Phylogeny and Historical Biogeography of the East Asian <i>Clematis</i> Group, Sect. <i>Tubulosae</i>, Inferred from Phylogenomic Data
The evolutionary history of <i>Clematis</i> section <i>Tubulosae</i>, an East Asian endemic lineage, has not been comprehensively studied. In this study, we reconstruct the phylogeny of this section with a complete sampling using a phylogenomic approach. The genome skimming m...
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MDPI AG
2023-02-01
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| Series: | International Journal of Molecular Sciences |
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| author | Rudan Lyu Jiamin Xiao Mingyang Li Yike Luo Jian He Jin Cheng Lei Xie |
| author_facet | Rudan Lyu Jiamin Xiao Mingyang Li Yike Luo Jian He Jin Cheng Lei Xie |
| author_sort | Rudan Lyu |
| collection | DOAJ |
| description | The evolutionary history of <i>Clematis</i> section <i>Tubulosae</i>, an East Asian endemic lineage, has not been comprehensively studied. In this study, we reconstruct the phylogeny of this section with a complete sampling using a phylogenomic approach. The genome skimming method was applied to obtain the complete plastome sequence, the nuclear ribosomal DNA (nrDNA), and the nuclear SNPs data for phylogenetic reconstruction. Using a Bayesian molecular clock approach and ancestral range reconstruction, we reconstruct biogeographical history and discuss the biotic and abiotic factors that may have shaped the distribution patterns of the section. Both nuclear datasets better resolved the phylogeny of the sect. <i>Tubulosae</i> than the plastome sequence. Sect. <i>Tubulosae</i> was resolved as a monophyletic group sister to a clade mainly containing species from the sect. <i>Clematis</i> and sect. <i>Aspidanthera</i>. Within sect. <i>Tubulosae</i>, two major clades were resolved by both nuclear datasets. Two continental taxa, <i>C. heracleifolia</i> and <i>C. tubulosa</i> var. <i>ichangensis</i>, formed one clade. One continental taxon, <i>C. tubulosa</i>, and all the other species from Taiwan island, the Korean peninsula, and the Japanese archipelago formed the other clade. Molecular dating results showed that sect. <i>Tubulosae</i> diverged from its sister clade in the Pliocene, and all the current species diversified during the Pleistocene. Our biogeographical reconstruction suggested that sect. <i>Tubulosae</i> evolved and began species diversification, most likely in mainland China, then dispersed to the Korean peninsula, and then expanded its range through the Japanese archipelago to Taiwan island. Island species diversity may arise through allopatric speciation by vicariance events following the range fragmentation triggered by the climatic oscillation and sea level change during the Pleistocene epoch. Our results highlight the importance of climatic oscillation during the Pleistocene to the spatial-temporal diversification patterns of the sect. <i>Tubulosae</i>. |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T09:38:49Z |
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| spelling | doaj.art-4814c64b1f054384b61581f8ef4dcb1a2023-11-16T17:06:23ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-02-01243305610.3390/ijms24033056Phylogeny and Historical Biogeography of the East Asian <i>Clematis</i> Group, Sect. <i>Tubulosae</i>, Inferred from Phylogenomic DataRudan Lyu0Jiamin Xiao1Mingyang Li2Yike Luo3Jian He4Jin Cheng5Lei Xie6School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaSchool of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaCollege of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, ChinaSchool of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaSchool of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaCollege of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, ChinaSchool of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, ChinaThe evolutionary history of <i>Clematis</i> section <i>Tubulosae</i>, an East Asian endemic lineage, has not been comprehensively studied. In this study, we reconstruct the phylogeny of this section with a complete sampling using a phylogenomic approach. The genome skimming method was applied to obtain the complete plastome sequence, the nuclear ribosomal DNA (nrDNA), and the nuclear SNPs data for phylogenetic reconstruction. Using a Bayesian molecular clock approach and ancestral range reconstruction, we reconstruct biogeographical history and discuss the biotic and abiotic factors that may have shaped the distribution patterns of the section. Both nuclear datasets better resolved the phylogeny of the sect. <i>Tubulosae</i> than the plastome sequence. Sect. <i>Tubulosae</i> was resolved as a monophyletic group sister to a clade mainly containing species from the sect. <i>Clematis</i> and sect. <i>Aspidanthera</i>. Within sect. <i>Tubulosae</i>, two major clades were resolved by both nuclear datasets. Two continental taxa, <i>C. heracleifolia</i> and <i>C. tubulosa</i> var. <i>ichangensis</i>, formed one clade. One continental taxon, <i>C. tubulosa</i>, and all the other species from Taiwan island, the Korean peninsula, and the Japanese archipelago formed the other clade. Molecular dating results showed that sect. <i>Tubulosae</i> diverged from its sister clade in the Pliocene, and all the current species diversified during the Pleistocene. Our biogeographical reconstruction suggested that sect. <i>Tubulosae</i> evolved and began species diversification, most likely in mainland China, then dispersed to the Korean peninsula, and then expanded its range through the Japanese archipelago to Taiwan island. Island species diversity may arise through allopatric speciation by vicariance events following the range fragmentation triggered by the climatic oscillation and sea level change during the Pleistocene epoch. Our results highlight the importance of climatic oscillation during the Pleistocene to the spatial-temporal diversification patterns of the sect. <i>Tubulosae</i>.https://www.mdpi.com/1422-0067/24/3/3056<i>Clematis</i> sect. <i>Tubulosae</i>genome skimminghistorical biogeographyphylogenomic analysisRanunculaceaeSino-Japanese Floristic Region |
| spellingShingle | Rudan Lyu Jiamin Xiao Mingyang Li Yike Luo Jian He Jin Cheng Lei Xie Phylogeny and Historical Biogeography of the East Asian <i>Clematis</i> Group, Sect. <i>Tubulosae</i>, Inferred from Phylogenomic Data International Journal of Molecular Sciences <i>Clematis</i> sect. <i>Tubulosae</i> genome skimming historical biogeography phylogenomic analysis Ranunculaceae Sino-Japanese Floristic Region |
| title | Phylogeny and Historical Biogeography of the East Asian <i>Clematis</i> Group, Sect. <i>Tubulosae</i>, Inferred from Phylogenomic Data |
| title_full | Phylogeny and Historical Biogeography of the East Asian <i>Clematis</i> Group, Sect. <i>Tubulosae</i>, Inferred from Phylogenomic Data |
| title_fullStr | Phylogeny and Historical Biogeography of the East Asian <i>Clematis</i> Group, Sect. <i>Tubulosae</i>, Inferred from Phylogenomic Data |
| title_full_unstemmed | Phylogeny and Historical Biogeography of the East Asian <i>Clematis</i> Group, Sect. <i>Tubulosae</i>, Inferred from Phylogenomic Data |
| title_short | Phylogeny and Historical Biogeography of the East Asian <i>Clematis</i> Group, Sect. <i>Tubulosae</i>, Inferred from Phylogenomic Data |
| title_sort | phylogeny and historical biogeography of the east asian i clematis i group sect i tubulosae i inferred from phylogenomic data |
| topic | <i>Clematis</i> sect. <i>Tubulosae</i> genome skimming historical biogeography phylogenomic analysis Ranunculaceae Sino-Japanese Floristic Region |
| url | https://www.mdpi.com/1422-0067/24/3/3056 |
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