151
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Du H, Liu M, Zhang S, Liu F, Zhang Z, Kong X. Lineage Divergence of Dendrolimus punctatus in Southern China Based on Mitochondrial Genome. Front Genet 2020; 11:65. [PMID: 32153637 PMCID: PMC7045034 DOI: 10.3389/fgene.2020.00065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/20/2020] [Indexed: 12/12/2022] Open
Abstract
In southern China, the masson pine caterpillar, Dendrolimus punctatus, has caused serious damage to the Pinus massoniana (Lamb.) pine forests. Here, the whole mitochondrial DNA (mtDNA) was employed to analyze the population evolution of D. punctatus and to understand the process underlying its current phylogenetic pattern. D. punctatus populations within its distribution range in China were categorized into five subgroups: central and eastern China (CEC), southwestern China (SWC), Yibin in Sichuan (SC), Baise in Guangxi (GX), and Luoding in Guangdong (GD), with a high level of haplotype diversity and nucleotide diversity among them. The genetic distances between subgroups are relatively large; however, the genetic distances between populations within the CEC subgroup were relatively small, suggesting that many populations were closely related in this subgroup. The mantel test showed that geographic distance had an important impact on the genetic distance of different geographic populations (r = 0.3633, P < 0.001). The neutrality tests, Bayesian skyline plot, and haplotype network showed that D. punctatus experienced a population expansion around 100,000 years ago. The divergence times of GX/SC, SWC, GD, and CEC were 0.347, 0.236, 0.200, and 0.110 million years ago, respectively. The SWC, CEC, and GD subgroups might have evolved from GX or SC subgroups. The population genetic structure of D. punctatus was closely related to its host tree species, geographic distance among populations, the weak flight capacity, and many eco-environment conditions.
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Affiliation(s)
- Huicong Du
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Man Liu
- Guizhou Institute of Biology, Guizhou Academy of Sciences, Guiyang, China
| | - Sufang Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Fu Liu
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Zhen Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Xiangbo Kong
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
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152
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Membrebe JV, Suchard MA, Rambaut A, Baele G, Lemey P. Bayesian Inference of Evolutionary Histories under Time-Dependent Substitution Rates. Mol Biol Evol 2020; 36:1793-1803. [PMID: 31004175 PMCID: PMC6657730 DOI: 10.1093/molbev/msz094] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Many factors complicate the estimation of time scales for phylogenetic histories, requiring increasingly complex evolutionary models and inference procedures. The widespread application of molecular clock dating has led to the insight that evolutionary rate estimates may vary with the time frame of measurement. This is particularly well established for rapidly evolving viruses that can accumulate sequence divergence over years or even months. However, this rapid evolution stands at odds with a relatively high degree of conservation of viruses or endogenous virus elements over much longer time scales. Building on recent insights into time-dependent evolutionary rates, we develop a formal and flexible Bayesian statistical inference approach that accommodates rate variation through time. We evaluate the novel molecular clock model on a foamy virus cospeciation history and a lentivirus evolutionary history and compare the performance to other molecular clock models. For both virus examples, we estimate a similarly strong time-dependent effect that implies rates varying over four orders of magnitude. The application of an analogous codon substitution model does not implicate long-term purifying selection as the cause of this effect. However, selection does appear to affect divergence time estimates for the less deep evolutionary history of the Ebolavirus genus. Finally, we explore the application of our approach on woolly mammoth ancient DNA data, which shows a much weaker, but still important, time-dependent rate effect that has a noticeable impact on node age estimates. Future developments aimed at incorporating more complex evolutionary processes will further add to the broad applicability of our approach.
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Affiliation(s)
- Jade Vincent Membrebe
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA.,Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.,Fogarty International Center, National Institutes of Health, Bethesda, MD
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
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153
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Gemmell MR, Trewick SA, Hills SFK, Morgan‐Richards M. Phylogenetic topology and timing of New Zealand olive shells are consistent with punctuated equilibrium. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael R. Gemmell
- Ecology Group School of Agriculture and Environment Massey University Palmerston North New Zealand
| | - Steven A. Trewick
- Ecology Group School of Agriculture and Environment Massey University Palmerston North New Zealand
| | - Simon F. K. Hills
- Ecology Group School of Agriculture and Environment Massey University Palmerston North New Zealand
| | - Mary Morgan‐Richards
- Ecology Group School of Agriculture and Environment Massey University Palmerston North New Zealand
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154
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Bateta R, Saarman NP, Okeyo WA, Dion K, Johnson T, Mireji PO, Okoth S, Malele I, Murilla G, Aksoy S, Caccone A. Phylogeography and population structure of the tsetse fly Glossina pallidipes in Kenya and the Serengeti ecosystem. PLoS Negl Trop Dis 2020; 14:e0007855. [PMID: 32092056 PMCID: PMC7058365 DOI: 10.1371/journal.pntd.0007855] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/05/2020] [Accepted: 10/17/2019] [Indexed: 02/06/2023] Open
Abstract
Glossina pallidipes is the main vector of animal African trypanosomiasis and a potential vector of human African trypanosomiasis in eastern Africa where it poses a large economic burden and public health threat. Vector control efforts have succeeded in reducing infection rates, but recent resurgence in tsetse fly population density raises concerns that vector control programs require improved strategic planning over larger geographic and temporal scales. Detailed knowledge of population structure and dispersal patterns can provide the required information to improve planning. To this end, we investigated the phylogeography and population structure of G. pallidipes over a large spatial scale in Kenya and northern Tanzania using 11 microsatellite loci genotyped in 600 individuals. Our results indicate distinct genetic clusters east and west of the Great Rift Valley, and less distinct clustering of the northwest separate from the southwest (Serengeti ecosystem). Estimates of genetic differentiation and first-generation migration indicated high genetic connectivity within genetic clusters even across large geographic distances of more than 300 km in the east, but only occasional migration among clusters. Patterns of connectivity suggest isolation by distance across genetic breaks but not within genetic clusters, and imply a major role for river basins in facilitating gene flow in G. pallidipes. Effective population size (Ne) estimates and results from Approximate Bayesian Computation further support that there has been recent G. pallidipes population size fluctuations in the Serengeti ecosystem and the northwest during the last century, but also suggest that the full extent of differences in genetic diversity and population dynamics between the east and the west was established over evolutionary time periods (tentatively on the order of millions of years). Findings provide further support that the Serengeti ecosystem and northwestern Kenya represent independent tsetse populations. Additionally, we present evidence that three previously recognized populations (the Mbeere-Meru, Central Kenya and Coastal "fly belts") act as a single population and should be considered as a single unit in vector control.
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Affiliation(s)
- Rosemary Bateta
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kikuyu, Nairobi, Kenya
| | - Norah P. Saarman
- Department of Ecology and Evolutionary Biology, Yale University, Connecticut, United States of America
| | - Winnie A. Okeyo
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kikuyu, Nairobi, Kenya
- Department of Biomedical Sciences and Technology, School of Public Health and Community Development, Maseno University, Maseno, Kisumu, Kenya
| | - Kirstin Dion
- Department of Ecology and Evolutionary Biology, Yale University, Connecticut, United States of America
| | - Thomas Johnson
- Department of Ecology and Evolutionary Biology, Yale University, Connecticut, United States of America
| | - Paul O. Mireji
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kikuyu, Nairobi, Kenya
- Centre for Geographic Medicine Research Coast, Kenya Medical Research Institute, Kilifi, Kenya
| | - Sylvance Okoth
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kikuyu, Nairobi, Kenya
| | - Imna Malele
- Vector and Vector Borne Diseases Research Institute, Tanzania Veterinary Laboratory Agency, Tanga, Tanzania
| | - Grace Murilla
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kikuyu, Nairobi, Kenya
| | - Serap Aksoy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Connecticut, United States of America
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, Connecticut, United States of America
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155
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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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156
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Yano K, Takenaka M, Tojo K. Genealogical Position of Japanese Populations of the Globally Distributed Mayfly Cloeon dipterum and Related Species (Ephemeroptera, Baetidae): A Molecular Phylogeographic Analysis. Zoolog Sci 2020; 36:479-489. [PMID: 31833319 DOI: 10.2108/zs190049] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/11/2019] [Indexed: 11/17/2022]
Abstract
In the present study, we add genetic data of the mayfly Cloeon dipterum collected from the Japanese Islands to the established molecular phylogenetic knowledge in the mitochondrial COI gene of Cloeon mayflies. Cloeon dipterum is a typical cosmopolitan species that includes six intraspecific haplotype groups. The present phylogenetic analysis revealed that haplotypes of the Japanese C. dipterum constitute a seventh group together with a haplotype from Korea. This East Asian group forms a sister group with previously known European and North American haplotype groups (i.e., the clade CT1 to CT3). The present phylogenetic analysis further revealed the occurrence of two described species (C. dipterum and Cloeon ryogokuensis) and possibly three species (Cloeon sp. 1 to 3) in Japan. Consideration is given to the degree of genetic differentiation, divergence time, and differentiation process among these seven genetic groups.
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Affiliation(s)
- Koki Yano
- Department of Biology, Graduate School of Science and Technology, Shinshu University, Matsumoto, Nagano 390-8621, Japan.,Department of Mountain and Environmental Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano 390-8621, Japan
| | - Masaki Takenaka
- Department of Mountain and Environmental Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano 390-8621, Japan
| | - Koji Tojo
- Department of Biology, Faculty of Science, Shinshu University, Matsumoto, Nagano 390-8621, Japan, .,Institute of Mountain Science, Interdisciplinary Cluster for Edge Research, Shinshu University, Matsumoto, Nagano 390-8621, Japan,
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157
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Brookes DR, Hereward JP, Walter GH, Furlong MJ. Origins, Divergence, and Contrasting Invasion History of the Sweet Potato Weevil Pests Cylas formicarius (Coleoptera: Brentidae) and Euscepes batatae (Coleoptera: Curculionidae) in the Asia-Pacific. JOURNAL OF ECONOMIC ENTOMOLOGY 2019; 112:2931-2939. [PMID: 31352482 DOI: 10.1093/jee/toz198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Indexed: 06/10/2023]
Abstract
Cylas formicarius F. and Euscepes batatae Waterhouse are the most damaging sweet potato insect pests globally. Both weevils are thought to have invaded the Pacific alongside the movement of sweet potato (Ipomoea batatas (L.) Lam. Convolvulaceae), with C. formicarius having originated in India and E. batatae in Central or South America. Here we compare the genetic relationships between populations of the pests, primarily in the Asia-Pacific, to understand better their contemporary population structure and their historical movement relative to that of sweet potato. Cylas formicarius has divergent mitochondrial lineages that indicate a more complex biogeographic and invasive history than is presently assumed for this insect, suggesting it was widespread across the Asia-Pacific before the arrival of sweet potato. Cylas formicarius must have originally fed on Ipomoea species other than I. batatas but the identity of these species is presently unknown. Cylas formicarius was formerly designated as three species or subspecies and the genetic data presented here suggests that these designations should be reinvestigated. Euscepes batatae has very low genetic diversity which is consistent with its historical association with sweet potato and a recent introduction to the Asia-Pacific from the Americas. The distribution of E. batatae may be narrower than that of C. formicarius in the Asia-Pacific because it has relied relatively more on human-assisted movement. Consequently, E. batatae may become more widespread in the future. Investigating the invasion history of both species will help to understand the probability and nature of future invasions.
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Affiliation(s)
- Dean R Brookes
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - James P Hereward
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Gimme H Walter
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Michael J Furlong
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
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158
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Camacho AI, Mas‐Peinado P, Iepure S, Perina G, Dorda BA, Casado A, Rey I. Novel sexual dimorphism in a new genus of Bathynellidae from Russia, with a revision of phylogenetic relationships. ZOOL SCR 2019. [DOI: 10.1111/zsc.12387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ana I. Camacho
- Dpto. Biodiversidad y Biología Evolutiva Museo Nacional de Ciencias Naturales (CSIC) Madrid Spain
| | - Paloma Mas‐Peinado
- Dpto. Biodiversidad y Biología Evolutiva Museo Nacional de Ciencias Naturales (CSIC) Madrid Spain
| | - Sanda Iepure
- Cavanilles Institute of Biodiversity and Evolutionary Biology University of Valencia Valencia Spain
- "Emil Racovita" Institute of Speleology Cluj Napoca Romania
| | - Giulia Perina
- Centre for Ecosystem Management Edith Cowan University Joondalup WA Australia
| | - Beatriz A. Dorda
- Dpto. Colecciones Colección de Tejidos y ADN Museo Nacional de Ciencias Naturales (CSIC) Madrid Spain
| | - Adrian Casado
- Dpto. Colecciones Colección de Tejidos y ADN Museo Nacional de Ciencias Naturales (CSIC) Madrid Spain
| | - Isabel Rey
- Dpto. Colecciones Colección de Tejidos y ADN Museo Nacional de Ciencias Naturales (CSIC) Madrid Spain
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159
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Riccieri A, Mancini E, Salvi D, Bologna MA. Phylogeny, biogeography and systematics of the hyper-diverse blister beetle genus Hycleus (Coleoptera: Meloidae). Mol Phylogenet Evol 2019; 144:106706. [PMID: 31830551 DOI: 10.1016/j.ympev.2019.106706] [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: 05/09/2019] [Revised: 10/01/2019] [Accepted: 12/08/2019] [Indexed: 10/25/2022]
Abstract
Hycleus is a hyper-diverse genus of blister beetles including ~500 species widely distributed in the Old World, currently divided into three "sections" and into 45 "phenetic" species groups according to morphological characters. Recently the monophyly of Hycleus was questioned pointing out its paraphyly with respect to the genera Ceroctis and Paractenodia. In this study, we built a time-calibrated phylogenetic tree based on DNA sequence data from mitochondrial and nuclear genes obtained from 125 species, to understand the phylogenetic relationships among the species of this genus, to infer the biogeographic processes behind their diversification, and to assess their taxonomy and classification. Our results identified four main lineages one of which included the species belonging to Ceroctis and Paractenodia; therefore, both taxa are now referred to Hycleus as new synonyms. The three described sections of Hycleus resulted polyphyletic and are rejected, whereas several species groups represented well supported clades. Hycleus likely originated in Africa during the Early Miocene (~20 Mya), and subsequently spread in Europe and western Asia. Later, in the Late Miocene (~6 Mya) a Saharo-Sindian group branched off from the Palaearctic lineage, whereas the Oriental Region was colonized following a dispersal event through the Arabian Peninsula from the Afrotropical Region (~5 Mya).
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Affiliation(s)
- Alessandra Riccieri
- Department of Sciences, University "Roma Tre", Viale G. Marconi 446, 00146 Roma, Italy.
| | - Emiliano Mancini
- Department of Biology and Biotechnology "C. Darwin", "Sapienza" University of Rome, Viale dell'Università 32, 00186 Roma, Italy
| | - Daniele Salvi
- Department of Health, Life & Environmental Sciences, University of L'Aquila, Via Vetoio snc, 67100 L'Aquila-Coppito, Italy; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Marco A Bologna
- Department of Sciences, University "Roma Tre", Viale G. Marconi 446, 00146 Roma, Italy
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160
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Gamboa M, Arrivillaga-HenrÍQuez J. Biochemical and molecular differentiation of Anacroneuria species (Plecoptera, Insecta) in Andean National Park, Venezuela. SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1687604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Maribet Gamboa
- Faculty of Engineering, Department of Civil and Environmental Engineering, Ehime University, Bunkyo-cho 3, Matsuyama 790-8577, Japan
| | - Jazzmin Arrivillaga-HenrÍQuez
- FACSO-Turismo THC, Área Ambiente y Territorio, Línea Salud y Calidad Ambiental, Grupo de Investigación Biodiversidad, Zoonosis y Salud Pública (GIBCIZ), Instituto de Investigación en Salud Pública y Zoonosis, Universidad Central del Ecuador, Quito, Ecuador
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161
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Mutun S, Dinç S. The Anatolian Diagonal and Paleoclimatic Changes Shaped the Phylogeography of Cynips quercus (Hymenoptera, Cynipidae). ANN ZOOL FENN 2019. [DOI: 10.5735/086.056.0107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Serap Mutun
- Department of Biology, Faculty of Science and Art, Bolu Abant İzzet Baysal University, TR-14030 Bolu, Turkey
| | - Serdar Dinç
- Department of Biology, Faculty of Science and Art, Bolu Abant İzzet Baysal University, TR-14030 Bolu, Turkey
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162
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Salces‐Castellano A, Patiño J, Alvarez N, Andújar C, Arribas P, Braojos‐Ruiz JJ, Arco‐Aguilar M, García‐Olivares V, Karger DN, López H, Manolopoulou I, Oromí P, Pérez‐Delgado AJ, Peterman WE, Rijsdijk KF, Emerson BC. Climate drives community‐wide divergence within species over a limited spatial scale: evidence from an oceanic island. Ecol Lett 2019; 23:305-315. [DOI: 10.1111/ele.13433] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/15/2019] [Accepted: 10/09/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Antonia Salces‐Castellano
- Island Ecology and Evolution Research Group Institute of Natural Products and Agrobiology (IPNA‐CSIC) C/Astrofísico Francisco Sánchez 3 La Laguna Tenerife Canary Islands 38206 Spain
- School of Doctoral and Postgraduate Studies University of La Laguna 38200 La Laguna Tenerife Canary Islands Spain
| | - Jairo Patiño
- Island Ecology and Evolution Research Group Institute of Natural Products and Agrobiology (IPNA‐CSIC) C/Astrofísico Francisco Sánchez 3 La Laguna Tenerife Canary Islands 38206 Spain
- Plant Conservation and Biogeography Group Department of Botany, Ecology and Plant Physiology University of La Laguna C/ Astrofísico Francisco Sánchez 38206La Laguna Tenerife Canary Islands Spain
| | - Nadir Alvarez
- Natural History Museum of Geneva 1 route de Malagnou 1208 Geneva Switzerland
| | - Carmelo Andújar
- Island Ecology and Evolution Research Group Institute of Natural Products and Agrobiology (IPNA‐CSIC) C/Astrofísico Francisco Sánchez 3 La Laguna Tenerife Canary Islands 38206 Spain
| | - Paula Arribas
- Island Ecology and Evolution Research Group Institute of Natural Products and Agrobiology (IPNA‐CSIC) C/Astrofísico Francisco Sánchez 3 La Laguna Tenerife Canary Islands 38206 Spain
| | - Juan José Braojos‐Ruiz
- Tenerife Insular Water Council (CIATF) C/ Leoncio Rodríguez 2 38003 Santa Cruz de Tenerife Spain
| | - Marcelino Arco‐Aguilar
- Plant Conservation and Biogeography Group Department of Botany, Ecology and Plant Physiology University of La Laguna C/ Astrofísico Francisco Sánchez 38206La Laguna Tenerife Canary Islands Spain
| | - Víctor García‐Olivares
- Island Ecology and Evolution Research Group Institute of Natural Products and Agrobiology (IPNA‐CSIC) C/Astrofísico Francisco Sánchez 3 La Laguna Tenerife Canary Islands 38206 Spain
- School of Doctoral and Postgraduate Studies University of La Laguna 38200 La Laguna Tenerife Canary Islands Spain
| | - Dirk N. Karger
- Swiss Federal Research Institute WSL Zürcherstrasse 1118903Birmensdorf Switzerland
| | - Heriberto López
- Island Ecology and Evolution Research Group Institute of Natural Products and Agrobiology (IPNA‐CSIC) C/Astrofísico Francisco Sánchez 3 La Laguna Tenerife Canary Islands 38206 Spain
| | | | - Pedro Oromí
- Department of Animal Biology, Edaphology and Geology University of Laguna C/ Astrofísico Francisco Sánchez 38206 La Laguna, Tenerife Canary Islands Spain
| | - Antonio J. Pérez‐Delgado
- Island Ecology and Evolution Research Group Institute of Natural Products and Agrobiology (IPNA‐CSIC) C/Astrofísico Francisco Sánchez 3 La Laguna Tenerife Canary Islands 38206 Spain
- School of Doctoral and Postgraduate Studies University of La Laguna 38200 La Laguna Tenerife Canary Islands Spain
| | - William E. Peterman
- School of Environmental and Natural Resources The Ohio State University Columbus OH USA
| | - Kenneth F. Rijsdijk
- Institute for Biodiversity and Ecosystem Dynamics University of Amsterdam Amsterdam Netherlands
| | - Brent C. Emerson
- Island Ecology and Evolution Research Group Institute of Natural Products and Agrobiology (IPNA‐CSIC) C/Astrofísico Francisco Sánchez 3 La Laguna Tenerife Canary Islands 38206 Spain
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163
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Lukić M, Delić T, Pavlek M, Deharveng L, Zagmajster M. Distribution pattern and radiation of the European subterranean genusVerhoeffiella(Collembola, Entomobryidae). ZOOL SCR 2019. [DOI: 10.1111/zsc.12392] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Marko Lukić
- Croatian Biospeleological Society Zagreb Croatia
- SubBioLab Department of Biology Biotechnical Faculty University of Ljubljana Ljubljana Slovenia
- Ruđer Bošković Institute Zagreb Croatia
| | - Teo Delić
- SubBioLab Department of Biology Biotechnical Faculty University of Ljubljana Ljubljana Slovenia
| | - Martina Pavlek
- Croatian Biospeleological Society Zagreb Croatia
- Ruđer Bošković Institute Zagreb Croatia
- Department of Evolutionary Biology, Ecology and Environmental Sciences & Biodiversity Research Institute Universitat de Barcelona Barcelona Spain
| | - Louis Deharveng
- Institut de Systématique, Evolution, Biodiversité ISYEB ‐ UMR 7205 ‐ CNRS MNHN, UPMC, EPHE, Museum national d'Histoire naturelle Sorbonne Universités Paris France
| | - Maja Zagmajster
- SubBioLab Department of Biology Biotechnical Faculty University of Ljubljana Ljubljana Slovenia
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164
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Sabatelli S, Liu M, Badano D, Mancini E, Trizzino M, Richard Cline A, Endrestøl A, Huang M, Audisio P. Molecular phylogeny and host‐plant use (Lamiaceae) of the
Thymogethes
pollen beetles (Coleoptera). ZOOL SCR 2019. [DOI: 10.1111/zsc.12384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Simone Sabatelli
- Department of Biology and Biotechnologies “C. Darwin” Sapienza Università degli Studi di Roma Rome Italy
| | - Meike Liu
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Entomological Museum Northwest A&F University Yangling China
- College of Agriculture Yangtze University Jingzhou China
| | | | - Emiliano Mancini
- Department of Biology and Biotechnologies “C. Darwin” Sapienza Università degli Studi di Roma Rome Italy
| | - Marco Trizzino
- Gene Expression and Regulation Program The Wistar Institute Philadelphia PA USA
| | - Andrew Richard Cline
- Plant Pest Diagnostics Center California Department of Food & Agriculture Sacramento CA USA
| | | | - Min Huang
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Entomological Museum Northwest A&F University Yangling China
| | - Paolo Audisio
- Department of Biology and Biotechnologies “C. Darwin” Sapienza Università degli Studi di Roma Rome Italy
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165
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Dool SE, Künzel S, Haase M, Picker MD, Eberhard MJB. Variable Molecular Markers for the Order Mantophasmatodea (Insecta). J Hered 2019; 109:477-483. [PMID: 29206981 DOI: 10.1093/jhered/esx109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 11/23/2017] [Indexed: 01/12/2023] Open
Abstract
The recently discovered insect order Mantophasmatodea currently comprises 19 Southern African species. These mainly occur in allopatry, have high levels of color polymorphism and communicate via species- and gender-specific vibratory signals. High levels of interspecific morphological conservatism mean that cryptic species are likely to be uncovered. These aspects of Mantophasmatodean biology make them an ideal group in which to investigate population divergence due to habitat-specific adaptation, sexual selection, and potentially sensory speciation. Lack of appropriate genetic markers has thus far rendered such studies unfeasible. To address this need, the first microsatellite loci for this order were developed. Fifty polymorphic loci were designed specifically for Karoophasma biedouwense (Austrophasmatidae), out of which 23 were labeled and tested for amplification across the order using 2-3 individuals from 10 species, representing all 4 currently known families. A Bayesian mitochondrially encoded cytochrome c oxidase I (COI) topology was reconstructed and divergence dates within the order were estimated for the first time. Amplification success and levels of polymorphism were compared with genetic divergence and time since divergence. In agreement with studies on vertebrate taxa, both amplification and variability were negatively correlated with distance (temporal and genetic). The high number of informative loci will offer sufficient resolution for both broad level population genetic analysis and individual based pedigree or parentage analyses for most species in Austrophasmatidae, with at least some loci available for the other families. This resource will facilitate research into the evolutionary biology of this understudied but fascinating group.
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Affiliation(s)
- Serena E Dool
- From the General and Systematic Zoology, Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | - Sven Künzel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Martin Haase
- Vogelwarte, Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | - Mike D Picker
- Department of Biological Sciences, University of Cape Town, Rondebosch, Cape Town, South Africa
| | - Monika J B Eberhard
- From the General and Systematic Zoology, Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
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166
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Bocek M, Kusy D, Motyka M, Bocak L. Persistence of multiple patterns and intraspecific polymorphism in multi-species Müllerian communities of net-winged beetles. Front Zool 2019; 16:38. [PMID: 31636689 PMCID: PMC6798367 DOI: 10.1186/s12983-019-0335-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 08/28/2019] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND In contrast to traditional models of purifying selection and a single aposematic signal in Müllerian complexes, some communities of unprofitable prey contain members with multiple aposematic patterns. Processes responsible for diversity in aposematic signaling are poorly understood and large multi-species communities are seldom considered. RESULTS We analyzed the phylogeny and aposematic patterns of closely related Eniclases net-winged beetles in New Guinea using mtDNA and nextRAD data. We suggest three clades of closely related and incompletely reproductively isolated lineages, detail the extent of polymorphism among Eniclases, and categorize their low-contrast aposematic patterns. The warning signal of Eniclases consists of body shape and color, with ambiguous color perception under some circumstances, i.e., when resting on the undersides of leaves. Field observations suggest that perception of the aposematic signal is affected by beetle behavior and environmental conditions. Local communities containing Eniclases consisted of 7-85 metriorrhynchine species assigned to 3-10 colour patterns. CONCLUSION As a result, we suggest that under certain light conditions the aposematic colour signal is less apparent than the body shape in net-winged beetle communities. We document variable environmental factors in our study area and highly diverse multi-species communities of other net-winged beetles. Which implies dynamically changing community structure in space and time. Variable environmental conditions and diverse community composition are suggested to be favorable for the persistence of multiple aposematic patterns, imperfect mimics, and intraspecific polymorphism. Further research should identify the relative effect of these factors on purifying selection and the alleles which are responsible for phenotypic differences.
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Affiliation(s)
- Matej Bocek
- Laboratory of Molecular Systematics, Faculty of Science, Palacky University, tr. 17. listopadu 50, 771 46 Olomouc, Czech Republic
| | - Dominik Kusy
- Laboratory of Molecular Systematics, Faculty of Science, Palacky University, tr. 17. listopadu 50, 771 46 Olomouc, Czech Republic
| | - Michal Motyka
- Laboratory of Molecular Systematics, Faculty of Science, Palacky University, tr. 17. listopadu 50, 771 46 Olomouc, Czech Republic
| | - Ladislav Bocak
- Laboratory of Molecular Systematics, Faculty of Science, Palacky University, tr. 17. listopadu 50, 771 46 Olomouc, Czech Republic
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167
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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.
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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
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168
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Techer MA, Rane RV, Grau ML, Roberts JMK, Sullivan ST, Liachko I, Childers AK, Evans JD, Mikheyev AS. Divergent evolutionary trajectories following speciation in two ectoparasitic honey bee mites. Commun Biol 2019; 2:357. [PMID: 31583288 PMCID: PMC6773775 DOI: 10.1038/s42003-019-0606-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 09/10/2019] [Indexed: 01/28/2023] Open
Abstract
Multispecies host-parasite evolution is common, but how parasites evolve after speciating remains poorly understood. Shared evolutionary history and physiology may propel species along similar evolutionary trajectories whereas pursuing different strategies can reduce competition. We test these scenarios in the economically important association between honey bees and ectoparasitic mites by sequencing the genomes of the sister mite species Varroa destructor and Varroa jacobsoni. These genomes were closely related, with 99.7% sequence identity. Among the 9,628 orthologous genes, 4.8% showed signs of positive selection in at least one species. Divergent selective trajectories were discovered in conserved chemosensory gene families (IGR, SNMP), and Halloween genes (CYP) involved in moulting and reproduction. However, there was little overlap in these gene sets and associated GO terms, indicating different selective regimes operating on each of the parasites. Based on our findings, we suggest that species-specific strategies may be needed to combat evolving parasite communities.
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Affiliation(s)
- Maeva A. Techer
- Okinawa Institute of Science and Technology, 1919-1 Tancha Onna-son, 904-0495 Okinawa, Japan
| | - Rahul V. Rane
- Commonwealth Scientific and Industrial Research Organisation, Clunies Ross St, (GPO Box 1700), Acton, ACT 2601 Australia
- Bio21 Institute, School of BioSciences, University of Melbourne, 30 Flemington Road, Parkville, VIC 3010 Australia
| | - Miguel L. Grau
- Okinawa Institute of Science and Technology, 1919-1 Tancha Onna-son, 904-0495 Okinawa, Japan
| | - John M. K. Roberts
- Commonwealth Scientific and Industrial Research Organisation, Clunies Ross St, (GPO Box 1700), Acton, ACT 2601 Australia
| | | | | | | | | | - Alexander S. Mikheyev
- Okinawa Institute of Science and Technology, 1919-1 Tancha Onna-son, 904-0495 Okinawa, Japan
- Australian National University, Canberra, ACT 2600 Australia
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169
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McCulloch GA, Waters JM. Phylogenetic divergence of island biotas: Molecular dates, extinction, and "relict" lineages. Mol Ecol 2019; 28:4354-4362. [PMID: 31544990 DOI: 10.1111/mec.15229] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/24/2019] [Accepted: 07/30/2019] [Indexed: 01/08/2023]
Abstract
Island formation is a key driver of biological evolution, and several studies have used geological ages of islands to calibrate rates of DNA change. However, many islands are home to "relict" lineages whose divergence apparently pre-dates island age. The geologically dynamic New Zealand (NZ) archipelago sits upon the ancient, largely submerged continent Zealandia, and the origin and age of its distinctive biota have long been contentious. While some researchers have interpreted NZ's biota as equivalent to that of a post-Oligocene island, a recent review of genetic studies identified a sizeable proportion of pre-Oligocene "relict" lineages, concluding that much of the biota survived an incomplete drowning event. Here, we assemble comparable genetic divergence data sets for two recently formed South Pacific archipelagos (Lord Howe; Chatham Islands) and demonstrate similarly substantial proportions of relict lineages. Similar to the NZ biota, our island reviews provide surprisingly little evidence for major genetic divergence "pulses" associated with island emergence. The dominance of Quaternary divergence estimates in all three biotas may highlight the importance of rapid biological turnover and new arrivals in response to recent climatic and/or geological disturbance and change. We provide a schematic model to help account for discrepancies between expected versus observed divergence-date distributions for island biotas, incorporating the effects of both molecular dating error and lineage extinction. We conclude that oceanic islands can represent both evolutionary "cradles" and "museums" and that the presence of apparently archaic island lineages does not preclude dispersal origins.
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170
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Goodman KR, Prost S, Bi K, Brewer MS, Gillespie RG. Host and geography together drive early adaptive radiation of Hawaiian planthoppers. Mol Ecol 2019; 28:4513-4528. [PMID: 31484218 DOI: 10.1111/mec.15231] [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: 03/14/2018] [Revised: 08/19/2019] [Accepted: 08/27/2019] [Indexed: 11/30/2022]
Abstract
The interactions between insects and their plant host have been implicated in driving diversification of both players. Early arguments highlighted the role of ecological opportunity, with the idea that insects "escape and radiate" on new hosts, with subsequent hypotheses focusing on the interplay between host shifting and host tracking, coupled with isolation and fusion, in generating diversity. Because it is rarely possible to capture the initial stages of diversification, it is particularly difficult to ascertain the relative roles of geographic isolation versus host shifts in initiating the process. The current study examines genetic diversity between populations and hosts within a single species of endemic Hawaiian planthopper, Nesosydne umbratica (Hemiptera, Delphacidae). Given that the species was known as a host generalist occupying unrelated hosts, Clermontia (Campanulaceae) and Pipturus (Urticaceae), we set out to determine the relative importance of geography and host in structuring populations in the early stages of differentiation on the youngest islands of the Hawaiian chain. Results from extensive exon capture data showed that N. umbratica is highly structured, both by geography, with discrete populations on each volcano, and by host plant, with parallel radiations on Clermontia and Pipturus leading to extensive co-occurrence. The marked genetic structure suggests that populations can readily become established on novel hosts provided opportunity; subsequent adaptation allows monopolization of the new host. The results support the role of geographic isolation in structuring populations and with host shifts occurring as discrete events that facilitate subsequent parallel geographic range expansion.
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Affiliation(s)
- Kari Roesch Goodman
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Stefan Prost
- Department of Integrative Biology, University of California, Berkeley, CA, USA.,LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg Research Institute, Frankfurt/Main, Germany
| | - Ke Bi
- Computational Genomics Resource Laboratory (CGRL), California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.,Ancestry, San Francisco, CA, USA.,Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
| | - Michael S Brewer
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Rosemary G Gillespie
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
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171
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Morgan-Richards M, Langton-Myers SS, Trewick SA. Loss and gain of sexual reproduction in the same stick insect. Mol Ecol 2019; 28:3929-3941. [PMID: 31386772 PMCID: PMC6852293 DOI: 10.1111/mec.15203] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 06/17/2019] [Accepted: 07/30/2019] [Indexed: 01/10/2023]
Abstract
The outcome of competition between different reproductive strategies within a single species can be used to infer selective advantage of the winning strategy. Where multiple populations have independently lost or gained sexual reproduction it is possible to investigate whether the advantage is contingent on local conditions. In the New Zealand stick insect Clitarchus hookeri, three populations are distinguished by recent change in reproductive strategy and we determine their likely origins. One parthenogenetic population has established in the United Kingdom and we provide evidence that sexual reproduction has been lost in this population. We identify the sexual population from which the parthenogenetic population was derived, but show that the UK females have a post‐mating barrier to fertilisation. We also demonstrate that two sexual populations have recently arisen in New Zealand within the natural range of the mtDNA lineage that otherwise characterizes parthenogenesis in this species. We infer independent origins of males at these two locations using microsatellite genotypes. In one population, a mixture of local and nonlocal alleles suggested males were the result of invasion. Males in another population were most probably the result of loss of an X chromosome that produced a male phenotype in situ. Two successful switches in reproductive strategy suggest local competitive advantage for outcrossing over parthenogenetic reproduction. Clitarchus hookeri provides remarkable evidence of repeated and rapid changes in reproductive strategy, with competitive outcomes dependent on local conditions.
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Affiliation(s)
| | | | - Steven A Trewick
- Wildlife & Ecology, Massey University, Palmerston North, New Zealand
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172
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Poveda-Martínez D, Aguirre MB, Logarzo G, Calderón L, de la Colina A, Hight S, Triapitsyn S, Diaz-Soltero H, Hasson E. Untangling the Hypogeococcus pungens species complex (Hemiptera: Pseudococcidae) for Argentina, Australia, and Puerto Rico based on host plant associations and genetic evidence. PLoS One 2019; 14:e0220366. [PMID: 31344099 PMCID: PMC6657911 DOI: 10.1371/journal.pone.0220366] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/15/2019] [Indexed: 11/18/2022] Open
Abstract
Hypogeococcus pungens, a mealybug native of southern South America, is devastating native cacti in Puerto Rico and threatening cactus diversity in the Caribbean, and potentially in Central and North America. The taxonomic status of H. pungens is controversial since it has been reported feeding not only on Cactaceae but also on other plant families throughout its distribution range. However, in Australia, where the species had been exported from Argentina to control weedy American cacti, it was never found on host plants other than Cactaceae. These conflicting pieces of evidence not only cast doubt on the species identity that invaded Puerto Rico, but also have a negative impact on the search for natural enemies to be used in biological control programs against this pest. Here we present reproductive incompatibility and phylogenetic evidences that give support to the hypothesis that H. pungens is a species complex in which divergence appears to be driven by the host plants. The nuclear EF1α and 18S and the mitochondrial COI genes were used as markers to evaluate the phylogenetic relationships among H. pungens populations collected in Argentina, Australia and Puerto Rico feeding on Cactaceae and/or Amaranthaceae. Additionally, we conducted reciprocal crosses between mealybugs from both hosts. Species delimitation analysis revealed two well-supported putative species within H. pungens, one including mealybugs feeding on Amaranthaceae (H. pungens sensu stricto), and a new undescribed species using Cactaceae as hosts. Additionally, we found asymmetric reproductive incompatibility between these putative species suggesting recent reproductive isolation. The Bayesian species delimitation also suggested that the Australian mealybug population may derive from another undescribed species. Overall, the patterns of genetic differentiation may be interpreted as the result of recent speciation events prompted by host plant shifts. Finally, the finding of a single haplotype in the Puerto Rico population suggests only one invasive event. We still need to identify the geographical origin of the pest in order to enable the use of biological control to reduce the threat to cacti diversity in the Caribbean.
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Affiliation(s)
- Daniel Poveda-Martínez
- Fundación para el Estudio de Especies Invasivas (FuEDEI), Hurlingham, Buenos Aires, Argentina
- Instituto de Ecología Genética y Evolución de Buenos Aires (IEGEBA), Departamento de Ecología Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
- Grupo de investigación en Evolución, Ecología y Conservación (EECO), Universidad del Quindío, Armenia, Colombia
- * E-mail: (DPM); (MBA)
| | - María Belén Aguirre
- Fundación para el Estudio de Especies Invasivas (FuEDEI), Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
- * E-mail: (DPM); (MBA)
| | - Guillermo Logarzo
- Fundación para el Estudio de Especies Invasivas (FuEDEI), Hurlingham, Buenos Aires, Argentina
| | - Luciano Calderón
- Fundación para el Estudio de Especies Invasivas (FuEDEI), Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Alicia de la Colina
- Instituto de Ecología Genética y Evolución de Buenos Aires (IEGEBA), Departamento de Ecología Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Stephen Hight
- U.S. Department of Agriculture-ARS, Tallahassee, Florida, United States of America
| | - Serguei Triapitsyn
- Department of Entomology, University of California, Riverside, California, United States of America
| | - Hilda Diaz-Soltero
- Caribbean Advisor to the APHIS Administrator, USDA, San Juan, Puerto Rico
| | - Esteban Hasson
- Instituto de Ecología Genética y Evolución de Buenos Aires (IEGEBA), Departamento de Ecología Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
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173
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Francischini FJB, Cordeiro EMG, de Campos JB, Alves-Pereira A, Viana JPG, Wu X, Wei W, Brown P, Joyce A, Murua G, Fogliata S, Clough SJ, Zucchi MI. Diatraea saccharalis history of colonization in the Americas. The case for human-mediated dispersal. PLoS One 2019; 14:e0220031. [PMID: 31339922 PMCID: PMC6656350 DOI: 10.1371/journal.pone.0220031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 07/08/2019] [Indexed: 11/28/2022] Open
Abstract
The sugarcane borer moth, Diatraea saccharalis, is one of the most important pests of sugarcane and maize crops in the Western Hemisphere. The pest is widespread throughout South and Central America, the Caribbean region and the southern United States. One of the most intriguing features of D. saccharalis population dynamics is the high rate of range expansion reported in recent years. To shed light on the history of colonization of D. saccharalis, we investigated the genetic structure and diversity in American populations using single nucleotide polymorphism (SNPs) markers throughout the genome and sequences of the mitochondrial gene cytochrome oxidase (COI). Our primary goal was to propose possible dispersal routes from the putative center of origin that can explain the spatial pattern of genetic diversity. Our findings showed a clear correspondence between genetic structure and the geographical distributions of this pest insect on the American continents. The clustering analyses indicated three distinct groups: one composed of Brazilian populations, a second group composed of populations from El Salvador, Mexico, Texas and Louisiana and a third group composed of the Florida population. The predicted time of divergence predates the agriculture expansion period, but the pattern of distribution of haplotype diversity suggests that human-mediated movement was most likely the factor responsible for the widespread distribution in the Americas. The study of the early history of D. saccharalis promotes a better understanding of range expansion, the history of invasion, and demographic patterns of pest populations in the Americas.
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Affiliation(s)
- Fabricio J. B. Francischini
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Erick M. G. Cordeiro
- Department of Entomology and Acarology, University of Sao Paulo, Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, São Paulo, Brazil
| | - Jaqueline B. de Campos
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | | | - João Paulo Gomes Viana
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Xing Wu
- Department of Crop Science, University of Illinois, Urbana, Illinois, United States of America
| | - Wei Wei
- Department of Crop Science, University of Illinois, Urbana, Illinois, United States of America
| | - Patrick Brown
- Department of Crop Science, University of Illinois, Urbana, Illinois, United States of America
| | - Andrea Joyce
- Department of Public Health, University of California, Merced, California, United States of America
| | - Gabriela Murua
- Instituto de Tecnología Agroindustrial del Noroeste Argentino, Estación Experimental Agroindustrial Obispo Colombres, Consejo Nacional de Investigaciones Científicas y Técnicas (ITANOA-EEAOC-CONICET), Tucumán, Argentina
| | - Sofia Fogliata
- Instituto de Tecnología Agroindustrial del Noroeste Argentino, Estación Experimental Agroindustrial Obispo Colombres, Consejo Nacional de Investigaciones Científicas y Técnicas (ITANOA-EEAOC-CONICET), Tucumán, Argentina
| | - Steven J. Clough
- Department of Crop Science, University of Illinois, Urbana, Illinois, United States of America
- US Department of Agriculture-Agricultural Research Service, Urbana, Illinois, United States of America
| | - Maria I. Zucchi
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, Brazil
- Laboratory of Conservation Genetics and Genomics, Agribusiness Technological Development of São Paulo (APTA), Piracicaba, São Paulo, Brazil
- * E-mail:
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174
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Du Z, Hasegawa H, Cooley JR, Simon C, Yoshimura J, Cai W, Sota T, Li H. Mitochondrial Genomics Reveals Shared Phylogeographic Patterns and Demographic History among Three Periodical Cicada Species Groups. Mol Biol Evol 2019; 36:1187-1200. [PMID: 30850829 PMCID: PMC6526903 DOI: 10.1093/molbev/msz051] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The mass application of whole mitogenome (MG) sequencing has great potential for resolving complex phylogeographic patterns that cannot be resolved by partial mitogenomic sequences or nuclear markers. North American periodical cicadas (Magicicada) are well known for their periodical mass emergence at 17- and 13-year intervals in the north and south, respectively. Magicicada comprises three species groups, each containing one 17-year species and one or two 13-year species. Within each life cycle, single-aged cohorts, called broods, of periodical cicadas emerge in different years, and most broods contain members of all three species groups. There are 12 and three extant broods of 17- and 13-year cicadas, respectively. The phylogeographic relationships among the populations and broods within the species groups have not been clearly resolved. We analyzed 125 whole MG sequences from all broods and seven species within three species groups to ascertain the divergence history of the geographic and allochronic populations and their life cycles. Our mitogenomic phylogeny analysis clearly revealed that each of the three species groups had largely similar phylogeographic subdivisions (east, middle, and west) and demographic histories (rapid population expansion after the last glacial period). The mitogenomic phylogeny also partly resolved the brood diversification process, which could be explained by hypothetical temporary life cycle shifts, and showed that none of the 13- and 17-year species within the species groups was monophyletic, possibly due to gene flow between them. Our findings clearly reveal phylogeographic structures in the three Magicicada species groups, demonstrating the advantage of whole MG sequence data in phylogeographic studies.
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Affiliation(s)
- Zhenyong Du
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Hiroki Hasegawa
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, Japan
| | - John R Cooley
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
| | - Jin Yoshimura
- Graduate School of Science and Technology and Department of Mathematical and Systems Engineering, Shizuoka University, Hamamatsu, Japan.,Department of Environmental and Forest Biology, State University of New York College of Environmental Science and Forestry, Syracuse, NY.,Marine Biosystems Research Center, Chiba University, Kamogawa, Chiba, Japan
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, Japan
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
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175
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Hinojosa JC, Koubínová D, Szenteczki MA, Pitteloud C, Dincă V, Alvarez N, Vila R. A mirage of cryptic species: Genomics uncover striking mitonuclear discordance in the butterfly Thymelicus sylvestris. Mol Ecol 2019; 28:3857-3868. [PMID: 31233646 DOI: 10.1111/mec.15153] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 06/07/2019] [Indexed: 10/26/2022]
Abstract
Mitochondrial DNA (mtDNA) sequencing has led to an unprecedented rise in the identification of cryptic species. However, it is widely acknowledged that nuclear DNA (nuDNA) sequence data are also necessary to properly define species boundaries. Next generation sequencing techniques provide a wealth of nuclear genomic data, which can be used to ascertain both the evolutionary history and taxonomic status of putative cryptic species. Here, we focus on the intriguing case of the butterfly Thymelicus sylvestris (Lepidoptera: Hesperiidae). We identified six deeply diverged mitochondrial lineages; three distributed all across Europe and found in sympatry, suggesting a potential case of cryptic species. We then sequenced these six lineages using double-digest restriction-site associated DNA sequencing (ddRADseq). Nuclear genomic loci contradicted mtDNA patterns and genotypes generally clustered according to geography, i.e., a pattern expected under the assumption of postglacial recolonization from different refugia. Further analyses indicated that this strong mtDNA/nuDNA discrepancy cannot be explained by incomplete lineage sorting, sex-biased asymmetries, NUMTs, natural selection, introgression or Wolbachia-mediated genetic sweeps. We suggest that this mitonuclear discordance was caused by long periods of geographic isolation followed by range expansions, homogenizing the nuclear but not the mitochondrial genome. These results highlight T. sylvestris as a potential case of multiple despeciation and/or lineage fusion events. We finally argue, since mtDNA and nuDNA do not necessarily follow the same mechanisms of evolution, their respective evolutionary history reflects complementary aspects of past demographic and biogeographic events.
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Affiliation(s)
| | - Darina Koubínová
- Unit of Research and Collection, Museum of Natural History, Geneva, Switzerland
| | - Mark A Szenteczki
- Laboratory of Functional Ecology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Camille Pitteloud
- Department of Environmental Systems Sciences, Institute of Terrestrial Ecosystems, ETHZ, Zürich, Switzerland
| | - Vlad Dincă
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Nadir Alvarez
- Unit of Research and Collection, Museum of Natural History, Geneva, Switzerland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
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176
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Ke F, You S, Huang S, Chen W, Liu T, He W, Xie D, Li Q, Lin X, Vasseur L, Gurr GM, You M. Herbivore range expansion triggers adaptation in a subsequently-associated third trophic level species and shared microbial symbionts. Sci Rep 2019; 9:10314. [PMID: 31311998 PMCID: PMC6635496 DOI: 10.1038/s41598-019-46742-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 06/14/2019] [Indexed: 01/12/2023] Open
Abstract
Invasive species may change the life history strategies, distribution, genetic configuration and trophic interactions of native species. The diamondback moth, Plutella xylostella L., is an invasive herbivore attacking cultivated and wild brassica plants worldwide. Here we present phylogeographic analyses of P. xylostella and one of its major parasitoids, Cotesia vestalis, using mitochondrial markers, revealing the genetic diversity and evolutionary history of these two species. We find evidence that C. vestalis originated in Southwest China, then adapted to P. xylostella as a new host by ecological sorting as P. xylostella expanded its geographic range into this region. Associated with the expansion of P. xylostella, Wolbachia symbionts were introduced into local populations of the parasitoid through horizontal transfer from its newly associated host. Insights into the evolutionary history and phylogeographic system of the herbivore and its parasitoid provide an important basis for better understanding the impacts of biological invasion on genetic configuration of local species.
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Affiliation(s)
- Fushi Ke
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China
| | - Shijun You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China.
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China.
| | - Sumei Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China
| | - Weijun Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China
| | - Tiansheng Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China
| | - Weiyi He
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China
| | - Dandan Xie
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China
| | - Qiang Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China
| | - Xijian Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China
| | - Liette Vasseur
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, L2S 3A1, Canada
| | - Geoff M Gurr
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
- Graham Centre, Charles Sturt University, Orange, NSW, 2800, Australia
| | - Minsheng You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China.
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China.
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177
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Singer D, Mitchell EAD, Payne RJ, Blandenier Q, Duckert C, Fernández LD, Fournier B, Hernández CE, Granath G, Rydin H, Bragazza L, Koronatova NG, Goia I, Harris LI, Kajukało K, Kosakyan A, Lamentowicz M, Kosykh NP, Vellak K, Lara E. Dispersal limitations and historical factors determine the biogeography of specialized terrestrial protists. Mol Ecol 2019; 28:3089-3100. [DOI: 10.1111/mec.15117] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 04/25/2019] [Accepted: 04/29/2019] [Indexed: 12/26/2022]
Affiliation(s)
- David Singer
- Laboratory of Soil Biodiversity, Institute of Biology University of Neuchâtel Neuchâtel Switzerland
- Department of Zoology, Institute of Biosciences University of São Paulo São Paulo Brazil
| | - Edward A. D. Mitchell
- Laboratory of Soil Biodiversity, Institute of Biology University of Neuchâtel Neuchâtel Switzerland
- Jardin Botanique de Neuchâtel Neuchâtel Switzerland
| | | | - Quentin Blandenier
- Laboratory of Soil Biodiversity, Institute of Biology University of Neuchâtel Neuchâtel Switzerland
- Real Jardín Botánico CSIC Madrid Spain
| | - Clément Duckert
- Laboratory of Soil Biodiversity, Institute of Biology University of Neuchâtel Neuchâtel Switzerland
| | - Leonardo D. Fernández
- Laboratory of Soil Biodiversity, Institute of Biology University of Neuchâtel Neuchâtel Switzerland
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS) Universidad Bernardo O'Higgins Santiago Chile
| | - Bertrand Fournier
- Community and Quantitative Ecology Laboratory, Department of Biology Concordia University Montreal QC Canada
| | - Cristián E. Hernández
- Facultad de Ciencias Naturales y Oceanográficas, Departamento de Zoología Universidad de Concepción Barrio Universitario de Concepción Chile
| | - Gustaf Granath
- Department of Ecology and Genetics Evolutionary Biology Centre Uppsala University Uppsala Sweden
| | - Håkan Rydin
- Department of Ecology and Genetics Evolutionary Biology Centre Uppsala University Uppsala Sweden
| | - Luca Bragazza
- WSL Swiss Federal Institute for Forest, Snow and Landscape Research Lausanne Switzerland
- Laboratory of Ecological Systems (ECOS), Ecole Polytechnique Féderale de Lausanne (EPFL) School of Architecture, Civil and Environmental Engineering (ENAC) Lausanne Switzerland
- Department of Life Science and Biotechnologies University of Ferrara Ferrara Italy
| | - Natalia G. Koronatova
- Laboratory of Biogeocenology, Institute of Soil Science and Agrochemistry Siberian Branch of Russian Academy of Sciences Novosibirsk Russia
| | - Irina Goia
- Department of Taxonomy and Ecology, Faculty of Biology and Geology Babeș‐Bolyai University Cluj‐Napoca Romania
| | - Lorna I. Harris
- School of Geography and Earth Sciences McMaster University Hamilton ON Canada
| | - Katarzyna Kajukało
- Laboratory of Wetland Ecology and Monitoring, Faculty of Geographical and Geological Sciences and Department of Biogeography and Paleoecology Adam Mickiewicz University Poznań Poland
| | - Anush Kosakyan
- Institute of Parasitology, Biology Center Czech Academy of Sciences České Budĕjovice Czech Republic
| | - Mariusz Lamentowicz
- Laboratory of Wetland Ecology and Monitoring, Faculty of Geographical and Geological Sciences and Department of Biogeography and Paleoecology Adam Mickiewicz University Poznań Poland
| | - Natalia P. Kosykh
- Laboratory of Biogeocenology, Institute of Soil Science and Agrochemistry Siberian Branch of Russian Academy of Sciences Novosibirsk Russia
| | - Kai Vellak
- Institute of Ecology and Earth Sciences, Natural History Museum University of Tartu Tartu Estonia
| | - Enrique Lara
- Laboratory of Soil Biodiversity, Institute of Biology University of Neuchâtel Neuchâtel Switzerland
- Real Jardín Botánico CSIC Madrid Spain
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178
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Ballinger MJ, Taylor DJ. Evolutionary persistence of insect bunyavirus infection despite host acquisition and expression of the viral nucleoprotein gene. Virus Evol 2019; 5:vez017. [PMID: 31308960 PMCID: PMC6620529 DOI: 10.1093/ve/vez017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
How insects combat RNA virus infection is a subject of intensive research owing to its importance in insect health, virus evolution, and disease transmission. In recent years, a pair of potentially linked phenomena have come to light as a result of this work-first, the pervasive production of viral DNA from exogenous nonretroviral RNA in infected individuals, and second, the widespread distribution of nonretroviral integrated RNA virus sequences (NIRVs) in the genomes of diverse eukaryotes. The evolutionary consequences of NIRVs for viruses are unclear and the field would benefit from studies of natural virus infections co-occurring with recent integrations, an exceedingly rare circumstance in the literature. Here, we provide evidence that a novel insect-infecting phasmavirus (Order Bunyavirales) has been persisting in a phantom midge host, Chaoborus americanus, for millions of years. Interestingly, the infection persists despite the host's acquisition (during the Pliocene), fixation, and expression of the viral nucleoprotein gene. We show that virus prevalence and geographic distribution are high and broad, comparable to the host-specific infections reported in other phantom midges. Short-read mapping analyses identified a lower abundance of the nucleoprotein-encoding genome segment in this virus relative to related viruses. Finally, the novel virus has facilitated the first substitution rate estimation for insect-infecting phasmaviruses. Over a period of approximately 16 million years, we find rates of (0.6 - 1.6) × 10-7 substitutions per site per year in protein coding genes, extraordinarily low for negative-sense RNA viruses, but consistent with the few estimates produced over comparable evolutionary timescales.
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Affiliation(s)
- Matthew J Ballinger
- Department of Biological Sciences, Mississippi State University, PO Box GY, Mississippi State, MS
| | - Derek J Taylor
- Department of Biological Sciences, The State University of New York at Buffalo, 109 Cooke Hall, Buffalo, NY
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179
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Cozzarolo CS, Balke M, Buerki S, Arrigo N, Pitteloud C, Gueuning M, Salamin N, Sartori M, Alvarez N. Biogeography and Ecological Diversification of a Mayfly Clade in New Guinea. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00233] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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180
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Brunetti M, Magoga G, Iannella M, Biondi M, Montagna M. Phylogeography and species distribution modelling of Cryptocephalusbarii (Coleoptera: Chrysomelidae): is this alpine endemic species close to extinction? Zookeys 2019; 856:3-25. [PMID: 31293347 PMCID: PMC6603993 DOI: 10.3897/zookeys.856.32462] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 02/18/2019] [Indexed: 11/13/2022] Open
Abstract
The alternation of glacial and interglacial cycles of the Quaternary period contributed in shaping the current species distribution. Cold-adapted organisms experienced range expansion and contraction in response to the temperature decrease and increase, respectively. In this study, a fragment of the mitochondrial marker COI was used to investigate the phylogeography of Cryptocephalusbarii, a cold-adapted alpine leaf beetle species endemic of Orobie Alps, northern Italy. The relationships among populations, their divergence time, and the most probable migration model were estimated and are discussed in light of the Pleistocene climate oscillations. Through a species distribution modelling analysis, the current habitat suitability was assessed and the distribution in a future global warming scenario predicted. The main divergence events that led to the actual population structure took place from ~750,000 to ~150,000 years ago, almost following the pattern of the climate oscillations that led to the increase of the connections between the populations during cold periods and the isolation on massifs in warm periods. The most supported migration model suggests that the species survived to past adverse climatic conditions within refugia inside and at the limit of the actual range. The species distribution modelling analysis showed that C.barii is extremely sensitive to air temperature variations, thus the increase of temperature caused by global warming will reduce the suitable areas within the species range, leading to its possible extinction in the next 50 years. Cryptocephalusbarii is a representative case of how cold adapted and limited distributed species have been and could be affected by climate change, that highlights the implementation of conservation actions.
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Affiliation(s)
- Matteo Brunetti
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Via Celoria, 2, 20133 Milan, Italy Università degli Studi di Milano Milan Italy
| | - Giulia Magoga
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Via Celoria, 2, 20133 Milan, Italy Università degli Studi di Milano Milan Italy
| | - Mattia Iannella
- Dipartimento di Medicina clinica, Sanità pubblica, Scienze della Vita e dell'Ambiente, Università degli Studi dell'Aquila, Via Vetoio, 67100 Coppito, Italy Università degli Studi dell'Aquila Coppito Italy
| | - Maurizio Biondi
- Dipartimento di Medicina clinica, Sanità pubblica, Scienze della Vita e dell'Ambiente, Università degli Studi dell'Aquila, Via Vetoio, 67100 Coppito, Italy Università degli Studi dell'Aquila Coppito Italy
| | - Matteo Montagna
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Via Celoria, 2, 20133 Milan, Italy Università degli Studi di Milano Milan Italy
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181
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Godefroid M, Meseguer AS, Sauné L, Genson G, Streito JC, Rossi JP, Zaldívar Riverón A, Mayer F, Cruaud A, Rasplus JY. Restriction-site associated DNA markers provide new insights into the evolutionary history of the bark beetle genus Dendroctonus. Mol Phylogenet Evol 2019; 139:106528. [PMID: 31176966 DOI: 10.1016/j.ympev.2019.106528] [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: 04/17/2019] [Revised: 06/02/2019] [Accepted: 06/05/2019] [Indexed: 10/26/2022]
Abstract
The bark beetle genus Dendroctonus contains some of the most economically important pests of conifers worldwide. Despite many attempts, there is no agreement today on the phylogenetic relationships within the genus, which limits our understanding of its evolutionary history. Here, using restriction-site associated DNA (RAD) markers from 70 specimens representing 17 species (85% of the known diversity) we inferred the phylogeny of the genus, its time of origin and biogeographic history, as well as the evolution of key ecological traits (host plants, larval behavior and adults' attack strategies). For all combinations of tested parameters (from 6444 to 23,570 RAD tags analyzed), the same, fully resolved topology was inferred. Our analyses suggest that the most recent common ancestor (mrca) of all extant Dendroctonus species was widely distributed across eastern Palearctic and western Nearctic during the early Miocene, from where species dispersed to other Holarctic regions. A first main inter-continental vicariance event occurred during early Miocene isolating the ancestors of D. armandi in the Palearctic, which was followed by the radiation of the main Dendroctonus lineages in North America. During the Late Miocene, the ancestor of the 'rufipennis' species group colonized north-east Palearctic regions from western North America, which was followed by a second main inter-continental vicariance event isolating Pleistocene populations in Asia (D. micans) and western North America (D. murrayanae and D. punctatus). The present study supports previous hypotheses explaining intercontinental range disjunctions across the Northern Hemisphere by the fragmentation of a continuous distribution due to climatic cooling, host range fragmentation and geological changes during the late Cenozoic. The reconstruction of ancestral ecological traits indicates that the mrca bored individual galleries and mass attacked the boles of pines. The gregarious feeding behavior of the larvae as well as the individual attack of the base of trees have apparently independently evolved twice in North America (in the 'rufipennis' and the 'valens' species groups), which suggests a higher adaptive potential than previously thought and may be of interest for plant protection and biodiversity conservation in a rapidly changing world.
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Affiliation(s)
- Martin Godefroid
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France; Consejo Superior de Investigaciones Cientificas - Instituto de Ciencias Agrarias (ICA - CSIC), Madrid, Spain.
| | - Andrea S Meseguer
- CNRS, UMR 5554 Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier
- CNRS
- IRD
- EPHE), Montpellier, France
| | - Laure Sauné
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Guenaëlle Genson
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Jean-Claude Streito
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Jean-Pierre Rossi
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Alejandro Zaldívar Riverón
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de Mexico, Mexico, D.F., Mexico
| | - François Mayer
- Biological Control and Spatial Ecology Laboratory (LUBIES), University of Brussels, Belgium
| | - Astrid Cruaud
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Jean-Yves Rasplus
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
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182
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Kundrata R, Bocak L. Molecular phylogeny reveals the gradual evolutionary transition to soft-bodiedness in click-beetles and identifies sub-Saharan Africa as a cradle of diversity for Drilini (Coleoptera: Elateridae). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz033] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Abstract
Drilini are soft-bodied predatory click-beetles (Elateridae: Agrypninae) with incompletely metamorphosed females. Due to divergent morphology, their classification has been contentious. We present the first densely sampled molecular phylogeny of Drilini based on nuclear and mitochondrial markers. Altogether, 44 species, representing all genera, were analysed using maximum likelihood and the Bayesian approach. Molecular analyses recovered five major clades that were also well supported by morphology. Afrotropical lineages mark deep splits. Most Palearctic species belong to a terminal clade. A few species of the predominantly Afrotropical Selasia are distributed from Arabia up to the Himalayas and Thailand. The origin of Drilini is dated to the Late Eocene (~35.5 Mya) and rapid radiation is identified from the Eocene/Oligocene to the Middle Miocene. We describe the gradual transformation of male morphological traits, e.g. the level of sclerotization, structure of mouthparts, loss of the thoracic interlocking mechanism, shortened elytra and expanded larviform abdomen. Five new genera, Austroselasia, Habeshaselasia, Illubaboria, Malacodrilus and Mashaselasia are proposed. Latoselasia, previously a subgenus of Wittmerselasia, is elevated to the genus rank. Five new species, Habeshaselasia nekemtensis, H. illubaborensis, Illubaboria bicolor, Malacodrilus hajeki and Mashaselasia aethiopica are described.
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Affiliation(s)
| | - Ladislav Bocak
- Department of Zoology, Faculty of Science, Palacky University, Olomouc, Czech Republic
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183
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Ding YH, Yu DY, Guo WB, Li JN, Zhang F. Molecular phylogeny of Entomobrya (Collembola: Entomobryidae) from China: Color pattern groups and multiple origins. INSECT SCIENCE 2019; 26:587-597. [PMID: 29135078 DOI: 10.1111/1744-7917.12559] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/30/2017] [Accepted: 10/22/2017] [Indexed: 06/07/2023]
Abstract
Highly diversified colorations among springtails (Collembola) have been widely used for species diagnosis, but their phylogenetic significance is poorly known. We addressed this issue in the largest Entomobryinae genus Entomobrya, which possesses variable color patterns among species. The relationships within the genus and to other genera have also rarely been studied. Based on material mainly from China, we have conducted a multilocus phylogeny and topology tests with likelihood and Bayesian algorithms, and accordingly demonstrated the non-monophyly of Chinese Entomobrya. The division of five clades, including Entomobrya and several related genera, coincided well with five types of colorations, respectively. Further analyses of divergence time and historical biogeography revealed that Chinese Entomobrya originated mainly from Palearctic (northern and western) China in the Paleocene and Eocene. This study highlights the great phylogenetic values as well as taxonomic uses of coloration in Chinese Entomobrya. Multiple phylogenetic and biogeographic origins of Entomobrya imply its complicated relationships with both scaled and unscaled genera of Entomobryinae.
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Affiliation(s)
- Yin-Huan Ding
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Dao-Yuan Yu
- Department of Ecology, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Wei-Bo Guo
- Nanjing Institute of Environmental Sciences under Ministry of Environmental Protection, Nanjing, China
| | - Jian-Nan Li
- Nanjing Institute of Environmental Sciences under Ministry of Environmental Protection, Nanjing, China
| | - Feng Zhang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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184
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Fujisawa T, Sasabe M, Nagata N, Takami Y, Sota T. Genetic basis of species-specific genitalia reveals role in species diversification. SCIENCE ADVANCES 2019; 5:eaav9939. [PMID: 31249868 PMCID: PMC6594765 DOI: 10.1126/sciadv.aav9939] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 05/22/2019] [Indexed: 06/09/2023]
Abstract
The diversity of genital morphology among closely related animals with internal fertilization is well known, but the genetic backgrounds are unclear. Here, we show that, in Carabus (Ohomopterus) beetles showing correlated evolution of male and female genital parts, only a few major quantitative trait loci (QTLs) determine differences in genital dimensions between sister species, and sequence divergence is pronounced in the genomic regions containing genital QTLs. The major QTLs for male and female genital dimensions reside in different locations within the same linkage group, implying that coevolution between the sexes is only loosely constrained and can respond to sexually antagonistic selection. The same genomic regions containing the major QTLs show elevated divergence between three pairs of parapatric species with marked differences in genital parts. Our study demonstrates that species diversification can follow coevolution of genitalia between the sexes, even without tight linkage of loci affecting male and female genital dimensions.
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Affiliation(s)
- Tomochika Fujisawa
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Masataka Sasabe
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Nobuaki Nagata
- Division of Collections Conservation, National Museum of Nature and Science, Tsukuba 305-0005, Japan
| | - Yasuoki Takami
- Graduate School of Human Development and Environment, Kobe University, Kobe 657-8501, Japan
| | - Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
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185
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Phylogeographic structures of the host insects of Ophiocordyceps sinensis. ZOOLOGY 2019; 134:27-37. [PMID: 31146905 DOI: 10.1016/j.zool.2019.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 03/20/2019] [Accepted: 03/25/2019] [Indexed: 11/22/2022]
Abstract
A fungus-insect complex, known as DongChong XiaCao, is formed from the infection of the hepialid larvae by the fungus Ophiocordyceps sinensis, which is endemic to the Qinghai-Tibetan Plateau (QTP). Due to previously limited sample collection size, the data about the diversity and structure of the host insect was insufficient and lacked details. The purpose of this study was aimed to discuss the diversity and phylogeography of the host insects of O. sinensis with a large-scale sampling. The mitochondrial cytochrome oxidase I gene (cox1) was sequenced and analyzed among 710 samples representing 88 geographic locations. 205 haplotypes of cox1 were identified from all the 710 samples and 4 phylogenetic clades with 12 subclades were identified. Instead of the single latitude-based divergence suggested previously, three distribution patterns were deduced to correspond to the phylogeographic structures, including but not limited to the co-existence of a wide and specific local phylogeographic distribution structures. Two separate genetic diversity and differentiation centers, namely the northwestern Yunnan and the southeastern Tibet were identified. Dating analyses from three calibrations supported that the divergence of the 4 clades occurred in the Oligocene-Miocene period (30.54-13.66 million years ago) (Ma), which were connected with the second and third geological movements of the QTP (17-25, 8-13 Ma). Our results provide a more detailed understanding of the divergence and distribution patterns of the host insects of O. sinensis.
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186
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Lee TRC, Anderson SJ, Tran-Nguyen LTT, Sallam N, Le Ru BP, Conlong D, Powell K, Ward A, Mitchell A. Towards a global DNA barcode reference library for quarantine identifications of lepidopteran stemborers, with an emphasis on sugarcane pests. Sci Rep 2019; 9:7039. [PMID: 31065024 PMCID: PMC6504866 DOI: 10.1038/s41598-019-42995-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/05/2019] [Indexed: 11/09/2022] Open
Abstract
Lepidopteran stemborers are among the most damaging agricultural pests worldwide, able to reduce crop yields by up to 40%. Sugarcane is the world’s most prolific crop, and several stemborer species from the families Noctuidae, Tortricidae, Crambidae and Pyralidae attack sugarcane. Australia is currently free of the most damaging stemborers, but biosecurity efforts are hampered by the difficulty in morphologically distinguishing stemborer species. Here we assess the utility of DNA barcoding in identifying stemborer pest species. We review the current state of the COI barcode sequence library for sugarcane stemborers, assembling a dataset of 1297 sequences from 64 species. Sequences were from specimens collected and identified in this study, downloaded from BOLD or requested from other authors. We performed species delimitation analyses to assess species diversity and the effectiveness of barcoding in this group. Seven species exhibited <0.03 K2P interspecific diversity, indicating that diagnostic barcoding will work well in most of the studied taxa. We identified 24 instances of identification errors in the online database, which has hampered unambiguous stemborer identification using barcodes. Instances of very high within-species diversity indicate that nuclear markers (e.g. 18S, 28S) and additional morphological data (genitalia dissection of all lineages) are needed to confirm species boundaries.
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Affiliation(s)
- Timothy R C Lee
- Department of Entomology, Australian Museum Research Institute, 1 William St, Darlinghurst, NSW, 2010, Australia.
| | - Stacey J Anderson
- Biosecurity Operations, NAQS, Department of Agriculture and Water Resources, 1 Pederson Road, Eaton, NT, 0812, Australia
| | - Lucy T T Tran-Nguyen
- Northern Territory Department of Primary Industry and Resources, GPO Box 3000, Darwin, NT, 0801, Australia
| | - Nader Sallam
- Department of Agriculture and Water Resources, 114 Catalina Crescent, Airport Business Park, Cairns Airport, Cairns, QLD, 4870, Australia
| | - Bruno P Le Ru
- African Insect Science for Food and Health (ICIPE), PO Box 30772-00100, Nairobi, Kenya.,IRD/CNRS, UMR IRD 247 EGCE, Laboratoire Evolution Génomes Comportement et Ecologie, Avenue de la terrasse, BP1, 91198, Gif-sur-Yvette, France and Université Paris-Sud 11, 91405, Orsay, France
| | - Desmond Conlong
- Department of Conservation Ecology and Entomology, Faculty of AgriSciences, University of Stellenbosch, Private Bag X1, Matieland, Western Cape, 7602, South Africa.,South African Sugarcane Research Institute, 170 Flanders Drive, Mount Edgecombe, KwaZulu-Natal, 4300, South Africa
| | - Kevin Powell
- Sugar Research Australia, 71378 Bruce Highway, Gordonvale, QLD, 4865, Australia
| | - Andrew Ward
- Sugar Research Australia, 50 Meiers Road, Indooroopilly, QLD, 4068, Australia
| | - Andrew Mitchell
- Department of Entomology, Australian Museum Research Institute, 1 William St, Darlinghurst, NSW, 2010, Australia
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187
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Mutun S, Dinç S, Çimen E. Population genetic structure and phylogeography of the oak gall wasp Andricus chodjaii (Hymenoptera: Cynipidae) in Turkey as inferred from mitochondrial and nuclear DNA sequences. ZOOLOGY IN THE MIDDLE EAST 2019. [DOI: 10.1080/09397140.2019.1609175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Serap Mutun
- Department of Biology, Faculty of Science and Arts, Bolu Abant İzzet Baysal University, Bolu, Turkey
| | - Serdar Dinç
- Department of Biology, Faculty of Science and Arts, Bolu Abant İzzet Baysal University, Bolu, Turkey
| | - Erhan Çimen
- Department of Biology, Faculty of Science and Arts, Bolu Abant İzzet Baysal University, Bolu, Turkey
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188
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Cox K, McKeown N, Antonini G, Harvey D, Solano E, Van Breusegem A, Thomaes A. Phylogeographic structure and ecological niche modelling reveal signals of isolation and postglacial colonisation in the European stag beetle. PLoS One 2019; 14:e0215860. [PMID: 31022224 PMCID: PMC6483211 DOI: 10.1371/journal.pone.0215860] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 04/09/2019] [Indexed: 12/13/2022] Open
Abstract
Lucanus cervus (L.), the stag beetle, is a saproxylic beetle species distributed widely across Europe. Throughout its distribution the species has exhibited pronounced declines and is widely considered threatened. Conservation efforts may be hindered by the lack of population genetic data and understanding of the spatial scale of population connectivity. To address this knowledge gap this research details the first broad scale phylogeographic study of L. cervus based on mitochondrial DNA (mtDNA) sequencing and microsatellite analysis of samples collected from 121 localities across Europe. Genetic data were complemented by palaeo-distribution models of spatial occupancy during the Last Glacial Maximum to strengthen inferences of refugial areas. A salient feature of the mtDNA was the identification of two lineages. Lineage I was widespread across Europe while lineage II was confined to Greece. Microsatellites supported the differentiation of the Greek samples and alongside palaeo-distribution models indicated this area was a glacial refuge. The genetic endemism of the Greek samples, and demographic results compatible with no signatures of spatial expansion likely reflects restricted dispersal into and out of the area. Lineage I exhibited a shallow star like phylogeny compatible with rapid population expansion across Europe. Demographic analysis indicated such expansions occurred after the Last Glacial Maximum. Nuclear diversity and hindcast species distribution models indicated a central Italian refuge for lineage I. Palaeo-distribution modelling results also suggested a western refuge in northern Iberia and south-west France. In conclusion the results provide evidence of glacial divergence in stag beetle while also suggesting high, at least on evolutionary timescales, gene flow across most of Europe. The data also provide a neutral genetic framework against which patterns of phenotypic variation may be assessed.
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Affiliation(s)
- Karen Cox
- Research Institute for Nature and Forest (INBO), Geraardsbergen, Belgium
| | - Niall McKeown
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth, United Kingdom
| | - Gloria Antonini
- Department of Biology and Biotechnology "Charles Darwin", Sapienza - University of Rome, Rome, Italy
| | - Deborah Harvey
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey, United Kingdom
| | - Emanuela Solano
- Department of Biology and Biotechnology "Charles Darwin", Sapienza - University of Rome, Rome, Italy
| | - An Van Breusegem
- Research Institute for Nature and Forest (INBO), Geraardsbergen, Belgium
| | - Arno Thomaes
- Research Institute for Nature and Forest (INBO), Brussels, Belgium
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189
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Copilaş-Ciocianu D, Sidorov D, Gontcharov A. Adrift across tectonic plates: molecular phylogenetics supports the ancient Laurasian origin of old limnic crangonyctid amphipods. ORG DIVERS EVOL 2019. [DOI: 10.1007/s13127-019-00401-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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190
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Jiruskova A, Motyka M, Bocek M, Bocak L. The Malacca Strait separates distinct faunas of poorly-flying Cautires net-winged beetles. PeerJ 2019; 7:e6511. [PMID: 30863675 PMCID: PMC6407506 DOI: 10.7717/peerj.6511] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 01/22/2019] [Indexed: 02/04/2023] Open
Abstract
We investigated the spatial and temporal patterns of Cautires diversification on the Malay Peninsula and Sumatra to understand if the narrow and frequently dry Malacca Strait separates different faunas. Moreover, we analyzed the origin of Cautires in Malayan and Sumatran mountains. We sampled 18 localities and present the mtDNA-based phylogeny of 76 species represented by 388 individuals. The phylogenetic tree was dated using mtDNA evolution rates and the ancestral ranges were estimated using the maximum likelihood approach. The phylogeny identified multiple lineages on the Malay Peninsula since the Upper Eocene (35 million years ago, mya) and a delayed evolution of diversity in Sumatra since the Upper Oligocene (26 mya). A limited number of colonization events across the Malacca Strait was identified up to the Pliocene and more intensive faunal exchange since the Pleistocene. The early colonization events were commonly followed by in situ diversification. As a result, the Malacca Strait now separates two faunas with a high species-level turnover. The montane fauna diversified in a limited space and seldom took part in colonization events across the Strait. Besides isolation by open sea or a savannah corridor, mimetic patterns could decrease the colonization capacity of Cautires. The Malay fauna is phylogenetically more diverse and has a higher value if conservation priorities should be defined.
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Affiliation(s)
- Alice Jiruskova
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Michal Motyka
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Matej Bocek
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Ladislav Bocak
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, Olomouc, Czech Republic
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191
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Loeza-Quintana T, Carr CM, Khan T, Bhatt YA, Lyon SP, Hebert PD, Adamowicz SJ. Recalibrating the molecular clock for Arctic marine invertebrates based on DNA barcodes. Genome 2019; 62:200-216. [DOI: 10.1139/gen-2018-0107] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Divergence times for species assemblages of Arctic marine invertebrates have often been estimated using a standard rate (1.4%/MY) of molecular evolution calibrated using a single sister pair of tropical crustaceans. Because rates of molecular evolution vary among taxa and environments, it is essential to obtain clock calibrations from northern lineages. The recurrent opening and closure of the Bering Strait provide an exceptional opportunity for clock calibration. Here, we apply the iterative calibration approach to investigate patterns of molecular divergence among lineages of northern marine molluscs and arthropods using publicly available sequences of the cytochrome c oxidase subunit I (COI) gene and compare these results with previous estimates of trans-Bering divergences for echinoderms and polychaetes. The wide range of Kimura two-parameter (K2P) divergences among 73 trans-Bering sister pairs (0.12%–16.89%) supports multiple pulses of migration through the Strait. Overall, the results indicate a rate of K2P divergence of 3.2%/MY in molluscs, 5%–5.2%/MY in arthropods, and 3.5%–4.7%/MY in polychaetes. While these rates are considerably higher than the often-adopted 1.4%/MY rate, they are similar to calibrations (3%–5%/MY) in several other studies of marine invertebrates. This upward revision in rates means there is a need both to reevaluate the evolutionary history of marine lineages and to reexamine the impact of prior climatic changes upon the diversification of marine life.
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Affiliation(s)
- Tzitziki Loeza-Quintana
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Christina M. Carr
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- University of Northern Iowa, 187 McCollum Science Hall, Cedar Falls, IA 50614, USA
| | - Tooba Khan
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Yash A. Bhatt
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Faculty of Science, University of Western Ontario, 1151 Richmond St, London, ON N6A 3K7, Canada
| | - Samantha P. Lyon
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Paul D.N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Sarah J. Adamowicz
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
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192
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Esquer-Garrigos Y, Streiff R, Party V, Nidelet S, Navascués M, Greenfield MD. Pleistocene origins of chorusing diversity in Mediterranean bush-cricket populations ( Ephippiger diurnus). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/bly195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Yareli Esquer-Garrigos
- CBGP, INRA, CIRAD, IRD, Université de Montpellier, Montpellier, France
- DGIMI, INRA, Université de Montpellier, Montpellier, France
- Université de Tours, Tours, France
| | - Réjane Streiff
- CBGP, INRA, CIRAD, IRD, Université de Montpellier, Montpellier, France
- DGIMI, INRA, Université de Montpellier, Montpellier, France
| | | | - Sabine Nidelet
- CBGP, INRA, CIRAD, IRD, Université de Montpellier, Montpellier, France
| | | | - Michael D Greenfield
- Université de Tours, Tours, France
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
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193
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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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194
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Bocek M, Bocak L. The origins and dispersal history of the trichaline net-winged beetles in Southeast Asia, Wallacea, New Guinea and Australia. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zly090] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Matej Bocek
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic
| | - Ladislav Bocak
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic
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195
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Gamboa M, Muranyi D, Kanmori S, Watanabe K. Molecular phylogeny and diversification timing of the Nemouridae family (Insecta, Plecoptera) in the Japanese Archipelago. PLoS One 2019; 14:e0210269. [PMID: 30633758 PMCID: PMC6329508 DOI: 10.1371/journal.pone.0210269] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 12/19/2018] [Indexed: 11/30/2022] Open
Abstract
The generation of the high species diversity of insects in Japan was profoundly influenced by the formation of the Japanese Archipelago. We explored the species diversification and biogeographical history of the Nemouridae Billberg, 1820 family in the Japanese Archipelago using mitochondrial DNA and nuclear DNA markers. We collected 49 species among four genera: Indonemoura Baumann, 1975; Protonemura Kempny, 1898; Amphinemura, Ris 1902 and Nemoura Latreille, 1796 in Japan, China, South Korea and North America. We estimated their divergence times-based on three molecular clock node calibrations-using Bayesian phylogeography approaches. Our results suggested that Japanese Archipelago formation events resulted in diversification events in the middle of the Cretaceous (<120 Ma), speciation in the Paleogene (<50 Ma) and intra-species diversification segregated into eastern and western Japan of the Fossa Magna region at late Neogene (20 Ma). The Indonemoura samples were genetically separated into two clades-that of Mainland China and that of Japan. The Japanese clade clustered with the Nemouridae species from North America, suggesting the possibility of a colonisation event prior to the formation of the Japanese Archipelago. We believe that our results enhanced the understanding both of the origin of the species and of local species distribution in the Japanese Archipelago.
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Affiliation(s)
- Maribet Gamboa
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, Japan
| | - David Muranyi
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, Japan
- Deparment of Zoology, Plant Protection Institute Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Shota Kanmori
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, Japan
| | - Kozo Watanabe
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, Japan
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196
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Liu Y, Dietrich CH, Wei C. Genetic divergence, population differentiation and phylogeography of the cicada Subpsaltria yangi based on molecular and acoustic data: an example of the early stage of speciation? BMC Evol Biol 2019; 19:5. [PMID: 30621591 PMCID: PMC6323834 DOI: 10.1186/s12862-018-1317-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 12/04/2018] [Indexed: 11/17/2022] Open
Abstract
Background Geographical isolation combined with historical climatic fluctuations have been identified as two major factors that contribute to the formation of new species. On the other hand, biotic factors such as competition and predation are also able to drive the evolution and diversification of organisms. To determine whether geographical barriers contributed to population divergence or speciation in the rare endemic cicada Subpsaltria yangi the population differentiation, genetic structure and phylogeography of the species were investigated in the Loess Plateau and adjacent areas of northwestern China by analysing mitochondrial and nuclear DNA and comparing the calling song structure of 161 male individuals. Results The results reveal a low level of genetic differentiation and relatively simple phylogeographic structure for this species, but two independent clades corresponding to geographically isolated populations were recognised. Genetic and geographical distances were significantly correlated among lineages. Results of divergence-time estimation are consistent with a scenario of isolation due to glacial refugia and interglacial climate oscillation in northwestern China. Significant genetic divergence was found between the population occurring in the Helan Mountains and other populations, and recent population expansion has occurred in the Helan Mountains and/or adjacent areas. This population is also significantly different in calling song structure from other populations. Conclusions Geographical barriers (i.e., the deserts and semi-deserts surrounding the Helan Mountains), possibly coupled with related ecological differences, may have driven population divergence and allopatric speciation. This provides a possible example of incipient speciation in Cicadidae, improves understanding of population differentiation, acoustic signal diversification and phylogeographic relationships of this rare cicada species of conservation concern, and informs future studies on population differentiation, speciation and phylogeography of other insects with a high degree of endemism in the Helan Mountains and adjacent areas. Electronic supplementary material The online version of this article (10.1186/s12862-018-1317-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yunxiang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, and Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Christopher H Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, 61820, USA
| | - Cong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, and Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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197
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Rizvanovic M, Kennedy JD, Nogués-Bravo D, Marske KA. Persistence of genetic diversity and phylogeographic structure of three New Zealand forest beetles under climate change. DIVERS DISTRIB 2019. [DOI: 10.1111/ddi.12834] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Mirnesa Rizvanovic
- Center for Macroecology, Evolution and Climate; Natural History Museum of Denmark; University of Copenhagen; Copenhagen Ø Denmark
| | - Jonathan D. Kennedy
- Center for Macroecology, Evolution and Climate; Natural History Museum of Denmark; University of Copenhagen; Copenhagen Ø Denmark
| | - David Nogués-Bravo
- Center for Macroecology, Evolution and Climate; Natural History Museum of Denmark; University of Copenhagen; Copenhagen Ø Denmark
| | - Katharine A. Marske
- Center for Macroecology, Evolution and Climate; Natural History Museum of Denmark; University of Copenhagen; Copenhagen Ø Denmark
- Department of Biology; University of Oklahoma; Norman Oklahoma USA
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198
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López-Estrada EK, Sanmartín I, García-París M, Zaldívar-Riverón A. High extinction rates and non-adaptive radiation explains patterns of low diversity and extreme morphological disparity in North American blister beetles (Coleoptera, Meloidae). Mol Phylogenet Evol 2019; 130:156-168. [DOI: 10.1016/j.ympev.2018.09.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 07/24/2018] [Accepted: 09/22/2018] [Indexed: 10/28/2022]
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Elias-Costa AJ, Confalonieri VA, Lanteri AA, Rodriguero MS. Game of clones: Is Wolbachia inducing speciation in a weevil with a mixed reproductive mode? Mol Phylogenet Evol 2018; 133:42-53. [PMID: 30583042 DOI: 10.1016/j.ympev.2018.12.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 10/08/2018] [Accepted: 12/20/2018] [Indexed: 12/20/2022]
Abstract
Parthenogenesis is widely distributed in Metazoa but it is especially frequent in weevils (Coleoptera, Curculionidae) with one fifth of all known cases. Previous studies have shown that in the tribe Naupactini parthenogenetic reproduction most likely originated with an infection of the endoparasitic bacterium Wolbachia pipientis. In particular, Pantomorus postfasciatus possess a mixed reproductive mode: some populations have males while in others they are absent, and females produce clones by thelytoky. To better understand this scenario, we studied the population structure and infection status in 64 individuals of P. postfasciatus from Argentina and Brazil. We sequenced two mitochondrial (COI and COII) and one nuclear (ITS-1) fragments and obtained two very divergent haplogroups, one corresponding to the sexual populations uninfected with Wolbachia, and another conforming a monophyletic parthenogenetic (or presumptively parthenogenetic) and infected clade. Each of these haplogroups was identified as an independently evolutionary unit by all species delimitation analyses accomplished: multilocus *BEAST and BP&P, and single locus GMYC and K/θ rule. Additionally, present evidence suggests that Wolbachia infection occurred at least twice in all-female populations of P. postfasciatus with two different bacterial strains. Speciation mediated by Wolbachia is a recently described phenomenon and the case of P. postfasciatus is the first known case in a diplo-diploid insect. A model that describes how thelytoky-inducing phenotypes of Wolbachia could generate new lineages is discussed.
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Affiliation(s)
- A J Elias-Costa
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IEGEBA (CONICET-UBA), Intendente Güiraldes y Av. Costanera Norte s/n, 4to. Piso, Pabellón II, Ciudad Universitaria, CI1428 EHA Ciudad Autónoma de Buenos Aires, Argentina.
| | - V A Confalonieri
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IEGEBA (CONICET-UBA), Intendente Güiraldes y Av. Costanera Norte s/n, 4to. Piso, Pabellón II, Ciudad Universitaria, CI1428 EHA Ciudad Autónoma de Buenos Aires, Argentina
| | - A A Lanteri
- División Entomología, Museo de La Plata, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del Bosque s/n, 1900 La Plata, Argentina
| | - M S Rodriguero
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IEGEBA (CONICET-UBA), Intendente Güiraldes y Av. Costanera Norte s/n, 4to. Piso, Pabellón II, Ciudad Universitaria, CI1428 EHA Ciudad Autónoma de Buenos Aires, Argentina
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200
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Ward CM, Baxter SW. Assessing Genomic Admixture between Cryptic Plutella Moth Species following Secondary Contact. Genome Biol Evol 2018; 10:2973-2985. [PMID: 30321345 PMCID: PMC6250210 DOI: 10.1093/gbe/evy224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2018] [Indexed: 12/30/2022] Open
Abstract
Cryptic species are genetically distinct taxa without obvious variation in morphology and are occasionally discovered using molecular or sequence data sets of populations previously thought to be a single species. The world-wide Brassica pest, Plutella xylostella (diamondback moth), has been a problematic insect in Australia since 1882, yet a morphologically cryptic species with apparent endemism (P. australiana) was only recognized in 2013. Plutella xylostella and P. australiana are able to hybridize under laboratory conditions, and it was unknown whether introgression of adaptive traits could occur in the field to improve fitness and potentially increase pressure on agriculture. Phylogenetic reconstruction of 29 nuclear genomes confirmed P. xylostella and P. australiana are divergent, and molecular dating with 13 mitochondrial genes estimated a common Plutella ancestor 1.96 ± 0.175 Ma. Sympatric Australian populations and allopatric Hawaiian P. xylostella populations were used to test whether neutral or adaptive introgression had occurred between the two Australian species. We used three approaches to test for genomic admixture in empirical and simulated data sets including 1) the f3 statistic at the level of the population, 2) pairwise comparisons of Nei's absolute genetic divergence (dXY) between populations, and 3) changes in phylogenetic branch lengths between individuals across 50-kb genomic windows. These complementary approaches all supported reproductive isolation of the Plutella species in Australia, despite their ability to hybridize. Finally, we highlight the most divergent genomic regions between the two cryptic Plutella species and find they contain genes involved with processes including digestion, detoxification, and DNA binding.
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Affiliation(s)
- Christopher M Ward
- Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, Australia
| | - Simon W Baxter
- Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, Australia
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