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Vafeiadou AM, Geldhof K, Barhdadi W, Baetens JM, De Baets B, Moens T, Daly AJ. Temperature-driven dynamics: unraveling the impact of climate change on cryptic species interactions within the Litoditis marina complex. PeerJ 2024; 12:e17324. [PMID: 38784398 PMCID: PMC11114120 DOI: 10.7717/peerj.17324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/10/2024] [Indexed: 05/25/2024] Open
Abstract
Anthropogenic climate change and the associated increase in sea temperatures are projected to greatly impact marine ecosystems. Temperature variation can influence the interactions between species, leading to cascading effects on the abundance, diversity and composition of communities. Such changes in community structure can have consequences on ecosystem stability, processes and the services it provides. Therefore, it is important to better understand the role of species interactions in the development of communities and how they are influenced by environmental factors like temperature. The coexistence of closely related cryptic species, with significant biological and ecological differences, makes this even more complex. This study investigated the effect of temperature on species growth and both intra- and interspecific interactions of three species within the free-living nematode Litoditis marina complex. To achieve this, closed microcosm experiments were conducted on the L. marina species Pm I, Pm III and Pm IV in monoculture and combined cultures at two temperature treatments of 15 °C and 20 °C. A population model was constructed to elucidate and quantify the effects of intra- and interspecific interactions on nematode populations. The relative competitive abilities of the investigated species were quantified using the Modern Coexistence Theory (MCT) framework. Temperature had strong and disparate effects on the population growth of the distinct L. marina species. This indicates temperature could play an important role in the distribution of these cryptic species. Both competitive and facilitative interactions were observed in the experiments. Temperature affected both the type and the strength of the species interactions, suggesting a change in temperature could impact the coexistence of these closely related species, alter community dynamics and consequently affect ecosystem processes and services.
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Affiliation(s)
- Anna-Maria Vafeiadou
- Department of Biology, Marine Biology Research Group, Universiteit Gent, Ghent, Belgium
| | - Kevin Geldhof
- Department of Biology, Marine Biology Research Group, Universiteit Gent, Ghent, Belgium
| | - Wissam Barhdadi
- Department of Data Analysis and Mathematical Modelling, Universiteit Gent, Ghent, Belgium
| | - Jan M. Baetens
- Department of Data Analysis and Mathematical Modelling, Universiteit Gent, Ghent, Belgium
| | - Bernard De Baets
- Department of Data Analysis and Mathematical Modelling, Universiteit Gent, Ghent, Belgium
| | - Tom Moens
- Department of Biology, Marine Biology Research Group, Universiteit Gent, Ghent, Belgium
| | - Aisling J. Daly
- Department of Data Analysis and Mathematical Modelling, Universiteit Gent, Ghent, Belgium
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2
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Walker MA, Bolek MG, Zieman EA, Langford GJ, Reyda FB, Jiménez FA. MOLECULAR PHYLOGENETIC ANALYSIS OF GYRINICOLA BATRACHIENSIS (NEMATODA: OXYUROIDEA) LENDS SUPPORT TO THE MONOPHYLY OF THE GENUS AND THE RESURRECTION OF GYRINICOLINAE. J Parasitol 2023; 109:622-632. [PMID: 38151050 DOI: 10.1645/22-108] [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: 12/29/2023] Open
Abstract
Gyrinicola Yamaguti, 1938, includes 6 species of oxyurid found within the intestinal tract of numerous, larval, anuran species in Europe, Asia, South America, and North America. The systematic placement and hierarchical treatment of the genus has shifted at least 5 times since its discovery; the group was first considered as its own family (Gyrinicolidae), then treated as a subfamily (Gyrinicolinae) of Cosmocercidae, then as a member of the Pharyngodonidae, followed by movement back to the Cosmocercidae, and finally a recent proposal suggested the resurrection of the Gyrinicolidae. Species in the genus vary widely in the morphology of the uterine tract, a characteristic often used to indicate membership in the genus, as it is tied to the reproductive mode. However, until recently very few genetic data were available to aid in the placement of this unique group of worms, and before this study to the best of our knowledge none existed for the North American species. To examine the monophyly and placement of the Gyrinicola we sampled populations of Gyrinicola batrachiensis across North America and screened them for genetic diversity using nuclear markers 18S and 28S. Phylogenies suggest at least 3 clades exist among the nematodes from North America and that these clades, alongside Gyrinicola japonica, form a well-supported group within Oxyuroidea. Further representation of Pharyngodonidae from other vertebrate classes may help clarify the relationship of this historical grouping to other members of the Oxyuroidea.
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Affiliation(s)
- Matthew A Walker
- School of Biological Sciences, Southern Illinois University, Carbondale, Illinois 62901
| | - Matthew G Bolek
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma 74078
| | - Elliott A Zieman
- Department of Biological Sciences, Eastern Illinois University, Charleston, Illinois 61920
| | - Gabriel J Langford
- Department of Biology, Florida Southern College, Lakeland, Florida 33801
| | - Florian B Reyda
- Biology Department & Biological Field Station, State University of New York, College at Oneonta, Ravine Parkway, Oneonta, New York 13820
| | - F Agustín Jiménez
- School of Biological Sciences, Southern Illinois University, Carbondale, Illinois 62901
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3
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Kang H, Ko HR, Lim YJ, Park EH, Kim EH, Park SK, Park BY, Han H. Haplotype diversity of Heterodera koreana (Tylenchida: Heteroderidae), affecting bamboo in Korea. RESEARCH SQUARE 2023:rs.3.rs-3205194. [PMID: 37720038 PMCID: PMC10503861 DOI: 10.21203/rs.3.rs-3205194/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
In a survey of plant-parasitic nematodes in agricultural fields, cyst-forming nematodes were found in soil planted bamboo in Korea. The aim of this study was to identify the cyst nematodes based on morphological and molecular characteristics. As the results, the morphology and morphometrics of cysts and second-stage juveniles (J2s) were consistent with those of previous descriptions of Heterodera koreana. In phylogenetic analyses based on DNA sequences, these cyst nematodes were clustered together with clade of H. koreana in internal transcribed spacer (ITS) region, and large subunit D2-D3 segments (LSU D2-D3). These nematodes were clustered together with clade of H. koreana in cytochrome c oxidase subunit I (COI) gene, but a haplotype was different when compared with previous reported haplotypes (haplotype A-C) in Japan. This study showed these cyst nematodes were identified as H. koreana, and a new haplotype of H. koreana is distributed in Korea. We suggest that the new haplotype of H. koreana name as haplotype D.
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Guo F, Slos D, Du H, Li K, Li H, Qing X. Transcriptomics of Cruznema velatum (Nematoda: Rhabditidae) with a redescription of the species. J Helminthol 2023; 97:e57. [PMID: 37470247 DOI: 10.1017/s0022149x23000342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Cruznema velatum isolated from soil in a chestnut orchard located at Guangdong province, China, is redescribed with morphology, molecular barcoding sequences, and transcriptome data. The morphological comparison for C. velatum and six other valid species is provided. Phylogeny analysis suggests genus Cruznema is monophyletic. The species is amphimix, can be cultured with Escherichia coli in 7-9 days from egg to egg-laying adult, and has a lifespan of 11 to 14 days at 20°C. The transcription data generated 45,366 unigenes; 29.9%, 31.3%, 24.8%, and 18.6% of unigenes were annotated in KOG, SwissProt, GO, and KEGG, respectively. Further gene function analysis demonstrated that C. velatum share the same riboflavin, lipoic acid, and vitamin B6 metabolic pathways with Caenorhabditis elegans and Pristionchus pacificus.
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Affiliation(s)
- F Guo
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing210095, China
| | - D Slos
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke9820, Belgium
| | - H Du
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing210095, China
| | - K Li
- College of Agriculture, Xinjiang Agricultural University, Urumqi830052, China
| | - H Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing210095, China
- College of Agriculture, Xinjiang Agricultural University, Urumqi830052, China
| | - X Qing
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing210095, China
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di Montanara AC, Baldrighi E, Franzo A, Catani L, Grassi E, Sandulli R, Semprucci F. Free-living nematodes research: State of the art, prospects, and future directions. A bibliometric analysis approach. ECOL INFORM 2022. [DOI: 10.1016/j.ecoinf.2022.101891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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6
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Ecological and morphological differentiation among COI haplotype groups in the plant parasitic nematode species Mesocriconema xenoplax. J Nematol 2022; 54:20220009. [PMID: 35860518 PMCID: PMC9260820 DOI: 10.2478/jofnem-2022-0009] [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: 12/08/2021] [Indexed: 11/20/2022] Open
Abstract
DNA barcoding with the mitochondrial COI gene reveals distinct haplotype subgroups within the monophyletic and parthenogenetic nematode species, Mesocriconema xenoplax. Biological attributes of these haplotype groups (HG) have not been explored. An analysis of M. xenoplax from 40 North American sites representing both native plant communities and agroecosystems was conducted to identify possible subgroup associations with ecological, physiological, or geographic factors. A dataset of 132 M. xenoplax specimens was used to generate sequences of a 712 bp region of the cytochrome oxidase subunit I gene. Maximum-likelihood and Bayesian phylogenies recognized seven COI HG (≥99/0.99 posterior probability/bootstrap value). Species delimitation metrics largely supported the genetic integrity of the HG. Discriminant function analysis of HG morphological traits identified stylet length, total body length, and stylet knob width as the strongest distinguishing features among the seven groups, with stylet length as the strongest single distinguishing morphological feature. Multivariate analysis identified land cover, ecoregion, and maximum temperature as predictors of 53.6% of the total variation (P = 0.001). Within land cover, HG categorized under “herbaceous,” “woody wetlands,” and “deciduous forest” were distinct in DAPC and RDA analyses and were significantly different (analysis of molecular variance P = 0.001). These results provide empirical evidence for molecular, morphological, and ecological differentiation associated with HG within the monophyletic clade that represents the species Mesocriconema xenoplax.
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HODDA M. Phylum Nematoda: trends in species descriptions, the documentation of diversity, systematics, and the species concept. Zootaxa 2022; 5114:290-317. [DOI: 10.11646/zootaxa.5114.1.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Indexed: 11/04/2022]
Abstract
This paper summarizes the trends in nematode species description and systematics emerging from a comparison of the latest comprehensive classification and census of Phylum Nematoda (Hodda 2022a, b) with earlier classifications (listed in Hodda 2007). It also offers some general observations on trends in nematode systematics emerging from the review of the voluminous literature used to produce the classification. The trends in nematodes can be compared with developments in the systematics of other organisms to shed light on many of the general issues confronting systematists now and into the future.
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8
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Shift from morphological to recent advanced molecular approaches for the identification of nematodes. Genomics 2022; 114:110295. [DOI: 10.1016/j.ygeno.2022.110295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 01/08/2022] [Accepted: 02/01/2022] [Indexed: 11/17/2022]
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Daly AJ, De Meester N, Baetens JM, Moens T, De Baets B. Untangling the mechanisms of cryptic species coexistence in a nematode community through individual‐based modelling. OIKOS 2021. [DOI: 10.1111/oik.07989] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Aisling J. Daly
- KERMIT, Dept of Data Analysis and Mathematical Modelling, Ghent Univ. Ghent Belgium
| | - Nele De Meester
- Marine Biology Unit, Dept of Biology, Ghent Univ. Ghent Belgium
| | - Jan M. Baetens
- KERMIT, Dept of Data Analysis and Mathematical Modelling, Ghent Univ. Ghent Belgium
| | - Tom Moens
- Marine Biology Unit, Dept of Biology, Ghent Univ. Ghent Belgium
| | - Bernard De Baets
- KERMIT, Dept of Data Analysis and Mathematical Modelling, Ghent Univ. Ghent Belgium
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Leduc D, Zhao ZQ. Morphological and molecular characterisation of Spirinia antipodea Leduc n. sp. (Nematoda: Desmodoridae), a cryptic species related to S. parasitifera, from the coast of New Zealand. NEMATOLOGY 2019. [DOI: 10.1163/15685411-00003199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Summary
Spirinia parasitifera is a common nematode species recorded from coastal habitats of the White, North and Barents Seas, the Northwest Atlantic, the Maldives and Australia, and exhibits a high degree of variability in some morphological characters. For these reasons it has been suggested that S. parasitifera is a species complex comprised of several distinct but potentially cryptic species. However, no study has yet combined molecular and morphological approaches to verify this assertion. Here, we describe S. antipodea n. sp., a species morphologically very similar to S. parasitifera, from the coast of New Zealand. Spirinia antipodea n. sp. differs from the original description of S. parasitifera as well as subsequent descriptions by other authors in at least one body dimension, but no single trait differs consistently between the New Zealand specimens and all descriptions of S. parasitifera. Phylogenetic analyses showed that the new species is distinct from other species of the genus, including S. parasitifera specimens sampled near the type locality. The S. antipodea n. sp. SSU sequence differed from other Spirinia sequence by 2.1-5.3%, whilst D2-D3 of LSU sequences differed by 12.5-18.9%. The consensus SSU tree also recovered three distinct S. parasitifera clades, which provides support for the existence of a species complex. Because it is not possible to determine whether the variability in morphological characters observed among descriptions of S. parasitifera is intra- or interspecific, and therefore to determine which trait can reliably be used to differentiate between S. antipodea n. sp. and S. parasitifera, the new species is best differentiated from S. parasitifera and other closely related species based on SSU sequences rather than morphological characters.
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Affiliation(s)
- Daniel Leduc
- 1National Institute of Water and Atmospheric Research (NIWA) Limited, Private Bag 14-901, Kilbirnie, Wellington, New Zealand
| | - Zeng Qi Zhao
- 2Landcare Research, Private Bag 92170, Auckland Mail Centre, Auckland 1142, New Zealand
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11
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Guden RM, Vafeiadou AM, De Meester N, Derycke S, Moens T. Living apart-together: Microhabitat differentiation of cryptic nematode species in a saltmarsh habitat. PLoS One 2018; 13:e0204750. [PMID: 30261070 PMCID: PMC6160205 DOI: 10.1371/journal.pone.0204750] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 09/13/2018] [Indexed: 11/26/2022] Open
Abstract
Coexistence of highly similar species is at odds with ecological theory of competition; coexistence, then, requires stabilizing mechanisms such as differences in ecological niche. In the bacterivore nematode Litoditis marina species complex, which occurs associated with macro-algae, four cryptic lineages (Pm I-IV) co-occur in the field along the south-western coast and estuaries of The Netherlands. Here we investigate the temporal and/or spatial niche differentiation in their natural environment using a qPCR-based detection and relative quantification method. We collected different algal species (i.e. two Fucus species and Ulva sp.) and separated algal structures (i.e. receptacula, thalli, non-fertile tips and bladders) at different sampling months and times (i.e. twice per sampling month), to examine differences in microhabitat use between coexisting L. marina species. Results demonstrate that the cryptic species composition varied among different algal species and algal structures, which was also subject to temporal shifts. Pm I dominated on Fucus spp., Pm II showed dominance on Ulva sp., while Pm III overall had the lowest frequencies. Microhabitat partitioning was most pronounced between the two cryptic species which had similar microbiomes (Pm I and Pm II), and less so between the two species which had significantly different microbiomes (Pm I and Pm III), suggesting that species which share the same microhabitats may avoid competition through resource partitioning. The interplay of microhabitat differentiation and temporal dynamics among the cryptic species of L. marina implies that there is a complex interaction between biotic components and abiotic factors which contributes to their coexistence in the field.
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Affiliation(s)
- Rodgee Mae Guden
- Ghent University, Marine Biology Lab, Ghent, Belgium
- Mindanao State University- Iligan Institute of Technology, Iligan, Philippines
| | - Anna-Maria Vafeiadou
- Ghent University, Marine Biology Lab, Ghent, Belgium
- Aristotle University of Thessaloniki, Biology Department, Thessaloniki, Greece
| | | | - Sofie Derycke
- Ghent University, Marine Biology Lab, Ghent, Belgium
- Institute for Agricultural and Fisheries Research, Aquatic Environment and Quality, Oostende, Belgium
| | - Tom Moens
- Ghent University, Marine Biology Lab, Ghent, Belgium
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12
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Schaeffner BC, Marques FPL. Integrative taxonomy unravels the species diversity of Parachristianella (Cestoda : Trypanorhyncha) from both sides of the Panamanian isthmus. INVERTEBR SYST 2018. [DOI: 10.1071/is17008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The uplift of the Panamanian isthmus in the Pliocene caused the termination of gene flow among members of many ancestral populations of marine lineages leading the diversification of geminate species confined to opposite sides of Central America. This palaeogeographical event has been evoked to explain the diversification of few lineages of batoids with trans-isthmian distribution. As such, there is the expectation that this vicariance event also affected lineages of parasites associated with them. Our study suggests that this event can explain the diversification of Parachristianella Dollfus, 1946 (Trypanorhyncha:Eutetrarhynchidae) in the Caribbean Sea and tropical eastern Pacific Ocean. We provide molecular, morphological and biogeographical evidence to recognise five lineages within this genus inhabiting the coastal waters of Panama, including P. parva Campbell & Beveridge, 2007 and four new species: P. mendozai, sp. nov., P. kuchtai, sp. nov., P. campbelli, sp. nov. and P. soldanovae, sp. nov. These species can be diagnosed by unambiguous sets of molecular characters. The morphological cohesiveness of sister species, which most likely diverged from around 3million years ago through the uplift of the Panamanian isthmus, suggests that the traditional emphasis on the tentacular armature to circumscribe species within trypanorhynchs might underestimate the diversity of recently diverged lineages.
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Apolônio Silva de Oliveira D, Decraemer W, Moens T, Dos Santos GAP, Derycke S. Low genetic but high morphological variation over more than 1000 km coastline refutes omnipresence of cryptic diversity in marine nematodes. BMC Evol Biol 2017; 17:71. [PMID: 28270090 PMCID: PMC5341416 DOI: 10.1186/s12862-017-0908-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 02/08/2017] [Indexed: 11/21/2022] Open
Abstract
Background The resilience of ecosystems to negative impacts is generally higher when high gene flow, species diversity and genetic diversity are present. Population genetic studies are suitable to investigate genetic diversity and estimate gene flow between populations. Seaweed beds form a dynamic shallow water ecosystem influenced by climate change and human exploitation, as such, seaweed beds are a particularly powerful model to investigate ecosystem resilience in coastal areas. We studied the population genetic structure of the new nematode species Paracanthonchus gynodiporata associated with seaweeds in northeastern Brazil. Nematodes are generally believed to have a limited dispersal capacity because of the lack of planktonic larvae. Yet, they can drift on seaweeds, and water currents might be a natural barrier for their dispersal. Populations of P. gynodiporata were sampled over more than 1000 km coastline in regions across major oceanic currents with and without historical exploitation of seaweed. Results P. gynodiporata is described in an integrative way using mitochondrial and nuclear sequences and morphological data. The 3D model of the head region shows for the first time a detailed view of the ventrosublateral teeth, a character often overlooked in older taxonomic studies of the genus. A total of 17 mitochondrial COI haplotypes were found with one haplotype representing 63 to 83% of the frequencies in each population. AMOVA showed overall little population genetic structure (FST = 0.05204), and no genetic subdivision between the populations under the influence of the two different water currents were found. Effects of historical seaweed exploitation on population genetic diversity were not detected. In contrast, significant differences between populations were found in morphometric characters. This discrepancy in genetic and morphological differentiation between populations across 1000 km of coastline is surprising in view of the frequently observed presence of several cryptic species at small geographical scale in other macroalgal associated nematodes. Conclusions Our results show that cryptic species are not omnipresent in marine nematode species, suggesting that nematodes associated with seaweeds have been able to disperse over large distances across well-known biogeographic barriers.
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Affiliation(s)
| | - Wilfrida Decraemer
- Faculty of Science, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.,Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny, Vautierstraat 29, 1000, Brussels, Belgium
| | - Tom Moens
- Faculty of Science, Department of Biology, Marine Biology, Ghent University, Krijgslaan 281 (S8), 9000, Ghent, Belgium
| | - Giovanni Amadeu Paiva Dos Santos
- Department of Biology, Federal University of Pernambuco, Av. Professor Morais Rego, 1235 - Cidade Universitária, CEP 50670-901, Recife, Brazil
| | - Sofie Derycke
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny, Vautierstraat 29, 1000, Brussels, Belgium.,Faculty of Science, Department of Biology, Marine Biology, Ghent University, Krijgslaan 281 (S8), 9000, Ghent, Belgium
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14
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Kolombia YA, Karssen G, Viaene N, Kumar PL, Joos L, Coyne DL, Bert W. Morphological and molecular characterisation of Scutellonema species from yam ( Dioscorea spp.) and a key to the species of the genus. NEMATOLOGY 2017; 19:751-787. [PMID: 32704234 PMCID: PMC7340491 DOI: 10.1163/15685411-00003084] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/30/2017] [Accepted: 06/01/2017] [Indexed: 11/24/2022]
Abstract
The yam nematode, Scutellonema bradys, is a major threat to yam (Dioscorea spp.) production across yam-growing regions. In West Africa, this species cohabits with many morphologically similar congeners and, consequently, its accurate diagnosis is essential for control and for monitoring its movement. In the present study, 46 Scutellonema populations collected from yam rhizosphere and yam tubers in different agro-ecological zones in Ghana and Nigeria were characterised by their morphological features and by sequencing of the D2-D3 region of the 28S rDNA gene and the mitochondrial COI genes. Molecular phylogeny, molecular species delimitation and morphology revealed S. bradys, S. cavenessi, S. clathricaudatum and three undescribed species from yam rhizosphere. Only S. bradys was identified from yam tuber tissue, however. For barcoding and identifying Scutellonema spp., the most suitable marker used was the COI gene. Additionally, 99 new Scutellonema sequences were generated using populations obtained also from banana, carrot, maize and tomato, including the first for S. paralabiatum and S. clathricaudatum, enabling the development of a dichotomous key for identification of Scutellonema spp. The implications of these results are discussed.
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Affiliation(s)
- Yao A Kolombia
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.,International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Road, Ibadan, Nigeria
| | - Gerrit Karssen
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.,National Plant Protection Organization, 6706 EA Wageningen, The Netherlands
| | - Nicole Viaene
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.,Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), B-9820 Merelbeke, Belgium
| | - P Lava Kumar
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Road, Ibadan, Nigeria
| | - Lisa Joos
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Danny L Coyne
- IITA, Kasarani, P.O. Box 30772-00100, Nairobi, Kenya
| | - Wim Bert
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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15
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Cryptic diversity and ecosystem functioning: a complex tale of differential effects on decomposition. Oecologia 2016; 182:559-71. [DOI: 10.1007/s00442-016-3677-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 06/11/2016] [Indexed: 10/21/2022]
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16
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Derycke S, De Meester N, Rigaux A, Creer S, Bik H, Thomas WK, Moens T. Coexisting cryptic species of theLitoditis marinacomplex (Nematoda) show differential resource use and have distinct microbiomes with high intraspecific variability. Mol Ecol 2016; 25:2093-110. [DOI: 10.1111/mec.13597] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 01/22/2016] [Accepted: 02/12/2016] [Indexed: 11/30/2022]
Affiliation(s)
- S. Derycke
- OD Taxonomy and Phylogeny; Royal Belgian Institute of Natural Sciences; Vautierstraat 29 1000 Brussels Belgium
- Department of Biology; Marine Biology Section; Ghent University; Krijgslaan 281 (S8) 9000 Ghent Belgium
| | - N. De Meester
- Department of Biology; Marine Biology Section; Ghent University; Krijgslaan 281 (S8) 9000 Ghent Belgium
- CeMoFE; Ghent University; K.L. Ledeganckstraat 35 9000 Ghent Belgium
| | - A. Rigaux
- Department of Biology; Marine Biology Section; Ghent University; Krijgslaan 281 (S8) 9000 Ghent Belgium
- CeMoFE; Ghent University; K.L. Ledeganckstraat 35 9000 Ghent Belgium
| | - S. Creer
- Environment Centre Wales Building; School of Biological Sciences; Bangor University; Gwynedd LL57 2UW UK
| | - H. Bik
- Center for Genomics and Systems Biology; New York University; 12 Waverly Place New York NY 10003 USA
| | - W. K. Thomas
- Hubbard Center for Genome Studies; University of New Hampshire; 35 Colovos Road 448 Greg Hall Durham NH 03824 USA
| | - T. Moens
- Environment Centre Wales Building; School of Biological Sciences; Bangor University; Gwynedd LL57 2UW UK
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17
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Grosemans T, Morris K, Thomas WK, Rigaux A, Moens T, Derycke S. Mitogenomics reveals high synteny and long evolutionary histories of sympatric cryptic nematode species. Ecol Evol 2016; 6:1854-70. [PMID: 26933490 PMCID: PMC4760989 DOI: 10.1002/ece3.1975] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/18/2015] [Accepted: 01/03/2016] [Indexed: 11/09/2022] Open
Abstract
Species with seemingly identical morphology but with distinct genetic differences are abundant in the marine environment and frequently co-occur in the same habitat. Such cryptic species are typically delineated using a limited number of mitochondrial and/or nuclear marker genes, which do not yield information on gene order and gene content of the genomes under consideration. We used next-generation sequencing to study the composition of the mitochondrial genomes of four sympatrically distributed cryptic species of the Litoditis marina species complex (PmI, PmII, PmIII, and PmIV). The ecology, biology, and natural occurrence of these four species are well known, but the evolutionary processes behind this cryptic speciation remain largely unknown. The gene order of the mitochondrial genomes of the four species was conserved, but differences in genome length, gene length, and codon usage were observed. The atp8 gene was lacking in all four species. Phylogenetic analyses confirm that PmI and PmIV are sister species and that PmIII diverged earliest. The most recent common ancestor of the four cryptic species was estimated to have diverged 16 MYA. Synonymous mutations outnumbered nonsynonymous changes in all protein-encoding genes, with the Complex IV genes (coxI-III) experiencing the strongest purifying selection. Our mitogenomic results show that morphologically similar species can have long evolutionary histories and that PmIII has several differences in genetic makeup compared to the three other species, which may explain why it is better adapted to higher temperatures than the other species.
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Affiliation(s)
- Tara Grosemans
- Marine Biology Section Biology Department Faculty of Science University of Ghent Krijgslaan 281 (S8) 9000 Gent Belgium
| | - Krystalynne Morris
- Department of Biochemistry and Molecular Biology Hubbard Center for Genome Studies University of New Hampshire 35 Colovos Road Durham New Hampshire 03824
| | - William Kelley Thomas
- Department of Biochemistry and Molecular Biology Hubbard Center for Genome Studies University of New Hampshire 35 Colovos Road Durham New Hampshire 03824
| | - Annelien Rigaux
- Marine Biology Section Biology Department Faculty of Science University of Ghent Krijgslaan 281 (S8) 9000 Gent Belgium; CeMoFe University of Ghent Karel Lodewijk Ledeganckstraat 359000 Gent Belgium
| | - Tom Moens
- Marine Biology Section Biology Department Faculty of Science University of Ghent Krijgslaan 281 (S8) 9000 Gent Belgium
| | - Sofie Derycke
- Marine Biology Section Biology Department Faculty of Science University of Ghent Krijgslaan 281 (S8) 9000 Gent Belgium; Royal Belgian Institute of Natural Sciences (RBINS) OD Taxonomy and Phylogeny Vautierstraat 291000 Brussels Belgium
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18
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Miljutin DM, Miljutina MA. Intraspecific variability of morphological characters in the species-rich deep-sea genus Acantholaimus Allgén, 1933 (Nematoda: Chromadoridae). NEMATOLOGY 2016. [DOI: 10.1163/15685411-00002970] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Acantholaimusis a species-rich genus of deep-sea nematodes, often with dozens of species found at the same locality but each represented by single or few individuals. Species discrimination by morphological characters in this genus is therefore often difficult due to transitional forms that may be referred to several species because of lack of data on intraspecific variability. The aim of this study was to evaluate the intraspecific variability of morphological characters that are most often used inAcantholaimustaxonomy, in order to distinguish those which are most informative for species differentiation. A reverse taxonomic approach was applied for initial species discrimination. Two loci, one each from small and large subunits of rRNA, were sequenced for 59Acantholaimusspecimens from two deep-sea locations. Twenty-seven Molecular Operational Taxonomic Units (MOTU) were identified, of which 12 were represented by more than one individual. These were then analysed for intraspecific variability in morphological characters. Some of the examined characters showed high intraspecific variability; specifically: length of cephalic setae; distance from anterior end to amphid; shape of anterior setae; position and arrangement of cervical setae. In the absence of genetic data, these characters should be used with caution for differential diagnoses or species discrimination. Other characters were more conservative within the same MOTU: body proportions; length of outer labial setae; amphidial diam.; appearance of lateral field; general arrangement of cervical setae; and shape of tail. These characters may be successfully used for species discrimination in the absence of molecular data.
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Affiliation(s)
- Dmitry M. Miljutin
- Senckenberg Nature Research Society, Senckenberg am Meer, German Centre for Marine Biodiversity Research, Südstrand 44, 26382 Wilhelmshaven, Germany
| | - Maria A. Miljutina
- Senckenberg Nature Research Society, Senckenberg am Meer, German Centre for Marine Biodiversity Research, Südstrand 44, 26382 Wilhelmshaven, Germany
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19
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Dell’Anno A, Carugati L, Corinaldesi C, Riccioni G, Danovaro R. Unveiling the Biodiversity of Deep-Sea Nematodes through Metabarcoding: Are We Ready to Bypass the Classical Taxonomy? PLoS One 2015; 10:e0144928. [PMID: 26701112 PMCID: PMC4699195 DOI: 10.1371/journal.pone.0144928] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 11/25/2015] [Indexed: 11/18/2022] Open
Abstract
Nematodes inhabiting benthic deep-sea ecosystems account for >90% of the total metazoan abundances and they have been hypothesised to be hyper-diverse, but their biodiversity is still largely unknown. Metabarcoding could facilitate the census of biodiversity, especially for those tiny metazoans for which morphological identification is difficult. We compared, for the first time, different DNA extraction procedures based on the use of two commercial kits and a previously published laboratory protocol and tested their suitability for sequencing analyses of 18S rDNA of marine nematodes. We also investigated the reliability of Roche 454 sequencing analyses for assessing the biodiversity of deep-sea nematode assemblages previously morphologically identified. Finally, intra-genomic variation in 18S rRNA gene repeats was investigated by Illumina MiSeq in different deep-sea nematode morphospecies to assess the influence of polymorphisms on nematode biodiversity estimates. Our results indicate that the two commercial kits should be preferred for the molecular analysis of biodiversity of deep-sea nematodes since they consistently provide amplifiable DNA suitable for sequencing. We report that the morphological identification of deep-sea nematodes matches the results obtained by metabarcoding analysis only at the order-family level and that a large portion of Operational Clustered Taxonomic Units (OCTUs) was not assigned. We also show that independently from the cut-off criteria and bioinformatic pipelines used, the number of OCTUs largely exceeds the number of individuals and that 18S rRNA gene of different morpho-species of nematodes displayed intra-genomic polymorphisms. Our results indicate that metabarcoding is an important tool to explore the diversity of deep-sea nematodes, but still fails in identifying most of the species due to limited number of sequences deposited in the public databases, and in providing quantitative data on the species encountered. These aspects should be carefully taken into account before using metabarcoding in quantitative ecological research and monitoring programmes of marine biodiversity.
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Affiliation(s)
- Antonio Dell’Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Laura Carugati
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Cinzia Corinaldesi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Giulia Riccioni
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
- * E-mail:
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20
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Van Campenhout J, Vanreusel A, Van Belleghem S, Derycke S. Transcription, Signaling Receptor Activity, Oxidative Phosphorylation, and Fatty Acid Metabolism Mediate the Presence of Closely Related Species in Distinct Intertidal and Cold-Seep Habitats. Genome Biol Evol 2015; 8:51-69. [PMID: 26637468 PMCID: PMC4758239 DOI: 10.1093/gbe/evv242] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Bathyal cold seeps are isolated extreme deep-sea environments characterized by low species diversity while biomass can be high. The Håkon Mosby mud volcano (Barents Sea, 1,280 m) is a rather stable chemosynthetic driven habitat characterized by prominent surface bacterial mats with high sulfide concentrations and low oxygen levels. Here, the nematode Halomonhystera hermesi thrives in high abundances (11,000 individuals 10 cm−2). Halomonhystera hermesi is a member of the intertidal Halomonhystera disjuncta species complex that includes five cryptic species (GD1-5). GD1-5’s common habitat is characterized by strong environmental fluctuations. Here, we compared the transcriptomes of H. hermesi and GD1, H. hermesi’s closest relative. Genes encoding proteins involved in oxidative phosphorylation are more strongly expressed in H. hermesi than in GD1, and many genes were only observed in H. hermesi while being completely absent in GD1. Both observations could in part be attributed to high sulfide concentrations and low oxygen levels. Additionally, fatty acid elongation was also prominent in H. hermesi confirming the importance of highly unsaturated fatty acids in this species. Significant higher amounts of transcription factors and genes involved in signaling receptor activity were observed in GD1 (many of which were completely absent in H. hermesi), allowing fast signaling and transcriptional reprogramming which can mediate survival in dynamic intertidal environments. GC content was approximately 8% higher in H. hermesi coding unigenes resulting in differential codon usage between both species and a higher proportion of amino acids with GC-rich codons in H. hermesi. In general our results showed that most pathways were active in both environments and that only three genes are under natural selection. This indicates that also plasticity should be taken in consideration in the evolutionary history of Halomonhystera species. Such plasticity, as well as possible preadaptation to low oxygen and high sulfide levels might have played an important role in the establishment of a cold-seep Halomonhystera population.
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Affiliation(s)
- Jelle Van Campenhout
- Research Group Marine Biology, Biology Department, Ghent University, Belgium Department of Biology, Center for Molecular Phylogenetics and Evolution (CeMoFe), Ghent University, Biology Department, Belgium
| | - Ann Vanreusel
- Research Group Marine Biology, Biology Department, Ghent University, Belgium
| | - Steven Van Belleghem
- Terrestrial Ecology Unit, Biology Department, Ghent University, Belgium OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Sofie Derycke
- Research Group Marine Biology, Biology Department, Ghent University, Belgium OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
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21
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Daily Temperature Fluctuations Alter Interactions between Closely Related Species of Marine Nematodes. PLoS One 2015; 10:e0131625. [PMID: 26147103 PMCID: PMC4492701 DOI: 10.1371/journal.pone.0131625] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 06/05/2015] [Indexed: 01/15/2023] Open
Abstract
In addition to an increase in mean temperature, climate change models predict decreasing amplitudes of daily temperature fluctuations. In temperate regions, where daily and seasonal fluctuations are prominent, such decreases in daily temperature fluctuations can have a pronounced effect on the fitness of species and on the outcome of species interactions. In this study, the effect of a temperature regime with daily fluctuations versus a constant temperature on the fitness and interspecific interactions of three cryptic species of the marine nematode species complex of Litoditis marina (Pm I, Pm III and Pm IV) were investigated. In a lab experiment, different combinations of species (monospecific treatment: Pm I and Pm IV and Pm III alone; two-species treatment: Pm I + Pm IV; three-species treatment: Pm I + Pm IV + Pm III) were subjected to two different temperature regimes: one constant and one fluctuating temperature. Our results showed that fluctuating temperature had minor or no effects on the population fitness of the three species in monocultures. In contrast, interspecific interactions clearly influenced the fitness of all three species, both positively and negatively. Temperature regime did have a substantial effect on the interactions between the species. In the two-species treatment, temperature regime altered the interaction from a sort of mutualism to commensalism. In addition, the strength of the interspecific interactions changed depending on the temperature regime in the three-species treatment. This experiment confirms that interactions between the species can change depending on the abiotic environment; these results show that it is important to incorporate the effect of fluctuations on interspecific interactions to predict the effect of climate change on biodiversity.
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22
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Carugati L, Corinaldesi C, Dell'Anno A, Danovaro R. Metagenetic tools for the census of marine meiofaunal biodiversity: An overview. Mar Genomics 2015; 24 Pt 1:11-20. [PMID: 25957694 DOI: 10.1016/j.margen.2015.04.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 04/27/2015] [Accepted: 04/27/2015] [Indexed: 01/30/2023]
Abstract
Marine organisms belonging to meiofauna (size range: 20-500 μm) are amongst the most abundant and highly diversified metazoans on Earth including 22 over 35 known animal Phyla and accounting for more than 2/3 of the abundance of metazoan organisms. In any marine system, meiofauna play a key role in the functioning of the food webs and sustain important ecological processes. Estimates of meiofaunal biodiversity have been so far almost exclusively based on morphological analyses, but the very small size of these organisms and, in some cases, the insufficient morphological distinctive features limit considerably the census of the biodiversity of this component. Molecular approaches recently applied also to small invertebrates (including meiofauna) can offer a new momentum for the census of meiofaunal biodiversity. Here, we provide an overview on the application of metagenetic approaches based on the use of next generation sequencing platforms to study meiofaunal biodiversity, with a special focus on marine nematodes. Our overview shows that, although such approaches can represent a useful tool for the census of meiofaunal biodiversity, there are still different shortcomings and pitfalls that prevent their extensive use without the support of the classical taxonomic identification. Future investigations are needed to address these problems and to provide a good match between the contrasting findings emerging from classical taxonomic and molecular/bioinformatic tools.
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Affiliation(s)
- Laura Carugati
- Department of Life and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Cinzia Corinaldesi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Antonio Dell'Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, 60131 Ancona, Italy; Stazione Zoologica Anton Dohrn, Naples, Italy
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23
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De Meester N, Derycke S, Rigaux A, Moens T. Active dispersal is differentially affected by inter- and intraspecific competition in closely related nematode species. OIKOS 2014. [DOI: 10.1111/oik.01779] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nele De Meester
- Dept of Biology; Ghent Univ.; Krijgslaan 281/S8 BE-9000 Ghent Belgium
- Center for Molecular Phylogeny and Evolution, Ghent Univ.; Krijgslaan 281/S8 BE-9000 Ghent Belgium
| | - Sofie Derycke
- Dept of Biology; Ghent Univ.; Krijgslaan 281/S8 BE-9000 Ghent Belgium
- Center for Molecular Phylogeny and Evolution, Ghent Univ.; Krijgslaan 281/S8 BE-9000 Ghent Belgium
| | - Annelien Rigaux
- Dept of Biology; Ghent Univ.; Krijgslaan 281/S8 BE-9000 Ghent Belgium
- Center for Molecular Phylogeny and Evolution, Ghent Univ.; Krijgslaan 281/S8 BE-9000 Ghent Belgium
| | - Tom Moens
- Dept of Biology; Ghent Univ.; Krijgslaan 281/S8 BE-9000 Ghent Belgium
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24
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Differences in life-histories refute ecological equivalence of cryptic species and provide clues to the origin of bathyal Halomonhystera (Nematoda). PLoS One 2014; 9:e111889. [PMID: 25384013 PMCID: PMC4226489 DOI: 10.1371/journal.pone.0111889] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 10/01/2014] [Indexed: 11/19/2022] Open
Abstract
The discovery of morphologically very similar but genetically distinct species complicates a proper understanding of the link between biodiversity and ecosystem functioning. Cryptic species have been frequently observed to co-occur and are thus expected to be ecological equivalent. The marine nematode Halomonhystera disjuncta contains five cryptic species (GD1-5) that co-occur in the Westerschelde estuary. In this study, we investigated the effect of three abiotic factors (salinity, temperature and sulphide) on life-history traits of three cryptic H. disjuncta species (GD1-3). Our results show that temperature had the most profound influence on all life-cycle parameters compared to a smaller effect of salinity. Life-history traits of closely related cryptic species were differentially affected by temperature, salinity and presence of sulphides which shows that cryptic H. disjuncta species are not ecologically equivalent. Our results further revealed that GD1 had the highest tolerance to a combination of sulphides, high salinities and low temperatures. The close phylogenetic position of GD1 to Halomonhystera hermesi, the dominant species in sulphidic sediments of the Håkon Mosby mud volcano (Barent Sea, 1280 m depth), indicates that both species share a recent common ancestor. Differential life-history responses to environmental changes among cryptic species may have crucial consequences for our perception on ecosystem functioning and coexistence of cryptic species.
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25
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Pante E, Schoelinck C, Puillandre N. From Integrative Taxonomy to Species Description: One Step Beyond. Syst Biol 2014; 64:152-60. [DOI: 10.1093/sysbio/syu083] [Citation(s) in RCA: 180] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- E. Pante
- Littoral, Environnement et Sociétés (LIENSs) UMR 7266 CNRS, Université de La Rochelle, La Rochelle, France; 2Fisheries and Oceans Canada, Aquatic animal health, 343, University Avenue E1C 9B6 Moncton N.B., Canada; and 3Muséum National d'Histoire Naturelle, Département Systématique et Evolution, ISyEB (UMR 7205 CNRS/UPMC/MNHN/EPHE), 43, Rue Cuvier, 75231 Paris, France
| | - C. Schoelinck
- Littoral, Environnement et Sociétés (LIENSs) UMR 7266 CNRS, Université de La Rochelle, La Rochelle, France; 2Fisheries and Oceans Canada, Aquatic animal health, 343, University Avenue E1C 9B6 Moncton N.B., Canada; and 3Muséum National d'Histoire Naturelle, Département Systématique et Evolution, ISyEB (UMR 7205 CNRS/UPMC/MNHN/EPHE), 43, Rue Cuvier, 75231 Paris, France
| | - N. Puillandre
- Littoral, Environnement et Sociétés (LIENSs) UMR 7266 CNRS, Université de La Rochelle, La Rochelle, France; 2Fisheries and Oceans Canada, Aquatic animal health, 343, University Avenue E1C 9B6 Moncton N.B., Canada; and 3Muséum National d'Histoire Naturelle, Département Systématique et Evolution, ISyEB (UMR 7205 CNRS/UPMC/MNHN/EPHE), 43, Rue Cuvier, 75231 Paris, France
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26
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A good compromise: rapid and robust species proxies for inventorying biodiversity hotspots using the Terebridae (Gastropoda: Conoidea). PLoS One 2014; 9:e102160. [PMID: 25003611 PMCID: PMC4086986 DOI: 10.1371/journal.pone.0102160] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 06/11/2014] [Indexed: 11/19/2022] Open
Abstract
Devising a reproducible approach for species delimitation of hyperdiverse groups is an ongoing challenge in evolutionary biology. Speciation processes combine modes of passive and adaptive trait divergence requiring an integrative taxonomy approach to accurately generate robust species hypotheses. However, in light of the rapid decline of diversity on Earth, complete integrative approaches may not be practical in certain species-rich environments. As an alternative, we applied a two-step strategy combining ABGD (Automated Barcode Gap Discovery) and Klee diagrams, to balance speed and accuracy in producing primary species hypotheses (PSHs). Specifically, an ABGD/Klee approach was used for species delimitation in the Terebridae, a neurotoxin-producing marine snail family included in the Conoidea. Delimitation of species boundaries is problematic in the Conoidea, as traditional taxonomic approaches are hampered by the high levels of variation, convergence and morphological plasticity of shell characters. We used ABGD to analyze gaps in the distribution of pairwise distances of 454 COI sequences attributed to 87 morphospecies and obtained 98 to 125 Primary Species Hypotheses (PSHs). The PSH partitions were subsequently visualized as a Klee diagram color map, allowing easy detection of the incongruences that were further evaluated individually with two other species delimitation models, General Mixed Yule Coalescent (GMYC) and Poisson Tree Processes (PTP). GMYC and PTP results confirmed the presence of 17 putative cryptic terebrid species in our dataset. The consensus of GMYC, PTP, and ABGD/Klee findings suggest the combination of ABGD and Klee diagrams is an effective approach for rapidly proposing primary species proxies in hyperdiverse groups and a reliable first step for macroscopic biodiversity assessment.
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27
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Armenteros M, Ruiz-Abierno A, Decraemer W. Taxonomy of Stilbonematinae (Nematoda: Desmodoridae): description of two new and three known species and phylogenetic relationships within the family. Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12126] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maickel Armenteros
- Centro de Investigaciones Marinas; Universidad de La Habana; 16 # 114, Playa CP 11300 Habana Cuba
| | - Alexei Ruiz-Abierno
- Centro de Investigaciones Marinas; Universidad de La Habana; 16 # 114, Playa CP 11300 Habana Cuba
| | - Wilfrida Decraemer
- Royal Belgian Institute of Natural Sciences; Rue Vautier # 29 B-1000 Brussels Belgium
- Biology Department; Ghent University; Ledeganckstraat # 35 B-9000 Ghent Belgium
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28
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Félix MA, Braendle C, Cutter AD. A streamlined system for species diagnosis in Caenorhabditis (Nematoda: Rhabditidae) with name designations for 15 distinct biological species. PLoS One 2014; 9:e94723. [PMID: 24727800 PMCID: PMC3984244 DOI: 10.1371/journal.pone.0094723] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 03/14/2014] [Indexed: 12/18/2022] Open
Abstract
The rapid pace of species discovery outstrips the rate of species description in many taxa. This problem is especially acute for Caenorhabditis nematodes, where the naming of distinct species would greatly improve their visibility and usage for biological research, given the thousands of scientists studying Caenorhabditis. Species description and naming has been hampered in Caenorhabditis, in part due to the presence of morphologically cryptic species despite complete biological reproductive isolation and often enormous molecular divergence. With the aim of expediting species designations, here we propose and apply a revised framework for species diagnosis and description in this group. Our solution prioritizes reproductive isolation over traditional morphological characters as the key feature in delineating and diagnosing new species, reflecting both practical considerations and conceptual justifications. DNA sequence divergence criteria help prioritize crosses for establishing patterns of reproductive isolation among the many species of Caenorhabditis known to science, such as with the ribosomal internal transcribed spacer-2 (ITS2) DNA barcode. By adopting this approach, we provide new species name designations for 15 distinct biological species, thus increasing the number of named Caenorhabditis species in laboratory culture by nearly 3-fold. We anticipate that the improved accessibility of these species to the research community will expand the opportunities for study and accelerate our understanding of diverse biological phenomena.
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Affiliation(s)
- Marie-Anne Félix
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), Paris, France
- CNRS UMR 8197, Paris, France
- Inserm U1024, Paris, France
| | - Christian Braendle
- Institut de Biologie Valrose, CNRS UMR7277, Parc Valrose, Nice, France
- INSERM U1091, Nice, France
- Université Nice Sophia Antipolis, UFR Sciences, Nice, France
| | - Asher D. Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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29
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Morgan MJ, Bass D, Bik H, Birky CW, Blaxter M, Crisp MD, Derycke S, Fitch D, Fontaneto D, Hardy CM, King AJ, Kiontke KC, Moens T, Pawlowski JW, Porazinska D, Tang CQ, Thomas WK, Yeates DK, Creer S. A critique of Rossberg et al.: Noise obscures the genetic signal of meiobiotal ecospecies in ecogenomic datasets. Proc Biol Sci 2014; 281:20133076. [PMID: 24671969 DOI: 10.1098/rspb.2013.3076] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- M J Morgan
- CSIRO Ecosystem Sciences, , Canberra, Australian Capital Territory, Australia, Department of Life Sciences, Natural History Museum, , Cromwell Road, London SW7 5BD, UK, UC Davis Genome Center, , Davis, CA 95616, USA, Department of Ecology and Evolutionary Biology, University of Arizona, , Tucson, AZ 85721, USA, Institute of Evolutionary Biology, University of Edinburgh, , Edinburgh EH9 3JT, UK, Research School of Biology, Australian National University, , Canberra, Australian Capital Territory 0200, Australia, Department of Biology, Ghent University, , Marine Biology Lab, Ghent 9000, Belgium, Department of Biology, New York University, , New York, NY 10003, USA, National Research Council, Institute of Ecosystem Study, , Largo Tonolli 50, 28922 Verbania Pallanza, Italy, Department of Genetics and Evolution, University of Geneva, , Sciences III, 30, Quai Ernest Ansermet, Geneva 1211, Switzerland, Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, , Boulder, CO 80309, USA, Department of Life Sciences, Imperial College London, , Ascot, Berkshire SL5 7PY, UK, Hubbard Center for Genome Studies, University of New Hampshire, , 35 Colovos Road, Durham, NH 03824, USA, School of Biological Sciences, Bangor University, , Environment Centre Wales Building, Deiniol Road, College of Natural Sciences, Gwynedd LL57 2UW, UK
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30
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Rossberg AG, Rogers T, McKane AJ. Current noise-removal methods can create false signals in ecogenomic data. Proc Biol Sci 2014; 281:20140191. [PMID: 24671979 DOI: 10.1098/rspb.2014.0191] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Axel G Rossberg
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), , Pakefield Road, Lowestoft NR33 0HT, UK, Department of Mathematical Sciences, University of Bath, , Claverton Down, Bath BA2 7AY, UK, Theoretical Physics Division, School of Physics and Astronomy, University of Manchester, , Manchester M13 9PL, UK
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Morphological and molecular characterization of Mermis nigrescens Dujardin, (Nematoda: Mermithidae) parasitizing the introduced European earwig (Dermaptera: Forficulidae) in New Zealand. J Helminthol 2014; 89:267-76. [PMID: 24503193 DOI: 10.1017/s0022149x14000017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Parasitic nematodes of the family Mermithidae were found to be infecting the introduced European earwig Forficula auricularia (Dermaptera: Forficulidae) in Dunedin, South Island, New Zealand. Adult females were later collected from various garden plants while depositing eggs. These mermithid specimens were identified morphologically as Mermis nigrescens Dujardin, 1842. A genetic distance of 0.7% between these specimens and a M. nigrescens isolate from Canada (18S rRNA gene), suggests that they have diverged genetically, but there are currently no available comparable sequences for the European M. nigrescens. Two additional nuclear fragments were also amplified, the 28S rRNA and the ribosomal DNA first internal transcribed spacer (ITS1), providing a basis for future studies. Bearing in mind the morphological similarity with other reported M. nigrescens and the lack of sequence data from other parts of the world, we retain the name M. nigrescens, and suggest that the species may be found to represent a complex of cryptic species when more worldwide data are available. Herein, we present a brief description of the post-parasitic worms and adult females, along with an inferred phylogeny using 18S rRNA gene sequences.
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Leduc D. Free-living nematodes of the genusHalomonhystera(Monhysteridae) from the Southwest Pacific region and Ross Sea. NEW ZEALAND JOURNAL OF ZOOLOGY 2014. [DOI: 10.1080/03014223.2013.827581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Jelle VC, Sofie D, Alexei T, Daria P, Ann V. The Halomonhystera disjuncta
population is homogeneous across the Håkon Mosby mud volcano (Barents Sea) but is genetically differentiated from its shallow-water relatives. J ZOOL SYST EVOL RES 2013. [DOI: 10.1111/jzs.12054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Van Campenhout Jelle
- Research Group Marine Biology; Biology Department; Ghent University; Ghent Belgium
- Center for Molecular Phylogenetics and Evolution (CeMoFe); Ghent University; Ghent Belgium
| | - Derycke Sofie
- Research Group Marine Biology; Biology Department; Ghent University; Ghent Belgium
- Center for Molecular Phylogenetics and Evolution (CeMoFe); Ghent University; Ghent Belgium
| | - Tchesunov Alexei
- Department of Invertebrate Zoology; Faculty of Biology; Lomonosov's Moscow State University; Moscow Russia
| | - Portnova Daria
- P.P. Shirshov Institute of Oceanology; Russian Academy of Sciences; Moscow Russia
| | - Vanreusel Ann
- Research Group Marine Biology; Biology Department; Ghent University; Ghent Belgium
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Ristau K, Steinfartz S, Traunspurger W. First evidence of cryptic species diversity and significant population structure in a widespread freshwater nematode morphospecies (Tobrilus gracilis). Mol Ecol 2013; 22:4562-75. [PMID: 23927432 DOI: 10.1111/mec.12414] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 05/08/2013] [Accepted: 05/09/2013] [Indexed: 11/30/2022]
Abstract
Free-living nematodes are ubiquitous and highly abundant in terrestrial and aquatic environments, where they sustain ecosystem functioning by mineralization processes and nutrient cycling. Nevertheless, very little is known about their true diversity and intraspecific population structure. Recent molecular studies on marine nematodes indicated cryptic diversity and strong genetic differentiation of distinct populations, but for freshwater nematode species, analogous studies are lacking. Here, we present the first extensive molecular study exploring cryptic species diversity and genetic population structure of a widespread freshwater nematode morphospecies, Tobrilus gracilis, from nine postglacially formed European lakes. Taxonomic species status of individuals, analysed for fragments of the mitochondrial COI gene and for the large (LSU) and small (SSU) ribosomal subunits, were determined by morphological characteristics. Mitochondrial and nuclear markers strongly supported the existence of three distinct genetic lineages (Tg I-III) within Tobrilus gracilis, suggesting that this morphospecies indeed represents a complex of highly differentiated biological species. High genetic diversity was also observed at the population level. Across the nine lakes, 19 mitochondrial, and seven (LSU) and four (SSU) nuclear haplotypes were determined. A phylogeographical analysis revealed remarkable genetic differentiation even among neighbouring lake populations for one cryptic lineage. Priority and persistent founder effects are possible explanations for the observed population structure in the postglacially colonized lakes, but ask for future studies providing direct estimates of freshwater nematode dispersal rates. Our study suggests therefore that overall diversity of limnetic nematodes has been so far drastically underestimated and challenges the assumed ubiquitous distribution of other, single freshwater nematode morphospecies.
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Affiliation(s)
- Kai Ristau
- Department for Animal Ecology, Bielefeld University, Morgenbreede 45, 33615, Bielefeld, Germany.
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Jorge F, Perera A, Carretero MA, James Harris D, Roca V. Cryptic species unveiled: the case of the nematode Spauligodon atlanticus. J ZOOL SYST EVOL RES 2013. [DOI: 10.1111/jzs.12019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fátima Jorge
- CIBIO-UP; Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências da; Universidade do Porto; Porto Portugal
| | - Ana Perera
- CIBIO-UP; Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Vairão Portugal
| | - Miguel A. Carretero
- CIBIO-UP; Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Vairão Portugal
| | - D. James Harris
- CIBIO-UP; Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Vairão Portugal
| | - Vicente Roca
- Departament de Zoologia; Facultat de Ciències Biològiques; Universitat de València; València Spain
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Derycke S, Backeljau T, Moens T. Dispersal and gene flow in free-living marine nematodes. Front Zool 2013; 10:1. [PMID: 23356547 PMCID: PMC3567977 DOI: 10.1186/1742-9994-10-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 01/21/2013] [Indexed: 11/10/2022] Open
Abstract
Dispersal and gene flow determine connectivity among populations, and can be studied through population genetics and phylogeography. We here review the results of such a framework for free-living marine nematodes. Although field experiments have illustrated substantial dispersal in nematodes at ecological time scales, analysis of the genetic diversity illustrated the importance of priority effects, founder effects and genetic bottlenecks for population structuring between patches <1 km apart. In contrast, only little genetic structuring was observed within an estuary (<50 km), indicating that these small scale fluctuations in genetic differentiation are stabilized over deeper time scales through extensive gene flow. Interestingly, nematode species with contrasting life histories (extreme colonizers vs persisters) or with different habitat preferences (algae vs sediment) show similar, low genetic structuring. Finally, historical events have shaped the genetic pattern of marine nematodes and show that gene flow is restricted at large geographical scales. We also discuss the presence of substantial cryptic diversity in marine nematodes, and end with highlighting future important steps to further unravel nematode evolution and diversity.
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Affiliation(s)
- Sofie Derycke
- Department of Biology, Marine Biology section, Ghent University, Krijgslaan 281, S8, 9000, Ghent, Belgium.
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The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna. Proc Natl Acad Sci U S A 2012; 109:16208-12. [PMID: 22988084 DOI: 10.1073/pnas.1209160109] [Citation(s) in RCA: 180] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molecular tools have revolutionized the exploration of biodiversity, especially in organisms for which traditional taxonomy is difficult, such as for microscopic animals (meiofauna). Environmental (eDNA) metabarcode surveys of DNA extracted from sediment samples are increasingly popular for surveying biodiversity. Most eDNA surveys use the nuclear gene-encoding small-subunit rDNA gene (18S) as a marker; however, different markers and metrics used for delimiting species have not yet been evaluated against each other or against morphologically defined species (morphospecies). We assessed more than 12,000 meiofaunal sequences of 18S and of the main alternatively used marker [Cytochrome c oxidase subunit I (COI) mtDNA] belonging to 55 datasets covering three taxonomic ranks. Our results show that 18S reduced diversity estimates by a factor of 0.4 relative to morphospecies, whereas COI increased diversity estimates by a factor of 7.6. Moreover, estimates of species richness using COI were robust among three of four commonly used delimitation metrics, whereas estimates using 18S varied widely with the different metrics. We show that meiofaunal diversity has been greatly underestimated by 18S eDNA surveys and that the use of COI provides a better estimate of diversity. The suitability of COI is supported by cross-mating experiments in the literature and evolutionary analyses of discreteness in patterns of genetic variation. Furthermore its splitting of morphospecies is expected from documented levels of cryptic taxa in exemplar meiofauna. We recommend against using 18S as a marker for biodiversity surveys and suggest that use of COI for eDNA surveys could provide more accurate estimates of species richness in the future.
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Derycke S, Sheibani Tezerji R, Rigaux A, Moens T. Investigating the ecology and evolution of cryptic marine nematode species through quantitative real-time PCR of the ribosomal ITS region. Mol Ecol Resour 2012; 12:607-19. [PMID: 22385909 DOI: 10.1111/j.1755-0998.2012.03128.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The presence of morphologically similar but genetically distinct species has impacted biogeographical and ecological paradigms. In marine sediments, free-living nematodes form one of the most abundant and diverse faunal groups. Inferring the importance of nematode diversity for ecosystem functioning requires species-level identification, which is hampered by the lack of easily observable diagnostic characters and the presence of cryptic species. New techniques are urgently needed to adequately study the ecology and evolution of cryptic species. The aim of the present study was to evaluate the potential of a quantitative real-time PCR (qPCR) assay using the internal transcribed spacer (ITS) region of the ribosomal DNA to detect and quantify cryptic species of the R. (P.) marina complex. All primer pairs proved to be highly specific, and each primer pair was able to detect a single juvenile in a pool of 100 nematodes. C(t) values were significantly different between developmental stages for all species except for PmIII. Despite differences between developmental stages, a strong correlation was observed between the amount of extracted DNA and the number of nematodes present. Relative and absolute quantification estimates were comparable and resulted in strong positive correlations between the qPCR estimate and the actual number of nematodes present in the samples. The qPCR assay developed here provides the ability to quickly identify and quantify cryptic nematode species and will facilitate their study in laboratory and field settings.
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Affiliation(s)
- S Derycke
- Department of Biology, Marine Biology section, Ghent University, Krijgslaan 281, S8, 9000 Ghent, Belgium.
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APOLÔNIO SILVA DE OLIVEIRA DANIEL, DECRAEMER WILFRIDA, HOLOVACHOV OLEKSANDER, BURR JAY, TANDINGAN DE LEY IRMA, DE LEY PAUL, MOENS TOM, DERYCKE SOFIE. An integrative approach to characterize cryptic species in the Thoracostoma trachygaster Hope, 1967 complex (Nematoda: Leptosomatidae). Zool J Linn Soc 2012. [DOI: 10.1111/j.1096-3642.2011.00758.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ndiaye A, Bâ K, Aniskin V, Benazzou T, Chevret P, Konečný A, Sembène M, Tatard C, Kergoat GJ, Granjon L. Evolutionary systematics and biogeography of endemic gerbils (Rodentia, Muridae) from Morocco: an integrative approach. ZOOL SCR 2011. [DOI: 10.1111/j.1463-6409.2011.00501.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Reveillaud J, van Soest R, Derycke S, Picton B, Rigaux A, Vanreusel A. Phylogenetic relationships among NE Atlantic Plocamionida Topsent (1927) (Porifera, Poecilosclerida): under-estimated diversity in reef ecosystems. PLoS One 2011; 6:e16533. [PMID: 21347368 PMCID: PMC3036665 DOI: 10.1371/journal.pone.0016533] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Accepted: 12/20/2010] [Indexed: 11/23/2022] Open
Abstract
Background Small and cryptic sponges associated with cold-water coral reefs are particularly numerous and challenging to identify, but their ecological and biochemical importance is likely to compete with megabenthic specimens. Methodology/Principal Findings Here we use a combination of the standard M1M6 and I3M11 partitions of the COI fragment, partial rDNA 28S sequences and morphology to delineate small encrusting Plocamionida species. In total, 46 specimens were retrieved from seven shallow to deep-water coral locations, crossing 3,000 km along the European margins. Our work provides evidence that the Plocamionida ambigua f. tylotata and f. grandichelata can be considered valid species, whereas Plocamionida ambigua f. tornata corresponds to the species P. ambigua. Within the monophyletic group of Plocamionida, P. microcionides is shown as really divergent from the other taxa, and four putative new Plocamionida species are suggested. Conclusions/Significance This study shows that the use of molecular and morphological information in an integrative approach is a powerful tool for the identification of sponge species, and suggests that an under-estimated biodiversity of sponges occurs in cold-water coral reefs.
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Affiliation(s)
- Julie Reveillaud
- Marine Biology Section, Biology Department, Ghent University, Ghent, Belgium.
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Vanreusel A, De Groote A, Gollner S, Bright M. Ecology and biogeography of free-living nematodes associated with chemosynthetic environments in the deep sea: a review. PLoS One 2010; 5:e12449. [PMID: 20805986 PMCID: PMC2929199 DOI: 10.1371/journal.pone.0012449] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 07/28/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Here, insight is provided into the present knowledge on free-living nematodes associated with chemosynthetic environments in the deep sea. It was investigated if the same trends of high standing stock, low diversity, and the dominance of a specialized fauna, as observed for macro-invertebrates, are also present in the nematodes in both vents and seeps. METHODOLOGY This review is based on existing literature, in combination with integrated analysis of datasets, obtained through the Census of Marine Life program on Biogeography of Deep-Water Chemosynthetic Ecosystems (ChEss). FINDINGS Nematodes are often thriving in the sulphidic sediments of deep cold seeps, with standing stock values ocassionaly exceeding largely the numbers at background sites. Vents seem not characterized by elevated densities. Both chemosynthetic driven ecosystems are showing low nematode diversity, and high dominance of single species. Genera richness seems inversely correlated to vent and seep fluid emissions, associated with distinct habitat types. Deep-sea cold seeps and hydrothermal vents are, however, highly dissimilar in terms of community composition and dominant taxa. There is no unique affinity of particular nematode taxa with seeps or vents. CONCLUSIONS It seems that shallow water relatives, rather than typical deep-sea taxa, have successfully colonized the reduced sediments of seeps at large water depth. For vents, the taxonomic similarity with adjacent regular sediments is much higher, supporting rather the importance of local adaptation, than that of long distance distribution. Likely the ephemeral nature of vents, its long distance offshore and the absence of pelagic transport mechanisms, have prevented so far the establishment of a successful and typical vent nematode fauna. Some future perspectives in meiofauna research are provided in order to get a more integrated picture of vent and seep biological processes, including all components of the marine ecosystem.
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Affiliation(s)
- Ann Vanreusel
- Marine Biology Research Group, Ghent University, Ghent, Belgium.
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Derycke S, De Ley P, Tandingan De Ley I, Holovachov O, Rigaux A, Moens T. Linking DNA sequences to morphology: cryptic diversity and population genetic structure in the marine nematodeThoracostoma trachygaster(Nematoda, Leptosomatidae). ZOOL SCR 2010. [DOI: 10.1111/j.1463-6409.2009.00420.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Pereira TJ, Fonseca G, Mundo-Ocampo M, Guilherme BC, Rocha-Olivares A. Diversity of free-living marine nematodes (Enoplida) from Baja California assessed by integrative taxonomy. MARINE BIOLOGY 2010; 157:1665-1678. [PMID: 24391248 PMCID: PMC3873033 DOI: 10.1007/s00227-010-1439-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2009] [Accepted: 03/30/2010] [Indexed: 05/29/2023]
Abstract
We used morphological and molecular approaches to evaluate the diversity of free-living marine nematodes (order Enoplida) at four coastal sites in the Gulf of California and three on the Pacific coast of Baja California, Mexico. We identified 22 morphological species belonging to six families, of which Thoracostomopsidae and Oncholaimidae were the most diverse. The genus Mesacanthion (Thoracostomopsidae) was the most widespread and diverse. Five allopatric species, genetically and morphologically differentiated, were found in two localities in the Gulf of California (M. sp1 and M. sp2) and three in the Pacific coast (M. sp3, M. sp4 and M. sp5). Overall, we produced 19 and 20 sequences for the 18S and 28S genes, respectively. Neither gene displayed intraspecific polymorphisms, which allowed us to establish that some morphological variation was likely either ontogenetic or due to phenotypic plasticity. Although 18S and 28S phylogenies were topologically congruent (incongruence length difference test, P > 0.05), divergences between species were much higher in the 28S gene. Moreover, this gene possessed a stronger phylogenetic signal to resolve relationships involving Rhabdodemania and Bathylaimus. On the other hand, the close relationship of Pareurystomina (Enchilidiidae) with oncholaimids warrants further study. The 28S sequences (D2D3 domain) may be better suited for DNA barcoding of marine nematodes than those from the 18S rDNA, particularly for differentiating closely related or cryptic species. Finally, our results underline the relevance of adopting an integrative approach encompassing morphological and molecular analyses to improve the assessment of marine nematode diversity and advance their taxonomy.
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Affiliation(s)
- Tiago José Pereira
- />Department of Biological Oceanography, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana 3918, Apdo. Postal 2732, CP 22860 Ensenada, Baja California Mexico
- />Department of Nematology, University of California, Riverside, CA 92521 USA
| | - Gustavo Fonseca
- />Centro de Biologia Marinha da Universidade de São Paulo, Rod. Manoel Hipolito do Rego km 131.5, São Sebastião, 11600-000 Brazil
| | - Manuel Mundo-Ocampo
- />Department of Nematology, University of California, Riverside, CA 92521 USA
| | - Betânia Cristina Guilherme
- />Centro de Educação e Saúde, CES, Universidade Federal de Campina Grande, Av. Olho D’Água da Bica s/n, Cuité, PB Brazil
| | - Axayácatl Rocha-Olivares
- />Department of Biological Oceanography, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana 3918, Apdo. Postal 2732, CP 22860 Ensenada, Baja California Mexico
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