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Chaitanya R, McGuire JA, Karanth P, Meiri S. Their fates intertwined: diversification patterns of the Asian gliding vertebrates may have been forged by dipterocarp trees. Proc Biol Sci 2023; 290:20231379. [PMID: 37583322 PMCID: PMC10427812 DOI: 10.1098/rspb.2023.1379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 07/19/2023] [Indexed: 08/17/2023] Open
Abstract
The repeated evolution of gliding in diverse Asian vertebrate lineages is hypothesized to have been triggered by the dominance of tall dipterocarp trees in the tropical forests of Southeast Asia. These dipterocarp forests have acted as both centres of diversification and climatic refugia for gliding vertebrates, and support most of their extant diversity. We predict similarities in the diversification patterns of dipterocarp trees and gliding vertebrates, and specifically test whether episodic diversification events such as rate shifts and/or mass extinctions were temporally congruent in these groups. We analysed diversification patterns in reconstructed timetrees of Asian dipterocarps, the most speciose gliding vertebrates from different classes (Draco lizards, gliding frogs and Pteromyini squirrels) and compared them with similar-sized clades of non-gliding relatives (Diploderma lizards, Philautus frogs and Callosciurinae squirrels) from Southeast Asia. We found significant declines in net-diversification rates of dipterocarps and the gliding vertebrates during the Pliocene-Pleistocene, but not in the non-gliding groups. We conclude that the homogeneity and temporal coincidence of these rate declines point to a viable ecological correlation between dipterocarps and the gliding vertebrates. Further, we suggest that while the diversification decay in dipterocarps was precipitated by post-Miocene aridification of Asia, the crises in the gliding vertebrates were induced by both events concomitantly.
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Affiliation(s)
| | - Jimmy A. McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Praveen Karanth
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Shai Meiri
- School of Zoology, Tel Aviv University 6997801, Tel Aviv, Israel
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Tian Z, Zeng P, Lu X, Zhou T, Han Y, Peng Y, Xiao Y, Zhou B, Liu X, Zhang Y, Yu Y, Li Q, Zong H, Zhang F, Jiang H, He J, Cai J. Thirteen Dipterocarpoideae genomes provide insights into their evolution and borneol biosynthesis. Plant Commun 2022; 3:100464. [PMID: 36303430 PMCID: PMC9700207 DOI: 10.1016/j.xplc.2022.100464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 09/26/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
Dipterocarpoideae, the largest subfamily of the Dipterocarpaceae, is a dominant component of Southeast Asian rainforests and is widely used as a source of wood, damar resin, medicine, and essential oil. However, many Dipterocarpoideae species are currently on the IUCN Red List owing to severe degradation of their habitats under global climate change and human disturbance. Genetic information regarding these taxa has only recently been reported with the sequencing of four Dipterocarp genomes, providing clues to the function and evolution of these species. Here, we report on 13 high-quality Dipterocarpoideae genome assemblies, ranging in size from 302.6 to 494.8 Mb and representing the five most species-rich genera in Dipterocarpoideae. Molecular dating analyses support the Western Gondwanaland origin of Dipterocarpaceae. Based on evolutionary analysis, we propose a three-step chromosome evolution scenario to describe the karyotypic evolution from an ancestor with six chromosomes to present-day species with 11 and 7 chromosomes. We discovered an expansion of genes encoding cellulose synthase (CesA), which is essential for cellulose biosynthesis and secondary cell-wall formation. We functionally identified five bornyl diphosphate synthase (BPPS) genes, which specifically catalyze the biosynthesis of borneol, a natural medicinal compound extracted from damar resin and oils, thus providing a basis for large-scale production of natural borneol in vitro.
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Affiliation(s)
- Zunzhe Tian
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Peng Zeng
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Xiaoyun Lu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China; Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Tinggan Zhou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yuwei Han
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yingmei Peng
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yunxue Xiao
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kuming 650223, China
| | - Botong Zhou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xue Liu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yongting Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yang Yu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Qiong Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Hang Zong
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Feining Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Huifeng Jiang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China.
| | - Juan He
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China.
| | - Jing Cai
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China.
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Yu Y, Han Y, Peng Y, Tian Z, Zeng P, Zong H, Zhou T, Cai J. Comparative and phylogenetic analyses of eleven complete chloroplast genomes of Dipterocarpoideae. Chin Med 2021; 16:125. [PMID: 34823565 PMCID: PMC8620154 DOI: 10.1186/s13020-021-00538-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/15/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND In South-east Asia, Dipterocarpoideae is predominant in most mature forest communities, comprising around 20% of all trees. As large quantity and high quality wood are produced in many species, Dipterocarpoideae plants are the most important and valuable source in the timber market. The d-borneol is one of the essential oil components from Dipterocarpoideae (for example, Dryobalanops aromatica or Dipterocarpus turbinatus) and it is also an important traditional Chinese medicine (TCM) formulation known as "Bingpian" in Chinese, with antibacterial, analgesic and anti-inflammatory effects and can enhance anticancer efficiency. METHODS In this study, we analyzed 20 chloroplast (cp) genomes characteristics of Dipterocarpoideae, including eleven newly reported genomes and nine cp genomes previously published elsewhere, then we explored the chloroplast genomic features, inverted repeats contraction and expansion, codon usage, amino acid frequency, the repeat sequences and selective pressure analyses. At last, we constructed phylogenetic relationships of Dipterocarpoideae and found the potential barcoding loci. RESULTS The cp genome of this subfamily has a typical quadripartite structure and maintains a high degree of consistency among species. There were slightly more tandem repeats in cp genomes of Dipterocarpus and Vatica, and the psbH gene was subjected to positive selection in the common ancestor of all the 20 species of Dipterocarpoideae compared with three outgroups. Phylogenetic tree showed that genus Shorea was not a monophyletic group, some Shorea species and genus Parashorea are placed in one clade. In addition, the rpoC2 gene can be used as a potential marker to achieve accurate and rapid species identification in subfamily Dipterocarpoideae. CONCLUSIONS Dipterocarpoideae had similar cp genomic features and psbM, rbcL, psbH may function in the growth of Dipterocarpoideae. Phylogenetic analysis suggested new taxon treatment is needed for this subfamily indentification. In addition, rpoC2 is potential to be a barcoding gene to TCM distinguish.
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Affiliation(s)
- Yang Yu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
| | - Yuwei Han
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
| | - Yingmei Peng
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
| | - Zunzhe Tian
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
| | - Peng Zeng
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, 999078 Macau, China
| | - Hang Zong
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
| | - Tinggan Zhou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
| | - Jing Cai
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
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Carneiro de Melo Moura C, Brambach F, Jair Hernandez Bado K, Krutovsky KV, Kreft H, Tjitrosoedirdjo SS, Siregar IZ, Gailing O. Integrating DNA Barcoding and Traditional Taxonomy for the Identification of Dipterocarps in Remnant Lowland Forests of Sumatra. Plants (Basel) 2019; 8:plants8110461. [PMID: 31671512 PMCID: PMC6918277 DOI: 10.3390/plants8110461] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/07/2019] [Accepted: 10/17/2019] [Indexed: 11/16/2022]
Abstract
DNA barcoding has been used as a universal tool for phylogenetic inferences and diversity assessments, especially in poorly studied species and regions. The aim of this study was to contrast morphological taxonomy and DNA barcoding, using the three frequently used markers matK, rbcL, and trnL-F, to assess the efficiency of DNA barcoding in the identification of dipterocarps in Sumatra, Indonesia. The chloroplast gene matK was the most polymorphic among these three markers with an average interspecific genetic distance of 0.020. The results of the molecular data were mostly in agreement with the morphological identification for the clades of Anthoshorea, Hopea, Richetia, Parashorea, and Anisoptera, nonetheless these markers were inefficient to resolve the relationships within the Rubroshorea group. The maximum likelihood and Bayesian inference phylogenies identified Shorea as a paraphyletic genus, Anthoshorea appeared as sister to Hopea, and Richetia was sister to Parashorea. A better discriminatory power among dipterocarp species provided by matK and observed in our study suggests that this marker has a higher evolutionary rate than the other two markers tested. However, a combination of several different barcoding markers is essential for reliable identification of the species at a lower taxonomic level.
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Affiliation(s)
- Carina Carneiro de Melo Moura
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany.
| | - Fabian Brambach
- Biodiversity, Macroecology and Biogeography, University of Göttingen, Büsgenweg 1, 37077 Göttingen, Germany.
| | - Kevin Jair Hernandez Bado
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany.
| | - Konstantin V Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany.
- Center for Integrated Breeding Research, University of Göttingen, Albrecht-Thaer-Weg 3, 37075 Göttingen, Germany.
- Laboratory of Population Genetics, N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin Str., Moscow 119333, Russian.
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 50a/2 Akademgorodok, Krasnoyarsk 660036, Russia.
- Department of Ecosystem Science and Management, Texas A&M University, College Station, TX 77843-2138, USA.
| | - Holger Kreft
- Biodiversity, Macroecology and Biogeography, University of Göttingen, Büsgenweg 1, 37077 Göttingen, Germany.
| | | | - Iskandar Z Siregar
- Department of Silviculture, Faculty of Forestry, Bogor Agricultural University, Dramaga Campus, Bogor 16680, Indonesia.
| | - Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany.
- Center for Integrated Breeding Research, University of Göttingen, Albrecht-Thaer-Weg 3, 37075 Göttingen, Germany.
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Heckenhauer J, Samuel R, Ashton PS, Abu Salim K, Paun O. Phylogenomics resolves evolutionary relationships and provides insights into floral evolution in the tribe Shoreeae (Dipterocarpaceae). Mol Phylogenet Evol 2018; 127:1-13. [PMID: 29778722 DOI: 10.1016/j.ympev.2018.05.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 05/11/2018] [Accepted: 05/11/2018] [Indexed: 10/16/2022]
Abstract
A supra-annual, community-level synchronous flowering prevails in several parts of the tropical forests of Southeast Asia and its evolution has been hypothesized to be linked to pollinator shifts. The aseasonal Southeast Asian lowland rainforests are dominated by Dipterocarpaceae, which exhibit great floral diversity, a range of pollination syndromes and include species with annual and supra-annual gregarious flowering. Phylogenetic relationships within this family are still unclear, especially in the tribe Shoreeae. Here, we develop a pipeline to maximize recovery of genome-wide SNPs from restriction-site associated DNA sequencing (RADseq) in non-model organisms across wide phylogenetic scales. We then infer phylogenomic relationships in the tribe Shoreeae using both traditional and coalescent analyses. The phylogenetic trees obtained with these methods are congruent to each other and highly resolved. They allow reconstructing the evolutionary patterns of floral traits (number of stamens, anther structure and anther/appendage size) in the group. Our inferences indicate that species with many stamens, but smaller, globose anthers and longer appendages and have evolved multiple times from species with fewer stamens, but larger, oblong anthers and shorter appendages. This could have happened in parallel to iterative shifts in pollinators across the uncovered phylogeny from larger, longer generation to smaller, shorter-generation insects that can quickly build up the necessary population sizes during mass flowering episodes.
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Affiliation(s)
- Jacqueline Heckenhauer
- University of Vienna, Department of Botany and Biodiversity Research, Rennweg 14, 1030 Vienna, Austria.
| | - Rosabelle Samuel
- University of Vienna, Department of Botany and Biodiversity Research, Rennweg 14, 1030 Vienna, Austria
| | - Peter S Ashton
- Harvard University, Department of Organismic and Evolutionary Biology, 26 Oxford St, Cambridge, MA 02138, United States
| | - Kamariah Abu Salim
- University of Brunei Darussalam, Environmental and Life Sciences, Faculty of Science, Tungku Link Road, Gadong 1410, Brunei Darussalam
| | - Ovidiu Paun
- University of Vienna, Department of Botany and Biodiversity Research, Rennweg 14, 1030 Vienna, Austria
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