1
|
Del Olmo I, Roma-Cavagliani J, Martín-Hervás MDR, Langeneck J, Cervera JL, Álvarez-Campos P. Integrative taxonomy in Syllis prolifera (Annelida, Syllidae): from a unique cosmopolitan species to a complex of pseudocryptic species. INVERTEBR SYST 2024; 38:IS24004. [PMID: 38909605 DOI: 10.1071/is24004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 05/21/2024] [Indexed: 06/25/2024]
Abstract
Syllis prolifera (Syllidae, Syllinae) is an abundant species of marine annelids commonly found in warm to temperate waters worldwide. Although morphological variability occurs among populations, S. prolifera has long been considered a cosmopolitan species, widely distributed in coastal environments, including acidified and polluted areas. However, the increasing number of cases of cryptic and pseudocryptic speciation in several polychaete families in recent years has led us to question whether S. prolifera represents a single globally distributed taxon or is a species complex. To address this question, we conducted an integrative study, combining morphological, ecological and molecular data of 52 S. prolifera specimens collected in different localities across the western Mediterranean Sea and the Gulf of Cadiz. Our phylogenetic and species delimitation analyses that included two mitochondrial DNA markers (COI and 16S rRNA ) were congruent in not considering S. prolifera a unique entity. Five distinct lineages that can also be recognised by certain morphological and ecological traits were identified from these analyses instead. Overall, our study does not support the homogeneity of S. prolifera across the Mediterranean Sea, providing a new example of pseudocrypticism in marine invertebrates.
Collapse
Affiliation(s)
- Irene Del Olmo
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid, Spain
| | - Josep Roma-Cavagliani
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Campus de Excelencia Internacional del Mar (CEI•MAR), Universidad de Cádiz, Avenida República Saharaui, s/n, E-11510 Puerto Real, Spain
| | - María Del Rosario Martín-Hervás
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid, Spain; and Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Campus de Excelencia Internacional del Mar (CEI•MAR), Universidad de Cádiz, Avenida República Saharaui, s/n, E-11510 Puerto Real, Spain
| | - Joachim Langeneck
- Consorzio Interuniversitario per le Scienze del Mare (CoNISMa), Unità Locale di Ricerca (ULR) di Lecce, c/o Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA), Palazzina A, Campus Ecotekne, strada provinciale Lecce-Monteroni, I-73100 Lecce, Italy
| | - Juan Lucas Cervera
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Campus de Excelencia Internacional del Mar (CEI•MAR), Universidad de Cádiz, Avenida República Saharaui, s/n, E-11510 Puerto Real, Spain; and Instituto Universitario de Investigación Marina (INMAR), CEI•MAR, Universidad de Cádiz, Avenida República Saharaui, s/n, E-11510 Puerto Real, Spain
| | - Patricia Álvarez-Campos
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid, Spain
| |
Collapse
|
2
|
Teixeira MAL, Fourreau CJL, Sempere-Valverde J, Carvalho S. Two new records and description of a new Perinereis (Annelida, Nereididae) species for the Saudi Arabian Red Sea region. Zookeys 2024; 1196:331-354. [PMID: 38726099 PMCID: PMC11079592 DOI: 10.3897/zookeys.1196.115260] [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: 11/05/2023] [Accepted: 01/26/2024] [Indexed: 05/12/2024] Open
Abstract
Annelid biodiversity studies in the Red Sea are limited and integrative taxonomy is needed to accurately improve reference libraries in the region. As part of the bioblitz effort in Saudi Arabia to assess the invertebrate biodiversity in the northern Red Sea and Gulf of Aqaba, Perinereis specimens from intertidal marine and lagoon-like rocky environments were selected for an independent assessment, given the known taxonomic ambiguities in this genus. This study used an integrative approach, combining molecular with morphological and geographic data. Our results demonstrate that specimens found mainly in the Gulf of Aqaba are not only morphologically different from other five similar Perinereis Group I species reported in the region, but phylogenetic analysis using available COI sequences from GenBank revealed different molecular operational taxonomic units, suggesting an undescribed species, P.kaustianasp. nov. The new species is genetically close and shares a similar paragnath pattern to the Indo-Pacific distributed P.helleri, in particular in Area III and Areas VII-VIII. Therefore, we suggest it may belong to the same species complex. However, P.kaustianasp. nov. differs from the latter mainly in the shorter length of the postero-dorsal tentacular cirri, median parapodia with much longer dorsal Tentacular cirri, posteriormost parapodia with much wider and greatly expanded dorsal ligules. Additionally, two new records are reported for the Saudi Neom area belonging to P.damietta and P.suezensis, previously described only for the Egyptian coast (Suez Canal) and are distributed sympatrically with the new species, but apparently not sympatric with each other.
Collapse
Affiliation(s)
- Marcos A. L. Teixeira
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Chloé Julie Loïs Fourreau
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Juan Sempere-Valverde
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Laboratorio de Biología Marina/Estación de Biología Marina del Estrecho (Ceuta), Departamento de Zoología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes s/n, 41012, Sevilla, Spain
| | - Susana Carvalho
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| |
Collapse
|
3
|
Lvarez R, Budaeva N. How complex is the Naineris setosa species complex? First integrative study of a presumed cosmopolitan and invasive annelid (Sedentaria: Orbiniidae). Zootaxa 2023; 5375:349-378. [PMID: 38220815 DOI: 10.11646/zootaxa.5375.3.3] [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: 11/22/2023] [Indexed: 01/16/2024]
Abstract
We performed a comparative study of the specimens from the Naineris setosa complex from the Pacific and the Atlantic Oceans and re-described the syntype of N. setosa, including the selection of the lectotype. Molecular phylogenetic and species delimitation analyses based on two mitochondrial (COI and 16S) and one nuclear (28S) marker revealed the presence of three species. One clade with wide Amphi-Atlantic distribution was attributed as Naineris setosa s. str. The second Atlantic clade restricted to Southern and Southeastern Brazil was described as a new species, Naineris lanai sp. n. The third clade, reported from the Northwestern Pacific, was identified as a new species but was not formally described due to the presence of only juvenile-sized worms in the studied material. Detailed morphological descriptions of several diagnostic characters in the Naineris setosa complex are provided.
Collapse
Affiliation(s)
- Ricardo Lvarez
- Graduate program in Oceanic Coastal Systems (PGSISCO); Federal University of Paran; Pontal do Paran; Paran; Brazil.
| | - Nataliya Budaeva
- Department of Natural History; University Museum of Bergen; University of Bergen; Allgaten 41; 5007 Bergen; Norway.
| |
Collapse
|
4
|
Population Genetic Structure of Marine Leech, Pterobdella arugamensis in Indo-West Pacific Region. Genes (Basel) 2022; 13:genes13060956. [PMID: 35741718 PMCID: PMC9222843 DOI: 10.3390/genes13060956] [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: 04/28/2022] [Revised: 05/18/2022] [Accepted: 05/24/2022] [Indexed: 02/01/2023] Open
Abstract
Grouper aquaculture is rapidly expanding in both tropical and subtropical regions. The presence of marine leeches (Pterobdella arugamensis; previously named Zeylanicobdella arugamensis) infesting cultured groupers, however, can have a fatal effect on grouper aquaculture production and cause significant economic loss. Understanding the marine leech’s population structure is therefore important to determine its possible distributional origin and distributional mechanisms, which will help monitor and mitigate the infestation. In this study, a total of 84 marine leeches collected from cultured hybrid groupers Epinephelus spp. in Brunei Darussalam, Malaysia and Indonesia were identified as P. arugamensis, based on morphological and mitochondrial cytochrome c oxidase subunit I gene sequence analyses. These leech samples, together with additional sequences from the GenBank database, were grouped into four genetically distinct haplogroups: (1) Asia Pacific, (2) Borneo, (3) Surabaya and (4) Iran. The four populations were found to be highly diverged from each other. The results also suggested that the samples from the Asia Pacific population could be dispersed and transported from Indonesia.
Collapse
|
5
|
Phillips JD, Gillis DJ, Hanner RH. Lack of Statistical Rigor in DNA Barcoding Likely Invalidates the Presence of a True Species' Barcode Gap. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.859099] [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
DNA barcoding has been largely successful in satisfactorily exposing levels of standing genetic diversity for a wide range of taxonomic groups through the employment of only one or a few universal gene markers. However, sufficient coverage of geographically-broad intra-specific haplotype variation within genomic databases like the Barcode of Life Data Systems (BOLD) and GenBank remains relatively sparse. As reference sequence libraries continue to grow exponentially in size, there is now the need to identify novel ways of meaningfully analyzing vast amounts of available DNA barcode data. This is an important issue to address promptly for the routine tasks of specimen identification and species discovery, which have seen broad adoption in areas as diverse as regulatory forensics and resource conservation. Here, it is demonstrated that the interpretation of DNA barcoding data is lacking in statistical rigor. To highlight this, focus is set specifically on one key concept that has become a household name in the field: the DNA barcode gap. Arguments outlined herein specifically center on DNA barcoding in animal taxa and stem from three angles: (1) the improper allocation of specimen sampling effort necessary to capture adequate levels of within-species genetic variation, (2) failing to properly visualize intra-specific and interspecific genetic distances, and (3) the inconsistent, inappropriate use, or absence of statistical inferential procedures in DNA barcoding gap analyses. Furthermore, simple statistical solutions are outlined which can greatly propel the use of DNA barcoding as a tool to irrefutably match unknowns to knowns on the basis of the barcoding gap with a high degree of confidence. Proposed methods examined herein are illustrated through application to DNA barcode sequence data from Canadian Pacific fish species as a case study.
Collapse
|
6
|
Aguado MT, Ponz-Segrelles G, Glasby CJ, Ribeiro RP, Nakamura M, Oguchi K, Omori A, Kohtsuka H, Fisher C, Ise Y, Jimi N, Miura T. Ramisyllis kingghidorahi n. sp., a new branching annelid from Japan. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-021-00538-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractAmong over 20,000 species of Annelida, only two branching species with a highly modified body-pattern are known until now: the Syllidae Syllis ramosa McIntosh, 1879, and Ramisyllis multicaudata Glasby et al. (Zoological Journal of the Linnean Society, 164, 481–497, 2012). Both have unusual ramified bodies with one head and multiple branches and live inside the canals of host sponges. Using an integrative approach (combining morphology, internal anatomy, ecology, phylogeny, genetic divergence, and the complete mitochondrial genome), we describe a new branching species from Japan, Ramisyllis kingghidorahi n. sp., inhabiting an undescribed species of Petrosia (Porifera: Demospongiae) from shallow waters. We compare the new species with its closest relative, R. multicaudata; emend the diagnosis of Ramisyllis; and discuss previous reports of S. ramosa. This study suggests a much higher diversity of branching syllids than currently known. Finally, we discuss possible explanations for the feeding behaviour in the new species in relation to its highly ciliated wall of the digestive tubes (especially at the distal branches and anus), and provide a hypothesis for the evolution of branching body patterns as the result of an adaptation to the host sponge labyrinthic canal system.
Collapse
|
7
|
Gonçalves LT, Bianchi FM, Deprá M, Calegaro-Marques C. Barcoding a can of worms: testing cox1 performance as a DNA barcode of Nematoda. Genome 2021; 64:705-717. [PMID: 33460338 DOI: 10.1139/gen-2020-0140] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Accurate taxonomic identifications and species delimitations are a fundamental problem in biology. The complex taxonomy of Nematoda is primarily based on morphology, which is often dubious. DNA barcoding emerged as a handy tool to identify specimens and assess diversity, but its applications in Nematoda are incipient. We evaluated cytochrome c oxidase subunit I (cox1) efficiency as a DNA barcode for nematodes scrutinising 5241 sequences retrieved from BOLD and GenBank. The samples included genera with medical, agricultural, or ecological relevance: Anguillicola, Caenorhabditis, Heterodera, Meloidogyne, Onchocerca, Strongyloides, and Trichinella. We assessed cox1 performance through barcode gap and Probability of Correct Identification (PCI) analyses, and estimated species richness through Automatic Barcode Gap Discovery (ABGD). Each genus presented distinct gap ranges, mirroring the evolutionary diversity within Nematoda. Thus, to survey the diversity of the phylum, a careful definition of thresholds for lower taxonomic levels should be considered. PCIs were around 70% for both databases, highlighting operational biases and challenges in nematode taxonomy. ABGD inferred higher richness than the taxonomic labels informed by databases. The prevalence of specimen misidentifications and dubious species delimitations emphasise the value of integrative approaches to nematode taxonomy and systematics. Overall, cox1 is a relevant tool for integrative taxonomy of nematodes.
Collapse
Affiliation(s)
- Leonardo Tresoldi Gonçalves
- Laboratório de Helmintologia, Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Filipe Michels Bianchi
- Laboratório de Entomologia Sistemática, Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Maríndia Deprá
- Laboratório de Drosophila, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Cláudia Calegaro-Marques
- Laboratório de Helmintologia, Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| |
Collapse
|
8
|
Zenker MM, Specht A, Fonseca VG. Assessing insect biodiversity with automatic light traps in Brazil: Pearls and pitfalls of metabarcoding samples in preservative ethanol. Ecol Evol 2020; 10:2352-2366. [PMID: 32184986 PMCID: PMC7069332 DOI: 10.1002/ece3.6042] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/23/2019] [Accepted: 12/27/2019] [Indexed: 12/24/2022] Open
Abstract
Automated species identification based on data produced with metabarcoding offers an alternative for assessing biodiversity of bulk insect samples obtained with traps. We used a standard two-step PCR approach to amplify a 313 bp fragment of the barcoding region of the mitochondrial COI gene. The PCR products were sequenced on an Illumina MiSeq platform, and the OTUs production and taxonomic identifications were performed with a customized pipeline and database. The DNA used in the PCR procedures was extracted directly from the preservative ethanol of bulk insect samples obtained with automatic light traps in 12 sampling areas located in different biomes of Brazil, during wet and dry seasons. Agricultural field and forest edge habitats were collected for all sampling areas. A total of 119 insect OTUs and nine additional OTUs assigned to other arthropod taxa were obtained at a ≥97% sequence similarity level. The alpha and beta diversity analyses comparing biomes, habitats, and seasons were mostly inconclusive, except for a significant difference in beta diversity between biomes. In this study, we were able to metabarcode and HTS adult insects from their preservative medium. Notwithstanding, our results underrepresent the true magnitude of insect diversity expected from samples obtained with automatic light traps in Brazil. Although biological and technical factors might have impacted our results, measures to optimize and standardize eDNA HTS should be in place to improve taxonomic coverage of samples of unknown diversity and stored in suboptimal conditions, which is the case of most eDNA samples.
Collapse
Affiliation(s)
- Mauricio M. Zenker
- Zoological Research Museum Alexander KoenigBonnGermany
- Present address:
Rua Eulo MaroniSão PauloBrazil
| | - Alexandre Specht
- Embrapa CerradosBrasiliaBrazil
- Present address:
Embrapa CerradosPlanaltinaFederal DistrictBrazil
| | - Vera G. Fonseca
- Zoological Research Museum Alexander KoenigBonnGermany
- Present address:
Centre for EnvironmentFisheries and Aquaculture Science (Cefas)WeymouthUK
| |
Collapse
|
9
|
Mack J, de Carle D, Kvist S. Prey, populations, and the pleistocene: evidence for low COI variation in a widespread North American leech. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:749-763. [DOI: 10.1080/24701394.2019.1634698] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Joseph Mack
- Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Danielle de Carle
- Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Sebastian Kvist
- Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
10
|
Guggolz T, Meißner K, Schwentner M, Brandt A. Diversity and distribution of Laonice species (Annelida: Spionidae) in the tropical North Atlantic and Puerto Rico Trench. Sci Rep 2019; 9:9260. [PMID: 31239511 PMCID: PMC6592887 DOI: 10.1038/s41598-019-45807-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 06/14/2019] [Indexed: 11/09/2022] Open
Abstract
Laonice Malmgren, 1867 (Annelida: Spionidae) is a common polychaete genus in the deep-sea. Although most species are quite well studied morphologically, fragmentation and other damage that occurs during sampling often hampers morphological species identification of deep-sea specimens. In this study, we employ three molecular markers (16S, COI and 18S) to study the biodiversity and the distribution patterns of Laonice from the tropical North Atlantic and the Puerto Rico Trench. Based upon different molecular analyses (Automated Barcode Gap Discovery, pairwise genetic distances, phylogenetics, haplotype networks) we were able to identify and differentiate eight Laonice species. Up to four of these species co-occurred sympatrically at the same station. The majority of species were found at multiple stations and two species in the eastern as well as western Atlantic had ranges of up to 4,000 km. Genetic differentiation across these extensive geographic distances was very low. Surprisingly, one 16S haplotype was shared between individuals 2,776 km apart and individuals from the Caribbean and the abyssal plain in the eastern Atlantic (>3,389 km) differed in only a single mutation in 16S. Our results suggest that members of this genus successfully disperse across large geographic distances and are largely unaffected by topographic barriers.
Collapse
Affiliation(s)
- Theresa Guggolz
- Zoological Museum Hamburg, Center of Natural History, Universität Hamburg, Martin-Luther-King-Platz 3, D-20146, Hamburg, Germany.
| | - Karin Meißner
- German Centre for Marine Biodiversity Research, Senckenberg am Meer, c/o Universität Hamburg, Martin-Luther-King-Platz 3, D-20146, Hamburg, Germany
| | - Martin Schwentner
- Zoological Museum Hamburg, Center of Natural History, Universität Hamburg, Martin-Luther-King-Platz 3, D-20146, Hamburg, Germany
| | - Angelika Brandt
- Senckenberg Naturmuseum, Senckenberganlage 25, 60325, Frankfurt, Germany
| |
Collapse
|
11
|
Mack J, Kvist S. Improved geographic sampling provides further evidence for the separation ofGlossiphonia complanataandGlossiphonia elegans(Annelida: Clitellata: Glossiphoniidae). J NAT HIST 2019. [DOI: 10.1080/00222933.2019.1590658] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Joseph Mack
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Sebastian Kvist
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
12
|
Jiao J, Huang W, Bai Z, Liu F, Ma C, Liang Z. DNA barcoding for the efficient and accurate identification of medicinal polygonati rhizoma in China. PLoS One 2018; 13:e0201015. [PMID: 30021015 PMCID: PMC6051646 DOI: 10.1371/journal.pone.0201015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 07/06/2018] [Indexed: 12/23/2022] Open
Abstract
Polygonati rhizoma (PR), a traditional medicinal and edible product with various bioactive components (Polygonatum polysaccharides, saponins, phenols, and flavonoids), is widely consumed in China. However, other species with morphological characteristics similar to those of the actual components are being used to replace or adulterate PR, causing issues with quality control and product safety. The morphological similarity of PR and its substitutes makes classic morphological identification challenging. To address this issue, DNA barcoding-based identification using ITS2 and psbA-trnH sequences was applied in this study to evaluate the efficiency and accuracy of this approach in identifying PR samples collected from 39 different regions in China. The identification of PR by this method was confirmed by other methods (phylogeny-based and character-based methods), and all the samples were clearly and accurately distinguished. This study highlights the efficient and accurate nature of DNA barcoding in PR identification. Applying this technique will provide a means to differentiate PR from other altered formulations, thus improving product quality and safety for consumers of PR and its products.
Collapse
Affiliation(s)
- Jie Jiao
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
| | - Wenli Huang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Zhenqing Bai
- College of Life Science, Yan'an University, Yan'an, Shaanxi, China
| | - Feng Liu
- Research Department, Buchang Pharma, Xi’an, Shaanxi, China
| | - Cunde Ma
- Research Department, Buchang Pharma, Xi’an, Shaanxi, China
| | - Zongsuo Liang
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
- College of Life Science, Zhejiang SCI-TECH University, Hangzhou, Zhejiang, China
- * E-mail:
| |
Collapse
|
13
|
Kara J, Macdonald AHH, Simon CA. Integrative taxonomic methods reveal an incorrect synonymisation of the South African Pseudonereis podocirra (Schmarda) as the widespread Pseudonereis variegata (Grube) from Chile. INVERTEBR SYST 2018. [DOI: 10.1071/is18016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The nereidid Pseudonereis variegata (Grube, 1866) described from Chile includes 14 synonymised species from 10 type localities with a discontinuous distribution, but no taxonomic or molecular studies have investigated the status of this species outside Chile. Two synonymised species, Mastigonereis podocirra Schmarda, 1861 and Nereis (Nereilepas) stimpsonis Grube, 1866, were described from South Africa and investigated here using morphological examination. MtCOI species delimitation analyses and morphology were used to determine the status of P. variegata in South Africa. Morphological examination revealed that museum and freshly collected specimens from South Africa that conform to the general description of P. variegata are similar to M. podocirra and N. stimpsonis with respect to the consistent absence of homogomph spinigers in the inferior neuropodial fascicle, expanded notopodial ligules and the subterminal attachment of dorsal cirri in posterior parapodia. The synonymy of M. podocirra and N. stimpsonis as P. variegata are rejected and P. podocirra, comb. nov. is reinstated. Morphologically, Pseudonereis podocirra differed from specimens from Chile with regard to the numbers of paragnaths, the absence of homogomph spinigers and changes in parapodial morphology along the body. Independence of these species was further supported by genetic distances, automatic barcode gap discovery and multi-rate Poisson tree process species delimitation analyses of 77 mtCOI sequences. Haplotype network revealed no genetic structuring within the South African populations. http://zoobank.org/urn:lsid:zoobank.org:pub:F0B1A5AF-9CE9-4A43-ACCF-17117E1C2F21
Collapse
|
14
|
Koroiva R, Pepinelli M, Rodrigues ME, Roque FDO, Lorenz-Lemke AP, Kvist S. DNA barcoding of odonates from the Upper Plata basin: Database creation and genetic diversity estimation. PLoS One 2017; 12:e0182283. [PMID: 28763495 PMCID: PMC5538745 DOI: 10.1371/journal.pone.0182283] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/14/2017] [Indexed: 11/18/2022] Open
Abstract
We present a DNA barcoding study of Neotropical odonates from the Upper Plata basin, Brazil. A total of 38 species were collected in a transition region of "Cerrado" and Atlantic Forest, both regarded as biological hotspots, and 130 cytochrome c oxidase subunit I (COI) barcodes were generated for the collected specimens. The distinct gap between intraspecific (0-2%) and interspecific variation (15% and above) in COI, and resulting separation of Barcode Index Numbers (BIN), allowed for successful identification of specimens in 94% of cases. The 6% fail rate was due to a shared BIN between two separate nominal species. DNA barcoding, based on COI, thus seems to be a reliable and efficient tool for identifying Neotropical odonate specimens down to the species level. These results underscore the utility of DNA barcoding to aid specimen identification in diverse biological hotspots, areas that require urgent action regarding taxonomic surveys and biodiversity conservation.
Collapse
Affiliation(s)
- Ricardo Koroiva
- Ecology and Conservation Graduate Program, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
- Laboratório de Ecologia, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Mateus Pepinelli
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Marciel Elio Rodrigues
- Laboratório de Organismos Aquáticos, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - Fabio de Oliveira Roque
- Laboratório de Ecologia, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Aline Pedroso Lorenz-Lemke
- Laboratório de Evolução e Biodiversidade, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Sebastian Kvist
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
15
|
Brasier MJ, Wiklund H, Neal L, Jeffreys R, Linse K, Ruhl H, Glover AG. DNA barcoding uncovers cryptic diversity in 50% of deep-sea Antarctic polychaetes. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160432. [PMID: 28018624 PMCID: PMC5180122 DOI: 10.1098/rsos.160432] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 09/30/2016] [Indexed: 05/20/2023]
Abstract
The Antarctic marine environment is a diverse ecosystem currently experiencing some of the fastest rates of climatic change. The documentation and management of these changes requires accurate estimates of species diversity. Recently, there has been an increased recognition of the abundance and importance of cryptic species, i.e. those that are morphologically identical but genetically distinct. This article presents the largest genetic investigation into the prevalence of cryptic polychaete species within the deep Antarctic benthos to date. We uncover cryptic diversity in 50% of the 15 morphospecies targeted through the comparison of mitochondrial DNA sequences, as well as 10 previously overlooked morphospecies, increasing the total species richness in the sample by 233%. Our ability to describe universal rules for the detection of cryptic species within polychaetes, or normalization to expected number of species based on genetic data is prevented by taxon-specific differences in phylogenetic outputs and genetic variation between and within potential cryptic species. These data provide the foundation for biogeographic and functional analysis that will provide insight into the drivers of species diversity and its role in ecosystem function.
Collapse
Affiliation(s)
- Madeleine J. Brasier
- School of Environmental Science, University of Liverpool, L69 3BX, Liverpool, UK
| | - Helena Wiklund
- Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Lenka Neal
- Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Rachel Jeffreys
- School of Environmental Science, University of Liverpool, L69 3BX, Liverpool, UK
| | - Katrin Linse
- BioSciences, British Antarctic Survey, Cambridge CB3 OET, UK
| | - Henry Ruhl
- National Oceanography Centre, University of Southampton, Waterfront Campus, Southampton SO14 3ZH, UK
| | - Adrian G. Glover
- Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| |
Collapse
|
16
|
Sundberg P, Kvist S, Strand M. Evaluating the Utility of Single-Locus DNA Barcoding for the Identification of Ribbon Worms (Phylum Nemertea). PLoS One 2016; 11:e0155541. [PMID: 27171471 PMCID: PMC4865114 DOI: 10.1371/journal.pone.0155541] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 04/29/2016] [Indexed: 11/22/2022] Open
Abstract
Whereas many nemerteans (ribbon worms; phylum Nemertea) can be identified from external characters if observed alive, many are still problematic. When it comes to preserved specimens (as in e.g. marine inventories), there is a particular need for specimen identifier alternatives. Here, we evaluate the utility of COI (cytochrome c oxidase subunit I) as a single-locus barcoding gene. We sequenced, data mined, and compared gene fragments of COI for 915 individuals representing 161 unique taxonomic labels for 71 genera, and subjected different constellations of these to both distance-based and character-based DNA barcoding approaches, as well as species delimitation analyses. We searched for the presence or absence of a barcoding gap at different taxonomic levels (phylum, subclass, family and genus) in an attempt to understand at what level a putative barcoding gap presents itself. This was performed both using the taxonomic labels as species predictors and using objectively inferred species boundaries recovered from our species delimitation analyses. Our data suggest that COI works as a species identifier for most groups within the phylum, but also that COI data are obscured by misidentifications in sequence databases. Further, our results suggest that the number of predicted species within the dataset is (in some cases substantially) higher than the number of unique taxonomic labels-this highlights the presence of several cryptic lineages within well-established taxa and underscores the urgency of an updated taxonomic backbone for the phylum.
Collapse
Affiliation(s)
- Per Sundberg
- Department of Marine Science, University of Gothenburg, Box 463, SE-405 30, Gothenburg, Sweden
| | - Sebastian Kvist
- Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, ON, M5S 2C6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 2B4, Canada
| | - Malin Strand
- Swedish Species Information Center, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden
| |
Collapse
|
17
|
Riesgo A, Taboada S, Avila C. Evolutionary patterns in Antarctic marine invertebrates: an update on molecular studies. Mar Genomics 2015; 23:1-13. [PMID: 26228311 DOI: 10.1016/j.margen.2015.07.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 07/17/2015] [Accepted: 07/17/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Ana Riesgo
- Department of Animal Biology and Biodiversity Research Institute (IrBIO), Faculty of Biology, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Catalonia, Spain.
| | - Sergi Taboada
- Department of Animal Biology and Biodiversity Research Institute (IrBIO), Faculty of Biology, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Catalonia, Spain
| | - Conxita Avila
- Department of Animal Biology and Biodiversity Research Institute (IrBIO), Faculty of Biology, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Catalonia, Spain
| |
Collapse
|
18
|
Achurra A, Rodriguez P, Erséus C. Pseudo-cryptic speciation in the subterranean medium: A new species of Stylodrilus Claparède, 1862, with a revision of the status of Bichaeta Bretscher, 1900 (Annelida, Clitellata, Lumbriculidae). ZOOL ANZ 2015. [DOI: 10.1016/j.jcz.2015.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|