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Huemer P, Karsholt O, Aarvik L, Berggren K, Bidzilya O, Junnilainen J, Landry JF, Mutanen M, Nupponen K, Segerer A, Šumpich J, Wieser C, Wiesmair B, Hebert PDN. DNA barcode library for European Gelechiidae (Lepidoptera) suggests greatly underestimated species diversity. Zookeys 2020; 921:141-157. [PMID: 32256152 PMCID: PMC7109146 DOI: 10.3897/zookeys.921.49199] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 02/06/2020] [Indexed: 11/12/2022] Open
Abstract
For the first time, a nearly complete barcode library for European Gelechiidae is provided. DNA barcode sequences (COI gene – cytochrome c oxidase 1) from 751 out of 865 nominal species, belonging to 105 genera, were successfully recovered. A total of 741 species represented by specimens with sequences ≥ 500bp and an additional ten species represented by specimens with shorter sequences were used to produce 53 NJ trees. Intraspecific barcode divergence averaged only 0.54% whereas distance to the Nearest-Neighbour species averaged 5.58%. Of these, 710 species possessed unique DNA barcodes, but 31 species could not be reliably discriminated because of barcode sharing or partial barcode overlap. Species discrimination based on the Barcode Index System (BIN) was successful for 668 out of 723 species which clustered from minimum one to maximum 22 unique BINs. Fifty-five species shared a BIN with up to four species and identification from DNA barcode data is uncertain. Finally, 65 clusters with a unique BIN remained unidentified to species level. These putative taxa, as well as 114 nominal species with more than one BIN, suggest the presence of considerable cryptic diversity, cases which should be examined in future revisionary studies.
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Affiliation(s)
- Peter Huemer
- Naturwissenschaftliche Sammlungen, Tiroler Landesmuseen Betriebsges.m.b.H., Innsbruck, Austria Tiroler Landesmuseen Betriebsges.m.b.H. Innsbruck Austria
| | - Ole Karsholt
- Zoological Museum, Natural History Museum of Denmark, Copenhagen, Denmark Natural History Museum of Denmark Copenhagen Denmark
| | - Leif Aarvik
- Natural History Museum, University of Oslo, Oslo, Norway University of Oslo Oslo Norway
| | - Kai Berggren
- Kristiansand, Norway Unaffiliated Kristiansand Norway
| | - Oleksiy Bidzilya
- Institute for Evolutionary Ecology of the National Academy of Sciences of Ukraine, Kiev, Ukraine Institute for Evolutionary Ecology, National Academy of Sciences of Ukraine Kiev Ukraine
| | - Jari Junnilainen
- Finnish Museum of Natural History, Zoology Unit, Helsinki, Finland Finnish Museum of Natural History Helsinki Finland
| | - Jean-François Landry
- Canadian National Collection of Insects, Arachnids, and Nematodes, Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Canada Agriculture and Agri-Food Canada Ottawa Canada
| | - Marko Mutanen
- Department of Ecology and Genetics, University of Oulu, Finland University of Oulu Oulu Finland
| | | | - Andreas Segerer
- SNSB-Zoological State Collection, Munich, Germany Zoological State Collection Munich Germany
| | - Jan Šumpich
- National Museum, Natural History Museum, Department of Entomology, Praha, Czech Republic Natural History Museum Prague Czech Republic
| | - Christian Wieser
- Landesmuseum Kärnten, Klagenfurt, Austria Landesmuseum Kärnten Klagenfurt am Wörthersee Austria
| | - Benjamin Wiesmair
- Naturwissenschaftliche Sammlungen, Tiroler Landesmuseen Betriebsges.m.b.H., Innsbruck, Austria Tiroler Landesmuseen Betriebsges.m.b.H. Innsbruck Austria
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada University of Guelph Guelph Canada
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Habel JC, Segerer A, Ulrich W, Torchyk O, Weisser WW, Schmitt T. Butterfly community shifts over two centuries. Conserv Biol 2016; 30:754-762. [PMID: 26743786 DOI: 10.1111/cobi.12656] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 10/14/2015] [Accepted: 10/15/2015] [Indexed: 06/05/2023]
Abstract
Environmental changes strongly impact the distribution of species and subsequently the composition of species assemblages. Although most community ecology studies represent temporal snap shots, long-term observations are rather rare. However, only such time series allow the identification of species composition shifts over several decades or even centuries. We analyzed changes in the species composition of a southeastern German butterfly and burnet moth community over nearly 2 centuries (1840-2013). We classified all species observed over this period according to their ecological tolerance, thereby assessing their degree of habitat specialisation. This classification was based on traits of the butterfly and burnet moth species and on their larval host plants. We collected data on temperature and precipitation for our study area over the same period. The number of species declined substantially from 1840 (117 species) to 2013 (71 species). The proportion of habitat specialists decreased, and most of these are currently endangered. In contrast, the proportion of habitat generalists increased. Species with restricted dispersal behavior and species in need of areas poor in soil nutrients had severe losses. Furthermore, our data indicated a decrease in species composition similarity between different decades over time. These data on species composition changes and the general trends of modifications may reflect effects from climate change and atmospheric nitrogen loads, as indicated by the ecological characteristics of host plant species and local changes in habitat configuration with increasing fragmentation. Our observation of major declines over time of currently threatened and protected species shows the importance of efficient conservation strategies.
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Affiliation(s)
- Jan Christian Habel
- Terrestrial Ecology Research Group, Department of Ecology and Ecosystem Management, School of Life Sciences Weihenstephan, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, D-85354, Freising, Germany
| | - Andreas Segerer
- Bavarian State Collection of Zoology, D-81247, Munich, Germany
| | - Werner Ulrich
- Chair of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Pl-87-100, Toruń, Poland
| | - Olena Torchyk
- Terrestrial Ecology Research Group, Department of Ecology and Ecosystem Management, School of Life Sciences Weihenstephan, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, D-85354, Freising, Germany
| | - Wolfgang W Weisser
- Terrestrial Ecology Research Group, Department of Ecology and Ecosystem Management, School of Life Sciences Weihenstephan, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, D-85354, Freising, Germany
| | - Thomas Schmitt
- Senckenberg German Entomological Institute, D-15374, Müncheberg, Germany
- Department of Zoology, Faculty of Natural Sciences, Institute of Biology, Martin Luther University Halle-Wittenberg, D-06099, Halle (Saale), Germany
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Mutanen M, Kivelä SM, Vos RA, Doorenweerd C, Ratnasingham S, Hausmann A, Huemer P, Dincă V, van Nieukerken EJ, Lopez-Vaamonde C, Vila R, Aarvik L, Decaëns T, Efetov KA, Hebert PDN, Johnsen A, Karsholt O, Pentinsaari M, Rougerie R, Segerer A, Tarmann G, Zahiri R, Godfray HCJ. Species-Level Para- and Polyphyly in DNA Barcode Gene Trees: Strong Operational Bias in European Lepidoptera. Syst Biol 2016; 65:1024-1040. [PMID: 27288478 PMCID: PMC5066064 DOI: 10.1093/sysbio/syw044] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 04/18/2016] [Accepted: 04/18/2016] [Indexed: 11/14/2022] Open
Abstract
The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service “Monophylizer” to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set of DNA barcodes analyzed from this regard. Particular attention was paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12% incidence of non-monophyly, a value significantly lower than that observed in previous studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded almost equal numbers of non-monophyletic species, but 24.1% of these cases of non-monophyly were only found by one of these methods. Non-monophyletic species tend to show either low genetic distances to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling effort, we estimate that the true incidence of non-monophyly is ∼23%, but with operational factors still being included. Within the operational factors, we separately assessed the frequency of taxonomic limitations (presence of overlooked cryptic and oversplit species) and identification uncertainties. We observed that operational factors are potentially present in more than half (58.6%) of the detected cases of non-monophyly. Furthermore, we observed that in about 20% of non-monophyletic species and entangled species, the lineages involved are either allopatric or parapatric—conditions where species delimitation is inherently subjective and particularly dependent on the species concept that has been adopted. These observations suggest that species-level non-monophyly in COI gene trees is less common than previously supposed, with many cases reflecting misidentifications, the subjectivity of species delimitation or other operational factors.
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Affiliation(s)
- Marko Mutanen
- Department of Genetics and Physiology, University of Oulu, Finland;
| | | | - Rutger A Vos
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | - Sujeevan Ratnasingham
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Canada
| | - Axel Hausmann
- SNSB - Bavarian State Collection of Zoology, Munich, Germany
| | - Peter Huemer
- Tiroler Landesmuseen-Betriebsgesellschaft m.b.H., Innsbruck, Austria
| | - Vlad Dincă
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Canada.,Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | | | - Carlos Lopez-Vaamonde
- INRA, UR633 Zoologie Forestière, 45075 Orléans, France.,Institut de Recherche sur la Biologie de l'Insecte, CNRS UMR 7261, Université François-Rabelais de Tours, UFR Sciences et Techniques, 37200 Tours, France
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Leif Aarvik
- Natural History Museum University of Oslo, Norway
| | - Thibaud Decaëns
- Centre d'Écologie Fonctionnelle et Évolutive, UMR 5175 CNRS / University of Montpellier / University of Montpellier 3 / EPHE / SupAgro Montpellier / INRA / IRD, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
| | | | - Paul D N Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Canada
| | | | - Ole Karsholt
- Zoologisk Museum, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | | | - Rodolphe Rougerie
- Département Systématique et Evolution, Muséum National d'Histoire Naturelle, Institut de Systématique, Evolution, Biodiversité, ISYEB-UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Paris, France
| | - Andreas Segerer
- SNSB - Bavarian State Collection of Zoology, Munich, Germany
| | - Gerhard Tarmann
- Tiroler Landesmuseen-Betriebsgesellschaft m.b.H., Innsbruck, Austria
| | - Reza Zahiri
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Canada.,Ottawa Plant Laboratory, Canadian Food Inspection Agency, Canada
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Abstract
Sulphur-dependent archaebacteria, which are found around nearly boiling continental solfataric springs and mud holes, can be assigned to two distinct branches: the aerobic, sulphur-oxidizing Sulfolobales and the strictly anaerobic sulphur-reducing Thermoproteales. Here, we report the isolation of a group of extremely thermophilic solfataric archaebacteria that are able to grow either strictly anaerobically by reduction, or fully aerobically by oxidation of molecular sulphur, depending on the oxygen supply. We have also established that the ability to grow in these two ways is shared by Sulfolobus brierleyi, a well-known less thermophilic sulphur-oxidizing archaebacterium capable of ore-leaching. The phenomenon may be dependent on a fundamental switch in genome expression. These organisms might represent the primitive fore-runners of sulphur-oxidizing archaebacteria, meeting their energy requirements either by oxidation or by reduction of the same element.
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