1
|
Fröhlich D, Bodner M, Raspotnig G, Hahn C. Simple protocol for combined extraction of exocrine secretions and RNA in small arthropods. Biol Methods Protoc 2024; 9:bpae054. [PMID: 39131584 PMCID: PMC11316613 DOI: 10.1093/biomethods/bpae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/19/2024] [Accepted: 07/29/2024] [Indexed: 08/13/2024] Open
Abstract
The integration of data from multiple sources and analytical techniques to obtain novel insights and answer challenging questions is a hallmark of modern science. In arthropods, exocrine secretions may act as pheromones, defensive substances, antibiotics, as well as surface protectants, and as such they play a crucial role in ecology and evolution. Exocrine chemical compounds are frequently characterized by gas chromatography-mass spectrometry. Technological advances of recent years now allow us to routinely characterize the total gene complement transcribed in a particular biological tissue, often in the context of experimental treatment, via RNAseq. We here introduce a novel methodological approach to successfully characterize exocrine secretions and full transcriptomes of one and the same individual of oribatid mites. We found that chemical extraction prior to RNA extraction had only minor effects on the total RNA integrity. De novo transcriptomes obtained from such combined extractions were of comparable quality to those assembled for samples that were subject to RNA extraction only, indicating that combined chemical/RNA extraction is perfectly suitable for phylotranscriptomic studies. However, in-depth analysis of RNA expression analysis indicates that chemical extraction prior to RNAseq may affect transcript degradation rates, similar to the effects reported in previous studies comparing RNA extraction protocols. With this pilot study, we demonstrate that profiling chemical secretions and RNA expression levels from the same individual is methodologically feasible, paving the way for future research to understand the genes and pathways underlying the syntheses of biogenic chemical compounds. Our approach should be applicable broadly to most arachnids, insects, and other arthropods.
Collapse
Affiliation(s)
- David Fröhlich
- Department of Biology, University of Graz, Graz, 8010, Austria
| | - Michaela Bodner
- Department of Biology, University of Graz, Graz, 8010, Austria
| | | | - Christoph Hahn
- Department of Biology, University of Graz, Graz, 8010, Austria
| |
Collapse
|
2
|
Zamani A, Dal Pos D, Fric ZF, Orfinger AB, Scherz MD, Bartoňová AS, Gante HF. The future of zoological taxonomy is integrative, not minimalist. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2063964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alireza Zamani
- Zoological Museum, Biodiversity Unit, University of Turku, 20500 Turku, Finland
| | - Davide Dal Pos
- Department of Biology, University of Central Florida, 4110 Libra dr. Rm 442, Orlando, FL 32816, USA
| | - Zdenek Faltýnek Fric
- Department of Biodiversity and Conservation Biology, Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, Ceske Budejovice, CZ-37005, Czech Republic
| | - Alexander B. Orfinger
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611, USA
- Center for Water Resources, Florida A&M University, Tallahassee, FL 32301, USA
| | - Mark D. Scherz
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, 1350, Denmark
| | - Alena Sucháčková Bartoňová
- Department of Biodiversity and Conservation Biology, Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, Ceske Budejovice, CZ-37005, Czech Republic
| | - Hugo F. Gante
- cE3c—Center for Ecology, Evolution and Environmental Changes, Universidade de Lisboa, Lisboa, Portugal
- Department of Biology, KU Leuven, Section Ecology, Evolution and Biodiversity Conservation, Charles Deberiotstraat 32 box 2439, Leuven, B-3000, Belgium
- Royal Museum for Central Africa, Leuvensesteenweg 17, Tervuren, 3080, Belgium
| |
Collapse
|
3
|
Hlebec D, Sivec I, Podnar M, Kučinić M. DNA barcoding for biodiversity assessment: Croatian stoneflies (Insecta: Plecoptera). PeerJ 2022; 10:e13213. [PMID: 35469200 PMCID: PMC9034701 DOI: 10.7717/peerj.13213] [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: 12/27/2021] [Accepted: 03/12/2022] [Indexed: 01/12/2023] Open
Abstract
Background The hemi-metabolous aquatic order Plecoptera (stoneflies) constitutes an indispensable part of terrestrial and aquatic food webs due to their specific life cycle and habitat requirements. Stoneflies are considered one of the most sensitive groups to environmental changes in freshwater ecosystems and anthropogenic changes have caused range contraction of many species. Given the critical threat to stoneflies, the study of their distribution, morphological variability and genetic diversity should be one of the priorities in conservation biology. However, some aspects about stoneflies, especially a fully resolved phylogeny and their patterns of distribution are not well known. A study that includes comprehensive field research and combines morphological and molecular identification of stoneflies has not been conducted in Croatia so far. Thus, the major aim of this study was to regenerate a comprehensive and taxonomically well-curated DNA barcode database for Croatian stoneflies, to highlight the morphological variability obtained for several species and to elucidate results in light of recent taxonomy. Methods A morphological examination of adult specimens was made using basic characteristics for distinguishing species: terminalia in males and females, head and pronotum patterns, penial morphology, and egg structures. DNA barcoding was applied to many specimens to help circumscribe known species, identify cryptic or yet undescribed species, and to construct a preliminary phylogeny for Croatian stoneflies. Results Sequences (658 bp in length) of 74 morphospecies from all families present in Croatia were recovered from 87% of the analysed specimens (355 of 410), with one partial sequence of 605 bp in length for Capnopsis schilleri balcanica Zwick, 1984. A total of 84% morphological species could be unambiguously identified using COI sequences. Species delineation methods confirmed the existence of five deeply divergent genetic lineages, with monophyletic origin, which also differ morphologically from their congeners and represent distinct entities. BIN (Barcode Index Number) assignment and species delineation methods clustered COI sequences into different numbers of operational taxonomic units (OTUs). ASAP delimited 76 putative species and achieved a maximum match score with morphology (97%). ABGD resulted in 62 and mPTP in 61 OTUs, indicating a more conservative approach. Most BINs were congruent with traditionally recognized species. Deep intraspecific genetic divergences in some clades highlighted the need for taxonomic revision in several species-complexes and species-groups. Research has yielded the first molecular characterization of nine species, with most having restricted distributions and confirmed the existence of several species which had been declared extinct regionally.
Collapse
Affiliation(s)
- Dora Hlebec
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia,Zoological Museum Hamburg, Leibniz Institute for the Analysis of Biodiversity Change, Hamburg, Germany,Croatian Biospeleological Society, Zagreb, Croatia
| | - Ignac Sivec
- Slovenian Museum of Natural History, Ljubljana, Slovenia
| | | | - Mladen Kučinić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| |
Collapse
|
4
|
Muster C, Spelda J, Rulik B, Thormann J, von der Mark L, Astrin JJ. The dark side of pseudoscorpion diversity: The German Barcode of Life campaign reveals high levels of undocumented diversity in European false scorpions. Ecol Evol 2021; 11:13815-13829. [PMID: 34707820 PMCID: PMC8525104 DOI: 10.1002/ece3.8088] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 11/12/2022] Open
Abstract
DNA barcoding is particularly useful for identification and species delimitation in taxa with conserved morphology. Pseudoscorpions are arachnids with high prevalence of morphological crypsis. Here, we present the first comprehensive DNA barcode library for Central European Pseudoscorpiones, covering 70% of the German pseudoscorpion fauna (35 out of 50 species). For 21 species, we provide the first publicly available COI barcodes, including the rare Anthrenochernes stellae Lohmander, a species protected by the FFH Habitats Directive. The pattern of intraspecific COI variation and interspecific COI variation (i.e., presence of a barcode gap) generally allows application of the DNA barcoding approach, but revision of current taxonomic designations is indicated in several taxa. Sequences of 36 morphospecies were assigned to 74 BINs (barcode index numbers). This unusually high number of intraspecific BINs can be explained by the presence of overlooked cryptic species and by the accelerated substitution rate in the mitochondrial genome of pseudoscorpions, as known from previous studies. Therefore, BINs may not be an appropriate proxy for species numbers in pseudoscorpions, while partitions built with the ASAP algorithm (Assemble Species by Automatic Partitioning) correspond well with putative species. ASAP delineated 51 taxonomic units from our data, an increase of 42% compared with the present taxonomy. The Neobisium carcionoides complex, currently considered a polymorphic species, represents an outstanding example of cryptic diversity: 154 sequences from our dataset were allocated to 23 BINs and 12 ASAP units.
Collapse
Affiliation(s)
- Christoph Muster
- Zoologisches Institut und MuseumUniversität GreifswaldGreifswaldGermany
| | - Jörg Spelda
- SNSB‐Zoologische Staatssammlung MünchenMunichGermany
| | - Björn Rulik
- Zoologisches Forschungsmuseum A. KoenigZFMKBonnGermany
| | - Jana Thormann
- Zoologisches Forschungsmuseum A. KoenigZFMKBonnGermany
| | | | | |
Collapse
|
5
|
Derkarabetian S, Castillo S, Koo PK, Ovchinnikov S, Hedin M. A demonstration of unsupervised machine learning in species delimitation. Mol Phylogenet Evol 2019; 139:106562. [PMID: 31323334 PMCID: PMC6880864 DOI: 10.1016/j.ympev.2019.106562] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 07/03/2019] [Accepted: 07/15/2019] [Indexed: 01/13/2023]
Abstract
One major challenge to delimiting species with genetic data is successfully differentiating population structure from species-level divergence, an issue exacerbated in taxa inhabiting naturally fragmented habitats. Many fields of science are now using machine learning, and in evolutionary biology supervised machine learning has recently been used to infer species boundaries. These supervised methods require training data with associated labels. Conversely, unsupervised machine learning (UML) uses inherent data structure and does not require user-specified training labels, potentially providing more objectivity in species delimitation. In the context of integrative taxonomy, we demonstrate the utility of three UML approaches (random forests, variational autoencoders, t-distributed stochastic neighbor embedding) for species delimitation in an arachnid taxon with high population genetic structure (Opiliones, Laniatores, Metanonychus). We find that UML approaches successfully cluster samples according to species-level divergences and not high levels of population structure, while model-based validation methods severely over-split putative species. UML offers intuitive data visualization in two-dimensional space, the ability to accommodate various data types, and has potential in many areas of systematic and evolutionary biology. We argue that machine learning methods are ideally suited for species delimitation and may perform well in many natural systems and across taxa with diverse biological characteristics.
Collapse
Affiliation(s)
- Shahan Derkarabetian
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, United States; Department of Biology, San Diego State University, San Diego, CA 92182, United States; Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA 92521, United States.
| | - Stephanie Castillo
- Department of Biology, San Diego State University, San Diego, CA 92182, United States; Department of Entomology, University of California, Riverside, Riverside, CA 92521, United States
| | - Peter K Koo
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, United States
| | - Sergey Ovchinnikov
- Center for Systems Biology, Harvard University, Cambridge, MA 02138, United States
| | - Marshal Hedin
- Department of Biology, San Diego State University, San Diego, CA 92182, United States
| |
Collapse
|
6
|
Liu T, Sun K, Csorba G, Zhang K, Zhang L, Zhao H, Jin L, Thong VD, Xiao Y, Feng J. Species delimitation and evolutionary reconstruction within an integrative taxonomic framework: A case study on Rhinolophus macrotis complex (Chiroptera: Rhinolophidae). Mol Phylogenet Evol 2019; 139:106544. [PMID: 31252069 DOI: 10.1016/j.ympev.2019.106544] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 10/26/2022]
Abstract
Species delimitation and evolutionary reconstruction remain challenging for non-model species that have experienced reticulate evolution and exhibit conflicting patterns of differentiation among multiple lines of evidence, such as mitochondrial and nuclear data and phenotypes. Here, we applied an integrative taxonomic approach to a case study of Rhinolophus macrotis complex, whose taxonomic status remains controversial, to provide insight into the systematics and evolutionary history of these species. By integrating traditional genetic markers with different modes of inheritance, genome-wide SNPs as well as phenotypic characteristics, we clarified the presence of three closely related species, R. episcopus, R. siamensis, and R. osgoodi, within this complex, and proposed a new taxonomic treatment for R. osgoodi. Our results suggested that hybridization and introgression are the main causes of low mtDNA divergence in these species. Combined with the demographic inference, we deduced that glacial-interglacial cycles drove geographic isolation and secondary contacts of these species, then promoted hybridization and lineage fusion among them, finally resulting in a reticulate evolutionary pattern. Overall, our study highlights the importance of combining multiple types of data to delimit species, especially those with conserved morphology, and to reveal the sophisticated processes of speciation.
Collapse
Affiliation(s)
- Tong Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China; Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China.
| | - Gábor Csorba
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
| | - Kangkang Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Lin Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Hanbo Zhao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Vu Dinh Thong
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Viet Nam; Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Viet Nam
| | - Yanhong Xiao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China; College of Life Science, Jilin Agricultural University, Changchun, China.
| |
Collapse
|
7
|
Steiner FM, Csősz S, Markó B, Gamisch A, Rinnhofer L, Folterbauer C, Hammerle S, Stauffer C, Arthofer W, Schlick-Steiner BC. Turning one into five: Integrative taxonomy uncovers complex evolution of cryptic species in the harvester ant Messor “structor”. Mol Phylogenet Evol 2018; 127:387-404. [DOI: 10.1016/j.ympev.2018.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 03/02/2018] [Accepted: 04/04/2018] [Indexed: 11/25/2022]
|
8
|
Noguerales V, Cordero PJ, Ortego J. Integrating genomic and phenotypic data to evaluate alternative phylogenetic and species delimitation hypotheses in a recent evolutionary radiation of grasshoppers. Mol Ecol 2018; 27:1229-1244. [DOI: 10.1111/mec.14504] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 12/16/2017] [Accepted: 01/05/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Víctor Noguerales
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM); Ciudad Real Spain
| | - Pedro J. Cordero
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM); Ciudad Real Spain
| | - Joaquín Ortego
- Department of Integrative Ecology; Estación Biológica de Doñana (EBD-CSIC); Seville Spain
| |
Collapse
|
9
|
Dupuis JR, Mcdonald CM, Acorn JH, Sperling FAH. Genomics-informed species delimitation to support morphological identification of anglewing butterflies (Lepidoptera: Nymphalidae: Polygonia). Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Julian R Dupuis
- Department of Plant and Environmental Protection Sciences, University of Hawai’i at Mānoa, Honolulu, HI, USA
- Department of Biological Sciences, CW 405 Biosciences Centre, University of Alberta, Edmonton, AB, Canada
| | - Christianne M Mcdonald
- Department of Biological Sciences, CW 405 Biosciences Centre, University of Alberta, Edmonton, AB, Canada
| | - John H Acorn
- Department of Renewable Resources, University of Alberta, Edmonton, AB, Canada
| | - Felix A H Sperling
- Department of Biological Sciences, CW 405 Biosciences Centre, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
10
|
Brückner A, Heethoff M, Blüthgen N. The relationship between epicuticular long-chained hydrocarbons and surface area - volume ratios in insects (Diptera, Hymenoptera, Lepidoptera). PLoS One 2017; 12:e0175001. [PMID: 28384308 PMCID: PMC5383148 DOI: 10.1371/journal.pone.0175001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/17/2017] [Indexed: 01/02/2023] Open
Abstract
Long-chain cuticular hydrocarbons (CHCs) are common components of the epicuticle of terrestrial arthropods. CHC serve as a protective barrier against environmental influences but also act as semiochemicals in animal communication. Regarding the latter aspect, species- or intra-functional group specific CHCs composition and variation are relatively well studied. However, comparative knowledge about the relationship of CHC quantity and their relation to surface area—volume ratios in the context of water loss and protection is fragmentary. Hence, we aim to study the taxon-specific relationship of the CHC amount and surface-area to volume ratio related to their functional role (e.g. in water loss). We focused on flower visiting insects and analyzed the CHC amounts of three insect orders (Hymenoptera, Lepidoptera and Diptera) using gas chromatography—mass spectrometry (GC-MS). We included 113 species from two grassland plots, quantified their CHCs, and measured their body mass and surface area. We found differences in the surface area, CHCs per body mass and the CHC density (= amount of CHCs per surface area) across the three insect taxa. Especially the Hymenoptera had a higher CHC density compared to Diptera and Lepidoptera. CHC density could be explained by surface area-volume ratios in Hymenoptera but not in Diptera and Lepidoptera. Unexpectedly, CHC density decreased with increasing surface area—volume ratios.
Collapse
Affiliation(s)
- Adrian Brückner
- Ecological Networks, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
- * E-mail:
| | - Michael Heethoff
- Ecological Networks, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Nico Blüthgen
- Ecological Networks, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| |
Collapse
|
11
|
Astrin JJ, Höfer H, Spelda J, Holstein J, Bayer S, Hendrich L, Huber BA, Kielhorn KH, Krammer HJ, Lemke M, Monje JC, Morinière J, Rulik B, Petersen M, Janssen H, Muster C. Towards a DNA Barcode Reference Database for Spiders and Harvestmen of Germany. PLoS One 2016; 11:e0162624. [PMID: 27681175 PMCID: PMC5040438 DOI: 10.1371/journal.pone.0162624] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 08/25/2016] [Indexed: 01/05/2023] Open
Abstract
As part of the German Barcode of Life campaign, over 3500 arachnid specimens have been collected and analyzed: ca. 3300 Araneae and 200 Opiliones, belonging to almost 600 species (median: 4 individuals/species). This covers about 60% of the spider fauna and more than 70% of the harvestmen fauna recorded for Germany. The overwhelming majority of species could be readily identified through DNA barcoding: median distances between closest species lay around 9% in spiders and 13% in harvestmen, while in 95% of the cases, intraspecific distances were below 2.5% and 8% respectively, with intraspecific medians at 0.3% and 0.2%. However, almost 20 spider species, most notably in the family Lycosidae, could not be separated through DNA barcoding (although many of them present discrete morphological differences). Conspicuously high interspecific distances were found in even more cases, hinting at cryptic species in some instances. A new program is presented: DiStats calculates the statistics needed to meet DNA barcode release criteria. Furthermore, new generic COI primers useful for a wide range of taxa (also other than arachnids) are introduced.
Collapse
Affiliation(s)
- Jonas J. Astrin
- ZFMK: Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
- * E-mail: (JJA); (HH); (JS); (JH)
| | - Hubert Höfer
- SMNK: Staatliches Museum für Naturkunde Karlsruhe, Karlsruhe, Germany
- * E-mail: (JJA); (HH); (JS); (JH)
| | - Jörg Spelda
- ZSM: Zoologische Staatssammlung München, München, Germany
- * E-mail: (JJA); (HH); (JS); (JH)
| | - Joachim Holstein
- SMNS: Staatliches Museum für Naturkunde Stuttgart, Stuttgart, Germany
- * E-mail: (JJA); (HH); (JS); (JH)
| | - Steffen Bayer
- SMNK: Staatliches Museum für Naturkunde Karlsruhe, Karlsruhe, Germany
| | - Lars Hendrich
- ZSM: Zoologische Staatssammlung München, München, Germany
| | | | | | | | | | - Juan Carlos Monje
- SMNS: Staatliches Museum für Naturkunde Stuttgart, Stuttgart, Germany
| | | | - Björn Rulik
- ZFMK: Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Malte Petersen
- ZFMK: Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Hannah Janssen
- ZFMK: Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Christoph Muster
- Zoologisches Institut und Museum, Universität Greifswald, Greifswald, Germany
| |
Collapse
|
12
|
Wachter GA, Papadopoulou A, Muster C, Arthofer W, Knowles LL, Steiner FM, Schlick-Steiner BC. Glacial refugia, recolonization patterns and diversification forces in Alpine-endemicMegabunusharvestmen. Mol Ecol 2016; 25:2904-19. [DOI: 10.1111/mec.13634] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 03/06/2016] [Accepted: 03/22/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Gregor A. Wachter
- Molecular Ecology Group; Institute of Ecology; University of Innsbruck; Technikerstraße 25 6020 Innsbruck Austria
| | - Anna Papadopoulou
- Department of Ecology and Evolutionary Biology; Museum of Zoology; University of Michigan; Ann Arbor MI 48109-1079 USA
- Department of Integrative Ecology; Estación Biológica de Doñana (CSIC); 41092 Seville Spain
| | - Christoph Muster
- Zoological Institute and Museum; University of Greifswald; Johann-Sebastian-Bach-Straße 11/12 17487 Greifswald Germany
| | - Wolfgang Arthofer
- Molecular Ecology Group; Institute of Ecology; University of Innsbruck; Technikerstraße 25 6020 Innsbruck Austria
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology; Museum of Zoology; University of Michigan; Ann Arbor MI 48109-1079 USA
| | - Florian M. Steiner
- Molecular Ecology Group; Institute of Ecology; University of Innsbruck; Technikerstraße 25 6020 Innsbruck Austria
| | - Birgit C. Schlick-Steiner
- Molecular Ecology Group; Institute of Ecology; University of Innsbruck; Technikerstraße 25 6020 Innsbruck Austria
| |
Collapse
|
13
|
Csősz S, Fisher BL. Toward Objective, Morphology-Based Taxonomy: A Case Study on the Malagasy Nesomyrmex sikorai Species Group (Hymenoptera: Formicidae). PLoS One 2016; 11:e0152454. [PMID: 27097219 PMCID: PMC4838242 DOI: 10.1371/journal.pone.0152454] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 03/15/2016] [Indexed: 11/18/2022] Open
Abstract
Madagascar is one of the world’s greatest biodiversity hotspots, meriting special attention from biodiversity scientists. It is an excellent testing ground for novel techniques in taxonomy that aim to increase classification objectivity and yield greater taxonomic resolving power. Here we reveal the diversity of a unique and largely unexplored fragment of the Malagasy ant fauna using an advanced combination of exploratory analyses on quantitative morphological data allowing for increased objectivity in taxonomic workflow. The diversity of the Nesomyrmex sikorai species-group was assessed via hypothesis-free nest-centroid-clustering combined with recursive partitioning to estimate the number of morphological clusters and determine the most probable boundaries between them. This combination of methods provides a highly automated and objective species delineation protocol based on continuous morphometric data. Delimitations of clusters recognized by these exploratory analyses were tested via confirmatory Linear Discriminant Analysis (LDA) and Multivariate Ratio Analysis (MRA). The final species hypotheses are corroborated by many qualitative characters, and the recognized species exhibit different spatial distributions and occupy different ecological regions. We describe and redescribe eight morphologically distinct species including six new species: Nesomyrmex excelsiorsp. n., N. modestussp. n., N. reticulatussp. n., N. retusispinosus (Forel, 1892), N. rugosussp. n., N. sikorai (Emery, 1896), N. striatussp. n., and N. tamatavensissp. n. An identification key for their worker castes using morphometric data is provided.
Collapse
Affiliation(s)
- Sándor Csősz
- Department of Entomology, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, United States of America
- * E-mail:
| | - Brian L. Fisher
- Department of Entomology, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, United States of America
| |
Collapse
|
14
|
Csősz S, Fisher BL. Taxonomic revision of the Malagasy members of the Nesomyrmex angulatus species group using the automated morphological species delineation protocol NC-PART-clustering. PeerJ 2016; 4:e1796. [PMID: 26989630 PMCID: PMC4793320 DOI: 10.7717/peerj.1796] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/22/2016] [Indexed: 11/20/2022] Open
Abstract
Background. Applying quantitative morphological approaches in systematics research is a promising way to discover cryptic biological diversity. Information obtained through twenty-first century science poses new challenges to taxonomy by offering the possibility of increased objectivity in independent and automated hypothesis formation. In recent years a number of promising new algorithmic approaches have been developed to recognize morphological diversity among insects based on multivariate morphometric analyses. These algorithms objectively delimit components in the data by automatically assigning objects into clusters. Method. In this paper, hypotheses on the diversity of the Malagasy Nesomyrmex angulatus group are formulated via a highly automated protocol involving a fusion of two algorithms, (1) Nest Centroid clustering (NC clustering) and (2) Partitioning Algorithm based on Recursive Thresholding (PART). Both algorithms assign samples into clusters, making the class assignment results of different algorithms readily inferable. The results were tested by confirmatory cross-validated Linear Discriminant Analysis (LOOCV-LDA). Results. Here we reveal the diversity of a unique and largely unexplored fragment of the Malagasy ant fauna using NC-PART-clustering on continuous morphological data, an approach that brings increased objectivity to taxonomy. We describe eight morphologically distinct species, including seven new species: Nesomyrmex angulatus (Mayr, 1862), N. bidentatus sp. n., N. clypeatus sp. n., N. devius sp. n., N. exiguus sp. n., N. fragilis sp. n., N. gracilis sp. n., and N. hirtellus sp. n.. An identification key for their worker castes using morphometric data is provided. Conclusions. Combining the dimensionality reduction feature of NC clustering with the assignment of samples into clusters by PART advances the automatization of morphometry-based alpha taxonomy.
Collapse
Affiliation(s)
- Sándor Csősz
- Entomology, California Academy of Sciences , San Francisco, CA , USA
| | - Brian L Fisher
- Entomology, California Academy of Sciences , San Francisco, CA , USA
| |
Collapse
|
15
|
Dejaco T, Gassner M, Arthofer W, Schlick-Steiner BC, Steiner FM. Taxonomist's Nightmare … Evolutionist's Delight : An Integrative Approach Resolves Species Limits in Jumping Bristletails Despite Widespread Hybridization and Parthenogenesis. Syst Biol 2016; 65:947-974. [PMID: 26869489 PMCID: PMC5066060 DOI: 10.1093/sysbio/syw003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 10/26/2015] [Accepted: 01/14/2016] [Indexed: 11/13/2022] Open
Abstract
Accurate species delimitation is fundamental to biology. Traditionally, species were delimited based on morphological characters, sometimes leading to taxonomic uncertainty in morphologically conserved taxa. Recently, multiple taxonomically challenging cases have benefited from integrative taxonomy-an approach that highlights congruence among different disciplines and invokes evolutionary explanations for incongruence, acknowledging that different methods can mirror different stages of the speciation continuum. Here, we used a cohesive protocol for integrative taxonomy to revise species limits in 20 nominal species and 4 morphospecies of an ancestrally wingless insect group, the jumping bristletail genus Machilis from the European Eastern Alps. Even though morphologically conserved, several small-scale endemic species have been described from the Eastern Alps based on variation in hypodermal pigmentation patterns-a highly questionable character. As valuable as these endemics are for conservation, they have never been verified by alternative methods. Using traditional morphometrics, mitochondrial DNA, ribosomal DNA, and amplified fragment-length polymorphism markers, we identify six nominal species as taxonomic junior synonyms (Machilis alpicola Janetschek, 1953 syn. n. under M. vagans Wygodzinsky, 1941; M. ladensis Janetschek, 1950 syn. n., M. robusta Wygodzinsky, 1941 syn. n., and M. vicina Wygodzinsky, 1941 syn. n. under M. inermis Wygodzinsky, 1941; M. aleamaculata Wygodzinsky, 1941 syn. n. under M. montana Wygodzinsky, 1941; M. pulchra Janetschek, 1950 syn. n. under M. helleri Verhoeff, 1910) and describe two new species (Machilis cryptoglacialis sp. n. and Machilis albida sp. n.), one uncovered from morphological crypsis and one never sampled before. Building on numerous cases of incongruence among data sources, we further shed light on complex evolutionary histories including hybrid speciation, historical and recent hybridization, and ongoing speciation. We hypothesize that an inherent affinity to hybridization, combined with parallel switches to parthenogenesis and repeated postglacial colonization events may have boosted endemicity in Eastern Alpine Machilis We thus emphasize the importance of integrative taxonomy for rigorous species delimitation and its implication for evolutionary research and conservation in taxonomically challenging taxa.
Collapse
Affiliation(s)
- Thomas Dejaco
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria .,Museum of Nature South Tyrol, Bindergasse 1, 39100 Bozen/Bolzano, Italy
| | - Melitta Gassner
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Wolfgang Arthofer
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Birgit C Schlick-Steiner
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Florian M Steiner
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| |
Collapse
|
16
|
Starrett J, Derkarabetian S, Richart CH, Cabrero A, Hedin M. A new monster from southwest Oregon forests: Cryptomaster behemoth sp. n. (Opiliones, Laniatores, Travunioidea). Zookeys 2016:11-35. [PMID: 26877685 PMCID: PMC4740820 DOI: 10.3897/zookeys.555.6274] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 11/15/2015] [Indexed: 12/03/2022] Open
Abstract
The monotypic genus Cryptomaster Briggs, 1969 was described based on individuals from a single locality in southwestern Oregon. The described species Cryptomasterleviathan Briggs, 1969 was named for its large body size compared to most travunioid Laniatores. However, as the generic name suggests, Cryptomaster are notoriously difficult to find, and few subsequent collections have been recorded for this genus. Here, we increase sampling of Cryptomaster to 15 localities, extending their known range from the Coast Range northeast to the western Cascade Mountains of southern Oregon. Phylogenetic analyses of mitochondrial and nuclear DNA sequence data reveal deep phylogenetic breaks consistent with independently evolving lineages. We use discovery and validation species delimitation approaches to generate and test species hypotheses, including a coalescent species delimitation method to test multi-species hypotheses. For delimited species, we use light microscopy and SEM to discover diagnostic morphological characters. Although Cryptomaster has a small geographic distribution, this taxon is consistent with other short-range endemics in having deep phylogenetic breaks indicative of species level divergences. Herein we describe Cryptomasterbehemothsp. n., and provide morphological diagnostic characters for identifying Cryptomasterleviathan and Cryptomasterbehemoth.
Collapse
Affiliation(s)
- James Starrett
- Department of Biology, 5500 Campanile Drive San Diego State University, San Diego, CA 92182, USA
| | - Shahan Derkarabetian
- Department of Biology, 5500 Campanile Drive San Diego State University, San Diego, CA 92182, USA; Department of Biology, 900 University Avenue, University of California, Riverside, Riverside, CA 92521, USA
| | - Casey H Richart
- Department of Biology, 5500 Campanile Drive San Diego State University, San Diego, CA 92182, USA; Department of Biology, 900 University Avenue, University of California, Riverside, Riverside, CA 92521, USA
| | - Allan Cabrero
- Department of Biology, 5500 Campanile Drive San Diego State University, San Diego, CA 92182, USA
| | - Marshal Hedin
- Department of Biology, 5500 Campanile Drive San Diego State University, San Diego, CA 92182, USA
| |
Collapse
|
17
|
Delfosse E, Iorio É. Les opilions (Arachnida: Opiliones) du Parc national du Mercantour et des Alpes méridionales françaises. ZOOSYSTEMA 2015. [DOI: 10.5252/z2015n4a9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
18
|
Csősz S, Fisher BL. Diagnostic survey of Malagasy Nesomyrmex species-groups and revision of hafahafa group species via morphology based cluster delimitation protocol. Zookeys 2015:19-59. [PMID: 26487823 PMCID: PMC4607843 DOI: 10.3897/zookeys.526.6037] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/27/2015] [Indexed: 12/02/2022] Open
Abstract
Madagascar and its surrounding islands are among the world’s greatest biodiversity hotspots, harboring predominantly endemic and threatened communities meriting special attention from biodiversity scientists. Building on the considerable efforts in recent years to inventory the Malagasy ant fauna, the myrmicine genus Nesomyrmex is reviewed and (1) subdivided into four major groups based on salient morphological features corroborated by numeric morphology: angulatus-, hafahafa-, madecassus- and sikorai-groups, and (2) the hafahafa species-group endemic to Madagascar is revised. Diversity within hafahafa species-group was assessed via hypothesis-free nest-centroid-clustering combined with gap statistic to assess the number of clusters and to determine the most probable boundaries between them. This combination of methods provides a highly automatized, objective species delineation protocol based on continuous morphometric data. Delimitations of clusters recognized by these exploratory analyses were tested via confirmatory Linear Discriminant Analysis. These results suggest the existence of four morphologically distinct species, Nesomyrmexcapricornissp. n., Nesomyrmexhafahafasp. n., Nesomyrmexmedusussp. n. and Nesomyrmexspinosussp. n.; all are described and an identification key for their worker castes using morphometric data is provided. Two members of the newly outlined hafahafa species-group, Nesomyrmexhafahafasp. n., Nesomyrmexmedusussp. n., are distributed along the southeastern coast Madagascar and occupy rather large ranges, but two other species, Nesomyrmexcapricornissp. n. and Nesomyrmexspinosussp. n., are only known to occur in small and isolated forest, highlighting the importance of small forest patches for conserving arthropod diversity.
Collapse
Affiliation(s)
- Sándor Csősz
- Entomology, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, U.S.A
| | - Brian L Fisher
- Entomology, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, U.S.A
| |
Collapse
|