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Cerretti P, Yan L, Narayanan Kutty S, Szpila K, Nania D, Tintea R, Mei M, Pape T. Phylogenomics resolves long-standing questions about the affinities of an endangered Corsican endemic fly. JOURNAL OF INSECT SCIENCE (ONLINE) 2024; 24:9. [PMID: 39052426 PMCID: PMC11271022 DOI: 10.1093/jisesa/ieae073] [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: 03/11/2024] [Revised: 05/25/2024] [Accepted: 06/24/2024] [Indexed: 07/27/2024]
Abstract
Recent studies on oestroidean Diptera (Brachycera) are providing a comprehensive and nuanced understanding of the evolutionary history of this remarkably diverse clade of holometabolous insects. The Oestroidea, which includes formidable pests such as various blowflies, botflies, and flesh flies that infest livestock, pets and humans, are mostly composed of beneficial species that act as scavengers or parasitoids on various pest insects. In our research, we used genomic methods to elucidate the phylogenetic position of Nesodexia corsicana Villeneuve, 1911 (Diptera: Calliphoridae), a mysterious oestroid species endemic to Corsica and characterized by distinctive morphological features that have puzzled taxonomists for years. Contrary to initial hypotheses, our results place Nesodexia Villeneuve, 1911 within the Calliphoridae subfamily Rhinophorinae, a small lineage of terrestrial isopod parasitoids. Through detailed morphological analysis of adults of both sexes and eggs, we uncovered significant insights consistent with our phylogenomic reconstruction. The unique morphological features of the species, coupled with its restricted and fragmented habitat, highlight its potential conservation importance. We delineated the area of occupancy for N. corsicana and assessed its "threatened" category using specific IUCN Red List criteria. In addition, we mapped the available habitat within its range and determined potential key biodiversity areas (KBA) triggered by N. corsicana. New potential KBAs are only partially covered by the Corsican Regional Park. Finally, we mapped the distribution of habitats on the island to assess the potential distribution of the species beyond its currently known geographic range.
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Affiliation(s)
- Pierfilippo Cerretti
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Roma, Italy
| | - Liping Yan
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | | | - Krzysztof Szpila
- Faculty of Biological and Veterinary Sciences, Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Dario Nania
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Roma, Italy
| | - Roxana Tintea
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Roma, Italy
| | - Maurizio Mei
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Roma, Italy
| | - Thomas Pape
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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Sota T, Takami Y, Ikeda H, Liang H, Karagyan G, Scholtz C, Hori M. Global dispersal and diversification in ground beetles of the subfamily Carabinae. Mol Phylogenet Evol 2021; 167:107355. [PMID: 34774762 DOI: 10.1016/j.ympev.2021.107355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/10/2021] [Accepted: 11/08/2021] [Indexed: 10/19/2022]
Abstract
The origin and diversification process of lineages of organisms that are currently widely distributed among continents is an interesting subject for exploring the evolutionary history of global species diversity. Ground beetles of the subfamily Carabinae are flightless except for one lineage, but nevertheless occur on all continents except Antarctica. Here, we used sequence data from ultraconserved elements to reconstruct the phylogeny, divergence time, biogeographical history, ancestral state of hind wings and changes in the speciation rate of Carabinae. Our results show that Carabinae originated in the Americas and diversified into four tribes during the period from the late Jurassic to the late Cretaceous, with two in South America (Celoglossini) and Australasia (Pamborini) and two in Laurasia (Cychrini and Carabini). The ancestral Carabinae were inferred to be winged; three of four tribes (Cychrini, Ceglossini and Pamborini) have completely lost their hind wings and flight capability. The remaining tribe, Carabini, diverged into the subtribes Carabina (wingless) and Calosomina (winged) in the Oligocene. Carabina originated in Europe, spread over Eurasia and diversified into approximately 1000 species, accounting for around 60% of all Carabinae species. Calosomina that were flight-capable dispersed from North America or Eurasia to South America, Australia, and Africa, and then flightless lineages evolved on oceanic islands and continental highlands. The speciation rate increased in the Cychrini and Carabini clades in Eurasia. Within Carabini, the speciation rate was higher for wingless than winged states. Our study showed that the global distribution of Carabinae resulted from ancient dispersal before the breakup of Gondwana and more recent dispersal through flight around the world. These patterns consequently illustrate the causal relationships of geographical history, evolution of flightlessness, and the global distribution and species diversity of Carabinae.
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Affiliation(s)
- Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.
| | - Yasuoki Takami
- Graduate School of Human Development and Environment, Kobe University, Nada, Kobe 657-8501, Japan
| | - Hiroshi Ikeda
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
| | - Hongbin Liang
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Gayane Karagyan
- Scientific Center of Zoology and Hydroecology, National Academy of Sciences of the Republic of Armenia, Yerevan 0014, Armenia
| | - Clarke Scholtz
- Department of Zoology and Entomology, University of Pretoria, Pretoria 0002, Republic of South Africa
| | - Michio Hori
- Kyoto University, Sakyo, Kyoto 606-8501, Japan
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Toussaint EFA, Gauthier J, Bilat J, Gillett CPDT, Gough HM, Lundkvist H, Blanc M, Muñoz-Ramírez CP, Alvarez N. HyRAD-X Exome Capture Museomics Unravels Giant Ground Beetle Evolution. Genome Biol Evol 2021; 13:6275686. [PMID: 33988685 PMCID: PMC8480185 DOI: 10.1093/gbe/evab112] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2021] [Indexed: 12/27/2022] Open
Abstract
Advances in phylogenomics contribute toward resolving long-standing evolutionary questions. Notwithstanding, genetic diversity contained within more than a billion biological specimens deposited in natural history museums remains recalcitrant to analysis owing to challenges posed by its intrinsically degraded nature. Yet that tantalizing resource could be critical in overcoming taxon sampling constraints hindering our ability to address major evolutionary questions. We addressed this impediment by developing phyloHyRAD, a new bioinformatic pipeline enabling locus recovery at a broad evolutionary scale from HyRAD-X exome capture of museum specimens of low DNA integrity using a benchtop RAD-derived exome-complexity-reduction probe set developed from high DNA integrity specimens. Our new pipeline can also successfully align raw RNAseq transcriptomic and ultraconserved element reads with the RAD-derived probe catalog. Using this method, we generated a robust timetree for Carabinae beetles, the lack of which had precluded study of macroevolutionary trends pertaining to their biogeography and wing-morphology evolution. We successfully recovered up to 2,945 loci with a mean of 1,788 loci across the exome of specimens of varying age. Coverage was not significantly linked to specimen age, demonstrating the wide exploitability of museum specimens. We also recovered fragmentary mitogenomes compatible with Sanger-sequenced mtDNA. Our phylogenomic timetree revealed a Lower Cretaceous origin for crown group Carabinae, with the extinct Aplothorax Waterhouse, 1841 nested within the genus Calosoma Weber, 1801 demonstrating the junior synonymy of Aplothorax syn. nov., resulting in the new combination Calosoma burchellii (Waterhouse, 1841) comb. nov. This study compellingly illustrates that HyRAD-X and phyloHyRAD efficiently provide genomic-level data sets informative at deep evolutionary scales.
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Affiliation(s)
| | | | - Julia Bilat
- Natural History Museum of Geneva, Switzerland
| | - Conrad P D T Gillett
- University of Hawai'i Insect Museum, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Harlan M Gough
- Florida Natural History Museum, University of Florida, Gainesville, Florida, USA
| | | | | | - Carlos P Muñoz-Ramírez
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Chile.,Centro de Investigación en Biodiversidad y Ambientes Sustentables (CIBAS), Universidad Católica de la Santísima Concepción, Chile
| | - Nadir Alvarez
- Natural History Museum of Geneva, Switzerland.,Department of Genetics and Evolution, University of Geneva, Switzerland
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Akiyama K, Jang TW, Park YH, Shinohara T, Konuma J, Liang H, Kubota K, Sota T, Ishikawa R, Kim JL, Kim JK, Takami Y. Phylogeographical analysis of character displacement in feeding phenotypes of snail-feeding Acoptolabrus ground beetles. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Ecological character displacement predicts that interspecific resource competition results in greater trait divergence between species in sympatry than in allopatry. However, other processes, such as ecological sorting, result in the same pattern of trait variation. In this study, we characterize character displacement in eight species of snail-feeding Acoptolabrus ground beetles in the Far East. Acoptolabrus exhibit divergent feeding phenotypes, including species with a slender forebody that is able to intrude into large shells and species with stout heads and mandibles for crushing small shells. The pattern of character displacement in feeding phenotypes was confirmed by multivariate analysis of body dimensions. Molecular phylogenetic analysis, divergence time estimation and biogeographical analysis revealed that sympatry and phenotypic divergence occurred repeatedly during the Pleistocene and almost simultaneously within each geographical area. Comparative analysis revealed that the evolution of feeding phenotypes best fitted a selective model with three adaptive optima, corresponding to the three cases of sympatry with a congener. Repeated coincidences of sympatry and adaptive differentiation in feeding phenotypes suggested causal relationships, although the precise order of events was difficult to discriminate. This study provides insight into the spatiotemporal dynamics of interspecific interactions and adaptive phenotypic diversification.
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Affiliation(s)
- Kazutoshi Akiyama
- Graduate School of Human Development and Environment, Kobe University, Nada, Kobe, Japan
| | - Tae Woong Jang
- College of Forest and Environmental Sciences, Kangwon National University, Chuncheon, Korea
| | - Yong Hwan Park
- Graduate School of Human Development and Environment, Kobe University, Nada, Kobe, Japan
- College of Forest and Environmental Sciences, Kangwon National University, Chuncheon, Korea
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Korea
| | - Tadashi Shinohara
- Graduate School of Human Development and Environment, Kobe University, Nada, Kobe, Japan
| | - Junji Konuma
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Hongbin Liang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Kohei Kubota
- Department of Forest Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, Japan
| | | | - Jung Lark Kim
- Department of Health Management, Uiduk University, Gyeongju, Korea
| | - Jong Kuk Kim
- College of Forest and Environmental Sciences, Kangwon National University, Chuncheon, Korea
| | - Yasuoki Takami
- Graduate School of Human Development and Environment, Kobe University, Nada, Kobe, Japan
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