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Dort H, van der Bijl W, Wahlberg N, Nylin S, Wheat CW. Genome-Wide Gene Birth-Death Dynamics Are Associated with Diet Breadth Variation in Lepidoptera. Genome Biol Evol 2024; 16:evae095. [PMID: 38976568 PMCID: PMC11229701 DOI: 10.1093/gbe/evae095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2024] [Indexed: 07/10/2024] Open
Abstract
Comparative analyses of gene birth-death dynamics have the potential to reveal gene families that played an important role in the evolution of morphological, behavioral, or physiological variation. Here, we used whole genomes of 30 species of butterflies and moths to identify gene birth-death dynamics among the Lepidoptera that are associated with specialist or generalist feeding strategies. Our work advances this field using a uniform set of annotated proteins for all genomes, investigating associations while correcting for phylogeny, and assessing all gene families rather than a priori subsets. We discovered that the sizes of several important gene families (e.g. those associated with pesticide resistance, xenobiotic detoxification, and/or protein digestion) are significantly correlated with diet breadth. We also found 22 gene families showing significant shifts in gene birth-death dynamics at the butterfly (Papilionoidea) crown node, the most notable of which was a family of pheromone receptors that underwent a contraction potentially linked with a shift to visual-based mate recognition. Our findings highlight the importance of uniform annotations, phylogenetic corrections, and unbiased gene family analyses in generating a list of candidate genes that warrant further exploration.
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Affiliation(s)
- Hanna Dort
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Wouter van der Bijl
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | | | - Sören Nylin
- Department of Zoology, Stockholm University, Stockholm, Sweden
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2
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He R, Wang S, Li Q, Wang Z, Mei Y, Li F. Phylogenomic analysis and molecular identification of true fruit flies. Front Genet 2024; 15:1414074. [PMID: 38974385 PMCID: PMC11224437 DOI: 10.3389/fgene.2024.1414074] [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: 04/08/2024] [Accepted: 05/30/2024] [Indexed: 07/09/2024] Open
Abstract
The family Tephritidae in the order Diptera, known as true fruit flies, are agriculturally important insect pests. However, the phylogenetic relationships of true fruit flies, remain controversial. Moreover, rapid identification of important invasive true fruit flies is essential for plant quarantine but is still challenging. To this end, we sequenced the genome of 16 true fruit fly species at coverage of 47-228×. Together with the previously reported genomes of nine species, we reconstructed phylogenetic trees of the Tephritidae using benchmarking universal single-copy ortholog (BUSCO), ultraconserved element (UCE) and anchored hybrid enrichment (AHE) gene sets, respectively. The resulting trees of 50% taxon-occupancy dataset for each marker type were generally congruent at 88% nodes for both concatenation and coalescent analyses. At the subfamily level, both Dacinae and Trypetinae are monophyletic. At the species level, Bactrocera dorsalis is more closely related to Bactrocera latifrons than Bactrocera tryoni. This is inconsistent with previous conclusions based on mitochondrial genes but consistent with recent studies based on nuclear data. By analyzing these genome data, we screened ten pairs of species-specific primers for molecular identification of ten invasive fruit flies, which PCR validated. In summary, our work provides draft genome data of 16 true fruit fly species, addressing the long-standing taxonomic controversies and providing species-specific primers for molecular identification of invasive fruit flies.
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Affiliation(s)
- Rong He
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Shuping Wang
- Technical Centre for Animal, Plant and Food Inspection and Quarantine, Shanghai Customs, Shanghai, China
| | - Qiang Li
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Zuoqi Wang
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yang Mei
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fei Li
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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3
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Shapoval NA, Kir’yanov AV, Krupitsky AV, Yakovlev RV, Romanovich AE, Zhang J, Cong Q, Grishin NV, Kovalenko MG, Shapoval GN. Phylogeography of Two Enigmatic Sulphur Butterflies, Colias mongola Alphéraky, 1897 and Colias tamerlana Staudinger, 1897 (Lepidoptera, Pieridae), with Relations to Wolbachia Infection. INSECTS 2023; 14:943. [PMID: 38132616 PMCID: PMC10743618 DOI: 10.3390/insects14120943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023]
Abstract
The genus Colias Fabricius, 1807 includes numerous taxa and forms with uncertain status and taxonomic position. Among such taxa are Colias mongola Alphéraky, 1897 and Colias tamerlana Staudinger, 1897, interpreted in the literature either as conspecific forms, as subspecies of different but morphologically somewhat similar Colias species or as distinct species-level taxa. Based on mitochondrial and nuclear DNA markers, we reconstructed a phylogeographic pattern of the taxa in question. We recover and include in our analysis DNA barcodes of the century-old type specimens, the lectotype of C. tamerlana deposited in the Natural History Museum (Museum für Naturkunde), Berlin, Germany (ZMHU) and the paralectotype of C. tamerlana and the lectotype of C. mongola deposited in the Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia (ZISP). Our analysis grouped all specimens within four (HP_I-HP_IV) deeply divergent but geographically poorly structured clades which did not support nonconspecifity of C. mongola-C. tamerlana. We also show that all studied females of the widely distributed haplogroup HP_II were infected with a single Wolbachia strain belonging to the supergroup B, while the males of this haplogroup, as well as all other investigated specimens of both sexes, were not infected. Our data highlight the relevance of large-scale sampling dataset analysis and the need for testing for Wolbachia infection to avoid erroneous phylogenetic reconstructions and species misidentification.
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Affiliation(s)
- Nazar A. Shapoval
- Department of Karyosystematics, Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab. 1, 199034 St. Petersburg, Russia
| | - Alexander V. Kir’yanov
- Photonics Department, Centro de Investigaciones en Optica, Lomas del Bosque 115, Leon 37150, Mexico;
| | - Anatoly V. Krupitsky
- Department of Entomology, Biological Faculty, Lomonosov Moscow State University, Leninskie Gory, GSP-1, korp. 12, 119991 Moscow, Russia;
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky Pr. 33, 119071 Moscow, Russia
| | - Roman V. Yakovlev
- Department of Ecology, Altai State University, Lenina Pr. 61, 656049 Barnaul, Russia;
- Institute of Biology, Tomsk State University, Lenina Pr. 36, 634050 Tomsk, Russia
| | - Anna E. Romanovich
- Resource Center for Development of Molecular and Cellular Technologies, St. Petersburg State University, Universitetskaya Nab., 7/9, 199034 St. Petersburg, Russia;
| | - Jing Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center, Harry Hines Blvd. 5323, Dallas, TX 75390-9050, USA; (J.Z.); (Q.C.); (N.V.G.)
- Department of Biochemistry, University of Texas Southwestern Medical Center, Harry Hines Blvd. 5323, Dallas, TX 75390-9050, USA
- Eugene McDermott Center For Human Growth & Development, University of Texas Southwestern Medical Center, Harry Hines Blvd. 5323, Dallas, TX 75390-9050, USA
| | - Qian Cong
- Department of Biophysics, University of Texas Southwestern Medical Center, Harry Hines Blvd. 5323, Dallas, TX 75390-9050, USA; (J.Z.); (Q.C.); (N.V.G.)
- Eugene McDermott Center For Human Growth & Development, University of Texas Southwestern Medical Center, Harry Hines Blvd. 5323, Dallas, TX 75390-9050, USA
| | - Nick V. Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Harry Hines Blvd. 5323, Dallas, TX 75390-9050, USA; (J.Z.); (Q.C.); (N.V.G.)
- Department of Biochemistry, University of Texas Southwestern Medical Center, Harry Hines Blvd. 5323, Dallas, TX 75390-9050, USA
| | - Margarita G. Kovalenko
- Research and Methodological Department of Entomology, All-Russian Plant Quarantine Center, Pogranichnaya 32, 140150 Bykovo, Russia;
| | - Galina N. Shapoval
- Department of Ecology, Altai State University, Lenina Pr. 61, 656049 Barnaul, Russia;
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Marino A, Reboud EL, Chevalier E, Tilak MK, Contreras-Garduño J, Nabholz B, Condamine FL. Genomics of the relict species Baronia brevicornis sheds light on its demographic history and genome size evolution across swallowtail butterflies. G3 (BETHESDA, MD.) 2023; 13:jkad239. [PMID: 37847748 PMCID: PMC10700114 DOI: 10.1093/g3journal/jkad239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 05/22/2023] [Accepted: 10/09/2023] [Indexed: 10/19/2023]
Abstract
Relict species, like coelacanth, gingko, tuatara, are the remnants of formerly more ecologically and taxonomically diverse lineages. It raises the questions of why they are currently species-poor, have restrained ecology, and are often vulnerable to extinction. Estimating heterozygosity level and demographic history can guide our understanding of the evolutionary history and conservation status of relict species. However, few studies have focused on relict invertebrates compared to vertebrates. We sequenced the genome of Baronia brevicornis (Lepidoptera: Papilionidae), which is an endangered species, the sister species of all swallowtail butterflies, and is the oldest lineage of all extant butterflies. From a dried specimen, we were able to generate both long-read and short-read data and assembled a genome of 406 Mb for Baronia. We found a fairly high level of heterozygosity (0.58%) compared to other swallowtail butterflies, which contrasts with its endangered and relict status. Taking into account the high ratio of recombination over mutation, demographic analyses indicated a sharp decline of the effective population size initiated in the last million years. Moreover, the Baronia genome was used to study genome size variation in Papilionidae. Genome sizes are mostly explained by transposable elements activities, suggesting that large genomes appear to be a derived feature in swallowtail butterflies as transposable elements activity is recent and involves different transposable elements classes among species. This first Baronia genome provides a resource for assisting conservation in a flagship and relict insect species as well as for understanding swallowtail genome evolution.
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Affiliation(s)
- Alba Marino
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Eliette L Reboud
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Emmanuelle Chevalier
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Marie-Ka Tilak
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Jorge Contreras-Garduño
- Universidad Nacional Autónoma de México, Escuela Nacional de Estudios Superiores, campus Morelia, Antigua Carretera a Pátzcuaro #8701, Col. Ex-Hacienda San José de la Huerta, 58190 Morelia, Michoacán, Mexico
| | - Benoit Nabholz
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
- Institut Universitaire de France (IUF), Paris, France
| | - Fabien L Condamine
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
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Chaturvedi S, Escalona M, Marimuthu MPA, Nguyen O, Chumchim N, Fairbairn CW, Seligmann W, Miller C, Bradley Shaffer H, Whiteman NK. A draft reference genome assembly of the Pipevine Swallowtail butterfly, Battus philenor hirsuta. J Hered 2023; 114:698-706. [PMID: 37428819 PMCID: PMC10650949 DOI: 10.1093/jhered/esad043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/08/2023] [Indexed: 07/12/2023] Open
Abstract
The California Pipevine Swallowtail Butterfly, Battus philenor hirsuta, and its host plant, the California Pipevine or Dutchman's Pipe, Aristolochia californica Torr., are an important California endemic species pair. While this species pair is an ideal system to study co-evolution, genomic resources for both are lacking. Here, we report a new, chromosome-level assembly of B. philenor hirsuta as part of the California Conservation Genomics Project (CCGP). Following the sequencing and assembly strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin proximity sequencing technology to produce a de novo assembled genome. Our genome assembly, the first for any species in the genus, contains 109 scaffolds spanning 443 mega base (Mb) pairs, with a contig N50 of 14.6 Mb, a scaffold N50 of 15.2 Mb, and BUSCO complete score of 98.9%. In combination with the forthcoming A. californica reference genome, the B. philenor hirsuta genome will be a powerful tool for documenting landscape genomic diversity and plant-insect co-evolution in a rapidly changing California landscape.
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Affiliation(s)
- Samridhi Chaturvedi
- Department of Integrative Biology, University of California, 142 Weill Hall #3200, Berkeley, CA 94720, United States
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, United States
| | - Merly Escalona
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States
| | - Noravit Chumchim
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States
| | - Colin W Fairbairn
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
| | - William Seligmann
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
| | - Courtney Miller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095-7239, United States
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095-7239, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095-7239, United States
| | - Noah K Whiteman
- Department of Integrative Biology, University of California, 142 Weill Hall #3200, Berkeley, CA 94720, United States
- Department of Molecular and Cell Biology, University of California, 142 Weill Hall #3200, Berkeley, CA 94720, United States
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6
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Li J, Han G, Tian X, Liang D, Zhang P. UPrimer: A Clade-Specific Primer Design Program Based on Nested-PCR Strategy and Its Applications in Amplicon Capture Phylogenomics. Mol Biol Evol 2023; 40:msad230. [PMID: 37832226 PMCID: PMC10630340 DOI: 10.1093/molbev/msad230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/12/2023] [Accepted: 10/09/2023] [Indexed: 10/15/2023] Open
Abstract
Amplicon capture is a promising target sequence capture approach for phylogenomic analyses, and the design of clade-specific nuclear protein-coding locus (NPCL) amplification primers is crucial for its successful application. In this study, we developed a primer design program called UPrimer that can quickly design clade-specific NPCL amplification primers based on genome data, without requiring manual intervention. Unlike other available primer design programs, UPrimer uses a nested-PCR strategy that greatly improves the amplification success rate of the designed primers. We examined all available metazoan genome data deposited in NCBI and developed NPCL primer sets for 21 metazoan groups with UPrimer, covering a wide range of taxa, including arthropods, mollusks, cnidarians, echinoderms, and vertebrates. On average, each clade-specific NPCL primer set comprises ∼1,000 NPCLs. PCR amplification tests were performed in 6 metazoan groups, and the developed primers showed a PCR success rate exceeding 95%. Furthermore, we demonstrated a phylogenetic case study in Lepidoptera, showing how NPCL primers can be used for phylogenomic analyses with amplicon capture. Our results indicated that using 100 NPCL probes recovered robust high-level phylogenetic relationships among butterflies, highlighting the utility of the newly designed NPCL primer sets for phylogenetic studies. We anticipate that the automated tool UPrimer and the developed NPCL primer sets for 21 metazoan groups will enable researchers to obtain phylogenomic data more efficiently and cost-effectively and accelerate the resolution of various parts of the Tree of Life.
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Affiliation(s)
- JiaXuan Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - GuangCheng Han
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xiao Tian
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Dan Liang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Peng Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
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San Jose M, Doorenweerd C, Geib S, Barr N, Dupuis JR, Leblanc L, Kauwe A, Morris KY, Rubinoff D. Interspecific gene flow obscures phylogenetic relationships in an important insect pest species complex. Mol Phylogenet Evol 2023; 188:107892. [PMID: 37524217 DOI: 10.1016/j.ympev.2023.107892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/07/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023]
Abstract
As genomic data proliferates, the prevalence of post-speciation gene flow is making species boundaries and relationships increasingly ambiguous. Although current approaches inferring fully bifurcating phylogenies based on concatenated datasets provide simple and robust answers to many species relationships, they may be inaccurate because the models ignore inter-specific gene flow and incomplete lineage sorting. To examine the potential error resulting from ignoring gene flow, we generated both a RAD-seq and a 500 protein-coding loci highly multiplexed amplicon (HiMAP) dataset for a monophyletic group of 12 species defined as the Bactrocera dorsalis sensu lato clade. With some of the world's worst agricultural pests, the taxonomy of the B. dorsalis s.l. clade is important for trade and quarantines. However, taxonomic confusion confounds resolution due to intra- and interspecific phenotypic variation and convergence, mitochondrial introgression across half of the species, and viable hybrids. We compared the topological convergence of our datasets using concatenated phylogenetic and various multispecies coalescent approaches, some of which account for gene flow. All analyses agreed on species delimitation, but there was incongruence between species relationships. Under concatenation, both datasets suggest identical species relationships with mostly high statistical support. However, multispecies coalescent and multispecies network approaches suggest markedly different hypotheses and detected significant gene flow. We suggest that the network approaches are likely more accurate because gene flow violates the assumptions of the concatenated phylogenetic analyses, but the data-reductive requirements of network approaches resulted in reduced statistical support and could not unambiguously resolve gene flow directions. Our study highlights the importance of testing for gene flow, particularly with phylogenomic datasets, even when concatenated approaches receive high statistical support.
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Affiliation(s)
- Michael San Jose
- University of Hawaii, College of Tropical Agriculture and Human Resources, Department of Plant and Environmental Protection Sciences, Entomology Section, 3050 Maile Way, Honolulu, HI, 96822-2231, USA.
| | - Camiel Doorenweerd
- University of Hawaii, College of Tropical Agriculture and Human Resources, Department of Plant and Environmental Protection Sciences, Entomology Section, 3050 Maile Way, Honolulu, HI, 96822-2231, USA
| | - Scott Geib
- Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye U.S. Pacific Basin Agricultural Center, USDA Agricultural Research Services, Hilo, HI, USA
| | - Norman Barr
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Plant Protection and Quarantine, Science & Technology, Insect Management and Molecular Diagnostics Laboratory, 22675 N. Moorefield Road, Edinburg, TX 78541, USA
| | - Julian R Dupuis
- University of Kentucky, Department of Entomology, S225 Ag Science Center North, 1100 South Limestone, Lexington, KY, 40546-0091, USA
| | - Luc Leblanc
- University of Idaho, Department of Entomology, Plant Pathology and Nematology, 875 Perimeter Drive, MS2329, Moscow, ID, 83844-2329, USA
| | - Angela Kauwe
- Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye U.S. Pacific Basin Agricultural Center, USDA Agricultural Research Services, Hilo, HI, USA
| | - Kimberley Y Morris
- University of Hawaii, College of Tropical Agriculture and Human Resources, Department of Plant and Environmental Protection Sciences, Entomology Section, 3050 Maile Way, Honolulu, HI, 96822-2231, USA; Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye U.S. Pacific Basin Agricultural Center, USDA Agricultural Research Services, Hilo, HI, USA
| | - Daniel Rubinoff
- University of Hawaii, College of Tropical Agriculture and Human Resources, Department of Plant and Environmental Protection Sciences, Entomology Section, 3050 Maile Way, Honolulu, HI, 96822-2231, USA
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Atencio GWG, Zanini R, Deprá M, Romanowski HP. Preliminary population studies of the grassland swallowtail butterfly Euryades corethrus (Lepidoptera, Papilionidae). AN ACAD BRAS CIENC 2023; 95:e20210503. [PMID: 37341269 DOI: 10.1590/0001-3765202320210503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/10/2021] [Indexed: 06/22/2023] Open
Abstract
Euryades corethrus is a Troidini butterfly (Papilionidae, Papilioninae), endemic to grasslands in southern Brazil, Uruguay, Argentina and Paraguay. Formerly abundant, nowadays it is in the Red list of endangered species for those areas. During its larval stage, it feeds on Aristolochia spp, commonly found in southern grasslands. These native grassland areas are diminishing, being converted to crops and pastures, causing habitat loss for Aristolochia and E. corethrus. This study aimed to assess the genetic diversity, population structure and demographic history of E. corethrus. We sampled eight populations from Rio Grande do Sul, Brazil and based on Cytochrome Oxidase subunit I (COI) molecular marker, our results suggest a low genetic variability between populations, presence of gene flow and, consequently, lack of population structure. A single maternally inherited-genetic marker is insufficient for population-level decisions, but barcoding is a useful tool during early stages of population investigation, bringing out genomic diversity patterns within the target species. Those populations likely faced a bottleneck followed by a rapid expansion during the last glaciation and subsequent stabilization in effective population size. Habitat loss is a threat, which might cause isolation, loss of genetic variability and, ultimately, extinction of E. corethrus if no habitat conservation policy is adopted.
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Affiliation(s)
- Guilherme Wagner G Atencio
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43433, Sala 214, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Zoologia, Laboratório de Ecologia de Insetos, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43435, Sala 218, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Universidade de Lisboa, Faculdade de Ciências, Centro de Ecologia, Evolução e Alterações Ambientais, Edifício C2, 5.º piso, Sala 2.5.46, Código Postal 1749-016, Campo Grande, Lisboa, Portugal
| | - Rebeca Zanini
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Drosophila, Av. Bento Gonçalves, 9500, Prédio 43323, Sala 210, Agronomia, 90650-001 Porto Alegre, RS, Brazil
- Universidade Nova de Lisboa, Faculdade de Ciências Médicas, Laboratório de Biomedicina Integrativa, Rua do Instituto Bacteriológico 5, Código Postal 1169-056, Lisboa, Portugal
| | - Maríndia Deprá
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43433, Sala 214, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Drosophila, Av. Bento Gonçalves, 9500, Prédio 43323, Sala 210, Agronomia, 90650-001 Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Prédio 43312 M, Caixa Postal 15053, Agronomia, 90650-001 Porto Alegre, RS, Brazil
| | - Helena P Romanowski
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43433, Sala 214, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Zoologia, Laboratório de Ecologia de Insetos, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43435, Sala 218, Agronomia, 91501-970 Porto Alegre, RS, Brazil
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9
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Kawahara AY, Storer C, Carvalho APS, Plotkin DM, Condamine FL, Braga MP, Ellis EA, St Laurent RA, Li X, Barve V, Cai L, Earl C, Frandsen PB, Owens HL, Valencia-Montoya WA, Aduse-Poku K, Toussaint EFA, Dexter KM, Doleck T, Markee A, Messcher R, Nguyen YL, Badon JAT, Benítez HA, Braby MF, Buenavente PAC, Chan WP, Collins SC, Rabideau Childers RA, Dankowicz E, Eastwood R, Fric ZF, Gott RJ, Hall JPW, Hallwachs W, Hardy NB, Sipe RLH, Heath A, Hinolan JD, Homziak NT, Hsu YF, Inayoshi Y, Itliong MGA, Janzen DH, Kitching IJ, Kunte K, Lamas G, Landis MJ, Larsen EA, Larsen TB, Leong JV, Lukhtanov V, Maier CA, Martinez JI, Martins DJ, Maruyama K, Maunsell SC, Mega NO, Monastyrskii A, Morais ABB, Müller CJ, Naive MAK, Nielsen G, Padrón PS, Peggie D, Romanowski HP, Sáfián S, Saito M, Schröder S, Shirey V, Soltis D, Soltis P, Sourakov A, Talavera G, Vila R, Vlasanek P, Wang H, Warren AD, Willmott KR, Yago M, Jetz W, Jarzyna MA, Breinholt JW, Espeland M, Ries L, Guralnick RP, Pierce NE, Lohman DJ. A global phylogeny of butterflies reveals their evolutionary history, ancestral hosts and biogeographic origins. Nat Ecol Evol 2023; 7:903-913. [PMID: 37188966 PMCID: PMC10250192 DOI: 10.1038/s41559-023-02041-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 03/16/2023] [Indexed: 05/17/2023]
Abstract
Butterflies are a diverse and charismatic insect group that are thought to have evolved with plants and dispersed throughout the world in response to key geological events. However, these hypotheses have not been extensively tested because a comprehensive phylogenetic framework and datasets for butterfly larval hosts and global distributions are lacking. We sequenced 391 genes from nearly 2,300 butterfly species, sampled from 90 countries and 28 specimen collections, to reconstruct a new phylogenomic tree of butterflies representing 92% of all genera. Our phylogeny has strong support for nearly all nodes and demonstrates that at least 36 butterfly tribes require reclassification. Divergence time analyses imply an origin ~100 million years ago for butterflies and indicate that all but one family were present before the K/Pg extinction event. We aggregated larval host datasets and global distribution records and found that butterflies are likely to have first fed on Fabaceae and originated in what is now the Americas. Soon after the Cretaceous Thermal Maximum, butterflies crossed Beringia and diversified in the Palaeotropics. Our results also reveal that most butterfly species are specialists that feed on only one larval host plant family. However, generalist butterflies that consume two or more plant families usually feed on closely related plants.
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Affiliation(s)
- Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
- Entomology and Nematology Department, University of Florida, Gainesville, FL, USA.
- Department of Biology, University of Florida, Gainesville, FL, USA.
| | - Caroline Storer
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Ana Paula S Carvalho
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - David M Plotkin
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, USA
| | - Fabien L Condamine
- CNRS, Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier), Montpellier, France
| | - Mariana P Braga
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Emily A Ellis
- McGuire Center for Lepidoptera and Biodiversity, 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, University of Florida, Gainesville, FL, USA
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Xuankun Li
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Center for Biodiversity Research, Department of Biological Sciences, University of Memphis, Memphis, TN, USA
| | - Vijay Barve
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Liming Cai
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Chandra Earl
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Hannah L Owens
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- 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
| | - Wendy A Valencia-Montoya
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Kwaku Aduse-Poku
- Biology Department, City College of New York, City University of New York, New York, NY, USA
- Department of Life and Earth Sciences, Perimeter College, Georgia State University, Decatur, GA, USA
| | - Emmanuel F A Toussaint
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Entomology, Natural History Museum of Geneva, Geneva, Switzerland
| | - Kelly M Dexter
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Tenzing Doleck
- Biology Department, City College of New York, City University of New York, New York, NY, USA
- PhD Program in Biology, Graduate Center, City University of New York, New York, NY, USA
| | - Amanda Markee
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Rebeccah Messcher
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Y-Lan Nguyen
- Biology Department, City College of New York, City University of New York, New York, NY, USA
| | - Jade Aster T Badon
- Animal Biology Division, Institute of Biological Sciences, University of the Philippines Los Baños, Laguna, Philippines
| | - Hugo A Benítez
- Laboratorio de Ecología y Morfometría Evolutiva, Centro de Investigación de Estudios Avanzados del Maule, Universidad Católica del Maule, Talca, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
| | - Michael F Braby
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
- Australian National Insect Collection, Canberra, Australian Capital Territory, Australia
| | | | - Wei-Ping Chan
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | | | - Richard A Rabideau Childers
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Even Dankowicz
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Rod Eastwood
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Zdenek F Fric
- Biology Centre CAS, České Budějovice, Czech Republic
| | - Riley J Gott
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, USA
| | - Jason P W Hall
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Winnie Hallwachs
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Nate B Hardy
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Rachel L Hawkins Sipe
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Alan Heath
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Iziko South African Museum, Cape Town, South Africa
| | - Jomar D Hinolan
- Botany and National Herbarium Division, National Museum of the Philippines, Manila, Philippines
| | - Nicholas T Homziak
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, USA
| | - Yu-Feng Hsu
- College of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | | | - Micael G A Itliong
- Biology Department, City College of New York, City University of New York, New York, NY, USA
| | - Daniel H Janzen
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Krushnamegh Kunte
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | - Gerardo Lamas
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Michael J Landis
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Elise A Larsen
- Department of Biology, Georgetown University, Washington, DC, USA
| | | | - Jing V Leong
- Biology Department, City College of New York, City University of New York, New York, NY, USA
- Biology Centre CAS, České Budějovice, Czech Republic
- Faculty of Science, Department of Zoology, University of South Bohemia, České Budějovice, Czech Republic
| | - Vladimir Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, St. Petersburg, Russia
| | - Crystal A Maier
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Jose I Martinez
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, USA
| | - Dino J Martins
- Turkana Basin Institute, Stony Brook University, Stony Brook, NY, USA
| | | | - Sarah C Maunsell
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Nicolás Oliveira Mega
- Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Alexander Monastyrskii
- Vietnam Programme, Fauna & Flora International, Hanoi, Vietnam
- Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ana B B Morais
- Centro de Ciências Naturais e Exatas, Pós-Graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, Brazil
| | | | - Mark Arcebal K Naive
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- University of Chinese Academy of Sciences, Beijing, China
- College of Arts and Sciences, Jose Rizal Memorial State University, Tampilisan, Philippines
| | | | - Pablo Sebastián Padrón
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Entomology Laboratory, Museo de Zoología, Universidad del Azuay, Cuenca, Ecuador
| | - Djunijanti Peggie
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong-Bogor, Indonesia
| | | | - Szabolcs Sáfián
- Institute of Silviculture and Forest Protection, University of West Hungary, Sopron, Hungary
| | - Motoki Saito
- The Research Institute of Evolutionary Biology (Insect Study Division), Setagaya, Japan
| | | | - Vaughn Shirey
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Doug Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Pamela Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Andrei Sourakov
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Gerard Talavera
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Univ. Pompeu Fabra), Barcelona, Spain
| | - Petr Vlasanek
- T.G. Masaryk Water Research Institute, Prague, Czech Republic
| | - Houshuai Wang
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Andrew D Warren
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Keith R Willmott
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Masaya Yago
- The University Museum, The University of Tokyo, Tokyo, Japan
| | - Walter Jetz
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Center for Biodiversity and Global Change, Yale University, New Haven, CT, USA
| | - Marta A Jarzyna
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH, USA
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Jesse W Breinholt
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- RAPiD Genomics, Gainesville, FL, USA
| | - Marianne Espeland
- Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Leslie Ries
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Robert P Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA.
| | - David J Lohman
- Biology Department, City College of New York, 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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10
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Pan Z, Ding Y, Zhang S, Li L, Ma F. Chromosome-Level Genome Assembly of Papilio elwesi Leech, 1889 (Lepidoptera: Papilionidae). INSECTS 2023; 14:304. [PMID: 36975989 PMCID: PMC10058580 DOI: 10.3390/insects14030304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
A rarely seen butterfly species, the large swallowtail butterfly Papilio elwesi Leech, 1889 (Lepidoptera: Papilionidae), endemic to the Chinese mainland, has been declared a state-protected animal in China since 2000, but its genome is not yet available. To obtain high-quality genome assembly and annotation, we sequenced the genome and transcriptome of P. elwesi using the PacBio and PromethION platforms, respectively. The final assembled genome was 358.51 Mb, of which 97.59% was anchored to chromosomes (30 autosomes and 1 Z sex chromosome), with a contig/scaffold N50 length of 6.79/12.32 Mb and 99.0% (n = 1367) BUSCO completeness. The genome annotation pointed to 36.82% (131.99 Mb) repetitive elements and 1296 non-coding RNAs in the genome, along with 13,681 protein-coding genes that cover 98.6% (1348) of the BUSCO genes. Among the 11,499 identified gene families, 104 underwent significantly rapid expansions or contractions, and these rapidly expanding families play roles in detoxification and metabolism. Additionally, strong synteny exists between the chromosomes of P. elwesi and P. machaon. The chromosome-level genome of P. elwesi could serve as an important genomic resource for furthering our understanding of butterfly evolution and for more in-depth genomic analyses.
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Affiliation(s)
- Zhixiang Pan
- School of Life Sciences, Taizhou University, Taizhou 318000, China
| | - Yinhuan Ding
- Department of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, China
| | - Shusheng Zhang
- The Management Center of Wuyanling National Natural Reserve in Zhejiang, Wenzhou 325500, China
| | - Luxian Li
- Zhejiang Environment Technology Company Limited, Hangzhou 311100, China
| | - Fangzhou Ma
- Nanjing Institute of Environmental Sciences under Ministry of Ecology and Environment, Nanjing 210042, China
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11
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A comprehensive phylogeny and revised taxonomy illuminate the origin and diversification of the global radiation of Papilio (Lepidoptera: Papilionidae). Mol Phylogenet Evol 2023; 183:107758. [PMID: 36907224 DOI: 10.1016/j.ympev.2023.107758] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/28/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023]
Abstract
The swallowtail genus Papilio (Lepidoptera: Papilionidae) is species rich, distributed worldwide, and has broad morphological habits and ecological niches. Because of its elevated species richness, it has been historically difficult to reconstruct a densely sampled phylogeny for this clade. Here we provide a taxonomic working list for the genus, resulting in 235 Papilio species, and assemble a molecular dataset of seven gene fragments representing ca. 80% of the currently described diversity. Phylogenetic analyses reconstructed a robust tree with highly supported relationships within subgenera, although a few nodes in the early history of the Old World Papilio remain unresolved. Contrasting with previous results, we found that Papilio alexanor is sister to all Old World Papilio and that the subgenus Eleppone is no longer monotypic. The latter includes the recently described Fijian Papilio natewa with the Australian Papilio anactus and is sister to subgenus Araminta (formerly included in subgenus Menelaides) occurring in Southeast Asia. Our phylogeny also includes rarely studied (P. antimachus, P. benguetana) or endangered species (P. buddha, P. chikae). Taxonomic changes resulting from this study are elucidated. Molecular dating and biogeographic analyses indicate that Papilio originated ca. 30 million years ago (Oligocene), in a northern region centered on Beringia. A rapid early Miocene radiation in the Paleotropics is revealed within Old World Papilio, potentially explaining their low early branch support. Most subgenera originated in the early to middle Miocene followed by synchronous southward biogeographic dispersals and repeated local extirpations in northern latitudes. This study provides a comprehensive phylogenetic framework for Papilio with clarification of subgeneric systematics and species taxonomic changes enumerated, which will facilitate further studies to address questions on their ecology and evolutionary biology using this model clade.
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12
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Spatio-Temporal Evolutionary Patterns of the Pieridae Butterflies (Lepidoptera: Papilionoidea) Inferred from Mitogenomic Data. Genes (Basel) 2022; 14:genes14010072. [PMID: 36672814 PMCID: PMC9858963 DOI: 10.3390/genes14010072] [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: 11/23/2022] [Revised: 12/17/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Pieridae is one of the largest and almost cosmopolitan groups of butterflies, which plays an important role in natural ecosystems; however, to date, its phylogeny and evolutionary history have not been fully resolved. In this study, we obtained the complete or nearly complete mitochondrial genomes of 100 pierid taxa (six newly sequenced, sixty extracted from the whole-genome data, and thirty-four directly available from GenBank). At the same time, for the first time, we conducted comparative mitogenomic and phylogenetic analyses based on these mitogenomic data, to further clarify their spatio-temporal evolutionary patterns. Comparative mitogenomic analysis showed that, except for cox2, the GC content of each of the 13 protein-coding genes (PCGs) in the rapidly diverging subfamily Pierinae was higher than in its sister group Coliadinae. Moreover, the dN/dS values of nine genes (atp6, atp8, cox1, cox3, cob, nad1, nad3, nad5, and nad6) in Pierinae were also relatively higher than those in its sister group, Coliadinae. Phylogenetic analysis showed that all the resultant phylogenetic trees were generally in agreement with those of previous studies. The Pierinae family contained six clades in total with the relationship of (Leptosiaini + (((Nepheroniini + Arthocharidini) + Teracolini) + (Pierini + Elodini))). The Pieridae originated in the Palearctic region approximately 72.3 million years ago in the late Cretaceous, and the subfamily Pierinae diverged from this family around 57.9 million years ago in the Oriental region, shortly after the K-Pg mass extinction event; in addition, the spatio-temporal evolutionary patterns of Pierinae were closely correlated with geological events and environmental changes, as well as the host plant coevolutionary scenario in Earth's history. However, some incongruencies were observed between our results and those of previous studies in terms of shallow phylogenies for a few taxa, and should be further investigated.
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13
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Costa FP, Schrago CG, Mello B. Assessing the relative performance of fast molecular dating methods for phylogenomic data. BMC Genomics 2022; 23:798. [PMID: 36460948 PMCID: PMC9719170 DOI: 10.1186/s12864-022-09030-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/21/2022] [Indexed: 12/05/2022] Open
Abstract
Advances in genome sequencing techniques produced a significant growth of phylogenomic datasets. This massive amount of data represents a computational challenge for molecular dating with Bayesian approaches. Rapid molecular dating methods have been proposed over the last few decades to overcome these issues. However, a comparative evaluation of their relative performance on empirical data sets is lacking. We analyzed 23 empirical phylogenomic datasets to investigate the performance of two commonly employed fast dating methodologies: penalized likelihood (PL), implemented in treePL, and the relative rate framework (RRF), implemented in RelTime. They were compared to Bayesian analyses using the closest possible substitution models and calibration settings. We found that RRF was computationally faster and generally provided node age estimates statistically equivalent to Bayesian divergence times. PL time estimates consistently exhibited low levels of uncertainty. Overall, to approximate Bayesian approaches, RelTime is an efficient method with significantly lower computational demand, being more than 100 times faster than treePL. Thus, to alleviate the computational burden of Bayesian divergence time inference in the era of massive genomic data, molecular dating can be facilitated using the RRF, allowing evolutionary hypotheses to be tested more quickly and efficiently.
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Affiliation(s)
- Fernanda P. Costa
- grid.8536.80000 0001 2294 473XDepartment of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-617 Brazil
| | - Carlos G. Schrago
- grid.8536.80000 0001 2294 473XDepartment of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-617 Brazil
| | - Beatriz Mello
- grid.8536.80000 0001 2294 473XDepartment of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-617 Brazil
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14
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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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15
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Zhang C, Mirarab S. Weighting by Gene Tree Uncertainty Improves Accuracy of Quartet-based Species Trees. Mol Biol Evol 2022; 39:6750035. [PMID: 36201617 PMCID: PMC9750496 DOI: 10.1093/molbev/msac215] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 09/20/2022] [Accepted: 10/03/2022] [Indexed: 01/07/2023] Open
Abstract
Phylogenomic analyses routinely estimate species trees using methods that account for gene tree discordance. However, the most scalable species tree inference methods, which summarize independently inferred gene trees to obtain a species tree, are sensitive to hard-to-avoid errors introduced in the gene tree estimation step. This dilemma has created much debate on the merits of concatenation versus summary methods and practical obstacles to using summary methods more widely and to the exclusion of concatenation. The most successful attempt at making summary methods resilient to noisy gene trees has been contracting low support branches from the gene trees. Unfortunately, this approach requires arbitrary thresholds and poses new challenges. Here, we introduce threshold-free weighting schemes for the quartet-based species tree inference, the metric used in the popular method ASTRAL. By reducing the impact of quartets with low support or long terminal branches (or both), weighting provides stronger theoretical guarantees and better empirical performance than the unweighted ASTRAL. Our simulations show that weighting improves accuracy across many conditions and reduces the gap with concatenation in conditions with low gene tree discordance and high noise. On empirical data, weighting improves congruence with concatenation and increases support. Together, our results show that weighting, enabled by a new optimization algorithm we introduce, improves the utility of summary methods and can reduce the incongruence often observed across analytical pipelines.
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Affiliation(s)
- Chao Zhang
- Bioinformatics and Systems Biology, UC San Diego, La Jolla, CA, USA
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16
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Gamboa S, Condamine FL, Cantalapiedra JL, Varela S, Pelegrín JS, Menéndez I, Blanco F, Hernández Fernández M. A phylogenetic study to assess the link between biome specialization and diversification in swallowtail butterflies. GLOBAL CHANGE BIOLOGY 2022; 28:5901-5913. [PMID: 35838418 PMCID: PMC9543414 DOI: 10.1111/gcb.16344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
The resource-use hypothesis, proposed by E.S. Vrba, states that habitat fragmentation caused by climatic oscillations would affect particularly biome specialists (species inhabiting only one biome), which might show higher speciation and extinction rates than biome generalists. If true, lineages would accumulate biome-specialist species. This effect would be particularly exacerbated for biomes located at the periphery of the global climatic conditions, namely, biomes that have high/low precipitation and high/low temperature such as rainforest (warm-humid), desert (warm-dry), steppe (cold-dry) and tundra (cold-humid). Here, we test these hypotheses in swallowtail butterflies, a clade with more than 570 species, covering all the continents but Antarctica, and all climatic conditions. Swallowtail butterflies are among the most studied insects, and they are a model group for evolutionary biology and ecology studies. Continental macroecological rules are normally tested using vertebrates, this means that there are fewer examples exploring terrestrial invertebrate patterns at global scale. Here, we compiled a large Geographic Information System database on swallowtail butterflies' distribution maps and used the most complete time-calibrated phylogeny to quantify diversification rates (DRs). In this paper, we aim to answer the following questions: (1) Are there more biome-specialist swallowtail butterflies than biome generalists? (2) Is DR related to biome specialization? (3) If so, do swallowtail butterflies inhabiting extreme biomes show higher DRs? (4) What is the effect of species distribution area? Our results showed that swallowtail family presents a great number of biome specialists which showed substantially higher DRs compared to generalists. We also found that biome specialists are unevenly distributed across biomes. Overall, our results are consistent with the resource-use hypothesis, species climatic niche and biome fragmentation as key factors promoting isolation.
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Affiliation(s)
- Sara Gamboa
- Centro de Investigación Mariña (CIM)Universidade de Vigo, Grupo de Ecoloxía Animal (GEA), MAPAS LabVigoPontevedraSpain
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias GeológicasUniversidad Complutense de MadridMadridSpain
- Departamento de Cambio MedioambientalInstituto de Geociencias (UCM, CSIC)MadridSpain
- CNRSUMR 5554 Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier)MontpellierFrance
| | - Fabien L. Condamine
- CNRSUMR 5554 Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier)MontpellierFrance
| | - Juan L. Cantalapiedra
- Departamento de Ciencias de la Vida, Edificio de Ciencias Campus Científico‐TecnológicoUniversidad de AlcaláAlcalá de HenaresSpain
| | - Sara Varela
- Centro de Investigación Mariña (CIM)Universidade de Vigo, Grupo de Ecoloxía Animal (GEA), MAPAS LabVigoPontevedraSpain
| | - Jonathan S. Pelegrín
- Área de Biología y Ciencias Ambientales Facultades de Ciencias Básicas y EducaciónUniversidad Santiago de CaliSantiago de CaliValle del CaucaColombia
- Departamento de Biología, Facultad de Ciencias Naturales y ExactasUniversidad del Valle, Campus MeléndezSantiago de CaliValle del CaucaColombia
| | - Iris Menéndez
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias GeológicasUniversidad Complutense de MadridMadridSpain
- Departamento de Cambio MedioambientalInstituto de Geociencias (UCM, CSIC)MadridSpain
| | - Fernando Blanco
- Museum für Naturkunde, Leibniz‐Institut für Evolutions und BiodiversitätsforschungBerlinGermany
| | - Manuel Hernández Fernández
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias GeológicasUniversidad Complutense de MadridMadridSpain
- Departamento de Cambio MedioambientalInstituto de Geociencias (UCM, CSIC)MadridSpain
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17
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Zheng X, Zhang R, Yue B, Wu Y, Yang N, Zhou C. Enhanced Resolution of Evolution and Phylogeny of the Moths Inferred from Nineteen Mitochondrial Genomes. Genes (Basel) 2022; 13:genes13091634. [PMID: 36140802 PMCID: PMC9498458 DOI: 10.3390/genes13091634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 11/21/2022] Open
Abstract
The vast majority (approximately 90%) of Lepidoptera species belong to moths whose phylogeny has been widely discussed and highly controversial. For the further understanding of phylogenetic relationships of moths, nineteen nearly complete mitochondrial genomes (mitogenomes) of moths involved in six major lineages were sequenced and characterized. These mitogenomes ranged from 15,177 bp (Cyclidia fractifasciata) to 15,749 bp (Ophthalmitis albosignaria) in length, comprising of the core 37 mitochondrial genes (13 protein-coding genes (PCGs) + 22 tRNAs + two rRNAs) and an incomplete control region. The order and orientation of genes showed the same pattern and the gene order of trnM-trnI-trnQ showed a typical rearrangement of Lepidoptera compared with the ancestral order of trnI-trnQ-trnM. Among these 13 PCGs, ATP8 exhibited the fastest evolutionary rate, and Drepanidae showed the highest average evolutionary rate among six families involved in 66 species. The phylogenetic analyses based on the dataset of 13 PCGs suggested the relationship of (Notodontidae + (Noctuidae + Erebidae)) + (Geometridae + (Sphingidae + Drepanidae)), which suggested a slightly different pattern from previous studies. Most groups were well defined in the subfamily level except Erebidae, which was not fully consistent across bayesian and maximum likelihood methods. Several formerly unassigned tribes of Geometridae were suggested based on mitogenome sequences despite a not very strong support in partial nodes. The study of mitogenomes of these moths can provide fundamental information of mitogenome architecture, and the phylogenetic position of moths, and contributes to further phylogeographical studies and the biological control of pests.
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Affiliation(s)
- Xiaofeng Zheng
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Rusong Zhang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Bisong Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Yongjie Wu
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Nan Yang
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu 610064, China
- Collaborative Innovation Center for Ecological Animal Husbandry of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu 610064, China
- Correspondence: (N.Y.); (C.Z.)
| | - Chuang Zhou
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
- Correspondence: (N.Y.); (C.Z.)
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18
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Mackintosh A, Laetsch DR, Baril T, Ebdon S, Jay P, Vila R, Hayward A, Lohse K. The genome sequence of the scarce swallowtail, Iphiclides podalirius. G3 GENES|GENOMES|GENETICS 2022; 12:6656352. [PMID: 35929795 PMCID: PMC9434224 DOI: 10.1093/g3journal/jkac193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/20/2022] [Indexed: 12/04/2022]
Abstract
The scarce swallowtail, Iphiclides podalirius (Linnaeus, 1758), is a species of butterfly in the family Papilionidae. Here, we present a chromosome-level genome assembly for Iphiclides podalirius as well as gene and transposable element annotations. We investigate how the density of genomic features differs between the 30 Iphiclides podalirius chromosomes. We find that shorter chromosomes have higher heterozygosity at four-fold-degenerate sites and a greater density of transposable elements. While the first result is an expected consequence of differences in recombination rate, the second suggests a counter-intuitive relationship between recombination and transposable element evolution. This high-quality genome assembly, the first for any species in the tribe Leptocircini, will be a valuable resource for population genomics in the genus Iphiclides and comparative genomics more generally.
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Affiliation(s)
- Alexander Mackintosh
- Institute of Ecology and Evolution, University of Edinburgh , Edinburgh EH9 3FL, UK
| | - Dominik R Laetsch
- Institute of Ecology and Evolution, University of Edinburgh , Edinburgh EH9 3FL, UK
| | - Tobias Baril
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus , Cornwall TR10 9FE, UK
| | - Sam Ebdon
- Institute of Ecology and Evolution, University of Edinburgh , Edinburgh EH9 3FL, UK
| | - Paul Jay
- Ecologie Systématique Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay , 91400 Orsay, France
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC—Universitat Pompeu Fabra) , Barcelona 08003, Spain
| | - Alex Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus , Cornwall TR10 9FE, UK
| | - Konrad Lohse
- Institute of Ecology and Evolution, University of Edinburgh , Edinburgh EH9 3FL, UK
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19
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Li J, Liang D, Zhang P. Simultaneously collecting coding and non-coding phylogenomic data using homemade full-length cDNA probes, tested by resolving the high-level relationships of Colubridae. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.969581] [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] Open
Abstract
Resolving intractable phylogenetic relationships often requires simultaneously analyzing a large number of coding and non-coding orthologous loci. To gather both coding and non-coding data, traditional sequence capture methods require custom-designed commercial probes. Here, we present a cost-effective sequence capture method based on homemade probes, to capture thousands of coding and non-coding orthologous loci simultaneously, suitable for all organisms. This approach, called “FLc-Capture,” synthesizes biotinylated full-length cDNAs from mRNA as capture probes, eliminates the need for costly commercial probe design and synthesis. To demonstrate the utility of FLc-Capture, we prepared full-length cDNA probes from mRNA extracted from a common colubrid snake. We performed capture experiments with these homemade cDNA probes and successfully obtained thousands of coding and non-coding genomic loci from 24 Colubridae species and 12 distantly related snake species of other families. The average capture specificity of FLc-Capture across all tested snake species is 35%, similar to the previously published EecSeq method. We constructed two phylogenomic data sets, one including 1,075 coding loci (∼817,000 bp) and the other including 1,948 non-coding loci (∼1,114,000 bp), to study the phylogeny of Colubridae. Both data sets yielded highly similar and well-resolved trees, with 85% of nodes having >95% bootstrap support. Our experimental tests show that FLc-Capture is a flexible, fast, and cost-effective sequence capture approach for simultaneously gathering coding and non-coding phylogenomic data sets to study intractable phylogenetic questions. We hope that this method will serve as a new data collection tool for evolutionary biologists working in the era of phylogenomics.
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20
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Hui-Yun T, Chiba H, Lohman DJ, Yen SH, Aduse-Poku K, Ohshima Y, Wu LW. Out of Asia: Intercontinental dispersals after the Eocene-Oligocene transition shaped the zoogeography of Limenitidinae butterflies (Lepidoptera: Nymphalidae). Mol Phylogenet Evol 2022; 170:107444. [DOI: 10.1016/j.ympev.2022.107444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/15/2022] [Accepted: 02/15/2022] [Indexed: 11/29/2022]
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21
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Wang Y, Yuan H, Huang J, Li C. Inline index helped in cleaning up data contamination generated during library preparation and the subsequent steps. Mol Biol Rep 2021; 49:385-392. [PMID: 34716505 DOI: 10.1007/s11033-021-06884-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 09/23/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND High-throughput sequencing involves library preparation and amplification steps, which may induce contamination across samples or between samples and the environment. METHODS We tested the effect of applying an inline-index strategy, in which DNA indices of 6 bp were added to both ends of the inserts at the ligation step of library prep for resolving the data contamination problem. RESULTS Our results showed that the contamination ranged from 0.29 to 1.25% in one experiment and from 0.83 to 27.01% in the other. We also found that contamination could be environmental or from reagents besides cross-contamination between samples. CONCLUSIONS Inline-index method is a useful experimental design to clean up the data and address the contamination problem which has been plaguing high-throughput sequencing data in many applications.
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Affiliation(s)
- Ying Wang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, 201306, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China
| | - Hao Yuan
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, 201306, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China
| | - Junman Huang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, 201306, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China
| | - Chenhong Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, 201306, China. .,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China.
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22
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Sharma S, Kumar S. Fast and accurate bootstrap confidence limits on genome-scale phylogenies using little bootstraps. NATURE COMPUTATIONAL SCIENCE 2021; 1:573-577. [PMID: 34734192 PMCID: PMC8560003 DOI: 10.1038/s43588-021-00129-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 08/13/2021] [Indexed: 12/30/2022]
Abstract
Felsenstein's bootstrap approach is widely used to assess confidence in species relationships inferred from multiple sequence alignments. It resamples sites randomly with replacement to build alignment replicates of the same size as the original alignment and infers a phylogeny from each replicate dataset. The proportion of phylogenies recovering the same grouping of species is its bootstrap confidence limit. But, standard bootstrap imposes a high computational burden in applications involving long sequence alignments. Here, we introduce the bag of little bootstraps approach to phylogenetics, bootstrapping only a few little samples, each containing a small subset of sites. We report that the median bagging of bootstrap confidence limits from little samples produces confidence in inferred species relationships similar to standard bootstrap but in a fraction of computational time and memory. Therefore, the little bootstraps approach can potentially enhance the rigor, efficiency, and parallelization of big data phylogenomic analyses.
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Affiliation(s)
- Sudip Sharma
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
- Department of Biology, Temple University, Philadelphia, PA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
- Department of Biology, Temple University, Philadelphia, PA
- Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
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23
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Podsiadlowski L, Tunström K, Espeland M, Wheat CW. The genome assembly and annotation of the Apollo butterfly Parnassius apollo, a flagship species for conservation biology. Genome Biol Evol 2021; 13:6296838. [PMID: 34115121 PMCID: PMC8536933 DOI: 10.1093/gbe/evab122] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Conservation genomics has made dramatic improvements over the past decade, leveraging the power of genomes to infer diverse parameters central to conservation management questions. However, much of this effort has focused upon vertebrate species, despite insects providing similar flagship status with the added benefit of smaller genomes, shorter generation times and extensive historical collections in museums. Here we present the genome of the Apollo butterfly (Parnassius apollo, Papilionidae), an iconic endangered butterfly, which like many species in this genus, needs conservation genomic attention yet lacks a genome. Using 68.7 Gb of long-read data (N50 = 15.2 kb) we assembled a 1.4 Gb genome for the Apollo butterfly, making this the largest sequenced Lepidopteran genome to date. The assembly was highly contiguous (N50 = 7.1 Mb) and complete (97% of Lepidopteran BUSCOs were single-copy and complete) and consisted of 1,707 contigs. Using RNAseq data and Arthropoda proteins, we annotated 28.3K genes. Alignment with the closest-related chromosome-level assembly, Papilio bianor, reveals a highly conserved chromosomal organization, albeit genome size is highly expanded in the Apollo butterfly, due primarily to a dramatic increase in repetitive element content. Using this alignment for superscaffolding places the P. apollo genome in to 31 chromosomal scaffolds, and together with our functional annotation, provides an essential resource for advancing conservation genomics in a flagship species for insect conservation.
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Affiliation(s)
| | - Kalle Tunström
- Department of Zoology, Stockholm University, Stockholm, Sweden
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24
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Ellis EA, Storer CG, Kawahara AY. De novo genome assemblies of butterflies. Gigascience 2021; 10:6291117. [PMID: 34076242 PMCID: PMC8170690 DOI: 10.1093/gigascience/giab041] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 07/22/2020] [Accepted: 05/05/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The availability of thousands of genomes has enabled new advancements in biology. However, many genomes have not been investigated for their quality. Here we examine quality trends in a taxonomically diverse and well-known group, butterflies (Papilionoidea), and provide draft, de novo assemblies for all available butterfly genomes. Owing to massive genome sequencing investment and taxonomic curation, this is an excellent group to explore genome quality. FINDINGS We provide de novo assemblies for all 822 available butterfly genomes and interpret their quality in terms of completeness and continuity. We identify the 50 highest quality genomes across butterflies and conclude that the ringlet, Aphantopus hyperantus, has the highest quality genome. Our post-processing of draft genome assemblies identified 118 butterfly genomes that should not be reused owing to contamination or extremely low quality. However, many draft genomes are of high utility, especially because permissibility of low-quality genomes is dependent on the objective of the study. Our assemblies will serve as a key resource for papilionid genomics, especially for researchers without computational resources. CONCLUSIONS Quality metrics and assemblies are typically presented with annotated genome accessions but rarely with de novo genomes. We recommend that studies presenting genome sequences provide the assembly and some metrics of quality because quality will significantly affect downstream results. Transparency in quality metrics is needed to improve the field of genome science and encourage data reuse.
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Affiliation(s)
- Emily A Ellis
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, 3215 Hull Road, Gainesville, FL 32611-2710, USA
| | - Caroline G Storer
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, 3215 Hull Road, Gainesville, FL 32611-2710, USA
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, 3215 Hull Road, Gainesville, FL 32611-2710, USA
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25
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Jeng ML, Chen MY, Wu LW. Two complete mitochondrial genomes of Papilio butterflies obtained from historical specimens (Lepidoptera: Papilionidae). Mitochondrial DNA B Resour 2021; 6:1341-1343. [PMID: 33898751 PMCID: PMC8023597 DOI: 10.1080/23802359.2021.1909443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Museum specimens are collected for education, exhibition, and various multiple scientific purposes. However, millions of specimens remain in their collection boxes for years without being analyzed. Historical specimens have been known to contain low-quality DNA; hence, it is difficult to utilize their sequence information in phylogenetic studies. However, recent advances in high-throughput sequencing (HTS) make these collections amenable to phylogenomic studies. In this study, two historical specimens (Papilio xuthus Linnaeus, 1767, and Papilio thoas Linnaeus, 1771) were sampled and DNA extracted for HTS via the Miseq platform. Two complete mitogenomes were assembled, even though the DNA quality of those specimens was highly fragmented, below 250 bp in length. The 37 genes of 60 mitogenomes were aligned and used for inferring the phylogenetic relationships of Papilioninae. These two newly sequenced mitogenomes are correctly grouped in the genus Papilio, and this result indicates that historical specimens show great potential for phylogenetic studies with HTS technology.
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Affiliation(s)
- Ming-Luen Jeng
- Department of Biology, National Museum of Natural Science, Taichung, Taiwan, ROC
| | - Ming-Yu Chen
- Department of Life Science, Tunghai University, Taichung, Taiwan, ROC
| | - Li-Wei Wu
- Department of Life Science, Tunghai University, Taichung, Taiwan, ROC
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26
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Chen XH, Tan SL, Liang YL, Huang L, Xiao HW, Luo HL, Xiong DJ, Yang BY, Ren ZX. The pollination of Habenaria rhodocheila (Orchidaceae) in South China: When butterflies take sides. Ecol Evol 2021; 11:2849-2861. [PMID: 33767841 PMCID: PMC7981216 DOI: 10.1002/ece3.7242] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/06/2021] [Accepted: 01/13/2021] [Indexed: 11/10/2022] Open
Abstract
Habenaria is one of the largest terrestrial genera in the family Orchidaceae. Most field studies on Habenaria species with greenish-white and nocturnal scented flowers are pollinated by nocturnal hawkmoths and settling moths. However, H. rhodocheila presents reddish flowers lacking a detectable scent and fails to fit the moth pollination syndrome. We investigated the pollinators, breeding system, and functional traits of H. rhodocheila in South China and found that two diurnal swallowtail butterflies Papilio helenus and Papilio nephelus (Papilionidae) were the effective pollinators. When butterflies foraged for nectar in the spur, the pollinia became attached between the palpi. A triangular projected median rostellar lobe was found at the entrance (sinus) of the spur of H. rhodocheila. This lobe divided the spur opening into two entrances forcing butterflies to enter their proboscides through the left or right side. When the projection of median rostellar lobe was removed, the site of pollinium attachment changed to the eyes of the butterflies, leading to a higher rate of pollinium removal but lower rate of pollinium deposition. Our quartz glass cylinder choice experiment suggested that visual rather than olfactory cues provided the major stimuli for butterflies to locate these flowers. Hand pollination experiments suggested this species was self-compatible but pollinator-dependent. However, the proportion of seeds with large embryos produced in self-pollinated fruits was significantly lower than in cross-pollinated fruits, indicating a significant inbreeding depression. Unlike many other orchid species, fruit set was higher than rates of pollinium removal, indicating a high level of pollination efficiency in a species with friable pollinia. Shifts from moth to butterfly pollination in the genus Habenaria parallel other orchid lineages providing insights into the potential for pollinator-mediated floral trait selection.
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Affiliation(s)
- Xing-Hui Chen
- Jiangxi Key Laboratory of Plant Resources School of Life Sciences Nanchang University Nanchang China
| | - Shao-Lin Tan
- Jiangxi Key Laboratory of Plant Resources School of Life Sciences Nanchang University Nanchang China
| | - Yue-Long Liang
- Jiulianshan National Natural Reserve Administration Bureau Ganzhou China
| | - Lang Huang
- Jiangxi Key Laboratory of Plant Resources School of Life Sciences Nanchang University Nanchang China
| | - Han-Wen Xiao
- Jiangxi Key Laboratory of Plant Resources School of Life Sciences Nanchang University Nanchang China
| | - Huo-Lin Luo
- Jiangxi Key Laboratory of Plant Resources School of Life Sciences Nanchang University Nanchang China
| | - Dong-Jin Xiong
- Jiangxi Key Laboratory of Plant Resources School of Life Sciences Nanchang University Nanchang China
| | - Bo-Yun Yang
- Jiangxi Key Laboratory of Plant Resources School of Life Sciences Nanchang University Nanchang China
| | - Zong-Xin Ren
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences Kunming China
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27
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Andrade Justi S, Soghigian J, Pecor DB, Caicedo-Quiroga L, Rutvisuttinunt W, Li T, Stevens L, Dorn PL, Wiegmann B, Linton YM. From e-voucher to genomic data: Preserving archive specimens as demonstrated with medically important mosquitoes (Diptera: Culicidae) and kissing bugs (Hemiptera: Reduviidae). PLoS One 2021; 16:e0247068. [PMID: 33630885 PMCID: PMC7906454 DOI: 10.1371/journal.pone.0247068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/29/2021] [Indexed: 12/26/2022] Open
Abstract
Scientific collections such as the U.S. National Museum (USNM) are critical to filling knowledge gaps in molecular systematics studies. The global taxonomic impediment has resulted in a reduction of expert taxonomists generating new collections of rare or understudied taxa and these large historic collections may be the only reliable source of material for some taxa. Integrated systematics studies using both morphological examinations and DNA sequencing are often required for resolving many taxonomic issues but as DNA methods often require partial or complete destruction of a sample, there are many factors to consider before implementing destructive sampling of specimens within scientific collections. We present a methodology for the use of archive specimens that includes two crucial phases: 1) thoroughly documenting specimens destined for destructive sampling—a process called electronic vouchering, and 2) the pipeline used for whole genome sequencing of archived specimens, from extraction of genomic DNA to assembly of putative genomes with basic annotation. The process is presented for eleven specimens from two different insect subfamilies of medical importance to humans: Anophelinae (Diptera: Culicidae)—mosquitoes and Triatominae (Hemiptera: Reduviidae)—kissing bugs. Assembly of whole mitochondrial genome sequences of all 11 specimens along with the results of an ortholog search and BLAST against the NCBI nucleotide database are also presented.
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Affiliation(s)
- Silvia Andrade Justi
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, Suitland, MD, United States of America
- Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Department of Entomology, Smithsonian Institution National Museum of Natural History, Washington, DC, United States of America
- * E-mail:
| | - John Soghigian
- Department of Entomology, North Carolina State University, Raleigh, NC, United States of America
| | - David B. Pecor
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, Suitland, MD, United States of America
- Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Department of Entomology, Smithsonian Institution National Museum of Natural History, Washington, DC, United States of America
| | - Laura Caicedo-Quiroga
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, Suitland, MD, United States of America
- Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Department of Entomology, Smithsonian Institution National Museum of Natural History, Washington, DC, United States of America
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Tao Li
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Lori Stevens
- Department of Biology, University of Vermont, Burlington, VT, United States of America
| | - Patricia L. Dorn
- Department of Biological Sciences, Loyola University New Orleans, New Orleans, LA, United States of America
| | - Brian Wiegmann
- Department of Entomology, North Carolina State University, Raleigh, NC, United States of America
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, Suitland, MD, United States of America
- Entomology Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Department of Entomology, Smithsonian Institution National Museum of Natural History, Washington, DC, United States of America
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Allio R, Tilak MK, Scornavacca C, Avenant NL, Kitchener AC, Corre E, Nabholz B, Delsuc F. High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox. eLife 2021; 10:e63167. [PMID: 33599612 PMCID: PMC7963486 DOI: 10.7554/elife.63167] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/16/2021] [Indexed: 12/26/2022] Open
Abstract
In a context of ongoing biodiversity erosion, obtaining genomic resources from wildlife is essential for conservation. The thousands of yearly mammalian roadkill provide a useful source material for genomic surveys. To illustrate the potential of this underexploited resource, we used roadkill samples to study the genomic diversity of the bat-eared fox (Otocyon megalotis) and the aardwolf (Proteles cristatus), both having subspecies with similar disjunct distributions in Eastern and Southern Africa. First, we obtained reference genomes with high contiguity and gene completeness by combining Nanopore long reads and Illumina short reads. Then, we showed that the two subspecies of aardwolf might warrant species status (P. cristatus and P. septentrionalis) by comparing their genome-wide genetic differentiation to pairs of well-defined species across Carnivora with a new Genetic Differentiation index (GDI) based on only a few resequenced individuals. Finally, we obtained a genome-scale Carnivora phylogeny including the new aardwolf species.
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Affiliation(s)
- Rémi Allio
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Marie-Ka Tilak
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Celine Scornavacca
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Nico L Avenant
- National Museum and Centre for Environmental Management, University of the Free StateBloemfonteinSouth Africa
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums ScotlandEdinburghUnited Kingdom
| | - Erwan Corre
- CNRS, Sorbonne Université, CNRS, ABiMS, Station Biologique de RoscoffRoscoffFrance
| | - Benoit Nabholz
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
- Institut Universitaire de France (IUF)ParisFrance
| | - Frédéric Delsuc
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
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29
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Allio R, Nabholz B, Wanke S, Chomicki G, Pérez-Escobar OA, Cotton AM, Clamens AL, Kergoat GJ, Sperling FAH, Condamine FL. Genome-wide macroevolutionary signatures of key innovations in butterflies colonizing new host plants. Nat Commun 2021; 12:354. [PMID: 33441560 PMCID: PMC7806994 DOI: 10.1038/s41467-020-20507-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 12/03/2020] [Indexed: 01/29/2023] Open
Abstract
The mega-diversity of herbivorous insects is attributed to their co-evolutionary associations with plants. Despite abundant studies on insect-plant interactions, we do not know whether host-plant shifts have impacted both genomic adaptation and species diversification over geological times. We show that the antagonistic insect-plant interaction between swallowtail butterflies and the highly toxic birthworts began 55 million years ago in Beringia, followed by several major ancient host-plant shifts. This evolutionary framework provides a valuable opportunity for repeated tests of genomic signatures of macroevolutionary changes and estimation of diversification rates across their phylogeny. We find that host-plant shifts in butterflies are associated with both genome-wide adaptive molecular evolution (more genes under positive selection) and repeated bursts of speciation rates, contributing to an increase in global diversification through time. Our study links ecological changes, genome-wide adaptations and macroevolutionary consequences, lending support to the importance of ecological interactions as evolutionary drivers over long time periods.
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Affiliation(s)
- Rémi Allio
- CNRS, IRD, EPHE, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France.
| | - Benoit Nabholz
- CNRS, IRD, EPHE, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20b, 01062, Dresden, Germany
| | - Guillaume Chomicki
- Department of Bioscience, Durham University, Stockton Road, Durham, DH1 3LE, UK
| | | | - Adam M Cotton
- 86/2 Moo 5, Tambon Nong Kwai, Hang Dong, Chiang Mai, Thailand
| | - Anne-Laure Clamens
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier, Montpellier, France
| | - Gaël J Kergoat
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier, Montpellier, France
| | - Felix A H Sperling
- Department of Biological Sciences, University of Alberta, Edmonton, T6G 2E9, AB, Canada
| | - Fabien L Condamine
- CNRS, IRD, EPHE, Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France.
- Department of Biological Sciences, University of Alberta, Edmonton, T6G 2E9, AB, Canada.
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Uckele KA, Adams RP, Schwarzbach AE, Parchman TL. Genome-wide RAD sequencing resolves the evolutionary history of serrate leaf Juniperus and reveals discordance with chloroplast phylogeny. Mol Phylogenet Evol 2020; 156:107022. [PMID: 33242585 DOI: 10.1016/j.ympev.2020.107022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 10/06/2020] [Accepted: 11/17/2020] [Indexed: 12/22/2022]
Abstract
Juniper (Juniperus) is an ecologically important conifer genus of the Northern Hemisphere, the members of which are often foundational tree species of arid regions. The serrate leaf margin clade is native to topologically variable regions in North America, where hybridization has likely played a prominent role in their diversification. Here we use a reduced-representation sequencing approach (ddRADseq) to generate a phylogenomic data set for 68 accessions representing all 22 species in the serrate leaf margin clade, as well as a number of close and distant relatives, to improve understanding of diversification in this group. Phylogenetic analyses using three methods (SVDquartets, maximum likelihood, and Bayesian) yielded highly congruent and well-resolved topologies. These phylogenies provided improved resolution relative to past analyses based on Sanger sequencing of nuclear and chloroplast DNA, and were largely consistent with taxonomic expectations based on geography and morphology. Calibration of a Bayesian phylogeny with fossil evidence produced divergence time estimates for the clade consistent with a late Oligocene origin in North America, followed by a period of elevated diversification between 12 and 5 Mya. Comparison of the ddRADseq phylogenies with a phylogeny based on Sanger-sequenced chloroplast DNA revealed five instances of pronounced discordance, illustrating the potential for chloroplast introgression, chloroplast transfer, or incomplete lineage sorting to influence organellar phylogeny. Our results improve understanding of the pattern and tempo of diversification in Juniperus, and highlight the utility of reduced-representation sequencing for resolving phylogenetic relationships in non-model organisms with reticulation and recent divergence.
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Affiliation(s)
- Kathryn A Uckele
- Department of Biology, MS 314, University of Nevada, Reno, Max Fleischmann Agriculture Building, 1664 N Virginia St., Reno, NV 89557, USA.
| | - Robert P Adams
- Baylor University, Utah Lab, 201 N 5500 W, Hurricane, UT 84790, USA.
| | - Andrea E Schwarzbach
- Department of Health and Biomedical Sciences, University of Texas - Rio Grande Valley, 1 W University Drive, Brownsville, TX 78520, USA.
| | - Thomas L Parchman
- Department of Biology, MS 314, University of Nevada, Reno, Max Fleischmann Agriculture Building, 1664 N Virginia St., Reno, NV 89557, USA.
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Toussaint EFA, Ellis EA, Gott RJ, Warren AD, Dexter KM, Storer C, Lohman DJ, Kawahara AY. Historical biogeography of Heteropterinae skippers via Beringian and post‐Tethyan corridors. ZOOL SCR 2020. [DOI: 10.1111/zsc.12457] [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)
- Emmanuel F. A. Toussaint
- Natural History Museum of Geneva Geneva Switzerland
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History University of Florida Gainesville FL USA
| | - Emily A. Ellis
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History University of Florida Gainesville FL USA
| | - Riley J. Gott
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History University of Florida Gainesville FL USA
| | - Andrew D. Warren
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History University of Florida Gainesville FL USA
| | - Kelly M. Dexter
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History University of Florida Gainesville FL USA
| | - Caroline Storer
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History University of Florida Gainesville FL USA
| | - David J. Lohman
- Biology Department City College of New YorkCity University of New York New York NY USA
- Ph.D. Program in Biology, Graduate Center City University of New York New York NY USA
- Entomology Section National Museum of Natural History Manila Philippines
| | - Akito Y. Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History University of Florida Gainesville FL USA
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Lukhtanov VA, Dubatolov VV. Phylogenetic position and taxonomic rearrangement of Davidina (Lepidoptera: Nymphalidae), an enigmatic butterfly genus new for Europe and America. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Davidina, an enigmatic butterfly genus described from China in the 19th century, has for a long time been considered a member of the family Pieridae due to its pierid-like wing pattern. In the 20th century, it was transferred to Satyridae (now subfamily Satyrinae of Nymphalidae) based on analysis of the structure of genitalia and placed next to the species-rich genus Oeneis (subtribe Satyrina), being separated from the latter by supposed differences in wing venation. We have conducted a phylogenetic and taxonomic study of the subtribe Satyrina using analysis of molecular and morphological characters. We show that the genus Oeneis is not monophyletic, and consists of two genetically diverged and morphologically differentiated groups that are not sister-groups (Oeneis s.s. and Protoeneis). We also demonstrate that Davidina is closely related to Protoeneis, but not to Oeneis s.s. To resolve this newly discovered non-monophyly and morphological heterogeneity, several species should be removed from Oeneis and transferred to the genus Davidina. As a consequence, we synonymize the name ProtoeneisGorbunov, 2001 with DavidinaOberthür, 1879. We conclude that Davidina is not a monotypic Chinese endemic genus, as has been previously supposed, but is composed of nine species that have a broad distribution area across the Holarctic region, extending to Europe and America.
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Affiliation(s)
- Vladimir A Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, St. Petersburg, Russia
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Miocene Diversification and High-Altitude Adaptation of Parnassius Butterflies (Lepidoptera: Papilionidae) in Qinghai-Tibet Plateau Revealed by Large-Scale Transcriptomic Data. INSECTS 2020; 11:insects11110754. [PMID: 33153157 PMCID: PMC7693471 DOI: 10.3390/insects11110754] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 12/01/2022]
Abstract
Simple Summary Parnassius butterflies have contributed to fundamental studies in biogeography, insect–plant interactions, and other fields of conservation biology and ecology. However, the early evolutionary pattern and molecular adaptation mechanism of this alpine butterfly group to high altitudes in Qinghai–Tibet Plateau are poorly understood up to now. In this study, we report for the first time, a relatively large-scale transcriptomic dataset of eight Parnassius species and their two closely related papilionid species, a dated phylogeny based on hundreds of gene sequences, and potential genetic mechanisms underlying the high-altitude adaptation by investigating changes in evolutionary rates and positively selected genes. Overall, our findings indicate that the transcriptome data sets reported here can provide some new insights into the spatiotemporally evolutionary pattern and high altitude adaptation of Parnassius butterflies from the extrinsic and intrinsic view, and will support further expressional and functional studies that will help interested researchers to address evolution, biodiversity and conservation questions concerning Parnassius and other butterfly species. Abstract The early evolutionary pattern and molecular adaptation mechanism of alpine Parnassius butterflies to high altitudes in Qinghai–Tibet Plateau are poorly understood up to now, due to difficulties in sampling, limited sequence data, and time calibration issues. Here, we present large-scale transcriptomic datasets of eight representative Parnassius species to reveal the phylogenetic timescale and potential genetic basis for high-altitude adaptation with multiple analytic strategies using 476 orthologous genes. Our phylogenetic results strongly supported that the subgenus Parnassius formed a well-resolved basal clade, and the subgenera Tadumia and Kailasius were closely related in the phylogenetic trees. In addition, molecular dating analyses showed that the Parnassius began to diverge at about 13.0 to 14.3 million years ago (middle Miocene), correlated with their hostplant’s spatiotemporal distributions, as well as geological and palaeoenvironmental changes of the Qinghai–Tibet Plateau. Moreover, the accelerated evolutionary rate, candidate positively selected genes and their potentially functional changes were detected, probably contributed to the high-altitude adaptation of Parnassius species. Overall, our study provided some new insights into the spatiotemporally evolutionary pattern and high altitude adaptation of Parnassius butterflies from the extrinsic and intrinsic view, which will help to address evolution, biodiversity, and conservation questions concerning Parnassius and other butterfly species.
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Wiemers M, Chazot N, Wheat CW, Schweiger O, Wahlberg N. A complete time-calibrated multi-gene phylogeny of the European butterflies. Zookeys 2020; 938:97-124. [PMID: 32550787 PMCID: PMC7289901 DOI: 10.3897/zookeys.938.50878] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/03/2020] [Indexed: 11/12/2022] Open
Abstract
With the aim of supporting ecological analyses in butterflies, the third most species-rich superfamily of Lepidoptera, this paper presents the first time-calibrated phylogeny of all 496 extant butterfly species in Europe, including 18 very localised endemics for which no public DNA sequences had been available previously. It is based on a concatenated alignment of the mitochondrial gene COI and up to eleven nuclear gene fragments, using Bayesian inferences of phylogeny. To avoid analytical biases that could result from our region-focussed sampling, our European tree was grafted upon a global genus-level backbone butterfly phylogeny for analyses. In addition to a consensus tree, the posterior distribution of trees and the fully concatenated alignment are provided for future analyses. Altogether a complete phylogenetic framework of European butterflies for use by the ecological and evolutionary communities is presented.
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Affiliation(s)
- Martin Wiemers
- Senckenberg Deutsches Entomologisches Institut, Eberswalder Straße 90, 15374, Müncheberg, Germany UFZ - Helmholtz Centre for Environmental Research Halle Germany.,UFZ - Helmholtz Centre for Environmental Research, Department of Community Ecology, Theodor-Lieser-Str. 4, 06120, Halle, Germany Senckenberg Deutsches Entomologisches Institut Müncheberg Germany
| | - Nicolas Chazot
- Department of Biology, Lund University, 22362, Lund, Sweden Lund University Lund Sweden.,Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30, Gothenburg, Sweden University of Gothenburg Gothenburg Sweden.,Gothenburg Global Biodiversity Centre, Box 461, 405 30, Gothenburg, Sweden Gothenburg Global Biodiversity Centre Gothenburg Sweden
| | - Christopher W Wheat
- Department of Zoology, Stockholm University, 10691, Stockholm, Sweden Stockholm University Stockholm Sweden
| | - Oliver Schweiger
- UFZ - Helmholtz Centre for Environmental Research, Department of Community Ecology, Theodor-Lieser-Str. 4, 06120, Halle, Germany Senckenberg Deutsches Entomologisches Institut Müncheberg Germany
| | - Niklas Wahlberg
- Department of Biology, Lund University, 22362, Lund, Sweden Lund University Lund Sweden
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Wen J, Yu Y, Xie DF, Peng C, Liu Q, Zhou SD, He XJ. A transcriptome-based study on the phylogeny and evolution of the taxonomically controversial subfamily Apioideae (Apiaceae). ANNALS OF BOTANY 2020; 125:937-953. [PMID: 32016402 PMCID: PMC7218814 DOI: 10.1093/aob/mcaa011] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 01/28/2020] [Indexed: 05/26/2023]
Abstract
BACKGROUND AND AIMS A long-standing controversy in the subfamily Apioideae concerns relationships among the major lineages, which has prevented a comprehensive study of their fruits and evolutionary history. Here we use single copy genes (SCGs) generated from transcriptome datasets to generate a reliable species tree and explore the evolutionary history of Apioideae. METHODS In total, 3351 SCGs were generated from 27 transcriptome datasets and one genome, and further used for phylogenetic analysis using coalescent-based methods. Fruit morphology and anatomy were studied in combination with the species tree. Eleven SCGs were screened out for dating analysis with two fossils selected for calibration. KEY RESULTS A well-supported species tree was generated with a topology [Chamaesieae, (Bupleureae, (Pleurospermeae, (Physospermopsis Clade, (Group C, (Group A, Group B)))))] that differed from previous trees. Daucinae and Torilidinae were not in the tribe Scandiceae and existed as sister groups to the Acronema Clade. Five branches (I-V) of the species tree showed low quartet support but strong local posterior probabilities. Dating analysis suggested that Apioideae originated around 56.64 Mya (95 % highest posterior density interval, 45.18-73.53 Mya). CONCLUSIONS This study resolves a controversial phylogenetic relationship in Apioideae based on 3351 SCGs and coalescent-based species tree estimation methods. Gene trees that contributed to the species tree may undergoing rapid evolutionary divergence and incomplete lineage sorting. Fruits of Apioideae might have evolved in two directions, anemochorous and hydrochorous, with epizoochorous as a derived mode. Molecular and morphological evidence suggests that Daucinae and Torilidinae should be restored to the tribe level. Our results provide new insights into the morphological evolution of this subfamily, which may contribute to a better understanding of species diversification in Apioideae. Molecular dating analysis suggests that uplift of the Qinghai-Tibetan Plateau (QTP) and climate changes probably drove rapid speciation and diversification of Apioideae in the QTP region.
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Affiliation(s)
- Jun Wen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, P.R. China
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, P.R. China
| | - Yan Yu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Deng-Feng Xie
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Chang Peng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Qing Liu
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, P.R. China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Xing-Jin He
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, P.R. China
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Allio R, Schomaker-Bastos A, Romiguier J, Prosdocimi F, Nabholz B, Delsuc F. MitoFinder: Efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics. Mol Ecol Resour 2020; 20:892-905. [PMID: 32243090 PMCID: PMC7497042 DOI: 10.1111/1755-0998.13160] [Citation(s) in RCA: 490] [Impact Index Per Article: 122.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 02/21/2020] [Accepted: 03/12/2020] [Indexed: 11/27/2022]
Abstract
Thanks to the development of high-throughput sequencing technologies, target enrichment sequencing of nuclear ultraconserved DNA elements (UCEs) now allows routine inference of phylogenetic relationships from thousands of genomic markers. Recently, it has been shown that mitochondrial DNA (mtDNA) is frequently sequenced alongside the targeted loci in such capture experiments. Despite its broad evolutionary interest, mtDNA is rarely assembled and used in conjunction with nuclear markers in capture-based studies. Here, we developed MitoFinder, a user-friendly bioinformatic pipeline, to efficiently assemble and annotate mitogenomic data from hundreds of UCE libraries. As a case study, we used ants (Formicidae) for which 501 UCE libraries have been sequenced whereas only 29 mitogenomes are available. We compared the efficiency of four different assemblers (IDBA-UD, MEGAHIT, MetaSPAdes, and Trinity) for assembling both UCE and mtDNA loci. Using MitoFinder, we show that metagenomic assemblers, in particular MetaSPAdes, are well suited to assemble both UCEs and mtDNA. Mitogenomic signal was successfully extracted from all 501 UCE libraries, allowing us to confirm species identification using CO1 barcoding. Moreover, our automated procedure retrieved 296 cases in which the mitochondrial genome was assembled in a single contig, thus increasing the number of available ant mitogenomes by an order of magnitude. By utilizing the power of metagenomic assemblers, MitoFinder provides an efficient tool to extract complementary mitogenomic data from UCE libraries, allowing testing for potential mitonuclear discordance. Our approach is potentially applicable to other sequence capture methods, transcriptomic data and whole genome shotgun sequencing in diverse taxa. The MitoFinder software is available from GitHub (https://github.com/RemiAllio/MitoFinder).
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Affiliation(s)
- Rémi Allio
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
| | - Alex Schomaker-Bastos
- Laboratório Multidisciplinar para Análise de Dados (LAMPADA), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jonathan Romiguier
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
| | - Francisco Prosdocimi
- Laboratório Multidisciplinar para Análise de Dados (LAMPADA), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Benoit Nabholz
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
| | - Frédéric Delsuc
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
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