tool to enable more flexible and comprehensive metabarcoding. Mol Ecol Resour 2024; 24:e13965. [PMID: 38733216 DOI: 10.1111/1755-0998.13965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/25/2024] [Accepted: 04/17/2024] [Indexed: 05/13/2024]
Abstract
The ITS-2-rRNA has been particularly useful for nematode metabarcoding but does not resolve all phylogenetic relationships, and reference sequences are not available for many nematode species. This is a particular issue when metabarcoding complex communities such as wildlife parasites or terrestrial and aquatic free-living nematode communities. We have used markerDB to produce four databases of distinct regions of the rRNA cistron: the 18S rRNA gene, the 28S rRNA gene, the ITS-1 intergenic spacer and the region spanning ITS-1_5.8S_ITS-2. These databases comprise 2645, 254, 13,461 and 10,107 unique full-length sequences representing 1391, 204, 1837 and 1322 nematode species, respectively. The comparative analysis illustrates the complementary value but also reveals a better representation of Clade III, IV and V than Clade I and Clade II nematodes in each case. Although the ITS-1 database includes the largest number of unique full-length sequences, the 18S rRNA database provides the widest taxonomic coverage. We also developed PrimerTC, a tool to assess primer sequence conservation across any reference sequence database, and have applied it to evaluate a large number of previously published rRNA cistron primers. We identified sets of primers that currently provide the broadest taxonomic coverage for each rRNA marker across the nematode phylum. These new resources will facilitate more comprehensive metabarcoding of nematode communities using either short-read or long-read sequencing platforms. Further, PrimerTC is available as a simple WebApp to guide or assess PCR primer design for any genetic marker and/or taxonomic group beyond the nematode phylum.
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Affiliation(s)
- Eléonore Charrier
- Faculty of Veterinary Medicine, Host Parasite Interaction Program, University of Calgary, Calgary, Alberta, Canada
| | - Rebecca Chen
- Faculty of Veterinary Medicine, Host Parasite Interaction Program, University of Calgary, Calgary, Alberta, Canada
| | - Noelle Thundathil
- Faculty of Veterinary Medicine, Host Parasite Interaction Program, University of Calgary, Calgary, Alberta, Canada
| | - John S Gilleard
- Faculty of Veterinary Medicine, Host Parasite Interaction Program, University of Calgary, Calgary, Alberta, Canada
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Allison PF, Pickich ET, Barnett ZC, Garrick RC. DNA barcoding is currently unreliable for species identification in most crayfishes. Ecol Evol 2024; 14:e70050. [PMID: 39041008 PMCID: PMC11260883 DOI: 10.1002/ece3.70050] [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: 02/07/2024] [Revised: 07/06/2024] [Accepted: 07/08/2024] [Indexed: 07/24/2024] Open
Abstract
DNA barcoding is commonly used for species identification. Despite this, there has not been a comprehensive assessment of the utility of DNA barcoding in crayfishes (Decapoda: Astacidea). Here we examined the extent to which local barcoding gaps (used for species identification) and global barcoding gaps (used for species discovery) exist among crayfishes, and whether global gaps met a previously suggested 10× threshold (mean interspecific difference being 10× larger than mean intra specific difference). We examined barcoding gaps using publicly available mitochondrial COI sequence data from the National Center for Biotechnology Information's nucleotide database. We created two versions of the COI datasets used for downstream analyses: one focused on the number of unique haplotypes (N H) per species, and another that focused on total number of sequences (N S; i.e., including redundant haplotypes) per species. A total of 81 species were included, with 58 species and five genera from the family Cambaridae and 23 species from three genera from the family Parastacidae. Local barcoding gaps were present in only 30 species (20 Cambaridae and 10 Parastacidae species). We detected global barcoding gaps in only four genera (Cambarus, Cherax, Euastacus, and Tenuibranchiurus), which were all below (4.2× to 5.2×) the previously suggested 10× threshold. We propose that a ~5× threshold would be a more appropriate working hypothesis for species discovery. While the N H and N S datasets yielded largely similar results, there were some discrepant inferences. To understand why some species lacked a local barcoding gap, we performed species delimitation analyses for each genus using the N H dataset. These results suggest that current taxonomy in crayfishes may be inadequate for the majority of examined species, and that even species with local barcoding gaps present may be in need of taxonomic revisions. Currently, the utility of DNA barcoding for species identification and discovery in crayfish is quite limited, and caution should be exercised when mitochondrial-based approaches are used in place of taxonomic expertise. Assessment of the evidence for local and global barcoding gaps is important for understanding the reliability of molecular species identification and discovery, but outcomes are dependent on the current state of taxonomy. As this improves (e.g., via resolving species complexes, possibly elevating some subspecies to the species-level status, and redressing specimen misidentifications in natural history and other collections), so too will the utility of DNA barcoding.
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Affiliation(s)
| | - Emily T. Pickich
- Department of BiologyUniversity of MississippiUniversityMississippiUSA
| | - Zanethia C. Barnett
- Southern Research StationUSDA Forest Service, Center for Bottomland Hardwoods ResearchClemsonSouth CarolinaUSA
| | - Ryan C. Garrick
- Department of BiologyUniversity of MississippiUniversityMississippiUSA
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Leigh DM, Vandergast AG, Hunter ME, Crandall ED, Funk WC, Garroway CJ, Hoban S, Oyler-McCance SJ, Rellstab C, Segelbacher G, Schmidt C, Vázquez-Domínguez E, Paz-Vinas I. Best practices for genetic and genomic data archiving. Nat Ecol Evol 2024; 8:1224-1232. [PMID: 38789640 DOI: 10.1038/s41559-024-02423-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 04/25/2024] [Indexed: 05/26/2024]
Abstract
Genetic and genomic data are collected for a vast array of scientific and applied purposes. Despite mandates for public archiving, data are typically used only by the generating authors. The reuse of genetic and genomic datasets remains uncommon because it is difficult, if not impossible, due to non-standard archiving practices and lack of contextual metadata. But as the new field of macrogenetics is demonstrating, if genetic data and their metadata were more accessible and FAIR (findable, accessible, interoperable and reusable) compliant, they could be reused for many additional purposes. We discuss the main challenges with existing genetic and genomic data archives, and suggest best practices for archiving genetic and genomic data. Recognizing that this is a longstanding issue due to little formal data management training within the fields of ecology and evolution, we highlight steps that research institutions and publishers could take to improve data archiving.
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Affiliation(s)
- Deborah M Leigh
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.
| | - Amy G Vandergast
- US Geological Survey, Western Ecological Research Center, San Diego, CA, USA
| | - Margaret E Hunter
- US Geological Survey, Wetland & Aquatic Research Center, Gainesville, FL, USA
| | - Eric D Crandall
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - W Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
| | - Colin J Garroway
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sean Hoban
- Center for Tree Science, The Morton Arboretum, Lisle, IL, USA
| | | | | | | | - Chloé Schmidt
- German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig, Leipzig, Germany
| | - Ella Vázquez-Domínguez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Ivan Paz-Vinas
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
- Universite Claude Bernard Lyon 1, LEHNA UMR 5023, CNRS, ENTPE, Villeurbanne, France
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40
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Liu WJ, Liu P, Lei W, Jia Z, He X, Shi W, Tan Y, Zou S, Wong G, Wang J, Wang F, Wang G, Qin K, Gao R, Zhang J, Li M, Xiao W, Guo Y, Xu Z, Zhao Y, Song J, Zhang J, Zhen W, Zhou W, Ye B, Song J, Yang M, Zhou W, Dai Y, Lu G, Bi Y, Tan W, Han J, Gao GF, Wu G. Surveillance of SARS-CoV-2 at the Huanan Seafood Market. Nature 2024; 631:402-408. [PMID: 37019149 DOI: 10.1038/s41586-023-06043-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/03/2023] [Indexed: 04/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019, emerged in December 2019. Its origins remain uncertain. It has been reported that a number of the early human cases of coronavirus disease 2019 had a history of contact with the Huanan Seafood Market. Here we present the results of surveillance for SARS-CoV-2 within the market. From 1 January 2020, after closure of the market, 923 samples were collected from the environment. From 18 January, 457 samples were collected from 18 species of animal, comprising unsold contents of refrigerators and freezers, swabs from stray animals and the contents of a fish tank. Using quantitative real-time polymerase chain reaction (RT-qPCR) and high-throughput sequencing (Bowtie2 analysis), SARS-CoV-2 was detected in 74 (70 RT-qPCR and 4 Bowtie2) environmental samples, but none of the animal samples. Three live viruses were successfully isolated. The viruses from the market shared a nucleotide identity of 99.99% to 100% with the human isolate HCoV-19/Wuhan/IVDC-HB-01/2019. SARS-CoV-2 lineage A (8782T and 28144C) was found in an environmental sample. RNA-sequencing analysis of SARS-CoV-2-positive and SARS-CoV-2-negative environmental samples showed an abundance of different vertebrate genera at the market. In summary, this study provides information about the distribution and prevalence of SARS-CoV-2 in the Huanan Seafood Market during the early stages of the outbreak of coronavirus disease 2019.
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Affiliation(s)
- William J Liu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China.
| | - Peipei Liu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Wenwen Lei
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Zhiyuan Jia
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Xiaozhou He
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Weifeng Shi
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University, and Shandong Academy of Medical Sciences, Tai'an, China
| | - Yun Tan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Ruijin Hospital Affiliated to Shanghai Jiao Tong University (SJTU) School of Medicine, Shanghai, China
| | - Shumei Zou
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Gary Wong
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Ji Wang
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Feng Wang
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Gang Wang
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Kun Qin
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Rongbao Gao
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Jie Zhang
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Min Li
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Wenling Xiao
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yuanyuan Guo
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Ziqian Xu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Yingze Zhao
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Jingdong Song
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Jing Zhang
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Wei Zhen
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Wenting Zhou
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Beiwei Ye
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Juan Song
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Mengjie Yang
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Weimin Zhou
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Yuting Dai
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Ruijin Hospital Affiliated to Shanghai Jiao Tong University (SJTU) School of Medicine, Shanghai, China
| | - Gang Lu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Ruijin Hospital Affiliated to Shanghai Jiao Tong University (SJTU) School of Medicine, Shanghai, China
| | - Yuhai Bi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Wenjie Tan
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Jun Han
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - George F Gao
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China.
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.
| | - Guizhen Wu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China.
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Kim BY, Gellert HR, Church SH, Suvorov A, Anderson SS, Barmina O, Beskid SG, Comeault AA, Crown KN, Diamond SE, Dorus S, Fujichika T, Hemker JA, Hrcek J, Kankare M, Katoh T, Magnacca KN, Martin RA, Matsunaga T, Medeiros MJ, Miller DE, Pitnick S, Schiffer M, Simoni S, Steenwinkel TE, Syed ZA, Takahashi A, Wei KHC, Yokoyama T, Eisen MB, Kopp A, Matute D, Obbard DJ, O’Grady PM, Price DK, Toda MJ, Werner T, Petrov DA. Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life. PLoS Biol 2024; 22:e3002697. [PMID: 39024225 PMCID: PMC11257246 DOI: 10.1371/journal.pbio.3002697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 06/03/2024] [Indexed: 07/20/2024] Open
Abstract
Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab. Here, we build upon our previous methods to perform amplification-free ONT sequencing of single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections, greatly improving the representation of lesser studied drosophilid taxa in whole-genome data. Using Illumina Novaseq X Plus and ONT P2 sequencers with R10.4.1 chemistry, we set a new benchmark for inexpensive hybrid genome assembly at US $150 per genome while assembling genomes from as little as 35 ng of genomic DNA from a single fly. We present 183 new genome assemblies for 179 species as a resource for drosophilid systematics, phylogenetics, and comparative genomics. Of these genomes, 62 are from pooled lab strains and 121 from single adult flies. Despite the sample limitations of working with small insects, most single-fly diploid assemblies are comparable in contiguity (>1 Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family.
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Affiliation(s)
- Bernard Y. Kim
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Hannah R. Gellert
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Samuel H. Church
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut United States of America
| | - Anton Suvorov
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Sean S. Anderson
- Department of Biology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Olga Barmina
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
| | - Sofia G. Beskid
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Aaron A. Comeault
- School of Environmental and Natural Sciences, Bangor University, Bangor, United Kingdom
| | - K. Nicole Crown
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Sarah E. Diamond
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Steve Dorus
- Center for Reproductive Evolution, Department of Biology, Syracuse University, Syracuse, New York, United States of America
| | - Takako Fujichika
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - James A. Hemker
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
| | - Jan Hrcek
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Maaria Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Toru Katoh
- Department of Biological Sciences, Hokkaido University, Sapporo, Japan
| | - Karl N. Magnacca
- Hawaii Invertebrate Program, Division of Forestry & Wildlife, Honolulu, Hawaii, United States of America
| | - Ryan A. Martin
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Teruyuki Matsunaga
- Department of Complexity Science and Engineering, The University of Tokyo, Tokyo, Japan
| | - Matthew J. Medeiros
- Pacific Biosciences Research Center, University of Hawaiʻi, Mānoa, Hawaii, United States of America
| | - Danny E. Miller
- Division of Genetic Medicine, Department of Pediatrics; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Scott Pitnick
- Center for Reproductive Evolution, Department of Biology, Syracuse University, Syracuse, New York, United States of America
| | - Michele Schiffer
- Daintree Rainforest Observatory, James Cook University, Townsville, Australia
| | - Sara Simoni
- Department of Biology, Stanford University, Stanford, California, United States of America
| | | | - Zeeshan A. Syed
- Center for Reproductive Evolution, Department of Biology, Syracuse University, Syracuse, New York, United States of America
| | - Aya Takahashi
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Kevin H-C. Wei
- Department of Zoology, The University of British Columbia, Vancouver, Canada
| | - Tsuya Yokoyama
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Michael B. Eisen
- Department of Cell and Molecular Biology, University of California Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California, United States of America
| | - Artyom Kopp
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
| | - Daniel Matute
- Department of Biology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Darren J. Obbard
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Patrick M. O’Grady
- Department of Entomology, Cornell University, Ithaca, New York, United States of America
| | - Donald K. Price
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, United States of America
| | | | - Thomas Werner
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Dmitri A. Petrov
- Department of Biology, Stanford University, Stanford, California, United States of America
- CZ Biohub, Investigator, San Francisco, California, United States of America
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Li Z, Xu K, Meng M, Xu Y, Ji D, Wang W, Xie C. Environmental heterogeneity caused by large-scale cultivation of Pyropia haitanensis shapes multi-group biodiversity distribution in coastal areas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172692. [PMID: 38663622 DOI: 10.1016/j.scitotenv.2024.172692] [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: 11/19/2023] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 05/09/2024]
Abstract
The response of marine biodiversity to mariculture has long been a research focus in marine ecology. However, the effects of seaweed cultivation on biological community assembly are poorly understood, especially in diverse communities with distinct ecological characteristics. In this study, we used environmental DNA metabarcoding to investigate the spatial distribution patterns of bacterial, protistan, and metazoan diversity, aiming to reveal the mechanisms of community assembly in the Pyropia haitanensis cultivation zone along the Fujian coast, China. We found that, compared with the biological communities in control zones, those in P. haitanensis cultivation zones exhibited stronger geographic distance-decay patterns and displayed more complex and stable network structures. Deterministic processes (environmental selection) played a more important role in the assembly of bacterial, protistan, and metazoan communities in P. haitanensis cultivation zones, especially metazoan communities. Variance partitioning analysis showed that environmental variables made greater contributions to the diversity of the three types of communities within the P. haitanensis cultivation zones than in the control zones. Partial least squares path modeling analysis identified nitrate‑nitrogen (NO3-N), pH, particulate organic carbon (POC), and dissolved organic carbon (DOC) as the key environmental variables affecting biodiversity. Overall, the environmental heterogeneity caused by the large-scale cultivation of P. haitanensis could be the crucial factor influencing the composition and structure of various biological communities. Our results highlight the importance of the responses of multi-group organisms to the cultivation of seaweed, and provide insights into the coexistence patterns of biodiversity at the spatial scale.
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Affiliation(s)
- Zongtang Li
- Fisheries College, Jimei University, Xiamen, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China; State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Ningde 352100, China
| | - Kai Xu
- Fisheries College, Jimei University, Xiamen, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China; State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Ningde 352100, China
| | - Muhan Meng
- Fisheries College, Jimei University, Xiamen, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Yan Xu
- Fisheries College, Jimei University, Xiamen, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China; State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Ningde 352100, China
| | - Dehua Ji
- Fisheries College, Jimei University, Xiamen, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China; State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Ningde 352100, China
| | - Wenlei Wang
- Fisheries College, Jimei University, Xiamen, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China; State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Ningde 352100, China.
| | - Chaotian Xie
- Fisheries College, Jimei University, Xiamen, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China; State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Ningde 352100, China.
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Li R, Ratnasingham S, Zarubiieva I, Somervuo P, Taylor GW. PROTAX-GPU: a scalable probabilistic taxonomic classification system for DNA barcodes. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230124. [PMID: 38705180 PMCID: PMC11070247 DOI: 10.1098/rstb.2023.0124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/23/2023] [Indexed: 05/07/2024] Open
Abstract
DNA-based identification is vital for classifying biological specimens, yet methods to quantify the uncertainty of sequence-based taxonomic assignments are scarce. Challenges arise from noisy reference databases, including mislabelled entries and missing taxa. PROTAX addresses these issues with a probabilistic approach to taxonomic classification, advancing on methods that rely solely on sequence similarity. It provides calibrated probabilistic assignments to a partially populated taxonomic hierarchy, accounting for taxa that lack references and incorrect taxonomic annotation. While effective on smaller scales, global application of PROTAX necessitates substantially larger reference libraries, a goal previously hindered by computational barriers. We introduce PROTAX-GPU, a scalable algorithm capable of leveraging the global Barcode of Life Data System (>14 million specimens) as a reference database. Using graphics processing units (GPU) to accelerate similarity and nearest-neighbour operations and the JAX library for Python integration, we achieve over a 1000 × speedup compared with the central processing unit (CPU)-based implementation without compromising PROTAX's key benefits. PROTAX-GPU marks a significant stride towards real-time DNA barcoding, enabling quicker and more efficient species identification in environmental assessments. This capability opens up new avenues for real-time monitoring and analysis of biodiversity, advancing our ability to understand and respond to ecological dynamics. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.
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Affiliation(s)
- Roy Li
- Vector Institute for Artificial Intelligence, Toronto, Canada M5G 0C6
- Department of Computer Science, University of Toronto, Toronto, Canada M5S 2E4
| | | | - Iuliia Zarubiieva
- Vector Institute for Artificial Intelligence, Toronto, Canada M5G 0C6
- School of Engineering, University of Guelph, Guelph, Canada N1G 2W1
| | - Panu Somervuo
- Department of Biosciences, University of Helsinki, Helsinki 00014, Finland
| | - Graham W. Taylor
- Vector Institute for Artificial Intelligence, Toronto, Canada M5G 0C6
- School of Engineering, University of Guelph, Guelph, Canada N1G 2W1
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van Klink R. Delivering on a promise: futureproofing automated insect monitoring methods. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230105. [PMID: 38705192 PMCID: PMC11070248 DOI: 10.1098/rstb.2023.0105] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/28/2023] [Indexed: 05/07/2024] Open
Abstract
Due to rapid technological innovations, the automated monitoring of insect assemblages comes within reach. However, this continuous innovation endangers the methodological continuity needed for calculating reliable biodiversity trends in the future. Maintaining methodological continuity over prolonged periods of time is not trivial, since technology improves, reference libraries grow and both the hard- and software used now may no longer be available in the future. Moreover, because data on many species are collected at the same time, there will be no simple way of calibrating the outputs of old and new devices. To ensure that reliable long-term biodiversity trends can be calculated using the collected data, I make four recommendations: (1) Construct devices to last for decades, and have a five-year overlap period when devices are replaced. (2) Construct new devices to resemble the old ones, especially when some kind of attractant (e.g. light) is used. Keep extremely detailed metadata on collection, detection and identification methods, including attractants, to enable this. (3) Store the raw data (sounds, images, DNA extracts, radar/lidar detections) for future reprocessing with updated classification systems. (4) Enable forward and backward compatibility of the processed data, for example by in-silico data 'degradation' to match the older data quality. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.
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Affiliation(s)
- Roel van Klink
- German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
- Department of Computer Science, Martin-Luther-University, Halle-Wittenberg, 06099 Halle, Germany
- WBBS Foundation, Kanaaldijk 36, 9409 TV Loon, The Netherlands
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Bertazzo-Silva FA, Putzke J, Furlan-Lopes C, D'ávila MF, Costa AL, Carvalho EL, Zorzi AF, Schaefer CEGR. Expanding geographic distribution knowledge of Galerinamarginata (Batsch) Kühner (Agaricales, Hymenogastraceae) with a novel Antarctic record. Biodivers Data J 2024; 12:e125727. [PMID: 38948134 PMCID: PMC11214013 DOI: 10.3897/bdj.12.e125727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/15/2024] [Indexed: 07/02/2024] Open
Abstract
Background The investigation of Agaricales diversity in the Antarctica is limited, with only seven genera reported for the region. Galerina stands out as the genus with the highest species diversity, including 12 species in Antarctica. This research reports the presence of G.marginata in the region, providing the first complete morphological description for the specimen developing in Antarctica. Sampling was conducted during the Austral summer of 2022/2023 as part of the XLI Brazilian Antarctic Operation in Point Smellie, Byers Peninsula, Livingston Island, South Shetland Archipelago, Antarctica. Phylogenetic relationships reconstructed by Maximum Likelihood demonstrate that G.marginata forms a monophyletic clade with over 60% bootstrap support in most branches. The isolate in this study was found to be internal to the main cluster. Evolutionary reconstructions using the Maximum Likelihood method indicate that the branches correspond to the Antarctic isolate being an internal clade within the marginata group. Recording fungal populations in polar regions offers information about their adaptation and survival in inhospitable environments. Understanding the species' distribution in Antarctica encourages future investigations into its ecology and interactions with other organisms. Here, data are presented to establish an initial foundation for monitoring the G.marginata population in Antarctica and assessing the potential impacts of climate change on its development and survival in the forthcoming years. New information We report the third occurrence of Galerinamarginata (Batsch) Kühner in Antarctica and provide, for the first time, a comprehensive morphological description of an individual of the species for the Antarctic continent, accompanied by phylogenetic analyses and comprehensive discussions regarding its diversity and global distribution.
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Affiliation(s)
- Fernando Augusto Bertazzo-Silva
- Laboratório de Taxonomia de Fungos, Universidade Federal do Pampa (UNIPAMPA), São Gabriel, RS, BrazilLaboratório de Taxonomia de Fungos, Universidade Federal do Pampa (UNIPAMPA)São Gabriel, RSBrazil
| | - Jair Putzke
- Laboratório de Taxonomia de Fungos, Universidade Federal do Pampa (UNIPAMPA), São Gabriel, RS, BrazilLaboratório de Taxonomia de Fungos, Universidade Federal do Pampa (UNIPAMPA)São Gabriel, RSBrazil
| | - Cassiane Furlan-Lopes
- Laboratório de Taxonomia de Fungos, Universidade Federal do Pampa (UNIPAMPA), São Gabriel, RS, BrazilLaboratório de Taxonomia de Fungos, Universidade Federal do Pampa (UNIPAMPA)São Gabriel, RSBrazil
| | - Maricia Fantinel D'ávila
- Universidade Federal do Pampa (UNIPAMPA), São Gabriel, RS, BrazilUniversidade Federal do Pampa (UNIPAMPA)São Gabriel, RSBrazil
| | - Alice Lemos Costa
- Laboratório de Taxonomia de Fungos, Universidade Federal do Pampa (UNIPAMPA), São Gabriel, RS, BrazilLaboratório de Taxonomia de Fungos, Universidade Federal do Pampa (UNIPAMPA)São Gabriel, RSBrazil
| | - Evelise Leis Carvalho
- Laboratório de Taxonomia de Fungos, Universidade Federal do Pampa (UNIPAMPA), São Gabriel, RS, BrazilLaboratório de Taxonomia de Fungos, Universidade Federal do Pampa (UNIPAMPA)São Gabriel, RSBrazil
| | - Ana Flavia Zorzi
- Laboratório de Taxonomia de Fungos, Universidade Federal do Pampa (UNIPAMPA), São Gabriel, RS, BrazilLaboratório de Taxonomia de Fungos, Universidade Federal do Pampa (UNIPAMPA)São Gabriel, RSBrazil
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Rewicz A, Monzalvo R, Myśliwy M, Tończyk G, Desiderato A, Ruchisansakun S, Rewicz T. Pollination biology of Impatiens capensis Meerb. in non-native range. PLoS One 2024; 19:e0302283. [PMID: 38900825 PMCID: PMC11189253 DOI: 10.1371/journal.pone.0302283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 04/02/2024] [Indexed: 06/22/2024] Open
Abstract
Pollination biology in the widespread species Impatiens capensis Meerb. has only been studied in America, specifically in zones of the U.S.A. and Canada. In this study, we investigated the pollination biology of I. capensis using an integrative identification approach using morphological and molecular tools in four populations of Northwest Poland. We also determined and compared the functional characteristics of the pollinators of the introduced species from the study sites and the native ones reported, for the latter collecting information from bibliographic sources. Visitors were identified using standard morphological keys, including identifying and classifying insect mouthparts. Molecular identification was carried out using mitochondrial DNA's cytochrome oxidase subunit I (COI). We morphologically identified 20 species of visitors constituted by 17 pollinators and three nectar robbers. DNA barcoding of 59 individuals proved the identification of 18 species (also 18 BINs). The frequency of pollinator species was primarily made up of representatives of both Hymenoptera (75%) and Diptera (21%). The morphological traits, such as the chewing and sucking mouthparts, small and big body height, and robber and pollinator behavior explained mainly the native and introduced visitors' arrangements that allow pollination success. However, to understand the process comprehensively, further investigation of other causalities in pollination success and understanding the diversity of pollinators in outer native ranges are necessary.
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Affiliation(s)
- Agnieszka Rewicz
- Department of Geobotany and Plant Ecology, University of Lodz, Łódź, Poland
| | - René Monzalvo
- Molecular Systematics Laboratory, Autonomous University of Hidalgo State, Biological Research Center., Carboneras, Mineral de la Reforma, Hidalgo, México
| | - Monika Myśliwy
- Institute of Marine and Environmental Sciences, University of Szczecin, Szczecin, Poland
| | - Grzegorz Tończyk
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
| | - Andrea Desiderato
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
| | - Saroj Ruchisansakun
- Department of Plant Science, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Tomasz Rewicz
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
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Goudarzi MH, Robinson SD, Cardoso FC, Mitchell ML, Cook LG, King GF, Walker AA. Phylogeny, envenomation syndrome, and membrane permeabilising venom produced by Australia's electric caterpillar Comana monomorpha. Sci Rep 2024; 14:14172. [PMID: 38898081 PMCID: PMC11187147 DOI: 10.1038/s41598-024-65078-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 06/17/2024] [Indexed: 06/21/2024] Open
Abstract
Zygaenoidea is a superfamily of lepidopterans containing many venomous species, including the Limacodidae (nettle caterpillars) and Megalopygidae (asp caterpillars). Venom proteomes have been recently documented for several species from each of these families, but further data are required to understand the evolution of venom in Zygaenoidea. In this study, we examined the 'electric' caterpillar from North-Eastern Australia, a limacodid caterpillar densely covered in venomous spines. We used DNA barcoding to identify this caterpillar as the larva of the moth Comana monomorpha (Turner, 1904). We report the clinical symptoms of C. monomorpha envenomation, which include acute pain, and erythema and oedema lasting for more than a week. Combining transcriptomics of venom spines with proteomics of venom harvested from the spine tips revealed a venom markedly different in composition from previously examined limacodid venoms that are rich in peptides. In contrast, the venom of C. monomorpha is rich in aerolysin-like proteins similar to those found in venoms of asp caterpillars (Megalopygidae). Consistent with this composition, the venom potently permeabilises sensory neurons and human neuroblastoma cells. This study highlights the diversity of venom composition in Limacodidae.
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Affiliation(s)
- Mohaddeseh H Goudarzi
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Protein and Peptide Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Samuel D Robinson
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Fernanda C Cardoso
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Protein and Peptide Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Michela L Mitchell
- Department of Toxinology, Women's and Children's Health Network, North Adelaide, SA, 5006, Australia
| | - Lyn G Cook
- School of the Environment, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia.
- Australian Research Council Centre of Excellence for Innovations in Protein and Peptide Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Andrew A Walker
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia.
- Australian Research Council Centre of Excellence for Innovations in Protein and Peptide Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
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DiBattista JD, Fowler AM, Shalders TC, Williams RJ, Wilkinson S. Tree of life metabarcoding can serve as a biotic benchmark for shifting baselines in urbanized estuaries. ENVIRONMENTAL RESEARCH 2024; 258:119454. [PMID: 38906450 DOI: 10.1016/j.envres.2024.119454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 06/23/2024]
Abstract
Urbanization of estuaries drastically changed existing shorelines and bathymetric contours, in turn modifying habitat for marine foundational species that host critical biodiversity. And yet we lack approaches to characterize a significant fraction of the biota that inhabit these ecosystems on time scales that align with rates of urbanization. Environmental DNA (or eDNA) metabarcoding that combines multiple assays targeting a broad range of taxonomic groups can provide a solution, but we need to determine whether the biological communities it detects ally with different habitats in these changing aquatic environments. In this study, we tested whether tree of life metabarcoding (ToL-metabarcoding) data extracted from filtered seawater samples correlated with four known geomorphic habitat zones across a heavily urbanized estuary (Sydney Harbour, Australia). Using this method, we substantially expanded our knowledge on the composition and spatial distribution of marine biodiversity across the tree of life in Sydney Harbour, particularly for organisms where existing records are sparse. Excluding terrestrial DNA inputs, we identified significant effects of both distance from the mouth of Sydney Harbour and geomorphic zone on biological community structure in the ToL-metabarcoding dataset (entire community), as well as in each of the taxonomic subgroups that we considered (fish, macroinvertebrates, algae and aquatic plants, bacteria). This effect appeared to be driven by taxa as a collective versus a few individual taxa, with each taxon explaining no more than 0.62% of the variation between geomorphic zones. Similarly, taxonomic richness was significantly higher within geomorphic zones with large sample sizes, but also decreased by 1% with each additional kilometer from the estuary mouth, a result consistent with a reduction in tidal inputs and available habitat in upper catchments. Based on these results, we suggest that ToL-metabarcoding can be used to benchmark biological monitoring in other urbanized estuaries globally, and in Sydney Harbour at future time points based on detection of bioindicators across the tree of life. We also suggest that robust biotic snapshots can be archived following extensive curation of taxonomic assignments that incorporates ecological affinities, supported by records from relevant and regional biodiversity repositories.
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Affiliation(s)
- Joseph D DiBattista
- School of Environment and Science, Griffith University, Southport, QLD, 4222, Australia; Australian Museum Research Institute, Australian Museum, Sydney, NSW, 2010, Australia.
| | - Ashley M Fowler
- New South Wales Department of Primary Industries, Sydney Institute of Marine Science, Mosman, NSW, 2088, Australia.
| | - Tanika C Shalders
- Faculty of Science and Engineering, National Marine Science Centre, Southern Cross University, Coffs Harbour, NSW, 2450, Australia.
| | - Robert J Williams
- New South Wales Department of Primary Industries, Fisheries (retired), Australia.
| | - Shaun Wilkinson
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6012, New Zealand.
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Vogel J, Sauren J, Peters RS. New evidence on the identity of the European Helorus species (Hymenoptera, Proctotrupoidea, Heloridae). Biodivers Data J 2024; 12:e122523. [PMID: 38919770 PMCID: PMC11196891 DOI: 10.3897/bdj.12.e122523] [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: 03/07/2024] [Accepted: 04/24/2024] [Indexed: 06/27/2024] Open
Abstract
Background Species of Helorus Latreille 1802 are rarely collected endoparasitoids of Chrysopidae larvae (Neuroptera). Previous work on the limits between the European species of this species-poor genus, based on morphology only, has left some uncertainties. Here, we approach these cases and revisit previous taxonomic decisions using freshly collected and museum material. New information We generated the first large-scale Heloridae DNA barcode dataset, combined these with morphological data in an integrative taxonomic approach, and added information from studying all relevant type material. We found five species, Helorusanomalipes (Panzer, 1798), H.coruscus Haliday, 1857 stat. rev., H.nigripes Förster, 1856, H.ruficornis Förster, 1856, and H.striolatus Cameron, 1906, for which we provide an updated identification key. DNA barcode data are added to publicly available DNA barcode reference databases, for all species, except H.nigripes.
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Affiliation(s)
- Jonathan Vogel
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Bonn, GermanyLeibniz Institute for the Analysis of Biodiversity Change, Museum Koenig BonnBonnGermany
| | - Jerome Sauren
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Bonn, GermanyLeibniz Institute for the Analysis of Biodiversity Change, Museum Koenig BonnBonnGermany
| | - Ralph S. Peters
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Bonn, GermanyLeibniz Institute for the Analysis of Biodiversity Change, Museum Koenig BonnBonnGermany
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Lilli G, Sirot C, Campbell H, Hermand F, Brophy D, Flot JF, Graham CT, George IF. Do fish gut microbiotas vary across spatial scales? A case study of Diplodus vulgaris in the Mediterranean Sea. Anim Microbiome 2024; 6:32. [PMID: 38872229 PMCID: PMC11177387 DOI: 10.1186/s42523-024-00319-2] [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: 03/28/2024] [Accepted: 05/29/2024] [Indexed: 06/15/2024] Open
Abstract
BACKGROUND Biogeography has been linked to differences in gut microbiota in several animals. However, the existence of such a relationship in fish is not clear yet. So far, it seems to depend on the fish species studied. However, most studies of fish gut microbiotas are based on single populations. In this study, we investigated the gut microbiota of fish from three wild populations of the two-banded sea bream Diplodus vulgaris (Geoffroy Saint-Hilaire, 1817) to determine whether its diversity, structure and potential functionality reflect the geographic origin of the fish, at large and small geographical scale. Additionally, we explored the host- and environmental-related factors explaining this relationship. RESULTS We showed that the taxonomy and potential functionality of the mucosa-associated gut microbiota of Diplodus vulgaris differ to varying degrees depending on the spatial scale considered. At large scale, we observed that both the taxonomical structure and the potential functionality of the fish microbiota differed significantly between populations. In contrast, the taxonomical diversity of the microbial community displayed a significant relationship with factors other than the geographic origin of the fish (i.e. sampling date). On the other hand, at small scale, the different composition and diversity of the microbiota differ according to the characteristics of the habitat occupied by the fish. Specifically, we identified the presence of Posidonia oceanica in the benthic habitat as predictor of both the microbiota composition and diversity. Lastly, we reported the enrichment of functions related to the metabolism of xenobiotics (i.e. drugs and 4-aminobenzoate) in a population and we indicated it as a potential target of future monitoring. CONCLUSIONS With this study, we confirmed the importance of investigating the gut microbiota of wild fish species using multiple populations, taking into account the different habitats occupied by the individuals. Furthermore, we underscored the use of the biodegradation potential of the gut microbiota as an alternative means of monitoring emerging contaminants in Mediterranean fish.
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Affiliation(s)
- Ginevra Lilli
- Laboratoire d'Ecologie des Systèmes Aquatiques (ESA), Université Libre de Bruxelles (ULB), 1050, Brussels, Belgium.
| | - Charlotte Sirot
- Centre de Recherches Insulaires et Observatoire de l'Environnement (CRIOBE), University of Perpignan, Perpignan, France
| | - Hayley Campbell
- Marine and Freshwater Research Centre, Atlantic Technological University, Dublin Road, Galway, Ireland
| | - Fanny Hermand
- Laboratoire d'Ecologie des Systèmes Aquatiques (ESA), Université Libre de Bruxelles (ULB), 1050, Brussels, Belgium
| | - Deirdre Brophy
- Marine and Freshwater Research Centre, Atlantic Technological University, Dublin Road, Galway, Ireland
| | - Jean-François Flot
- Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels - (IB)², 1050, Brussels, Belgium
| | - Conor T Graham
- Marine and Freshwater Research Centre, Atlantic Technological University, Dublin Road, Galway, Ireland
| | - Isabelle F George
- Laboratoire d'Ecologie des Systèmes Aquatiques (ESA), Université Libre de Bruxelles (ULB), 1050, Brussels, Belgium
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