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Guo ZQ, Gao YJ, Chen YX, Zhan LM, Storey KB, Yu DN, Zhang JY. Comparative Mitogenome of Phylogenetic Relationships and Divergence Time Analysis within Potamanthidae (Insecta: Ephemeroptera). INSECTS 2024; 15:357. [PMID: 38786913 PMCID: PMC11122660 DOI: 10.3390/insects15050357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
Potamanthidae belongs to the superfamily Ephemeroidea but has no complete mt genome released in the NCBI (except for two unchecked and one partial mt genome). Since the sister clade to Potamanthidae has always been controversial, we sequenced seven mt genomes of Potamanthidae (two species from Rhoenanthus and five species from Potamanthus) in order to rebuild the phylogenetic relationships of Potamanthidae in this study. The divergence time of Potamanthidae was also investigated by utilizing five fossil calibration points because of the indeterminate origin time. In addition, because Rhoenanthus coreanus and Potamanthus luteus are always in low-temperature environments, we aimed to explore whether these two species were under positive selection at the mt genome level. Amongst the 13 PCGs, CGA was used as the start codon in COX1, whereas other genes conformed to initiating with an ATN start codon. From this analysis, UUA (L), AUU (I), and UUU (F) had the highest usage. Furthermore, the DHU arm was absent in the secondary structure of S1 in all species. By combining the 13 PCGs and 2 rRNAs, we reconstructed the phylogenetic relationship of Potamanthidae within Ephemeroptera. The monophyly of Potamanthidae and the monophyly of Rhoenanthus and Potamanthus were supported in the results. The phylogenetic relationship of Potamanthidae + (Ephemeridae + Polymitarcyidae) was also recovered with a high prior probability. The divergence times of Potamanthidae were traced to be 90.44 Mya (95% HPD, 62.80-121.74 Mya), and the divergence times of Rhoenanthus and Potamanthus originated at approximately 64.77 Mya (95% HPD, 43.82-88.68 Mya), thus belonging to the late Pliocene Epoch or early Miocene Epoch. In addition, the data indicated that R. coreanus was under negative selection and that ATP8 and ND2 in Potamanthidae had a high evolutionary rate.
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Affiliation(s)
- Zhi-Qiang Guo
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Ya-Jie Gao
- School of Bioengineering, Aksu Vocational Technical College, Aksu 843000, China
| | - Yu-Xin Chen
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Le-Mei Zhan
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Dan-Na Yu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Covnservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Jia-Yong Zhang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Covnservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
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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.
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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
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Takenaka M, Yano K, Tojo K. Phylogeography of the true freshwater crab, Geothelphusa dehaani: Detected dual dispersal routes via land and sea. ZOOLOGY 2023; 160:126118. [PMID: 37683516 DOI: 10.1016/j.zool.2023.126118] [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] [Received: 04/17/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023]
Abstract
Dispersal is an important factor that determines the potential for colonization to pioneer sites. Although most decapods employ seaward migration for reproduction with a planktonic larval phase, true freshwater crabs spend their entire life cycle in freshwater. Therefore, it is expected that genetic regionality can be easily detected. In this study, we focused on true freshwater crabs, Geothelphusa Stimpson, 1858. Herein, we reveal the evolutionary history and dispersal patterns of freshwater crustaceans. We collected and genetically analyzed 283 specimens at 138 localities across the Japanese Islands. Phylogenetic analyses were conducted on the combined dataset (mtDNA COI, 16S, and nDNA ITS1, histone H3 regions) and the data set based on the mtDNA COI region. The phylogenetic relationships detected 10 clades that were highly monophyletic. The highlights of this study were the discovery of several cryptic species or undescribed species, and the completely different heterogeneous dual dispersal pathways within a single species; i.e., both land and ocean routes. Although it was concluded that Japanese crabs are basically genetically divided by straits, strong evidence for dispersion via ocean currents was also detected (i.e., a "sweepstake"). It was also confirmed that Geothelphusa dehaani (White, 1847) could survive in seawater.
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Affiliation(s)
- Masaki Takenaka
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto 390-8621, Japan; Institute of Mountain Science, Shinshu University, Asahi 3-1-1, Matsumoto 390-8621, Japan; Faculty of Life and Environmental Sciences, University of Tsukuba, Sugadairakogen 1278-294, Ueda 386-2204, Japan
| | - Koki Yano
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto 390-8621, Japan; Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Nishigonaka 38, Okazaki 444-0867, Japan
| | - Koji Tojo
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto 390-8621, Japan; Institute of Mountain Science, Shinshu University, Asahi 3-1-1, Matsumoto 390-8621, Japan.
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4
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Ranarilalatiana T, Razafindraleva HA, Granath G, Bukontaite Malm R, Rakotonirina JC, Razafindranaivo V, Ravaomanarivo LHR, Johansson F, Bergsten J. Remaining forests on the Central Highlands of Madagascar—Endemic and endangered aquatic beetle fauna uncovered. Ecol Evol 2022; 12:e9580. [PMCID: PMC9745264 DOI: 10.1002/ece3.9580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022] Open
Abstract
Madagascar is known for its high endemism and as many as 90% of this unique diversity are forest‐dwellers. Unfortunately, the forest cover of Madagascar is decreasing at an alarming rate. This decrease can also affect aquatic insects, but our knowledge on aquatic insect diversity and distribution on Madagascar are limited. Although the eastern rainforests are considered the most diverse, the Central Highlands of Madagascar also harbors unique microendemic fauna but has been less studied. Here, we analyze the aquatic Adephaga beetle fauna of three remaining protected forests of the Central Highlands. Diversity, abundance, and uniqueness are compared between and within natural forests and surrounding grasslands. At least 15 undescribed species were found, highlighting the Central Highlands as an important area for endemism. The natural forests and the surrounding grasslands differed significantly in species assemblages. Interestingly, the three remaining forests differed in their assemblages with the geographically more distant Manjakatompo Ankaratra having the most unique fauna but also the highest altitude span. By contrast, the species composition was similar between the peripheral zones of each of the three remaining forests. The similarity of the fauna in the peripheral open habitats illustrates how some local forest endemics are replaced with widespread generalists in degraded habitats. Our study shows that the remaining forests of the Central Highlands of Madagascar are important refuges of unique fauna at high risk of extinction.
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Affiliation(s)
| | | | - Gustaf Granath
- Department of Ecology and GeneticsUppsala UniversityUppsalaSweden
| | - Rasa Bukontaite Malm
- Department of Bioinformatics and GeneticsSwedish Museum of Natural HistoryStockholmSweden
| | | | - Victor Razafindranaivo
- Department of Entomology, Faculty of SciencesAntananarivo UniversityAntananarivoMadagascar
| | | | - Frank Johansson
- Department of Ecology and GeneticsUppsala UniversityUppsalaSweden
| | - Johannes Bergsten
- Department of ZoologySwedish Museum of Natural HistoryStockholmSweden
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5
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Dambri BM, Benhadji N, Vuataz L, Sartori M. Ecdyonurusaurasius sp. nov. (Insecta, Ephemeroptera, Heptageniidae, Ecdyonurinae), a new micro-endemic mayfly species from Aurès Mountains (north-eastern Algeria). Zookeys 2022; 1121:17-37. [PMID: 36760764 PMCID: PMC9848610 DOI: 10.3897/zookeys.1121.89613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/10/2022] [Indexed: 11/12/2022] Open
Abstract
Ecdyonurusaurasius sp. nov., a micro-endemic species reported from several streams within the Aurès Mountains (north-eastern Algeria), is described and illustrated at nymphal, subimaginal and imaginal stages of both sexes. Critical morphological diagnostic characters distinguishing the new species are presented, together with molecular affinities as well as notes on the biology and distribution of the species.
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Affiliation(s)
- Besma M. Dambri
- Department of Ecology and Environment, Faculty of Natural and Life Sciences, University of Batna 2, 05078 Fesdis, Batna, AlgeriaUniversity of Batna 2BatnaAlgeria
| | - Nadhira Benhadji
- Department of Hydrobiology, Institute of Biology, University of Szczecin, Felczaka street 3 c, 71- 412 Szczecin, PolandUniversity of SzczecinSzczecinPoland
| | - Laurent Vuataz
- Musée cantonal de zoologie, Palais de Rumine, Place de la Riponne 6, 1014 Lausanne, SwitzerlandMusée cantonal de zoologieLausanneSwitzerland,Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, SwitzerlandUniversity of LausanneLausanneSwitzerland
| | - Michel Sartori
- Musée cantonal de zoologie, Palais de Rumine, Place de la Riponne 6, 1014 Lausanne, SwitzerlandMusée cantonal de zoologieLausanneSwitzerland,Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, SwitzerlandUniversity of LausanneLausanneSwitzerland
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6
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Zhang W, Li R, Zhou C. Complete mitochondrial genomes of Epeorus carinatus and E. dayongensis (Ephemeroptera: Heptageniidae): Genomic comparison and phylogenetic inference. Gene 2021; 777:145467. [PMID: 33524519 DOI: 10.1016/j.gene.2021.145467] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 01/12/2021] [Accepted: 01/22/2021] [Indexed: 11/26/2022]
Abstract
The current research on Ephemeroptera is mainly based on its morphology, since only small numbers of mitogenomes have been reported. In this study, the mitogenomes of Epeorus carinatus (15,338 bp) and E. dayongensis (15,609 bp) were sequenced, annotated and compared to genome data from congeners. Both mitogenomes had 23 tRNA genes including standard 22 and one extra tRNAMet. The duplicated tRNAMet gene had been found in other heptageniid species except Paegniodes cupulatus, suggesting it could be used as a molecular synapomorphy for partial Heptageniidae. The phylogenetic analyses based on Bayesian Inference (BI) and Maximum Likelihood (ML) showed that Heptageniidae was monophyletic and the relationships among known Epeorus species were ((E. carinatus + E. herklotsi) + (E. dayongensis + E. sp. 1)), which implied the focal species E. carinatus and E. dayongensis should be grouped into different subgenera.
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Affiliation(s)
- Wei Zhang
- The Key Laboratory of Jiangsu Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Ran Li
- The Key Laboratory of Jiangsu Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Changfa Zhou
- The Key Laboratory of Jiangsu Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
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7
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Nieto C, Boldrini R, Gonzalez JC, Pes AM, Salles FF. The genus Camelobaetidius Demoulin (Ephemeroptera: Baetidae) in America: Phylogenic and biogeographic analyses. ZOOL ANZ 2020. [DOI: 10.1016/j.jcz.2020.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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8
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Taylor CL, Barker NP, Barber-James HM, Villet MH, Pereira-da-Conceicoa LL. Habitat requirements affect genetic variation in three species of mayfly (Ephemeroptera, Baetidae) from South Africa. Zookeys 2020; 936:1-24. [PMID: 32547291 PMCID: PMC7272479 DOI: 10.3897/zookeys.936.38587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 11/04/2019] [Indexed: 12/23/2022] Open
Abstract
This study investigates genetic diversity in three species of Ephemeroptera, one eurytopic and therefore widespread (Afroptilumsudafricanum) and two stenotopic and thus endemic (Demoreptusnatalensis and Demoreptuscapensis) species, all of which co-occur in the southern Great Escarpment, South Africa. Mitochondrial DNA was analysed to compare the genetic diversity between the habitat generalist and the two habitat specialists. Afroptilumsudafricanum showed no indication of population genetic structure due to geographic location, while both Demoreptus species revealed clear genetic differentiation between geographic localities and catchments, evident from phylogenetic analyses and high FST values from AMOVA. In addition, the phylogenetic analyses indicate some deeper haplotype divergences within A.sudafricanum and Demoreptus that merit taxonomic attention. These results give important insight into evolutionary processes occurring through habitat specialisation and population isolation. Further research and sampling across a wider geographic setting that includes both major mountain blocks of the Escarpment and lowland non-Escarpment sites will allow for refined understanding of biodiversity and associated habitat preferences, and illuminate comparative inferences into gene flow and cryptic speciation.
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Affiliation(s)
- Chantal L Taylor
- Department of Zoology and Entomology, Rhodes University, Somerset Street, Makhanda (Grahamstown), 6140, South Africa
| | - Nigel P Barker
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, 0028, South Africa
| | - Helen M Barber-James
- Department of Zoology and Entomology, Rhodes University, Somerset Street, Makhanda (Grahamstown), 6140, South Africa.,Department of Freshwater Invertebrates, Albany Museum, Somerset Street, Makhanda (Grahamstown), 6140, South Africa
| | - Martin H Villet
- Department of Zoology and Entomology, Rhodes University, Somerset Street, Makhanda (Grahamstown), 6140, South Africa
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9
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Garces JM, Sartori M, Freitag H. Integrative taxonomy of the genus Dudgeodes Sartori, 2008 (Insecta, Ephemeroptera, Teloganodidae) from the Philippines with description of new species and supplementary descriptions of Southeast Asian species. Zookeys 2020; 910:93-129. [PMID: 32099517 PMCID: PMC7026199 DOI: 10.3897/zookeys.910.48659] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 01/05/2020] [Indexed: 11/12/2022] Open
Abstract
COI sequences were used as an initial clustering method to delimit putative species of the genus Dudgeodes in the Philippines. An overview of the diagnostic characters of Philippine species and characters with high intraspecific variability are given. Six new species of Dudgeodes are described and illustrated: D. bauernfeindi Garces & Sartori, sp. nov., D. freitagi Garces & Sartori, sp. nov., D. luntian Garces & Sartori, sp. nov., D. pangantihoni Garces & Sartori, sp. nov., D. tabang Garces & Sartori, sp. nov., and D. vonrinteleni Garces & Sartori, sp. nov., all known from the nymphal stage. Supplementary descriptions are provided for D. pescadori Sartori, 2008, D. hutanis Sartori, 2008, D. stephani Sartori, 2008, D. ulmeri Sartori, 2008, and D. celebensis Sartori, 2008. A key to the nymphs of Philippine Dudgeodes species is proposed.
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Affiliation(s)
- Jhoana M. Garces
- Department of Biology, School of Science and Engineering, Ateneo de Manila University, Quezon City, PhilippinesAteneo de Manila UniversityQuezon CityPhilippines
| | - Michel Sartori
- Museum of Zoology, Palais de Rumine, Place Riponne 6, CH-1014 Lausanne, SwitzerlandMuseum of ZoologyLausanneSwitzerland
- Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, SwitzerlandUniversity of LausanneLausanneSwitzerland
| | - Hendrik Freitag
- Department of Biology, School of Science and Engineering, Ateneo de Manila University, Quezon City, PhilippinesAteneo de Manila UniversityQuezon CityPhilippines
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10
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Hrivniak Ľ, Sroka P, Bojková J, Godunko RJ, Soldán T, Staniczek AH. The impact of Miocene orogeny for the diversification of Caucasian Epeorus (Caucasiron) mayflies (Ephemeroptera: Heptageniidae). Mol Phylogenet Evol 2020; 146:106735. [PMID: 32001364 DOI: 10.1016/j.ympev.2020.106735] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 11/26/2022]
Abstract
A common hypothesis for the high biodiversity of mountains is the diversification driven by orogeny creating conditions for rapid in situ speciation of resident lineages. The Caucasus is a young mountain system considered as a biodiversity hotspot; however, the origin and evolution of its diversity remain poorly understood. This study focuses on mayflies of the subgenus Caucasiron, one of the most diversified stenotopic mayflies inhabiting various types of streams throughout the Caucasus. Using the time-calibrated phylogeny based on two mitochondrial (COI, 16S) and three nuclear (EF-1α, wg, 28S) gene fragments, we tested the role of Caucasian orogeny in biogeography, diversification patterns, and altitudinal diversification of Caucasiron mayflies. We found that orogeny promoted the lineage diversification of Caucasiron in the Miocene. The highest diversification rate corresponding with the uplift of mountains was followed by a significant slowdown towards the present suggesting minor influence of Pleistocene climatic oscillations on the speciation. The Caucasiron lineages cluster into three principal clades originating in the Upper Miocene. We found a strong support that one of the three clades diversified via allopatric speciation in the Greater Caucasus isolated in the Parathetys Sea. The other two clades originating most likely outside the Greater Caucasus diversified towards high and low altitude, respectively, indicating possible role of climatic factors and/or passive uplift on their differentiation. Current high Caucasiron diversity in the Greater Caucasus is a result of in situ speciation and later immigration from adjacent mountain ranges after the Parathetys Sea retreat. Our phylogeny supported the monophyly of Rhithrogeninae, Epeorus s.l., Caucasiron, and Iron. Epeorus subgenus Ironopsis was found paraphyletic, with its European representatives more closely related to Epeorus s.str. than to Iron. Therefore, we re-arranged taxa treated within Ironopsis to comply with the phylogeny recovered herein.
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Affiliation(s)
- Ľuboš Hrivniak
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 37005 České Budějovice, Czech Republic; Faculty of Sciences, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic.
| | - Pavel Sroka
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Jindřiška Bojková
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Roman J Godunko
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 37005 České Budějovice, Czech Republic; Department of Invertebrate Zoology and Hydrobiology, University of Łódź, Banacha 12/16, 90237 Łódź, Poland
| | - Tomáš Soldán
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Arnold H Staniczek
- Department of Entomology, State Museum of Natural History Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
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11
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Platania L, Cardoso A, Gómez-Zurita J. Diversity and evolution of New Caledonian endemic Taophila subgenus Lapita (Coleoptera: Chrysomelidae: Eumolpinae). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
New Caledonia is an important biodiversity hotspot, where numerous plant and animal groups show high levels of species diversity and endemicity, while facing multiple threats to their habitats. Leaf beetles in the subfamily Eumolpinae illustrate this pattern, with species estimates higher than the number of described taxa and distribution ranges that are often consistent with microendemicity. In this study, we increase the knowledge of this group by focusing on the Taophila subgenus Lapita, known from three species but here expanded to eleven with eight new species: T. atlantis sp. nov., T. hermes sp. nov., T. kronos sp. nov., T. oceanica sp. nov., T. olympica sp. nov., T. ouranos sp. nov., T. riberai sp. nov., and T. tridentata sp. nov. Additionally, we infer the evolutionary history of the group using mtDNA markers (COI and rrnS). This phylogeny and the species distribution help hypothesize a model of evolution for this lineage in the context of historical climatic and geological changes of New Caledonia.
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Affiliation(s)
- Leonardo Platania
- Animal Biodiversity and Evolution, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Anabela Cardoso
- Animal Biodiversity and Evolution, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Jesús Gómez-Zurita
- Animal Biodiversity and Evolution, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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12
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Massariol FC, Takiya DM, Salles FF. Global classification and evolution of brushlegged mayflies (Insecta: Ephemeroptera: Oligoneuriidae): phylogenetic analyses of morphological and molecular data and dated historical biogeography. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
AbstractOligoneuriidae is a Pantropical family of Ephemeroptera, with 68 species described in 12 genera. Three subfamilies are recognized: Chromarcyinae, with a single species from East Asia; Colocrurinae, with two fossil species from Brazil; and Oligoneuriinae, with the remaining species distributed in the Neotropical, Nearctic, Afrotropical and Palaearctic regions. Phylogenetic and biogeographical analyses were performed for the family based on 2762 characters [73 morphological and 2689 molecular (COI, 16S, 18S and 28S)]. Four major groups were recovered in all analyses (parsimony, maximum likelihood and Bayesian inference), and they were assigned to tribal level, namely Oligoneuriini, Homoeoneuriini trib. nov., Oligoneuriellini trib. nov. and Elassoneuriini trib. nov. In addition, Yawari and Madeconeuria were elevated to genus level. According to Statistical Dispersal-Vicariance (S-DIVA), Dispersal Extinction Cladogenesis (DEC) and divergence time estimation analyses, Oligoneuriidae originated ~150 Mya in the Gondwanan supercontinent, but was probably restricted to the currently delimited Neotropical region. The initial divergence of Oligoneuriidae involved a range expansion to Oriental and Afrotropical areas, sometime between 150 and 118 Mya. At ~118 Mya, the family started its diversification, reaching the Nearctic through dispersal from the Neotropical region and the Palaearctic and Madagascar from the Afrotropical region.
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Affiliation(s)
- Fabiana Criste Massariol
- Laboratório de Sistemática e Ecologia de Insetos, Universidade Federal do Espírito Santo, Departamento de Ciências Agrárias e Biológicas, São Mateus, ES, Brazil
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Espírito Santo, Vitória, Brazil
| | - Daniela Maeda Takiya
- Laboratório de Entomologia, Departamento de Zoologia, Universidade Federal do Rio de Janeiro, Caixa Postal, Rio de Janeiro, RJ, Brazil
| | - Frederico Falcão Salles
- Museu de Entomologia, Departamento de Entomologia, Universidade Federal de Viçosa, Viçosa, MG, Brazil
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Sroka P, Bojková J, Godunko RJ, Soldán T, Namin JI, Nejat F, Abdoli A, Staniczek AH. New Oligoneuriidae (Insecta, Ephemeroptera) from Iran. Zookeys 2019; 872:101-126. [PMID: 31528118 PMCID: PMC6718370 DOI: 10.3897/zookeys.872.36098] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/11/2019] [Indexed: 12/25/2022] Open
Abstract
Two new species of the mayfly family Oligoneuriidae are described based on larval specimens recently collected in Iran. The first new species, Oligoneuriellatuberculata Godunko & Staniczek, sp. nov., can be distinguished from all its congeners by the presence of pronounced protuberances posteromedially on abdominal terga, highly reduced paracercus, large lamella of gill I, and setation on hind margin of middle and hind femora confined to their basal halves. The second species, Oligoneuriopsisvillosus Bojková, Godunko, & Staniczek, sp. nov., remarkably belongs to a mostly Afrotropical genus. The new species clearly differs from all its congeners in the shape of setae on the surface of gills and terga, pattern of body colouration, and the shape of posterolateral projections of abdominal segments. Except for the species description, the generic diagnosis of Oligoneuriopsis Crass, 1947 is briefly discussed. COI barcode sequences of both new species are provided and molecular species delimitation is tested using distance-based and likelihood-based approaches, with both new species unambiguously recognised as separate lineages. The analysis of COI also corroborates the respective affinities of both new species, estimated based on morphology. The two new species of Oligoneuriidae described herein highlight the importance of the Middle East as a centre of diversity of this mayfly family within the Palaearctic.
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Affiliation(s)
- Pavel Sroka
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 37005 České Budějovice, Czech Republic Biology Centre of the Czech Academy of Sciences České Budějovice Czech Republic
| | - Jindřiška Bojková
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic Masaryk University Brno Czech Republic
| | - Roman J Godunko
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 37005 České Budějovice, Czech Republic Biology Centre of the Czech Academy of Sciences České Budějovice Czech Republic.,Department of Invertebrate Zoology and Hydrobiology, University of Łódź, Banacha 12/16, 90237 Łódź, Poland University of Łódź Łódź Poland
| | - Tomáš Soldán
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 37005 České Budějovice, Czech Republic Biology Centre of the Czech Academy of Sciences České Budějovice Czech Republic
| | - Javid Imanpour Namin
- Department of Fishery, Faculty of Natural Resources, University of Guilan, POB 1144, Sowmehsara-Rasht, Iran University of Guilan Sowmehsara-Rasht Iran
| | - Farshad Nejat
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, Daneshjou Boulevard, 1983969411 Tehran, Iran Shahid Beheshti University Tehran Iran
| | - Ashgar Abdoli
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, Daneshjou Boulevard, 1983969411 Tehran, Iran Shahid Beheshti University Tehran Iran
| | - Arnold H Staniczek
- Department of Entomology, State Museum of Natural History Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany State Museum of Natural History Stuttgart Stuttgart Germany
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14
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Abstract
Abstract
Sexual reproduction is overwhelmingly the most common reproductive mode among Metazoans, although it has been secondarily lost in some organisms. Ephoron shigae is a geographically parthenogenetic mayfly. Here, we provide details of the frequency of bisexual and parthenogenetic strains of E. shigae together with data on their sex ratios in the Abukuma-gawa River and one of its downstream tributaries, the Surikami-gawa River, in Japan. In a previous study in the 1990s, bisexual populations were observed in both rivers. The present study clearly shows that sex ratios have since changed to be almost entirely unisexual within the downstream area of the Abukuma-gawa River and the Surikami-gawa River. Our genetic analyses also show that these females are of a parthenogenetic strain, and that the original bisexual strains were overwhelmed within a period of <20 years. However, it was recently observed that many males and females of the bisexual strains continue to inhabit upstream areas of the Abukuma-gawa River. Therefore, we suggest that the parthenogenetic strains have increased in abundance primarily downstream. We show that a drastic change has occurred over a short period, involving the replacement of one strain and a corresponding change in reproductive mode along a riverine environment.
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Affiliation(s)
- K Sekiné
- Faculty of Geo-Environmental Science, Rissho University, Kumagaya, Saitama Prefecture, Japan
| | - K Tojo
- Department of Biology, Faculty of Science, Shinshu University, Matsumoto, Nagano, Japan
- Institute of Mountain Science, Shinshu University, Matsumoto, Nagano, Japan
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15
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Takenaka M, Tojo K. Ancient origin of a dipteromimid mayfly family endemic to the Japanese Islands and its genetic differentiation across tectonic faults. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/bly192] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Masaki Takenaka
- Department of Mountain and Environmental Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University, Asahi, Matsumoto, Nagano, Japan
| | - Koji Tojo
- Department of Mountain and Environmental Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University, Asahi, Matsumoto, Nagano, Japan
- Department of Biology, Faculty of Science, Shinshu University, Asahi, Matsumoto, Nagano, Japan
- Institute of Mountain Science, Shinshu University, Asahi, Matsumoto, Nagano, Japan
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16
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Zembrzuski DC, Anderson FE. Clarifying the phylogenetic relationships and taxonomy of Stenonema, Stenacron and Maccaffertium, three common eastern North American mayfly genera. Mol Phylogenet Evol 2018; 128:212-220. [PMID: 30099062 DOI: 10.1016/j.ympev.2018.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 07/01/2018] [Accepted: 08/03/2018] [Indexed: 11/29/2022]
Abstract
Stenonema, Stenacron, and Maccaffertium are three closely related genera of mayflies (Ephemeroptera:Heptageniidae) commonly found across North America. Due to their primarily aquatic life history and sensitivity to aquatic pollutants, these mayflies are often used as water quality indicators. However, there is little morphological variation within these genera, leading to difficulties in identification and rampant taxonomic confusion, limiting their utility as bioindicators. In an attempt to resolve the phylogenetic relationships of Stenonema, Stenacron, and Maccaffertium, and to clarify their higher-level classifications, we sequenced regions of two mitochondrial genes (cytochrome oxidase subunit 1 (cox1) and 16S ribosomal RNA (rrnl)) and two nuclear genes (Wingless (Wg) and histone H3) from 60 individuals representing most of the described species in these genera and included data from representatives of three heptageniid genera (Kageronia, Macdunnoa and Pseudiron) proposed in previous studies to be closely related to our focal taxa as well as two more distantly related heptageniid genera (Epeorus and Heptagenia) to root the phylogenies. Maximum likelihood and Bayesian analysis were conducted on single-gene and concatenated multi-gene data sets and species tree methods were utilized to resolve relationships. These analyses resolved Stenacron as a monophyletic group sister to a clade comprising Macdunnoa, Maccaffertium and Stenonema. Maccaffertium was found to be paraphyletic, with Stenonema femoratum resolved within Maccaffertium as sister to M. mexicanum. Many relationships remained unresolved or varied across analyses, making revision of the classification based on phylogenetic considerations challenging. To minimize confusion while naming clades and acknowledging uncertainty in our phylogenetic conclusions, we redefine Stenonema to include Maccaffertium and propose three subgenera-Stenonema, Maccaffertium and Lewisa- for key well-supported clades.
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Affiliation(s)
- Deanna C Zembrzuski
- Department of Zoology, Southern Illinois University, Carbondale, IL 62901, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Frank E Anderson
- Department of Zoology, Southern Illinois University, Carbondale, IL 62901, USA.
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17
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DNA barcoding for molecular identification of Demodex based on mitochondrial genes. Parasitol Res 2017; 116:3285-3290. [PMID: 29032499 DOI: 10.1007/s00436-017-5641-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/02/2017] [Indexed: 01/20/2023]
Abstract
There has been no widely accepted DNA barcode for species identification of Demodex. In this study, we attempted to solve this issue. First, mitochondrial cox1-5' and 12S gene fragments of Demodex folloculorum, D. brevis, D. canis, and D. caprae were amplified, cloned, and sequenced for the first time; intra/interspecific divergences were computed and phylogenetic trees were reconstructed. Then, divergence frequency distribution plots of those two gene fragments were drawn together with mtDNA cox1-middle region and 16S obtained in previous studies. Finally, their identification efficiency was evaluated by comparing barcoding gap. Results indicated that 12S had the higher identification efficiency. Specifically, for cox1-5' region of the four Demodex species, intraspecific divergences were less than 2.0%, and interspecific divergences were 21.1-31.0%; for 12S, intraspecific divergences were less than 1.4%, and interspecific divergences were 20.8-26.9%. The phylogenetic trees demonstrated that the four Demodex species clustered separately, and divergence frequency distribution plot showed that the largest intraspecific divergence of 12S (1.4%) was less than cox1-5' region (2.0%), cox1-middle region (3.1%), and 16S (2.8%). The barcoding gap of 12S was 19.4%, larger than cox1-5' region (19.1%), cox1-middle region (11.3%), and 16S (13.0%); the interspecific divergence span of 12S was 6.2%, smaller than cox1-5' region (10.0%), cox1-middle region (14.1%), and 16S (11.4%). Moreover, 12S has a moderate length (517 bp) for sequencing at once. Therefore, we proposed mtDNA 12S was more suitable than cox1 and 16S to be a DNA barcode for classification and identification of Demodex at lower category level.
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18
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Che Y, Gui S, Lo N, Ritchie A, Wang Z. Species Delimitation and Phylogenetic Relationships in Ectobiid Cockroaches (Dictyoptera, Blattodea) from China. PLoS One 2017; 12:e0169006. [PMID: 28046038 PMCID: PMC5207705 DOI: 10.1371/journal.pone.0169006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 12/10/2016] [Indexed: 11/23/2022] Open
Abstract
We collected Ectobiidae cockroach specimens from 44 locations in the south of the Yangtze valley. We obtained 297 COI sequences specimens and carried out phylogenetic and divergence dating analyses, as well as species delimitation analysis using a General Mixed Yule Coalescent (GMYC) framework. The intraspecific and interspecific sequence divergence in Ectobiidae cockroaches ranged from 0.0 to 7.0% and 4.6 to 30.8%, respectively. GMYC analysis resulted in 53 (confidence interval: 37-65) entities (likelihood ratio = 103.63) including 14 downloaded species. The COI GMYC groups partly corresponded to the ectobiid species and 52 ectobiid species were delimited successfully based on the combination of GMYC result with morphological information. We used the molecular data and 6 cockroach fossil calibrations to obtain a preliminary estimate of the timescale of ectobiid evolution. The major subfamilies in the group were found to have diverged between ~125-110 Ma, and morphospecies pairs were found to have diverged ~10 or more Ma.
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Affiliation(s)
- Yanli Che
- College of Plant Protection, Southwest University, Beibei, Chongqing, P. R. China
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Shunhua Gui
- College of Plant Protection, Southwest University, Beibei, Chongqing, P. R. China
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Andrew Ritchie
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Zongqing Wang
- College of Plant Protection, Southwest University, Beibei, Chongqing, P. R. China
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19
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Rutschmann S, Detering H, Simon S, Funk DH, Gattolliat JL, Hughes SJ, Raposeiro PM, DeSalle R, Sartori M, Monaghan MT. Colonization and diversification of aquatic insects on three Macaronesian archipelagos using 59 nuclear loci derived from a draft genome. Mol Phylogenet Evol 2016; 107:27-38. [PMID: 27742475 DOI: 10.1016/j.ympev.2016.10.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 09/23/2016] [Accepted: 10/10/2016] [Indexed: 12/20/2022]
Abstract
The study of processes driving diversification requires a fully sampled and well resolved phylogeny, although a lack of phylogenetic markers remains a limitation for many non-model groups. Multilocus approaches to the study of recent diversification provide a powerful means to study the evolutionary process, but their application remains restricted because multiple unlinked loci with suitable variation for phylogenetic or coalescent analysis are not available for most non-model taxa. Here we identify novel, putative single-copy nuclear DNA (nDNA) phylogenetic markers to study the colonization and diversification of an aquatic insect species complex, Cloeon dipterum L. 1761 (Ephemeroptera: Baetidae), in Macaronesia. Whole-genome sequencing data from one member of the species complex were used to identify 59 nDNA loci (32,213 base pairs), followed by Sanger sequencing of 29 individuals sampled from 13 islands of three Macaronesian archipelagos. Multispecies coalescent analyses established six putative species. Three island species formed a monophyletic clade, with one species occurring on the Azores, Europe and North America. Ancestral state reconstruction indicated at least two colonization events from the mainland (to the Canaries, respectively Azores) and one within the archipelago (between Madeira and the Canaries). Random subsets of the 59 loci showed a positive linear relationship between number of loci and node support. In contrast, node support in the multispecies coalescent tree was negatively correlated with mean number of phylogenetically informative sites per locus, suggesting a complex relationship between tree resolution and marker variability. Our approach highlights the value of combining genomics, coalescent-based phylogeography, species delimitation, and phylogenetic reconstruction to resolve recent diversification events in an archipelago species complex.
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Affiliation(s)
- Sereina Rutschmann
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587 Berlin, Germany; Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Straße 6-8, 14195 Berlin, Germany; Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain.
| | - Harald Detering
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587 Berlin, Germany; Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Straße 6-8, 14195 Berlin, Germany; Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Sabrina Simon
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY 10024, USA; Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - David H Funk
- Stroud Water Research Center, Avondale, PA 19311, USA
| | - Jean-Luc Gattolliat
- Musée cantonal de zoologie, Palais de Rumine, Place de la Riponne 6, 1014 Lausanne, Switzerland; Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, Switzerland
| | - Samantha J Hughes
- Centro de Investigação e de Tecnologias Agro-Ambientais e Biológicas (CITAB), Universidade de Trás-os-Montes e Alto Douro, Quinta de Prados, Apartado 1013, 5001-801 Vila Real, Portugal
| | - Pedro M Raposeiro
- Research Centre in Biodiversity and Genetic Resources (CIBIO)-Açores and the Biology Department, University of Azores, Rua Mãe de Deus 13A, 9501-855 Ponta Delgada, Portugal
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY 10024, USA
| | - Michel Sartori
- Musée cantonal de zoologie, Palais de Rumine, Place de la Riponne 6, 1014 Lausanne, Switzerland; Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, Switzerland
| | - Michael T Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587 Berlin, Germany; Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Straße 6-8, 14195 Berlin, Germany
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20
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Vuataz L, Rutschmann S, Monaghan MT, Sartori M. Molecular phylogeny and timing of diversification in Alpine Rhithrogena (Ephemeroptera: Heptageniidae). BMC Evol Biol 2016; 16:194. [PMID: 27654122 PMCID: PMC5031269 DOI: 10.1186/s12862-016-0758-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 09/01/2016] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Larvae of the Holarctic mayfly genus Rhithrogena Eaton, 1881 (Ephemeroptera, Heptageniidae) are a diverse and abundant member of stream and river communities and are routinely used as bio-indicators of water quality. Rhithrogena is well diversified in the European Alps, with a number of locally endemic species, and several cryptic species have been recently detected. While several informal species groups are morphologically well defined, a lack of reliable characters for species identification considerably hampers their study. Their relationships, origin, timing of speciation and mechanisms promoting their diversification in the Alps are unknown. RESULTS Here we present a species-level phylogeny of Rhithrogena in Europe using two mitochondrial and three nuclear gene regions. To improve sampling in a genus with many cryptic species, individuals were selected for analysis according to a recent DNA-based taxonomy rather than traditional nomenclature. A coalescent-based species tree and a reconstruction based on a supermatrix approach supported five of the species groups as monophyletic. A molecular clock, mapped on the most resolved phylogeny and calibrated using published mitochondrial evolution rates for insects, suggested an origin of Alpine Rhithrogena in the Oligocene/Miocene boundary. A diversification analysis that included simulation of missing species indicated a constant speciation rate over time, rather than any pronounced periods of rapid speciation. Ancestral state reconstructions provided evidence for downstream diversification in at least two species groups. CONCLUSIONS Our species-level analyses of five gene regions provide clearer definitions of species groups within European Rhithrogena. A constant speciation rate over time suggests that the paleoclimatic fluctuations, including the Pleistocene glaciations, did not significantly influence the tempo of diversification of Alpine species. A downstream diversification trend in the hybrida and alpestris species groups supports a previously proposed headwater origin hypothesis for aquatic insects.
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Affiliation(s)
- Laurent Vuataz
- Musée cantonal de zoologie, Palais de Rumine, Place de la Riponne 6, 1014, Lausanne, Switzerland.
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland.
| | - Sereina Rutschmann
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587, Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, 14195, Berlin, Germany
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
| | - Michael T Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587, Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, 14195, Berlin, Germany
| | - Michel Sartori
- Musée cantonal de zoologie, Palais de Rumine, Place de la Riponne 6, 1014, Lausanne, Switzerland
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland
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21
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Rutschmann S, Detering H, Simon S, Fredslund J, Monaghan MT. discomark: nuclear marker discovery from orthologous sequences using draft genome data. Mol Ecol Resour 2016; 17:257-266. [PMID: 27454666 DOI: 10.1111/1755-0998.12576] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 07/05/2016] [Accepted: 07/11/2016] [Indexed: 11/28/2022]
Abstract
High-throughput sequencing has laid the foundation for fast and cost-effective development of phylogenetic markers. Here we present the program discomark, which streamlines the development of nuclear DNA (nDNA) markers from whole-genome (or whole-transcriptome) sequencing data, combining local alignment, alignment trimming, reference mapping and primer design based on multiple sequence alignments to design primer pairs from input orthologous sequences. To demonstrate the suitability of discomark, we designed markers for two groups of species, one consisting of closely related species and one group of distantly related species. For the closely related members of the species complex of Cloeon dipterum s.l. (Insecta, Ephemeroptera), the program discovered a total of 78 markers. Among these, we selected eight markers for amplification and Sanger sequencing. The exon sequence alignments (2526 base pairs) were used to reconstruct a well-supported phylogeny and to infer clearly structured haplotype networks. For the distantly related species, we designed primers for the insect order Ephemeroptera, using available genomic data from four sequenced species. We developed primer pairs for 23 markers that are designed to amplify across several families. The discomark program will enhance the development of new nDNA markers by providing a streamlined, automated approach to perform genome-scale scans for phylogenetic markers. The program is written in Python, released under a public licence (GNU GPL version 2), and together with a manual and example data set available at: https://github.com/hdetering/discomark.
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Affiliation(s)
- Sereina Rutschmann
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Straße 6-8, 14195, Berlin, Germany.,Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
| | - Harald Detering
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Straße 6-8, 14195, Berlin, Germany.,Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
| | - Sabrina Simon
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY, 10024, USA.,Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | | | - Michael T Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Straße 6-8, 14195, Berlin, Germany
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22
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Bukontaite R, Ranarilalatiana T, Randriamihaja JH, Bergsten J. In or out-of-Madagascar?--Colonization patterns for large-bodied diving beetles (Coleoptera: Dytiscidae). PLoS One 2015; 10:e0120777. [PMID: 25794184 PMCID: PMC4368551 DOI: 10.1371/journal.pone.0120777] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 02/01/2015] [Indexed: 12/21/2022] Open
Abstract
High species diversity and endemism within Madagascar is mainly the result of species radiations following colonization from nearby continents or islands. Most of the endemic taxa are thought to be descendants of a single or small number of colonizers that arrived from Africa sometime during the Cenozoic and gave rise to highly diverse groups. This pattern is largely based on vertebrates and a small number of invertebrate groups. Knowledge of the evolutionary history of aquatic beetles on Madagascar is lacking, even though this species-rich group is often a dominant part of invertebrate freshwater communities in both standing and running water. Here we focus on large bodied diving beetles of the tribes Hydaticini and Cybistrini. Our aims with this study were to answer the following questions 1) How many colonization events does the present Malagasy fauna originate from? 2) Did any colonization event lead to a species radiation? 3) Where did the colonizers come from--Africa or Asia--and has there been any out-of-Madagascar event? 4) When did these events occur and were they concentrated to any particular time interval? Our results suggest that neither in Hydaticini nor in Cybistrini was there a single case of two or more endemic species forming a monophyletic group. The biogeographical analysis indicated different colonization histories for the two tribes. Cybistrini required at least eight separate colonization events, including the non-endemic species, all comparatively recent except the only lotic (running water) living Cybister operosus with an inferred colonization at 29 Ma. In Hydaticini the Madagascan endemics were spread out across the tree, often occupying basal positions in different species groups. The biogeographical analyses therefore postulated the very bold hypothesis of a Madagascan origin at a very deep basal node within Hydaticus and multiple out-of-Madagascar dispersal events. This hypothesis needs to be tested with equally intense taxon sampling of mainland Africa as for Madagascar.
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Affiliation(s)
- Rasa Bukontaite
- Department of Zoology, Swedish Museum of Natural History, Box 50007, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Tolotra Ranarilalatiana
- Departement d’Entomologie, Faculté des Sciences, B.P. 906, Université d’Antananarivo, Antananarivo, Madagascar
- Programme National de Lutte contre le Paludisme de Madagascar, Androhibe, Antananarivo (101), Madagascar
| | - Jacquelin Herisahala Randriamihaja
- Departement d’Entomologie, Faculté des Sciences, B.P. 906, Université d’Antananarivo, Antananarivo, Madagascar
- Programme National de Lutte contre le Paludisme de Madagascar, Androhibe, Antananarivo (101), Madagascar
| | - Johannes Bergsten
- Department of Zoology, Swedish Museum of Natural History, Box 50007, Stockholm, Sweden
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23
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Maddison DR, Cooper KW. Species delimitation in the ground beetle subgenusLiocosmius(Coleoptera: Carabidae:Bembidion), including standard and next-generation sequencing of museum specimens. Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12188] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- David R. Maddison
- Department of Integrative Biology; Oregon State University; 3029 Cordley Hall Corvallis OR 97331 USA
| | - Kenneth W. Cooper
- Department of Biology; University of California; Riverside CA 92521 USA
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24
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Sartori M. On the validity of Epeorella Ulmer, 1939 (Ephemeroptera, Heptageniidae) with general considerations on the Heptageniidae of the Sunda Islands. Zookeys 2014:97-106. [PMID: 25349509 PMCID: PMC4205742 DOI: 10.3897/zookeys.445.8370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 09/26/2014] [Indexed: 11/24/2022] Open
Abstract
The type material of Epeorellaborneonia Ulmer, 1939, the sole species of the genus Epeorella Ulmer, 1939 is reinvestigated and a lectotype (male imago) is designated. Based on several morphological structures, the synonymy with Epeorus Eaton, 1881 (Rhithrogeninae) is rejected. Epeorella stat. prop., known only at the winged stages, belongs to the subfamily Ecdyonurinae, and is a probable endemic of the island of Borneo. The newly erected genus Darthus Webb & McCafferty, 2007, also endemic to Borneo and only known by one species at the nymphal stage, is shown to be a junior subjective synonym of Epeorella. The new combination Epeorellavadora (Webb & McCafferty, 2007) is proposed for the species. The distribution of known heptageniid species from the Sunda Islands is discussed.
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Affiliation(s)
- Michel Sartori
- Zoologisches Museum und Biozentrum Grindel, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany ; Museum of Zoology, Palais de Rumine, Place Riponne 6, CH-1005 Lausanne, Switzerland
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Čandek K, Kuntner M. DNA barcoding gap: reliable species identification over morphological and geographical scales. Mol Ecol Resour 2014; 15:268-77. [DOI: 10.1111/1755-0998.12304] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 07/06/2014] [Accepted: 07/16/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Klemen Čandek
- Institute of Biology; Scientific Research Centre of the Slovenian Academy of Sciences and Arts; Novi Trg 2 1000 Ljubljana Slovenia
| | - Matjaž Kuntner
- Institute of Biology; Scientific Research Centre of the Slovenian Academy of Sciences and Arts; Novi Trg 2 1000 Ljubljana Slovenia
- Centre for Behavioural Ecology and Evolution; College of Life Sciences; Hubei University; 368 Youyi Road 430062 Wuhan China
- Department of Entomology; National Museum of Natural History; Smithsonian Institution; PO Box 37012 Washington DC 20013-7012 USA
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Sartori M. Status of the enigmatic Oriental genus Rhithrogeniella Ulmer, 1939 (Ephemeroptera, Heptageniidae). Zookeys 2014:47-61. [PMID: 25147469 PMCID: PMC4137297 DOI: 10.3897/zookeys.429.8116] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 07/23/2014] [Indexed: 11/12/2022] Open
Abstract
Based on historic collections and new material from Sumatra and Java, the species Rhithrogeniella ornata Ulmer, 1939, type species of the genus Rhithrogeniella, is reinvestigated. The nymph is described for the first time and is closely related to the continental Southeast Asian species Rhithrogeniella tonkinensis Soldán and Braasch, 1986. Rhithrogeniella belongs to the subfamily Ecdyonurinae, and is related to the genera Nixe Flowers, 1980 and/or Paracinygmula Bajkova, 1975 based on characters of the nymphal stage. Species described from Taiwan in the genus Nixe are transferred to the genus Rhithrogeniella: Rh. littoralis (Kang and Yang, 1994) comb. n., Rh. mitifica (Kang and Yang, 1994) comb. n. and Rh. obscura (Kang and Yang, 1994) comb. n.
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Affiliation(s)
- Michel Sartori
- Zoologisches Museum und Biozentrum Grindel, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany ; Museum of Zoology, Palais de Rumine, Place Riponne 6, CH-1005 Lausanne, Switzerland
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Sartori M. The species of Thalerosphyrus Eaton, 1881 (Insecta, Ephemeroptera, Heptageniidae, Ecdyonurinae) in Java and Sumatra, with some comments on the diversity of the genus in the Oriental Realm. Zookeys 2014:19-39. [PMID: 25061369 PMCID: PMC4109478 DOI: 10.3897/zookeys.420.7904] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 06/13/2014] [Indexed: 11/26/2022] Open
Abstract
Three species belonging to the genus Thalerosphyrus Eaton, 1881 are reported from Java and Sumatra. The nymphs of Th. determinatus (Walker, 1853) from Java, Th. sinuosus (Navás, 1933) from Java and Sumatra and Th. lamuriensis Sartori, 2014 from Sumatra are redescribed. The egg morphology of the three species is also presented for the first time. A key to the nymphs is proposed. General considerations on the composition of the genus Thalerosphyrus in the Oriental Realm are given. The distribution of the genus is greatly expended, and currently ranges over the Himalaya and Sumbawa in the Sunda Islands.
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Affiliation(s)
- Michel Sartori
- Zoologisches Museum und Biozentrum Grindel, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany ; Museum of Zoology, Palais de Rumine, Place Riponne 6, CH-1005 Lausanne, Switzerland
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Sivaramakrishnan KG, Janarthanan S, Selvakumar C, Arumugam M. Aquatic insect conservation: a molecular genetic approach. CONSERV GENET RESOUR 2014. [DOI: 10.1007/s12686-014-0250-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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The towering orogeny of New Guinea as a trigger for arthropod megadiversity. Nat Commun 2014; 5:4001. [DOI: 10.1038/ncomms5001] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 04/29/2014] [Indexed: 11/08/2022] Open
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Dijkstra KDB, Monaghan MT, Pauls SU. Freshwater biodiversity and aquatic insect diversification. ANNUAL REVIEW OF ENTOMOLOGY 2014; 59:143-63. [PMID: 24160433 PMCID: PMC4816856 DOI: 10.1146/annurev-ento-011613-161958] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Inland waters cover less than 1% of Earth's surface but harbor more than 6% of all insect species: Nearly 100,000 species from 12 orders spend one or more life stages in freshwater. Little is known about how this remarkable diversity arose, although allopatric speciation and ecological adaptation are thought to be primary mechanisms. Freshwater habitats are highly susceptible to environmental change and exhibit marked ecological gradients. Standing waters appear to harbor more dispersive species than running waters, but there is little understanding of how this fundamental ecological difference has affected diversification. In contrast to the lack of evolutionary studies, the ecology and habitat preferences of aquatic insects have been intensively studied, in part because of their widespread use as bioindicators. The combination of phylogenetics with the extensive ecological data provides a promising avenue for future research, making aquatic insects highly suitable models for the study of ecological diversification.
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Affiliation(s)
- Klaas-Douwe B. Dijkstra
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The
Netherlands, and University Museum of Zoology, Cambridge, CB2 3EJ, United Kingdom
| | - Michael T. Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB),
12587 Berlin, Germany;
| | - Steffen U. Pauls
- Biodiversity and Climate Research Centre, Frankfurt, Germany and
Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt,
Germany;
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Jordal BH. Deep phylogenetic divergence between Scolytoplatypus and Remansus, a new genus of Scolytoplatypodini from Madagascar (Coleoptera, Curculionidae, Scolytinae). Zookeys 2013:9-33. [PMID: 24294090 PMCID: PMC3837396 DOI: 10.3897/zookeys.352.6212] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Accepted: 11/06/2013] [Indexed: 11/30/2022] Open
Abstract
Scolytoplatypodini Blandford is a monotypic tribe of ambrosia beetles found in Asia, Madagascar and Africa. Only three species are currently known from Madagascar and four additional species are here described as new to science. Phylogenetic analyses of morphological and molecular data revealed that four of the seven endemic species are deeply separated from all other species by genetic and distinct morphological characters and therefore placed in a new genus Remansus Jordal. The split between this ancient lineage and Scolytoplatypus Schaufuss was estimated to approximate Palaeocene age (63 Ma), extending the minimum age of ambrosia feeding for this tribe to the beginning of the Palaeocene‒Eocene thermal maximum (PETM). In addition to the ancient origin of Remansus in Madagascar during the Palaeocene, a second origin occurred in Scolytoplatypus no more than 13 Ma. A geographical origin of the latter in South-Eastern Africa was unequivocally inferred from the phylogenies.
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Affiliation(s)
- Bjarte H Jordal
- Natural History Museum, University Museum of Bergen, PB 7800, NO-5020 Bergen, Norway
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