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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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Che Y, Deng W, Li W, Zhang J, Kinjo Y, Tokuda G, Bourguignon T, Lo N, Wang Z. Vicariance and dispersal events inferred from mitochondrial genomes and nuclear genes (18S, 28S) shaped global Cryptocercus distributions. Mol Phylogenet Evol 2021; 166:107318. [PMID: 34562575 DOI: 10.1016/j.ympev.2021.107318] [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: 05/02/2021] [Revised: 09/19/2021] [Accepted: 09/20/2021] [Indexed: 10/20/2022]
Abstract
Cryptocercus Scudder, a genus of wingless, subsocial cockroaches, has low vagility but exhibits a disjunct distribution in eastern and western North America, and in China, South Korea and the Russian Far East. This distribution provides an ideal model for testing hypotheses of vicariance through plate tectonics or other natural barriers versus dispersal across oceans or other natural barriers. We sequenced 45 samples of Cryptocercus to resolve phylogenetic relationships among members of the genus worldwide. We identified four types of tRNA rearrangements among samples from the Qin-Daba Mountains. Our maximum-likelihood and Bayesian phylogenetic trees, based on mitochondrial genomes and nuclear genes (18S, 28S), strongly supported six major lineages of Cryptocercus, which displayed a clear geographical distribution pattern. We used Bayesian molecular dating to estimate the evolutionary timescale of the genus, and reconstructed Cryptocercus ancestral ranges using statistical dispersal-vicariance analysis (S-DIVA) in RASP. Two dispersal events and six vicariance events for Cryptocercus were inferred with high support. The initial vicariance event occurred between American and Asian lineages at 80.5 Ma (95% credibility interval: 60.0-104.7 Ma), followed by one vicariance event within the American lineage 43.8 Ma (95% CI: 32.0-57.5 Ma), and two dispersal 31.9 Ma (95% CI: 25.8-39.5 Ma), 21.7 Ma (95% CI: 17.3-27.1 Ma) plus four vicariance events c. 29.3 Ma, 27.2 Ma, 24.8 Ma and 16.7 Ma within the Asian lineage. Our analyses provide evidence that both vicariance and dispersal have played important roles in shaping the distribution and diversity of these woodroaches.
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Affiliation(s)
- Yanli Che
- College of Plant Protection, Southwest University, Beibei, Chongqing 400716, PR China
| | - Wenbo Deng
- College of Plant Protection, Southwest University, Beibei, Chongqing 400716, PR China
| | - Weijun Li
- College of Plant Protection, Southwest University, Beibei, Chongqing 400716, PR China
| | - Jiawei Zhang
- College of Plant Protection, Southwest University, Beibei, Chongqing 400716, PR China
| | - Yukihiro Kinjo
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Gaku Tokuda
- Tropical Biosphere Research Center, Center of Molecular Biosciences, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Thomas Bourguignon
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan; Faculty of Tropical AgriSciences, Czech University of Life Sciences, Kamycka 129, Prague CZ-165 00, Czech Republic
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
| | - Zongqing Wang
- College of Plant Protection, Southwest University, Beibei, Chongqing 400716, PR China.
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Rewinding the molecular clock in the genus Carabus (Coleoptera: Carabidae) in light of fossil evidence and the Gondwana split: A reanalysis. PLoS One 2021; 16:e0256679. [PMID: 34550988 PMCID: PMC8457462 DOI: 10.1371/journal.pone.0256679] [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] [Received: 05/25/2020] [Accepted: 06/16/2021] [Indexed: 11/19/2022] Open
Abstract
Molecular clocks have become powerful tools given increasing sequencing and fossil resources. However, calibration analyses outcomes depend on the choice of priors. Here, we revisited the seminal dating study published by Andújar and coworkers of the genus Carabus proposing that prior choices need re-evaluation. We hypothesized that reflecting fossil evidence and the Gondwanan split properly significantly rewinds the molecular clock. We re-used the dataset including five mitochondrial and four nuclear DNA fragments with a total length of 7888 nt. Fossil evidence for Oligocene occurrence of Calosoma was considered. Root age was set based on the fossil evidence of Harpalinae ground beetles in the Upper Cretaceous. Paleogene divergence of the outgroup taxa Ceroglossini and Pamborini is introduced as a new prior based on current paleontological and geological literature. The ultrametric time-calibrated tree of the extended nd5 dataset resulted in a median TMRCA Carabus of 53.92 Ma (HPD 95% 45.01–63.18 Ma), roughly 30 Ma older than in the Andújar study. The splits among C. rugosus and C. morbillosus (A), C. riffensis from the European Mesocarabus (B), and Eurycarabus and Nesaeocarabus (C) were dated to 17.58 (12.87–22.85), 24.14 (18.02–30.58), and 21.6 (16.44–27.43) Ma. They were decidedly older than those previously reported (7.48, 10.93, and 9.51 Ma). These changes were driven almost entirely by constraining the Carabidae time-tree root with a Harpalinae amber fossil at ~99 Ma. Utilizing the nd5 dating results of three well-supported Carabus clades as secondary calibration points for the complete MIT-NUC dataset led to a TMRCA of Carabus of 44.72 (37.54–52.22) Ma, compared with 25.16 Ma (18.41–33.04 Ma) in the previous study. Considering fossil evidence for Oligocene Calosoma and Late Cretaceous Harpalini together with the Gondwanan split as a new prior, our new approach supports the origin of genus Carabus in the Eocene. Our results are preliminary because of the heavy reliance on the nd5 gene, and thus will have to be tested with a sufficient set of nuclear markers. Additionally, uncertainties due to dating root age of the tree based on a single fossil and outgroup taxon affect the results. Improvement of the fossil database, particularly in the supertribe Carabitae, is needed to reduce these uncertainties in dating Carabus phylogeny.
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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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Sota T, Hori M, Scholtz C, Karagyan G, Liang HB, Ikeda H, Takami Y. The origin of the giant ground beetle Aplothorax burchelli on St Helena Island. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa093] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Some highly isolated oceanic islands harbour endemic ground beetles that have lost the ability to fly. Here, we investigated the origin of the possibly extinct flightless giant ground beetle Aplothorax burchelli on St Helena Island in the South Atlantic. Aplothorax burchelli was initially considered to be a member of the subtribe Calosomina (=genus Calosoma) of the subfamily Carabinae (Coleoptera: Carabidae) closely related to the genus Ctenosta (=Calosoma subgenus Ctenosta), but this proposition was questioned due to its unique external and genital morphology. We conducted a phylogenetic analysis of mitogenome sequences using historical specimens of A. burchelli and samples of representative species of Carabinae. Our analysis of 13 protein-coding gene sequences revealed that A. burchelli is definitely a member of Calosomina, most closely related to a species of Ctenosta. Further analysis using NADH dehydrogenase subunit 5 gene sequences from most groups in Calosomina showed that A. burchelli formed a monophyletic group with Ctenosta species from Africa and Madagascar. Our results suggest that the ancestor of A. burchelli, which had the ability to fly, colonized St Helena from Africa after the emergence of the island 14 Mya, and has since undergone evolutionary changes in conjunction with loss of flight.
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Affiliation(s)
- Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, Japan
| | | | - Clarke Scholtz
- Department of Zoology and Entomology, University of Pretoria, Pretoria, Republic of South Africa
| | - Gayane Karagyan
- Scientific Center of Zoology and Hydroecology, National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia
| | - Hong-Bin Liang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hiroshi Ikeda
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - Yasuoki Takami
- Graduate School of Human Development and Environment, Kobe University, Nada, Kobe, Japan
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Gillett CPDT, Toussaint EFA. Macroevolution and shifts in the feeding biology of the New World scarab beetle tribe Phanaeini (Coleoptera: Scarabaeidae: Scarabaeinae). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The New World scarab beetle tribe Phanaeini contains coprophagous, necrophagous, mycetophagous and suspected myrmecophilous species. We analyse the largest tribal molecular dataset assembled, incorporating, for the first time, the enigmatic monobasic genus Megatharsis, the thalassinus group of the subgenus Coprophanaeus (Metallophanaeus), and the subgenus Dendropaemon (Eurypodea) (formerly Tetramereia), unveiling their macroevolutionary and biogeographical history in light of Cenozoic abiotic changes and inferring shifts in feeding biology through time. We recover the contentious genus Gromphas outside an otherwise monophyletic Phanaeini. We infer Megatharsis in a clade containing the apparent myrmecophilous genus Dendropaemon, within the Coprophanaeus clade, and demonstrate that the subgenus Coprophanaeus (Metallophanaeus) is polyphyletic, whilst species groups within the subgenus Coprophanaeus (Coprophanaeus) are monophyletic. Our divergence time analyses and ancestral range estimation indicate an eastern South American origin for Phanaeini in the early Eocene, with subsequent colonization of Central America and the Nearctic during the Oligocene, long before a Panamanian land bridge. A shift to necrophagy in Coprophanaeus is possibly linked to increasing Neotropical small vertebrate diversity since the Eocene and, astonishingly, myrmecophily evolved from necrophagy 35 Mya. These drastic shifts in lifestyle are not concordant with variations in diversification rates and appear unlinked to Quaternary extinction of large mammals.
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Affiliation(s)
- Conrad P D T Gillett
- University of Hawaiʻi Insect Museum, College of Tropical Agriculture and Human Resources, University of Hawaiʻi at Mānoa, Maile Way, Honolulu, HI, USA
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Sugiura S, Takanashi T. Hornworm counterattacks: defensive strikes and sound production in response to invertebrate attackers. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/blx156] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Shinji Sugiura
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Takuma Takanashi
- Department of Forest Entomology, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
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