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Liu Y, Lai YJ, Ye JF, Hu HH, Peng DX, Lu LM, Sun H, Chen ZD. The Sino-Himalayan flora evolved from lowland biomes dominated by tropical floristic elements. BMC Biol 2023; 21:239. [PMID: 37904140 PMCID: PMC10617089 DOI: 10.1186/s12915-023-01746-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 10/24/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND The Sino-Himalayan flora harbors highly diverse high-elevation biotas, but our understanding of its evolutionary history in temporal and spatial dimensions is limited. In this study, we integrated a dated phylogenetic tree with comprehensive species distribution data to investigate changes over time and space in floristic elements, including the tropical, Tethys, northern temperate, and East Asian floristic elements, across the entire Sino-Himalaya and its three floristic regions: the Yunnan Plateau, Hengduan Mountains, and East Himalaya regions. RESULTS Our results revealed that the Sino-Himalayan flora developed from lowland biomes and was predominantly characterized by tropical floristic elements before the collision between the Indian subcontinent and Eurasia during the Early Cenozoic. Subsequently, from the Late Eocene onwards, the uplifts of the Himalaya and Hengduan Mountains transformed the Sino-Himalayan region into a wet and cold plateau, on which harsh and diverse ecological conditions forced the rapid evolution of local angiosperms, giving birth to characteristic taxa adapted to the high altitudes and cold habitat. The percentage of temperate floristic elements increased and exceeded that of tropical floristic elements by the Late Miocene. CONCLUSIONS The Sino-Himalayan flora underwent four significant formation periods and experienced a considerable increase in endemic genera and species in the Miocene, which remain crucial to the present-day patterns of plant diversity. Our findings support the view that the Sino-Himalayan flora is relatively young but has ancient origins. The three major shifts in the divergence of genera and species during the four formation periods were primarily influenced by the uplifts of the Himalaya and Hengduan Mountains and the onset and intensification of the Asian monsoon system. Additionally, the temporal patterns of floristic elements differed among the three floristic regions of the Sino-Himalaya, indicating that the uplift of the Himalaya and surrounding areas was asynchronous. Compared to the Yunnan Plateau region, the East Himalaya and Hengduan Mountains experienced more recent and drastic uplifts, resulting in highly intricate topography with diverse habitats that promoted the rapid radiation of endemic genera and species in these regions.
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Affiliation(s)
- Yun Liu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang-Jun Lai
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Jian-Fei Ye
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Hai-Hua Hu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Dan-Xiao Peng
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Li-Min Lu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Hang Sun
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
| | - Zhi-Duan Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, 430074, China.
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Nguyen HQ, Ho PT, Kong S, Bae Y, Pham TH, La HT, Jang Y. A time-calibrated mitogenomic phylogeny suggests that Korean Hyalessa fuscata is a bridge between Chinese and Japanese H. maculaticollis. J Genet 2022. [DOI: 10.1007/s12041-022-01405-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Zhang JY, Liao M, Cheng YH, Feng Y, Ju WB, Deng HN, Li X, Plenković-Moraj A, Xu B. Comparative Chloroplast Genomics of Seven Endangered Cypripedium Species and Phylogenetic Relationships of Orchidaceae. FRONTIERS IN PLANT SCIENCE 2022; 13:911702. [PMID: 35812969 PMCID: PMC9257239 DOI: 10.3389/fpls.2022.911702] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
The species in the genus Cypripedium (Orchidaceae) are considered endangered, mainly distributed in the temperate regions of the Northern Hemisphere, with high ornamental and economic value. Despite previous extensive studies based on both morphology and molecular data, species and sections relationships within Cypripedium remain controversial. Here, we employed two newly generated Cypripedium chloroplast genomes with five other published genomes to elucidate their genomic characteristics. The two genomes were 162,773-207,142 bp in length and contained 128-130 genes, including 82-84 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. We identified 2,192 simple sequence repeats, 786 large repeat sequences, and 7,929 variable loci. The increase of repeat sequences (simple sequence repeats and large repeat sequences) causes a significant amplification in the chloroplast genome size of Cypripedium. The expansion of the IR region led to the pseudogenization or loss of genes in the SSC region. In addition, we identified 12 highly polymorphic loci (Pi > 0.09) suitable for inferring the phylogeny of Cypripedium species. Based on data sets of whole chloroplast genomes (IRa excluded) and protein-coding sequences, a well-supported phylogenetic tree was reconstructed, strongly supporting the five subfamilies of Orchidaceae and the genus Cypripedium as monophyletic taxa. Our findings also supported that C. palangshanense belonged to sect. Palangshanensia rather than sect. Retinervia. This study also enriched the genomic resources of Cypripedium, which may help to promote the conservation efforts of these endangered species.
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Affiliation(s)
- Jun-Yi Zhang
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Min Liao
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yue-Hong Cheng
- Wolong National Natural Reserve Administration Bureau, Sichuan, China
| | - Yu Feng
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Wen-Bing Ju
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Heng-Ning Deng
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xiong Li
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | - Bo Xu
- China-Croatia “Belt and Road” Joint Laboratory on Biodiversity and Ecosystem Services, CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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Ye Y, Kitayama K, Onoda Y. A cost-benefit analysis of leaf carbon economy with consideration of seasonal changes in leaf traits for sympatric deciduous and evergreen congeners: implications for their coexistence. THE NEW PHYTOLOGIST 2022; 234:1047-1058. [PMID: 35133649 DOI: 10.1111/nph.18022] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
Deciduous and evergreen species, which have evolved repeatedly across different clades, can coexist in a given environment despite substantial differences in their leaf traits. It remains unclear how these two groups differ in the development of leaf traits over their lifespans or how their carbon economy - the balance between lifetime carbon gain and leaf construction cost - is determined. We determined the photosynthetic rate (Aarea ), leaf mass per area (LMA), leaf mechanical strength and leaf water potentials and estimated the lifetime carbon gain and leaf construction cost of five closely related pairs of evergreen and deciduous species co-occurring in a temperate forest. Aarea of evergreen species was lower during their first spring, similar in summer and higher than the autumn until the following spring than their deciduous counterparts. Leaf mechanical strength, osmotic pressures and LMA increased continuously towards winter in evergreen species while remaining largely constant in deciduous species. The ratio of lifetime carbon gain to leaf construction cost was similar between the two groups. The additional cost associated with enduring winter is paid back by a longer revenue of photosynthesis in evergreen species, allowing evergreen and deciduous leaf habits to coexist in the seasonal environment.
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Affiliation(s)
- Yunhan Ye
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Kanehiro Kitayama
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Yusuke Onoda
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
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Phylogenomics and diversification drivers of the Eastern Asian – Eastern North American disjunct Podophylloideae. Mol Phylogenet Evol 2022; 169:107427. [DOI: 10.1016/j.ympev.2022.107427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/02/2021] [Accepted: 12/25/2021] [Indexed: 11/17/2022]
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Cai R, Ané C. Assessing the fit of the multi-species network coalescent to multi-locus data. Bioinformatics 2021; 37:634-641. [PMID: 33027508 DOI: 10.1093/bioinformatics/btaa863] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/14/2020] [Accepted: 09/22/2020] [Indexed: 01/25/2023] Open
Abstract
MOTIVATION With growing genome-wide molecular datasets from next-generation sequencing, phylogenetic networks can be estimated using a variety of approaches. These phylogenetic networks include events like hybridization, gene flow or horizontal gene transfer explicitly. However, the most accurate network inference methods are computationally heavy. Methods that scale to larger datasets do not calculate a full likelihood, such that traditional likelihood-based tools for model selection are not applicable to decide how many past hybridization events best fit the data. We propose here a goodness-of-fit test to quantify the fit between data observed from genome-wide multi-locus data, and patterns expected under the multi-species coalescent model on a candidate phylogenetic network. RESULTS We identified weaknesses in the previously proposed TICR test, and proposed corrections. The performance of our new test was validated by simulations on real-world phylogenetic networks. Our test provides one of the first rigorous tools for model selection, to select the adequate network complexity for the data at hand. The test can also work for identifying poorly inferred areas on a network. AVAILABILITY AND IMPLEMENTATION Software for the goodness-of-fit test is available as a Julia package at https://github.com/cecileane/QuartetNetworkGoodnessFit.jl. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ruoyi Cai
- Department of Statistics, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Cécile Ané
- Department of Statistics, University of Wisconsin - Madison, Madison, WI 53706, USA.,Department of Botany, University of Wisconsin - Madison, Madison, WI 53706, USA
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