1
|
Vuataz L, Reding JP, Reding A, Roesti C, Stoffel C, Vinçon G, Gattolliat JL. A comprehensive DNA barcoding reference database for Plecoptera of Switzerland. Sci Rep 2024; 14:6322. [PMID: 38491157 PMCID: PMC10943188 DOI: 10.1038/s41598-024-56930-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 03/12/2024] [Indexed: 03/18/2024] Open
Abstract
DNA barcoding is an essential tool in modern biodiversity sciences. Despite considerable work to barcode the tree of life, many groups, including insects, remain partially or totally unreferenced, preventing barcoding from reaching its full potential. Aquatic insects, especially the three orders Ephemeroptera, Plecoptera, and Trichoptera (EPT), are key freshwater quality indicators worldwide. Among them, Plecoptera (stoneflies), which are among the most sensitive aquatic insects to habitat modification, play a central role in river monitoring surveys. Here, we present an update of the Plecoptera reference database for (meta)barcoding in Switzerland, now covering all 118 species known from this country. Fresh specimens, mostly from rare or localized species, were collected, and 151 new CO1 barcodes were generated. These were merged with the 422 previously published sequences, resulting in a dataset of 573 barcoded specimens. Our CO1 dataset was delimited in 115 CO1 clusters based on a priori morphological identifications, of which 17% are newly reported for Switzerland, and 4% are newly reported globally. Among the 115 CO1 clusters, 85% showed complete congruence with morphology. Distance-based analysis indicated local barcoding gaps in 97% of the CO1 clusters. This study significantly improves the Swiss reference database for stoneflies, enhancing future species identification accuracy and biodiversity monitoring. Additionally, this work reveals cryptic diversity and incongruence between morphology and barcodes, both presenting valuable opportunities for future integrative taxonomic studies. Voucher specimens, DNA extractions and reference barcodes are available for future developments, including metabarcoding and environmental DNA surveys.
Collapse
Affiliation(s)
- Laurent Vuataz
- Département de zoologie, Palais de Rumine, Muséum cantonal des sciences naturelles, Place Riponne 6, 1005, Lausanne, Switzerland.
- Department of Ecology and Evolution, University of Lausanne (UNIL), 1015, Lausanne, Switzerland.
| | | | | | | | - Céline Stoffel
- Département de zoologie, Palais de Rumine, Muséum cantonal des sciences naturelles, Place Riponne 6, 1005, Lausanne, Switzerland
- Department of Ecology and Evolution, University of Lausanne (UNIL), 1015, Lausanne, Switzerland
| | | | - Jean-Luc Gattolliat
- Département de zoologie, Palais de Rumine, Muséum cantonal des sciences naturelles, Place Riponne 6, 1005, Lausanne, Switzerland
- Department of Ecology and Evolution, University of Lausanne (UNIL), 1015, Lausanne, Switzerland
| |
Collapse
|
2
|
Ahrens D. Species Diagnosis and DNA Taxonomy. Methods Mol Biol 2024; 2744:33-52. [PMID: 38683310 DOI: 10.1007/978-1-0716-3581-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
The use of DNA has helped to improve and speed up species identification and delimitation. However, it also provides new challenges to taxonomists. Incongruence of outcome from various markers and delimitation methods, bias from sampling and skewed species distribution, implemented models, and the choice of methods/priors may mislead results and also may, in conclusion, increase elements of subjectivity in species taxonomy. The lack of direct diagnostic outcome from most contemporary molecular delimitation approaches and the need for a reference to existing and best sampled trait reference systems reveal the need for refining the criteria of species diagnosis and diagnosability in the current framework of nomenclature codes and good practices to avoid nomenclatorial instability, parallel taxonomies, and consequently more and new taxonomic impediment.
Collapse
Affiliation(s)
- Dirk Ahrens
- Museum A. Koenig Bonn, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany.
| |
Collapse
|
3
|
Kayastha P, Szydło W, Mioduchowska M, Kaczmarek Ł. Morphological and genetic variability in cosmopolitan tardigrade species-Paramacrobiotus fairbanksi Schill, Förster, Dandekar & Wolf, 2010. Sci Rep 2023; 13:17672. [PMID: 37848470 PMCID: PMC10582252 DOI: 10.1038/s41598-023-42653-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 09/13/2023] [Indexed: 10/19/2023] Open
Abstract
Paramacrobiotus fairbanksi was described from Alaska (USA) based on integrative taxonomy and later reported from various geographical localities making it a true cosmopolitan species. The 'Everything is Everywhere' (EiE) hypothesis assumes that the geographic distribution of microscopic organisms is not limited by dispersal but by local environmental conditions, making them potentially cosmopolitan. In the present work we report four new populations of P. fairbanksi from the Northern Hemisphere which suggests that the 'EiE' hypothesis is true, at least for some tardigrade species. We also compared all known populations of P. fairbanksi at the genetic and morphological levels. The p-distances between COI haplotypes of all sequenced P. fairbanksi populations from Albania, Antarctica, Canada, Italy, Madeira, Mongolia, Spain, USA and Poland ranged from 0.002 to 0.005%. In total, twelve haplotypes (H1-H12) of COI gene fragments were identified. We also report statistically significant morphometrical differences of species even though they were cultured and bred in the same laboratory conditions. Furthermore, we also discuss differences in the potential distribution of two Paramacrobiotus species.
Collapse
Affiliation(s)
- Pushpalata Kayastha
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
| | - Wiktoria Szydło
- Center for Advanced Technology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 10, 61-614, Poznań, Poland
- Population Ecology Lab, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Monika Mioduchowska
- Department of Evolutionary Genetics and Biosystematics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308, Gdańsk, Poland
| | - Łukasz Kaczmarek
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| |
Collapse
|
4
|
Liu JX, Reshchikov A, Chen HY. Descriptions of Three New Species of the Genus Acerataspis Uchida, 1934 (Hymenoptera, Ichneumonidae, Metopiinae), with an Illustrated Identification Key to Extant Species. INSECTS 2023; 14:389. [PMID: 37103204 PMCID: PMC10142930 DOI: 10.3390/insects14040389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/06/2023] [Accepted: 04/10/2023] [Indexed: 06/19/2023]
Abstract
The Asian genus Acerataspis Uchida, 1934 is reviewed based on both morphology and DNA barcodes. Ten species are recognized in total, of which three species from Yunnan Province of China are described as new: Acerataspis maliae sp. nov., A. seperata sp. nov. and A. similis sp. nov. The male of A. fukienensis Chao, 1957 is described and illustrated for the first time. The genus is recorded from Thailand and Southeast Asia for the first time. An illustrated key to all known extant species is provided. With the supplement of DNA barcodes, a few diagnostic morphological characters are found useful in species identification.
Collapse
Affiliation(s)
- Jing-Xian Liu
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Alexey Reshchikov
- Institute of Eastern Himalaya Biodiversity Research, Dali University, Dali 671003, China
| | - Hua-Yan Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| |
Collapse
|
5
|
Crowley L, Allen H, Barnes I, Boyes D, Broad GR, Fletcher C, Holland PW, Januszczak I, Lawniczak M, Lewis OT, Macadam CR, Mulhair PO, Pereira da Conceicoa L, Price BW, Raper C, Sivell O, Sivess L. A sampling strategy for genome sequencing the British terrestrial arthropod fauna. Wellcome Open Res 2023. [DOI: 10.12688/wellcomeopenres.18925.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
Abstract
The Darwin Tree of Life (DToL) project aims to sequence and assemble high-quality genomes from all eukaryote species in Britain and Ireland, with the first phase of the project concentrating on family-level coverage plus species of particular ecological, biomedical or evolutionary interest. We summarise the processes involved in (1) assessing the UK arthropod fauna and the status of individual species on UK lists; (2) prioritising and collecting species for initial genome sequencing; (3) handling methods to ensure that high-quality genomic DNA is preserved; and (4) compiling standard operating procedures for processing specimens for genome sequencing, identification verification and voucher specimen curation. We briefly explore some lessons learned from the pilot phase of DToL and the impact of the Covid-19 pandemic.
Collapse
|
6
|
Takasuka K, Arakawa K. The Method of Eliminating the Wolbachia Endosymbiont Genomes from Insect Samples Prior to a Long-Read Sequencing. Methods Mol Biol 2023; 2632:101-112. [PMID: 36781724 DOI: 10.1007/978-1-0716-2996-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
When extracting DNA of invertebrates for long-read sequencing, not only enough quantity and size of the DNA but, depending on the species, elimination of contamination of endosymbiotic Wolbachia genome also has to be achieved. These requirements become troublesome, especially in small-sized species with a limited number of individuals available for the experiment. In this chapter, using tiny parasitoid wasps (Reclinervellus nielseni) parasitizing spiders as hosts, we developed a method of eliminating the Wolbachia genomes by means of an antibiotic administration to adult wasps via honey solution. Twenty days of rifampicin treatment since their emergence from cocoons resulted in a significant decrease in the Wolbachia genomes while keeping good DNA conditions for nanopore sequencing. An adequate quantity of DNA was then gained by pooling several individuals. The method could be applied to other insects or invertebrates that can be maintained by laboratory feeding with liquid food.
Collapse
Affiliation(s)
- Keizo Takasuka
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan.,Graduate School of Media and Governance, Keio University, Kanagawa, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan.,Graduate School of Media and Governance, Keio University, Kanagawa, Japan
| |
Collapse
|
7
|
Rodrigues BL, Galati EAB. Molecular taxonomy of phlebotomine sand flies (Diptera, Psychodidae) with emphasis on DNA barcoding: A review. Acta Trop 2023; 238:106778. [PMID: 36435214 DOI: 10.1016/j.actatropica.2022.106778] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022]
Abstract
The taxonomy and systematics of sand flies (Diptera, Psychodidae, Phlebotominae) are one of the pillars of research aimed to identifying vector populations and the agents transmitted by these insects. Traditionally, the use of morphological traits has been the main line of evidence for the definition of species, but the use of DNA sequences is useful as an integrative approach for their delimitation. Here, we discuss the current status of the molecular taxonomy of sand flies, including their most sequenced molecular markers and the main results. Only about 37% of all sand fly species have been processed for any molecular marker and are publicly available in the NCBI GenBank or BOLD Systems databases. The genera Phlebotomus, Nyssomyia, Psathyromyia and Psychodopygus are well-sampled, accounting for more than 56% of their sequenced species. However, less than 34% of the species of Sergentomyia, Lutzomyia, Trichopygomyia and Trichophoromyia have been sampled, representing a major gap in the knowledge of these groups. The most sequenced molecular markers are those within mtDNA, especially the DNA barcoding fragment of the cytochrome c oxidase subunit I (coi) gene, which has shown promising results in detecting cryptic diversity within species. Few sequences of conserved genes have been generated, which hampers higher-level phylogenetic inferences. We argue that sand fly species should be sequenced for at least the coi DNA barcoding marker, but multiple markers with different mutation rates should be assessed, whenever possible, to generate multilocus analysis.
Collapse
Affiliation(s)
- Bruno Leite Rodrigues
- Programa de Pós-Graduação em Saúde Pública, Faculdade de Saúde Pública da Universidade de São Paulo (FSP/USP). Av. Dr. Arnaldo, 715 - Cerqueira César, São Paulo SP, Brazil, 01246-904.
| | - Eunice Aparecida Bianchi Galati
- Programa de Pós-Graduação em Saúde Pública, Faculdade de Saúde Pública da Universidade de São Paulo (FSP/USP). Av. Dr. Arnaldo, 715 - Cerqueira César, São Paulo SP, Brazil, 01246-904
| |
Collapse
|
8
|
Urfer K, Spasojevic T, Klopfstein S, Baur H, Lasut L, Kropf C. Incongruent molecular and morphological variation in the crab spider Synemaglobosum (Araneae, Thomisidae) in Europe. Zookeys 2021; 1078:107-134. [PMID: 35068955 PMCID: PMC8709837 DOI: 10.3897/zookeys.1078.64116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 10/29/2021] [Indexed: 11/12/2022] Open
Abstract
Establishing species boundaries is one of the challenges taxonomists around the world have been tackling for centuries. The relation between intraspecific and interspecific variability is still under discussion and in many taxa it remains understudied. Here the hypothesis of single versus multiple species of the crab spider Synemaglobosum (Fabricius) is tested. The wide distribution range as well as its high morphological variability makes this species an interesting candidate for re-evaluation using an integrative approach. This study combines information from barcoding, phylogenetic reconstruction based on mitochondrial CO1 and ITS2 of more than 60 specimens collected over a wide range of European localities, and morphology. The findings show deep clades with up to 6% mean pairwise distance in the CO1 barcode without any biogeographical pattern. The nuclear ITS2 gene did not support the CO1 clades. Morphological assessment of somatic and genital characters in males and females and a morphometric analysis of the male palp uncovered high intraspecific variation that does not match the CO1 or ITS2 phylogenies or biogeography either. Screening for endosymbiotic Wolbachia bacteria was conducted and only a single infected specimen was found. Several scenarios might explain these inconsistent patterns. While the deep divergences in the barcoding marker might suggest cryptic or ongoing speciation or geographical isolation in the past, the lack of congruent variation in the nuclear ITS2 gene or the studied morphological character systems, especially the male palp, indicates that S.globosum might simply be highly polymorphic both in terms of its mtDNA and morphology. Therefore, more data on ecology and behaviour and full genome sequences are necessary to ultimately resolve this taxonomically intriguing case.
Collapse
Affiliation(s)
- Karin Urfer
- Natural History Museum Bern, Bernastrasse 15, 3005 Bern, SwitzerlandNatural History Museum BernBernSwitzerland
- University of Bern, Institute of Ecology and Evolution, Baltzerstrasse 6, 3012 Bern, SwitzerlandUniversity of BernBernSwitzerland
- Natural History Museum St.Gallen, Rorschacher Strasse 263, 9016 St.Gallen, SwitzerlandNatural History Museum BaselBaselSwitzerland
- Natural History Museum Basel, Augustinergasse 2, 4051 Basel, SwitzerlandNatural History Museum St.GallenSt.GallenSwitzerland
| | - Tamara Spasojevic
- University of Bern, Institute of Ecology and Evolution, Baltzerstrasse 6, 3012 Bern, SwitzerlandUniversity of BernBernSwitzerland
- Natural History Museum Basel, Augustinergasse 2, 4051 Basel, SwitzerlandNatural History Museum St.GallenSt.GallenSwitzerland
| | - Seraina Klopfstein
- University of Bern, Institute of Ecology and Evolution, Baltzerstrasse 6, 3012 Bern, SwitzerlandUniversity of BernBernSwitzerland
- Natural History Museum Basel, Augustinergasse 2, 4051 Basel, SwitzerlandNatural History Museum St.GallenSt.GallenSwitzerland
| | - Hannes Baur
- Natural History Museum Bern, Bernastrasse 15, 3005 Bern, SwitzerlandNatural History Museum BernBernSwitzerland
- University of Bern, Institute of Ecology and Evolution, Baltzerstrasse 6, 3012 Bern, SwitzerlandUniversity of BernBernSwitzerland
| | - Liana Lasut
- Natural History Museum Bern, Bernastrasse 15, 3005 Bern, SwitzerlandNatural History Museum BernBernSwitzerland
- University of Bern, Institute of Ecology and Evolution, Baltzerstrasse 6, 3012 Bern, SwitzerlandUniversity of BernBernSwitzerland
| | - Christian Kropf
- Natural History Museum Bern, Bernastrasse 15, 3005 Bern, SwitzerlandNatural History Museum BernBernSwitzerland
- University of Bern, Institute of Ecology and Evolution, Baltzerstrasse 6, 3012 Bern, SwitzerlandUniversity of BernBernSwitzerland
| |
Collapse
|
9
|
Lue CH, Buffington ML, Scheffer S, Lewis M, Elliott TA, Lindsey ARI, Driskell A, Jandova A, Kimura MT, Carton Y, Kula RR, Schlenke TA, Mateos M, Govind S, Varaldi J, Guerrieri E, Giorgini M, Wang X, Hoelmer K, Daane KM, Abram PK, Pardikes NA, Brown JJ, Thierry M, Poirié M, Goldstein P, Miller SE, Tracey WD, Davis JS, Jiggins FM, Wertheim B, Lewis OT, Leips J, Staniczenko PPA, Hrcek J. DROP: Molecular voucher database for identification of Drosophila parasitoids. Mol Ecol Resour 2021; 21:2437-2454. [PMID: 34051038 DOI: 10.1111/1755-0998.13435] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 01/03/2023]
Abstract
Molecular identification is increasingly used to speed up biodiversity surveys and laboratory experiments. However, many groups of organisms cannot be reliably identified using standard databases such as GenBank or BOLD due to lack of sequenced voucher specimens identified by experts. Sometimes a large number of sequences are available, but with too many errors to allow identification. Here, we address this problem for parasitoids of Drosophila by introducing a curated open-access molecular reference database, DROP (Drosophila parasitoids). Identifying Drosophila parasitoids is challenging and poses a major impediment to realize the full potential of this model system in studies ranging from molecular mechanisms to food webs, and in biological control of Drosophila suzukii. In DROP, genetic data are linked to voucher specimens and, where possible, the voucher specimens are identified by taxonomists and vetted through direct comparison with primary type material. To initiate DROP, we curated 154 laboratory strains, 856 vouchers, 554 DNA sequences, 16 genomes, 14 transcriptomes, and six proteomes drawn from a total of 183 operational taxonomic units (OTUs): 114 described Drosophila parasitoid species and 69 provisional species. We found species richness of Drosophila parasitoids to be heavily underestimated and provide an updated taxonomic catalogue for the community. DROP offers accurate molecular identification and improves cross-referencing between individual studies that we hope will catalyse research on this diverse and fascinating model system. Our effort should also serve as an example for researchers facing similar molecular identification problems in other groups of organisms.
Collapse
Affiliation(s)
- Chia-Hua Lue
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
- Department of Biology, Brooklyn College, City University of New York (CUNY), Brooklyn, NY, USA
| | - Matthew L Buffington
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Sonja Scheffer
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Matthew Lewis
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Tyler A Elliott
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Amy Driskell
- Laboratories of Analytical Biology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Anna Jandova
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
| | | | - Yves Carton
- "Évolution, Génomes, Comportement, Écologie", CNRS et Université Paris-Saclay, Paris, France
| | - Robert R Kula
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Todd A Schlenke
- Department of Entomology, University of Arizona, Tucson, AZ, USA
| | - Mariana Mateos
- Wildlife and Fisheries Sciences Department, Texas A&M University, College Station, TX, USA
| | - Shubha Govind
- The Graduate Center of the City University of New York, New York, NY, USA
| | - Julien Varaldi
- CNRS, Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université de Lyon, Université Lyon 1, Villeurbanne, France
| | - Emilio Guerrieri
- CNR-Institute for Sustainable Plant Protection (CNR-IPSP), National Research Council of Italy, Portici, Italy
| | - Massimo Giorgini
- CNR-Institute for Sustainable Plant Protection (CNR-IPSP), National Research Council of Italy, Portici, Italy
| | - Xingeng Wang
- United States Department of Agriculture, Agricultural Research Services, Beneficial Insects Introduction Research Unit, Newark, DE, USA
| | - Kim Hoelmer
- United States Department of Agriculture, Agricultural Research Services, Beneficial Insects Introduction Research Unit, Newark, DE, USA
| | - Kent M Daane
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Paul K Abram
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, Agassiz, BC, Canada
| | - Nicholas A Pardikes
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
| | - Joel J Brown
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branisovska 31, Czech Republic
| | - Melanie Thierry
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branisovska 31, Czech Republic
| | - Marylène Poirié
- INRAE, CNRS. and Evolution and Specificity of Multitrophic Interactions (ESIM) Sophia Agrobiotech Institute, Université "Côte d'Azur", Sophia Antipolis, France
| | - Paul Goldstein
- Systematic Entomology Laboratory, ARS/USDA c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Scott E Miller
- Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - W Daniel Tracey
- Department of Biology, Indiana University Bloomington, Bloomington, IN, USA
- Gill Center for Biomolecular Science, Indiana University Bloomington, Bloomington, IN, USA
| | - Jeremy S Davis
- Department of Biology, Indiana University Bloomington, Bloomington, IN, USA
- Biology Department, University of Kentucky, Lexington, KY, USA
| | | | - Bregje Wertheim
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands
| | - Owen T Lewis
- Department of Zoology, University of Oxford, Oxford, UK
| | - Jeff Leips
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Phillip P A Staniczenko
- Department of Biology, Brooklyn College, City University of New York (CUNY), Brooklyn, NY, USA
| | - Jan Hrcek
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branisovska 31, Czech Republic
| |
Collapse
|
10
|
Mioduchowska M, Nitkiewicz B, Roszkowska M, Kačarević U, Madanecki P, Pinceel T, Namiotko T, Gołdyn B, Kaczmarek Ł. Taxonomic classification of the bacterial endosymbiont Wolbachia based on next-generation sequencing: is there molecular evidence for its presence in tardigrades? Genome 2021; 64:951-958. [PMID: 34015229 DOI: 10.1139/gen-2020-0036] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We used high-throughput sequencing of 16S rRNA to test whether tardigrade species are infected with Wolbachia parasites. We applied SILVA and Greengenes databases that allowed taxonomic classification of bacterial sequences to OTUs. The results obtained from both databases differed considerably in the number of OTUs, and only the Greengenes database allowed identification of Wolbachia (infection was also supported by comparison of sequences to NCBI database). The putative bacterial endosymbiont Wolbachia was discovered only in adult eutardigrades, while bacteria identified down to the order Rickettsiales were detected in both eutardigrade eggs and adult specimens. Nevertheless, the frequency of Wolbachia in the bacterial communities of the studied eutardigrades was low. Similarly, in our positive control, i.e., a fairy shrimp Streptocephalus cafer, which was found to be infected with Wolbachia in our previous study using Sanger sequencing, only the Rickettsiales were detected. We also carried out phylogenetic reconstruction using Wolbachia sequences from the SILVA and Greengenes databases, Alphaproteobacteria putative endosymbionts and Rickettsiales OTUs obtained in previous studies on the microbial community of tardigrades, and Rickettsiales and Wolbachia OTUs obtained in the current study. Our discovery of Wolbachia in tardigrades can fuel new research to uncover the specifics of this interaction.
Collapse
Affiliation(s)
- Monika Mioduchowska
- Department of Genetics and Biosystematics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland.,Department of Marine Plankton Research, Institute of Oceanography, University of Gdansk, Marszałka Piłsudskiego 46, 81-378 Gdynia, Poland; Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland
| | - Bartosz Nitkiewicz
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury, M. Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - Milena Roszkowska
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland.,Department of Bioenergetics, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Uroš Kačarević
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia
| | - Piotr Madanecki
- Department of Biology and Pharmaceutical Botany, Faculty of Pharmacy, Medical University of Gdansk, J. Hallera 107, 80-416 Gdansk, Poland
| | - Tom Pinceel
- Animal Ecology, Global Change and Sustainable Development, KU Leuven, Charles Deberiotstraat 32, 3000 Leuven, Belgium.,Centre for Environmental Management, University of the Free State, Bloemfontein, South Africa
| | - Tadeusz Namiotko
- Department of Genetics and Biosystematics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Bartłomiej Gołdyn
- Department of General Zoology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Łukasz Kaczmarek
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| |
Collapse
|
11
|
Sharkey M, Brown B, Baker A, Mutanen M. Response to Zamani et al. (2020): The omission of critical data in the pursuit of "revolutionary" methods to accelerate the description of species. Zookeys 2021; 1033:191-201. [PMID: 33958926 PMCID: PMC8084859 DOI: 10.3897/zookeys.1033.66186] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 04/04/2021] [Indexed: 11/30/2022] Open
Abstract
Here we respond to the criticisms leveled against a proposal that suggested an efficient solution to the taxonomic impediment. We clarify some of our objectives and demonstrate that many of the criticisms apply more to traditional approaches to taxonomy rather than to our minimalist approach.
Collapse
Affiliation(s)
- Michael Sharkey
- The Hymenoptera Institute, 116 Franklin Ave., Redlands, CA 92373, USAThe Hymenoptera InstituteRedlandsUnited States of America
| | - Brian Brown
- Entomology Section, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, CA 90007, USANatural History Museum of Los Angeles CountyLos AngelesUnited States of America
| | - Austin Baker
- Department of Entomology, University of California, Riverside, CA, USAUniversity of CaliforniaRiversideUnited States of America
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, FinlandUniversity of OuluOuluFinland
| |
Collapse
|
12
|
Shimizu S, Broad GR, Maeto K. Integrative taxonomy and analysis of species richness patterns of nocturnal Darwin wasps of the genus Enicospilus Stephens (Hymenoptera, Ichneumonidae, Ophioninae) in Japan. Zookeys 2020; 990:1-144. [PMID: 33269011 PMCID: PMC7674391 DOI: 10.3897/zookeys.990.55542] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/10/2020] [Indexed: 11/24/2022] Open
Abstract
The predominantly tropical ophionine genus Enicospilus Stephens, 1835 is one of the largest genera of Darwin wasps (Hymenoptera, Ichneumonidae), with more than 700 extant species worldwide that are usually crepuscular or nocturnal and are parasitoids of Lepidoptera larvae. In the present study, the Japanese species of Enicospilus are revised using an integrative approach (combined morphology and DNA barcoding). On the basis of 3,110 specimens, 47 Enicospilus species are recognised in Japan, eight of which are new species (E.acutus Shimizu, sp. nov., E.kunigamiensis Shimizu, sp. nov., E.limnophilus Shimizu, sp. nov., E.matsumurai Shimizu, sp. nov., E.pseudopuncticulatus Shimizu, sp. nov., E.sharkeyi Shimizu, sp. nov., E.takakuwai Shimizu, sp. nov., and E.unctus Shimizu, sp. nov.), seven are new records from Japan (E.jilinensis Tang, 1990, E.laqueatus (Enderlein, 1921), E.multidens Chiu, 1954, stat. rev., E.puncticulatus Tang, 1990, E.stenophleps Cushman, 1937, E.vestigator (Smith, 1858), and E.zeugos Chiu, 1954, stat. rev.), 32 had already been recorded in Japan; three (E.biharensis Townes, Townes & Gupta, 1961, E.flavicaput (Morley, 1912), and E.merdarius (Gravenhorst, 1829)) have been erroneously recorded from Japan based on misidentifications, and four names that were previously on the Japanese list are deleted through synonymy. The following taxonomic changes are proposed: E.vacuus Gauld & Mitchell, 1981, syn. nov. (= E.formosensis (Uchida, 1928)); E.multidensstat. rev.; E.striatus Cameron, 1899, syn. nov. = E.lineolatus (Roman, 1913), syn. nov. = E.uniformis Chiu, 1954, syn. nov. = E.flatus Chiu, 1954, syn. nov. = E.gussakovskii Viktorov, 1957, syn. nov. = E.striolatus Townes, Townes & Gupta, 1961, syn. nov. = E.unicornis Rao & Nikam, 1969, syn. nov. = E.unicornis Rao & Nikam, 1970, syn. nov. (= E.pungens (Smith, 1874)); E.iracundus Chiu, 1954, syn. nov. (= E.sakaguchii (Matsumura & Uchida, 1926)); E.sigmatoides Chiu, 1954, syn. nov. (= E.shikokuensis (Uchida, 1928)); E.yamanakai (Uchida, 1930), syn. nov. (= E.shinkanus (Uchida, 1928)); E.ranunculus Chiu, 1954, syn. nov. (= E.yezoensis (Uchida, 1928)); and E.zeugosstat. rev. = E.henrytownesi Chao & Tang, 1991, syn. nov. In addition, the following new regional and country records are also provided: E.flavocephalus (Kirby, 1900), E.puncticulatus, and E.vestigator from the Eastern Palaearctic region, E.laqueatus from the Eastern Palaearctic and Oceanic regions, and E.maruyamanus (Uchida, 1928) from the Oriental region; E.abdominalis (Szépligeti, 1906) from Nepal, E.flavocephalus from Laos, E.formosensis from Laos and Malaysia, E.insinuator (Smith, 1860) from Taiwan, E.maruyamanus from India and Philippines, E.nigronotatus Cameron, 1903, E.riukiuensis (Matsumura & Uchida, 1926), and E.sakaguchii from Indonesia, E.pungens from 14 countries (Australia, Bhutan, Brunei, Indonesia, Laos, Malaysia, Nepal, New Caledonia, Papua New Guinea, Philippines, Solomon Islands, Sri Lanka, Tajikistan, and Taiwan), and E.yezoensis from South Korea. An identification key to all Japanese species of Enicospilus is proposed. Although 47 species are recognised in the present study, approximately 55 species could potentially be found in Japan based on ACE and Chao 1 estimators. The latitudinal diversity gradient of Enicospilus species richness is also tested in the Japanese archipelago based on the constructed robust taxonomic framework and extensive samples. Enicospilus species richness significantly increases towards the south, contrary to the ‘anomalous’ pattern of some other ichneumonid subfamilies.
Collapse
Affiliation(s)
- So Shimizu
- Laboratory of Insect Biodiversity and Ecosystem Science, Graduate School of Agricultural Science, Kôbe University, Rokkôdaichô 1-1, Nada, Kôbe, Hyôgo 657-8501, Japan Kôbe University Kôbe Japan.,DC and Overseas Challenge Program for Young Researchers, Japan Society for the Promotion of Science, Tôkyô, Japan The Natural History Museum London United Kingdom.,Depertment of Life Sciences, the Natural History Museum, Cromwell Road, London SW7 5BD, UK Japan Society for the Promotion of Science Tokyo Japan
| | - Gavin R Broad
- Depertment of Life Sciences, the Natural History Museum, Cromwell Road, London SW7 5BD, UK Japan Society for the Promotion of Science Tokyo Japan
| | - Kaoru Maeto
- Laboratory of Insect Biodiversity and Ecosystem Science, Graduate School of Agricultural Science, Kôbe University, Rokkôdaichô 1-1, Nada, Kôbe, Hyôgo 657-8501, Japan Kôbe University Kôbe Japan
| |
Collapse
|
13
|
Raupach MJ, Hannig K, Morinière J, Hendrich L. A DNA barcode library for ground beetles of Germany: the genus Pterostichus Bonelli, 1810 and allied taxa (Insecta, Coleoptera, Carabidae). Zookeys 2020; 980:93-117. [PMID: 33192140 PMCID: PMC7642132 DOI: 10.3897/zookeys.980.55979] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/04/2020] [Indexed: 11/12/2022] Open
Abstract
Species of the ground beetle genus Pterostichus Bonelli, 1810 are some of the most common carabids in Europe. This publication provides a first comprehensive DNA barcode library for this genus and allied taxa including Abax Bonelli, 1810, Molops Bonelli, 1810, Poecilus Bonelli, 1810, and Stomis Clairville, 1806 for Germany and Central Europe in general. DNA barcodes were analyzed from 609 individuals that represent 51 species, including sequences from previous studies as well as more than 198 newly generated sequences. The results showed a 1:1 correspondence between BIN and traditionally recognized species for 44 species (86%), whereas two (4%) species were characterized by two BINs. Three BINs were found for one species (2%), while one BIN for two species was revealed for two species pairs (8%). Low interspecific distances with maximum pairwise K2P values below 2.2% were found for four species pairs. Haplotype sharing was found for two closely related species pairs: Pterostichusadstrictus Eschscholtz, 1823/Pterostichusoblongopunctatus (Fabricius, 1787) and Pterostichusnigrita Paykull, 1790/Pterostichusrhaeticus Heer, 1837. In contrast to this, high intraspecific sequence divergences with values above 2.2% were shown for three species (Molopspiceus (Panzer, 1793), Pterostichuspanzeri (Panzer, 1805), Pterostichusstrenuus (Panzer, 1793)). Summarizing the results, the present DNA barcode library does not only allow the identification of most of the analyzed species, but also provides valuable information for alpha-taxonomy as well as for ecological and evolutionary research. This library represents another step in building a comprehensive DNA barcode library of ground beetles as part of modern biodiversity research.
Collapse
Affiliation(s)
- Michael J Raupach
- Sektion Hemiptera, Bavarian State Collection of Zoology (SNSB - ZSM), Münchhausenstraße 21, 81247 München, Germany
| | | | - Jérome Morinière
- AIM - Advanced Identification Methods GmbH, Spinnereistraße 11, 04179 Leipzig
| | - Lars Hendrich
- Sektion Insecta varia, Bavarian State Collection of Zoology (SNSB - ZSM), Münchhausenstraße 21, 81247 München, Germany
| |
Collapse
|
14
|
Gueuning M, Frey JE, Praz C. Ultraconserved yet informative for species delimitation: Ultraconserved elements resolve long-standing systematic enigma in Central European bees. Mol Ecol 2020; 29:4203-4220. [PMID: 32916006 DOI: 10.1111/mec.15629] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 12/21/2022]
Abstract
Accurate and testable species hypotheses are essential for measuring, surveying and managing biodiversity. Taxonomists often rely on mitochondrial DNA barcoding to complement morphological species delimitations. Although COI-barcoding has largely proven successful in assisting identifications for most animal taxa, there are nevertheless numerous cases where mitochondrial barcodes do not reflect species hypotheses. For instance, what is regarded as a single species can be associated with two distinct DNA barcodes, which can point either to cryptic diversity or to within-species mitochondrial divergences without reproductive isolation. In contrast, two or more species can share barcodes, for instance due to mitochondrial introgression. These intrinsic limitations of DNA barcoding are commonly addressed with nuclear genomic markers, which are expensive, may have low repeatability and often require high-quality DNA. To overcome these limitations, we examined the use of ultraconserved elements (UCEs) as a quick and robust genomic approach to address such problematic cases of species delimitation in bees. This genomic method was assessed using six different species complexes suspected to harbour cryptic diversity, mitochondrial introgression or mitochondrial paraphyly. The sequencing of UCEs recovered between 686 and 1,860 homologous nuclear loci and provided explicit species delimitation in all investigated species complexes. These results provide strong evidence for the suitability of UCEs as a fast method for species delimitation even in recently diverged lineages. Furthermore, we provide the first evidence for both mitochondrial introgression among distinct bee species, and mitochondrial paraphyly within a single bee species.
Collapse
Affiliation(s)
- Morgan Gueuning
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland.,Institute of Biology, University of Neuchatel, Neuchatel, Switzerland
| | - Juerg E Frey
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland
| | - Christophe Praz
- Institute of Biology, University of Neuchatel, Neuchatel, Switzerland
| |
Collapse
|
15
|
Salvi D, Berrilli E, D'Alessandro P, Biondi M. Sharpening the DNA barcoding tool through a posteriori taxonomic validation: The case of Longitarsus flea beetles (Coleoptera: Chrysomelidae). PLoS One 2020; 15:e0233573. [PMID: 32437469 PMCID: PMC7241800 DOI: 10.1371/journal.pone.0233573] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/07/2020] [Indexed: 11/30/2022] Open
Abstract
The accuracy of the DNA barcoding tool depends on the existence of a comprehensive archived library of sequences reliably determined at species level by expert taxonomists. However, misidentifications are not infrequent, especially following large-scale DNA barcoding campaigns on diverse and taxonomically complex groups. In this study we used the species-rich flea beetle genus Longitarsus, that requires a high level of expertise for morphological species identification, as a case study to assess the accuracy of the DNA barcoding tool following several optimization procedures. We built a cox1 reference database of 1502 sequences representing 78 Longitarsus species, among which 117 sequences (32 species) were newly generated using a non-invasive DNA extraction method that allows keeping reference voucher specimens. Within this dataset we identified 69 taxonomic inconsistencies using barcoding gap analysis and tree topology methods. Threshold optimisation and a posteriori taxonomic revision based on newly generated reference sequences and metadata allowed resolving 44 sequences with ambiguous and incorrect identification and provided a significant improvement of the DNA barcoding accuracy and identification efficacy. Unresolved taxonomic uncertainties, due to overlapping intra- and inter-specific levels of divergences, mainly regards the Longitarsus pratensis species complex and polyphyletic groups L. melanocephalus, L. nigrofasciatus and L. erro. Such type of errors indicates either poorly established taxonomy or any biological processes that make mtDNA groups poorly predictive of species boundaries (e.g. recent speciation or interspecific hybridisation), thus providing directions for further integrative taxonomic and evolutionary studies. Overall, this study underlines the importance of reference vouchers and high-quality metadata associated to sequences in reference databases and corroborates, once again, the key role of taxonomists in any step of the DNA barcoding pipeline in order to generate and maintain a correct and functional reference library.
Collapse
Affiliation(s)
- Daniele Salvi
- Department of Health, Life and Environmental Sciences, University of L'Aquila, Coppito, L'Aquila, Italy
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Emanuele Berrilli
- Department of Health, Life and Environmental Sciences, University of L'Aquila, Coppito, L'Aquila, Italy
| | - Paola D'Alessandro
- Department of Health, Life and Environmental Sciences, University of L'Aquila, Coppito, L'Aquila, Italy
| | - Maurizio Biondi
- Department of Health, Life and Environmental Sciences, University of L'Aquila, Coppito, L'Aquila, Italy
| |
Collapse
|
16
|
Akankunda T, To H, Rodriguez Lopez C, Leijs R, Hogendoorn K. A method to generate multilocus barcodes of pinned insect specimens using MiSeq. Mol Ecol Resour 2020; 20. [PMID: 32104992 DOI: 10.1111/1755-0998.13143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/20/2020] [Accepted: 02/03/2020] [Indexed: 01/03/2023]
Abstract
For molecular insect identification, amplicon sequencing methods are recommended because they offer a cost-effective approach for targeting small sets of informative genes from multiple samples. In this context, high-throughput multilocus amplicon sequencing has been achieved using the MiSeq Illumina sequencing platform. However, this approach generates short gene fragments of <500 bp, which then have to be overlapped using bioinformatics to achieve longer sequence lengths. This increases the risk of generating chimeric sequences or leads to the formation of incomplete loci. Here, we propose a modified nested amplicon sequencing method for targeting multiple loci from pinned insect specimens using the MiSeq Illumina platform. The modification exists in using a three-step nested PCR approach targeting near full-length loci in the initial PCR and subsequently amplifying short fragments of between 300 and 350 bp for high-throughput sequencing using Illumina chemistry. Using this method, we generated 407 sequences of three loci from 86% of all the specimens sequenced. Out of 103 pinned bee specimens of replicated species, 71% passed the 95% sequence similarity threshold between species replicates. This method worked best for pinned specimens aged between 0 and 5 years, with a limit of 10 years for pinned and 14 years for ethanol-preserved specimens. Hence, our method overcomes some of the challenges of amplicon sequencing using short read next generation sequencing and improves the possibility of creating high-quality multilocus barcodes from insect collections.
Collapse
Affiliation(s)
- Trace Akankunda
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
| | - Hien To
- The Bioinformatics Hub, The University of Adelaide, Adelaide, SA, Australia
| | - Carlos Rodriguez Lopez
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia.,Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Remko Leijs
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia.,South Australian Museum, North Terrace, Adelaide, SA, Australia
| | - Katja Hogendoorn
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
| |
Collapse
|
17
|
Kaczmarek Ł, Roszkowska M, Poprawa I, Janelt K, Kmita H, Gawlak M, Fiałkowska E, Mioduchowska M. Integrative description of bisexual Paramacrobiotus experimentalis sp. nov. (Macrobiotidae) from republic of Madagascar (Africa) with microbiome analysis. Mol Phylogenet Evol 2020; 145:106730. [PMID: 31904510 DOI: 10.1016/j.ympev.2019.106730] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 12/31/2019] [Accepted: 12/31/2019] [Indexed: 12/26/2022]
Abstract
In a moss samples collected on Madagascar two populations of Paramacrobiotus experimentalis sp. nov. were found. Paramacrobiotus experimentalis sp. nov. with the presence of a microplacoid and areolatus type of eggs is similar to Pam. danielae, Pam. garynahi, Pam. hapukuensis, Pam. peteri, Pam. rioplatensis and Pam. savai, but it differs from them by some morphological and morphometric characters of the eggs. The p-distance between two COI haplotypes of Pam. experimentalis sp. nov. was 0.17%. In turn, the ranges of uncorrected genetic p-distances of all Paramacrobiotus species available in GenBank was from 18.27% (for Pam. lachowskae) to 25.26% (for Pam. arduus) with an average distance of 20.67%. We also found that Pam. experimentalis sp. nov. is bisexual. This observation was congruent on three levels: (i) morphological - specimen size dimorphism; (ii) structural (primary sexual characteristics) - females have an unpaired ovary while males have an unpaired testis and (iii) molecular - heterozygous and homozygous strains of the ITS-2 marker. Although symbiotic associations of hosts with bacteria (including endosymbiotic bacteria) are common in nature and these interactions exert various effects on the evolution, biology and reproductive ecology of hosts, there is still very little information on the bacterial community associated with tardigrades. To fill this gap and characterise the bacterial community of Pam. experimentalis sp. nov. populations and microbiome of its microhabitat, high throughput sequencing of the V3-V4 hypervariable regions in the bacterial 16S rRNA gene fragment was performed. The obtained 16S rRNA gene sequences ranged from 92,665 to 131,163. In total, 135 operational taxonomic units (OTUs) were identified across the rarefied dataset. Overall, both Pam. experimentalis sp. nov. populations were dominated by OTUs ascribed to the phylum Proteobacteria (89-92%) and Firmicutes (6-7%). In the case of samples from tardigrades' laboratory habitat, the most abundant bacterial phylum was Proteobacteria (51-90%) and Bacteroides (9-48%). In all compared microbiome profiles, only 16 of 137 OTUs were shared. We found also significant differences in beta diversity between the partly species-specific microbiome of Pam. experimentalis sp. nov. and its culturing environment. Two OTUs belonging to a putative bacterial endosymbiont were identified - Rickettsiales and Polynucleobacter. We also demonstrated that each bacterial community was rich in genes involved in membrane transport, amino acid metabolism, and carbohydrate metabolism.
Collapse
Affiliation(s)
- Łukasz Kaczmarek
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University, Poznan, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland.
| | - Milena Roszkowska
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University, Poznan, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; Department of Bioenergetics, Faculty of Biology, Adam Mickiewicz University, Poznan, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland.
| | - Izabela Poprawa
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007 Katowice, Poland.
| | - Kamil Janelt
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Bankowa 9, 40-007 Katowice, Poland
| | - Hanna Kmita
- Department of Bioenergetics, Faculty of Biology, Adam Mickiewicz University, Poznan, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland.
| | - Magdalena Gawlak
- The Institute of Plant Protection-National Research Institute, Węgorka 20, 60-318 Poznań, Poland.
| | - Edyta Fiałkowska
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland.
| | - Monika Mioduchowska
- Department of Genetics and Biosystematics, Faculty of Biology, University of Gdańsk, Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland.
| |
Collapse
|
18
|
Blattner L, Gerecke R, von Fumetti S. Hidden biodiversity revealed by integrated morphology and genetic species delimitation of spring dwelling water mite species (Acari, Parasitengona: Hydrachnidia). Parasit Vectors 2019; 12:492. [PMID: 31639027 PMCID: PMC6805402 DOI: 10.1186/s13071-019-3750-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 10/12/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Water mites are among the most diverse organisms inhabiting freshwater habitats and are considered as substantial part of the species communities in springs. As parasites, Hydrachnidia influence other invertebrates and play an important role in aquatic ecosystems. In Europe, 137 species are known to appear solely in or near springheads. New species are described frequently, especially with the help of molecular species identification and delimitation methods. The aim of this study was to verify the mainly morphology-based taxonomic knowledge of spring-inhabiting water mites of central Europe and to build a genetic species identification library. METHODS We sampled 65 crenobiontic species across the central Alps and tested the suitability of mitochondrial (cox1) and nuclear (28S) markers for species delimitation and identification purposes. To investigate both markers, distance- and phylogeny-based approaches were applied. The presence of a barcoding gap was tested by using the automated barcoding gap discovery tool and intra- and interspecific genetic distances were investigated. Furthermore, we analyzed phylogenetic relationships between different taxonomic levels. RESULTS A high degree of hidden diversity was observed. Seven taxa, morphologically identified as Bandakia concreta Thor, 1913, Hygrobates norvegicus (Thor, 1897), Ljania bipapillata Thor, 1898, Partnunia steinmanni Walter, 1906, Wandesia racovitzai Gledhill, 1970, Wandesia thori Schechtel, 1912 and Zschokkea oblonga Koenike, 1892, showed high intraspecific cox1 distances and each consisted of more than one phylogenetic clade. A clear intraspecific threshold between 5.6-6.0% K2P distance is suitable for species identification purposes. The monophyly of Hydrachnidia and the main superfamilies is evident with different species clearly separated into distinct clades. cox1 separates water mite species but is unsuitable for resolving higher taxonomic levels. CONCLUSIONS Water mite species richness in springs is higher than has been suggested based on morphological species identification alone and further research is needed to evaluate the true diversity. The standard molecular species identification marker cox1 can be used to identify species but should be complemented by a nuclear marker, e.g. 28S, to resolve taxonomic relationships. Our results contribute to the taxonomical knowledge on spring inhabiting Hydrachnida, which is indispensable for the development and implementation of modern environment assessment methods, e.g. metabarcoding, in spring ecology.
Collapse
Affiliation(s)
- Lucas Blattner
- Department of Environmental Sciences, Geoecology Research Group, University of Basel, St. Johanns-Vorstadt 10, 4056 Basel, Switzerland
| | - Reinhard Gerecke
- Department of Biology, University of Tübingen, Auf der Morgenstelle 28E, 72076 Tübingen, Germany
| | - Stefanie von Fumetti
- Department of Environmental Sciences, Geoecology Research Group, University of Basel, St. Johanns-Vorstadt 10, 4056 Basel, Switzerland
| |
Collapse
|
19
|
Fagan-Jeffries EP, Cooper SJB, Bradford TM, Austin AD. Intragenomic internal transcribed spacer 2 variation in a genus of parasitoid wasps (Hymenoptera: Braconidae): implications for accurate species delimitation and phylogenetic analysis. INSECT MOLECULAR BIOLOGY 2019; 28:485-498. [PMID: 30632223 DOI: 10.1111/imb.12564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A recent DNA barcoding study of Australian microgastrines (Hymenoptera: Braconidae) sought to use next-generation sequencing of the cytochrome c oxidase subunit 1 (COI) barcoding gene region, the wingless (WG) gene and the internal transcribed spacer 2 (ITS2) to delimit molecular species in a highly diverse group of parasitic wasps. Large intragenomic distances between ITS2 variants, often larger than the average interspecific variation, caused difficulties in using ITS2 for species delimitation in both threshold and tree-based approaches, and the gene was not included in the reported results of the previous DNA barcoding study. We here report on the intragenomic, and the intra- and interspecies, variation in ITS2in the microgastrine genus Diolcogasterto further investigate the value of ITS2as a marker for species delimitation and phylogenetics of the Microgastrinae. Distinctive intragenomic variant patterns were found in different species of Diolcogaster, with some species possessing a single major variant, and others possessing many divergent variants. Characterizing intragenomic variation of ITS2is critical as it is a widely used marker in hymenopteran phylogenetics and species delimitation, and large intragenomic distances such as those found in this study may obscure phylogenetic signal.
Collapse
Affiliation(s)
- E P Fagan-Jeffries
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - S J B Cooper
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, University of Adelaide, Adelaide, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, Australia
| | - T M Bradford
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, University of Adelaide, Adelaide, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, Australia
| | - A D Austin
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, University of Adelaide, Adelaide, Australia
| |
Collapse
|
20
|
Hill GE. Reconciling the Mitonuclear Compatibility Species Concept with Rampant Mitochondrial Introgression. Integr Comp Biol 2019; 59:912-924. [DOI: 10.1093/icb/icz019] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Abstract
The mitonuclear compatibility species concept defines a species as a population that is genetically isolated from other populations by uniquely coadapted mitochondrial (mt) and nuclear genes. A key prediction of this hypothesis is that the mt genotype of each species will be functionally distinct and that introgression of mt genomes will be prevented by mitonuclear incompatibilities that arise when heterospecific mt and nuclear genes attempt to cofunction to enable aerobic respiration. It has been proposed, therefore, that the observation of rampant introgression of mt genotypes from one species to another constitutes a strong refutation of the mitonuclear speciation. The displacement of a mt genotype from a nuclear background with which it co-evolved to a foreign nuclear background will necessarily lead to fitness loss due to mitonuclear incompatibilities. Here I consider two potential benefits of mt introgression between species that may, in some cases, overcome fitness losses arising from mitonuclear incompatibilities. First, the introgressed mt genotype may be better adapted to the local environment than the native mt genotype such that higher fitness is achieved through improved adaptation via introgression. Second, if the mitochondria of the recipient taxa carry a high mutational load, then introgression of a foreign, less corrupt mt genome may enable the recipient taxa to escape its mutational load and gain a fitness advantage. Under both scenarios, fitness gains from novel mt genotypes could theoretically compensate for the fitness that is lost via mitonuclear incompatibility. I also consider the role of endosymbionts in non-adaptive rampant introgression of mt genomes. I conclude that rampant introgression is not necessarily evidence against the idea of tight mitonuclear coadaptation or the mitonuclear compatibility species concept. Rampant mt introgression will typically lead to erasure of species but in some cases could lead to hybrid speciation.
Collapse
Affiliation(s)
- Geoffrey E Hill
- Department of Biological Sciences, 331 Funchess Hall, Auburn University, Auburn, AL 36849-5414, USA
| |
Collapse
|
21
|
Vuataz L, Sanchez A, Wyler S, Blanc M, Chittaro Y. Diversity and relationships of Ampedini Gistel, 1848 (Coleoptera : Elateridae) in Switzerland and Europe. INVERTEBR SYST 2019. [DOI: 10.1071/is18055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The click-beetle family Elateridae is an abundant and ecologically important component of the saproxylic fauna, and many species are used as key indicators of old-growth forests, a rare and endangered habitat in Europe. Among Elateridae, the tribe Ampedini includes several species with unclear taxonomic status. Here we examined the species status and the relationships between 26 of the 29 Ampedini species recorded in Switzerland using both mitochondrial (CO1) and nuclear (ITS2) markers, and compared our results with the CO1 data publicly available for Europe. Our tree-based species-delimitation analysis was largely congruent with traditional, morphology-based species, with the ITS2 and the combined (CO1+ITS2) datasets corresponding more precisely to morphology than the CO1 dataset. As expected, species with unclear or debated taxonomic status generally corresponded to closely related DNA-based species pairs. Our results support the taxonomic status of some of these ambiguous species, while others require further investigations, including a more exhaustive sampling and new morphological examinations. The Ampedini species tree provided here, which is the first attempt of a DNA-based Ampedini phylogeny, did not support the genera Brachygonus and Ampedus as monophyletic, but further investigations are necessary to confirm this result.
Collapse
|
22
|
Magoga G, Sahin DC, Fontaneto D, Montagna M. Barcoding of Chrysomelidae of Euro-Mediterranean area: efficiency and problematic species. Sci Rep 2018; 8:13398. [PMID: 30194432 PMCID: PMC6128942 DOI: 10.1038/s41598-018-31545-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 08/03/2018] [Indexed: 11/16/2022] Open
Abstract
Leaf beetles (Coleoptera: Chrysomelidae), with more than 37,000 species worldwide and about 2,300 in the Euro-Mediterranean region, are an ecological and economical relevant family, making their molecular identification of interest also in agriculture. This study, part of the Mediterranean Chrysomelidae Barcoding project (www.c-bar.org), aims to: (i) develop a reference Cytochrome c oxidase I (COI) library for the molecular identification of the Euro-Mediterranean Chrysomelidae; (ii) test the efficiency of DNA barcoding for leaf beetles identification; (iii) develop and compare optimal thresholds for distance-based identifications estimated at family and subfamily level, minimizing false positives and false negatives. Within this study, 889 COI nucleotide sequences of 261 species were provided; after the inclusion of information from other sources, a dataset of 7,237 sequences (542 species) was analysed. The average intra-interspecific distances were in the range of those recorded for Coleoptera: 1.6–24%. The estimated barcoding efficiency (~94%) confirmed the usefulness of this tool for Chrysomelidae identification. The few cases of failure were recorded for closely related species (e.g., Cryptocephalus marginellus superspecies, Cryptocephalus violaceus - Cryptocephalus duplicatus and some Altica species), even with morphologically different species sharing the same COI haplotype. Different optimal thresholds were achieved for the tested taxonomic levels, confirming that group-specific thresholds significantly improve molecular identifications.
Collapse
Affiliation(s)
- Giulia Magoga
- Dipartimento di Scienze Agrarie e Ambientali - Università degli Studi di Milano, Via Celoria 2, 20133, Milano, Italy
| | - Didem Coral Sahin
- Directorate of Plant Protection Central Research Institute, Yenimahalle, Ankara, Turkey
| | - Diego Fontaneto
- Consiglio Nazionale delle Ricerche-Istituto per lo Studio degli Ecosistemi, Largo Tonolli 50, 28922, Verbania, Italy
| | - Matteo Montagna
- Dipartimento di Scienze Agrarie e Ambientali - Università degli Studi di Milano, Via Celoria 2, 20133, Milano, Italy.
| |
Collapse
|
23
|
Fagan-Jeffries EP, Cooper SJB, Bertozzi T, Bradford TM, Austin AD. DNA barcoding of microgastrine parasitoid wasps (Hymenoptera: Braconidae) using high-throughput methods more than doubles the number of species known for Australia. Mol Ecol Resour 2018; 18:1132-1143. [PMID: 29791787 DOI: 10.1111/1755-0998.12904] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/07/2018] [Indexed: 01/10/2023]
Abstract
The Microgastrinae are a hugely diverse subfamily of endoparasitoid wasps of lepidopteran caterpillars. They are important in agriculture as biological control agents and play a significant ecological role in the regulation of caterpillar populations. Whilst the group has been the focus of intensive rearing and DNA barcoding studies in the Northern Hemisphere, the Australian fauna has received little attention. In total, 99 species have been described from or have been introduced into Australia, but the real species diversity for the region is clearly much larger than this. In this study, museum ethanol samples and recent field collections were mined for hundreds of specimens of microgastrine wasps, which were then barcoded for the COI region, ITS2 ribosomal spacer and the wingless nuclear genes, using a pooled sequencing approach on an Illumina Miseq system. Full COI sequences were obtained for 525 individuals which, when combined with 162 publicly available sequences, represented 417 haplotypes, and a total of 236 species were delimited using a consensus approach. By more than doubling the number of known microgastrine wasp species in Australia, our study highlights the value of DNA barcoding in the context of employing high-throughput sequencing methods of bulk ethanol museum collections for biodiversity assessment.
Collapse
Affiliation(s)
- Erinn P Fagan-Jeffries
- Department of Ecology and Evolutionary Biology, Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Steven J B Cooper
- Department of Ecology and Evolutionary Biology, Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, SA, Australia
| | - Terry Bertozzi
- Department of Ecology and Evolutionary Biology, Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, SA, Australia
| | - Tessa M Bradford
- Department of Ecology and Evolutionary Biology, Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, SA, Australia
| | - Andrew D Austin
- Department of Ecology and Evolutionary Biology, Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| |
Collapse
|
24
|
Klopfstein S, van Der Schyff G, Tierney S, Austin AD. Wolbachia infections in Australian ichneumonid parasitoid wasps (Hymenoptera: Ichneumonidae): evidence for adherence to the global equilibrium hypothesis. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/blx157] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Seraina Klopfstein
- Naturhistorisches Museum der Burgergemeinde Bern, Bern, Switzerland
- University of Bern, Institute of Ecology and Evolution, Bern, Switzerland
- Australian Centre for Evolutionary Biology and Biodiversity; School of Biological Sciences, The University of Adelaide, Adelaide, SA Australia
| | - Gwen van Der Schyff
- Australian Centre for Evolutionary Biology and Biodiversity; School of Biological Sciences, The University of Adelaide, Adelaide, SA Australia
| | - Simon Tierney
- Australian Centre for Evolutionary Biology and Biodiversity; School of Biological Sciences, The University of Adelaide, Adelaide, SA Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Andrew D Austin
- Australian Centre for Evolutionary Biology and Biodiversity; School of Biological Sciences, The University of Adelaide, Adelaide, SA Australia
| |
Collapse
|
25
|
Weigand H, Weiss M, Cai H, Li Y, Yu L, Zhang C, Leese F. Deciphering the origin of mito-nuclear discordance in two sibling caddisfly species. Mol Ecol 2017; 26:5705-5715. [PMID: 28792677 DOI: 10.1111/mec.14292] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/20/2017] [Accepted: 08/03/2017] [Indexed: 01/15/2023]
Abstract
An increasing number of phylogenetic studies have reported discordances among nuclear and mitochondrial markers. These discrepancies are highly relevant to widely used biodiversity assessment approaches, such as DNA barcoding, that rely almost exclusively on mitochondrial markers. Although the theoretical causes of mito-nuclear discordances are well understood, it is often extremely challenging to determine the principal underlying factor in a given study system. In this study, we uncovered significant mito-nuclear discordances in a pair of sibling caddisfly species. Application of genome sequencing, ddRAD and DNA barcoding revealed ongoing hybridization, as well as historical hybridization in Pleistocene refugia, leading us to identify introgression as the ultimate cause of the observed discordance pattern. Our novel genomic data, the discovery of a European-wide hybrid zone and the availability of established techniques for laboratory breeding make this species pair an ideal model system for studying species boundaries with ongoing gene flow.
Collapse
Affiliation(s)
- Hannah Weigand
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
| | - Martina Weiss
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
| | - Huimin Cai
- BGI-Shenzhen, Shenzhen, China.,Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | | | - Lili Yu
- BGI-Shenzhen, Shenzhen, China
| | | | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
| |
Collapse
|
26
|
Grzywacz A, Wyborska D, Piwczyński M. DNA barcoding allows identification of European Fanniidae (Diptera) of forensic interest. Forensic Sci Int 2017; 278:106-114. [DOI: 10.1016/j.forsciint.2017.06.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 06/19/2017] [Accepted: 06/20/2017] [Indexed: 11/26/2022]
|
27
|
Hill GE. Mitonuclear coevolution as the genesis of speciation and the mitochondrial DNA barcode gap. Ecol Evol 2016; 6:5831-42. [PMID: 27547358 PMCID: PMC4983595 DOI: 10.1002/ece3.2338] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 06/27/2016] [Accepted: 06/30/2016] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial genes are widely used in taxonomy and systematics because high mutation rates lead to rapid sequence divergence and because such changes have long been assumed to be neutral with respect to function. In particular, the nucleotide sequence of the mitochondrial gene cytochrome c oxidase subunit 1 has been established as a highly effective DNA barcode for diagnosing the species boundaries of animals. Rarely considered in discussions of mitochondrial evolution in the context of systematics, speciation, or DNA barcodes, however, is the genomic architecture of the eukaryotes: Mitochondrial and nuclear genes must function in tight coordination to produce the complexes of the electron transport chain and enable cellular respiration. Coadaptation of these interacting gene products is essential for organism function. I extend the hypothesis that mitonuclear interactions are integral to the process of speciation. To maintain mitonuclear coadaptation, nuclear genes, which code for proteins in mitochondria that cofunction with the products of mitochondrial genes, must coevolve with rapidly changing mitochondrial genes. Mitonuclear coevolution in isolated populations leads to speciation because population-specific mitonuclear coadaptations create between-population mitonuclear incompatibilities and hence barriers to gene flow between populations. In addition, selection for adaptive divergence of products of mitochondrial genes, particularly in response to climate or altitude, can lead to rapid fixation of novel mitochondrial genotypes between populations and consequently to disruption in gene flow between populations as the initiating step in animal speciation. By this model, the defining characteristic of a metazoan species is a coadapted mitonuclear genotype that is incompatible with the coadapted mitochondrial and nuclear genotype of any other population.
Collapse
Affiliation(s)
- Geoffrey E. Hill
- Department Biological ScienceAuburn University331 Funchess HallAuburnAlabama36849‐5414
| |
Collapse
|