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Bolshakov V, Prokin A, Ivanova E, Movergoz E. The first record of Chironomusnuditarsis Keyl, 1961 from Sevan Lake (Armenia) confirmed by morphology, karyotype and COI gene sequence. COMPARATIVE CYTOGENETICS 2024; 18:123-141. [PMID: 39045233 PMCID: PMC11263815 DOI: 10.3897/compcytogen.18.126130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 06/27/2024] [Indexed: 07/25/2024]
Abstract
Chironomusnuditarsis Keyl, 1961 is recorded from Sevan Lake for the first time. This species is widespread in Europe, the Caucasus, and Siberia. For species identification, we used a comprehensive approach that included morphological, cytogenetic and molecular genetic analyses. Morphological analysis showed a high similarity with the description. Nine chromosome banding sequences ndtA1, ndtA2, ndtB2, ndtC1, ndtD1, ndtE1, ndtF1, ndtG1, and ndtG2 were found. The banding sequences ndtA1, ndtA2, ndtG1, and ndtG2 are species-specific for C.nuditarsis and allow us to accurately distinguish it from the sibling species Ch.curabilis Belyanina, Sigareva et Loginova, 1990. Molecular-genetic analysis of the COI gene sequences has shown low genetic distances of 0.38-0.95% in the sibling species Ch.nuditarsis and Ch.curabilis complex and the insufficiency of using a single COI as a molecular marker for their separation.
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Affiliation(s)
- Viktor Bolshakov
- Papanin Institute for Biology of Inland Waters Russian Academy of Sciences, Yaroslavl reg., Nekouz dist., Borok, 152742, RussiaRussian Academy of SciencesBorokRussia
| | - Alexander Prokin
- Papanin Institute for Biology of Inland Waters Russian Academy of Sciences, Yaroslavl reg., Nekouz dist., Borok, 152742, RussiaRussian Academy of SciencesBorokRussia
| | - Elena Ivanova
- Cherepovets State University, Lunacharski 5, Cherepovets 162600, RussiaCherepovets State UniversityCherepovetsRussia
| | - Ekaterina Movergoz
- Papanin Institute for Biology of Inland Waters Russian Academy of Sciences, Yaroslavl reg., Nekouz dist., Borok, 152742, RussiaRussian Academy of SciencesBorokRussia
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Chimeno C, Rulik B, Manfrin A, Kalinkat G, Hölker F, Baranov V. Facing the infinity: tackling large samples of challenging Chironomidae (Diptera) with an integrative approach. PeerJ 2023; 11:e15336. [PMID: 37250705 PMCID: PMC10211366 DOI: 10.7717/peerj.15336] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/11/2023] [Indexed: 05/31/2023] Open
Abstract
Background Integrative taxonomy is becoming ever more significant in biodiversity research as scientists are tackling increasingly taxonomically challenging groups. Implementing a combined approach not only guarantees more accurate species identification, but also helps overcome limitations that each method presents when applied on its own. In this study, we present one application of integrative taxonomy for the highly abundant and particularly diverse fly taxon Chironomidae (Diptera). Although non-biting midges are key organisms in merolimnic systems, they are often cast aside in ecological surveys because they are very challenging to identify and extremely abundant. Methods Here, we demonstrate one way of applying integrative methods to tackle this highly diverse taxon. We present a three-level subsampling method to drastically reduce the workload of bulk sample processing, then apply morphological and molecular identification methods in parallel to evaluate species diversity and to examine inconsistencies across methods. Results Our results suggest that using our subsampling approach, identifying less than 10% of a sample's contents can reliably detect >90% of its diversity. However, despite reducing the processing workload drastically, the performance of our taxonomist was affected by mistakes, caused by large amounts of material. We conducted misidentifications for 9% of vouchers, which may not have been recovered had we not applied a second identification method. On the other hand, we were able to provide species information in cases where molecular methods could not, which was the case for 14% of vouchers. Therefore, we conclude that when wanting to implement non-biting midges into ecological frameworks, it is imperative to use an integrative approach.
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Affiliation(s)
- Caroline Chimeno
- Bavarian State Collection of Zoology (SNSB-ZSM), Munich, Germany
| | - Björn Rulik
- Zoological Research Museum Alexander Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
| | - Alessandro Manfrin
- Institute for Environmental Sciences, iES Landau, RPTU University of Kaiserslautern-Landau, Landau, Germany
| | - Gregor Kalinkat
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Franz Hölker
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Viktor Baranov
- Estación Biológica de Doñana-CSIC/Doñana Biological Station-CSIC, Seville, Spain
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Duan Q, Liu F, Gui D, Fan W, Cui G, Jia W, Zhu A, Wang J. Phylogenetic Analysis of Wild Species and the Maternal Origin of Cultivars in the Genus Lilium Using 114 Plastid Genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:865606. [PMID: 35937320 PMCID: PMC9355515 DOI: 10.3389/fpls.2022.865606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/16/2022] [Indexed: 05/24/2023]
Abstract
Lilies are one of the most important ornamental flowers worldwide with approximately 100 wild species and numerous cultivars, but the phylogenetic relationships among wild species and their contributions to these cultivars are poorly resolved. We collected the major Lilium species and cultivars and assembled their plastome sequences. Our phylogenetic reconstruction using 114 plastid genomes, including 70 wild species representing all sections and 42 cultivars representing six hybrid divisions and two outgroups, uncovered well-supported genetic relationships within Lilium. The wild species were separated into two distinct groups (groups A and B) associated with geographical distribution, which further diversified into eight different clades that were phylogenetically well supported. Additional support was provided by the distributions of indels and single-nucleotide variants, which were consistent with the topology. The species of sections Archelirion, Sinomartagon III, and Leucolirion 6a and 6b were the maternal donors for Oriental hybrids, Asiatic hybrids, Trumpet hybrids, and Longiflorum hybrids, respectively. The maternal donors of the OT hybrids originated from the two sections Archelirion and Leucolirion 6a, and LA hybrids were derived from the two sections Leucolirion 6b and Sinomartagon. Our study provides an important basis for clarifying the infrageneric classification and the maternal origin of cultivars in Lilium.
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Affiliation(s)
- Qing Duan
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming, China
- Joint Lab of Yunnan Seed Industry, Kunming, China
| | - Fang Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Daping Gui
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Weishu Fan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Guangfen Cui
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming, China
- Joint Lab of Yunnan Seed Industry, Kunming, China
| | - Wenjie Jia
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming, China
- Joint Lab of Yunnan Seed Industry, Kunming, China
| | - Andan Zhu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jihua Wang
- Flower Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Kunming, China
- Joint Lab of Yunnan Seed Industry, Kunming, China
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Improved Chironomid Barcode Database Enhances Identification of Water Mite Dietary Content. DIVERSITY 2022. [DOI: 10.3390/d14020065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chironomids are one of the most biodiverse and abundant members of freshwater ecosystems. They are a food source for many organisms, including fish and water mites. The accurate identification of chironomids is essential for many applications in ecological research, including determining which chironomid species are present in the diets of diverse predators. Larval and adult chironomids from diverse habitats, including lakes, rivers, inland gardens, coastal vegetation, and nearshore habitats of the Great Lakes, were collected from 2012 to 2019. After morphological identification of chironomids, DNA was extracted and cytochrome oxidase I (COI) barcodes were PCR amplified and sequenced. Here we describe an analysis of biodiverse adult and larval chironomids in the Great Lakes region of North America based on new collections to improve chironomid identification by curating a chironomid DNA barcode database, thereby expanding the diversity and taxonomic specificity of DNA reference libraries for the Chironomidae family. In addition to reporting many novel chironomid DNA barcodes, we demonstrate here the use of this chironomid COI barcode database to improve the identification of DNA barcodes of prey in the liquefied diets of water mites. The species identifications of the COI barcodes of chironomids ingested by Lebertia davidcooki and L. quinquemaculosa are more diverse for L. davidcooki and include Parachironomus abortivus, Cryptochironomus ponderosus. Parachironomus tenuicaudatus, Glyptotendipes senilis, Dicrotendipes modestus, Chironomus riparius, Chironomus entis/plumosus, Chironomus maturus, Chironomus crassicaudatus, Endochironomus subtendens, Cricotopus sylvestris, Cricotopus festivellus, Orthocladius obumbratus, Tanypus punctipennis, Rheotanytarsus exiguus gr., and Paratanytarsus nr. bituberculatus.
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5
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Ge Y, Xia C, Wang J, Zhang X, Ma X, Zhou Q. The efficacy of DNA barcoding in the classification, genetic differentiation, and biodiversity assessment of benthic macroinvertebrates. Ecol Evol 2021; 11:5669-5681. [PMID: 34026038 PMCID: PMC8131818 DOI: 10.1002/ece3.7470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 02/26/2021] [Accepted: 03/05/2021] [Indexed: 11/19/2022] Open
Abstract
Macroinvertebrates have been recognized as key ecological indicators of aquatic environment and are the most commonly used approaches for water quality assessment. However, species identification of macroinvertebrates (especially of aquatic insects) proves to be very difficult due to the lack of taxonomic expertise in some regions and can become time-consuming. In this study, we evaluated the feasibility of DNA barcoding for the classification of benthic macroinvertebrates and investigated the genetic differentiation in seven orders (Insecta: Ephemeroptera, Plecoptera, Trichoptera, Diptera, Hemiptera, Coleoptera, and Odonata) from four large transboundary rivers of northwest China and further explored its potential application to biodiversity assessment. A total of 1,144 COI sequences, belonging to 176 species, 112 genera, and 53 families were obtained and analyzed. The barcoding gap analysis showed that COI gene fragment yielded significant intra- and interspecific divergences and obvious barcoding gaps. NJ phylogenetic trees showed that all species group into monophyletic species clusters whether from the same population or not, except two species (Polypedilum. laetum and Polypedilum. bullum). The distance-based (ABGD) and tree-based (PTP and MPTP) methods were utilized for grouping specimens into Operational Taxonomic Units (OTUs) and delimiting species. The ABGD, PTP, and MPTP analysis were divided into 177 (p = .0599), 197, and 195 OTUs, respectively. The BIN analysis generated 186 different BINs. Overall, our study showed that DNA barcoding offers an effective framework for macroinvertebrate species identification and sheds new light on the biodiversity assessment of local macroinvertebrates. Also, the construction of DNA barcode reference library of benthic macroinvertebrates in Eurasian transboundary rivers provides a solid backup for bioassessment studies of freshwater habitats using modern high-throughput technologies in the near future.
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Affiliation(s)
- Yihao Ge
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
- The Key Laboratory of Aquatic Biodiversity and ConservationInstitute of HydrobiologyChinese Academy of SciencesWuhanChina
| | - Chengxing Xia
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
| | - Jun Wang
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- The Key Laboratory of Aquatic Biodiversity and ConservationInstitute of HydrobiologyChinese Academy of SciencesWuhanChina
| | - Xiujie Zhang
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
| | - Xufa Ma
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
| | - Qiong Zhou
- Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of FisheriesHuazhong Agricultural UniversityWuhanChina
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationWuhanChina
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Takamura K, Ueno R, Kondo NI, Ohbayashi K. Pond chironomid communities revealed by molecular species delimitation reflect eutrophication. Ecol Evol 2021; 11:4193-4204. [PMID: 33976803 PMCID: PMC8093717 DOI: 10.1002/ece3.7315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 11/26/2022] Open
Abstract
Farm ponds, a valued habitat for freshwater organisms, are being negatively affected by the recent changes in the environment as well as anthropological activities. In these ponds, biodiversity researchers have tended to focus on species that prefer natural habitats and/or can be identified based on morphological characters. In contrast, this study focused on the insect family Chironomidae, which is widely distributed from clear to polluted waters of ponds, but is hard to identify morphologically as an aquatic larva. We adopted DNA barcoding and molecular species delimitation to identify every single specimen of quantitative collections. From bottom sediments of 17 ponds in summer in the Banshu Plain of Japan, a total of 62 species were delimited based on the DNA sequences of the mitochondrial COI region. Chironomid communities from these ponds were classified into four groups in a two-dimensional ordination of multivariate analysis (NMDS). One of the dimensions was well correlated with the gradient of eutrophication, while another dimension was not clearly assigned to any general feature of the environmental gradient, but rice cultivation could possibly be involved.
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Affiliation(s)
- Kenzi Takamura
- Center for Environmental Biology and EcosystemNational Institute for Environmental StudiesTsukubaJapan
| | - Ryuhei Ueno
- Center for Environmental Biology and EcosystemNational Institute for Environmental StudiesTsukubaJapan
| | - Natsuko Ito Kondo
- Center for Environmental Biology and EcosystemNational Institute for Environmental StudiesTsukubaJapan
| | - Kako Ohbayashi
- Center for Environmental Biology and EcosystemNational Institute for Environmental StudiesTsukubaJapan
- Graduate School of Arts and SciencesThe University of TokyoKomabaJapan
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7
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Lencioni V, Rodriguez‐Prieto A, Allegrucci G. Congruence between molecular and morphological systematics of Alpine non‐biting midges (Chironomidae, Diamesinae). ZOOL SCR 2021. [DOI: 10.1111/zsc.12480] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Valeria Lencioni
- Department of Invertebrate Zoology and Hydrobiology MUSE‐Museo delle Scienze Trento Italy
| | - Ana Rodriguez‐Prieto
- Department of Invertebrate Zoology and Hydrobiology MUSE‐Museo delle Scienze Trento Italy
- WonderGene S.r.l Trento Italy
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8
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Sevigny JL, Norenburg JL, Leasi F. A Bioinformatics Tutorial for Comparative Development Genomics in Diverse Meiofauna. Methods Mol Biol 2021; 2219:289-305. [PMID: 33074549 DOI: 10.1007/978-1-0716-0974-3_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Miniaturization, which is a common feature in animals, is particularly manifest in meiofauna-animals sharing peculiar phenotypic features that evolved as adaptations to the highly specialized aquatic interstitial habitat. While revealing much about the extreme phyletic diversity of meiofauna, the genome structure of meiofaunal species could also characterize the phenotype of ancestral states as well as explain the origin and evolution of miniaturization. Here, we present a practical bioinformatics tutorial for genome assembly, genome comparison, and characterization of Hox clusters in meiofaunal species.
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Affiliation(s)
- Joseph L Sevigny
- Hubbard Center for Genome Studies, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Jon L Norenburg
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC, USA
| | - Francesca Leasi
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, TN, USA.
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9
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Molecular and morphometric divergence of four species of butterflies (Nymphalidae and Pieridae) from the Western Himalaya, India. Mol Biol Rep 2020; 47:8687-8699. [PMID: 33070284 DOI: 10.1007/s11033-020-05913-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 10/10/2020] [Indexed: 10/23/2022]
Abstract
Morphometric and molecular divergence among four butterfly species of the families Nymphalidae and Pieridae from the western Himalaya region were investigated using molecular tools, traditional morphometric measures and a truss network system. The considered species were Danaus chrysippus, Vanessa cardui, Pieris brassicae and Pieris canidia. Traditional taxonomy is sometimes unable to discriminate cryptic species or species that have close morphological features. Although taxonomists carefully examine external body features to differentiate the species; however, there is a risk for misidentification during a visual assessment of cryptic species. Therefore, we aimed to use the truss network system of 14 morphological landmarks interconnected to yield 90 variables about molecular taxonomy. Principal component analysis (PCA), discriminant function analysis (DFA) and cluster analysis (CA) were employed to determine morphometric variations. In the traditional analysis, 79, 68, 16 and 5 characters out of 90 were found significant (p < 0.05) for D. chrysippus, V. cardui, P. brassicae and P. canidia, respectively. One to seven principal components were extracted through PCA; they explained 87.5-100% of the total variance in samples. Notably, DFA correctly classified 100% of the original grouped cases and 100% of the cross-validated grouped cases. However, the variations were not the same for the two different methods (truss and traditional) employed for the analysis. We correctly identified all the species; the interspecies sequence divergence was between 0.1034 and 0.1398, and the intra-species sequence divergence range was 0.0001 to 0.0128 using the Cytochrome c oxidase subunit-I (COI) gene. The present study provides useful information about the application and complementary role of traditional with truss morphometric analysis for the precise identification and classification of the selected species.
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10
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Jiang KW, Zhang R, Zhang ZF, Pan B, Tian B. DNA barcoding and molecular phylogeny of Dumasia (Fabaceae: Phaseoleae) reveals a cryptic lineage. PLANT DIVERSITY 2020; 42:376-385. [PMID: 33134622 PMCID: PMC7584798 DOI: 10.1016/j.pld.2020.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/24/2020] [Accepted: 07/26/2020] [Indexed: 06/11/2023]
Abstract
Dumasia taxonomy and classification have long been problematic. Species within this genus have few morphological differences and plants without flowers or fruits are difficult to accurately identify. In this study, we evaluated the ability of six DNA barcoding sequences, one nuclear (ITS) and five chloroplast regions (trnH-psbA, matK, rbcL, trnL-trnF, psbB-psbF), to efficiently identify Dumasia species. Most single markers or their combinations identify obvious barcoding gaps between intraspecific and interspecific genetic variation. Most combined analyses including ITS showed good species resolution and identification efficiency. We therefore suggest that ITS alone or a combination of ITS with any cpDNA marker are most suitable for DNA barcoding of Dumasia. The phylogenetic analyses clearly indicated that Dumasia yunnanensis is not monophyletic and is separated as two independent branches, which may result from cryptic differentiation. Our results demonstrate that molecular data can deepen the comprehension of taxonomy of Dumasia and provide an efficient approach for identification of the species.
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Affiliation(s)
- Kai-Wen Jiang
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, 650224, China
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhong-Fu Zhang
- Department of Wetland, Southwest Forestry University, Kunming, 650224, China
| | - Bo Pan
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, 666303, China
| | - Bin Tian
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, 650224, China
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030, Vienna, Austria
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11
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A protocol for fast identification of larval tephritid flies with a community-wide COI reference bank. CONSERV GENET RESOUR 2019. [DOI: 10.1007/s12686-019-01120-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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12
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Morinière J, Balke M, Doczkal D, Geiger MF, Hardulak LA, Haszprunar G, Hausmann A, Hendrich L, Regalado L, Rulik B, Schmidt S, Wägele JW, Hebert PDN. A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding-based biomonitoring. Mol Ecol Resour 2019; 19:900-928. [PMID: 30977972 PMCID: PMC6851627 DOI: 10.1111/1755-0998.13022] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 11/29/2022]
Abstract
This study summarizes results of a DNA barcoding campaign on German Diptera, involving analysis of 45,040 specimens. The resultant DNA barcode library includes records for 2,453 named species comprising a total of 5,200 barcode index numbers (BINs), including 2,700 COI haplotype clusters without species‐level assignment, so called “dark taxa.” Overall, 88 out of 117 families (75%) recorded from Germany were covered, representing more than 50% of the 9,544 known species of German Diptera. Until now, most of these families, especially the most diverse, have been taxonomically inaccessible. By contrast, within a few years this study provided an intermediate taxonomic system for half of the German Dipteran fauna, which will provide a useful foundation for subsequent detailed, integrative taxonomic studies. Using DNA extracts derived from bulk collections made by Malaise traps, we further demonstrate that species delineation using BINs and operational taxonomic units (OTUs) constitutes an effective method for biodiversity studies using DNA metabarcoding. As the reference libraries continue to grow, and gaps in the species catalogue are filled, BIN lists assembled by metabarcoding will provide greater taxonomic resolution. The present study has three main goals: (a) to provide a DNA barcode library for 5,200 BINs of Diptera; (b) to demonstrate, based on the example of bulk extractions from a Malaise trap experiment, that DNA barcode clusters, labelled with globally unique identifiers (such as OTUs and/or BINs), provide a pragmatic, accurate solution to the “taxonomic impediment”; and (c) to demonstrate that interim names based on BINs and OTUs obtained through metabarcoding provide an effective method for studies on species‐rich groups that are usually neglected in biodiversity research projects because of their unresolved taxonomy.
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Affiliation(s)
| | | | | | - Matthias F Geiger
- Zoological Research Museum Alexander Koenig - Leibniz Institute for Animal Biodiversity, Bonn, Germany
| | | | | | | | | | | | - Björn Rulik
- Zoological Research Museum Alexander Koenig - Leibniz Institute for Animal Biodiversity, Bonn, Germany
| | | | - Johann-Wolfgang Wägele
- Zoological Research Museum Alexander Koenig - Leibniz Institute for Animal Biodiversity, Bonn, Germany
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
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13
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Ospina‐Pérez EM, Campeón‐Morales OI, Richardi VS, Rivera‐Páez FA. Histological description of immature
Chironomus columbiensis
(Diptera: Chironomidae): A potential contribution to environmental monitoring. Microsc Res Tech 2019; 82:1277-1289. [DOI: 10.1002/jemt.23278] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/12/2019] [Accepted: 04/03/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Erika M. Ospina‐Pérez
- Grupo de Investigación GEBIOME, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y NaturalesUniversidad de Caldas Caldas Colombia
| | - Oscar I. Campeón‐Morales
- Grupo de Investigación GEBIOME, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y NaturalesUniversidad de Caldas Caldas Colombia
| | - Vinicius S. Richardi
- Laboratório de Morfologia e Fisiologia de Culicidae e Chironomidae, Departamento de ZoologiaUniversidade Federal do Paraná – UFPR Curitiba Paraná Brazil
| | - Fredy A. Rivera‐Páez
- Grupo de Investigación GEBIOME, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y NaturalesUniversidad de Caldas Caldas Colombia
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Foucault Q, Wieser A, Heumann-Kiesler C, Diogo J, Cocchiararo B, Nowak C, Waldvogel AM, Pfenninger M. An experimental assessment of reproductive isolation and its consequences for seasonal hybridization dynamics. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly177] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Quentin Foucault
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage, Frankfurt am Main, Germany
- Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg, Mainz, Germany
| | - Andreas Wieser
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage, Frankfurt am Main, Germany
- Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg, Mainz, Germany
| | - Clara Heumann-Kiesler
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage, Frankfurt am Main, Germany
- Institut für Ökologie, Evolution und Diversität, Goethe-Universität, Frankfurt am Main, Germany
| | - Joao Diogo
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage, Frankfurt am Main, Germany
| | - Berardino Cocchiararo
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystraße, Gelnhausen, Germany
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystraße, Gelnhausen, Germany
| | - Ann-Marie Waldvogel
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage, Frankfurt am Main, Germany
| | - Markus Pfenninger
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage, Frankfurt am Main, Germany
- Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg, Mainz, Germany
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15
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Li XY, Chen YO, Wang QK, Li K, Pape T, Zhang D. Molecular and morphological characterization of third instar Palaearctic horse stomach bot fly larvae (Oestridae: Gasterophilinae, Gasterophilus). Vet Parasitol 2018; 262:56-74. [DOI: 10.1016/j.vetpar.2018.09.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 09/19/2018] [Accepted: 09/22/2018] [Indexed: 01/17/2023]
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16
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Sales NG, Mariani S, Salvador GN, Pessali TC, Carvalho DC. Hidden Diversity Hampers Conservation Efforts in a Highly Impacted Neotropical River System. Front Genet 2018; 9:271. [PMID: 30087693 PMCID: PMC6066647 DOI: 10.3389/fgene.2018.00271] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 07/03/2018] [Indexed: 11/13/2022] Open
Abstract
Neotropical Rivers host a highly diverse ichthyofauna, but taxonomic uncertainty prevents appropriate conservation measures. The Doce River Basin (DRB), lying within two Brazilian threatened hotspots (Atlantic Forest and Brazilian Savanna) in south-east Brazil, faced the worst ever environmental accident reported for South American catchments, due to a dam collapse that spread toxic mining tailings along the course of its main river. Its ichthyofauna was known to comprise 71 native freshwater fish species, of which 13 endemic. Here, we build a DNA barcode library for the DRB ichthyofauna, using samples obtained before the 2015 mining disaster, in order to provide a more robust biodiversity record for this basin, as a baseline for future management actions. Throughout the whole DRB, we obtained a total of 306 barcodes, assigned to 69 putative species (with a mean of 4.54 barcodes per species), belonging to 45 genera, 18 families, and 5 orders. Average genetic distances within species, genus, and families were 2.59, 11.4, and 20.5%, respectively. The 69 species identified represent over 76% of the known DRB ichthyofauna, comprising 43 native (five endemic, of which three threatened by extinction), 13 already known introduced species, and 13 unknown species (such as Characidium sp., Neoplecostomus sp., and specimens identified only at the sub-family level Neoplecostominae, according to morphological identification provided by the museum collections). Over one fifth of all analyzed species (N = 16) had a mean intraspecific genetic divergence higher than 2%. An integrative approach, combining NND (nearest neighbor distance), BIN (barcode index number), ABGD (automatic barcode gap discovery), and bPTP (Bayesian Poisson Tree Processes model) analyses, suggested the occurrence of potential cryptic species, species complex, or historical errors in morphological identification. The evidence presented calls for a more robust, DNA-assisted cataloging of biodiversity-rich ecosystems, in order to enable effective monitoring and informed actions to preserve and restore these delicate habitats.
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Affiliation(s)
- Naiara G Sales
- Ecosystems and Environment Research Centre, School of Environment & Life Sciences, University of Salford, Salford, United Kingdom
| | - Stefano Mariani
- Ecosystems and Environment Research Centre, School of Environment & Life Sciences, University of Salford, Salford, United Kingdom
| | - Gilberto N Salvador
- Laboratório de Ecologia e Conservação, Universidade Federal do Pará, Belém, Brazil
| | - Tiago C Pessali
- Museu de Ciências Naturais PUC Minas, Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, Brazil
| | - Daniel C Carvalho
- Programa de Pós-graduação em Biologia de Vertebrados, Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, Brazil
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17
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Waldvogel AM, Wieser A, Schell T, Patel S, Schmidt H, Hankeln T, Feldmeyer B, Pfenninger M. The genomic footprint of climate adaptation in Chironomus riparius. Mol Ecol 2018; 27:1439-1456. [PMID: 29473242 DOI: 10.1111/mec.14543] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 02/09/2018] [Accepted: 02/09/2018] [Indexed: 12/31/2022]
Abstract
The gradual heterogeneity of climatic factors poses varying selection pressures across geographic distances that leave signatures of clinal variation in the genome. Separating signatures of clinal adaptation from signatures of other evolutionary forces, such as demographic processes, genetic drift and adaptation, to nonclinal conditions of the immediate local environment is a major challenge. Here, we examine climate adaptation in five natural populations of the harlequin fly Chironomus riparius sampled along a climatic gradient across Europe. Our study integrates experimental data, individual genome resequencing, Pool-Seq data and population genetic modelling. Common-garden experiments revealed significantly different population growth rates at test temperatures corresponding to the population origin along the climate gradient, suggesting thermal adaptation on the phenotypic level. Based on a population genomic analysis, we derived empirical estimates of historical demography and migration. We used an FST outlier approach to infer positive selection across the climate gradient, in combination with an environmental association analysis. In total, we identified 162 candidate genes as genomic basis of climate adaptation. Enriched functions among these candidate genes involved the apoptotic process and molecular response to heat, as well as functions identified in studies of climate adaptation in other insects. Our results show that local climate conditions impose strong selection pressures and lead to genomic adaptation despite strong gene flow. Moreover, these results imply that selection to different climatic conditions seems to converge on a functional level, at least between different insect species.
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Affiliation(s)
- Ann-Marie Waldvogel
- Molecular Ecology Group, Institute for Ecology, Evolution & Diversity, Goethe-University, Frankfurt am Main, Hesse, Germany.,Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hesse, Germany
| | - Andreas Wieser
- Molecular Ecology Group, Institute for Ecology, Evolution & Diversity, Goethe-University, Frankfurt am Main, Hesse, Germany.,Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hesse, Germany
| | - Tilman Schell
- Molecular Ecology Group, Institute for Ecology, Evolution & Diversity, Goethe-University, Frankfurt am Main, Hesse, Germany.,Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hesse, Germany
| | - Simit Patel
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hesse, Germany
| | - Hanno Schmidt
- Pathology, Microbiology & Immunology, University of California - Davis, Davis, CA, USA
| | - Thomas Hankeln
- Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, Johannes Gutenberg-University, Mainz, Rhineland-Palatinate, Germany
| | - Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hesse, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hesse, Germany
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18
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Gale SW, Duangjai S, Li J, Ito Y, Watthana S, Termwutthipreecha P, Cheuk ML, Suddee S. Integrative analyses of Nervilia (Orchidaceae) section Linervia reveal further undescribed cryptic diversity in Thailand. SYST BIODIVERS 2018. [DOI: 10.1080/14772000.2017.1415233] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Stephan W. Gale
- Kadoorie Farm and Botanic Garden, Lam Kam Road, Tai Po, New Territories, Hong Kong
| | - Sutee Duangjai
- Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Jihong Li
- Kadoorie Farm and Botanic Garden, Lam Kam Road, Tai Po, New Territories, Hong Kong
| | - Yu Ito
- Plant Phylogenetics and Conservation Group, Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Santi Watthana
- School of Biology, Institute of Science, Suranaree University of Technology, 111 University Avenue, Muang District, Nakhon Ratchasima 30000, Thailand
| | - Phatsara Termwutthipreecha
- Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Mang Lung Cheuk
- Kadoorie Farm and Botanic Garden, Lam Kam Road, Tai Po, New Territories, Hong Kong
| | - Somran Suddee
- Forest Herbarium, Department of National Parks, Wildlife and Plant Conservation, Chatuchak, Bangkok 10900, Thailand
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19
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Pedrosa JAM, Cocchiararo B, Verdelhos T, Soares AMVM, Pestana JLT, Nowak C. Population genetic structure and hybridization patterns in the cryptic sister species Chironomus riparius and Chironomus piger across differentially polluted freshwater systems. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 141:280-289. [PMID: 28359994 DOI: 10.1016/j.ecoenv.2017.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 03/02/2017] [Accepted: 03/06/2017] [Indexed: 06/07/2023]
Abstract
Chironomids are an integral and functionally important part of many freshwater ecosystems. Yet, to date, there is limited understanding of their microevolutionary processes under chemically polluted natural environments. In this study, we investigated the genetic variation within populations of the ecotoxicological model species Chironomus riparius and its cryptic sister species Chironomus piger at 18 metal-contaminated and reference sites in northwestern Portugal. Microsatellite analysis was conducted on 909 samples to answer if metal contamination affects genetic variation in natural chironomid populations as previously suggested from controlled laboratory experiments. Similarly high levels of genetic diversity and significant but weak genetic substructuring were found across all sites and temporal replicates, with no effects of metal contamination on the genetic variation or species' abundance, although C. piger tended to be less frequent at highly contaminated sites. Our results indicate that high levels of gene flow and population dynamic processes may overlay potential pollutant effects. At least for our study species, we conclude that the "genetic erosion hypothesis", which suggests that chemical pollution will reduce genome-wide genetic variability in affected populations, does not hold under natural conditions. Interestingly, our study provides evidence of successful hybridization between the two sister species under natural conditions.
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Affiliation(s)
- João A M Pedrosa
- Department of Biology & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal; Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystrasse 12, 63571 Gelnhausen, Germany.
| | - Berardino Cocchiararo
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystrasse 12, 63571 Gelnhausen, Germany
| | - Tiago Verdelhos
- MARE - Marine and Environmental Sciences Centre, Faculty of Sciences and Technology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Amadeu M V M Soares
- Department of Biology & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - João L T Pestana
- Department of Biology & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystrasse 12, 63571 Gelnhausen, Germany
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20
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Pedrosa J, Campos D, Cocchiararo B, Nowak C, Soares AMVM, Barata C, L T Pestana J. Evolutionary consequences of historical metal contamination for natural populations of Chironomus riparius (Diptera: Chironomidae). ECOTOXICOLOGY (LONDON, ENGLAND) 2017; 26:534-546. [PMID: 28353160 DOI: 10.1007/s10646-017-1784-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/15/2017] [Indexed: 06/06/2023]
Abstract
Populations inhabiting metal-impacted freshwater systems located nearby industrial and urban areas may be under intense selection. The present study aims to address two fundamental microevolutionary aspects of metal contamination in the midge Chironomus riparius (Meigen): Are populations inhabiting historically metal contaminated sites genetically adapted to metals? And, are populations from these sites genetically eroded? To answer these questions, C. riparius populations were sampled from three sites with well-known histories of metal contamination and three nearby-located references. Genetic adaptation to metals was investigated through acute and chronic exposures to cadmium (Cd), after rearing all populations for at least six generations under laboratory clean conditions. Genetic diversity was estimated based on the allelic variation of seven microsatellite markers. Results showed higher acute tolerance to Cd in populations originating from metal contaminated sites compared to their respective references and significant differences in two out of three pairwise comparisons. However, there was a mismatch between acute and chronic tolerance to Cd with results of the partial life-cycle tests suggesting fitness costs under control clean conditions in two metal-adapted populations. Despite no evidences of genetic erosion in populations sampled from metal contaminated sites, our results suggest genetically inherited tolerance to Cd in populations inhabiting historically contaminated sites. These findings lend support to the use of C. riparius as a model organism in evolutionary toxicology and highlight the importance of coupling measures of neutral genetic diversity with assessments of chemical tolerance of populations for a better understanding of contaminant-induced adaptation and evolutionary processes.
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Affiliation(s)
- João Pedrosa
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193, Aveiro, Portugal
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum of Frankfurt, Clamecystrasse 12, 63571, Gelnhausen, Germany
| | - Diana Campos
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193, Aveiro, Portugal
| | - Berardino Cocchiararo
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum of Frankfurt, Clamecystrasse 12, 63571, Gelnhausen, Germany
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum of Frankfurt, Clamecystrasse 12, 63571, Gelnhausen, Germany
| | - Amadeu M V M Soares
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193, Aveiro, Portugal
| | - Carlos Barata
- Department of Environmental Chemistry (IDAEA-CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
| | - João L T Pestana
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193, Aveiro, Portugal.
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21
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Oppold AM, Schmidt H, Rose M, Hellmann SL, Dolze F, Ripp F, Weich B, Schmidt-Ott U, Schmidt E, Kofler R, Hankeln T, Pfenninger M. Chironomus riparius
(Diptera) genome sequencing reveals the impact of minisatellite transposable elements on population divergence. Mol Ecol 2017; 26:3256-3275. [DOI: 10.1111/mec.14111] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 02/23/2017] [Accepted: 03/06/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Ann-Marie Oppold
- Molecular Ecology Group; Institute for Ecology, Evolution & Diversity; Goethe-University Frankfurt am Main; Max-von-Laue-Str. 9, 60438 Frankfurt am Main Hessen Germany
- Senckenberg Biodiversity and Climate Research Centre; Georg-Voigt-Str. 14-16 60325 Frankfurt am Main Hessen Germany
| | - Hanno Schmidt
- Senckenberg Biodiversity and Climate Research Centre; Georg-Voigt-Str. 14-16 60325 Frankfurt am Main Hessen Germany
| | - Marcel Rose
- Molecular Ecology Group; Institute for Ecology, Evolution & Diversity; Goethe-University Frankfurt am Main; Max-von-Laue-Str. 9, 60438 Frankfurt am Main Hessen Germany
| | - Sören Lukas Hellmann
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Florian Dolze
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Fabian Ripp
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Bettina Weich
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Urs Schmidt-Ott
- Department of Organismal Biology and Anatomy; University of Chicago; 920 E. 58th Street, 1061C Chicago IL 60637 USA
| | - Erwin Schmidt
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Robert Kofler
- Institut für Populationsgenetik; Vetmeduni Vienna 1210 Vienna Austria
| | - Thomas Hankeln
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Markus Pfenninger
- Molecular Ecology Group; Institute for Ecology, Evolution & Diversity; Goethe-University Frankfurt am Main; Max-von-Laue-Str. 9, 60438 Frankfurt am Main Hessen Germany
- Senckenberg Biodiversity and Climate Research Centre; Georg-Voigt-Str. 14-16 60325 Frankfurt am Main Hessen Germany
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22
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Cariani A, Messinetti S, Ferrari A, Arculeo M, Bonello JJ, Bonnici L, Cannas R, Carbonara P, Cau A, Charilaou C, El Ouamari N, Fiorentino F, Follesa MC, Garofalo G, Golani D, Guarniero I, Hanner R, Hemida F, Kada O, Lo Brutto S, Mancusi C, Morey G, Schembri PJ, Serena F, Sion L, Stagioni M, Tursi A, Vrgoc N, Steinke D, Tinti F. Improving the Conservation of Mediterranean Chondrichthyans: The ELASMOMED DNA Barcode Reference Library. PLoS One 2017; 12:e0170244. [PMID: 28107413 PMCID: PMC5249125 DOI: 10.1371/journal.pone.0170244] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/30/2016] [Indexed: 11/18/2022] Open
Abstract
Cartilaginous fish are particularly vulnerable to anthropogenic stressors and environmental change because of their K-selected reproductive strategy. Accurate data from scientific surveys and landings are essential to assess conservation status and to develop robust protection and management plans. Currently available data are often incomplete or incorrect as a result of inaccurate species identifications, due to a high level of morphological stasis, especially among closely related taxa. Moreover, several diagnostic characters clearly visible in adult specimens are less evident in juveniles. Here we present results generated by the ELASMOMED Consortium, a regional network aiming to sample and DNA-barcode the Mediterranean Chondrichthyans with the ultimate goal to provide a comprehensive DNA barcode reference library. This library will support and improve the molecular taxonomy of this group and the effectiveness of management and conservation measures. We successfully barcoded 882 individuals belonging to 42 species (17 sharks, 24 batoids and one chimaera), including four endemic and several threatened ones. Morphological misidentifications were found across most orders, further confirming the need for a comprehensive DNA barcoding library as a valuable tool for the reliable identification of specimens in support of taxonomist who are reviewing current identification keys. Despite low intraspecific variation among their barcode sequences and reduced samples size, five species showed preliminary evidence of phylogeographic structure. Overall, the ELASMOMED initiative further emphasizes the key role accurate DNA barcoding libraries play in establishing reliable diagnostic species specific features in otherwise taxonomically problematic groups for biodiversity management and conservation actions.
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Affiliation(s)
- Alessia Cariani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Silvia Messinetti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Alice Ferrari
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Marco Arculeo
- Department STEBICEF, University of Palermo, Palermo, Italy
| | | | | | - Rita Cannas
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | | | - Alessandro Cau
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Charis Charilaou
- Department of Fisheries and Marine Research, Ministry of Agriculture, Rural Development and Environment, Nicosia, Republic of Cyprus
| | - Najib El Ouamari
- Centre Régional de Institut National Recherche Halieutique, Nador, Morocco
| | - Fabio Fiorentino
- Institute for Coastal Marine Environment (IAMC) National Research Council (CNR), Mazara del Vallo, Italy
| | | | - Germana Garofalo
- Institute for Coastal Marine Environment (IAMC) National Research Council (CNR), Mazara del Vallo, Italy
| | - Daniel Golani
- Department of Evolution, Systematics and Ecology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ilaria Guarniero
- Department DIMEVET, University of Bologna, Ozzano dell'Emilia, Italy
| | - Robert Hanner
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Farid Hemida
- Ecole Nationale Superieure des Sciences de la Mer et d'Amenagement du Littoral, Campus Universitaire de Dely Ibrahim, Alger, Algeria
| | - Omar Kada
- Centre Régional de Institut National Recherche Halieutique, Nador, Morocco
| | | | - Cecilia Mancusi
- Regional Agency for Environmental Protection-Toscana (ARPAT), Livorno, Italy
| | | | | | - Fabrizio Serena
- Regional Agency for Environmental Protection-Toscana (ARPAT), Livorno, Italy
| | - Letizia Sion
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
| | - Marco Stagioni
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Angelo Tursi
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
| | - Nedo Vrgoc
- Institute of Oceanography and Fisheries, Split, Croatia
| | - Dirk Steinke
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Fausto Tinti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
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23
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Pedrosa JAM, Cocchiararo B, Bordalo MD, Rodrigues ACM, Soares AMVM, Barata C, Nowak C, Pestana JLT. The role of genetic diversity and past-history selection pressures in the susceptibility of Chironomus riparius populations to environmental stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 576:807-816. [PMID: 27810765 DOI: 10.1016/j.scitotenv.2016.10.100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/21/2016] [Accepted: 10/14/2016] [Indexed: 06/06/2023]
Abstract
Natural populations experiencing intense selection and genetic drift may exhibit limited potential to adapt to environmental change. The present study addresses the following aspects of the "genetic erosion" hypothesis in the midge Chironomus riparius: does long-term mercury (Hg) contamination affect the Hg tolerance of midge populations inhabiting such impacted areas? If so, is there any fitness cost under changing environmental conditions? And does genetic impoverishment influence the susceptibility of C. riparius to cope with environmental stressful conditions? For this end, we tested the acute and chronic tolerance to Hg and salinity in four C. riparius populations differing in their levels of genetic diversity (assessed through microsatellite markers) and past-histories of Hg exposure. Results showed that the midge population collected from a heavily Hg-contaminated site had higher Hg tolerance compared to the population collected from a closely-located reference site suggesting directional selection for Hg-tolerant traits in its native environment despite no genetic erosion in the field. No increased susceptibility under changing environmental conditions of salinity stress was observed. Moreover, results also showed that populations with higher genetic diversity performed better in the partial life-cycle assays providing evidence on the key role that genetic diversity plays as mediator of populations' susceptibility to environmental stress. Our findings are discussed in terms of the suitability of C. riparius as a model organism in evolutionary toxicology studies as well as the validity of ecotoxicological assessments using genetically eroded laboratory populations.
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Affiliation(s)
- João A M Pedrosa
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal; Conservation Genetics Group, Senckenberg Research Institute, Clamecystrasse 12, 63571 Gelnhausen, Germany
| | - Berardino Cocchiararo
- Conservation Genetics Group, Senckenberg Research Institute, Clamecystrasse 12, 63571 Gelnhausen, Germany
| | - Maria D Bordalo
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Andreia C M Rodrigues
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal; Department of Environmental Chemistry (IDAEA-CSIC), Jordi Girona, 18-26, 08034 Barcelona, Spain
| | - Amadeu M V M Soares
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Carlos Barata
- Department of Environmental Chemistry (IDAEA-CSIC), Jordi Girona, 18-26, 08034 Barcelona, Spain
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute, Clamecystrasse 12, 63571 Gelnhausen, Germany
| | - João L T Pestana
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal.
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24
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Towards resolving the double classification in Erythraeus (Actinotrichida: Erythraeidae): matching larvae with adults using 28S sequence data and experimental rearing. ORG DIVERS EVOL 2016. [DOI: 10.1007/s13127-016-0283-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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25
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Oppold AM, Pedrosa JAM, Bálint M, Diogo JB, Ilkova J, Pestana JLT, Pfenninger M. Support for the evolutionary speed hypothesis from intraspecific population genetic data in the non-biting midge Chironomus riparius. Proc Biol Sci 2016; 283:20152413. [PMID: 26888029 DOI: 10.1098/rspb.2015.2413] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The evolutionary speed hypothesis (ESH) proposes a causal mechanism for the latitudinal diversity gradient. The central idea of the ESH is that warmer temperatures lead to shorter generation times and increased mutation rates. On an absolute time scale, both should lead to an acceleration of selection and drift. Based on the ESH, we developed predictions regarding the distribution of intraspecific genetic diversity: populations of ectothermic species with more generations per year owing to warmer ambient temperatures should be more differentiated from each other, accumulate more mutations and show evidence for increased mutation rates compared with populations in colder regions. We used the multivoltine insect species Chironomus riparius to test these predictions with cytochrome oxidase I (COI) sequence data and found that populations from warmer regions are indeed significantly more differentiated and have significantly more derived haplotypes than populations from colder regions. We also found a significant correlation of the annual mean temperature with the population mutation parameter θ that serves as a proxy for the per generation mutation rate under certain assumptions. This pattern could be corroborated with two nuclear loci. Overall, our results support the ESH and indicate that the thermal regime experienced may be crucially driving the evolution of ectotherms and may thus ultimately govern their speciation rate.
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Affiliation(s)
- Ann-Marie Oppold
- Molecular Ecology Group, Institute for Ecology, Evolution and Diversity, Goethe-University Frankfurt am Main, Hessen, Germany Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hessen, Germany
| | - João A M Pedrosa
- Departamento de Biologia and CESAM, Universidade de Aveiro, Campus Universitário de Santiago, Aveiro, Portugal Conservation Genetics Group, Senckenberg Research Institute, Gelnhausen, Hessen, Germany
| | - Miklós Bálint
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hessen, Germany
| | - João B Diogo
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hessen, Germany
| | - Julia Ilkova
- Institute of Biodiversity and Ecosystem research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - João L T Pestana
- Departamento de Biologia and CESAM, Universidade de Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Markus Pfenninger
- Molecular Ecology Group, Institute for Ecology, Evolution and Diversity, Goethe-University Frankfurt am Main, Hessen, Germany Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Hessen, Germany
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Castelin M, Van Steenkiste N, Pante E, Harbo R, Lowe G, Gilmore SR, Therriault TW, Abbott CL. A new integrative framework for large-scale assessments of biodiversity and community dynamics, using littoral gastropods and crabs of British Columbia, Canada. Mol Ecol Resour 2016; 16:1322-1339. [DOI: 10.1111/1755-0998.12534] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/18/2016] [Accepted: 03/18/2016] [Indexed: 11/27/2022]
Affiliation(s)
- M. Castelin
- Pacific Biological Station; Fisheries and Oceans Canada; 3190 Hammond Bay Road Nanaimo BC Canada V9T 6N7
| | - N. Van Steenkiste
- Pacific Biological Station; Fisheries and Oceans Canada; 3190 Hammond Bay Road Nanaimo BC Canada V9T 6N7
| | - E. Pante
- LIENSs Laboratory; UMR 7266 CNRS-Université de La Rochelle; 2 rue Olympe de Gouges La Rochelle 17000 France
| | - R. Harbo
- Invertebrate Zoology; Royal BC Museum; 675 Belleville Street Victoria BC Canada V8W 9W2
| | - G. Lowe
- Pacific Biological Station; Fisheries and Oceans Canada; 3190 Hammond Bay Road Nanaimo BC Canada V9T 6N7
| | - S. R. Gilmore
- Pacific Biological Station; Fisheries and Oceans Canada; 3190 Hammond Bay Road Nanaimo BC Canada V9T 6N7
| | - T. W. Therriault
- Pacific Biological Station; Fisheries and Oceans Canada; 3190 Hammond Bay Road Nanaimo BC Canada V9T 6N7
| | - C. L. Abbott
- Pacific Biological Station; Fisheries and Oceans Canada; 3190 Hammond Bay Road Nanaimo BC Canada V9T 6N7
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Barley AJ, Thomson RC. Assessing the performance of DNA barcoding using posterior predictive simulations. Mol Ecol 2016; 25:1944-57. [PMID: 26915049 DOI: 10.1111/mec.13590] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/05/2016] [Accepted: 01/18/2016] [Indexed: 02/05/2023]
Abstract
Accurate estimates of biodiversity are required for research in a broad array of biological subdisciplines including ecology, evolution, systematics, conservation and biodiversity science. The use of statistical models and genetic data, particularly DNA barcoding, has been suggested as an important tool for remedying the large gaps in our current understanding of biodiversity. However, the reliability of biodiversity estimates obtained using these approaches depends on how well the statistical models that are used describe the evolutionary process underlying the genetic data. In this study, we utilize data from the Barcode of Life Database and posterior predictive simulations to assess the performance of DNA barcoding under commonly used substitution models. We demonstrate that the success of DNA barcoding varies widely across DNA substitution models and that model choice has a substantial impact on the number of operational taxonomic units identified (changing results by ~4-31%). Additionally, we demonstrate that the widely followed practice of a priori assuming the Kimura 2-parameter model for DNA barcoding is statistically unjustified and should be avoided. Using both data-based and inference-based test statistics, we detect variation in model performance across taxonomic groups, clustering algorithms, genetic divergence thresholds and substitution models. Taken together, these results illustrate the importance of considering both model selection and model adequacy in studies quantifying biodiversity.
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Affiliation(s)
- Anthony J Barley
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Robert C Thomson
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
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28
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Montagna M, Mereghetti V, Lencioni V, Rossaro B. Integrated Taxonomy and DNA Barcoding of Alpine Midges (Diptera: Chironomidae). PLoS One 2016; 11:e0149673. [PMID: 26938660 PMCID: PMC4777558 DOI: 10.1371/journal.pone.0149673] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/02/2016] [Indexed: 11/19/2022] Open
Abstract
Rapid and efficient DNA-based tools are recommended for the evaluation of the insect biodiversity of high-altitude streams. In the present study, focused principally on larvae of the genus Diamesa Meigen 1835 (Diptera: Chironomidae), the congruence between morphological/molecular delimitation of species as well as performances in taxonomic assignments were evaluated. A fragment of the mitochondrial cox1 gene was obtained from 112 larvae, pupae and adults (Diamesinae, Orthocladiinae and Tanypodinae) that were collected in different mountain regions of the Alps and Apennines. On the basis of morphological characters 102 specimens were attributed to 16 species, and the remaining ten specimens were identified to the genus level. Molecular species delimitation was performed using: i) distance-based Automatic Barcode Gap Discovery (ABGD), with no a priori assumptions on species identification; and ii) coalescent tree-based approaches as the Generalized Mixed Yule Coalescent model, its Bayesian implementation and Bayesian Poisson Tree Processes. The ABGD analysis, estimating an optimal intra/interspecific nucleotide distance threshold of 0.7%-1.4%, identified 23 putative species; the tree-based approaches, identified between 25-26 entities, provided nearly identical results. All species belonging to zernyi, steinboecki, latitarsis, bertrami, dampfi and incallida groups, as well as outgroup species, are recovered as separate entities, perfectly matching the identified morphospecies. In contrast, within the cinerella group, cases of discrepancy arose: i) the two morphologically separate species D. cinerella and D. tonsa are neither monophyletic nor diagnosable exhibiting low values of between-taxa nucleotide mean divergence (0.94%); ii) few cases of larvae morphological misidentification were observed. Head capsule color is confirmed to be a valid character able to discriminate larvae of D. zernyi, D. tonsa and D. cinerella, but it is here better defined as a color gradient between the setae submenti and genal setae. DNA barcodes performances were high: average accuracy was ~89% and precision of ~99%. On the basis of the present data, we can thus conclude that molecular identification represents a promising tool that could be effectively adopted in evaluating biodiversity of high-altitude streams.
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Affiliation(s)
- Matteo Montagna
- Dipartimento di Scienze Agrarie e Ambientali—Università degli Studi di Milano, Via Celoria 2, I-20133, Milano, Italy
| | - Valeria Mereghetti
- Dipartimento di Scienze Agrarie e Ambientali—Università degli Studi di Milano, Via Celoria 2, I-20133, Milano, Italy
| | - Valeria Lencioni
- MUSE—Museo delle Scienze, Corso del Lavoro e della Scienza 3, I-38122, Trento, Italy
| | - Bruno Rossaro
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente—Università degli Studi di Milano, Via Celoria 2, I-20133, Milano, Italy
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Failla AJ, Vasquez AA, Hudson P, Fujimoto M, Ram JL. Morphological identification and COI barcodes of adult flies help determine species identities of chironomid larvae (Diptera, Chironomidae). BULLETIN OF ENTOMOLOGICAL RESEARCH 2016; 106:34-46. [PMID: 26072670 DOI: 10.1017/s0007485315000486] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Establishing reliable methods for the identification of benthic chironomid communities is important due to their significant contribution to biomass, ecology and the aquatic food web. Immature larval specimens are more difficult to identify to species level by traditional morphological methods than their fully developed adult counterparts, and few keys are available to identify the larval species. In order to develop molecular criteria to identify species of chironomid larvae, larval and adult chironomids from Western Lake Erie were subjected to both molecular and morphological taxonomic analysis. Mitochondrial cytochrome c oxidase I (COI) barcode sequences of 33 adults that were identified to species level by morphological methods were grouped with COI sequences of 189 larvae in a neighbor-joining taxon-ID tree. Most of these larvae could be identified only to genus level by morphological taxonomy (only 22 of the 189 sequenced larvae could be identified to species level). The taxon-ID tree of larval sequences had 45 operational taxonomic units (OTUs, defined as clusters with >97% identity or individual sequences differing from nearest neighbors by >3%; supported by analysis of all larval pairwise differences), of which seven could be identified to species or 'species group' level by larval morphology. Reference sequences from the GenBank and BOLD databases assigned six larval OTUs with presumptive species level identifications and confirmed one previously assigned species level identification. Sequences from morphologically identified adults in the present study grouped with and further classified the identity of 13 larval OTUs. The use of morphological identification and subsequent DNA barcoding of adult chironomids proved to be beneficial in revealing possible species level identifications of larval specimens. Sequence data from this study also contribute to currently inadequate public databases relevant to the Great Lakes region, while the neighbor-joining analysis reported here describes the application and confirmation of a useful tool that can accelerate identification and bioassessment of chironomid communities.
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Affiliation(s)
- A J Failla
- Department of Physiology,Wayne State University School of Medicine,5374 Scott Hall,540 E. Canfield St.,Detroit,MI 48201
| | - A A Vasquez
- Department of Physiology,Wayne State University School of Medicine,5374 Scott Hall,540 E. Canfield St.,Detroit,MI 48201
| | - P Hudson
- Great Lakes Science Center,U.S. Geological Survey,1451 Green Road,Ann Arbor,MI 48105,USA
| | - M Fujimoto
- Department of Physiology,Wayne State University School of Medicine,5374 Scott Hall,540 E. Canfield St.,Detroit,MI 48201
| | - J L Ram
- Department of Physiology,Wayne State University School of Medicine,5374 Scott Hall,540 E. Canfield St.,Detroit,MI 48201
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30
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Rockney HJ, Ofori-Boateng C, Porcino N, Leaché AD. A comparison of DNA barcoding markers in West African frogs. AFR J HERPETOL 2015. [DOI: 10.1080/21564574.2015.1114530] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Heidi J. Rockney
- Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, USA
- Department of Biology, University of Washington, Seattle, Washington, USA
| | - Caleb Ofori-Boateng
- Forestry Research Institute of Ghana, Kumasi, Ghana
- Wildlife and Range Management Department, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Natsuko Porcino
- Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, USA
- Department of Biology, University of Washington, Seattle, Washington, USA
| | - Adam D. Leaché
- Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, USA
- Department of Biology, University of Washington, Seattle, Washington, USA
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31
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Gutiérrez-Cánovas C, Sánchez-Fernández D, Velasco J, Millan A, Bonada N. Similarity in the difference: changes in community functional features along natural and anthropogenic stress gradients. Ecology 2015; 96:2458-66. [PMID: 26594702 DOI: 10.1890/14-1447.1] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The effect of stressors on biodiversity can vary in relation to the degree to which biological communities have adapted over evolutionary time. We compared the responses of functional features of stream insect communities along chronic stress gradients with contrasting time persistence. Water salinity and land use intensification were used as examples of natural (long-term persistent) and anthropogenic (short-term persistent) stressors, respectively. A new trait-based approach was applied to quantify functional diversity components and functional redundancy within the same multidimensional space, using metrics at the taxon and community levels. We found similar functional responses along natural and anthropogenic stress gradients. In both cases, the mean taxon functional richness and functional similarity between taxa increased with stress, whereas community functional richness and functional redundancy decreased. Despite the differences in evolutionary persistence, both chronic stressors act as strong nonrandom environmental filters, producing convergent functional responses. These results can improve our ability to predict functional effects of novel stressors at ecoloiical and evolutionary scales.
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Wirta H, Várkonyi G, Rasmussen C, Kaartinen R, Schmidt NM, Hebert PDN, Barták M, Blagoev G, Disney H, Ertl S, Gjelstrup P, Gwiazdowicz DJ, Huldén L, Ilmonen J, Jakovlev J, Jaschhof M, Kahanpää J, Kankaanpää T, Krogh PH, Labbee R, Lettner C, Michelsen V, Nielsen SA, Nielsen TR, Paasivirta L, Pedersen S, Pohjoismäki J, Salmela J, Vilkamaa P, Väre H, von Tschirnhaus M, Roslin T. Establishing a community-wide DNA barcode library as a new tool for arctic research. Mol Ecol Resour 2015; 16:809-22. [PMID: 26602739 DOI: 10.1111/1755-0998.12489] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 11/09/2015] [Accepted: 11/17/2015] [Indexed: 12/18/2022]
Abstract
DNA sequences offer powerful tools for describing the members and interactions of natural communities. In this study, we establish the to-date most comprehensive library of DNA barcodes for a terrestrial site, including all known macroscopic animals and vascular plants of an intensively studied area of the High Arctic, the Zackenberg Valley in Northeast Greenland. To demonstrate its utility, we apply the library to identify nearly 20 000 arthropod individuals from two Malaise traps, each operated for two summers. Drawing on this material, we estimate the coverage of previous morphology-based species inventories, derive a snapshot of faunal turnover in space and time and describe the abundance and phenology of species in the rapidly changing arctic environment. Overall, 403 terrestrial animal and 160 vascular plant species were recorded by morphology-based techniques. DNA barcodes (CO1) offered high resolution in discriminating among the local animal taxa, with 92% of morphologically distinguishable taxa assigned to unique Barcode Index Numbers (BINs) and 93% to monophyletic clusters. For vascular plants, resolution was lower, with 54% of species forming monophyletic clusters based on barcode regions rbcLa and ITS2. Malaise catches revealed 122 BINs not detected by previous sampling and DNA barcoding. The insect community was dominated by a few highly abundant taxa. Even closely related taxa differed in phenology, emphasizing the need for species-level resolution when describing ongoing shifts in arctic communities and ecosystems. The DNA barcode library now established for Zackenberg offers new scope for such explorations, and for the detailed dissection of interspecific interactions throughout the community.
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Affiliation(s)
- H Wirta
- Department of Agricultural Sciences, University of Helsinki, Latokartanonkaari 5, 00790, Helsinki, Finland
| | - G Várkonyi
- Finnish Environment Institute, Natural Environment Centre, Friendship Park Research Centre, Lentiirantie 342B, 88900, Kuhmo, Finland
| | - C Rasmussen
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus, Denmark
| | - R Kaartinen
- Department of Ecology, Swedish University of Agricultural Sciences, Box 7044, 750 07, Uppsala, Sweden
| | - N M Schmidt
- Arctic Research Centre, Department of Bioscience, Aarhus University, Frederiksborgvej 399, DK-4000, Roskilde, Denmark
| | - P D N Hebert
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - M Barták
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 165 21, Praha 6 - Suchdol, Czech Republic
| | - G Blagoev
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - H Disney
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - S Ertl
- Division of Conservation Biology, Vegetation Ecology and Landscape Ecology, Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Vienna, Austria
| | - P Gjelstrup
- Department of Bioscience, Aarhus University, Vejlsøvej 25, Silkeborg, DK-8600, Denmark
| | - D J Gwiazdowicz
- Department of Forest Pathology, University of Life Sciences, Wojska Polskiego 71c, Poznan, 60625, Poland
| | - L Huldén
- Finnish Museum of Natural History, Zoology Unit, University of Helsinki, Pohjoinen Rautatiekatu 13, 00100, Helsinki, Finland
| | - J Ilmonen
- Metsähallitus, Parks & Wildlife Finland, PO Box 94, 01301, Vantaa, Finland
| | - J Jakovlev
- Finnish Environment Institute, Mechelininkatu 34A, 00250, Helsinki, Finland
| | - M Jaschhof
- Station Linné, Ölands Skogsby 161, 38693, Färjestaden, Sweden
| | - J Kahanpää
- Finnish Museum of Natural History, Zoology Unit, University of Helsinki, Pohjoinen Rautatiekatu 13, 00100, Helsinki, Finland
| | - T Kankaanpää
- Department of Agricultural Sciences, University of Helsinki, Latokartanonkaari 5, 00790, Helsinki, Finland
| | - P H Krogh
- Department of Bioscience, Aarhus University, Vejlsøvej 25, Silkeborg, DK-8600, Denmark
| | - R Labbee
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - C Lettner
- Division of Conservation Biology, Vegetation Ecology and Landscape Ecology, Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Vienna, Austria
| | - V Michelsen
- Zoological Museum of the University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - S A Nielsen
- Department of Environmental, Social and Spatial Change, Roskilde University, Universitetsvej 1, PO Box 260, DK-4000, Roskilde, Denmark
| | | | | | - S Pedersen
- Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - J Pohjoismäki
- Department of Biology, University of Eastern Finland, P.O. Box 11, 80101, Joensuu, Finland
| | - J Salmela
- Metsähallitus, Ounasjoentie 6, 96101, Rovaniemi, Finland
| | - P Vilkamaa
- Finnish Museum of Natural History, Zoology Unit, University of Helsinki, Pohjoinen Rautatiekatu 13, 00100, Helsinki, Finland
| | - H Väre
- Finnish Museum of Natural History, Botany Unit, University of Helsinki, Unioninkatu 44, 00140, Helsinki, Finland
| | - M von Tschirnhaus
- Fakultät Biologie, Universität Bielefeld, Universitätsstrasse 25, 33615, Bielefeld, Germany
| | - T Roslin
- Department of Agricultural Sciences, University of Helsinki, Latokartanonkaari 5, 00790, Helsinki, Finland.,Department of Ecology, Swedish University of Agricultural Sciences, Box 7044, 750 07, Uppsala, Sweden
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Muhammad Tahir H, Akhtar S. Services of DNA barcoding in different fields. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4463-4474. [DOI: 10.3109/19401736.2015.1089572] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Samreen Akhtar
- Department of Zoology, University of Sargodha, Sargodha, Pakistan
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Andriollo T, Naciri Y, Ruedi M. Two Mitochondrial Barcodes for one Biological Species: The Case of European Kuhl's Pipistrelles (Chiroptera). PLoS One 2015; 10:e0134881. [PMID: 26241944 PMCID: PMC4524706 DOI: 10.1371/journal.pone.0134881] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/14/2015] [Indexed: 11/18/2022] Open
Abstract
The Kuhl's pipistrelle (Pipistrellus kuhlii) is a Western Palaearctic species of bat that exhibits several deeply divergent mitochondrial lineages across its range. These lineages could represent cryptic species or merely ancient polymorphism, but no nuclear markers have been studied so far to properly assess the taxonomic status of these lineages. We examined here two lineages occurring in Western Europe, and used both mitochondrial and nuclear markers to measure degrees of genetic isolation between bats carrying them. The sampling focused on an area of strict lineage sympatry in Switzerland but also included bats from further south, in North Africa. All individuals were barcoded for the COI gene to identify their mitochondrial lineages and five highly polymorphic microsatellite loci were used to cluster them according to their nuclear genotypes. Despite this low number of nuclear markers, all North African nuclear genotypes were grouped in a highly distinct subpopulation when compared with European samples sharing the same mitochondrial barcodes. The reverse situation prevailed in Switzerland where bats carrying distinct barcodes had similar nuclear genotypes. There was a weak east/west nuclear structure of populations, but this was independent of mitochondrial lineages as bats carrying either variant were completely admixed. Thus, the divergent mitochondrial barcodes present in Western Europe do not represent cryptic species, but are part of a single biological species. We argue that these distinct barcodes evolved in allopatry and came recently into secondary contact in an area of admixture north of the Alps. Historical records from this area and molecular dating support such a recent bipolar spatial expansion. These results also highlight the need for using appropriate markers before claiming the existence of cryptic species based on highly divergent barcodes.
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Affiliation(s)
- Tommy Andriollo
- Muséum d’histoire naturelle de la Ville de Genève, BP 6434, 1211 Geneva 6, Switzerland
- Université de Genève, Faculté des Sciences, Section de biologie, 1211 Geneva 4, Switzerland
- * E-mail:
| | - Yamama Naciri
- Université de Genève, Faculté des Sciences, Section de biologie, 1211 Geneva 4, Switzerland
- Conservatoire et Jardin botaniques de la Ville de Genève and University of Geneva, BP 60, 1292 Chambésy, Geneva, Switzerland
| | - Manuel Ruedi
- Muséum d’histoire naturelle de la Ville de Genève, BP 6434, 1211 Geneva 6, Switzerland
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Grosjean S, Ohler A, Chuaynkern Y, Cruaud C, Hassanin A. Improving biodiversity assessment of anuran amphibians using DNA barcoding of tadpoles. Case studies from Southeast Asia. C R Biol 2015; 338:351-61. [DOI: 10.1016/j.crvi.2015.03.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 03/19/2015] [Accepted: 03/25/2015] [Indexed: 10/23/2022]
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Robuchon M, Valero M, Gey D, Le Gall L. How does molecular-assisted identification affect our estimation of α, β and γ biodiversity? An example from understory red seaweeds (Rhodophyta) of Laminaria kelp forests in Brittany, France. Genetica 2015; 143:207-23. [PMID: 25351554 DOI: 10.1007/s10709-014-9796-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 10/15/2014] [Indexed: 12/18/2022]
Abstract
Using two distinct identification methods, one based on morphological characters only and the other combining morphological and molecular characters (integrative identification method), we investigated the differences in the biodiversity patterns of red seaweed communities associated with kelp forests at various spatial scales: the regional diversity of Brittany, France (γ-diversity), the local diversity at different Breton sites (α-diversity) and the differentiation in species diversity and abundances among those sites (β-diversity). To characterise α and β diversities, we conducted an initial survey in winter 2011 at 20 sites belonging to four different sub-regions, with specimens collected from six quadrats of 0.10 m(2) at each site, three in the tidal zone dominated by Laminaria digitata and three in the zone dominated by Laminaria hyperborea. To further characterise the regional diversity, we carried out another survey combining several sampling methods (quadrats and visual census) in different seasons (winter, spring and summer) and different years (2011 and 2012). In all, we collected 1990 specimens that were assigned to 76 taxa with the identification method based on morphological characters and 139 taxa using the integrative method. For γ and α diversity, the use of molecular characters revealed several cases of cryptic diversity and both increased the number of identified taxa and improved their taxonomic resolution. However, the addition of molecular characters for specimen identification only slightly affected estimates of β-diversity.
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Affiliation(s)
- Marine Robuchon
- Institut de Systématique, Evolution, Biodiversité, UMR 7205 CNRS, EPHE, MNHN, UPMC, Equipe Exploration, Espèces, Evolution, Muséum National d'Histoire Naturelle, Case Postale N° 39, 57 rue Cuvier, 75231, Cedex 05 Paris, France,
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González Medina A, Soriano Hernando Ó, Jiménez Ríos G. The Use of the Developmental Rate of the Aquatic Midge Chironomus riparius (Diptera, Chironomidae) in the Assessment of the Postsubmersion Interval. J Forensic Sci 2015; 60:822-6. [PMID: 25613586 DOI: 10.1111/1556-4029.12707] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 04/12/2014] [Accepted: 04/27/2014] [Indexed: 11/29/2022]
Abstract
Nonbiting midges (Diptera, Chironomidae) are the most abundant members of the fauna associated with submerged carcasses, but their use in the medicolegal context is very restricted because of their complex ontogeny. In this case, the corpse of a woman was recovered in late spring from a river in Granada (Iberian Peninsula). It showed obvious signs of long permanence in the aquatic environment and, along with pulmonary and microscopical analyses, led to the conclusion that the cause of death was drowning. Several larvae-like specimens were sampled from the scalp and later identified by morphological external features as IV instar larvae of Chironomus riparius Meigen, 1804 (Diptera, Chironomidae). Sequencing of cytochrome oxidase subunit I was performed to confirm the identification. The knowledge of the biology of C. riparius at low temperatures was critical to assess a postsubmersion interval of 16-17 days.
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Oh JT, Epler JH, Bentivegna CS. A rapid method of species identification of wild chironomids (Diptera: Chironomidae) via electrophoresis of hemoglobin proteins in sodium dodecyl sulfate polyacrylamide gel (SDS-PAGE). BULLETIN OF ENTOMOLOGICAL RESEARCH 2014; 104:639-651. [PMID: 24923437 DOI: 10.1017/s0007485314000431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Studying aquatic benthic macroinvertebrates (BMIs) in the field requires accurate taxonomic identification, which can be difficult and time consuming. Conventionally, head capsule morphology has been used to identify wild larvae of Chironomidae. However, due to the number of species and possible damage and/or deformity of their head capsules, another supporting approach for identification is needed. Here, we provide hemoglobin (Hb) protein in hemolymph of chironomids as a new biomarker that may help resolve some of the ambiguities and difficulties encountered during taxonomic identification. Chironomids collected from two locations in Maine and New Jersey, USA were identified to the genus level and in some cases to the species-level using head capsule and body morphologies. The head capsule for a particular individual was then associated with a corresponding Hb protein profile generated from sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Distinct Hb profiles were observed from one group (Thienemannimyia) and four genera (Chironomus, Cricotopus, Dicrotendipes, and Glyptotendipes) of chironomids. Several species were polymorphic, having more than one Hb profile and/or having bands of the same size as those of other species. However, major bands and the combination of bands could distinguish individuals at the genus and sometimes species-level. Overall, this study showed that Hb profiles can be used in combination with head capsule morphology to identify wild chironomids.
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Affiliation(s)
- J T Oh
- Department of Biological Sciences,Seton Hall University,South Orange, New Jersey 07079,USA
| | - J H Epler
- 461 Tiger Hammock Road, Crawfordville, Florida 32327,USA
| | - C S Bentivegna
- Department of Biological Sciences,Seton Hall University,South Orange, New Jersey 07079,USA
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Sivaramakrishnan KG, Janarthanan S, Selvakumar C, Arumugam M. Aquatic insect conservation: a molecular genetic approach. CONSERV GENET RESOUR 2014. [DOI: 10.1007/s12686-014-0250-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Wong WH, Tay YC, Puniamoorthy J, Balke M, Cranston PS, Meier R. 'Direct PCR' optimization yields a rapid, cost-effective, nondestructive and efficient method for obtaining DNA barcodes without DNA extraction. Mol Ecol Resour 2014; 14:1271-80. [PMID: 24816169 DOI: 10.1111/1755-0998.12275] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 05/05/2014] [Accepted: 05/05/2014] [Indexed: 02/04/2023]
Abstract
Macroinvertebrates that are collected in large numbers pose major problems in basic and applied biodiversity research: identification to species via morphology is often difficult, slow and/or expensive. DNA barcodes are an attractive alternative or complementary source of information. Unfortunately, obtaining DNA barcodes from specimens requires many steps and thus time and money. Here, we promote a short cut to DNA barcoding, that is, a nondestructive PCR method that skips DNA extraction ('direct PCR') and that can be used for a broad range of invertebrate taxa. We demonstrate how direct PCR can be optimized for the larvae and adults of nonbiting midges (Diptera: Chironomidae), a typical invertebrate group that is abundant, contains important bioindicator species, but is difficult to identify based on morphological features. After optimization, direct PCR yields high PCR success rates (>90%), preserves delicate morphological features (e.g. details of genitalia, and larval head capsules) while allowing for the recovery of genomic DNA. We also document that direct PCR can be successfully optimized for a wide range of other invertebrate taxa that need routine barcoding (flies: Culicidae, Drosophilidae, Dolichopodidae, Sepsidae; sea stars: Oreasteridae). Key for obtaining high PCR success rates is optimizing (i) tissue quantity, (ii) body part, (iii) primer pair and (iv) type of Taq polymerase. Unfortunately, not all invertebrates appear suitable because direct PCR has low success rates for other taxa that were tested (e.g. Coleoptera: Dytiscidae, Copepoda, Hymenoptera: Formicidae and Odonata). It appears that the technique is less successful for heavily sclerotized insects and/or those with many exocrine glands.
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Affiliation(s)
- Wing Hing Wong
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
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Hu J, Chen YD, Jiang ZL, Nardi F, Yang TY, Jin J, Zhang ZK. Global haplotype analysis of the whitefly Bemisia tabaci cryptic species Asia I in Asia. ACTA ACUST UNITED AC 2014; 26:232-41. [PMID: 24460161 DOI: 10.3109/19401736.2013.830289] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The whitefly, Bemisia tabaci (Hemiptera: Aleyrodidiae), is a cryptic species complex comprising a minimum of 24 cryptic species. Some members of this complex are important agricultural pests, causing considerable damage to vegetable as well as ornamental and horticultural crops. Asia I, one of the cryptic species of B. tabaci, is widely distributed in Asia. One hundred and sixty mitochondrial cytochrome oxidase I (COI) sequences from eight countries have been analyzed to investigate the geographic origin and current genetic structure of this cryptic species. Sixty different haplotypes were identified, with levels of genetic distances ranging from 0.001 to 0.021. A sign of possible genetic differentiation emerges from the differential distribution of dominant haplotypes in Indonesia and India compared to China. A possible ancient separation between Asia I in India and Indonesia and secondary contact in China has been hypothesized.
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Affiliation(s)
- Jian Hu
- Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Yunnan Provincial Key Lab of Agricultural Biotechnology, Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences , Kunming , China
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Lopardo L, Uhl G. Testing mitochondrial marker efficacy for DNA barcoding in spiders: a test case using the dwarf spider genus Oedothorax (Araneae : Linyphiidae : Erigoninae). INVERTEBR SYST 2014. [DOI: 10.1071/is14017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The present study focusses on comparatively assessing the efficacy for DNA barcoding of the two most commonly used mitochondrial markers (cox1 and 16S) in a genus of erigonine spiders. In total, 53 specimens representing five species, including four multi-sampled species, were sampled from several European localities. Initial evaluation of species monophyly was performed through parsimony and Bayesian phylogenetic analyses. Efficacy of mitochondrial markers was tested using operational (including distance-, tree-based measures and Barcode Gap) and evolutionary criteria (using the General Mixed Yule-coalescent Model) for species delimitation. We propose that the cox1 marker can potentially overestimate analyses of biodiversity and thus might not be the preferred marker for DNA species identification and delimitation methods in Oedothorax. Instead, our results suggest that the 16S marker appears to be a promising candidate for such endeavour. Evaluating the contribution and suitability of markers to the re-identification of species, measured by their recovery of well established morphological species, is critical for future studies and for reliable results in species identification in spiders.
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Sohal HS, Goyal A, Sharma R, Khare R, Kumar S. Glycerol mediated, one pot, multicomponent synthesis of dihydropyrano[2,3-c]pyrazoles. ACTA ACUST UNITED AC 2013. [DOI: 10.5155/eurjchem.4.4.450-453.769] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Carew ME, Pettigrove VJ, Metzeling L, Hoffmann AA. Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species. Front Zool 2013; 10:45. [PMID: 23919569 PMCID: PMC3750358 DOI: 10.1186/1742-9994-10-45] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 06/05/2013] [Indexed: 11/25/2022] Open
Abstract
Introduction Invertebrate communities are central to many environmental monitoring programs. In freshwater ecosystems, aquatic macroinvertebrates are collected, identified and then used to infer ecosystem condition. Yet the key step of species identification is often not taken, as it requires a high level of taxonomic expertise, which is lacking in most organizations, or species cannot be identified as they are morphologically cryptic or represent little known groups. Identifying species using DNA sequences can overcome many of these issues; with the power of next generation sequencing (NGS), using DNA sequences for routine monitoring becomes feasible. Results In this study, we test if NGS can be used to identify species from field-collected samples in an important bioindicator group, the Chironomidae. We show that Cytochrome oxidase I (COI) and Cytochrome B (CytB) sequences provide accurate DNA barcodes for chironomid species. We then develop a NGS analysis pipeline to identifying species using megablast searches of high quality sequences generated using 454 pyrosequencing against comprehensive reference libraries of Sanger-sequenced voucher specimens. We find that 454 generated COI sequences successfully identified up to 96% of species in samples, but this increased up to 99% when combined with CytB sequences. Accurate identification depends on having at least five sequences for a species; below this level species not expected in samples were detected. Incorrect incorporation of some multiplex identifiers (MID’s) used to tag samples was a likely cause, and most errors could be detected when using MID tags on forward and reverse primers. We also found a strong quantitative relationship between the number of 454 sequences and individuals showing that it may be possible to estimate the abundance of species from 454 pyrosequencing data. Conclusions Next generation sequencing using two genes was successful for identifying chironomid species. However, when detecting species from 454 pyrosequencing data sets it was critical to include known individuals for quality control and to establish thresholds for detecting species. The NGS approach developed here can lead to routine species-level diagnostic monitoring of aquatic ecosystems.
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Affiliation(s)
- Melissa E Carew
- Department of Zoology, Victorian Centre for Aquatic Pollution Identification and Management (CAPIM), The University of Melbourne, Victoria 3010, Australia.
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Schmidt H, Greshake B, Feldmeyer B, Hankeln T, Pfenninger M. Genomic basis of ecological niche divergence among cryptic sister species of non-biting midges. BMC Genomics 2013; 14:384. [PMID: 23758757 PMCID: PMC3685581 DOI: 10.1186/1471-2164-14-384] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/30/2013] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND There is a lack of understanding the evolutionary forces driving niche segregation of closely related organisms. In addition, pinpointing the genes driving ecological divergence is a key goal in molecular ecology. Here, larval transcriptome sequences obtained by next-generation-sequencing are used to address these issues in a morphologically cryptic sister species pair of non-biting midges (Chironomus riparius and C. piger). RESULTS More than eight thousand orthologous open reading frames were screened for interspecific divergence and intraspecific polymorphisms. Despite a small mean sequence divergence of 1.53% between the sister species, 25.1% of 18,115 observed amino acid substitutions were inferred by α statistics to be driven by positive selection. Applying McDonald-Kreitman tests to 715 alignments of gene orthologues identified eleven (1.5%) genes driven by positive selection. CONCLUSIONS Three candidate genes were identified as potentially responsible for the observed niche segregation concerning nitrite concentration, habitat temperature and water conductivity. Additionally, signs of positive selection in the hydrogen sulfide detoxification pathway were detected, providing a new plausible hypothesis for the species' ecological differentiation. Finally, a divergently selected, nuclear encoded mitochondrial ribosomal protein may contribute to reproductive isolation due to cytonuclear coevolution.
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Affiliation(s)
- Hanno Schmidt
- Molecular Ecology Group, Biodiversity and Climate Research Centre (BiK-F) by Senckenberg Gesellschaft für Naturforschung and Goethe University, Biocampus Siesmayerstraße, Frankfurt am Main, 60054, Germany
- Institute of Molecular Genetics, Biosafety Research and Consulting, Johannes Gutenberg-University, Becherweg 30a, Mainz, 55128, Germany
| | - Bastian Greshake
- Molecular Ecology Group, Biodiversity and Climate Research Centre (BiK-F) by Senckenberg Gesellschaft für Naturforschung and Goethe University, Biocampus Siesmayerstraße, Frankfurt am Main, 60054, Germany
| | - Barbara Feldmeyer
- Molecular Ecology Group, Biodiversity and Climate Research Centre (BiK-F) by Senckenberg Gesellschaft für Naturforschung and Goethe University, Biocampus Siesmayerstraße, Frankfurt am Main, 60054, Germany
- Current address: Department of Evolutionary Biology, Johannes Gutenberg-University, Johannes-von-Müller-Weg 6, Mainz, 55128, Germany
| | - Thomas Hankeln
- Institute of Molecular Genetics, Biosafety Research and Consulting, Johannes Gutenberg-University, Becherweg 30a, Mainz, 55128, Germany
| | - Markus Pfenninger
- Molecular Ecology Group, Biodiversity and Climate Research Centre (BiK-F) by Senckenberg Gesellschaft für Naturforschung and Goethe University, Biocampus Siesmayerstraße, Frankfurt am Main, 60054, Germany
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Chen CW, Huang YM, Kuo LY, Nguyen QD, Luu HT, Callado JR, Farrar DR, Chiou WL. trnL-F is a powerful marker for DNA identification of field vittarioid gametophytes (Pteridaceae). ANNALS OF BOTANY 2013; 111:663-73. [PMID: 23380240 PMCID: PMC3605945 DOI: 10.1093/aob/mct004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Accepted: 12/11/2012] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS The gametophyte phase of ferns plays an important role in habitat selection, dispersal, adaptation and evolution. However, ecological studies on fern gametophytes have been impeded due to the difficulty of species identification of free-living gametophytes. DNA barcoding provides an alternative approach to identifying fern gametophytes but is rarely applied to field studies. In this study, an example of field vittarioid gametophyte identification using DNA barcoding, which has not been done before, is given. METHODS A combination of distance-based and tree-based approaches was performed to evaluate the discriminating power of three candidate barcodes (matK, rbcL and trnL-F) on 16 vittarioid sporophytes. Sequences of the trnL-F region were generated from 15 fern gametophyte populations by tissue-direct PCR and were compared against the sporophyte dataset, using BLAST. KEY RESULTS trnL-F earns highest primer universality and discriminatory ability scores, whereas PCR success rates were very low for matK and rbcL regions (10·8 % and 41·3 %, respectively). BLAST analyses showed that all the sampled field gametophytes could be successfully identified to species level. Three gametophyte populations were also discovered to be living beyond the known occurrence of their sporophyte counterparts. CONCLUSIONS This study demonstrates that DNA barcoding (i.e. reference databasing, tissue-direct PCR and molecular analysis), especially the trnL-F region, is an efficient tool to identify field gametophytes, and has considerable potential in exploring the ecology of fern gametophytes.
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Affiliation(s)
- Cheng Wei Chen
- Division of Silviculture, Taiwan Forestry Research Institute, Taipei 10066, Taiwan
| | - Yao Moan Huang
- Division of Silviculture, Taiwan Forestry Research Institute, Taipei 10066, Taiwan
| | - Li Yaung Kuo
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Quoc Dat Nguyen
- Southern Institute of Ecology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Hong Truong Luu
- Southern Institute of Ecology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | | | - Donald R. Farrar
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011-1020 USA
| | - Wen Liang Chiou
- Division of Botanical Garden, Taiwan Forestry Research Institute, Taipei 10066, Taiwan
- For correspondence. E-mail
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Pereira LHG, Hanner R, Foresti F, Oliveira C. Can DNA barcoding accurately discriminate megadiverse Neotropical freshwater fish fauna? BMC Genet 2013; 14:20. [PMID: 23497346 PMCID: PMC3608943 DOI: 10.1186/1471-2156-14-20] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 03/05/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The megadiverse Neotropical freshwater ichthyofauna is the richest in the world with approximately 6,000 recognized species. Interestingly, they are distributed among only 17 orders, and almost 80% of them belong to only three orders: Characiformes, Siluriformes and Perciformes. Moreover, evidence based on molecular data has shown that most of the diversification of the Neotropical ichthyofauna occurred recently. These characteristics make the taxonomy and identification of this fauna a great challenge, even when using molecular approaches. In this context, the present study aimed to test the effectiveness of the barcoding methodology (COI gene) to identify the mega diverse freshwater fish fauna from the Neotropical region. For this purpose, 254 species of fishes were analyzed from the Upper Parana River basin, an area representative of the larger Neotropical region. RESULTS Of the 254 species analyzed, 252 were correctly identified by their barcode sequences (99.2%). The main K2P intra- and inter-specific genetic divergence values (0.3% and 6.8%, respectively) were relatively low compared with similar values reported in the literature, reflecting the higher number of closely related species belonging to a few higher taxa and their recent radiation. Moreover, for 84 pairs of species that showed low levels of genetic divergence (<2%), application of a complementary character-based nucleotide diagnostic approach proved useful in discriminating them. Additionally, 14 species displayed high intra-specific genetic divergence (>2%), pointing to at least 23 strong candidates for new species. CONCLUSIONS Our study is the first to examine a large number of freshwater fish species from the Neotropical area, including a large number of closely related species. The results confirmed the efficacy of the barcoding methodology to identify a recently radiated, megadiverse fauna, discriminating 99.2% of the analyzed species. The power of the barcode sequences to identify species, even with low interspecific divergence, gives us an idea of the distribution of inter-specific genetic divergence in these megadiverse fauna. The results also revealed hidden genetic divergences suggestive of reproductive isolation and putative cryptic speciation in some species (23 candidates for new species). Finally, our study constituted an important contribution to the international Barcoding of Life (iBOL.org) project, providing barcode sequences for use in identification of these species by experts and non-experts, and allowing them to be available for use in other applications.
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Affiliation(s)
- Luiz H G Pereira
- Laboratory of Biology and Genetic of Fish, Department of Morphology, Biosciences Institute, State University of São Paulo, São Paulo, Brazil.
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Brodin Y, Ejdung G, Strandberg J, Lyrholm T. Improving environmental and biodiversity monitoring in the Baltic Sea using DNA barcoding of Chironomidae (Diptera). Mol Ecol Resour 2012; 13:996-1004. [PMID: 23280321 DOI: 10.1111/1755-0998.12053] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 11/07/2012] [Accepted: 11/08/2012] [Indexed: 11/30/2022]
Abstract
As for many other regions, environmental and biodiversity monitoring of the brackish Baltic Sea suffers from low species resolution for several taxa. One such case is the benthic larvae of midges Chironomidae (Diptera), which are estimated to constitute about 30% of the macrozoobenthos species of the Baltic Sea and are important indicators of environmental quality. We assessed the usefulness of COI (cytochrome oxidase I) gene barcoding to improve species resolution and its potential for implementation in monitoring programmes. Neighbour-Joining, Maximum parsimony and Bayesian-inference analyses all provided high congruency with morphological analyses of adult males for almost all 42 species studied. Barcoding was helpful to elucidate some cases of taxonomical difficulties, such as synonyms. In contrast to the high identification accuracy when using our local database, there were a number of cases where matching with GenBank and BOLD provided puzzling results. For reliable species identification at least 15-30 specimens from 5-10 well-distributed sites within the geographical range of the species might be needed in a database to adequately cover the intraspecific variability of chironomids. Implementation of DNA barcoding, as applied here, in monitoring would result in an increase from at present less than 10% to more than 90% successful chironomid species identification of Baltic Sea benthic samples, as it also would for many nearby lakes. Routine monitoring of benthic environmental samples based on Next-Generation sequencing techniques would provide a cost effective way to obtain a taxonomically much more complete assessment of environmental quality and biodiversity, as required by EU directives and national legislation.
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Affiliation(s)
- Y Brodin
- The Swedish Museum of Natural History, Box 50007, Stockholm, 104 05, Sweden
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Leite LAR. Mitochondrial pseudogenes in insect DNA barcoding: differing points of view on the same issue. BIOTA NEOTROPICA 2012. [DOI: 10.1590/s1676-06032012000300029] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Molecular tools have been used in taxonomy for the purpose of identification and classification of living organisms. Among these, a short sequence of the mitochondrial DNA, popularly known as DNA barcoding, has become very popular. However, the usefulness and dependability of DNA barcodes have been recently questioned because mitochondrial pseudogenes, non-functional copies of the mitochondrial DNA incorporated into the nuclear genome, have been found in various taxa. When these paralogous sequences are amplified together with the mitochondrial DNA, they may go unnoticed and end up being analyzed as if they were orthologous sequences. In this contribution the different points of view regarding the implications of mitochondrial pseudogenes for entomology are reviewed and discussed. A discussion of the problem from a historical and conceptual perspective is presented as well as a discussion of strategies to keep these nuclear mtDNA copies out of sequence analyzes.
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Cruz-Barraza JA, Carballo JL, Rocha-Olivares A, Ehrlich H, Hog M. Integrative taxonomy and molecular phylogeny of genus Aplysina (Demospongiae: Verongida) from Mexican Pacific. PLoS One 2012; 7:e42049. [PMID: 22912682 PMCID: PMC3418280 DOI: 10.1371/journal.pone.0042049] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 07/02/2012] [Indexed: 11/18/2022] Open
Abstract
Integrative taxonomy provides a major approximation to species delimitation based on integration of different perspectives (e.g. morphology, biochemistry and DNA sequences). The aim of this study was to assess the relationships and boundaries among Eastern Pacific Aplysina species using morphological, biochemical and molecular data. For this, a collection of sponges of the genus Aplysina from the Mexican Pacific was studied on the basis of their morphological, chemical (chitin composition), and molecular markers (mitochondrial COI and nuclear ribosomal rDNA: ITS1-5.8-ITS2). Three morphological species were identified, two of which are new to science. A. clathrata sp. nov. is a yellow to yellow-reddish or -brownish sponge, characterized by external clathrate-like morphology; A. revillagigedi sp. nov. is a lemon yellow to green, cushion-shaped sometimes lobate sponge, characterized by conspicuous oscules, which are slightly elevated and usually linearly distributed on rims; and A. gerardogreeni a known species distributed along the Mexican Pacific coast. Chitin was identified as the main structural component within skeletons of the three species using FTIR, confirming that it is shared among Verongida sponges. Morphological differences were confirmed by DNA sequences from nuclear ITS1-5.8-ITS2. Mitochondrial COI sequences showed extremely low but diagnostic variability for Aplysina revillagigedi sp. nov., thus our results corroborate that COI has limited power for DNA-barcoding of sponges and should be complemented with other markers (e.g. rDNA). Phylogenetic analyses of Aplysina sequences from the Eastern Pacific and Caribbean, resolved two allopatric and reciprocally monophyletic groups for each region. Eastern Pacific species were grouped in general accordance with the taxonomic hypothesis based on morphological characters. An identification key of Eastern Pacific Aplysina species is presented. Our results constitute one of the first approximations to integrative taxonomy, phylogeny and evolutionary biogeography of Eastern Pacific marine sponges; an approach that will significantly contribute to our better understanding of their diversity and evolutionary history.
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Affiliation(s)
- José Antonio Cruz-Barraza
- Unidad Académica Mazatlán, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mazatlán Sinaloa, México.
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