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Niu M, Liu Y, Xue L, Cai B, Zhao Q, Wei J. Improving DNA barcoding library of armored scale insects (Hemiptera: Diaspididae) in China. PLoS One 2024; 19:e0301499. [PMID: 38814962 PMCID: PMC11139323 DOI: 10.1371/journal.pone.0301499] [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: 12/27/2023] [Accepted: 03/18/2024] [Indexed: 06/01/2024] Open
Abstract
DNA barcoding is used to identify cryptic species, survey environmental samples, and estimate phyletic and genetic diversity. Armored scale insects are phytophagous insects and are the most species-rich taxa in the Coccoidea superfamily. This study developed a DNA barcode library for armored scale insect species collected from southern China during 2021-2022. We sequenced a total of 239 specimens, recognized as 50 morphological species, representing two subfamilies and 21 genera. Sequencing analysis revealed that the average G + C content of the cytochrome oxidase subunit I (COI) gene sequence was very low (~18.06%) and that the average interspecific divergence was 10.07% while intraspecific divergence was 3.20%. The intraspecific divergence value was inflated by the high intraspecific divergence in ten taxa, which may indicate novel species overlooked by current taxonomic treatments. All the Automated Barcode Gap Discovery, Assemble Species by Automatic Partitioning, Taxon DNA analysis and Bayesian Poisson Tree Process methods yielded largely consistent results, indicating a robust and credible species delimitation. Based on these results, an intergeneric distance threshold of ≤ 5% was deemed appropriate for the differentiation of armored scale insect species in China. This study establishes a comprehensive barcode library for the identification of armored scale insects, future research, and application.
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Affiliation(s)
- Minmin Niu
- College of Plant Protection, Shanxi Agricultural University, Taigu, China
| | - Yubo Liu
- College of Plant Protection, Shanxi Agricultural University, Taigu, China
| | - Linjia Xue
- College of Plant Protection, Shanxi Agricultural University, Taigu, China
| | - Bo Cai
- Hainan Province Engineering Research Center for Quarantine, Prevention and Control of Exotic Pests, Haikou, China
| | - Qing Zhao
- College of Plant Protection, Shanxi Agricultural University, Taigu, China
| | - Jiufeng Wei
- College of Plant Protection, Shanxi Agricultural University, Taigu, China
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Sharma R, Nath PC, Lodh BK, Mukherjee J, Mahata N, Gopikrishna K, Tiwari ON, Bhunia B. Rapid and sensitive approaches for detecting food fraud: A review on prospects and challenges. Food Chem 2024; 454:139817. [PMID: 38805929 DOI: 10.1016/j.foodchem.2024.139817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 05/13/2024] [Accepted: 05/22/2024] [Indexed: 05/30/2024]
Abstract
Precise and reliable analytical techniques are required to guarantee food quality in light of the expanding concerns regarding food safety and quality. Because traditional procedures are expensive and time-consuming, quick food control techniques are required to ensure product quality. Various analytical techniques are used to identify and detect food fraud, including spectroscopy, chromatography, DNA barcoding, and inotrope ratio mass spectrometry (IRMS). Due to its quick findings, simplicity of use, high throughput, affordability, and non-destructive evaluations of numerous food matrices, NI spectroscopy and hyperspectral imaging are financially preferred in the food business. The applicability of this technology has increased with the development of chemometric techniques and near-infrared spectroscopy-based instruments. The current research also discusses the use of several multivariate analytical techniques in identifying food fraud, such as principal component analysis, partial least squares, cluster analysis, multivariate curve resolutions, and artificial intelligence.
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Affiliation(s)
- Ramesh Sharma
- Bioproducts Processing Research Laboratory (BPRL), Department of Bio Engineering, National Institute of Technology, Agartala 799046, India; Department of Food Technology, Sri Shakthi Institute of Engineering and Technology, Coimbatore, Tamil Nadu-641062, India.
| | - Pinku Chandra Nath
- Bioproducts Processing Research Laboratory (BPRL), Department of Bio Engineering, National Institute of Technology, Agartala 799046, India.
| | - Bibhab Kumar Lodh
- Department of Chemical Engineering, National Institute of Technology, Agartala-799046, India.
| | - Jayanti Mukherjee
- Department of Pharmaceutical Chemistry, CMR College of Pharmacy, Hyderabad- 501401, Telangana, India.
| | - Nibedita Mahata
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur-713209.
| | - Konga Gopikrishna
- SEED Division, Department of Science and Technology, New Delhi, 110016, India.
| | - Onkar Nath Tiwari
- Centre for Conservation and Utilisation of Blue Green Algae (CCUBGA), Division of Microbiology, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India.
| | - Biswanath Bhunia
- Bioproducts Processing Research Laboratory (BPRL), Department of Bio Engineering, National Institute of Technology, Agartala 799046, India.
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Zhigila DA, Elliott TL, Schmiedel U, Muasya AM. Do phylogenetic community metrics reveal the South African quartz fields as terrestrial-habitat islands? ANNALS OF BOTANY 2024; 133:833-850. [PMID: 38401154 PMCID: PMC11082514 DOI: 10.1093/aob/mcae027] [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: 08/15/2023] [Accepted: 02/23/2024] [Indexed: 02/26/2024]
Abstract
BACKGROUND AND AIMS The quartz fields of the Greater Cape Floristic Region (GCFR) are arid and island-like special habitats, hosting ~142 habitat-specialized plant species, of which 81 % are local endemics, characterized by a rapid turnover of species between and among sites. We use several phylogenetic community metrics: (1) to examine species diversity and phylogenetic structure within and among quartz fields; (2) to investigate whether quartz field specialists are evolutionarily drawn from local species pools, whereas the alternative hypothesis posits that there is no significant evolutionary connection between quartz field specialists and the local species pools; and (3) to determine whether there is an association between certain traits and the presence of species in quartz fields. METHODS We sampled and developed dated phylogenies for six species-rich angiosperm families (Aizoaceae, Asteraceae, Crassulaceae, Cyperaceae, Fabaceae and Santalaceae) represented in the quartz field floras of southern Africa. Specifically, we focused on the flora of three quartz field regions in South Africa (Knersvlakte, Little Karoo and Overberg) and their surrounding species pools to address our research questions by scoring traits associated with harsh environments. KEY RESULTS We found that the Overberg and Little Karoo had the highest level of species overlap for families Aizoaceae and Fabaceae, whereas the Knersvlakte and the Overberg had the highest species overlap for families Asteraceae, Crassulaceae and Santalaceae. Although our phylogenetic community structure and trait analyses showed no clear patterns, relatively low pairwise phylogenetic distances between specialists and their local species pools for Aizoaceae suggest that quartz species could be drawn evolutionarily from their surrounding areas. We also found that families Aizoaceae and Crassulaceae in Knersvlakte and Little Karoo were phylogenetically even. CONCLUSIONS Despite their proximity to one another within the GCFR, the studied areas differ in their species pools and the phylogenetic structure of their specialists. Our work provides further justification for increased conservation focus on these unique habitats under future scenarios of global change.
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Affiliation(s)
- Daniel A Zhigila
- Department of Botany, Gombe State University, PMB 127, Tudun Wada, Gombe, Gombe State, Nigeria
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA 02138, USA
| | - Tammy L Elliott
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Ute Schmiedel
- Organismic Botany and Mycology, Institute of Plant Science and Microbiology, University of Hamburg, Germany
| | - A Muthama Muasya
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa
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Kou L, Yang N, Yan H, Niklas KJ, Sun S. Insect root feeders incur negative density-dependent damage across plant species in an alpine meadow. Ecology 2024; 105:e4285. [PMID: 38523437 DOI: 10.1002/ecy.4285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 12/07/2023] [Accepted: 02/01/2024] [Indexed: 03/26/2024]
Abstract
Although herbivores are well known to incur positive density-dependent damage and mortality, thereby likely shaping plant community assembly, the response of belowground root feeders to changes in plant density has seldom been addressed. Locally rare plant species (with lower plant biomass per area) are often smaller with shallower roots than common species (with higher plant biomass per area) in competition-intensive grasslands. Likewise, root feeders are often distributed in the upper soil layers. We hypothesized, therefore, that root feeders would incur negative density (biomass)-dependent damage across plant species. To test this hypothesis, we investigated the diversity and abundance of plant and root feeder species in an alpine meadow and determined the diet of the root feeders using metabarcoding. Across all species, root feeder load decreased with increasing aboveground plant biomass, root biomass, and total plant biomass per area, indicating a negative density dependence of damage across plant species. Aboveground plant biomass per area increased with increasing individual plant biomass and root depth per area across species, suggesting that rare plant species were smaller in size and had shallower root systems compared to common plant species. Both root biomass per area and root feeder biomass per area decreased with soil depth, but the root feeder biomass decreased disproportionately faster compared to root biomass with increasing root depth. Root feeder load decreased with increasing root depth but was not correlated with the feeding preference of root feeder species. Moreover, the prediction derived from a random process incorporating vertical distributions of root biomass and root feeder biomass significantly accounted for interspecific variation in root feeder load. In conclusion, the data indicate that root feeders incur negative density-dependent damage across plant species. On this basis, we suggest that manipulative experiments should be conducted to determine the effect of the negative density-dependent damage on plant community structure and that different types of plant-animal interactions should be concurrently examined to fully understand the effect of plant density on overall herbivore damage across plant species.
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Affiliation(s)
- Lixuan Kou
- Department of Ecology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Nan Yang
- Department of Ecology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Han Yan
- Department of Ecology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Karl J Niklas
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Shucun Sun
- Department of Ecology, School of Life Sciences, Nanjing University, Nanjing, China
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Espinosa Prieto A, Hardion L, Debortoli N, Beisel JN. Finding the perfect pairs: A matchmaking of plant markers and primers for multi-marker eDNA metabarcoding. Mol Ecol Resour 2024; 24:e13937. [PMID: 38363053 DOI: 10.1111/1755-0998.13937] [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: 09/20/2023] [Revised: 12/14/2023] [Accepted: 01/09/2024] [Indexed: 02/17/2024]
Abstract
As the scope of plant eDNA metabarcoding diversifies, so do the primers, markers and methods. A wealth of primers exists today, but their comparative evaluation is lacking behind. Similarly, multi-marker approaches are recommended but debates persist regarding barcode complementarity and optimal combinations. After a literature compilation of used primers, we compared in silico 102 primer pairs based on amplicon size, coverage and specificity, followed by an experimental evaluation of 15 primer pairs on a mock community sample covering 268 plant species and genera, and about 100 families. The analysis was done for the four most common plant metabarcoding markers, rbcL, trnL, ITS1 and ITS2 and their complementarity was assessed based on retrieved species. By focusing on existing primers, we identify common designs, promote alternatives and enhance prior-supported primers for immediate applications. The ITS2 was the best-performing marker for flowering vascular plants and was congruent to ITS1. However, the combined taxonomic breadth of ITS2 and rbcL surpassed any other combination, highlighting their high complementarity across Streptophyta. Overall, our study underscores the significance of comprehensive primer and barcode evaluations tailored to metabarcoding applications.
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Affiliation(s)
- Armando Espinosa Prieto
- University of Strasbourg, CNRS, Laboratoire Image Ville Environnement, UMR 7362, Strasbourg, France
| | - Laurent Hardion
- University of Strasbourg, CNRS, Laboratoire Image Ville Environnement, UMR 7362, Strasbourg, France
| | - Nicolas Debortoli
- Namur Molecular Tech, CHU UCL Namur, Yvoir, Belgium
- E-BIOM SA, Namur, Belgium
| | - Jean-Nicolas Beisel
- University of Strasbourg, CNRS, Laboratoire Image Ville Environnement, UMR 7362, Strasbourg, France
- École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES), Strasbourg, France
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Lehmann Albornoz P, Bartzen CS, Malabarba LR. The barcode trap-Description of a new species of Microglanis, with a review of the status of Microglanis cibelae (Siluriformes: Pseudopimelodidae). JOURNAL OF FISH BIOLOGY 2024. [PMID: 38646664 DOI: 10.1111/jfb.15764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 03/27/2024] [Accepted: 04/02/2024] [Indexed: 04/23/2024]
Abstract
In a recent study based on the generalized mixed Yule coalescent method for delimiting species, a threshold of 2% genetic distance using cytochrome c oxidase subunit I sequences was used to delimit the species of Microglanis. That action resulted in assembling several populations of Microglanis from Atlantic coastal rivers between Rio Grande do Sul and São Paulo states as a single species, Microglanis cottoides, including Microglanis cibelae as a junior synonym. We reexamined these populations and found three species diagnosed by their morphology and that constitute separate mtDNA lineages, including a new species. The synonym of M. cibelae and M. cottoides is reviewed and refuted based on morphological and molecular evidence. M. cibelae and the new species are sympatric and occasionally syntopic in the Tramandaí, Mampituba, and Araranguá river basins. The new species is distinguished from M. cibelae and M. cottoides by the anterior margin of the posttemporosupracleitrum narrow articulated with the epioccipital, the short mental and maxillary barbels, and depressed head and body.
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Affiliation(s)
| | - César Sá Bartzen
- Universidade do Vale do Rio dos Sinos (Unisinos), São Leopoldo, Brazil
| | - Luiz R Malabarba
- Departamento de Zoologia, IB, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Nascimento MHS, Birindelli JLO, Fraga E, Barros MC. Exploring hidden diversity: Molecular insights into the Leporinus species of the rivers of the Brazilian states of Maranhão and Piauí. JOURNAL OF FISH BIOLOGY 2024. [PMID: 38590289 DOI: 10.1111/jfb.15753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 03/10/2024] [Accepted: 03/27/2024] [Indexed: 04/10/2024]
Abstract
The present study delved into the world of hidden diversity by examining specimens identified as Leporinus piau from the river basins of the northern Brazilian states of Maranhão and Piauí. Using genetic analyses that combined data from three mitochondrial markers and one nuclear marker, the study identified two well-supported groups, reinforcing the findings of previous publications. The first group, found in samples from the Itapecuru, Mearim, Turiaçu, and Pericumã basins, in Maranhão, appears to represent a relatively ancient diversification and the possibility of concealed cryptic diversity. The second group, comprising specimens from the Parnaíba (Piauí) and Mearim (Maranhão) basins, appears to have resulted from a more recent process of diversification and has a close relationship with Leporinus friderici from the type locality. Our findings not only confirm the existence of a complex scenario of cryptic diversity in the genus Leporinus from the study basins but also underscore the taxonomic inconsistencies within this group of fish. This study offers a comprehensive analysis of the species diversity of the Maranhão and Piauí basins, which are critical regions for the conservation of Amazonian fish, providing valuable insights for the sustainable management and conservation of these fish.
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Affiliation(s)
- Maria Histelle Sousa Nascimento
- Departamento de Desenvolvimento e Ensino, Instituto Federal de Educação, Ciência e Tecnologia do Maranhão, Caxias, Brazil
- Rede de Biodiversidade e Biotecnologia da Amazônia Legal, Universidade Federal do Maranhão, São Luis, Brazil
- Departamento de Química e Biologia, Universidade Estadual do Maranhão, Caxias, Brazil
| | | | - Elmary Fraga
- Departamento de Química e Biologia, Universidade Estadual do Maranhão, Caxias, Brazil
| | - Maria Claudene Barros
- Rede de Biodiversidade e Biotecnologia da Amazônia Legal, Universidade Federal do Maranhão, São Luis, Brazil
- Departamento de Química e Biologia, Universidade Estadual do Maranhão, Caxias, Brazil
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Gajski D, Wolff JO, Melcher A, Weber S, Prost S, Krehenwinkel H, Kennedy SR. Facilitating taxonomy and phylogenetics: An informative and cost-effective protocol integrating long amplicon PCRs and third-generation sequencing. Mol Phylogenet Evol 2024; 192:107988. [PMID: 38072140 DOI: 10.1016/j.ympev.2023.107988] [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: 08/03/2023] [Revised: 10/22/2023] [Accepted: 12/07/2023] [Indexed: 12/31/2023]
Abstract
Phylogenetic inference has become a standard technique in integrative taxonomy and systematics, as well as in biogeography and ecology. DNA barcodes are often used for phylogenetic inference, despite being strongly limited due to their low number of informative sites. Also, because current DNA barcodes are based on a fraction of a single, fast-evolving gene, they are highly unsuitable for resolving deeper phylogenetic relationships due to saturation. In recent years, methods that analyse hundreds and thousands of loci at once have improved the resolution of the Tree of Life, but these methods require resources, experience and molecular laboratories that most taxonomists do not have. This paper introduces a PCR-based protocol that produces long amplicons of both slow- and fast-evolving unlinked mitochondrial and nuclear gene regions, which can be sequenced by the affordable and portable ONT MinION platform with low infrastructure or funding requirements. As a proof of concept, we inferred a phylogeny of a sample of 63 spider species from 20 families using our proposed protocol. The results were overall consistent with the results from approaches based on hundreds and thousands of loci, while requiring just a fraction of the cost and labour of such approaches, making our protocol accessible to taxonomists worldwide.
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Affiliation(s)
- Domagoj Gajski
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno 611 37, Czech Republic
| | - Jonas O Wolff
- Evolutionary Biomechanics, Zoological Institute and Museum, University of Greifswald, Loitzer Str. 26, Greifswald 17489, Germany; School of Natural Sciences, Macquarie University, NSW 2109, Sydney, Australia
| | - Anja Melcher
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Sven Weber
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Stefan Prost
- Ecology and Genetics Research Unit, University of Oulu, Pentti Kaiteran katu 1, Linnanmaa, Finland
| | - Henrik Krehenwinkel
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Susan R Kennedy
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany.
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Modeel S, Negi RK, Sharma M, Dolkar P, Yadav S, Siwach S, Yadav P, Negi T. A comprehensive DNA barcoding of Indian freshwater fishes of the Indus River system, Beas. Sci Rep 2024; 14:2763. [PMID: 38307873 PMCID: PMC10837433 DOI: 10.1038/s41598-024-52519-0] [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: 07/07/2023] [Accepted: 01/19/2024] [Indexed: 02/04/2024] Open
Abstract
The Beas River is one of the important rivers of the Indus River system located in Himachal Pradesh, India, that harbors a diverse range of freshwater fish species. The present study employed COI gene to investigate the ichthyofaunal diversity of river Beas. Through the sequencing of 203 specimens from Beas River, we identified 43 species, belonging to 31 genera, 16 families, and 10 orders. To analyze the genetic divergence and phylogeny of identified species, 485 sequences of Indian origin were retrieved from BOLD, resulting in a dataset of 688 sequences. Our findings consistently revealed a hierarchical increase in the mean K2P genetic divergence within species (0.80%), genus (9.06%), and families (15.35%). Automated Barcode Gap discovery, Neighbour Joining, and Bayesian inference consensus tree methodologies were employed to determine the putative species and their phylogeny, successfully delimiting most of the species with only a few exceptions. The results unveiled six species exhibiting high intra-species divergence (> 2%), suggesting the presence of sibling species and falsely identified sequences on online databases. The present study established the first DNA barcoding-based inventory of freshwater fish species in the Beas River providing comprehensive insights into economically exploited endangered and vulnerable species. In order to ensure the sustainable use of aquatic resources in the Beas River, we recommend the implementation of species measures to protect biodiversity and genetic resources.
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Affiliation(s)
- Sonakshi Modeel
- Fish Molecular Biology Lab, Department of Zoology, University of Delhi, North Campus, Delhi, 110007, India
| | - Ram Krishan Negi
- Fish Molecular Biology Lab, Department of Zoology, University of Delhi, North Campus, Delhi, 110007, India.
| | - Monika Sharma
- Fish Molecular Biology Lab, Department of Zoology, University of Delhi, North Campus, Delhi, 110007, India
| | - Padma Dolkar
- Fish Molecular Biology Lab, Department of Zoology, University of Delhi, North Campus, Delhi, 110007, India
| | - Sheetal Yadav
- Fish Molecular Biology Lab, Department of Zoology, University of Delhi, North Campus, Delhi, 110007, India
| | - Sneha Siwach
- Fish Molecular Biology Lab, Department of Zoology, University of Delhi, North Campus, Delhi, 110007, India
| | - Pankaj Yadav
- Fish Molecular Biology Lab, Department of Zoology, University of Delhi, North Campus, Delhi, 110007, India
| | - Tarana Negi
- Department of Zoology, Govt. College Dujana, District Jhajjar, Beri, Haryana, India
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Budrys E, Orlovskytė S, Budrienė A. Ecological Speciation without Morphological Differentiation? A New Cryptic Species of Diodontus Curtis (Hymenoptera, Pemphredonidae) from the Centre of Europe. INSECTS 2024; 15:86. [PMID: 38392506 PMCID: PMC10888621 DOI: 10.3390/insects15020086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 12/29/2023] [Accepted: 01/16/2024] [Indexed: 02/24/2024]
Abstract
Upon exploring the mitotype diversity of the aphid-hunting wasp, Diodontus tristis, we revealed specimens with highly divergent mitotypes from two localities in Lithuania and nesting in clayey substrate, while the specimens with typical mitotypes were found nesting in sandy sites. The comparison of inter- and intra-specific distances and application of delimitation algorithms supported the species status of the clay-nesting populations. Using a set of DNA markers that included complete or partial sequences of six mitochondrial genes, three markers of ribosomal operon, two homeobox genes, and four other nuclear genes, we clarified the phylogenetic relationships of the new cryptic species. The endosymbiotic bacteria infestation was checked, considering the option that the divergent populations may represent clades isolated by Wolbachia infection; however, it did not demonstrate any specificity. We found only subtle morphological differences in the new clay-nesting species, D. argillicola sp. nov.; the discriminant analysis of morphometric measurements did not reliably segregate it as well. Thus, we provide the molecular characters of the cryptic species, which allow confident identification, its phylogenetic position within the genus, and an updated identification key for the D. tristis species group.
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Affiliation(s)
- Eduardas Budrys
- Institute of Ecology, Nature Research Centre, Akademijos 2, 08412 Vilnius, Lithuania
| | - Svetlana Orlovskytė
- Institute of Ecology, Nature Research Centre, Akademijos 2, 08412 Vilnius, Lithuania
| | - Anna Budrienė
- Institute of Ecology, Nature Research Centre, Akademijos 2, 08412 Vilnius, Lithuania
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Cheng R, Luo A, Orr M, Ge D, Hou Z, Qu Y, Guo B, Zhang F, Sha Z, Zhao Z, Wang M, Shi X, Han H, Zhou Q, Li Y, Liu X, Shao C, Zhang A, Zhou X, Zhu C. Cryptic diversity begets challenges and opportunities in biodiversity research. Integr Zool 2024. [PMID: 38263700 DOI: 10.1111/1749-4877.12809] [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] [Indexed: 01/25/2024]
Abstract
How many species of life are there on Earth? This is a question that we want to know but cannot yet answer. Some scholars speculate that the number of species may reach 2.2 billion when considering cryptic diversity and that each morphology-based insect species may contain an average of 3.1 cryptic species. With nearly two million described species, such high estimates of cryptic diversity would suggest that cryptic species are widespread. The development of molecular species delimitation has led to the discovery of a large number of cryptic species, and cryptic biodiversity has gradually entered our field of vision and attracted more attention. This paper introduces the concept of cryptic species, how they evolve, and methods by which they may be discovered and confirmed, and provides theoretical and methodological guidance for the study of hidden species. A workflow of how to confirm cryptic species is provided. In addition, the importance and reliability of multi-evidence-based integrated taxonomy are reaffirmed as a way to better standardize decision-making processes. Special focus on cryptic diversity and increased funding for taxonomy is needed to ensure that cryptic species in hyperdiverse groups are discoverable and described. An increased focus on cryptic species in the future will naturally arise as more difficult groups are studied, and thereby, we may finally better understand the rules governing the evolution and maintenance of cryptic biodiversity.
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Affiliation(s)
- Rui Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Arong Luo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Michael Orr
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Entomologie, Staatliches Museum für Naturkunde Stuttgart, Stuttgart, Germany
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhong'e Hou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Baocheng Guo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Feng Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zhongli Sha
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Zhe Zhao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Mingqiang Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xiaoyu Shi
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hongxiang Han
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qingsong Zhou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yuanning Li
- Institute of Oceanography, Shandong University, Qingdao, China
| | - Xingyue Liu
- Department of Entomology, China Agricultural University, Beijing, China
| | - Chen Shao
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Aibing Zhang
- College of Life Science, Capital Normal University, Beijing, China
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing, China
| | - Chaodong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences/International College, University of Chinese Academy of Sciences, Beijing, China
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12
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Vences M, Patmanidis S, Fedosov A, Miralles A, Puillandre N. iTaxoTools 1.0: Improved DNA Barcode Exploration with TaxI2. Methods Mol Biol 2024; 2744:281-296. [PMID: 38683326 DOI: 10.1007/978-1-0716-3581-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
The overall availability of user-friendly software tools tailored to the analysis of DNA barcodes is limited. Several obvious functions such as detecting and visualizing the DNA barcode gap, the calculation of matrices of pairwise distances at the level of species, or the filtering and decontaminating of sets of sequences based on comparisons with reference databases can typically be carried out only by complex procedures that involve various programs and/or a substantial manual work of formatting. The iTaxoTools project aims at contributing user-friendly software solutions to improve the speed and quality of the workflow of alpha-taxonomy. In this chapter, we provide detailed protocols for the use of a substantially improved version of the tool TaxI2 for distance-based exploration of DNA barcodes. The program calculates genetic distances from prealigned data sets, or based on pairwise alignments, or with an alignment-free approach. Sequence and metadata input can be formatted as tab-delimited files and TaxI2 then computes tables, matrices and graphs of distances, and distance summary statistics within and between species and genera. TaxI2 also includes modes to compare a set of sequences against one or two reference data sets and output lists of best matches or filter data according to thresholds or reciprocal matches. Here, detailed step-by-step protocols are provided for the use of TaxI2, as well as for the interpretation of the program's output.
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Affiliation(s)
- Miguel Vences
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany.
| | - Stefanos Patmanidis
- School of Electrical and Computer Engineering, National Technical University of Athens, Athens, Greece
| | - Alexander Fedosov
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Aurélien Miralles
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
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13
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Singh D, Mittal N, Verma S, Singh A, Siddiqui MH. Applications of some advanced sequencing, analytical, and computational approaches in medicinal plant research: a review. Mol Biol Rep 2023; 51:23. [PMID: 38117315 DOI: 10.1007/s11033-023-09057-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023]
Abstract
The potential active chemicals found in medicinal plants, which have long been employed as natural medicines, are abundant. Exploring the genes responsible for producing these compounds has given new insights into medicinal plant research. Previously, the authentication of medicinal plants was done via DNA marker sequencing. With the advancement of sequencing technology, several new techniques like next-generation sequencing, single molecule sequencing, and fourth-generation sequencing have emerged. These techniques enshrined the role of molecular approaches for medicinal plants because all the genes involved in the biosynthesis of medicinal compound(s) could be identified through RNA-seq analysis. In several research insights, transcriptome data have also been used for the identification of biosynthesis pathways. miRNAs in several medicinal plants and their role in the biosynthesis pathway as well as regulation of the disease-causing genes were also identified. In several research articles, an in silico study was also found to be effective in identifying the inhibitory effect of medicinal plant-based compounds against virus' gene(s). The use of advanced analytical methods like spectroscopy and chromatography in metabolite proofing of secondary metabolites has also been reported in several recent research findings. Furthermore, advancement in molecular and analytic methods will give new insight into studying the traditionally important medicinal plants that are still unexplored.
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Affiliation(s)
- Dhananjay Singh
- Department of Biosciences, Integral University, Lucknow, Uttar Pradesh, 226026, India
| | - Nishu Mittal
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, 225003, India
| | - Swati Verma
- College of Horticulture and Forestry Thunag, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan, Himachal Pradesh, 173230, India
| | - Anjali Singh
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, 225003, India
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14
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Wildermuth B, Seifert CL, Husemann M, Schuldt A. Metabarcoding reveals that mixed forests mitigate negative effects of non-native trees on canopy arthropod diversity. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2921. [PMID: 37776039 DOI: 10.1002/eap.2921] [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: 01/31/2023] [Revised: 07/13/2023] [Accepted: 08/18/2023] [Indexed: 10/01/2023]
Abstract
Averting climate change-induced forest diebacks increasingly relies on tree species planted outside of their natural range and on the addition of non-native tree species to mixed-species forests. However, the consequences of such changes for associated biodiversity remain poorly understood, especially for the forest canopy as a largely understudied forest stratum. Here, we used flight interception traps and a metabarcoding approach to study the taxonomic and functional (trophic guilds) composition and taxon richness of canopy arthropods. We sampled 15 monospecific and mixed stands of native European beech, native Norway spruce-planted outside its natural range-and non-native Douglas fir in northwest Germany. We found that the diversity of arthropods was lower in non-native Douglas fir compared with native beech stands. Taxon richness of herbivores was reduced by both conifer species. Other functional guilds, however, were not affected by stand type. Arthropod composition differed strongly between native broadleaved beech and monospecific coniferous (native spruce or non-native Douglas fir) stands, with less pronounced differences between the native and non-native conifers. Beech-conifer mixtures consistently hosted intermediate arthropod diversity and community composition compared with the respective monospecific stands. Moreover, arthropod diversity had a positive relationship with the number of canopy microhabitats. Our study shows that considering arthropod taxa of multiple functional groups reveals the multifaceted impact of non-native tree species on forest canopy arthropod communities. Contrasting with previous studies that primarily focused on the forest floor, we found that native beech hosts a rich diversity of arthropods, compared with lower diversity and distinct communities in economically attractive, and especially in non-native, conifers with few canopy microhabitats. Broadleaf-conifer mixtures did not perform better than native beech stands, but mitigated the negative effects of conifers, making such mixtures a compromise to foster both forest-associated diversity and economic yield.
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Affiliation(s)
- Benjamin Wildermuth
- Department of Forest Nature Conservation, University of Göttingen, Göttingen, Germany
| | - Carlo L Seifert
- Department of Forest Nature Conservation, University of Göttingen, Göttingen, Germany
| | - Martin Husemann
- Museum of Nature, Leibniz Institute for the Analysis of Biodiversity Change, Hamburg, Germany
| | - Andreas Schuldt
- Department of Forest Nature Conservation, University of Göttingen, Göttingen, Germany
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15
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de Souza Oliveira L, de Araújo Bitencourt J, Galdino JH, Sampaio I, Souza Carneiro PL, Antunes de Mello Affonso PR. Genetic Diversity in Natural Populations of the Near-Threatened Species Lignobrycon myersi (Characiformes, Triportheidae): Implications for Species Conservation. Zebrafish 2023; 20:271-279. [PMID: 38011710 DOI: 10.1089/zeb.2023.0036] [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: 11/29/2023] Open
Abstract
The river basins of Brazil contain a highly diverse ichthyofauna of remarkable endemism, including several threatened species. Accordingly, Lignobrycon myersi is a fish species distributed only in a few rivers from the state of Bahia, northeastern Brazil. Since this species is classified as Near Threatened and is poorly studied, efforts to understand the genetic structure of populations and putative cryptic forms should help define efficient strategies of management and conservation. Herein, the molecular identification and the population genetic diversity of specimens of L. myersi across their range (Almada, Contas, and Cachoeira river basins) were assessed using mitochondrial markers (16S rDNA and D-Loop, respectively). The inferences based on phylogenetics, genetic distance, and species delimitation methods invariably identified all samples as L. myersi. In addition, sequencing of D-loop fragments revealed significant haplotype diversity and a considerable level of population genetic structure. Despite their geographic isolation, these data suggested that populations from Almada and Contas rivers represent a single evolutionary lineage that could be managed as a whole. In contrast, the population from Cachoeira River was highly differentiated from the others and should be managed separately as a unique and endemic unit, particularly focused on the conservation of native habitats.
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Affiliation(s)
| | | | - José Henrique Galdino
- Department of Biological Sciences, State University of Southwestern Bahia, Jequié, Brazil
| | - Iracilda Sampaio
- Department of Coastal Studies, Federal University of Pará, Bragança, Brazil
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16
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Tadmor‐Levi R, Feldstein‐Farkash T, Milstein D, Golani D, Leader N, Goren M, David L. Revisiting the species list of freshwater fish in Israel based on DNA barcoding. Ecol Evol 2023; 13:e10812. [PMID: 38125953 PMCID: PMC10731390 DOI: 10.1002/ece3.10812] [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: 02/27/2023] [Revised: 11/07/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
Israel's region forms a continental bridge; hence, the freshwater fish fauna in Israel consists of unique populations of species that originated from Africa, Asia, or Europe and are often endemic or at the edge of their distribution range. Worldwide, fish biodiversity suffers significantly from pressures and disturbances of freshwater habitats, especially in arid regions, such as in parts of Israel. Biodiversity conservation requires efficient tools for monitoring changes in populations. DNA barcoding, by complementing and enhancing species identification, provides such monitoring tools. In this study, over 200 specimens representing over 28 species were DNA barcoded and together with previously available records, a DNA barcoding database for freshwater fish of Israel was established. Of the 71 distinct barcodes generated, 37% were new, attesting to the uniqueness of fish populations in Israel. For most species, morphological and molecular species identifications agreed. However, discrepancies were found for five genera. Based on DNA barcoding, we propose Acanthobrama telavivensis as a junior synonym for Acanthobrama lissneri. In Garra spp., we propose splitting Garra nana into two species and assigning Garra rufa in the region to Garra jordanica, or possibly to two species. Israeli Pseudophoxinus kervillei is not the same species as in Syria and Lebanon. However, Pseudophoxinus syriacus might not be endangered since it is genetically very similar to Pseudophoxinus drusensis. In Israel, instead of five reported Oxynoemacheilus species, combining DNA barcoding with morphology suggests only three. Genetic and geographic separation suggested that Aphanius mento is likely a species complex. The study provides a thorough barcoding database, suggests significant species reconsiderations in the region, and highlights the Sea of Galilee and the Beit She'an valley streams as biodiversity "hotspots." This study will therefore promote further studying of the fish species in the region and their ecology, as well as the monitoring and conservation of freshwater fish biodiversity in Israel and the region.
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Affiliation(s)
- Roni Tadmor‐Levi
- Department of Animal SciencesRobert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of JerusalemRehovotIsrael
- National Natural History Collections, Department of Ecology, Evolution and BehaviorThe Hebrew University of JerusalemJerusalemIsrael
| | - Tamar Feldstein‐Farkash
- The Steinhardt Museum of Natural History and School of ZoologyTel Aviv UniversityTel AvivIsrael
| | - Dana Milstein
- Science and Conservation DivisionIsrael Nature and Parks AuthorityJerusalemIsrael
| | - Daniel Golani
- National Natural History Collections, Department of Ecology, Evolution and BehaviorThe Hebrew University of JerusalemJerusalemIsrael
| | - Noam Leader
- Science and Conservation DivisionIsrael Nature and Parks AuthorityJerusalemIsrael
| | - Menachem Goren
- The Steinhardt Museum of Natural History and School of ZoologyTel Aviv UniversityTel AvivIsrael
| | - Lior David
- Department of Animal SciencesRobert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of JerusalemRehovotIsrael
- National Natural History Collections, Department of Ecology, Evolution and BehaviorThe Hebrew University of JerusalemJerusalemIsrael
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17
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Fell A, Silva T, Duthie AB, Dent D. A global systematic review of frugivorous animal tracking studies and the estimation of seed dispersal distances. Ecol Evol 2023; 13:e10638. [PMID: 37915807 PMCID: PMC10616751 DOI: 10.1002/ece3.10638] [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: 06/13/2023] [Revised: 09/25/2023] [Accepted: 10/08/2023] [Indexed: 11/03/2023] Open
Abstract
Seed dispersal is one of the most important ecosystem functions globally. It shapes plant populations, enhances forest succession, and has multiple, indirect benefits for humans, yet it is one of the most threatened processes in plant regeneration, worldwide. Seed dispersal distances are determined by the diets, seed retention times and movements of frugivorous animals. Hence, understanding how we can most effectively describe frugivore movement and behaviour with rapidly developing animal tracking technology is key to quantifying seed dispersal. To assess the current use of animal tracking in frugivory studies and to provide a baseline for future studies, we provide a comprehensive review and synthesis on the existing primary literature of global tracking studies that monitor movement of frugivorous animals. Specifically, we identify studies that estimate dispersal distances and how they vary with body mass and environmental traits. We show that over the last two decades there has been a large increase in frugivore tracking studies that determine seed dispersal distances. However, some taxa (e.g. reptiles) and geographic locations (e.g. Africa and Central Asia) are poorly studied. Furthermore, we found that certain morphological and environmental traits can be used to predict seed dispersal distances. We demonstrate that flight ability and increased body mass both significantly increase estimated seed dispersal mean and maximum distances. Our results also suggest that protected areas have a positive effect on mean seed dispersal distances when compared to unprotected areas. We anticipate that this review will act as a reference for future frugivore tracking studies, specifically to target current taxonomic and geographic data gaps, and to further explore how seed dispersal relates to key frugivore and fruit traits.
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Affiliation(s)
- Adam Fell
- Biological and Environmental SciencesUniversity of StirlingStirlingUK
| | - Thiago Silva
- Biological and Environmental SciencesUniversity of StirlingStirlingUK
| | - A. Bradley Duthie
- Biological and Environmental SciencesUniversity of StirlingStirlingUK
| | - Daisy Dent
- Department of Environmental Systems ScienceInstitute of Integrative Biology, ETH ZurichZurichSwitzerland
- Max Planck Institute for Animal BehaviourKonstanzGermany
- Smithsonian Tropical Research InstituteBalboaPanama
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18
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Jourdan J, Bundschuh M, Copilaș-Ciocianu D, Fišer C, Grabowski M, Hupało K, Jemec Kokalj A, Kabus J, Römbke J, Soose LJ, Oehlmann J. Cryptic Species in Ecotoxicology. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023; 42:1889-1914. [PMID: 37314101 DOI: 10.1002/etc.5696] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/20/2023] [Accepted: 06/12/2023] [Indexed: 06/15/2023]
Abstract
The advent of genetic methods has led to the discovery of an increasing number of species that previously could not be distinguished from each other on the basis of morphological characteristics. Even though there has been an exponential growth of publications on cryptic species, such species are rarely considered in ecotoxicology. Thus, the particular question of ecological differentiation and the sensitivity of closely related cryptic species is rarely addressed. Tackling this question, however, is of key importance for evolutionary ecology, conservation biology, and, in particular, regulatory ecotoxicology. At the same time, the use of species with (known or unknown) cryptic diversity might be a reason for the lack of reproducibility of ecotoxicological experiments and implies a false extrapolation of the findings. Our critical review includes a database and literature search through which we investigated how many of the species most frequently used in ecotoxicological assessments show evidence of cryptic diversity. We found a high proportion of reports indicating overlooked species diversity, especially in invertebrates. In terrestrial and aquatic realms, at least 67% and 54% of commonly used species, respectively, were identified as cryptic species complexes. The issue is less prominent in vertebrates, in which we found evidence for cryptic species complexes in 27% of aquatic and 6.7% of terrestrial vertebrates. We further exemplified why different evolutionary histories may significantly determine cryptic species' ecology and sensitivity to pollutants. This in turn may have a major impact on the results of ecotoxicological tests and, consequently, the outcome of environmental risk assessments. Finally, we provide a brief guideline on how to deal practically with cryptic diversity in ecotoxicological studies in general and its implementation in risk assessment procedures in particular. Environ Toxicol Chem 2023;42:1889-1914. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
- Jonas Jourdan
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
| | - Mirco Bundschuh
- iES Landau, Institute for Environmental Sciences, University of Kaiserslautern-Landau, Landau, Germany
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Denis Copilaș-Ciocianu
- Laboratory of Evolutionary Ecology of Hydrobionts, Nature Research Centre, Vilnius, Lithuania
| | - Cene Fišer
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Michał Grabowski
- Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
| | - Kamil Hupało
- Department of Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Anita Jemec Kokalj
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jana Kabus
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
| | - Jörg Römbke
- ECT Oekotoxikologie, Flörsheim am Main, Germany
| | - Laura J Soose
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
| | - Jörg Oehlmann
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
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Mroue-Ruiz FH, Pacheco-Sandoval A, Lago-Lestón A, Giffard-Mena I, Abadía-Cardoso A, Chong-Robles J, Schramm Y. Metabarcoding Used for the First Time to Identify Prey of Wild Totoaba macdonaldi. Integr Comp Biol 2023; 63:276-287. [PMID: 37164934 DOI: 10.1093/icb/icad030] [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: 02/17/2023] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/12/2023] Open
Abstract
Totoaba macdonaldi is an endangered endemic fish of the Gulf of California. Overexploitation resulted in the Mexican government banning the fishing of this species in 1975, and it being listed as endangered. However, the species is still subject to illegal fishing. Despite its conservation status, little is known about totoaba biology. The present study aimed to implement, for the first time, a metabarcoding protocol to describe the totoaba diet. Four wild totoaba individuals, seized by Mexican law enforcement agents, were dissected, and their stomach contents were collected. Three representative amplicon libraries were generated for cephalopods, chordates, and eukaryotes. After sequencing, 18 different taxa were identified, of which 11 species were recognized as prey. The totoaba were found to have consumed Pacific anchovy (Cetengraulis mysticetus), flathead grey mullet (Mugil cephalus), bigeye croaker (Micropogonias megalops), northern anchovy (Engraulis mordax), ocean whitefish (Caulolatilus princeps), milkfish (Chanos chanos), and Pacific sardine (Sardinops sagax). Members of the Euphausiidae family (krill) were also identified. This study identified up to four times more species in much fewer samples than previous studies based on morphological recognition, thus confirming metabarcoding as an effective method for studying the feeding habits of this species and one providing the tools required for further analysis of the totoaba diet.
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Affiliation(s)
- F H Mroue-Ruiz
- Facultad de Ciencias, Universidad Autónoma de Baja California, 22860 Ensenada, Baja California, Mexico
| | - A Pacheco-Sandoval
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, 22860 Ensenada, Baja California, Mexico
- Posgrado en Ciencias de la Vida, Centro de Investigación Científica y de Educación Superior de Ensenada, 22860 Ensenada, Baja California, Mexico
| | - A Lago-Lestón
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, 22860 Ensenada, Baja California, Mexico
| | - I Giffard-Mena
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, 22860 Ensenada, Baja California, Mexico
| | - A Abadía-Cardoso
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, 22860 Ensenada, Baja California, Mexico
| | - J Chong-Robles
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, 22860 Ensenada, Baja California, Mexico
| | - Y Schramm
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, 22860 Ensenada, Baja California, Mexico
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20
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Kabus J, Cunze S, Dombrowski A, Karaouzas I, Shumka S, Jourdan J. Uncovering the Grinnellian niche space of the cryptic species complex Gammarus roeselii. PeerJ 2023; 11:e15800. [PMID: 37551343 PMCID: PMC10404395 DOI: 10.7717/peerj.15800] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 07/05/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND The discovery of cryptic species complexes within morphologically established species comes with challenges in the classification and handling of these species. We hardly know to what extent species within a species complex differ ecologically. Such knowledge is essential to assess the vulnerability of individual genetic lineages in the face of global change. The abiotic conditions, i.e., the Grinnellian niche that a genetic lineage colonizes, provides insights into how diverse the ecological requirements of each evolutionary lineage are within a species complex. MATERIAL AND METHODS We sampled the cryptic species complex of the amphipod Gammarus roeselii from Central Germany to Greece and identified genetic lineages based on cytochrome c oxidase subunit I (COI) barcoding. At the same time, we recorded various abiotic parameters and local pollution parameters using a series of in vitro assays to then characterize the Grinnellian niches of the morphospecies (i.e., Gammarus roeselii sensu lato) as well as each genetic lineage. Local pollution can be a significant factor explaining current and future distributions in times of increasing production and release of chemicals into surface waters. RESULTS We identified five spatially structured genetic lineages in our dataset that differed to varying degrees in their Grinnellian niche. In some cases, the niches were very similar despite the geographical separation of lineages, supporting the hypothesis of niche conservatism while being allopatrically separated. In other cases, we found a small niche that was clearly different from those of other genetic lineages. CONCLUSION The variable niches and overlaps of different dimensions make the G. roeselii species complex a promising model system to further study ecological, phenotypic and functional differentiation within this species complex. In general, our results show that the Grinnellian niches of genetically distinct molecular operational taxonomic units (MOTUs) within a cryptic species complex can differ significantly between each other, calling for closer inspection of cryptic species in a conservational and biodiversity context.
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Affiliation(s)
- Jana Kabus
- Department Aquatic Ecotoxicology, Johann Wolfgang Goethe Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - Sarah Cunze
- Department of Integrative Parasitology and Zoophysiology, Johann Wolfgang Goethe Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - Andrea Dombrowski
- Department Aquatic Ecotoxicology, Johann Wolfgang Goethe Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - Ioannis Karaouzas
- Institute of Marine Biological Resources and Inland Waters, Hellenic Centre for Marine Research, Anavyssos, Greece
| | - Spase Shumka
- Faculty of Biotechnology and Food, Agricultural University of Tirana, Tirana, Albania
| | - Jonas Jourdan
- Department Aquatic Ecotoxicology, Johann Wolfgang Goethe Universität Frankfurt am Main, Frankfurt am Main, Germany
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21
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Jiang RH, Liang SQ, Wu F, Tang LM, Qin B, Chen YY, Huang YH, Li KX, Zhang XC. Phylogenomic analysis, cryptic species discovery, and DNA barcoding of the genus Cibotium in China based on plastome data. FRONTIERS IN PLANT SCIENCE 2023; 14:1183653. [PMID: 37346120 PMCID: PMC10279961 DOI: 10.3389/fpls.2023.1183653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/02/2023] [Indexed: 06/23/2023]
Abstract
Germplasm resources are the source of herbal medicine production. The cultivation of superior germplasm resources helps to resolve the conflict between long-term population persistence and growing market demand by consistently producing materials with high quality. The fern species Cibotium barometz is the original plant of cibotii rhizoma ("Gouji"), a traditional Chinese medicine used in the therapy of pain, weakness, and numbness in the lower extremities. Long-history medicinal use has caused serious wild population decline in China. Without sufficient understanding of the species and lineage diversity of Cibotium, it is difficult to propose a targeted conservation scheme at present, let alone select high-quality germplasm resources. In order to fill such a knowledge gap, this study sampled C. barometz and relative species throughout their distribution in China, performed genome skimming to obtain plastome data, and conducted phylogenomic analyses. We constructed a well-supported plastome phylogeny of Chinese Cibotium, which showed that three species with significant genetic differences are distributed in China, namely C. barometz, C. cumingii, and C. sino-burmaense sp. nov., a cryptic species endemic to NW Yunnan and adjacent regions of NE Myanmar. Moreover, our results revealed two differentiated lineages of C. barometz distributed on the east and west sides of a classic phylogeographic boundary that was probably shaped by monsoons and landforms. We also evaluated the resolution of nine traditional barcode loci and designed five new DNA barcodes based on the plastome sequence that can distinguish all these species and lineages of Chinese Cibotium accurately. These novel findings on a genetic basis will guide conservation planners and medicinal plant breeders to build systematic conservation plans and exploit the germplasm resources of Cibotium in China.
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Affiliation(s)
- Ri-Hong Jiang
- Guangxi Key Laboratory of Special Non-wood Forest Cultivation and Utilization, Guangxi Engineering and Technology Research Center for Woody Spices, Guangxi Forestry Research Institute, Nanning, China
| | - Si-Qi Liang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Fei Wu
- China National Botanical Garden, Beijing, China
- Beijing Botanical Garden, Beijing, China
- Beijing Floriculture Engineering Technology Research Centre, Beijing, China
| | - Li-Ming Tang
- Guangxi Forestry Industry Group Stock Corporation, Nanning, China
| | - Bo Qin
- Guangxi Key Laboratory of Special Non-wood Forest Cultivation and Utilization, Guangxi Engineering and Technology Research Center for Woody Spices, Guangxi Forestry Research Institute, Nanning, China
| | - Ying-Ying Chen
- Guangxi Key Laboratory of Special Non-wood Forest Cultivation and Utilization, Guangxi Engineering and Technology Research Center for Woody Spices, Guangxi Forestry Research Institute, Nanning, China
| | - Yao-Heng Huang
- Guangxi Key Laboratory of Special Non-wood Forest Cultivation and Utilization, Guangxi Engineering and Technology Research Center for Woody Spices, Guangxi Forestry Research Institute, Nanning, China
| | - Kai-Xiang Li
- Guangxi Key Laboratory of Special Non-wood Forest Cultivation and Utilization, Guangxi Engineering and Technology Research Center for Woody Spices, Guangxi Forestry Research Institute, Nanning, China
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
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22
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Nascimento MHS, Aragão DG, Silva JLN, Lima RC, Birindelli JLO, Fraga EC, Barros MC. The DNA barcode reveals cryptic diversity and a new record for the genus Leporinus (Characiformes, Anostomidae) in the hydrographic basins of central northern Brazil. PeerJ 2023; 11:e15184. [PMID: 37250713 PMCID: PMC10225125 DOI: 10.7717/peerj.15184] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/15/2023] [Indexed: 05/31/2023] Open
Abstract
Leporinus is one of the most speciose genera of the order Characiformes, with 81 valid species distributed throughout much of Central and South America. The considerable diversity of this genus has generated extensive debate on its classification and internal arrangement. In the present study, we investigated the species diversity of the genus Leporinus in central northern Brazil, and conclude that six valid species-Leporinus maculatus, Leporinus unitaeniatus, Leporinus affinis, Leporinus venerei, Leporinus cf. friderici, and Leporinus piau-are found in the hydrographic basins of the Brazilian states of Maranhão, Piauí, and Tocantins. We analyzed 182 sequences of the Cytochrome Oxidase subunit I gene, of which, 157 were obtained from Leporinus specimens collected from the basins of the Itapecuru, Mearim, Turiaçu, Pericumã, Periá, Preguiças, Parnaíba, and Tocantins rivers. The species delimitation analyses, based on the ABGD, ASAP, mPTP, bPTP, and GMYC methods, revealed the presence of four distinct molecular operational taxonomic units (MOTUs), identified as L. maculatus, L. unitaeniatus, L. affinis, and L. piau (from the Parnaíba River). The bPTP method restricted L. venerei to a single MOTU, and confirmed the occurrence of this species in the rivers of Maranhão for the first time. The separation of L. cf. friderici into two clades and the subsequent formation of different operational taxonomic units was consistent with polyphyly in this species, which indicates the existence of cryptic diversity. The arrangement of L. cf. friderici and L. piau in two different clades supports the conclusion that the L. piau specimens from Maranhão were misidentified, based on their morphological traits, reflecting the taxonomic inconsistencies that exist among morphologically similar species. Overall, then, the species delimitation methods employed in the present study indicated the presence of six MOTUs-L. maculatus, L. unitaenitus, L. affinis, L. cf. friderici, L. venerei, and L. piau. In the case of two other MOTUs identified in the present study, one (L. venerei) is a new record for the state of Maranhão, and we believe that the other represents a population of L. piau from the basin of the Parnaíba River.
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Affiliation(s)
- Maria Histelle Sousa Nascimento
- Department of Chemistry and Biology, Maranhão State University, Caxias, Maranhão, Brazil
- Graduate Network Program in the Biodiversity and Biotechnology of Legal Amazonia, Biological Sciences Institute, Belem, Pará, Brazil
| | - Deborah Gaído Aragão
- Department of Chemistry and Biology, Maranhão State University, Caxias, Maranhão, Brazil
| | | | - Renato Correia Lima
- Graduate Program in Genetics, Conservation, and Evolutionary Biology, National Amazonian Research Institute, Manaus, Amazonas, Brazil
| | | | - Elmary Costa Fraga
- Department of Chemistry and Biology, Maranhão State University, Caxias, Maranhão, Brazil
| | - Maria Claudene Barros
- Department of Chemistry and Biology, Maranhão State University, Caxias, Maranhão, Brazil
- Graduate Network Program in the Biodiversity and Biotechnology of Legal Amazonia, Biological Sciences Institute, Belem, Pará, Brazil
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23
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Kumar S, Gahramanov V, Patel S, Yaglom J, Kaczmarczyk L, Alexandrov IA, Gerlitz G, Salmon-Divon M, Sherman MY. Evolution of Resistance to Irinotecan in Cancer Cells Involves Generation of Topoisomerase-Guided Mutations in Non-Coding Genome That Reduce the Chances of DNA Breaks. Int J Mol Sci 2023; 24:ijms24108717. [PMID: 37240063 DOI: 10.3390/ijms24108717] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/01/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
Resistance to chemotherapy is a leading cause of treatment failure. Drug resistance mechanisms involve mutations in specific proteins or changes in their expression levels. It is commonly understood that resistance mutations happen randomly prior to treatment and are selected during the treatment. However, the selection of drug-resistant mutants in culture could be achieved by multiple drug exposures of cloned genetically identical cells and thus cannot result from the selection of pre-existent mutations. Accordingly, adaptation must involve the generation of mutations de novo upon drug treatment. Here we explored the origin of resistance mutations to a widely used Top1 inhibitor, irinotecan, which triggers DNA breaks, causing cytotoxicity. The resistance mechanism involved the gradual accumulation of recurrent mutations in non-coding regions of DNA at Top1-cleavage sites. Surprisingly, cancer cells had a higher number of such sites than the reference genome, which may define their increased sensitivity to irinotecan. Homologous recombination repairs of DNA double-strand breaks at these sites following initial drug exposures gradually reverted cleavage-sensitive "cancer" sequences back to cleavage-resistant "normal" sequences. These mutations reduced the generation of DNA breaks upon subsequent exposures, thus gradually increasing drug resistance. Together, large target sizes for mutations and their Top1-guided generation lead to their gradual and rapid accumulation, synergistically accelerating the development of resistance.
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Affiliation(s)
- Santosh Kumar
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
| | - Valid Gahramanov
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
| | - Shivani Patel
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
| | - Julia Yaglom
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
| | - Lukasz Kaczmarczyk
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
| | - Ivan A Alexandrov
- Department of Anatomy and Anthropology & Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Gabi Gerlitz
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
| | | | - Michael Y Sherman
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
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24
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Wu YH, Hou SB, Yuan ZY, Jiang K, Huang RY, Wang K, Liu Q, Yu ZB, Zhao HP, Zhang BL, Chen JM, Wang LJ, Stuart BL, Chambers EA, Wang YF, Gao W, Zou DH, Yan F, Zhao GG, Fu ZX, Wang SN, Jiang M, Zhang L, Ren JL, Wu YY, Zhang LY, Yang DC, Jin JQ, Yin TT, Li JT, Zhao WG, Murphy RW, Huang S, Guo P, Zhang YP, Che J. DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs. Mol Ecol Resour 2023. [PMID: 36924341 DOI: 10.1111/1755-0998.13784] [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: 10/03/2022] [Revised: 02/25/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023]
Abstract
DNA barcoding has greatly facilitated studies of taxonomy, biodiversity, biological conservation, and ecology. Here, we establish a reliable DNA barcoding library for Chinese snakes, unveiling hidden diversity with implications for taxonomy, and provide a standardized tool for conservation management. Our comprehensive study includes 1638 cytochrome c oxidase subunit I (COI) sequences from Chinese snakes that correspond to 17 families, 65 genera, 228 named species (80.6% of named species) and 36 candidate species. A barcode gap analysis reveals gaps, where all nearest neighbour distances exceed maximum intraspecific distances, in 217 named species and all candidate species. Three species-delimitation methods (ABGD, sGMYC, and sPTP) recover 320 operational taxonomic units (OTUs), of which 192 OTUs correspond to named and candidate species. Twenty-eight other named species share OTUs, such as Azemiops feae and A. kharini, Gloydius halys, G. shedaoensis, and G. intermedius, and Bungarus multicinctus and B. candidus, representing inconsistencies most probably caused by imperfect taxonomy, recent and rapid speciation, weak taxonomic signal, introgressive hybridization, and/or inadequate phylogenetic signal. In contrast, 43 species and candidate species assign to two or more OTUs due to having large intraspecific distances. If most OTUs detected in this study reflect valid species, including the 36 candidate species, then 30% more species would exist than are currently recognized. Several OTU divergences associate with known biogeographic barriers, such as the Taiwan Strait. In addition to facilitating future studies, this reliable and relatively comprehensive reference database will play an important role in the future monitoring, conservation, and management of Chinese snakes.
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Affiliation(s)
- Yun-He Wu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Shao-Bing Hou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Zhi-Yong Yuan
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ke Jiang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ru-Yi Huang
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Kai Wang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Qin Liu
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin, Sichuan, 644007, China
| | - Zhong-Bin Yu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Hai-Peng Zhao
- School of Life Science, Henan University, Kaifeng, Henan, 475001, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jin-Min Chen
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Li-Jun Wang
- School of Life Sciences, Hainan Normal University, Haikou, Hainan, 571158, China
| | - Bryan L Stuart
- Section of Research & Collections, North Carolina Museum of Natural Sciences, Raleigh, North Carolina, 27601, USA
| | - E Anne Chambers
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, 94720, USA
| | - Yu-Fan Wang
- Zhejiang Forest Resource Monitoring Center, Hangzhou, Zhejiang, 310020, China
| | - Wei Gao
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Da-Hu Zou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- College of Science, Tibet University, Lhasa, Tibet, 850000, China
| | - Fang Yan
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Gui-Gang Zhao
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Zhong-Xiong Fu
- Yunnan Senye Biotechnology Co., Ltd, Xishuangbanna, Yunnan, 666100, China
| | - Shao-Neng Wang
- Bureau of Guangxi Mao'er Mountain Nature Reserve, Guilin, Guangxi, 541316, China
| | - Ming Jiang
- Gongshan Bureau of Gaoligongshan National Nature Reserve, Gongshan, Yunnan, 650224, China
| | - Liang Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510260, China
| | - Jin-Long Ren
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China
| | - Ya-Yong Wu
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin, Sichuan, 644007, China
| | - Lu-Yang Zhang
- Beijing Mountains & Seas Eco Technology Co. Ltd, Beijing, 101100, China
| | - Dian-Cheng Yang
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jia-Tang Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China
| | - Wen-Ge Zhao
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, 150025, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Reptilia Zoo and Education Centre, Vaughn, Ontario, L4K 2N6, Canada
| | - Song Huang
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China
| | - Peng Guo
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin, Sichuan, 644007, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
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25
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Prudnikow L, Pannicke B, Wünschiers R. A primer on pollen assignment by nanopore-based DNA sequencing. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1112929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023] Open
Abstract
The possibility to identify plants based on the taxonomic information coming from their pollen grains offers many applications within various biological disciplines. In the past and depending on the application or research in question, pollen origin was analyzed by microscopy, usually preceded by chemical treatment methods. This procedure for identification of pollen grains is both time-consuming and requires expert knowledge of morphological features. Additionally, these microscopically recognizable features usually have a low resolution at species-level. Since a few decades, DNA has been used for the identification of pollen taxa, as sequencing technologies evolved both in their handling and affordability. We discuss advantages and challenges of pollen DNA analyses compared to traditional methods. With readers with little experience in this field in mind, we present a hands-on primer for genetic pollen analysis by nanopore sequencing. As our lab mainly works with pollen collected within agroecological research projects, we focus on pollen collected by pollinating insects. We briefly consider sample collection, storage and processing in the laboratory as well as bioinformatic aspects. Currently, pollen metabarcoding is mostly conducted with next-generation sequencing methods that generate short sequence reads (<1 kb). Increasingly, however, pollen DNA analysis is carried out using the long-read generating (several kb), low-budget and mobile MinION nanopore sequencing platform by Oxford Nanopore Technologies. Therefore, we are focusing on aspects for palynology with the MinION DNA sequencing device.
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26
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DNA barcoding reveals hidden nemertean diversity from the marine protected area Namuncurá–Burdwood Bank, Southwestern Atlantic. Polar Biol 2023. [DOI: 10.1007/s00300-023-03117-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
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27
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Assessment of the Diversity, Distinctiveness and Conservation of Australia’s Central Queensland Coastal Rainforests Using DNA Barcoding. DIVERSITY 2023. [DOI: 10.3390/d15030378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Globally threatened dry rainforests are poorly studied and conserved when compared to mesic rainforests. Investigations of dry rainforest communities within Australia are no exception. We assessed the community diversity, distinctiveness and level of conservation in Central Queensland coastal dry rainforest communities. Our three-marker DNA barcode-based phylogeny, based on rainforest species from the Central Queensland Coast, was combined with the phylogeny from Southeast Queensland. The phylogenetic tree and Central Queensland Coast (CQC) community species lists were used to evaluate phylogenetic diversity (PD) estimates and species composition to pinpoint regions of significant rainforest biodiversity. We evaluated the patterns and relationships between rainforest communities of the biogeographical areas of Central Queensland Coast and Southeast Queensland, and within and between Subregions. Subsequently, we identified areas of the highest distinctiveness and diversity in phylogenetically even rainforest communities, consistent with refugia, and areas significantly more related than random, consistent with expansion into disturbed or harsher areas. We found clear patterns of phylogenetic clustering that suggest that selection pressures for moisture and geology were strong drivers of rainforest distribution and species diversity. These results showed that smaller dry rainforests in Central Queensland Coast (CQC) represented areas of regional plant migration but were inadequately protected. To sustain species diversity and distribution under intense selection pressures of moisture availability and substrate type throughout this dry and geologically complex region, the future conservation of smaller patches is essential.
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28
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Baião GC, Schneider DI, Miller WJ, Klasson L. Multiple introgressions shape mitochondrial evolutionary history in Drosophila paulistorum and the Drosophila willistoni group. Mol Phylogenet Evol 2023; 180:107683. [PMID: 36574824 DOI: 10.1016/j.ympev.2022.107683] [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: 08/17/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022]
Abstract
Hybridization and the consequent introgression of genomic elements is an important source of genetic diversity for biological lineages. This is particularly evident in young clades in which hybrid incompatibilities are still incomplete and mixing between species is more likely to occur. Drosophila paulistorum, a representative of the Neotropical Drosophila willistoni subgroup, is a classic model of incipient speciation. The species is divided into six semispecies that show varying degrees of pre- and post-mating incompatibility with each other. In the present study, we investigate the mitochondrial evolutionary history of D. paulistorum and the willistoni subgroup. For that, we perform phylogenetic and comparative analyses of the complete mitochondrial genomes and draft nuclear assemblies of 25 Drosophila lines of the willistoni and saltans species groups. Our results show that the mitochondria of D. paulistorum are polyphyletic and form two non-sister clades that we name α and β. Identification and analyses of nuclear mitochondrial insertions further reveal that the willistoni subgroup has an α-like mitochondrial ancestor and strongly suggest that both the α and β mitochondria of D. paulistorum were acquired through introgression from unknown fly lineages of the willistoni subgroup. We also uncover multiple mitochondrial introgressions across D. paulistorum semispecies and generate novel insight into the evolution of the species.
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Affiliation(s)
- Guilherme C Baião
- Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Husargatan 3, 751 24 Uppsala, Sweden.
| | - Daniela I Schneider
- Lab Genome Dynamics, Department Cell & Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstraße 17, 1090 Vienna, Austria.
| | - Wolfgang J Miller
- Lab Genome Dynamics, Department Cell & Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstraße 17, 1090 Vienna, Austria.
| | - Lisa Klasson
- Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Husargatan 3, 751 24 Uppsala, Sweden.
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29
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Theissinger K, Fernandes C, Formenti G, Bista I, Berg PR, Bleidorn C, Bombarely A, Crottini A, Gallo GR, Godoy JA, Jentoft S, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Secomandi S, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Jarvis ED, Bálint M, Ciofi C, Waterhouse RM, Mazzoni CJ, Höglund J. How genomics can help biodiversity conservation. Trends Genet 2023:S0168-9525(23)00020-3. [PMID: 36801111 DOI: 10.1016/j.tig.2023.01.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/08/2022] [Accepted: 01/19/2023] [Indexed: 02/18/2023]
Abstract
The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.
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Affiliation(s)
- Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Carlos Fernandes
- CE3C - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Faculdade de Psicologia, Universidade de Lisboa, Alameda da Universidade, 1649-013 Lisboa, Portugal
| | - Giulio Formenti
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Iliana Bista
- Naturalis Biodiversity Center, Darwinweg 2, 2333, CR, Leiden, The Netherlands; Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Paul R Berg
- NIVA - Norwegian Institute for Water Research, Økernveien, 94, 0579 Oslo, Norway; Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Christoph Bleidorn
- University of Göttingen, Department of Animal Evolution and Biodiversity, Untere Karspüle, 2, 37073, Göttingen, Germany
| | | | - Angelica Crottini
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Rua Padre Armando Quintas, 7, 4485-661, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Guido R Gallo
- Department of Biosciences, University of Milan, Milan, Italy
| | - José A Godoy
- Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Joanna Malukiewicz
- Primate Genetics Laborator, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany
| | - Alice Mouton
- InBios - Conservation Genetics Lab, University of Liege, Chemin de la Vallée 4, 4000, Liege, Belgium
| | - Rebekah A Oomen
- Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Sadye Paez
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Per J Palsbøll
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh, 9747, AG, Groningen, The Netherlands; Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA 02657, USA
| | - Christophe Pampoulie
- Marine and Freshwater Research Institute, Fornubúðir, 5,220, Hanafjörður, Iceland
| | - María J Ruiz-López
- Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), Spain
| | | | - Hannes Svardal
- Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium
| | - Constantina Theofanopoulou
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA; Hunter College, City University of New York, NY, USA
| | - Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), Campus Institute Data Science (CIDAS), Goldschmidtstr. 1, 37077, Goettingen, Germany
| | - Ann-Marie Waldvogel
- Institute of Zoology, University of Cologne, Zülpicherstrasse 47b, D-50674, Cologne, Germany
| | - Guojie Zhang
- Evolutionary & Organismal Biology Research Center, Zhejiang University School of Medicine, Hangzhou, 310058, China; Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Erich D Jarvis
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Claudio Ciofi
- University of Florence, Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino, (FI) 50019, Italy
| | - Robert M Waterhouse
- University of Lausanne, Department of Ecology and Evolution, Le Biophore, UNIL-Sorge, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Camila J Mazzoni
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str 17, 10315 Berlin, Germany; Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Koenigin-Luise-Str 6-8, 14195 Berlin, Germany
| | - Jacob Höglund
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75246, Uppsala, Sweden.
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Rongier G, Sagne A, Etienne S, Petitclerc F, Jaouen G, Murienne J, Orivel J. Ants of French Guiana: 16S rRNA sequence dataset. Biodivers Data J 2023; 11:e91577. [PMID: 38327367 PMCID: PMC10848834 DOI: 10.3897/bdj.11.e91577] [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: 08/12/2022] [Accepted: 11/30/2022] [Indexed: 02/10/2023] Open
Abstract
This dataset represents a reference library of DNA sequences for ants from French Guiana. A total of 3931 new sequences from the 16S rRNA gene has been generated. The reference library covers 344 species distributed in 57 genera. Overall, 3920 sequences have been assigned at the species level and 11 at the genus level. All these sequences were submitted to DDBJ/EMBL/GenBank databases in the Bioproject: PRJNA779056: 16S French Guiana Ants (Hymenoptera: Formicidae), sequence identifier KFFS00000000.
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Affiliation(s)
- Gaëtan Rongier
- UMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles), Kourou, French GuianaUMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles)KourouFrench Guiana
| | - Audrey Sagne
- UMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles), Kourou, French GuianaUMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles)KourouFrench Guiana
| | - Sandrine Etienne
- UMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles), Kourou, French GuianaUMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles)KourouFrench Guiana
| | - Frederic Petitclerc
- UMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles), Kourou, French GuianaUMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles)KourouFrench Guiana
| | - Gaelle Jaouen
- UMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles), Kourou, French GuianaUMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles)KourouFrench Guiana
| | - Jerome Murienne
- Laboratoire Evolution et Diversité Biologique (EDB UMR5174) CNRS, Université Paul Sabatier Toulouse 3, IRD, Toulouse, FranceLaboratoire Evolution et Diversité Biologique (EDB UMR5174) CNRS, Université Paul Sabatier Toulouse 3, IRDToulouseFrance
| | - Jerome Orivel
- UMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles), Kourou, French GuianaUMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles)KourouFrench Guiana
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Setsuko S, Yoshimura K, Ueno S, Worth JRP, Ujino-Ihara T, Katsuki T, Noshiro S, Fujii T, Arai T, Yoshimaru H. A DNA barcode reference library for the native woody seed plants of Japan. Mol Ecol Resour 2023; 23:855-871. [PMID: 36694075 DOI: 10.1111/1755-0998.13748] [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: 04/12/2022] [Revised: 10/25/2022] [Accepted: 12/08/2022] [Indexed: 01/26/2023]
Abstract
DNA barcode databases are increasingly available for a range of organisms, facilitating the wide application of DNA barcode-based studies. Here we announce the development of a comprehensive DNA barcode reference library of Japanese native woody seed plants representing 43 orders, 99 families, 303 genera and 834 species, and comprising 77.3% of the genera and 72.2% of the species of native woody seed plants in Japan. A total of 6216 plant specimens were collected from 223 sites across the subtropical, temperate, boreal and alpine biomes in Japan with most species represented by multiple accessions. This reference library utilized three chloroplast DNA regions (rbcL, trnH-psbA and matK) and consists of 14,403 barcode sequences. Individual regions varied in their identification rates, with species-level and genus-level rates for rbcL, trnH-psbA and matK based on blast being 57.4%/96.2%, 78.5%/99.1% and 67.8%/98.1%, respectively. Identification rates were higher using region combinations, with total species-level rates for two region combinations (rbcL & trnH-psbA, rbcL & matK and trnH-psbA & matK) ranging between 90.6% and 95.8%, and for all three regions being equal to 98.6%. Genus-level identification rates were even higher, ranging between 99.7% and 100% for two region combinations and being 100% for the three regions. These results indicate that this DNA barcode reference library is an effective resource for investigations of native woody seed plants in Japan using DNA barcodes and provides a useful template for the development of libraries for other components of the Japanese flora.
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Affiliation(s)
- Suzuki Setsuko
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Kensuke Yoshimura
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Saneyoshi Ueno
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - James Raymond Peter Worth
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Tokuko Ujino-Ihara
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Toshio Katsuki
- Tama Forest Science Garden, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tokyo, Japan
| | - Shuichi Noshiro
- Department of Wood Properties and Processing
- , Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Tomoyuki Fujii
- Department of Wood Properties and Processing
- , Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Takahisa Arai
- Tohoku University Botanical Gardens, Tohoku University, Miyagi, Japan
| | - Hiroshi Yoshimaru
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
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Pauperio J, Gonzalez LM, Martinez J, González MA, Martins FMS, Veríssimo J, Puppo P, Pinto J, Chaves C, Pinho CJ, Grosso-Silva JM, Quaglietta L, Silva TLL, Sousa P, Alves PC, Fonseca N, Beja P, Ferreira S. The InBIO barcoding initiative database: DNA barcodes of Iberian Trichoptera, documenting biodiversity for freshwater biomonitoring in a Mediterranean hotspot. Biodivers Data J 2023; 11:e97484. [PMID: 38327295 PMCID: PMC10848855 DOI: 10.3897/bdj.11.e97484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 12/28/2022] [Indexed: 01/20/2023] Open
Abstract
Background The Trichoptera are an important component of freshwater ecosystems. In the Iberian Peninsula, 380 taxa of caddisflies are known, with nearly 1/3 of the total species being endemic in the region. A reference collection of morphologically identified Trichoptera specimens, representing 142 Iberian taxa, was constructed. The InBIO Barcoding Initiative (IBI) Trichoptera 01 dataset contains records of 438 sequenced specimens. The species of this dataset correspond to about 37% of Iberian Trichoptera species diversity. Specimens were collected between 1975 and 2018 and are deposited in the IBI collection at the CIBIO (Research Center in Biodiversity and Genetic Resources, Portugal) or in the collection Marcos A. González at the University of Santiago de Compostela (Spain). New information Twenty-nine species, from nine different families, were new additions to the Barcode of Life Data System (BOLD). A success identification rate of over 80% was achieved when comparing morphological identifications and DNA barcodes for the species analysed. This encouraging step advances incorporation of informed Environmental DNA tools in biomonitoring schemes, given the shortcomings of morphological identifications of larvae and adult Caddisflies in such studies. DNA barcoding was not successful in identifying species in six Trichoptera genera: Hydropsyche (Hydropsychidae), Athripsodes (Leptoceridae), Wormaldia (Philopotamidae), Polycentropus (Polycentropodidae) Rhyacophila (Rhyacophilidae) and Sericostoma (Sericostomatidae). The high levels of intraspecific genetic variability found, combined with a lack of a barcode gap and a challenging morphological identification, rendered these species as needing additional studies to resolve their taxonomy.
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Affiliation(s)
- Joana Pauperio
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, United KingdomEuropean Molecular Biology Laboratory, European Bioinformatics InstituteHinxton, CambridgeUnited Kingdom
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
| | - Luis Martin Gonzalez
- Departamento de Zoología, Genética y Antropología Física, Facultad de Biología. Universidad de Santiago de Compostela, Santiago de Compostela, SpainDepartamento de Zoología, Genética y Antropología Física, Facultad de Biología. Universidad de Santiago de CompostelaSantiago de CompostelaSpain
| | - Jesus Martinez
- Departamento de Zoología, Genética y Antropología Física, Facultad de Biología. Universidad de Santiago de Compostela, Santiago de Compostela, SpainDepartamento de Zoología, Genética y Antropología Física, Facultad de Biología. Universidad de Santiago de CompostelaSantiago de CompostelaSpain
| | - Marcos A González
- Departamento de Zoología, Genética y Antropología Física, Facultad de Biología. Universidad de Santiago de Compostela, Santiago de Compostela, SpainDepartamento de Zoología, Genética y Antropología Física, Facultad de Biología. Universidad de Santiago de CompostelaSantiago de CompostelaSpain
| | - Filipa MS Martins
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
| | - Joana Veríssimo
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, PortugalDepartamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007PortoPortugal
| | - Pamela Puppo
- Marshall University, Department of Biological Sciences, Huntington, United States of AmericaMarshall University, Department of Biological SciencesHuntingtonUnited States of America
| | - Joana Pinto
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
| | - Cátia Chaves
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
| | - Catarina J. Pinho
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, PortugalDepartamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007PortoPortugal
| | - José Manuel Grosso-Silva
- Museu de História Natural e da Ciência da Universidade do Porto, Porto, PortugalMuseu de História Natural e da Ciência da Universidade do PortoPortoPortugal
| | - Lorenzo Quaglietta
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia, Universidade de LisboaLisboaPortugal
| | - Teresa Luísa L Silva
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
| | - Pedro Sousa
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
| | - Paulo Celio Alves
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
- EBM, Estação Biológica de Mértola, Praça Luís de Camões, Mértola, PortugalEBM, Estação Biológica de Mértola, Praça Luís de CamõesMértolaPortugal
| | - Nuno Fonseca
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
| | - Pedro Beja
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto Superior de Agronomia, Universidade de LisboaLisboaPortugal
| | - Sónia Ferreira
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Vila do Conde, PortugalBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 VairãoVila do CondePortugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, PortugalCIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 VairãoVila do CondePortugal
- EBM, Estação Biológica de Mértola, Praça Luís de Camões, Mértola, PortugalEBM, Estação Biológica de Mértola, Praça Luís de CamõesMértolaPortugal
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Ji W, Dou F, Zhang C, Xiao Y, Yin W, Yu J, Kurenshchikov DK, Zhu X, Shi J. Improvement in the Identification Technology for Asian Spongy Moth, Lymantria dispar Linnaeus, 1758 (Lepidoptera: Erebidae) Based on SS-COI. INSECTS 2023; 14:94. [PMID: 36662022 PMCID: PMC9867181 DOI: 10.3390/insects14010094] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/05/2023] [Accepted: 01/11/2023] [Indexed: 06/17/2023]
Abstract
Lymantria dispar (Linnaeus, 1758), which is commonly known as spongy moth, with two subspecies, is found in Asia: Lymantria dispar asiatica and Lymantria dispar japonica, collectively referred to as the Asian spongy moth (ASM). The subspecies Lymantria dispar dispar occurs in Europe and is commonly known as the European spongy moth (ESM). The ASM is on the quarantine list of many countries because it induces greater economic losses than the ESM. Accurate identification is essential to prevent the invasion of ASM into new areas. Although several techniques for identifying ASMs have been developed, the recent discovery of complex patterns of genetic variation among ASMs in China as well as new subspecies in some areas has necessitated the development of new, improved identification techniques, as previously developed techniques are unable to accurately identify ASMs from all regions in China. Here, we demonstrate the efficacy of an improved technique for the identification of the ASM using ASM-specific primers, which were designed based on cytochrome oxidase I sequences from samples obtained from all sites where ASMs have been documented to occur in China. We show that these primers are effective for identifying a single ASM at all life stages and from all ASM populations in China, and the minimum detectable concentration of genomic DNA was 30 pg. The inclusion of other Lymantria samples in our analysis confirmed the high specificity of the primers. Our improved technique allows the spread of ASMs to be monitored in real time and will help mitigate the spread of ASMs to other areas.
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Affiliation(s)
- Wenzhuai Ji
- Beijing Key Laboratory for Forest Pest Control and Sino-French Joint Laboratory for Invasive Forest Pests in Eurasia, College of Forestry, Beijing Forestry University, Beijing 100107, China
| | - Fengrui Dou
- Beijing Key Laboratory for Forest Pest Control and Sino-French Joint Laboratory for Invasive Forest Pests in Eurasia, College of Forestry, Beijing Forestry University, Beijing 100107, China
| | - Chunhua Zhang
- Agricultural Integrated Service Centre, Agriculture and Rural Affairs Bureau, Fugong 673400, China
| | - Yuqian Xiao
- Beijing Key Laboratory for Forest Pest Control and Sino-French Joint Laboratory for Invasive Forest Pests in Eurasia, College of Forestry, Beijing Forestry University, Beijing 100107, China
| | - Wenqi Yin
- Beijing Key Laboratory for Forest Pest Control and Sino-French Joint Laboratory for Invasive Forest Pests in Eurasia, College of Forestry, Beijing Forestry University, Beijing 100107, China
| | - Jinyong Yu
- Guizhou Academy of Forestry, Guiyang 550005, China
| | - D. K. Kurenshchikov
- Institute for Aquatic and Ecological Problems, Far East Brunch of Russian Academy of Science, 680000 Khabarovsk, Russia
| | - Xiue Zhu
- Guizhou Academy of Forestry, Guiyang 550005, China
| | - Juan Shi
- Beijing Key Laboratory for Forest Pest Control and Sino-French Joint Laboratory for Invasive Forest Pests in Eurasia, College of Forestry, Beijing Forestry University, Beijing 100107, China
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Botha D, du Plessis M, Siebert F, Barnard S. Introducing an rbcL and a trnL reference library to aid in the metabarcoding analysis of foraged plants from two semi-arid eastern South African savanna bioregions. PLoS One 2023; 18:e0286144. [PMID: 37205700 DOI: 10.1371/journal.pone.0286144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/10/2023] [Indexed: 05/21/2023] Open
Abstract
Success of a metabarcoding study is determined by the extent of taxonomic coverage and the quality of records available in the DNA barcode reference database used. This study aimed to create an rbcL and a trnL (UAA) DNA barcode sequence reference database of plant species that are potential herbivore foraging targets and commonly found in semi-arid savannas of eastern South Africa. An area-specific species list of 765 species was compiled according to plant collection records available and areas comparable to an eastern semi-arid South African savanna. Thereafter, rbcL and trnL sequences of species from this list were mined from GenBank and BOLD sequence databases according to specific quality criteria to ensure accurate taxonomic coverage and resolution. These were supplemented with sequences of 24 species sequenced for this study. A phylogenetic approach, employing Neighbor-Joining, was used to verify the topology of the reference libraries to known angiosperm phylogeny. The taxonomic reliability of these reference libraries was evaluated by testing for the presence of a barcode gap, identifying a data-appropriate identification threshold, and determining the identification accuracy of reference sequences via primary distance-based criteria. The final rbcL reference dataset consisted of 1238 sequences representing 318 genera and 562 species. The final trnL dataset consisted of 921 sequences representing 270 genera and 461 species. Barcode gaps were found for 76% of the taxa in the rbcL barcode reference dataset and 68% of the taxa in the trnL barcode reference dataset. The identification success rate, calculated with the k-nn criterion was 85.86% for the rbcL dataset and 73.72% for the trnL dataset. The datasets for rbcL and trnL combined during this study are not presented as complete DNA reference libraries, but rather as two datasets that should be used in unison to identify plants present in the semi-arid eastern savannas of South Africa.
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Affiliation(s)
- Danielle Botha
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Mornè du Plessis
- Core Sequencing Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham, Johannesburg, South Africa
| | - Frances Siebert
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Sandra Barnard
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
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Grover A, Sharma P, Sharma R, Sinha R. Ultrastructural and molecular approach as a tool for taxonomic identification of aquatic macroinvertebrates: A review. Heliyon 2022; 8:e12236. [DOI: 10.1016/j.heliyon.2022.e12236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 10/16/2022] [Accepted: 12/01/2022] [Indexed: 12/14/2022] Open
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Kestel JH, Field DL, Bateman PW, White NE, Allentoft ME, Hopkins AJM, Gibberd M, Nevill P. Applications of environmental DNA (eDNA) in agricultural systems: Current uses, limitations and future prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157556. [PMID: 35882340 DOI: 10.1016/j.scitotenv.2022.157556] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/29/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Global food production, food supply chains and food security are increasingly stressed by human population growth and loss of arable land, becoming more vulnerable to anthropogenic and environmental perturbations. Numerous mutualistic and antagonistic species are interconnected with the cultivation of crops and livestock and these can be challenging to identify on the large scales of food production systems. Accurate identifications to capture this diversity and rapid scalable monitoring are necessary to identify emerging threats (i.e. pests and pathogens), inform on ecosystem health (i.e. soil and pollinator diversity), and provide evidence for new management practices (i.e. fertiliser and pesticide applications). Increasingly, environmental DNA (eDNA) is providing rapid and accurate classifications for specific organisms and entire species assemblages in substrates ranging from soil to air. Here, we aim to discuss how eDNA is being used for monitoring of agricultural ecosystems, what current limitations exist, and how these could be managed to expand applications into the future. In a systematic review we identify that eDNA-based monitoring in food production systems accounts for only 4 % of all eDNA studies. We found that the majority of these eDNA studies target soil and plant substrates (60 %), predominantly to identify microbes and insects (60 %) and are biased towards Europe (42 %). While eDNA-based monitoring studies are uncommon in many of the world's food production systems, the trend is most pronounced in emerging economies often where food security is most at risk. We suggest that the biggest limitations to eDNA for agriculture are false negatives resulting from DNA degradation and assay biases, as well as incomplete databases and the interpretation of abundance data. These require in silico, in vitro, and in vivo approaches to carefully design, test and apply eDNA monitoring for reliable and accurate taxonomic identifications. We explore future opportunities for eDNA research which could further develop this useful tool for food production system monitoring in both emerging and developed economies, hopefully improving monitoring, and ultimately food security.
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Affiliation(s)
- Joshua H Kestel
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia.
| | - David L Field
- Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia
| | - Philip W Bateman
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Behavioural Ecology Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Nicole E White
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Anna J M Hopkins
- Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia
| | - Mark Gibberd
- Centre for Crop Disease Management (CCDM), School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
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Safhi FA, ALshamrani SM, Jalal AS, El-Moneim DA, Alyamani AA, Ibrahim AA. Genetic Characterization of Some Saudi Arabia's Accessions from Commiphora gileadensis Using Physio-Biochemical Parameters, Molecular Markers, DNA Barcoding Analysis and Relative Gene Expression. Genes (Basel) 2022; 13:2099. [PMID: 36421774 PMCID: PMC9690626 DOI: 10.3390/genes13112099] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/29/2022] [Accepted: 11/07/2022] [Indexed: 09/02/2023] Open
Abstract
Commiphora gileadensis L. is a medicinal plant, known as balsam, with pharmaceutical potential for its phytochemical activities and chemical constituents. Genetic diversity is a genetic tool used in medicinal plant evolution and conservation. Three accessions from C. gileadensis were collected from three localities in Saudi Arabia (Jeddah, Jizan and Riyadh). Genetic characterization was carried out using physio-biochemical parameters, molecular markers (inter-simple sequence repeat (ISSR) and start codon targeted (SCoT)), DNA barcoding (18 S rRNA and ITS rDNA regions), relative gene expressions (phenylalanine ammonia-lyase 1 (PAL1), defensin (PR-12)) and pathogenesis-related protein (AFPRT). The results of this study showed that C. gileadensis accession C3, collected from Riyadh, had the highest content from the physio-biochemical parameters perspective, with values of 92.54 mg/g and 77.13 mg/g for total phenolic content (TPC) and total flavonoid content (TFC), respectively. Furthermore, the highest content of antioxidant enzyme activity was present in accession C3 with values of 16.87, 60.87, 35.76 and 27.98 U mg-1 for superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) (mol/min/mg FW) and ascorbate peroxidase (APX) (U mg-1 protein), respectively. The highest total number of bands and number of unique bands were 138 and 59, respectively, for the SCoT marker. The SCoT marker was the most efficient for the genetic diversity of C. gileadensis by producing the highest polymorphism (75.63%). DNA barcoding using 18 S and ITS showed the nearby Commiphora genus and clustered C. gileadensis accessions from Jeddah and Jizan in one clade and the C. gileadensis accession from Ryiadh in a separate cluster. Moreover, relative gene expression of the PAL1, defensin (PR-12) and AFPRT (PR1) genes was upregulated in the C. gileadensis accession from Ryiadh. In conclusion, ecological and environmental conditions in each locality affect the genomic expression and genetic diversity, which can help the evolution of important medicinal plants and improve breeding and conservation systems.
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Affiliation(s)
- Fatmah Ahmed Safhi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | | | - Areej Saud Jalal
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Diaa Abd El-Moneim
- Department of Plant Production(Genetic Branch), Faculty of Environmental and Agricultural Sciences, Arish University, El-Arish 45511, Egypt
| | - Amal A. Alyamani
- Department of Biotechnology, Faculty of Science, Taif University, Taif 21974, Saudi Arabia
| | - Amira A. Ibrahim
- Botany and Microbiology Department, Faculty of Science, Arish University, El-Arish 45511, Egypt
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Okuno S, Yin T, Nanami S, Matsuyama S, Kamiya K, Tan S, Davies SJ, Mohamad M, Yamakura T, Itoh A. Community phylogeny and spatial scale affect phylogenetic diversity metrics in a species‐rich rainforest in Borneo. Ecol Evol 2022; 12:e9536. [DOI: 10.1002/ece3.9536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/24/2022] Open
Affiliation(s)
- Seiya Okuno
- Graduate School of Science Osaka City University Osaka Japan
| | - Tingting Yin
- Graduate School of Science Osaka City University Osaka Japan
| | - Satoshi Nanami
- Graduate School of Science Osaka City University Osaka Japan
- Graduate School of Science Osaka Metropolitan University Osaka Japan
| | - Shuhei Matsuyama
- College of Agriculture, Food and Environmental Sciences Rakuno Gakuen University Ebetsu Japan
| | - Koichi Kamiya
- Graduate School of Agriculture Ehime University Matsuyama Japan
| | - Sylvester Tan
- Global Earth Observatory (ForestGEO) Smithsonian Tropical Research Institute Washington USA
| | - Stuart J. Davies
- Global Earth Observatory (ForestGEO) Smithsonian Tropical Research Institute Washington USA
| | | | - Takuo Yamakura
- Graduate School of Science Osaka City University Osaka Japan
| | - Akira Itoh
- Graduate School of Science Osaka City University Osaka Japan
- Graduate School of Science Osaka Metropolitan University Osaka Japan
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Zhu S, Liu Q, Qiu S, Dai J, Gao X. DNA barcoding: an efficient technology to authenticate plant species of traditional Chinese medicine and recent advances. Chin Med 2022; 17:112. [PMID: 36171596 PMCID: PMC9514984 DOI: 10.1186/s13020-022-00655-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022] Open
Abstract
Traditional Chinese medicine (TCM) plays an important role in the global traditional health systems. However, adulterated and counterfeit TCM is on the rise. DNA barcoding is an effective, rapid, and accurate technique for identifying plant species. In this study, we collected manuscripts on DNA barcoding published in the last decade and summarized the use of this technique in identifying 50 common Chinese herbs listed in the Chinese pharmacopoeia. Based on the dataset of the major seven DNA barcodes of plants in the NCBI database, the strengths and limitations of the barcodes and their derivative barcoding technology, including single-locus barcode, multi-locus barcoding, super-barcoding, meta-barcoding, and mini-barcoding, were illustrated. In addition, the advances in DNA barcoding, particularly identifying plant species for TCM using machine learning technology, are also reviewed. Finally, the selection process of an ideal DNA barcoding technique for accurate identification of a given TCM plant species was also outlined.
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Affiliation(s)
- Shuang Zhu
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Qiaozhen Liu
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Simin Qiu
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Jiangpeng Dai
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Xiaoxia Gao
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China.
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40
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Tadmor-Levi R, Cummings D, Borovski T, Shapira R, Marcos-Hadad E, David L. A method for quick and efficient identification of cichlid species by high resolution DNA melting analysis of minibarcodes. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1010838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Freshwater bodies are key in supporting aquatic and terrestrial life. Ecological balance of freshwater habitats is very vulnerable, hence, often significantly disrupted by climatic changes and anthropogenic acts. In Israel, due to its relatively arid climate, many freshwater resources have been disrupted and still are under great pressure. The Sea of Galilee is the largest surface freshwater body in the Middle East and a habitat to unique populations of several fishes, including six cichlid species. Studies on the ecology of these fish and their conservation require effective monitoring tools. In this study, a simple and efficient molecular method was developed to identify the species of these lake cichlids using high resolution melting analysis of mini DNA barcodes. The species of an individual sample can be identified by a single tube PCR reaction. This assay successfully identified sequence differences both among and within species. Here, this method identified the species for 279 small cichlid fry that could not be morphologically identified, allowing to estimate relative species abundance and map their distribution in time and location. The results are key to understand not only the ecology of young stages but also their recruitment potential to adult fish populations and their sustainability. This method can be readily implemented in further ecological studies and surveys related to these species, in the lake and its surroundings, as a tool to enhance understanding and protection of these species.
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Xiao TW, Ge XJ. Plastome structure, phylogenomics, and divergence times of tribe Cinnamomeae (Lauraceae). BMC Genomics 2022; 23:642. [PMID: 36076185 PMCID: PMC9461114 DOI: 10.1186/s12864-022-08855-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tribe Cinnamomeae is a species-rich and ecologically important group in tropical and subtropical forests. Previous studies explored its phylogenetic relationships and historical biogeography using limited loci, which might result in biased molecular dating due to insufficient parsimony-informative sites. Thus, 15 plastomes were newly sequenced and combined with published plastomes to study plastome structural variations, gene evolution, phylogenetic relationships, and divergence times of this tribe. RESULTS Among the 15 newly generated plastomes, 14 ranged from 152,551 bp to 152,847 bp, and the remaining one (Cinnamomum chartophyllum XTBGLQM0164) was 158,657 bp. The inverted repeat (IR) regions of XTBGLQM0164 contained complete ycf2, trnICAU, rpl32, and rpl2. Four hypervariable plastid loci (ycf1, ycf2, ndhF-rpl32-trnLUAG, and petA-psbJ) were identified as candidate DNA barcodes. Divergence times based on a few loci were primarily determined by prior age constraints rather than by DNA data. In contrast, molecular dating using complete plastid protein-coding genes (PCGs) was determined by DNA data rather than by prior age constraints. Dating analyses using PCGs showed that Cinnamomum sect. Camphora diverged from C. sect. Cinnamomum in the late Oligocene (27.47 Ma). CONCLUSIONS This study reports the first case of drastic IR expansion in tribe Cinnamomeae, and indicates that plastomes have sufficient parsimony-informative sites for molecular dating. Besides, the dating analyses provide preliminary insights into the divergence time within tribe Cinnamomeae and can facilitate future studies on its historical biogeography.
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Affiliation(s)
- Tian-Wen Xiao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China. .,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China.
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42
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Genetic differentiation pattern and evidence of an early speciation process in the genus Reithrodon (Rodentia: Sigmodontinae). Mamm Biol 2022. [DOI: 10.1007/s42991-022-00297-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Guo M, Yuan C, Tao L, Cai Y, Zhang W. Life barcoded by DNA barcodes. CONSERV GENET RESOUR 2022; 14:351-365. [PMID: 35991367 PMCID: PMC9377290 DOI: 10.1007/s12686-022-01291-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/05/2022] [Indexed: 11/15/2022]
Abstract
The modern concept of DNA-based barcoding for cataloguing biodiversity was proposed in 2003 by first adopting an approximately 600 bp fragment of the mitochondrial COI gene to compare via nucleotide alignments with known sequences from specimens previously identified by taxonomists. Other standardized regions meeting barcoding criteria then are also evolving as DNA barcodes for fast, reliable and inexpensive assessment of species composition across all forms of life, including animals, plants, fungi, bacteria and other microorganisms. Consequently, global DNA barcoding campaigns have resulted in the formation of many online workbenches and databases, such as BOLD system, as barcode references, and facilitated the development of mini-barcodes and metabarcoding strategies as important extensions of barcode techniques. Here we intend to give an overview of the characteristics and features of these barcode markers and major reference libraries existing for barcoding the planet’s life, as well as to address the limitations and opportunities of DNA barcodes to an increasingly broader community of science and society.
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Lance RF, Guan X, Swift JF, Edwards CE, Lindsay DL, Britzke ER. Multifaceted DNA Metabarcoding of Guano to Uncover Multiple Classes of Ecological Data in Two Different Bat Communities. Evol Appl 2022; 15:1189-1200. [PMID: 35899252 PMCID: PMC9309442 DOI: 10.1111/eva.13425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 11/30/2022] Open
Abstract
DNA contained in animal scat provides a wealth of information about the animal, and DNA metabarcoding of scat collections can provide key information about animal populations and communities. Next‐generation DNA sequencing technologies and DNA metabarcoding provide an efficient means for obtaining information available in scat samples. We used multifaceted DNA metabarcoding (MDM) of noninvasively collected bat guano pellets from a Myotis lucifugus colony on Fort Drum Military Installation, New York, USA, and from two mixed‐species bat roosts on Fort Huachuca Military Installation, Arizona, USA, to identify attributes such as bat species composition, sex ratios, diet, and the presence of pathogens and parasites. We successfully identified bat species for nearly 98% of samples from Fort Drum and 90% of samples from Fort Huachuca, and identified the sex for 84% and 67% of samples from these same locations, respectively. Species and sex identification matched expectations based on prior censuses of bat populations utilizing those roosts, though samples from some species were more or less common than anticipated within Fort Huachuca roosts. Nearly 62% of guano samples from Fort Drum contained DNA from Pseudogymnoascus destructans, where bats with wing damage from White‐nose Syndrome were commonly observed. Putative dietary items were detected in a majority of samples from insectivorous bats on Fort Drum (81%) and Fort Huachuca (63%). A minority of guano samples identified as the nectarivorous Leptonycteris yerbabuenae (28%) provided DNA sequences from putative forage plant species. Finally, DNA sequences from both putative ecto‐ and endoparasite taxa were detected in 35% and 56% of samples from Fort Drum and Fort Huachuca, respectively. This study demonstrates that the combination of noninvasive sampling, DNA metabarcoding, and sample and locus multiplexing provide a wide array of data that are otherwise difficult to obtain.
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Affiliation(s)
- Richard F. Lance
- Environmental Laboratory US Army Engineer Research & Development Center 3909 Halls Ferry Road Vicksburg MS 39180 USA
| | - Xin Guan
- Bennett Aerospace 3909 Halls Ferry Road Vicksburg MS 39180 USA
- Moderna, Inc Cambridge MA USA
| | - Joel F. Swift
- Center for Conservation and Sustainable Development Missouri Botanical Garden 4344 Shaw Blvd St. Louis MO 63110 USA
- Department of Biology St. Louis University St. Louis MO USA
| | - Christine E. Edwards
- Center for Conservation and Sustainable Development Missouri Botanical Garden 4344 Shaw Blvd St. Louis MO 63110 USA
| | - Denise L. Lindsay
- Environmental Laboratory US Army Engineer Research & Development Center 3909 Halls Ferry Road Vicksburg MS 39180 USA
| | - Eric R. Britzke
- Environmental Laboratory US Army Engineer Research & Development Center 3909 Halls Ferry Road Vicksburg MS 39180 USA
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45
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DNA Barcoding Medicinal Plant Species from Indonesia. PLANTS 2022; 11:plants11101375. [PMID: 35631799 PMCID: PMC9147630 DOI: 10.3390/plants11101375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 11/17/2022]
Abstract
Over the past decade, plant DNA barcoding has emerged as a scientific breakthrough and is often used to help with species identification or as a taxonomical tool. DNA barcoding is very important in medicinal plant use, not only for identification purposes but also for the authentication of medicinal products. Here, a total of 61 Indonesian medicinal plant species from 30 families and a pair of ITS2, matK, rbcL, and trnL primers were used for a DNA barcoding study consisting of molecular and sequence analyses. This study aimed to analyze how the four identified DNA barcoding regions (ITS2, matK, rbcL, and trnL) aid identification and conservation and to investigate their effectiveness for DNA barcoding for the studied species. This study resulted in 212 DNA barcoding sequences and identified new ones for the studied medicinal plant species. Though there is no ideal or perfect region for DNA barcoding of the target species, we recommend matK as the main region for Indonesian medicinal plant identification, with ITS2 and rbcL as alternative or complementary regions. These findings will be useful for forensic studies that support the conservation of medicinal plants and their national and global use.
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Saccò M, Guzik MT, van der Heyde M, Nevill P, Cooper SJB, Austin AD, Coates PJ, Allentoft ME, White NE. eDNA in subterranean ecosystems: Applications, technical aspects, and future prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153223. [PMID: 35063529 DOI: 10.1016/j.scitotenv.2022.153223] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
Monitoring of biota is pivotal for the assessment and conservation of ecosystems. Environments worldwide are being continuously and increasingly exposed to multiple adverse impacts, and the accuracy and reliability of the biomonitoring tools that can be employed shape not only the present, but more importantly, the future of entire habitats. The analysis of environmental DNA (eDNA) metabarcoding data provides a quick, affordable, and reliable molecular approach for biodiversity assessments. However, while extensively employed in aquatic and terrestrial surface environments, eDNA-based studies targeting subterranean ecosystems are still uncommon due to the lack of accessibility and the cryptic nature of these environments and their species. Recent advances in genetic and genomic analyses have established a promising framework for shedding new light on subterranean biodiversity and ecology. To address current knowledge and the future use of eDNA methods in groundwaters and caves, this review explores conceptual and technical aspects of the application and its potential in subterranean systems. We briefly introduce subterranean biota and describe the most used traditional sampling techniques. Next, eDNA characteristics, application, and limitations in the subsurface environment are outlined. Last, we provide suggestions on how to overcome caveats and delineate some of the research avenues that will likely shape this field in the near future. We advocate that eDNA analyses, when carefully conducted and ideally combined with conventional sampling techniques, will substantially increase understanding and enable crucial expansion of subterranean community characterisation. Given the importance of groundwater and cave ecosystems for nature and humans, eDNA can bring to the surface essential insights, such as study of ecosystem assemblages and rare species detection, which are critical for the preservation of life below, as well as above, the ground.
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Affiliation(s)
- Mattia Saccò
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia.
| | - Michelle T Guzik
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide 5005, SA, Australia
| | - Mieke van der Heyde
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Steven J B Cooper
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide 5005, SA, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide 5000, SA, Australia
| | - Andrew D Austin
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide 5005, SA, Australia
| | - Peterson J Coates
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, 1 Challenger Drive, 1006, Dartmouth, Nova Scotia B2Y 4A2, Canada
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Nicole E White
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
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Verkuil YI, Nicolaus M, Ubels R, Dietz MW, Samplonius JM, Galema A, Kiekebos K, de Knijff P, Both C. DNA metabarcoding quantifies the relative biomass of arthropod taxa in songbird diets: Validation with camera‐recorded diets. Ecol Evol 2022; 12:e8881. [PMID: 35571761 PMCID: PMC9077022 DOI: 10.1002/ece3.8881] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/06/2022] [Accepted: 04/15/2022] [Indexed: 11/24/2022] Open
Abstract
Ecological research is often hampered by the inability to quantify animal diets. Diet composition can be tracked through DNA metabarcoding of fecal samples, but whether (complex) diets can be quantitatively determined with metabarcoding is still debated and needs validation using free‐living animals. This study validates that DNA metabarcoding of feces can retrieve actual ingested taxa, and most importantly, that read numbers retrieved from sequencing can also be used to quantify the relative biomass of dietary taxa. Validation was done with the hole‐nesting insectivorous Pied Flycatcher whose diet was quantified using camera footage. Size‐adjusted counts of food items delivered to nestlings were used as a proxy for provided biomass of prey orders and families, and subsequently, nestling feces were assessed through DNA metabarcoding. To explore potential effects of digestion, gizzard and lower intestine samples of freshly collected birds were subjected to DNA metabarcoding. For metabarcoding with Cytochrome Oxidase subunit I (COI), we modified published invertebrate COI primers LCO1490 and HCO1777, which reduced host reads to 0.03%, and amplified Arachnida DNA without significant changing the recovery of other arthropod taxa. DNA metabarcoding retrieved all commonly camera‐recorded taxa. Overall, and in each replicate year (N = 3), the relative scaled biomass of prey taxa and COI read numbers correlated at R = .85 (95CI:0.68–0.94) at order level and at R = .75 (CI:0.67–0.82) at family level. Similarity in arthropod community composition between gizzard and intestines suggested limited digestive bias. This DNA metabarcoding validation demonstrates that quantitative analyses of arthropod diet is possible. We discuss the ecological applications for insectivorous birds.
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Affiliation(s)
- Yvonne I. Verkuil
- Conservation Ecology Group Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
| | - Marion Nicolaus
- Conservation Ecology Group Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
| | - Richard Ubels
- Conservation Ecology Group Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
| | - Maurine W. Dietz
- Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
| | - Jelmer M. Samplonius
- Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
| | - Annabet Galema
- Conservation Ecology Group Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
| | - Kim Kiekebos
- Conservation Ecology Group Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
| | - Peter de Knijff
- Department of Human Genetics Leiden University Medical Centre Leiden The Netherlands
| | - Christiaan Both
- Conservation Ecology Group Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
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Ashfaq M, Khan AM, Rasool A, Akhtar S, Nazir N, Ahmed N, Manzoor F, Sones J, Perez K, Sarwar G, Khan AA, Akhter M, Saeed S, Sultana R, Tahir HM, Rafi MA, Iftikhar R, Naseem MT, Masood M, Tufail M, Kumar S, Afzal S, McKeown J, Samejo AA, Khaliq I, D’Souza ML, Mansoor S, Hebert PDN. A DNA barcode survey of insect biodiversity in Pakistan. PeerJ 2022; 10:e13267. [PMID: 35497186 PMCID: PMC9048642 DOI: 10.7717/peerj.13267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/23/2022] [Indexed: 01/15/2023] Open
Abstract
Although Pakistan has rich biodiversity, many groups are poorly known, particularly insects. To address this gap, we employed DNA barcoding to survey its insect diversity. Specimens obtained through diverse collecting methods at 1,858 sites across Pakistan from 2010-2019 were examined for sequence variation in the 658 bp barcode region of the cytochrome c oxidase 1 (COI) gene. Sequences from nearly 49,000 specimens were assigned to 6,590 Barcode Index Numbers (BINs), a proxy for species, and most (88%) also possessed a representative image on the Barcode of Life Data System (BOLD). By coupling morphological inspections with barcode matches on BOLD, every BIN was assigned to an order (19) and most (99.8%) were placed to a family (362). However, just 40% of the BINs were assigned to a genus (1,375) and 21% to a species (1,364). Five orders (Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera) accounted for 92% of the specimens and BINs. More than half of the BINs (59%) are so far only known from Pakistan, but others have also been reported from Bangladesh (13%), India (12%), and China (8%). Representing the first DNA barcode survey of the insect fauna in any South Asian country, this study provides the foundation for a complete inventory of the insect fauna in Pakistan while also contributing to the global DNA barcode reference library.
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Affiliation(s)
- Muhammad Ashfaq
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, Canada
| | - Arif M. Khan
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | - Akhtar Rasool
- Centre for Animal Sciences and Fisheries, University of Swat, Mingora, Pakistan
| | - Saleem Akhtar
- Directorate of Entomology, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Naila Nazir
- Department of Entomology, University of Poonch, Rawalakot, Azad Kashmir, Pakistan
| | - Nazeer Ahmed
- Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan
| | - Farkhanda Manzoor
- Department of Zoology, Lahore College for Women University, Lahore, Pakistan
| | - Jayme Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
| | - Kate Perez
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
| | - Ghulam Sarwar
- Institute of Zoology, University of the Punjab, Lahore, Pakistan
| | - Azhar A. Khan
- College of Agriculture, Bahauddin Zakariya University Bahadur Campus, Layyah, Pakistan
| | - Muhammad Akhter
- Pulses Research Institute, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Shafqat Saeed
- Faculty of Agriculture and Environmental Sciences, MNS University of Agriculture, Multan, Pakistan
| | - Riffat Sultana
- Department of Zoology, University of Sindh, Jamshoro, Pakistan
| | | | - Muhammad A. Rafi
- National Insect Museum, National Agricultural Research Center, Islamabad, Pakistan
| | - Romana Iftikhar
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | | | - Mariyam Masood
- Government College Women University Faisalabad, Faisalabad, Pakistan
| | | | - Santosh Kumar
- Department of Zoology, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Sabila Afzal
- Department of Zoology, University of Narowal, Narowal, Pakistan
| | - Jaclyn McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
| | | | | | | | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, Canada
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49
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Yu Y, Wang Q, Zhou P, Lv N, Li W, Zhao F, Zhu S, Liu D. First Glimpse of Gut Microbiota of Quarantine Insects in China. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:394-404. [PMID: 35623445 PMCID: PMC9684152 DOI: 10.1016/j.gpb.2022.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 04/11/2022] [Accepted: 04/19/2022] [Indexed: 01/05/2023]
Abstract
Quarantine insects are economically important pests that frequently invade new habitats. A rapid and accurate monitoring method to trace the geographical sources of invaders is required for their prevention, detection, and eradication. Current methods based on genetics are typically time-consuming. Here, we developed a novel tracing method based on insect gut microbiota. The source location of the insect gut microbiota can be used to rapidly determine the geographical origin of the insect. We analyzed 179 gut microbiota samples from 591 individuals of 22 quarantine insect species collected from 36 regions in China. The gut microbiota of these insects primarily included Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, Proteobacteria, and Tenericutes. The diversity of the insect gut microbiota was closely associated with geographical and environmental factors. Different insect species could be distinguished based on the composition of gut microbiota at the phylum level. Populations of individual insect species from different regions could be distinguished based on the composition of gut microbiota at the phylum, class, and order levels. A method for determining the geographical origins of invasive insect species has been established; however, its practical application requires further investigations before implementation.
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Affiliation(s)
- Yanxue Yu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Qi Wang
- Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, China,Computational Virology Group, Center for Bacteria and Virus Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Zhou
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Na Lv
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Li
- Computational Virology Group, Center for Bacteria and Virus Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangqing Zhao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 102206, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuifang Zhu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China,Corresponding authors.
| | - Di Liu
- Computational Virology Group, Center for Bacteria and Virus Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China,Corresponding authors.
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50
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Challenges in eDNA detection of the invasive European green crab, Carcinus maenas. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02757-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
AbstractThe early detection of invasive species is essential to cease the spread of the species before it can cause irreversible damage to the environment. The analysis of environmental DNA (eDNA) has emerged as a non-harmful method to detect the presence of a species before visual detection and is a promising approach to monitor invasive species. Few studies have investigated the use of eDNA for arthropods, as their exoskeleton is expected to limit the release of eDNA into the environment. We tested published primers for the invasive European green crab, Carcinus maenas, in the Gulf of Maine and found them not species-specific enough for reliable use outside of the area for which they were designed for. We then designed new primers, tested them against a broad range of local faunal species, and validated these primers in a field study. We demonstrate that eDNA analyses can be used for crustaceans with an exoskeleton and suggest that primers and probe sequences must be tested on local fauna at each location of use to ensure no positive amplification of these other species.
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