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Raman G, Choi KS, Lee EM, Morden CW, Shim H, Kang JS, Yang TJ, Park S. Extensive characterization of 28 complete chloroplast genomes of Hydrangea species: A perspective view of their organization and phylogenetic and evolutionary relationships. Comput Struct Biotechnol J 2023; 21:5073-5091. [PMID: 37867966 PMCID: PMC10589384 DOI: 10.1016/j.csbj.2023.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023] Open
Abstract
The tribe Hydrangeeae displays a unique, distinctive disjunct distribution encompassing East Asia, North America and Hawaii. Despite its complex trait variations and polyphyletic nature, comprehensive phylogenomic and biogeographical studies on this tribe have been lacking. To address this gap, we sequenced and characterized 28 plastomes of Hydrangeeae. Our study highlights the highly conserved nature of Hydrangeaceae chloroplast (cp) genomes in terms of gene content and arrangement. Notably, synapomorphic characteristics of tandem repeats in the conserved domain of accD were observed in the Macrophyllae, Chinenses, and Dichroa sections within the Hydrangeeae tribe. Additionally, we found lower expression of accD in these sections using structure prediction and quantitative real-time PCR analysis. Phylogenomic analyses revealed the subdivision of the Hydrangeeae tribe into two clades with robust support values. Consistent with polyphyletic relationships, sect. Broussaisia was identified as the basal group in the tribe Hydrangeeae. Our study also provides insights into the phylogenetic relationships of Hydrangea petiolaris in the Jeju and Ulleung Island populations, suggesting the need for further studies with more samples and molecular data. Divergence time estimation and biogeographical analyses suggested that the common ancestors of the tribe Hydrangeeae likely originated from North America and East Asia during the Paleocene period via the Bering Land Bridge, potentially facilitating migration within the tribe between these regions. In conclusion, this study enhances our understanding of the evolutionary history and biogeography of the tribe Hydrangeeae, shedding light on the dispersal patterns and origins of this intriguing plant group with its unique disjunct distribution.
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Affiliation(s)
- Gurusamy Raman
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
| | - Kyoung-Su Choi
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
- Plant Research Team, Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - Eun Mi Lee
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
| | - Clifford W. Morden
- School of Life Sciences, University of Hawai]i at Mānoa, Honolulu, HI, USA
| | - Hyeonah Shim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jong-Soo Kang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
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2
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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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3
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Gamboa M, Muranyi D, Kanmori S, Watanabe K. Molecular phylogeny and diversification timing of the Nemouridae family (Insecta, Plecoptera) in the Japanese Archipelago. PLoS One 2019; 14:e0210269. [PMID: 30633758 PMCID: PMC6329508 DOI: 10.1371/journal.pone.0210269] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 12/19/2018] [Indexed: 11/30/2022] Open
Abstract
The generation of the high species diversity of insects in Japan was profoundly influenced by the formation of the Japanese Archipelago. We explored the species diversification and biogeographical history of the Nemouridae Billberg, 1820 family in the Japanese Archipelago using mitochondrial DNA and nuclear DNA markers. We collected 49 species among four genera: Indonemoura Baumann, 1975; Protonemura Kempny, 1898; Amphinemura, Ris 1902 and Nemoura Latreille, 1796 in Japan, China, South Korea and North America. We estimated their divergence times-based on three molecular clock node calibrations-using Bayesian phylogeography approaches. Our results suggested that Japanese Archipelago formation events resulted in diversification events in the middle of the Cretaceous (<120 Ma), speciation in the Paleogene (<50 Ma) and intra-species diversification segregated into eastern and western Japan of the Fossa Magna region at late Neogene (20 Ma). The Indonemoura samples were genetically separated into two clades-that of Mainland China and that of Japan. The Japanese clade clustered with the Nemouridae species from North America, suggesting the possibility of a colonisation event prior to the formation of the Japanese Archipelago. We believe that our results enhanced the understanding both of the origin of the species and of local species distribution in the Japanese Archipelago.
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Affiliation(s)
- Maribet Gamboa
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, Japan
| | - David Muranyi
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, Japan
- Deparment of Zoology, Plant Protection Institute Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Shota Kanmori
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, Japan
| | - Kozo Watanabe
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, Japan
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4
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Siahaan SA, Sakamoto H, Shinoda T, Takamatsu S. Geographic and temporal distributions of four genotypes found in Erysiphe gracilis var. gracilis , a powdery mildew of evergreen oaks (Erysiphales). MYCOSCIENCE 2018. [DOI: 10.1016/j.myc.2017.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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5
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Toussaint Fls EFA, Gillett CPDT. Rekindling Jeannel’s Gondwanan vision? Phylogenetics and evolution of Carabinae with a focus on Calosoma caterpillar hunter beetles. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx128] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Imai S, Kobayashi K, Ohkubo Y, Yagi N, Hasegawa E. Difference in evolutionary patterns of strongly or weakly selected characters among ant populations. Sci Rep 2016; 6:39451. [PMID: 27995972 PMCID: PMC5171879 DOI: 10.1038/srep39451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 11/23/2016] [Indexed: 11/28/2022] Open
Abstract
Despite being a central issue in evolutionary biology, few studies have examined the stasis of characters in populations with no gene flow. A possible mechanism of such stasis is stabilizing selection with similar peaks in each population. This study examined the evolutionary patterns of morphological characters with and without strong selection in ant populations. We show that compared to a character that seems to be less important, characters that are more important were less variable within and among populations. Microsatellite analyses showed significant genetic differences between populations, implying limited gene flow between them. The observed levels of genetic differentiation cannot be attributed to recent population separations. Thus, the observed differences in morphological variance seem to reflect the degree of selection on each character. The less important character changed proportionately with time, but such a pattern was not observed in more important characters. These results suggest that stabilizing selection maintains morphological stasis between populations of the same species with minimal gene flow independent of divergence times.
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Affiliation(s)
- Shuichiro Imai
- Laboratory of Animal Ecology, Department of Ecology and Systematics, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
| | - Kazuya Kobayashi
- Laboratory of Animal Ecology, Department of Ecology and Systematics, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
| | - Yusaku Ohkubo
- Laboratory of Animal Ecology, Department of Ecology and Systematics, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
| | - Norihiro Yagi
- Laboratory of Animal Ecology, Department of Ecology and Systematics, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
| | - Eisuke Hasegawa
- Laboratory of Animal Ecology, Department of Ecology and Systematics, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060-8589, Japan
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7
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OSAWA S, SU ZH, NISHIKAWA M, TOMINAGA O. Silent evolution. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2016; 92:455-461. [PMID: 27840392 PMCID: PMC5328790 DOI: 10.2183/pjab.92.455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/07/2016] [Indexed: 06/06/2023]
Abstract
Phylogenetic analyses using mitochondrial DNA sequences of several kinds of beetles have shown that their evolution included a silent stage in which no morphological changes took place. We thus propose a new category of evolutionary process called "silent evolution".
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Affiliation(s)
- Syozo OSAWA
- 1003, 2-4-7, Ushita-Asahi, Higashi-ku, Hiroshima, Japan
| | - Zhi-Hui SU
- JT Biohistory Research Hall, Murasaki-cho, Takatsuki, Osaka, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Machikaneyama, Toyonaka, Osaka, Japan
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Andújar C, Soria-Carrasco V, Serrano J, Gómez-Zurita J. Congruence test of molecular clock calibration hypotheses based on Bayes factor comparisons. Methods Ecol Evol 2014. [DOI: 10.1111/2041-210x.12151] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carmelo Andújar
- Departamento de Zoología y Antropología Física; Facultad de Veterinaria; Universidad de Murcia; 30071 Murcia Spain
| | - Víctor Soria-Carrasco
- Animal Biodiversity and Evolution; Institut de Biologia Evolutiva (CSIC-Univ. Pompeu Fabra); Pg. Marítim de la Barceloneta 37 08003 Barcelona Spain
| | - José Serrano
- Departamento de Zoología y Antropología Física; Facultad de Veterinaria; Universidad de Murcia; 30071 Murcia Spain
| | - Jesús Gómez-Zurita
- Animal Biodiversity and Evolution; Institut de Biologia Evolutiva (CSIC-Univ. Pompeu Fabra); Pg. Marítim de la Barceloneta 37 08003 Barcelona Spain
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Sekiné K, Hayashi F, Tojo K. Phylogeography of the East Asian polymitarcyid mayfly genusEphoron(Ephemeroptera: Polymitarcyidae): a comparative analysis of molecular and ecological characteristics. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12033] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Kazuki Sekiné
- Research Fellow of the Japan Society for the Promotion of Science (Division of Insect Sciences, National Institute of Agrobiological Sciences); Tsukuba; Ibaraki; 305-8634; Japan
| | - Fumio Hayashi
- Department of Biology; Tokyo Metropolitan University; Hachioji; Tokyo; 192-0397; Japan
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10
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Andújar C, Serrano J, Gómez-Zurita J. Winding up the molecular clock in the genus Carabus (Coleoptera: Carabidae): assessment of methodological decisions on rate and node age estimation. BMC Evol Biol 2012; 12:40. [PMID: 22455387 PMCID: PMC3368785 DOI: 10.1186/1471-2148-12-40] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 03/28/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rates of molecular evolution are known to vary across taxa and among genes, and this requires rate calibration for each specific dataset based on external information. Calibration is sensitive to evolutionary model parameters, partitioning schemes and clock model. However, the way in which these and other analytical aspects affect both the rates and the resulting clade ages from calibrated phylogenies are not yet well understood. To investigate these aspects we have conducted calibration analyses for the genus Carabus (Coleoptera, Carabidae) on five mitochondrial and four nuclear DNA fragments with 7888 nt total length, testing different clock models and partitioning schemes to select the most suitable using Bayes Factors comparisons. RESULTS We used these data to investigate the effect of ambiguous character and outgroup inclusion on both the rates of molecular evolution and the TMRCA of Carabus. We found considerable variation in rates of molecular evolution depending on the fragment studied (ranging from 5.02% in cob to 0.26% divergence/My in LSU-A), but also on analytical conditions. Alternative choices of clock model, partitioning scheme, treatment of ambiguous characters, and outgroup inclusion resulted in rate increments ranging from 28% (HUWE1) to 1000% (LSU-B and ITS2) and increments in the TMRCA of Carabus ranging from 8.4% (cox1-A) to 540% (ITS2). Results support an origin of the genus Carabus during the Oligocene in the Eurasian continent followed by a Miocene differentiation that originated all main extant lineages. CONCLUSIONS The combination of several genes is proposed as the best strategy to minimise both the idiosyncratic behaviors of individual markers and the effect of analytical aspects in rate and age estimations. Our results highlight the importance of estimating rates of molecular evolution for each specific dataset, selecting for optimal clock and partitioning models as well as other methodological issues potentially affecting rate estimation.
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Affiliation(s)
- Carmelo Andújar
- Departamento de Zoología y Antropología Física. Facultad de Veterinaria, Universidad de Murcia, 30071 Murcia, Spain
| | - José Serrano
- Departamento de Zoología y Antropología Física. Facultad de Veterinaria, Universidad de Murcia, 30071 Murcia, Spain
| | - Jesús Gómez-Zurita
- Institut de Biologia Evolutiva (CSIC-UPF), Pg. Marítim de la Barceloneta 37, 08003 Barcelona, Spain
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11
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Su ZH, Okamoto M, Tominaga O, Akita K, Kashiwai N, Imura Y, Ojika T, Nagahata Y, Osawa S. Establishment of hybrid-derived offspring populations in the Ohomopterus ground beetles through unidirectional hybridization. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2006; 82:232-250. [PMID: 25792787 PMCID: PMC4343062 DOI: 10.2183/pjab.82.232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2006] [Accepted: 09/12/2006] [Indexed: 06/04/2023]
Abstract
An approach to deduce the mechanism of stabilization of the hybrid-derived populations in the Ohomopterus ground beetles has been made by comparative studies on the phylogenetic trees of the mitochondrial and nuclear DNA. A phylogenetic tree based on the internal transcribed spacer (ITS) of nuclear ribosomal gene roughly reflects the relations of morphological species group, while mitochondrial NADH dehydrogenase subunit 5 (ND5) gene shows a considerable different topology on the tree; there exist several geographically-linked lineages, most of which consist of more than one species. These results suggest that the replacement of mitochondria has occurred widely in the Ohomopterus species. In most cases, hybridization is unidirectional, i.e., the species A (♂) hybridized with another species B (♀) and not vice versa, with accompanied replacement of mitochondria of A by those of B. The results also suggest that partial or complete occupation of the distribution territory by a hybrid-derived morphological species. The morphological appearance of the resultant hybrid-derivatives are recognized as that of the original species A. Emergence of a morphological new species from a hybrid-derived population has been exemplified.
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Affiliation(s)
- Zhi-Hui Su
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125,
Japan
| | - Munehiro Okamoto
- Department of Laboratory Animal Science, School of Veterinary Medicine, Faculty of Agriculture, Tottori University, Tottori 680-8553,
Japan
| | | | - Katsumi Akita
- Hisaiiba-cho 66, D-304, Tsu-shi, Mie 514-1108,
Japan
| | - Noboru Kashiwai
- Hosen-Gakuen High School, Chuo, Nakano-ku, Tokyo 164-8628,
Japan
| | - Yûki Imura
- Shinohara-chô 1249-8, Kôhoku-ku, Yokohama 222-0026,
Japan
| | - Tooru Ojika
- Sato-machi, Gantotsuka 3-40, Anjo-shi, Aichi 446-0008,
Japan
| | | | - Syozo Osawa
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125,
Japan
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12
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Kiyoshi T, Sota T. Differentiation of the dragonfly genus Davidius (Odonata: Gomphidae) in Japan inferred from mitochondrial and nuclear gene genealogies. Zoolog Sci 2006; 23:1-8. [PMID: 16547400 DOI: 10.2108/zsj.23.1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
To infer the differentiation of Japanese Davidius dragonflies, we investigated the genealogies of the mitochondrial cytochrome oxidase subunit I gene (COI) and the nuclear ribosomal RNA gene region encompassing 18S, ITS1, 5.8S, and ITS2 sequences for three species endemic to Japan--Davidius nanus, D. fujiama, and D. moiwanus--as well as D. lunatus from the Korean Peninsula. According to the mitochondrial and nuclear gene genealogies, D. nanus and D. moiwanus are closely related and are sister to the continental species D. lunatus, whereas D. fujiama differentiated from an ancestor of the other three species. Although the mitochondrial DNA data did not resolve the relationships between D. nanus and three D. moiwanus subspecies, the nuclear DNA data indicate the monophyly of D. moiwanus and its subspecies. The nuclear gene genealogy suggests that isolated wetlands used by larval D. moiwanus derive from the ancestral riverine habitats of D. nanus and other Davidius species. The COI sequence divergence among local populations was much greater in D. moiwanus than in D. nanus, which may be the result of differences in the dispersal ranges associated with the habitat types of these species.
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Affiliation(s)
- Takuya Kiyoshi
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
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13
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Su ZH, Imura Y, Okamoto M, Kim CG, Zhou HZ, Paik JC, Osawa S. Phylogeny and evolution of Digitulati ground beetles (Coleoptera, Carabidae) inferred from mitochondrial ND5 gene sequences. Mol Phylogenet Evol 2004; 30:152-66. [PMID: 15022766 DOI: 10.1016/s1055-7903(03)00163-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Genealogical trees have been constructed using mitochondrial ND5 gene sequences of 87 specimens consisting of 32 species which have been believed to belong to the division Digitulati (one of the lineages of the subtribe Carabina) of the world. There have been recognized six lineages, which are well separated from each other. Each lineage contains the following genus: (1) the lineage A: Ohomopterus from Japan; (2) the lineage B: Isiocarabus from eastern Eurasian Continent; (3) the lineage C: Carabus from China which are further subdivided into three sublineages; (4) the lineage D: Carabus from USA; (5) the lineage E: Carabus from the Eurasian Continent, Japan and North America; and (6) the lineage F: Eucarabus from the Eurasian Continent. Additionally, the genus Acrocarabus which had been treated as a constituent of the division Archicarabomorphi has been recognized to be the 7th lineage of the division Digitulati from the ND5 genealogical analysis as well as morphology. These lineages are assumed to have radiated within a short period and are largely linked to their geographic distribution.
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Affiliation(s)
- Zhi-Hui Su
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan.
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14
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Su ZH, Imura Y, Okamoto M, Osawa S. Pattern of phylogenetic diversification of the Cychrini ground beetles in the world as deduced mainly from sequence comparisons of the mitochondrial genes. Gene 2004; 326:43-57. [PMID: 14729262 DOI: 10.1016/j.gene.2003.10.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The phylogenetic position of the tribe Cychrini within the subfamily Carabinae (the family Carabidae) was estimated by comparing the nucleotide sequences of the mitochondrial NADH dehydrogenase subunit 5 (ND5) gene and the nuclear 28S ribosomal DNA (rDNA). The phylogenetic trees suggest that the Cychrini would most probably be the oldest line within the Carabinae. Phylogenetic trees were constructed by comparing the mitochondrial cytochrome C oxidase subunit I (COI) gene sequences from 33 species of the Cychrini from various localities that include the whole distribution ranges of the representative species within all the known genera in the world. The trees suggest that the Cychrini members radiated into a number of phylogenetic lineages within a short period, starting about 44 million years ago (MYA). Most of the phylogenetic lineages or sublineages are geographically linked, each consisting of a single or only a few species without scarce morphological differentiation in spite of their long evolutionary histories (silent or near-silent evolution [see Adv. Biophys. 36 (1999) 65; J. Mol. Evol. 53 (2001) 517]). The fact suggests that the geographic isolation per se did not bring about conspicuous morphological differentiation. The phylogenetic lineages of the Cychrini well correspond to the taxonomically defined genera and the subgenera.
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Affiliation(s)
- Zhi-Hui Su
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan.
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15
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Su ZH, Imura Y, Zhou HZ, Okamoto M, Osawa S. Mode of morphological differentiation in the Latitarsi-ground beetles (Coleoptera, Carabidae) of the world inferred from a phylogenetic tree of mitochondrial ND5 gene sequences. Genes Genet Syst 2003; 78:53-70. [PMID: 12655138 DOI: 10.1266/ggs.78.53] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Latitarsi is one large division of the subtribe Carabina (subfamily Carabinae, family Carabidae), and has been considered as a discrete morphological group consisting of 17 genera. The phylogenetic relationships and evolutionary pattern of the Latitarsi ground beetles have been investigated by analyzing mitochondrial NADH dehydrogenase subunit 5 (ND5) gene sequences. The phylogenetic tree suggests that the Latitarsi members do not form a single cluster, i.e., not monophyletic and at least 16 lineages belonging to the so-called Latitarsi emerged at about the same time of the Carabina radiation together with the members of other divisions. This suggests that these lineages (A, B, C, H, L, N, O, P, Q, R, S, T, U, V, W and X in Fig. 2a) may be treated each as a phylogenetically distinct division equivalent to other divisions. The group with bootstrap value of more than 80 percent has been considered as a single lineage (division) with two exceptions, V and X. The independency of each lineage has been assumed by the traditional morphology as well as a single clustering on the trees constructed by independent methods, unchanged topology by replacement of outgroups, etc. Generally speaking, the members in a single lineage are geographically linked. Many phylogenetic lineages are composed of a single or only a few species without conspicuous morphological differentiation. In contrast to such a "silent morphological evolution", a remarkable morphological differentiation occasionally took place in several lineages.
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Affiliation(s)
- Zhi-Hui Su
- JT Biohistory Research Hall, Takatsuki, Osaka, Japan.
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Yagi T, Katoh T, Chichvarkhin A, Shinkawa T, Omoto K. Molecular phylogeny of butterflies Parnassius glacialis and P. stubbendorfii at various localities in East Asia. Genes Genet Syst 2001; 76:229-34. [PMID: 11732631 DOI: 10.1266/ggs.76.229] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The phylogeny of butterflies, Parnassius stubbendorfii and P. glacialis, collected at various localities in the Japan archipelago and the eastern part of the Asian continent was analyzed using mitochondrial DNA sequences coding for NADH dehydrogenase subunit 5 (805 bp). The molecular phylogenetic trees revealed that P. glacialis and P. stubbendorfii diverged from a common ancestor, and then the populations inhabiting the Japan archipelago and the Asian continent diverged in each species. The reliability of these divergences was supported by high bootstrap values. The divergences within the Japan archipelago and within the Asian continent in each species were unclear because of low bootstrap values. The genetic distance and a rough time-estimation in the UPGMA tree suggest that the both populations of P. glacialis and P. stubbendorfii may have been isolated in the Japan archipelago at the early time (about 1.7-2.0 Mya) of the glacial period in the Pleistocene. The genetic distance between the Japanese and the continental subspecies may be large enough that they can be classified as different species, in comparison with the genetic distances among some other parnassian species.
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Affiliation(s)
- T Yagi
- Research Institute for Advanced Science and Technology, Osaka Prefecture University, Sakai, Japan.
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Kim CG, Tominaga O, Su ZH, Osawa S. Differentiation within the genus Leptocarabus (excl. L. kurilensis) in the Japanese Islands as deduced from mitochondrial ND5 gene sequences (Coleoptera, Carabidae). Genes Genet Syst 2000; 75:335-42. [PMID: 11280008 DOI: 10.1266/ggs.75.335] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The phylogenetic trees have been constructed for the mitochondrial ND5 gene sequences from the Japanese Leptocarabus ground beetles, which contain 101 specimens collected from nearly the complete distribution ranges of them consisting of five morphological species, i.e., Leptocarabus procerulus, L. kumagaii, L. hiurai, L. kyushuensis and L. arboreus. On the trees, there are recognized two major lineages, each of which is further divided into two or more sublineages. The phylogenetic lines are geographically linked. Two or more species occur in a single lineage, and the same species appear in different lines. We suggest that transformation from one type of morphology to another took place in parallel in various periods of evolution of the Japanese Leptocarabus. From the phylogenetic tree and the dating from the nucleotide substitution rate and the geohistorical data it is inferred that the ancestry of all the Japanese Leptocarabus species was derived from a protoform of L. kyushuensis inhabited the ancient Japan area, followed by separation into two lineages after split of the Japanese Islands from the Eurasian Continent. They then propagated distribution to occupy their own habitat ranges, during which the morphological transformation took place in some lineages.
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Affiliation(s)
- C G Kim
- Lab. of Evolutionary Genetics, National Institute of Genetics, Mishima, 411-8540, Japan
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