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Karimifard S, Saberi-Pirooz R, Ahmadzadeh F, Aghamir F. Investigating the impacts of agricultural land use on soil earthworm communities: A case study of northern Zagros Mountains of Iran. Heliyon 2024; 10:e23523. [PMID: 38173494 PMCID: PMC10761580 DOI: 10.1016/j.heliyon.2023.e23523] [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: 03/30/2023] [Revised: 12/05/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
Earthworms play a crucial role in the invertebrate community of soil by contributing to the belowground biomass and biogeochemical cycle. Environmental stresses, such as human activities and land use changes, have been found to negatively affect their abundance and diversity. To investigate the impact of agricultural land use and pastures on earthworms' genetic diversity in the Northern Zagros Mountains, we used COI molecular marker and DNA barcoding approaches. We collected earthworm specimens from four farmland sites and six pastures and assessed the abundance and species composition of earthworm communities across the two land uses using quadrat sampling. Using the barcoding method, we identified 13 molecular operational taxonomic units (MOTUs) among the captured earthworms. Our results showed that the number of total MOTUs, density, and earthworm communities differed significantly between the two land uses. We also found that pastures had more abundant earthworms, while farmlands had greater diversity. The diversity of OTUs in the Lumbricidae family was dominant in the agricultural system. Overall, the population of invasive earthworm species in cultivation systems is influenced by chemical inputs and organic materials from plant residues, cover crops, manure, or organic fertilizers. Given the rapid rate of land use change worldwide, especially in Iran, it is crucial to understand the impact of disturbances on earthworms.
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Affiliation(s)
- Shadi Karimifard
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, 1983963113, Iran
| | - Reihaneh Saberi-Pirooz
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, 1983963113, Iran
| | - Faraham Ahmadzadeh
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, 1983963113, Iran
| | - Fatemeh Aghamir
- Department of Agroecology, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, 1983963113, Iran
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Cryptic Clitellata: Molecular Species Delimitation of Clitellate Worms (Annelida): An Overview. DIVERSITY-BASEL 2021. [DOI: 10.3390/d13020036] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Methods for species delimitation using molecular data have developed greatly and have become a staple in systematic studies of clitellate worms. Here we give a historical overview of the data and methods used to delimit clitellates from the mid-1970s to today. We also discuss the taxonomical treatment of the cryptic species, including the recommendation that cryptic species, as far as possible, should be described and named. Finally, we discuss the prospects and further development of the field.
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Involvement of sphaeractinomyxon in the life cycle of mugiliform-infecting Myxobolus (Cnidaria, Myxosporea) reveals high functionality of actinospore morphotype in promoting transmission. Parasitology 2020; 147:1320-1329. [PMID: 32594944 DOI: 10.1017/s0031182020001043] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Four new actinospore types belonging to the sphaeractinomyxon collective group (Cnidaria, Myxosporea) are described from the coelomic cavity of a marine Baltidrilus sp. (Oligochaeta, Naididae) inhabiting a northern Portuguese estuary. Host identification supports the usage of marine oligochaetes, namely of the family Naididae Ehrenberg, 1828, as definitive hosts for myxosporeans inhabiting estuarine/marine environments. The absence of mixed infections in the host specimens analysed is suggested to reflect the influence of host-, parasite- and environmental-related factors regulating myxosporean-annelid interactions. Molecular analyses matched the SSU rDNA sequences of three of the four new types with those of mugiliform-infecting Myxobolus spp., namely Myxobolus mugiliensis and a Myxobolus sp. from flathead grey mullet Mugil cephalus, and Myxobolus labrosus from thicklip grey mullet Chelon labrosus. These results directly link, for the first time, the sphaeractinomyxon collective group to a myxospore counterpart, further confirming their previously hypothesized specific involvement in the life cycle of myxobolids that infect mullets. Acknowledging this life cycle relationship, the functionality of the sphaeractinomyxon morphotype is suggested to have been decisive for the evolutionary hyperdiversification of the genus Myxobolus in mullets. Unlike other actinospore morphotypes, sphaeractinomyxon lack valvular processes, which implies a limited capability for buoyancy. Considering the benthic-feeding nature of mullets, this feature is most likely crucial in promoting successful transmission to the vertebrate host.
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High-throughput DNA barcoding of oligochaetes for abundance-based indices to assess the biological quality of sediments in streams and lakes. Sci Rep 2020; 10:2041. [PMID: 32029757 PMCID: PMC7005023 DOI: 10.1038/s41598-020-58703-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 01/20/2020] [Indexed: 12/25/2022] Open
Abstract
Aquatic oligochaete communities are valuable indicators of the biological quality of sediments in streams and lakes, but identification of specimens to the species level based on morphological features requires solid expertise in taxonomy and is possible only for a fraction of specimens present in a sample. The identification of aquatic oligochaetes using DNA barcodes would facilitate their use in biomonitoring and allow a wider use of this taxonomic group for ecological diagnoses. Previous approaches based on DNA metabarcoding of samples composed of total sediments or pools of specimens have been proposed for assessing the biological quality of ecosystems, but such methods do not provide precise information on species abundance, which limits the value of resulting ecological diagnoses. Here, we tested how a DNA barcoding approach based on high-throughput sequencing of sorted and genetically tagged specimens performed to assess oligochaete species diversity and abundance and the biological quality of sediments in streams and lakes. We applied both molecular and morphological approaches at 13 sites in Swiss streams and at 7 sites in Lake Geneva. We genetically identified 33 or 66 specimens per site. For both approaches, we used the same index calculations. We found that the ecological diagnoses derived from the genetic approach matched well with those of the morphological approach and that the genetic identification of only 33 specimens per site provided enough ecological information for correctly estimating the biological quality of sediments in streams and lakes.
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Molecular data infers the involvement of a marine aurantiactinomyxon in the life cycle of the myxosporean parasite Paramyxidium giardi (Cnidaria, Myxozoa). Parasitology 2019; 146:1555-1563. [DOI: 10.1017/s0031182019000866] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
AbstractAn aurantiactinomyxon type is described from the marine naidid Tubificoides pseudogaster (Dahl, 1960), collected from the lower estuary of a Northern Portuguese River. This type constitutes the first of its collective group to be reported from Portugal, and only the fourth described from a marine oligochaete worldwide. Extensive morphological comparisons of new aurantiactinomyxon isolates to all known types without available molecular data are proposed to be unnecessary, given the artificiality of the usage of morphological criteria for actinosporean differentiation and the apparent strict host specificity of the group. Recognition of naidid oligochaetes as the hosts of choice for marine types of aurantiactinomyxon and other collective groups, suggests that the family Naididae played a preponderant role in the myxosporean colonization of estuarine communities. Molecular analyses of the type in study further infer its involvement in the life cycle of Paramyxidium giardi (Cépède, 1906) Freeman and Kristmundsson, 2018, a species that infects the kidney of European eel Anguilla anguilla (Linnaeus, 1758) and that has been reported globally, including from Portuguese waters. The low intraspecific difference registered in relation to Icelandic isolates of P. giardi (0.6%) is hypothesized to result from the emergence of genotypically different subspecies due to geographic isolation.
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Martin P, Martinsson S, Wuillot J, Erséus C. Integrative species delimitation and phylogeny of the branchiate wormBranchiodrilus(Clitellata, Naididae). ZOOL SCR 2018. [DOI: 10.1111/zsc.12316] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Patrick Martin
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny; Brussels Belgium
| | - Svante Martinsson
- Department of Biological and Environmental Sciences; University of Gothenburg; Göteborg Sweden
| | | | - Christer Erséus
- Department of Biological and Environmental Sciences; University of Gothenburg; Göteborg Sweden
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Darling JA, Carlton JT. A Framework for Understanding Marine Cosmopolitanism in the Anthropocene. FRONTIERS IN MARINE SCIENCE 2018; 5:293. [PMID: 31019910 PMCID: PMC6475922 DOI: 10.3389/fmars.2018.00293] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Recent years have witnessed growing appreciation for the ways in which human-mediated species introductions have reshaped marine biogeography. Despite this we have yet to grapple fully with the scale and impact of anthropogenic dispersal in both creating and determining contemporary distributions of marine taxa. In particular, the past several decades of research on marine biological invasions have revealed that broad geographic distributions of coastal marine organisms-historically referred to simply as "cosmopolitanism"-may belie complex interplay of both natural and anthropogenic processes. Here we describe a framework for understanding contemporary cosmopolitanism, informed by a synthesis of the marine bioinvasion literature. Our framework defines several novel categories in an attempt to provide a unified terminology for discussing cosmopolitan distributions in the world's oceans. We reserve the term eucosmopolitan to refer to those species for which data exist to support a true, natural, and prehistorically global (or extremely broad) distribution. While in the past this has been the default assumption for species observed to exhibit contemporary cosmopolitan distributions, we argue that given recent advances in marine invasion science this assignment should require positive evidence. In contrast, neocosmopolitan describes those species that have demonstrably achieved extensive geographic ranges only through historical anthropogenic dispersal, often facilitated over centuries of human maritime traffic. We discuss the history and human geography underpinning these neocosmopolitan distributions, and illustrate the extent to which these factors may have altered natural biogeographic patterns. We define the category pseudocosmopolitan to encompass taxa for which a broad distribution is determined (typically after molecular investigation) to reflect multiple, sometimes regionally endemic, lineages with uncertain taxonomic status; such species may remain cosmopolitan only so long as taxonomic uncertainty persists, after which they may splinter into multiple geographically restricted species. We discuss the methods employed to identify such species and to resolve both their taxonomic status and their biogeographic histories. We argue that recognizing these different types of cosmopolitanism, and the important role that invasion science has played in understanding them, is critically important for the future study of both historical and modern marine biogeography, ecology, and biodiversity.
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Affiliation(s)
- John A. Darling
- United States Environmental Protection Agency, National Exposure Research Laboratory, Research Triangle Park, NC, United States
| | - James T. Carlton
- Maritime Studies Program, Williams College-Mystic Seaport, Mystic, CT, United States
- Department of Biology, Williams College, Williamstown, MA, United States
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Liu Y, Erséus C. New specific primers for amplification of the Internal Transcribed Spacer region in Clitellata (Annelida). Ecol Evol 2017; 7:10421-10439. [PMID: 29238565 PMCID: PMC5723599 DOI: 10.1002/ece3.3212] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 06/05/2017] [Accepted: 06/06/2017] [Indexed: 11/11/2022] Open
Abstract
Nuclear molecular evidence, for example, the rapidly evolving Internal Transcribed Spacer region (ITS), integrated with maternally inherited (mitochondrial) COI barcodes, has provided new insights into the diversity of clitellate annelids. PCR amplification and sequencing of ITS, however, are often hampered by poor specificity of primers used. Therefore, new clitellate‐specific primers for amplifying the whole ITS region (ITS: 29F/1084R) and a part of it (ITS2: 606F/1082R) were developed on the basis of a collection of previously published ITS sequences with flanking rDNA coding regions. The specificity of these and other ITS primers used for clitellates were then tested in silico by evaluating their mismatches with all assembled and annotated sequences (STD, version r127) from EMBL, and the new primers were also tested in vitro for a taxonomically broad sample of clitellate species (71 specimens representing 11 families). The in silico analyses showed that the newly designed primers have a better performance than the universal ones when amplifying clitellate ITS sequences. In vitro PCR and sequencing using the new primers were successful, in particular, for the 606F/1082R pair, which worked well for 65 of the 71 specimens. Thus, using this pair for amplifying the ITS2 will facilitate further molecular systematic investigation of various clitellates. The other pair (29F/1084R), will be a useful complement to existing ITS primers, when amplifying ITS as a whole.
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Affiliation(s)
- Yingkui Liu
- Department of Biological and Environmental Sciences University of Gothenburg Göteborg Sweden
| | - Christer Erséus
- Department of Biological and Environmental Sciences University of Gothenburg Göteborg Sweden
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Vivien R, Holzmann M, Werner I, Pawlowski J, Lafont M, Ferrari BJD. Cytochrome c oxidase barcodes for aquatic oligochaete identification: development of a Swiss reference database. PeerJ 2017; 5:e4122. [PMID: 29230362 PMCID: PMC5723135 DOI: 10.7717/peerj.4122] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 11/13/2017] [Indexed: 11/20/2022] Open
Abstract
Introduction Aquatic oligochaetes represent valuable indicators of the quality of sediments of watercourses and lakes, but their difficult identification based on morphological criteria compromises their more common use for eco-diagnostic analyses. This issue could be overcome by using DNA barcodes for species identification. A 10% threshold of cytochrome c oxidase (COI) divergence was proposed for differentiating between oligochaete species based on molecular and morphological data. A Swiss database of COI sequences of aquatic oligochaetes was initiated in 2012. The aim of this study is to complement the Swiss oligochaete database of COI sequences and to confirm the relevance of this threshold for species delimitation. Methods We sequenced the COI sequence of 216 specimens collected in different regions of Switzerland and ITS2 region of some lineages whose delimitation with COI data was doubtful. Results We distinguished 53 lineages, among which 34 were new for Switzerland and 17 sequenced for the first time. All the lineages were separated by more than 10% of COI variation, with the exception of some species within Nais and Uncinais. In these two genera, the threshold was lowered to 8% to be congruent with the morphological analysis. The total number of lineages reported so far for Switzerland is 75, including 59 morphospecies or unidentified species and 16 cryptic species. Discussion Our study shows that the threshold of 10% of COI divergence is generally appropriate to distinguish aquatic oligochaete lineages, but that it must be adjusted for some species. The database reported here will be complemented in the future in parallel to the development of genetic oligochaete indices.
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Affiliation(s)
- Régis Vivien
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre) Eawag-EPFL, Lausanne/Dübendorf, Switzerland
| | - Maria Holzmann
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Inge Werner
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre) Eawag-EPFL, Lausanne/Dübendorf, Switzerland
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Michel Lafont
- Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, Université Lyon I, Villeurbanne, France
| | - Benoit J D Ferrari
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre) Eawag-EPFL, Lausanne/Dübendorf, Switzerland
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Álvarez-Campos P, Giribet G, Riesgo A. The Syllis gracilis species complex: A molecular approach to a difficult taxonomic problem (Annelida, Syllidae). Mol Phylogenet Evol 2017; 109:138-150. [DOI: 10.1016/j.ympev.2016.12.036] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 12/27/2016] [Accepted: 12/28/2016] [Indexed: 11/26/2022]
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Description of new types of sphaeractinomyxon actinospores (Myxozoa: Myxosporea) from marine tubificid oligochaetes, with a discussion on the validity of the tetraspora and the endocapsa as actinospore collective group names. Parasitol Res 2016; 115:2341-51. [DOI: 10.1007/s00436-016-4983-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 03/03/2016] [Indexed: 11/26/2022]
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Vivien R, Lejzerowicz F, Pawlowski J. Next-Generation Sequencing of Aquatic Oligochaetes: Comparison of Experimental Communities. PLoS One 2016; 11:e0148644. [PMID: 26866802 PMCID: PMC4750909 DOI: 10.1371/journal.pone.0148644] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 01/20/2016] [Indexed: 11/26/2022] Open
Abstract
Aquatic oligochaetes are a common group of freshwater benthic invertebrates known to be very sensitive to environmental changes and currently used as bioindicators in some countries. However, more extensive application of oligochaetes for assessing the ecological quality of sediments in watercourses and lakes would require overcoming the difficulties related to morphology-based identification of oligochaetes species. This study tested the Next-Generation Sequencing (NGS) of a standard cytochrome c oxydase I (COI) barcode as a tool for the rapid assessment of oligochaete diversity in environmental samples, based on mixed specimen samples. To know the composition of each sample we Sanger sequenced every specimen present in these samples. Our study showed that a large majority of OTUs (Operational Taxonomic Unit) could be detected by NGS analyses. We also observed congruence between the NGS and specimen abundance data for several but not all OTUs. Because the differences in sequence abundance data were consistent across samples, we exploited these variations to empirically design correction factors. We showed that such factors increased the congruence between the values of oligochaetes-based indices inferred from the NGS and the Sanger-sequenced specimen data. The validation of these correction factors by further experimental studies will be needed for the adaptation and use of NGS technology in biomonitoring studies based on oligochaete communities.
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Affiliation(s)
- Régis Vivien
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre), Eawag/EPFL, 1015, Lausanne, Switzerland
- * E-mail:
| | - Franck Lejzerowicz
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
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Martinsson S, Rhodén C, Erséus C. Barcoding gap, but no support for cryptic speciation in the earthworm Aporrectodea longa (Clitellata: Lumbricidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:147-155. [PMID: 26709635 DOI: 10.3109/19401736.2015.1115487] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
DNA-barcoding, using the mitochondrial marker COI, has been found successful for the identification of specimens in many animal groups, but may not be suited for species discovery and delimitation if used alone. In this study, we investigate whether two observed COI haplogroups in the earthworm Aporrectodea longa correspond to two cryptic species or if the variation is intraspecific. This is done by complementing COI with two nuclear markers, ITS2 and Histone 3. The variation is studied using distance methods, parsimony networks and Bayesian coalescent trees, and the statistical distinctness of the groups is tested on gene trees using the genealogical sorting index, Rosenberg's PAB and Rodrigo et al.'s P(RD). We also applied multilocus species delimitation based on the multispecies coalescence model. The two haplogroups were found in COI, and all tests except P(RD) found them to be significantly distinct. However, in ITS2, the same groups were not recovered in any analyses or tests. H3 was invariable in A. longa, and was, therefore, included only in the multilocus analysis, which preferred a model treating A. longa as one species over a model splitting it into two. We also compared two measurements of size, body length, and no. of segments between the groups. No difference in body length was found, and although a significant difference in no. of segments was noted the haplogroup with the lower mean showed both the highest and the lowest value. When combined, these results led us to the conclusion that there is no support for the separation of A. longa into two cryptic species. This study again highlights the importance of complementing mitochondrial barcodes with more data when establishing species boundaries.
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Affiliation(s)
- Svante Martinsson
- a Division of Systematics and Biodiversity, Department of Biological and Environmental Sciences , University of Gothenburg , Göteborg , Sweden
| | - Caroline Rhodén
- a Division of Systematics and Biodiversity, Department of Biological and Environmental Sciences , University of Gothenburg , Göteborg , Sweden
| | - Christer Erséus
- a Division of Systematics and Biodiversity, Department of Biological and Environmental Sciences , University of Gothenburg , Göteborg , Sweden
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Vivien R, Wyler S, Lafont M, Pawlowski J. Molecular barcoding of aquatic oligochaetes: implications for biomonitoring. PLoS One 2015; 10:e0125485. [PMID: 25856230 PMCID: PMC4391796 DOI: 10.1371/journal.pone.0125485] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 03/14/2015] [Indexed: 11/18/2022] Open
Abstract
Aquatic oligochaetes are well recognized bioindicators of quality of sediments and water in watercourses and lakes. However, the difficult taxonomic determination based on morphological features compromises their more common use in eco-diagnostic analyses. To overcome this limitation, we investigated molecular barcodes as identification tool for broad range of taxa of aquatic oligochaetes. We report 185 COI and 52 ITS2 rDNA sequences for specimens collected in Switzerland and belonging to the families Naididae, Lumbriculidae, Enchytraeidae and Lumbricidae. Phylogenetic analyses allowed distinguishing 41 lineages separated by more than 10 % divergence in COI sequences. The lineage distinction was confirmed by Automatic Barcode Gap Discovery (ABGD) method and by ITS2 data. Our results showed that morphological identification underestimates the oligochaete diversity. Only 26 of the lineages could be assigned to morphospecies, of which seven were sequenced for the first time. Several cryptic species were detected within common morphospecies. Many juvenile specimens that could not be assigned morphologically have found their home after genetic analysis. Our study showed that COI barcodes performed very well as species identifiers in aquatic oligochaetes. Their easy amplification and good taxonomic resolution might help promoting aquatic oligochaetes as bioindicators for next generation environmental DNA biomonitoring of aquatic ecosystems.
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Affiliation(s)
- Régis Vivien
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- * E-mail:
| | - Sofia Wyler
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | | | - Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
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Mejlon E, De Wit P, Matamoros L, Erséus C. DNA-based phylogeny of the marine genus Heterodrilus
(Annelida, Clitellata, Naididae). J ZOOL SYST EVOL RES 2015. [DOI: 10.1111/jzs.12092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Erica Mejlon
- Museum of Evolution; Uppsala University; Uppsala Sweden
| | - Pierre De Wit
- Department of Biological and Environmental Sciences; University of Gothenburg; Göteborg Sweden
| | - Lisa Matamoros
- Department of Biological and Environmental Sciences; University of Gothenburg; Göteborg Sweden
| | - Christer Erséus
- Department of Biological and Environmental Sciences; University of Gothenburg; Göteborg Sweden
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Nithaniyal S, Newmaster SG, Ragupathy S, Krishnamoorthy D, Vassou SL, Parani M. DNA barcode authentication of wood samples of threatened and commercial timber trees within the tropical dry evergreen forest of India. PLoS One 2014; 9:e107669. [PMID: 25259794 PMCID: PMC4178033 DOI: 10.1371/journal.pone.0107669] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 08/22/2014] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND India is rich with biodiversity, which includes a large number of endemic, rare and threatened plant species. Previous studies have used DNA barcoding to inventory species for applications in biodiversity monitoring, conservation impact assessment, monitoring of illegal trading, authentication of traded medicinal plants etc. This is the first tropical dry evergreen forest (TDEF) barcode study in the World and the first attempt to assemble a reference barcode library for the trees of India as part of a larger project initiated by this research group. METHODOLOGY/PRINCIPAL FINDINGS We sampled 429 trees representing 143 tropical dry evergreen forest (TDEF) species, which included 16 threatened species. DNA barcoding was completed using rbcL and matK markers. The tiered approach (1st tier rbcL; 2nd tier matK) correctly identified 136 out of 143 species (95%). This high level of species resolution was largely due to the fact that the tree species were taxonomically diverse in the TDEF. Ability to resolve taxonomically diverse tree species of TDEF was comparable among the best match method, the phylogenetic method, and the characteristic attribute organization system method. CONCLUSIONS We demonstrated the utility of the TDEF reference barcode library to authenticate wood samples from timber operations in the TDEF. This pilot research study will enable more comprehensive surveys of the illegal timber trade of threatened species in the TDEF. This TDEF reference barcode library also contains trees that have medicinal properties, which could be used to monitor unsustainable and indiscriminate collection of plants from the wild for their medicinal value.
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Affiliation(s)
- Stalin Nithaniyal
- Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Chennai, India
- Interdisciplinary School of Indian System of Medicine, SRM University, Chennai, India
| | - Steven G. Newmaster
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | | | - Sophie Lorraine Vassou
- Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Chennai, India
| | - Madasamy Parani
- Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Chennai, India
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Jörger KM, Schrödl M. How to describe a cryptic species? Practical challenges of molecular taxonomy. Front Zool 2013; 10:59. [PMID: 24073641 PMCID: PMC4015967 DOI: 10.1186/1742-9994-10-59] [Citation(s) in RCA: 180] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 09/03/2013] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Molecular methods of species delineation are rapidly developing and widely considered as fast and efficient means to discover species and face the 'taxonomic impediment' in times of biodiversity crisis. So far, however, this form of DNA taxonomy frequently remains incomplete, lacking the final step of formal species description, thus enhancing rather than reducing impediments in taxonomy. DNA sequence information contributes valuable diagnostic characters and -at least for cryptic species - could even serve as the backbone of a taxonomic description. To this end solutions for a number of practical problems must be found, including a way in which molecular data can be presented to fulfill the formal requirements every description must meet. Multi-gene barcoding and a combined molecular species delineation approach recently revealed a radiation of at least 12 more or less cryptic species in the marine meiofaunal slug genus Pontohedyle (Acochlidia, Heterobranchia). All identified candidate species are well delimited by a consensus across different methods based on mitochondrial and nuclear markers. RESULTS The detailed microanatomical redescription of Pontohedyle verrucosa provided in the present paper does not reveal reliable characters for diagnosing even the two major clades identified within the genus on molecular data. We thus characterize three previously valid Pontohedyle species based on four genetic markers (mitochondrial cytochrome c oxidase subunit I, 16S rRNA, nuclear 28S and 18S rRNA) and formally describe nine cryptic new species (P. kepii sp. nov., P. joni sp. nov., P. neridae sp. nov., P. liliae sp. nov., P. wiggi sp. nov., P. wenzli sp. nov., P. peteryalli sp. nov., P. martynovi sp. nov., P. yurihookeri sp. nov.) applying molecular taxonomy, based on diagnostic nucleotides in DNA sequences of the four markers. Due to the minute size of the animals, entire specimens were used for extraction, consequently the holotype is a voucher of extracted DNA ('DNA-type'). We used the Character Attribute Organization System (CAOS) to determine diagnostic nucleotides, explore the dependence on input data and data processing, and aim for maximum traceability in our diagnoses for future research. Challenges, pitfalls and necessary considerations for applied DNA taxonomy are critically evaluated. CONCLUSIONS To describe cryptic species traditional lines of evidence in taxonomy need to be modified. DNA sequence information, for example, could even serve as the backbone of a taxonomic description. The present contribution demonstrates that few adaptations are needed to integrate into traditional taxonomy novel diagnoses based on molecular data. The taxonomic community is encouraged to join the discussion and develop a quality standard for molecular taxonomy, ideally in the form of an automated final step in molecular species delineation procedures.
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Affiliation(s)
- Katharina M Jörger
- Mollusca Section, SNSB-Bavarian State Collection of Zoology, Münchhausenstr 21, 81247 München, Germany
- Department Biology II, Ludwig-Maximilians-University, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - Michael Schrödl
- Mollusca Section, SNSB-Bavarian State Collection of Zoology, Münchhausenstr 21, 81247 München, Germany
- Department Biology II, Ludwig-Maximilians-University, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
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Martinsson S, Achurra A, Svensson M, Erséus C. Integrative taxonomy of the freshwater wormRhyacodrilus falciformiss.l. (Clitellata: Naididae), with the description of a new species. ZOOL SCR 2013. [DOI: 10.1111/zsc.12032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Svante Martinsson
- Department of Biological and Environmental Sciences; University of Gothenburg; Box 463; SE-405 30; Göteborg; Sweden
| | | | - Marcus Svensson
- Department of Biological and Environmental Sciences; University of Gothenburg; Box 463; SE-405 30; Göteborg; Sweden
| | - Christer Erséus
- Department of Biological and Environmental Sciences; University of Gothenburg; Box 463; SE-405 30; Göteborg; Sweden
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Revision of Bryodrilus glandulosus () and Mesenchytraeus kuehnelti (Oligochaeta: Enchytraeidae) using morphological and molecular data. ZOOL ANZ 2012. [DOI: 10.1016/j.jcz.2011.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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ENVALL IDA, GUSTAVSSON LENAM, ERSÉUS CHRISTER. Genetic and chaetal variation in Nais worms (Annelida, Clitellata, Naididae). Zool J Linn Soc 2012. [DOI: 10.1111/j.1096-3642.2012.00828.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kvist S, Oceguera-Figueroa A, Siddall ME, Erséus C. Barcoding, types and theHirudofiles: Using information content to critically evaluate the identity of DNA barcodes. ACTA ACUST UNITED AC 2010; 21:198-205. [DOI: 10.3109/19401736.2010.529905] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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