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Huang Z, Chiba H, Hu Y, Deng X, Fei W, Sáfián S, Wu L, Wang M, Fan X. Molecular phylogeny of Hesperiidae (Lepidoptera) with an emphasis on Asian and African genera. Mol Phylogenet Evol 2024; 198:108119. [PMID: 38849065 DOI: 10.1016/j.ympev.2024.108119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 05/20/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024]
Abstract
Despite considerable research efforts in recent years, the deeper phylogenetic relationships among skipper butterflies (Hesperiidae) remain unresolved. This is primarily because of limited sampling, especially within Asian and African lineages. In this study, we consolidated previous data and extensively sampled Asian and African taxa to elucidate the phylogenetic relationships within Hesperiidae. The molecular dataset comprised sequences from two mitochondrial and two nuclear gene regions from 563 species that represented 353 genera. Our analyses revealed seven subfamilies within Hesperiidae: Coeliadinae, Euschemoninae, Eudaminae, Pyrginae, Heteropterinae, Trapezitinae, and Hesperiinae. The systematics of most tribes and genera aligned with those of prior studies. However, notable differences were observed in several tribes and genera. Overall, the position of taxa assigned to incertae sedis in Hesperiinae is largely clarified in this study. Our results strongly support the monophyly of the tribe Tagiadini (Pyrginae), and the systematics of some genera are clarified with comprehensive discussion. We recognize 15 tribes within the subfamily Hesperiinae. Of these, nine tribes are discussed in detail: Aeromachini, Astictopterini, Erionotini, Unkanini (new status), Ancistroidini, Ismini (confirmed status), Plastingini (new status), Gretnini (confirmed status), and Eetionini (confirmed status). We propose four subtribes within Astictopterini: Hypoleucina subtrib.n., Aclerosina, Cupithina, and Astictopterina. Furthermore, we describe a new genus (Hyarotoidesgen.n.) and reinstate two genera (Zeareinst.stat. and Separeinst.stat.) as valid. Additionally, we propose several new combinations: Zea mythecacomb.n.,Sepa bononiacomb.n. & reinst.stat., and Sepa umbrosacomb.n. This study, with extensive sampling of Asian and African taxa, greatly enhances the understanding of the knowledge of the skipper tree of life.
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Affiliation(s)
- Zhenfu Huang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China; Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Hideyuki Chiba
- B. P. Bishop Museum, 1525 Bernice Street, Honolulu, HI 96817-0916, USA
| | - Yanqing Hu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Xiaohua Deng
- Zunyi Agricultural Technology Extension Station, Zunyi, Guizhou 563000, China
| | - Wen Fei
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Szabolcs Sáfián
- Department of Zoology, Hungarian Natural History Museum, H-1088 Budapest, Baross utca 13, Hungary
| | - Liwei Wu
- Department of Life Science, Tunghai University, Taichung, Taiwan
| | - Min Wang
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China.
| | - Xiaoling Fan
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China.
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Ali M, Dey R, Das M, Kumar V, Chandra K, Uniyal VP, Gupta SK. Unique among high passes: Phylogenetic inferences from DNA barcoding of the butterfly fauna of Ladakh Trans-Himalaya, India. RESEARCH SQUARE 2024:rs.3.rs-4392854. [PMID: 38826425 PMCID: PMC11142357 DOI: 10.21203/rs.3.rs-4392854/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The butterfly assemblage of Ladakh Trans-Himalaya demands a thorough analysis of their population genetic structure owing to their typical biogeographic affinity and their adaptability to extreme cold-desert climates. No such effort has been taken till date, and in this backdrop, we created a barcode reference library of 60 specimens representing 23 species. Barcodes were generated from freshly collected leg samples using the Sanger sequencing method, followed by phylogenetic clade analyses and divergence calculation. Our data represents 22% of Ladakh's Rhopaloceran fauna with the novel barcode submission for six species, including one Schedule II species, Paralasa mani . Contrary to the 3% threshold rule, the interspecific divergence between two species pairs of typical mountain genus Hyponephele and Karanasa was found to be 2.3% and 2.2%, respectively. The addition of conspecific global barcodes revealed that most species showed little increase in divergence value, while a two-fold increase was noted in a few species. Bayesian clade clustering outcomes largely aligned with current morphological classifications, forming monophyletic clades of conspecific barcodes, with only minor exceptions observed for the taxonomically complicated genus Polyommatus and misidentified records of Aulocera in the database. We also observed variations within the same phylogenetic clades forming nested lineages, which may be attributed to the taxonomic intricacies present at the subspecies level globally, mostly among Eurasian species. Overall, our effort not only substantiated the effectiveness of DNA Barcoding for the identification and conservation of this climatically vulnerable assemblage but also highlighted the significance of deciphering the unique genetic composition among this geographically isolated population of Ladakh butterflies.
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Carvalho APS, Owens HL, St Laurent RA, Earl C, Dexter KM, Messcher RL, Willmott KR, Aduse-Poku K, Collins SC, Homziak NT, Hoshizaki S, Hsu YF, Kizhakke AG, Kunte K, Martins DJ, Mega NO, Morinaka S, Peggie D, Romanowski HP, Sáfián S, Vila R, Wang H, Braby MF, Espeland M, Breinholt JW, Pierce NE, Kawahara AY, Lohman DJ. Comprehensive phylogeny of Pieridae butterflies reveals strong correlation between diversification and temperature. iScience 2024; 27:109336. [PMID: 38500827 PMCID: PMC10945170 DOI: 10.1016/j.isci.2024.109336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/28/2023] [Accepted: 02/21/2024] [Indexed: 03/20/2024] Open
Abstract
Temperature is thought to be a key factor influencing global species richness patterns. We investigate the link between temperature and diversification in the butterfly family Pieridae by combining next generation DNA sequences and published molecular data with fine-grained distribution data. We sampled nearly 600 pierid butterfly species to infer the most comprehensive molecular phylogeny of the family and curated a distribution dataset of more than 800,000 occurrences. We found strong evidence that species in environments with more stable daily temperatures or cooler maximum temperatures in the warm seasons have higher speciation rates. Furthermore, speciation and extinction rates decreased in tandem with global temperatures through geological time, resulting in a constant net diversification.
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Affiliation(s)
- Ana Paula S. Carvalho
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, Gainesville, FL, USA
| | - Hannah L. Owens
- Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Macroecology, Evolution, and Climate, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Ryan A. St Laurent
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, Gainesville, FL, USA
- Department of Entomology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Chandra Earl
- Department of Natural Sciences, Bernice Pauahi Bishop Museum, Honolulu, HI, USA
| | - Kelly M. Dexter
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, Gainesville, FL, USA
| | - Rebeccah L. Messcher
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, Gainesville, FL, USA
| | - Keith R. Willmott
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, Gainesville, FL, USA
| | | | | | - Nicholas T. Homziak
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, Gainesville, FL, USA
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
| | - Sugihiko Hoshizaki
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yu-Feng Hsu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan, R.O.C
| | - Athulya G. Kizhakke
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bengaluru, India
| | - Krushnamegh Kunte
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bengaluru, India
| | - Dino J. Martins
- Turkana Basin Institute, Stony Brook University, Stony Brook, NY, USA
- Insect Committee of Nature Kenya, The East Africa Natural History Society, Nairobi, Kenya
| | - Nicolás O. Mega
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Sadaharu Morinaka
- Saitama Study Center, The Open University of Japan, Omiya-ku, Saitama City, Japan
| | - Djunijanti Peggie
- Museum Zoologi Bogor, Research Center for Biosystematics and Evolution, Research Organization for Life Sciences and Environment, National Research and Innovation Agency, Cibinong, Bogor, Indonesia
| | - Helena P. Romanowski
- Laboratório de Ecologia de Insetos, Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Szabolcs Sáfián
- African Butterfly Research Institute, Karen, Nairobi, Kenya
- Institute of Silviculture and Forest Protection, University of Sopron, Sopron, Hungary
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Univ. Pompeu Fabra), Barcelona, Spain
| | - Houshuai Wang
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Michael F. Braby
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
- Australian National Insect Collection, National Research Collections Australia, Canberra, ACT, Australia
| | - Marianne Espeland
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| | - Jesse W. Breinholt
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, Gainesville, FL, USA
- Intermountain Healthcare, Intermountain Precision Genomics, St. George, UT, USA
| | - Naomi E. Pierce
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Akito Y. Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, Gainesville, FL, USA
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - David J. Lohman
- Department of Biology, City University of New York, New York, NY, USA
- PhD Program in Biology, Graduate Center, City University of New York, New York, NY, USA
- Entomology Section, National Museum of Natural History, Manila, Philippines
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Portik DM, Streicher JW, Wiens JJ. Frog phylogeny: A time-calibrated, species-level tree based on hundreds of loci and 5,242 species. Mol Phylogenet Evol 2023; 188:107907. [PMID: 37633542 DOI: 10.1016/j.ympev.2023.107907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 08/15/2023] [Accepted: 08/15/2023] [Indexed: 08/28/2023]
Abstract
Large-scale, time-calibrated phylogenies from supermatrix studies have become crucial for evolutionary and ecological studies in many groups of organisms. However, in frogs (anuran amphibians), there is a serious problem with existing supermatrix estimates. Specifically, these trees are based on a limited number of loci (15 or fewer), and the higher-level relationships estimated are discordant with recent phylogenomic estimates based on much larger numbers of loci. Here, we attempted to rectify this problem by generating an expanded supermatrix and combining this with data from phylogenomic studies. To assist in aligning ribosomal sequences for this supermatrix, we developed a new program (TaxonomyAlign) to help perform taxonomy-guided alignments. The new combined matrix contained 5,242 anuran species with data from 307 markers, but with 95% missing data overall. This dataset represented a 71% increase in species sampled relative to the previous largest supermatrix analysis of anurans (adding 2,175 species). Maximum-likelihood analyses generated a tree in which higher-level relationships (and estimated clade ages) were generally concordant with those from phylogenomic analyses but were more discordant with the previous largest supermatrix analysis. We found few obvious problems arising from the extensive missing data in most species. We also generated a set of 100 time-calibrated trees for use in comparative analyses. Overall, we provide an improved estimate of anuran phylogeny based on the largest number of combined taxa and markers to date. More broadly, we demonstrate the potential to combine phylogenomic and supermatrix analyses in other groups of organisms.
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Affiliation(s)
- Daniel M Portik
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721 USA; California Academy of Sciences, San Francisco, CA 94118, USA
| | | | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721 USA.
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Lemes JRA, Siewert RR, Mielke OHH, Casagrande MM, Warren AD. Description of Uniphylus gen. nov., a new genus of Carcharodini (Lepidoptera, Hesperiidae, Pyrginae) for Staphylus evemerus Godman & Salvin, 1896. AN ACAD BRAS CIENC 2023; 95:e20221099. [PMID: 37909609 DOI: 10.1590/0001-3765202320221099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/03/2023] [Indexed: 11/03/2023] Open
Abstract
Staphylus evemerus Godman & Salvin, 1896 is a species with a unique set of morphological characters within Carcharodini. Also, mitochondrial cytochrome oxidase subunit 1 (COI) sequences analysis demonstrated a large genetic distance with other related genera of the tribe. Therefore, this paper aims to describe a new genus for this species, which is named as Uniphylus gen. nov. Besides the morphological redescription of the male of Uniphylus evemerus (Godman & Salvin, 1896) new comb., the description of the female is provided for the first time, as well as an updated distributional map with all records known so far for this species.
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Affiliation(s)
- José Ricardo A Lemes
- Universidade Federal do Paraná, Departamento de Zoologia, Laboratório de Estudos de Lepidoptera Neotropical, Caixa Postal 19020, 81531-980 Curitiba, PR, Brazil
| | - Ricardo Russo Siewert
- Universidade Estadual de Campinas, Departamento de Biologia Animal e Museu de Diversidade Biológica, Instituto de Biologia, Rua Monteiro Lobato, 255, 13083-862 Campinas, SP, Brazil
| | - Olaf H H Mielke
- Universidade Federal do Paraná, Departamento de Zoologia, Laboratório de Estudos de Lepidoptera Neotropical, Caixa Postal 19020, 81531-980 Curitiba, PR, Brazil
| | - Mirna M Casagrande
- Universidade Federal do Paraná, Departamento de Zoologia, Laboratório de Estudos de Lepidoptera Neotropical, Caixa Postal 19020, 81531-980 Curitiba, PR, Brazil
| | - Andrew David Warren
- University of Florida, Florida Museum of Natural History, McGuire Center for Lepidoptera and Biodiversity, 3215 Hull Rd., UF Cultural Plaza, PO Box 112710, Gainesville, FL 32611-2710, USA
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Hu GL, Brown J, Heikkilä M, Aarvik L, Mutanen M. Molecular phylogeny, divergence time, biogeography and trends in host plant usage in the agriculturally important tortricid tribe Grapholitini (Lepidoptera: Tortricidae: Olethreutinae). Cladistics 2023; 39:359-381. [PMID: 37209356 DOI: 10.1111/cla.12543] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 03/27/2023] [Accepted: 04/25/2023] [Indexed: 05/22/2023] Open
Abstract
The leaf-roller moth tribe Grapholitini comprises about 1200 described species and contains numerous notorious pests of fruits and seeds. The phylogeny of the tribe has been little studied using contemporary methods, and the monophyly of several genera remains questionable. In order to provide a more robust phylogenetic framework for the group, we conducted a multiple-gene phylogenetic analysis of 104 species representing 27 genera of Grapholitini and 29 outgroup species. Divergence time, ancestral area, and host plant usage were also inferred to explore evolutionary trends in the tribe. Our analyses indicate that Larisa and Corticivora, traditionally assigned to Grapholitini, are best excluded from the tribe. After removal of these two genera, the tribe is found to be monophyletic, represented by two major lineages-a Dichrorampha clade and a Cydia clade, the latter of which can be divided into seven generic groups. The genus Grapholita was found to be polyphyletic, comprising three different clades, and we propose three genera to accommodate these groups: Grapholita (sensu stricto), Aspila (formerly a subgenus of Grapholita) and Ephippiphora (formerly considered a synonym of Grapholita). We summarize each generic group, including related genera not included in our analysis, providing morphological, pheromone and food plant characters that support particular branches within the molecular hypotheses. Biogeographical analyses indicate that Grapholitini probably originated in the Nearctic, Afrotropical and Neotropical regions in the Lutetian of the middle Eocene (ca. 44.3 Ma). Our results also indicate that most groups in Grapholitini originated from Fabaceae-feeding monophagous or oligophagous ancestors, and that host plant shifts probably promoted species diversification within the tribe.
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Affiliation(s)
- Gui-Lin Hu
- School of Life Sciences, Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou, China
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - John Brown
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Maria Heikkilä
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Leif Aarvik
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
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Kamimura Y, Nishikawa M, Yamasako J. DNA barcoding of Japanese earwig species (Insecta, Dermaptera), with sequence diversity analyses of three species of Anisolabididae. Biodivers Data J 2023; 11:e107001. [PMID: 38318508 PMCID: PMC10840520 DOI: 10.3897/bdj.11.e107001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/19/2023] [Indexed: 02/07/2024] Open
Abstract
Dermaptera is a polyneopteran insect order that includes more than 2,000 described species, commonly known as earwigs, that mainly inhabit tropical, subtropical and warm temperate regions. Although 40 species have been found in Japan, their distribution and habitat preferences have remained ambiguous due to sample misidentification, particularly amongst immature specimens. To overcome this problem, we sequenced and analysed the DNA barcoding region of the mitochondrial cytochrome oxidase I gene (cox1) of dermapteran species recorded from Japan. Including publicly available data, 72.5% of known Japanese dermapteran species were subjected to molecular identification. We extensively sampled three wingless species of subfamily Anisolabidinae (Anisolabididae): Anisolabismaritima, Anisolabellamarginalis and Euborelliapallipes. Although these species exhibit similar habitat preferences as semi-synanthropes, A.maritima, a cosmopolitan species with the highest affinity to seashore, had significantly higher sequence diversity than the latter two species, which are considered endemic to East Asia. A similar trend was observed for (at least partly) winged cosmopolitan species of other families. Introgression with the congener Anisolabisseirokui is also suggested for A.maritima. Possible causes of the varying levels of sequence diversity are discussed.
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Affiliation(s)
| | - Masaru Nishikawa
- Ehime University, Matsuyama, JapanEhime UniversityMatsuyamaJapan
| | - Junsuke Yamasako
- National Agriculture and Food Research Organization, Tsukuba, JapanNational Agriculture and Food Research OrganizationTsukubaJapan
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Lukhtanov VA, Shapoval NA, Dantchenko AV, Eckweiler W. Phylogenetic Structure Revealed through Combining DNA Barcodes with Multi-Gene Data for Agrodiaetus Blue Butterflies (Lepidoptera, Lycaenidae). INSECTS 2023; 14:769. [PMID: 37754737 PMCID: PMC10532069 DOI: 10.3390/insects14090769] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/28/2023]
Abstract
The need for multi-gene analysis in evolutionary and taxonomic studies is generally accepted. However, the sequencing of multiple genes is not always possible. For various reasons, short mitochondrial DNA barcodes are the only source of molecular information for some species in many genera, although multi-locus data are available for other species of the same genera. In particular, such situation exists in the species-rich butterfly subgenus Polyommatus (Agrodiaetus). Here, we analyzed the partitioning of this subgenus into species groups by using three data sets. The first data set was represented by short mitochondrial DNA barcodes for all analyzed samples. The second and third data sets were represented by a combination of short mitochondrial DNA barcodes for part of the taxa with longer mitochondrial sequences COI + tRNA-Leu + COII (data set 2) and with longer mitochondrial COI + tRNA-Leu + COII and nuclear 5.8S rDNA + ITS2 + 28S rDNA sequences (data set 3) for the remaining species. We showed that the DNA barcoding approach (data set 1) failed to reveal the phylogenetic structure, resulting in numerous polytomies in the tree obtained. Combined analysis of the mitochondrial and nuclear sequences (data sets 2 and 3) revealed the species groups and the position within these species groups, even for the taxa for which only short DNA barcodes were available.
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Affiliation(s)
- Vladimir A. Lukhtanov
- Department of Karyosystematics, Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab. 1, 199034 Saint-Petersburg, Russia;
| | - Nazar A. Shapoval
- Department of Karyosystematics, Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab. 1, 199034 Saint-Petersburg, Russia;
| | - Alexander V. Dantchenko
- Department of Karyosystematics, Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab. 1, 199034 Saint-Petersburg, Russia;
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Pazhenkova EA, Lukhtanov VA. Chromosomal conservatism vs chromosomal megaevolution: enigma of karyotypic evolution in Lepidoptera. Chromosome Res 2023; 31:16. [PMID: 37300756 DOI: 10.1007/s10577-023-09725-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 05/21/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023]
Abstract
In the evolution of many organisms, periods of slow genome reorganization (= chromosomal conservatism) are interrupted by bursts of numerous chromosomal changes (= chromosomal megaevolution). Using comparative analysis of chromosome-level genome assemblies, we investigated these processes in blue butterflies (Lycaenidae). We demonstrate that the phase of chromosome number conservatism is characterized by the stability of most autosomes and dynamic evolution of the sex chromosome Z, resulting in multiple variants of NeoZ chromosomes due to autosome-sex chromosome fusions. In contrast during the phase of rapid chromosomal evolution, the explosive increase in chromosome number occurs mainly through simple chromosomal fissions. We show that chromosomal megaevolution is a highly non-random canalized process, and in two phylogenetically independent Lysandra lineages, the drastic parallel increase in number of fragmented chromosomes was achieved, at least partially, through reuse of the same ancestral chromosomal breakpoints. In species showing chromosome number doubling, we found no blocks of duplicated sequences or duplicated chromosomes, thus refuting the hypothesis of polyploidy. In the studied taxa, long blocks of interstitial telomere sequences (ITSs) consist of (TTAGG)n arrays interspersed with telomere-specific retrotransposons. ITSs are sporadically present in rapidly evolving Lysandra karyotypes, but not in the species with ancestral chromosome number. Therefore, we hypothesize that the transposition of telomeric sequences may be triggers of the rapid chromosome number increase. Finally, we discuss the hypothetical genomic and population mechanisms of chromosomal megaevolution and argue that the disproportionally high evolutionary role of the Z sex chromosome can be additionally reinforced by sex chromosome-autosome fusions and Z-chromosome inversions.
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Affiliation(s)
- Elena A Pazhenkova
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna Pot 111, 1000, Ljubljana, Slovenia.
| | - Vladimir A Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Universitetskaya Nab. 1, 199034, St. Petersburg, Russia.
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Montgelard C, Muller T, Arnal V, Maree S, Taylor PJ, Sands AF, Robinson TJ, Matthee CA. Diversification and evolutionary history of the African laminated-toothed rats (Rodentia, Otomyini). Mol Phylogenet Evol 2023; 183:107779. [PMID: 37019420 DOI: 10.1016/j.ympev.2023.107779] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 03/23/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023]
Abstract
The African continent was subjected to periodic climatic shifts during the Pliocene and Pleistocene. These habitat changes greatly affected the evolutionary processes and tempo of diversification in numerous, widely distributed mammals. The Otomyini (Family Muridae) comprises three African rodent genera, Parotomys, Otomys and Myotomys, characterized by unique laminated-shaped molars. Species within this tribe generally prefer open-habitat and show low dispersal capabilities, with previous studies suggesting that their diversification was closely associated with climatic oscillations over the last four million years. Our phylogenetic reconstructions, based on three mitochondrial (mtDNA) genes (Cytb, COI and 12S) and four nuclear introns (EF, SPTBN, MGF and THY), identified eight major genetic clades that are distributed across southern, eastern and western Africa. Our data permit the re-examination of the taxonomic status of the three genera as well as the previously proposed mesic-arid dichotomy of the 10 South African species. Moreover, multiple mtDNA species delimitation methods incorporating 168 specimens estimated the number of Otomyini species to be substantially higher than the ∼30 recognized, suggesting that the current taxonomy will necessitate an integrative approach to delimit extant species diversity within the Otomyini. The data suggests that the origin of the tribe can be dated back to ∼5.7 million years ago (Ma) in southern Africa. The distribution and phylogenetic associations among the eight major otomyine evolutionary lineages can best be explained by several waves of northward colonization from southern Africa, complemented by independent reversed dispersals from eastern back to southern Africa at different time periods. There is strong support for the hypothesis that the radiation, dispersion, and diversification of the otomyine rodents is closely linked to recent Plio-Pleistocene climatic oscillations.
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Wu YH, Hou SB, Yuan ZY, Jiang K, Huang RY, Wang K, Liu Q, Yu ZB, Zhao HP, Zhang BL, Chen JM, Wang LJ, Stuart BL, Chambers EA, Wang YF, Gao W, Zou DH, Yan F, Zhao GG, Fu ZX, Wang SN, Jiang M, Zhang L, Ren JL, Wu YY, Zhang LY, Yang DC, Jin JQ, Yin TT, Li JT, Zhao WG, Murphy RW, Huang S, Guo P, Zhang YP, Che J. DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs. Mol Ecol Resour 2023. [PMID: 36924341 DOI: 10.1111/1755-0998.13784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/25/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023]
Abstract
DNA barcoding has greatly facilitated studies of taxonomy, biodiversity, biological conservation, and ecology. Here, we establish a reliable DNA barcoding library for Chinese snakes, unveiling hidden diversity with implications for taxonomy, and provide a standardized tool for conservation management. Our comprehensive study includes 1638 cytochrome c oxidase subunit I (COI) sequences from Chinese snakes that correspond to 17 families, 65 genera, 228 named species (80.6% of named species) and 36 candidate species. A barcode gap analysis reveals gaps, where all nearest neighbour distances exceed maximum intraspecific distances, in 217 named species and all candidate species. Three species-delimitation methods (ABGD, sGMYC, and sPTP) recover 320 operational taxonomic units (OTUs), of which 192 OTUs correspond to named and candidate species. Twenty-eight other named species share OTUs, such as Azemiops feae and A. kharini, Gloydius halys, G. shedaoensis, and G. intermedius, and Bungarus multicinctus and B. candidus, representing inconsistencies most probably caused by imperfect taxonomy, recent and rapid speciation, weak taxonomic signal, introgressive hybridization, and/or inadequate phylogenetic signal. In contrast, 43 species and candidate species assign to two or more OTUs due to having large intraspecific distances. If most OTUs detected in this study reflect valid species, including the 36 candidate species, then 30% more species would exist than are currently recognized. Several OTU divergences associate with known biogeographic barriers, such as the Taiwan Strait. In addition to facilitating future studies, this reliable and relatively comprehensive reference database will play an important role in the future monitoring, conservation, and management of Chinese snakes.
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Affiliation(s)
- Yun-He Wu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Shao-Bing Hou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Zhi-Yong Yuan
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ke Jiang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ru-Yi Huang
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Kai Wang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Qin Liu
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin, Sichuan, 644007, China
| | - Zhong-Bin Yu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Hai-Peng Zhao
- School of Life Science, Henan University, Kaifeng, Henan, 475001, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jin-Min Chen
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Li-Jun Wang
- School of Life Sciences, Hainan Normal University, Haikou, Hainan, 571158, China
| | - Bryan L Stuart
- Section of Research & Collections, North Carolina Museum of Natural Sciences, Raleigh, North Carolina, 27601, USA
| | - E Anne Chambers
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, 94720, USA
| | - Yu-Fan Wang
- Zhejiang Forest Resource Monitoring Center, Hangzhou, Zhejiang, 310020, China
| | - Wei Gao
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Da-Hu Zou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- College of Science, Tibet University, Lhasa, Tibet, 850000, China
| | - Fang Yan
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Gui-Gang Zhao
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Zhong-Xiong Fu
- Yunnan Senye Biotechnology Co., Ltd, Xishuangbanna, Yunnan, 666100, China
| | - Shao-Neng Wang
- Bureau of Guangxi Mao'er Mountain Nature Reserve, Guilin, Guangxi, 541316, China
| | - Ming Jiang
- Gongshan Bureau of Gaoligongshan National Nature Reserve, Gongshan, Yunnan, 650224, China
| | - Liang Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510260, China
| | - Jin-Long Ren
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China
| | - Ya-Yong Wu
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin, Sichuan, 644007, China
| | - Lu-Yang Zhang
- Beijing Mountains & Seas Eco Technology Co. Ltd, Beijing, 101100, China
| | - Dian-Cheng Yang
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jia-Tang Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China
| | - Wen-Ge Zhao
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, 150025, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Reptilia Zoo and Education Centre, Vaughn, Ontario, L4K 2N6, Canada
| | - Song Huang
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China
| | - Peng Guo
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin, Sichuan, 644007, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
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12
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Pazhenkova EA, Lukhtanov VA. Whole-Genome Analysis Reveals the Dynamic Evolution of Holocentric Chromosomes in Satyrine Butterflies. Genes (Basel) 2023; 14:437. [PMID: 36833364 PMCID: PMC9956908 DOI: 10.3390/genes14020437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Butterfly chromosomes are holocentric, i.e., lacking a localized centromere. Potentially, this can lead to rapid karyotypic evolution through chromosome fissions and fusions, since fragmented chromosomes retain kinetic activity, while fused chromosomes are not dicentric. However, the actual mechanisms of butterfly genome evolution are poorly understood. Here, we analyzed chromosome-scale genome assemblies to identify structural rearrangements between karyotypes of satyrine butterfly species. For the species pair Erebia ligea-Maniola jurtina, sharing the ancestral diploid karyotype 2n = 56 + ZW, we demonstrate a high level of chromosomal macrosynteny and nine inversions separating these species. We show that the formation of a karyotype with a low number of chromosomes (2n = 36 + ZW) in Erebia aethiops was based on ten fusions, including one autosome-sex chromosome fusion, resulting in a neo-Z chromosome. We also detected inversions on the Z sex chromosome that were differentially fixed between the species. We conclude that chromosomal evolution is dynamic in the satyrines, even in the lineage that preserves the ancestral chromosome number. We hypothesize that the exceptional role of Z chromosomes in speciation may be further enhanced by inversions and sex chromosome-autosome fusions. We argue that not only fusions/fissions but also inversions are drivers of the holocentromere-mediated mode of chromosomal speciation.
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Affiliation(s)
- Elena A. Pazhenkova
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Vladimir A. Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Universitetskaya nab. 1, St. Petersburg 199034, Russia
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13
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Williams PH, Françoso E, Martinet B, Orr MC, Ren Z, Júnior JS, Thanoosing C, Vandame R. When did bumblebees reach South America? Unexpectedly old montane species may be explained by Mexican stopover (Hymenoptera: Apidae). SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2092229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
| | - Elaine Françoso
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK
| | - Baptiste Martinet
- Avenue F.D, Université Libre de Bruxelles, Roosevelt 50, Brussels, B-1050, Belgium
| | - Michael C. Orr
- Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang, 100101, Beijing, China
| | - Zongxin Ren
- Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, Yunnan, China
| | - José Santos Júnior
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Rémy Vandame
- El Colegio de la Frontera Sur, San Cristóbal de Las Casas, Chiapas, 29290, México
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14
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Lukhtanov VA, Gagarina AV. Molecular Phylogeny and Taxonomy of the Butterfly Subtribe Scolitantidina with Special Focus on the Genera Pseudophilotes, Glaucopsyche and Iolana (Lepidoptera, Lycaenidae). INSECTS 2022; 13:1110. [PMID: 36555020 PMCID: PMC9782982 DOI: 10.3390/insects13121110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
The Palearctic blue butterfly genus Pseudophilotes Beuret, 1958 is not homogenous regarding the morphology of its genital structures. For this reason, some of its species have been considered to be representatives of other genera of the subtribe Scolitantidina (subfamily Polyommatinae). Here, we address these taxonomic problems by analyzing the phylogenetic relationships between the genera, subgenera, and species of this subtribe inferred via the analysis of five nuclear and two mitochondrial DNA sequences. We demonstrate that the enigmatic Asian species P. panope (Eversmann, 1851) belongs to the genus Pseudophilotes but not to Praephilotes Forster, 1938 or Palaeophilotes Forster, 1938 and does not represent the independent genus Inderskia Korshunov, 2000, as hypothesized previously. We synonymize P. svetlana Yakovlev, 2003 (syn. nov.) and P. marina Zhdanko, 2004 (syn. nov.) with P. panope. We demonstrate a deep genetic divergence between lineages that were previously considered as subspecies of the single species Iolana iolas (Ochsenheimer, 1816). As a result, we confirm the multispecies concept of the genus Iolana Bethune-Baker, 1914. We show that the Holarctic genus Glaucopsyche can be divided into four subgenera: Glaucopsyche Scudder, 1872 (=Shijimiaeoides Beuret, 1958), Apelles Hemming, 1931, Bajluana Korshunov and Ivonin, 1990, and Phaedrotes Scudder, 1876.
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15
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Nunes R, Storer C, Doleck T, Kawahara AY, Pierce NE, Lohman DJ. Predictors of sequence capture in a large-scale anchored phylogenomics project. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.943361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Abstract
Next-generation sequencing (NGS) technologies have revolutionized phylogenomics by decreasing the cost and time required to generate sequence data from multiple markers or whole genomes. Further, the fragmented DNA of biological specimens collected decades ago can be sequenced with NGS, reducing the need for collecting fresh specimens. Sequence capture, also known as anchored hybrid enrichment, is a method to produce reduced representation libraries for NGS sequencing. The technique uses single-stranded oligonucleotide probes that hybridize with pre-selected regions of the genome that are sequenced via NGS, culminating in a dataset of numerous orthologous loci from multiple taxa. Phylogenetic analyses using these sequences have the potential to resolve deep and shallow phylogenetic relationships. Identifying the factors that affect sequence capture success could save time, money, and valuable specimens that might be destructively sampled despite low likelihood of sequencing success. We investigated the impacts of specimen age, preservation method, and DNA concentration on sequence capture (number of captured sequences and sequence quality) while accounting for taxonomy and extracted tissue type in a large-scale butterfly phylogenomics project. This project used two probe sets to extract 391 loci or a subset of 13 loci from over 6,000 butterfly specimens. We found that sequence capture is a resilient method capable of amplifying loci in samples of varying age (0–111 years), preservation method (alcohol, papered, pinned), and DNA concentration (0.020 ng/μl - 316 ng/ul). Regression analyses demonstrate that sequence capture is positively correlated with DNA concentration. However, sequence capture and DNA concentration are negatively correlated with sample age and preservation method. Our findings suggest that sequence capture projects should prioritize the use of alcohol-preserved samples younger than 20 years old when available. In the absence of such specimens, dried samples of any age can yield sequence data, albeit with returns that diminish with increasing age.
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16
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Nitta JH, Schuettpelz E, Ramírez-Barahona S, Iwasaki W. An open and continuously updated fern tree of life. FRONTIERS IN PLANT SCIENCE 2022; 13:909768. [PMID: 36092417 PMCID: PMC9449725 DOI: 10.3389/fpls.2022.909768] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/12/2022] [Indexed: 05/31/2023]
Abstract
Ferns, with about 12,000 species, are the second most diverse lineage of vascular plants after angiosperms. They have been the subject of numerous molecular phylogenetic studies, resulting in the publication of trees for every major clade and DNA sequences from nearly half of all species. Global fern phylogenies have been published periodically, but as molecular systematics research continues at a rapid pace, these become quickly outdated. Here, we develop a mostly automated, reproducible, open pipeline to generate a continuously updated fern tree of life (FTOL) from DNA sequence data available in GenBank. Our tailored sampling strategy combines whole plastomes (few taxa, many loci) with commonly sequenced plastid regions (many taxa, few loci) to obtain a global, species-level fern phylogeny with high resolution along the backbone and maximal sampling across the tips. We use a curated reference taxonomy to resolve synonyms in general compliance with the community-driven Pteridophyte Phylogeny Group I classification. The current FTOL includes 5,582 species, an increase of ca. 40% relative to the most recently published global fern phylogeny. Using an updated and expanded list of 51 fern fossil constraints, we find estimated ages for most families and deeper clades to be considerably older than earlier studies. FTOL and its accompanying datasets, including the fossil list and taxonomic database, will be updated on a regular basis and are available via a web portal (https://fernphy.github.io) and R packages, enabling immediate access to the most up-to-date, comprehensively sampled fern phylogeny. FTOL will be useful for anyone studying this important group of plants over a wide range of taxonomic scales, from smaller clades to the entire tree. We anticipate FTOL will be particularly relevant for macroecological studies at regional to global scales and will inform future taxonomic systems with the most recent hypothesis of fern phylogeny.
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Affiliation(s)
- Joel H. Nitta
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Eric Schuettpelz
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Santiago Ramírez-Barahona
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
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17
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Jardim de Queiroz L, Doenz CJ, Altermatt F, Alther R, Borko Š, Brodersen J, Gossner MM, Graham C, Matthews B, McFadden IR, Pellissier L, Schmitt T, Selz OM, Villalba S, Rüber L, Zimmermann NE, Seehausen O. Climate, immigration and speciation shape terrestrial and aquatic biodiversity in the European Alps. Proc Biol Sci 2022; 289:20221020. [PMID: 35946161 PMCID: PMC9363983 DOI: 10.1098/rspb.2022.1020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Quaternary climate fluctuations can affect speciation in regional biodiversity assembly in two non-mutually exclusive ways: a glacial species pump, where isolation in glacial refugia accelerates allopatric speciation, and adaptive radiation in underused adaptive zones during ice-free periods. We detected biogeographic and genetic signatures associated with both mechanisms in the assembly of the biota of the European Alps. Age distributions of endemic and widespread species within aquatic and terrestrial taxa (amphipods, fishes, amphibians, butterflies and flowering plants) revealed that endemic fish evolved only in lakes, are highly sympatric, and mainly of Holocene age, consistent with adaptive radiation. Endemic amphipods are ancient, suggesting preglacial radiation with limited range expansion and local Pleistocene survival, perhaps facilitated by a groundwater-dwelling lifestyle. Terrestrial endemics are mostly of Pleistocene age and are thus more consistent with the glacial species pump. The lack of evidence for Holocene adaptive radiation in the terrestrial biome is consistent with faster recolonization through range expansion of these taxa after glacial retreats. More stable and less seasonal ecological conditions in lakes during the Holocene may also have contributed to Holocene speciation in lakes. The high proportion of young, endemic species makes the Alpine biota vulnerable to climate change, but the mechanisms and consequences of species loss will likely differ between biomes because of their distinct evolutionary histories.
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Affiliation(s)
- Luiz Jardim de Queiroz
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland.,Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Carmela J Doenz
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland.,Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Florian Altermatt
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8006 Zürich, Switzerland
| | - Roman Alther
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8006 Zürich, Switzerland
| | - Špela Borko
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Jakob Brodersen
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland.,Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Martin M Gossner
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903 Birmensdorf, Switzerland.,Department of Environmental Systems Science, Swiss Federal Institute of Technology in Zürich, 8092 Zürich, Switzerland
| | - Catherine Graham
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903 Birmensdorf, Switzerland
| | - Blake Matthews
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland.,Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Ian R McFadden
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903 Birmensdorf, Switzerland.,Department of Environmental Systems Science, Swiss Federal Institute of Technology in Zürich, 8092 Zürich, Switzerland
| | - Loïc Pellissier
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903 Birmensdorf, Switzerland.,Department of Environmental Systems Science, Swiss Federal Institute of Technology in Zürich, 8092 Zürich, Switzerland
| | - Thomas Schmitt
- Senckenberg German Entomological Institute, 15374 Müncheberg, Germany.,Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Oliver M Selz
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland
| | - Soraya Villalba
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland
| | - Lukas Rüber
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Naturhistorisches Museum Bern, 3005 Bern, Switzerland
| | - Niklaus E Zimmermann
- Swiss Federal Institute for Forest, Snow and Landscape Research, 8903 Birmensdorf, Switzerland.,Department of Environmental Systems Science, Swiss Federal Institute of Technology in Zürich, 8092 Zürich, Switzerland
| | - Ole Seehausen
- Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum/8600 Dübendorf, Switzerland.,Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
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18
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Toro-Delgado E, Hernández-Roldán J, Dincă V, Vicente JC, Shaw MR, Quicke DL, Vodă R, Albrecht M, Fernández-Triana J, Vidiella B, Valverde S, Dapporto L, Hebert PDN, Talavera G, Vila R. Butterfly–parasitoid–hostplant interactions in Western Palaearctic Hesperiidae: a DNA barcoding reference library. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The study of ecological interactions between plants, phytophagous insects and their natural enemies is an essential but challenging component for understanding ecosystem dynamics. Molecular methods such as DNA barcoding can help elucidate these interactions. In this study, we employed DNA barcoding to establish hostplant and parasitoid interactions with hesperiid butterflies, using a complete reference library for Hesperiidae of continental Europe and north-western Africa (53 species, 100% of those recorded) based on 2934 sequences from 38 countries. A total of 233 hostplant and parasitoid interactions are presented, some recovered by DNA barcoding larval remains or parasitoid cocoons. Combining DNA barcode results with other lines of evidence allowed 94% species-level identification for Hesperiidae, but success was lower for parasitoids, in part due to unresolved taxonomy. Potential cases of cryptic diversity, both in Hesperiidae and Microgastrinae, are discussed. We briefly analyse the resulting interaction networks. Future DNA barcoding initiatives in this region should focus attention on north-western Africa and on parasitoids, because in these cases barcode reference libraries and taxonomy are less well developed.
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Affiliation(s)
| | - Juan Hernández-Roldán
- Institut de Biologia Evolutiva (CSIC-UPF) , 03008 Barcelona , Spain
- Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid , c/ Darwin, 2, ES - 28049 Madrid , Spain
| | - Vlad Dincă
- Ecology and Genetics Research Unit, PO Box 3000, University of Oulu , 90014 Oulu , Finland
- Research Institute of the University of Bucharest (ICUB), University of Bucharest , Bucharest , Romania
| | | | - Mark R Shaw
- National Museums of Scotland , Edinburgh , UK
| | - Donald Lj Quicke
- Department of Biology, Faculty of Life Sciences, Chulalongkorn University , Bangkok , Thailand
| | | | | | | | - Blai Vidiella
- Centre de Recerca Matemàtica , Edifici C , Campus de Bellaterra, Barcelona , Spain
| | - Sergi Valverde
- Institut de Biologia Evolutiva (CSIC-UPF) , 03008 Barcelona , Spain
- European Centre for Living Technology , Venice , Italy
| | - Leonardo Dapporto
- Dipartimento di Biologia, University of Florence , 50019 Sesto Fiorentino , Italy
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph , Guelph, ON N1G 2W1 , Canada
| | - Gerard Talavera
- Institut Botànic de Barcelona (IBB), CSIC-Ajuntament de Barcelona , Passeig del Migdia s/n, 08038 Barcelona , Spain
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF) , 03008 Barcelona , Spain
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19
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Wu H, Yang JB, Liu JX, Li DZ, Ma PF. Organelle Phylogenomics and Extensive Conflicting Phylogenetic Signals in the Monocot Order Poales. FRONTIERS IN PLANT SCIENCE 2022; 12:824672. [PMID: 35173754 PMCID: PMC8841755 DOI: 10.3389/fpls.2021.824672] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
The Poales is one of the largest orders of flowering plants with significant economic and ecological values. Reconstructing the phylogeny of the Poales is important for understanding its evolutionary history that forms the basis for biological studies. However, due to sparse taxon sampling and limited molecular data, previous studies have resulted in a variety of contradictory topologies. In particular, there are three nodes surrounded by incongruence: the phylogenetic ambiguity near the root of the Poales tree, the sister family of Poaceae, and the delimitation of the xyrid clade. We conducted a comprehensive sampling and reconstructed the phylogenetic tree using plastid and mitochondrial genomic data from 91 to 66 taxa, respectively, representing all the 16 families of Poales. Our analyses support the finding of Bromeliaceae and Typhaceae as the earliest diverging groups within the Poales while having phylogenetic relationships with the polytomy. The clade of Ecdeiocoleaceae and Joinvilleaceae is recovered as the sister group of Poaceae. The three families, Mayacaceae, Eriocaulaceae, and Xyridaceae, of the xyrid assembly diverged successively along the backbone of the Poales phylogeny, and thus this assembly is paraphyletic. Surprisingly, we find substantial phylogenetic conflicts within the plastid genomes of the Poales, as well as among the plastid, mitochondrial, and nuclear data. These conflicts suggest that the Poales could have a complicated evolutionary history, such as rapid radiation and polyploidy, particularly allopolyploidy through hybridization. In sum, our study presents a new perspicacity into the complex phylogenetic relationships and the underlying phylogenetic conflicts within the Poales.
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Affiliation(s)
- Hong Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jing-Xia Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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20
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Motyka M, Kusy D, Bocek M, Bilkova R, Bocak L. Phylogenomic and mitogenomic data can accelerate inventorying of tropical beetles during the current biodiversity crisis. eLife 2021; 10:71895. [PMID: 34927586 PMCID: PMC8798050 DOI: 10.7554/elife.71895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/18/2021] [Indexed: 11/13/2022] Open
Abstract
Conservation efforts must be evidence-based, so rapid and economically feasible methods should be used to quantify diversity and distribution patterns. We have attempted to overcome current impediments to the gathering of biodiversity data by using integrative phylogenomic and three mtDNA fragment analyses. As a model, we sequenced the Metriorrhynchini beetle fauna, sampled from ~700 localities in three continents. The species-rich dataset included ~6,500 terminals, ~1,850 putative species delimited at 5% uncorrected pairwise threshold, possibly ~1,000 of them unknown to science. Neither type of data could alone answer our questions on biodiversity and phylogeny. The phylogenomic backbone enabled the integrative delimitation of robustly defined natural genus-group units that will inform future research. Using constrained mtDNA analysis, we identified the spatial structure of species diversity, very high species-level endemism, and a biodiversity hotspot in New Guinea. We suggest that focused field research and subsequent laboratory and bioinformatic workflow steps would substantially accelerate the inventorying of any hyperdiverse tropical group with several thousand species. The outcome would be a scaffold for the incorporation of further data from environmental sequencing and ecological studies. The database of sequences could set a benchmark for the spatiotemporal evaluation of biodiversity, would support evidence-based conservation planning, and would provide a robust framework for systematic, biogeographic, and evolutionary studies.
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Affiliation(s)
- Michal Motyka
- Laboratory of Biodiversity and Molecular Evolution, Czech Advanced Technology Research Institute, Olomouc, Czech Republic
| | - Dominik Kusy
- Laboratory of Biodiversity and Molecular Evolution, Czech Advanced Technology Research Institute, Olomouc, Czech Republic
| | - Matej Bocek
- Laboratory of Biodiversity and Molecular Evolution, Czech Advanced Technology Research Institute, Olomouc, Czech Republic
| | - Renata Bilkova
- Laboratory of Biodiversity and Molecular Evolution, Czech Advanced Technology Research Institute, Olomouc, Czech Republic
| | - Ladislav Bocak
- ZoologyLaboratory of Biodiversity and Molecular Evolution, Czech Advanced Technology Research Institute, Olomouc, Czech Republic
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21
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Li X, St Laurent R, Earl C, Doorenweerd C, van Nieukerken EJ, Davis DR, Johns CA, Kawakita A, Kobayashi S, Zwick A, Lopez-Vaamonde C, Ohshima I, Kawahara AY. Phylogeny of gracillariid leaf-mining moths: evolution of larval behaviour inferred from phylogenomic and Sanger data. Cladistics 2021; 38:277-300. [PMID: 34710244 DOI: 10.1111/cla.12490] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 11/27/2022] Open
Abstract
Gracillariidae is the most taxonomically diverse cosmopolitan leaf-mining moth family, consisting of nearly 2000 named species in 105 described genera, classified into eight extant subfamilies. The majority of gracillariid species are internal plant feeders as larvae, creating mines and galls in plant tissue. Despite their diversity and ecological adaptations, their phylogenetic relationships, especially among subfamilies, remain uncertain. Genomic data (83 taxa, 589 loci) were integrated with Sanger data (130 taxa, 22 loci), to reconstruct a phylogeny of Gracillariidae. Based on analyses of both datasets combined and analyzed separately, monophyly of Gracillariidae and all its subfamilies, monophyly of the clade "LAMPO" (subfamilies: Lithocolletinae, Acrocercopinae, Marmarinae, Phyllocnistinae, and Oecophyllembiinae) and relationships of its subclade "AMO" (subfamilies: Acrocercopinae, Marmarinae, and Oecophyllembiinae) were strongly supported. A sister-group relationship of Ornixolinae to the remainder of the family, and a monophyletic leaf roller lineage (Callicercops Vári + Parornichinae) + Gracillariinae, as sister to the "LAMPO" clade were supported by the most likely tree. Dating analyses indicate a mid-Cretaceous (105.3 Ma) origin of the family, followed by a rapid diversification into the nine subfamilies predating the Cretaceous-Palaeogene extinction. We hypothesize that advanced larval behaviours, such as making keeled or tentiform blotch mines, rolling leaves and galling, allowed gracillariids to better avoid larval parasitoids allowing them to further diversify. Finally, we stabilize the classification by formally re-establishing the subfamily ranks of Marmarinae stat.rev., Oecophyllembiinae stat.rev. and Parornichinae stat.rev., and erect a new subfamily, Callicercopinae Li, Ohshima and Kawahara to accommodate the enigmatic genus Callicercops.
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Affiliation(s)
- Xuankun Li
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Ryan St Laurent
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Chandra Earl
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Camiel Doorenweerd
- Department of Plant and Environmental Protection Services, University of Hawaii, 3050 Maile Way, Honolulu, HI, 96822-2231, USA
| | | | - Donald R Davis
- Department of Entomology, NHB 105, Smithsonian Institution, Washington, DC, USA
| | - Chris A Johns
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Atsushi Kawakita
- The Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, 112-0001, Japan
| | - Shigeki Kobayashi
- Entomological Laboratory, Graduate School of life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan
| | - Andreas Zwick
- Australian National Insect Collection, National Research Collections Australia, CSIRO, Canberra, ACT, 2601, Australia
| | - Carlos Lopez-Vaamonde
- INRAE, URZF, Orléans, France.,IRBI, UMR 7261, CNRS-Université de Tours, Tours, France
| | - Issei Ohshima
- Department of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo, Kyoto, 606-8522, Japan.,Center for Frontier Natural History, Kyoto Prefectural University, Sakyo, Kyoto, 606-8522, Japan
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA.,Entomology and Nematology Department, University of Florida, Gainesville, FL, 32608, USA
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