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Kuo HC, Schoneman T, Gao LM, Gruezo WS, Amoroso VB, Yang Y, Yang KC, Chien CT, Möller M, Wang CN. A leading-edge scenario in the phylogeography and evolutionary history of East Asian insular Taxus in Taiwan and the Philippines. Front Genet 2024; 15:1372309. [PMID: 38756448 PMCID: PMC11096487 DOI: 10.3389/fgene.2024.1372309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/15/2024] [Indexed: 05/18/2024] Open
Abstract
The cool temperate origin of gymnosperm Taxus species in East Asia is specifically diverse and widespread. Certain lineages have managed to extend their distribution further south to subtropical and tropical islands such as Taiwan and the Philippines. To address questions including whether these insular lineages, recently identified as T. phytonii, have become genetically distinct from each other and from their continental relatives, and when and how they colonized their residing islands, we sampled over 11 populations, covering 179 Taxus individuals from Taiwan and the Philippines. Using four cpDNA and one nuclear marker, we showed in population genetic and genealogical analyses that the two insular lineages were genetically distinct from each other and also from other continental Taxus and that they represented each other's closest relative. Estimated with the coalescent-based multi-type tree (MTT) analyses, we inferred an origin of Taiwanese T. phytonii more ancient than 2.49 Mya and that of Philippine T. phytonii more ancient than 1.08 Mya. In addition, the divergence demographic history revealed by both MTT and isolation with migration (IM) analyses indicated the presence of recent post-split migrations from a continental taxon, T. mairei, to Taiwanese T. phytonii, as well as from Taiwanese T. phytonii to Philippine T. phytonii. Overall, this study suggests Taiwan as a stepping stone through which the temperate-origin yew trees can extend their distributions to tropical regions such as the Philippines.
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Affiliation(s)
- Hao-Chih Kuo
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Travis Schoneman
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Lian-Ming Gao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - William Sm. Gruezo
- Plant Biology Division, College of Arts and Sciences, Institute of Biological Sciences, University of the Philippines at Los Baños, Laguna, Philippines
| | - Victor B. Amoroso
- Center for Biodiversity Research and Extension in Mindanao (CEBREM), Central Mindanao University, Mindanao, Philippines
| | - Yang Yang
- Tainan District Agricultural Research and Extension Station, Ministry of Agriculture, Tainan, Taiwan
| | - Kuo-Cheng Yang
- General Education Center, Providence University, Taichung, Taiwan
| | - Ching-Te Chien
- Botanical Garden Division, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Michael Möller
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
| | - Chun-Neng Wang
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
- Department of Life Science, National Taiwan University, Taipei, Taiwan
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Kou Y, Fan D, Cheng S, Yang Y, Wang M, Wang Y, Zhang Z. Peripatric speciation within Torreya fargesii (Taxaceae) in the Hengduan Mountains inferred from multi-loci phylogeography. BMC Ecol Evol 2023; 23:74. [PMID: 38087226 PMCID: PMC10714551 DOI: 10.1186/s12862-023-02183-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND The Hengduan Mountains (HDM) are one of the major global biodiversity hotspots in the world. Several evolutionary scenarios, especially in-situ diversification, have been proposed to account for the high species richness of temperate plants. However, peripatric speciation, an important mode of allopatric speciation, has seldom been reported in this region. RESULTS Here, two chloroplast DNA regions and 14 nuclear loci were sequenced for 112 individuals from 10 populations of Torreya fargesii var. fargesii and 63 individuals from 6 populations of T. fargesii var. yunnanensis. Population genetic analyses revealed that the two varieties are well differentiated genetically (FST, 0.5765) and have uneven genetic diversity (π, 0.00221 vs. 0.00073 on an average of nuclear loci). The gene genealogical relationship showed that T. fargesii var. yunnanensis is inferred as derived from T. fargesii var. fargesii, which was further supported by the coalescent simulations (DIYABC, fastsimcoal2 and IMa2). By the coalescent simulations, the divergence time (~ 2.50-3.65 Ma) and the weak gene flow between the two varieties were detected. The gene flow was asymmetrical and only occurred in later stages of divergence, which is caused by second contact due to the population expansion (~ 0.61 Ma) in T. fargesii var. fargesii. In addition, niche modeling indicated that the two varieties are differentiated geographically and ecologically and have unbalanced distribution range. CONCLUSIONS Overall, T. fargesii var. fargesii is always parapatric with respect to T. fargesii var. yunnanensis, and the latter derived from the former in peripatry of the HDM following a colonization from central China during the late Pliocene. Our findings demonstrate that peripatric speciation following dispersal events may be an important evolutionary scenario for the formation of biodiversity hotspot of the HDM.
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Affiliation(s)
- Yixuan Kou
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, China
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Dengmei Fan
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Shanmei Cheng
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Yi Yang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Meixia Wang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Yujin Wang
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China.
| | - Zhiyong Zhang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, China.
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, China.
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China.
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Su Y, Liu L, Deng Q, Lü Z, Wang Z, He Z, Wang T. Epigenetic architecture of Pseudotaxus chienii: Revealing the synergistic effects of climate and soil variables. Ecol Evol 2023; 13:e10511. [PMID: 37701023 PMCID: PMC10493196 DOI: 10.1002/ece3.10511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 07/27/2023] [Accepted: 08/07/2023] [Indexed: 09/14/2023] Open
Abstract
Whether conifers can withstand environmental changes especially temperature fluctuations has been controversial. Epigenetic analysis may provide new perspectives for solving the issue. Pseudotaxus chienii is an endangered gymnosperm species endemic to China. In this study, we have examined the genetic and epigenetic variations in its natural populations aiming to disentangle the synergistic effects of climate and soil on its population (epi)genetic differentiation by using amplified fragment length polymorphism (AFLP) and methylation-sensitive AFLP (MSAP) techniques. We identified 23 AFLP and 26, 7, and 5 MSAP outliers in P. chienii. Twenty-one of the putative adaptive AFLP loci were found associated with climate and/or soil variables including precipitation, temperature, K, Fe, Zn, and Cu, whereas 21, 7, and 4 MSAP outliers were significantly related to precipitation of wettest month (Bio13), precipitation driest of month (Bio14), percent tree cover (PTC), and soil Fe, Mn, and Cu compositions. Total precipitation and precipitation in the driest seasons were the most influential factors for genetic and epigenetic variation, respectively. In addition, a high full-methylation level and a strong correlation between genetic and epigenetic variation were detected in P. chienii. Climate is found of greater importance than soil in shaping adaptive (epi)genetic differentiation, and the synergistic effects of climate and climate-soil variables were also observed. The identified climate and soil variables should be considered when applying ex situ conservation.
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Affiliation(s)
- Yingjuan Su
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
- Research Institute of Sun Yat‐sen University in ShenzhenShenzhenChina
| | - Li Liu
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Qi Deng
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
- School of MedicineGuangxi University of Science and TechnologyLiuzhouChina
| | - Zhuyan Lü
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Zhen Wang
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Ziqing He
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Ting Wang
- Research Institute of Sun Yat‐sen University in ShenzhenShenzhenChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
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4
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Ye J, Li D. Diversification of East Asian subtropical evergreen broadleaved forests over the last 8 million years. Ecol Evol 2022; 12:e9451. [PMID: 36329812 PMCID: PMC9618824 DOI: 10.1002/ece3.9451] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 09/26/2022] [Accepted: 10/10/2022] [Indexed: 11/25/2022] Open
Abstract
The evolution of subtropical evergreen broadleaved forests (EBLFs) in East Asia is interesting while complicated. Genus‐level phylogenies indicate that the origins of EBLFs could trace back to the Oligocene–Miocene boundary or even the Eocene, while population‐level phylogeographic evidence suggests that they diversified after the Miocene, particularly in the Pleistocene. Here, we review the origins of dominant plant species to better understand the evolution of EBLFs. We compiled published estimates of the timing of origin of dominant species and diversification of evergreen relict genera from East Asian EBLFs. We also traced and visualized the evolution of EBLFs in the region using dated phylogenies and geographic distributions of the reviewed taxa. Most (76.1%) of the dominant species originated after the late Miocene, ca. 8 million years ago. Of the 10 evergreen relict genera, eight diverged near the late Miocene–Pliocene boundary or during the late Pliocene, and the remaining two diverged during the Pleistocene. Over the past 8 million years, geo‐climatic changes have triggered origins of most of the dominant EBLF species and provided refugia for evergreen relict genera. Three pulsed phases of evolution are suggested by genetic studies at the genus, species, and population levels. Fossil evidence and spatiotemporal investigations should be integrated to fully understand the evolution of EBLFs in East Asia.
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Affiliation(s)
- Jun‐Wei Ye
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of BotanyChinese Academy of SciencesKunmingChina,Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of EducationSouthwest Forestry UniversityKunmingChina
| | - De‐Zhu Li
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of BotanyChinese Academy of SciencesKunmingChina
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Hodel RGJ, Massatti R, Knowles LL. Hybrid enrichment of adaptive variation revealed by genotype-environment associations in montane sedges. Mol Ecol 2022; 31:3722-3737. [PMID: 35560840 PMCID: PMC9327521 DOI: 10.1111/mec.16502] [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: 05/19/2021] [Revised: 04/20/2022] [Accepted: 05/05/2022] [Indexed: 12/04/2022]
Abstract
The role of hybridization in diversification is complex and may result in many possible outcomes. Not only can hybridization produce new lineages, but those lineages may contain unique combinations of adaptive genetic variation derived from parental taxa that allow hybrid‐origin lineages to occupy unique environmental space relative to one (or both) parent(s). We document such a case of hybridization between two sedge species, Carex nova and Carex nelsonii (Cyperaceae), that occupy partially overlapping environmental space in the southern Rocky Mountains, USA. In the region hypothesized to be the origin of the hybrid lineage, one parental taxon (C. nelsonii) is at the edge of its environmental tolerance. Hybrid‐origin individuals display mixed ancestry between the parental taxa—of nearly 7000 unlinked loci sampled, almost 30% showed evidence of excess ancestry from one parental lineage—approximately half displayed a genomic background skewed towards one parent, and half skewed towards the other. To test whether excess ancestry loci may have conferred an adaptive advantage to the hybrid‐origin lineage, we conducted genotype–environment association analyses on different combinations of loci—with and without excess ancestry—and with multiple contrasts between the hybrids and parental taxa. Loci with skewed ancestry showed significant environmental associations distinguishing the hybrid lineage from one parent (C. nelsonii), whereas loci with relatively equal representation of parental ancestries showed no such environmental associations. Moreover, the overwhelming majority of candidate adaptive loci with respect to environmental gradients also had excess ancestry from a parental lineage, implying these loci have facilitated the persistence of the hybrid lineage in an environment unsuitable to at least one parent.
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Affiliation(s)
- Richard G J Hodel
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.,Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, USA
| | - Rob Massatti
- U.S. Geological Survey, Southwest Biological Science Center, Flagstaff, AZ, USA
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
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Fan D, Lei S, Liang H, Yao Q, Kou Y, Cheng S, Yang Y, Qiu Y, Zhang Z. More opportunities more species: Pleistocene differentiation and northward expansion of an evergreen broad-leaved tree species Machilus thunbergii (Lauraceae) in Southeast China. BMC PLANT BIOLOGY 2022; 22:35. [PMID: 35038992 PMCID: PMC8762935 DOI: 10.1186/s12870-021-03420-9] [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: 07/01/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND The broad continuum between tropical and temperate floras in Eastern Asia (EAS) are thought to be one of the main factors responsible for a prominent species diversity anomaly of temperate plants between EAS and eastern North America (ENS). However, how the broad continuum and niche evolution between tropical and temperate floras in EAS contributes to lineage divergence and species diversity remains largely unknown. RESULTS Population genetic structure, demography, and determinants of genetic structure [i.e., isolation-by-distance (IBD), isolation-by-resistance (IBR), and isolation-by-environment (IBE)] of Machilus thunbergii Sieb. et Zucc. (Lauraceae) were evaluated by examining sequence variation of ten low-copy nuclear genes across 43 populations in southeast China. Climatic niche difference and potential distributions across four periods (Current, mid-Holocene, the last glacial maximum, the last interglacial) of two genetic clusters were determined by niche modelling. North and south clusters of populations in M. thunbergii were revealed and their demarcation line corresponds well with the northern boundary of tropical zone in China of Zhu & Wan. The divergence time between the clusters and demographic expansion of M. thunbergii occurred after the mid-Pleistocene climate transition (MPT, 0.8-1.2 Ma). Migration rates between clusters were asymmetrical, being much greater from north to south than the reverse. Significant effects of IBE, but non-significant effects of IBD and IBR on population genetic divergence were detected. The two clusters have different ecological niches and require different temperature regimes. CONCLUSIONS The north-south genetic differentiation may be common across the temperate-tropical boundary in southeast China. Divergent selection under different temperature regimes (possibly above and below freezing temperature in winter) could account for this divergence pattern. The broad continuum between tropical and temperate floras in EAS may have provided ample opportunities for tropical plant lineages to acquire freezing tolerance and to colonize the temperate regions during the late-Cenozoic global cooling. Our findings shed deeper insights into the high temperate plant species diversity in EAS.
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Affiliation(s)
- Dengmei Fan
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Shuqing Lei
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Hua Liang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Qi Yao
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yixuan Kou
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China.
| | - Shanmei Cheng
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yi Yang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yingxiong Qiu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhiyong Zhang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, Jiangxi, China.
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Phylotranscriptomics reveals the evolutionary history of subtropical East Asian white pines: further insights into gymnosperm diversification. Mol Phylogenet Evol 2022; 168:107403. [PMID: 35031461 DOI: 10.1016/j.ympev.2022.107403] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 11/15/2021] [Accepted: 12/25/2021] [Indexed: 11/20/2022]
Abstract
Floristic composition within a geographic area is driven by a wide array of factors from local biotic interactions to biogeographical processes. Subtropical East Asia is a key biodiversity hotspot of the world, and harbors the most families of extant gymnosperms and a large number of endemic genera with ancient origins, but rare phylogenetic studies explored whether it served as a diversification center for gymnosperms. Here, we investigated the evolutionary and biogeographical history of subtropical East Asian white pines using an integrative approach that combines phylotranscriptomic and ecological analyses. Using 2,606 orthologous nuclear genes, we reconstructed a fully resolved and dated phylogeny of these species. Two main clades first diverged in the early Miocene, and by the late Miocene, all species appeared. Two white pines endemic to Taiwan Island experienced independent colonization events and regional extinction, which resulted in the present disjunctive distribution from mainland China. Ecological and biogeographical analyses indicate that the monsoon-driven assembly of evergreen broadleaved forests (EBLFs) might have significantly affected the diversification of subtropical East Asian white pines. Our study highlights the interactions of biotic and abiotic forces in the diversification and speciation of subtropical East Asian white pines. These findings indicate that subtropical East Asia is not only a floristic museum, but also a diversification center for gymnosperms. Our study also demonstrates the importance of phylotranscriptomics on species delimitation and biodiversity conservation, particularly for closely related species.
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Cheng S, Zeng W, Wang J, Liu L, Liang H, Kou Y, Wang H, Fan D, Zhang Z. Species Delimitation of Asteropyrum (Ranunculaceae) Based on Morphological, Molecular, and Ecological Variation. FRONTIERS IN PLANT SCIENCE 2021; 12:681864. [PMID: 34567021 PMCID: PMC8461316 DOI: 10.3389/fpls.2021.681864] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/23/2021] [Indexed: 05/30/2023]
Abstract
Objectively evaluating different lines of evidence within a formalized framework is the most efficient and theoretically grounded approach for defining robust species hypotheses. Asteropyrum Drumm. et Hutch. is a small genus of perennial herb containing two species, A. cavaleriei and A. peltatum. The distinction of these two species mainly lies in the shape and size of leaf blades. However, these characters have been considered labile and could not differentiate the two species reliably. In this study, we investigated the variation of the leaf blades of 28 populations across the whole range of Asteropyrum using the landmark-based geometric morphometrics (GMM), sought genetic gaps within this genus using DNA barcoding, phylogenetic reconstruction and population genetic methods, and compared the predicted ecological niches of the two species. The results showed that the leaf form (shape and size) was overlapped between the two species; barcode gap was not detected within the genus Asteropyrum; and little ecological and geographical differentiation was found between the two taxa. Two genetic clusters detected by population genetic analysis did not match the two morphospecies. The results suggest that there are no distinct boundaries between the two species of Asteropyrum in terms of morphology, genetics and ecology and this present classification should be abandoned. We anticipate that range-wide population genomic studies would properly delineate the species boundaries and help to understand the evolution and speciation within Asteropyrum.
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Affiliation(s)
- Shanmei Cheng
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Weidong Zeng
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Jing Wang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Lei Liu
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Hua Liang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Yixuan Kou
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Dengmei Fan
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Zhiyong Zhang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
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Wang Z, Zhong C, Li D, Yan C, Yao X, Li Z. Cytotype distribution and chloroplast phylogeography of the Actinidia chinensis complex. BMC PLANT BIOLOGY 2021; 21:325. [PMID: 34229602 PMCID: PMC8259359 DOI: 10.1186/s12870-021-03099-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Plant phylogeographic studies of species in subtropical China have mainly focused on rare and endangered species, whereas few studies have been conducted on taxa with relatively wide distribution, especially polyploid species. We investigated the cytotype and haplotype distribution pattern of the Actinidia chinensis complex, a widespread geographically woody liana with variable ploidy in subtropical China comprising two varieties, with three chloroplast fragments DNA (ndhF-rpl132, rps16-trnQ and trnE-trnT). Macroevolutionary, microevolutionary and niche modeling tools were also combined to disentangle the origin and the demographic history of the species or cytotypes. RESULTS The ploidy levels of 3338 individuals from 128 populations sampled throughout the species distribution range were estimated with flow cytometry. The widespread cytotypes were diploids followed by tetraploids and hexaploids, whereas triploids and octoploids occurred in a few populations. Thirty-one chloroplast haplotypes were detected. The genetic diversity and genetic structure were found to be high between varieties (or ploidy races) chinensis and deliciosa. Our results revealed that these two varieties inhabit significantly different climatic niche spaces. Ecological niche models (ENMs) indicate that all varieties' ranges contracted during the Last Inter Glacial (LIG), and expanded eastward or northward during the Last Glacial Maximum (LGM). CONCLUSIONS Pliocene and Plio-Pleistocene climatic fluctuations and vicariance appear to have played key roles in shaping current population structure and historical demography in the A. chinensis complex. The polyploidization process also appears to have played an important role in the historical demography of the complex through improving their adaptability to environmental changes.
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Affiliation(s)
- Zhi Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Caihong Zhong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Dawei Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Chunlin Yan
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Xiaohong Yao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
| | - Zuozhou Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
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10
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Li S, Wang Z, Su Y, Wang T. EST-SSR-based landscape genetics of Pseudotaxus chienii, a tertiary relict conifer endemic to China. Ecol Evol 2021; 11:9498-9515. [PMID: 34306638 PMCID: PMC8293779 DOI: 10.1002/ece3.7769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/04/2021] [Accepted: 05/19/2021] [Indexed: 12/12/2022] Open
Abstract
Pseudotaxus chienii, belonging to the monotypic genus Pseudotaxus (Taxaceae), is a relict conifer endemic to China. Its populations are usually small and patchily distributed, having a low capacity of natural regeneration. To gain a clearer understanding of how landscape variables affect the local adaptation of P. chienii, we applied EST-SSR markers in conjunction with landscape genetics methods: (a) to examine the population genetic pattern and spatial genetic structure; (b) to perform genome scan and selection scan to identify outlier loci and the associated landscape variables; and (c) to model the ecological niche under climate change. As a result, P. chienii was found to have a moderate level of genetic variation and a high level of genetic differentiation. Its populations displayed a significant positive relationship between the genetic and geographical distance (i.e., "isolation by distance" pattern) and a strong fine-scale spatial genetic structure within 2 km. A putatively adaptive locus EMS6 (functionally annotated to cellulose synthase A catalytic subunit 7) was identified, which was found significantly associated with soil Cu, K, and Pb content and the combined effects of temperature and precipitation. Moreover, P. chienii was predicted to experience significant range contractions in future climate change scenarios. Our results highlight the potential of specific soil metal content and climate variables as the driving force of adaptive genetic differentiation in P. chienii. The data would also be useful to develop a conservation action plan for P. chienii.
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Affiliation(s)
- Shufeng Li
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Zhen Wang
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Yingjuan Su
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
- Research Institute of Sun Yat‐sen University in ShenzhenShenzhenChina
| | - Ting Wang
- Research Institute of Sun Yat‐sen University in ShenzhenShenzhenChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
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11
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Liu L, Wang Z, Su Y, Wang T. Population transcriptomic sequencing reveals allopatric divergence and local adaptation in Pseudotaxus chienii (Taxaceae). BMC Genomics 2021; 22:388. [PMID: 34039278 PMCID: PMC8157689 DOI: 10.1186/s12864-021-07682-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/05/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Elucidating the effects of geography and selection on genetic variation is critical for understanding the relative importance of adaptation in driving differentiation and identifying the environmental factors underlying its occurrence. Adaptive genetic variation is common in tree species, especially widely distributed long-lived species. Pseudotaxus chienii can occupy diverse habitats with environmental heterogeneity and thus provides an ideal material for investigating the process of population adaptive evolution. Here, we characterize genetic and expression variation patterns and investigate adaptive genetic variation in P. chienii populations. RESULTS We generated population transcriptome data and identified 13,545 single nucleotide polymorphisms (SNPs) in 5037 unigenes across 108 individuals from 10 populations. We observed lower nucleotide diversity (π = 0.000701) among the 10 populations than observed in other gymnosperms. Significant negative correlations between expression diversity and nucleotide diversity in eight populations suggest that when the species adapts to the surrounding environment, gene expression and nucleotide diversity have a reciprocal relationship. Genetic structure analyses indicated that each distribution region contains a distinct genetic group, with high genetic differentiation among them due to geographical isolation and local adaptation. We used FST outlier, redundancy analysis, and latent factor mixed model methods to detect molecular signatures of local adaptation. We identified 244 associations between 164 outlier SNPs and 17 environmental variables. The mean temperature of the coldest quarter, soil Fe and Cu contents, precipitation of the driest month, and altitude were identified as the most important determinants of adaptive genetic variation. Most candidate unigenes with outlier signatures were related to abiotic and biotic stress responses, and the monoterpenoid biosynthesis and ubiquitin-mediated proteolysis KEGG pathways were significantly enriched in certain populations and deserve further attention in other long-lived trees. CONCLUSIONS Despite the strong population structure in P. chienii, genomic data revealed signatures of divergent selection associated with environmental variables. Our research provides SNPs, candidate unigenes, and biological pathways related to environmental variables to facilitate elucidation of the genetic variation in P. chienii in relation to environmental adaptation. Our study provides a promising tool for population genomic analyses and insights into the molecular basis of local adaptation.
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Affiliation(s)
- Li Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhen Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, Guangdong, China.
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China.
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Xu R, Wang Z, Su Y, Wang T. Characterization and Development of Microsatellite Markers in Pseudotaxus chienii (Taxaceae) Based on Transcriptome Sequencing. Front Genet 2020; 11:574304. [PMID: 33193679 PMCID: PMC7593448 DOI: 10.3389/fgene.2020.574304] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/21/2020] [Indexed: 12/12/2022] Open
Abstract
Pseudotaxus chienii (Taxaceae) is an endangered conifer species endemic to China. However, a lack of suitable molecular markers hinders the genomic and genetic studies on this species. Here, we characterized and developed the microsatellite markers from a newly sequenced P. chienii transcriptome. A total of 21,835 microsatellite loci were detected from 161,131 non-redundant unigene sequences, and the frequency of SSRs was 13.55%, with an average of one SSR loci per 9.18 kb. Mono-nucleotide, di-nucleotide, and tri-nucleotide were the dominant repeat types, accounting for 50.06, 13.49, and 29.39% of the total SSRs, respectively. In terms of distribution location, the coding regions (CDS) with few microsatellites and mainly consisted of tri-nucleotides. There were significant differences in the length of microsatellite among genic regions and motif types. Functional annotation showed that the unigenes containing microsatellites had a wide range of biological functions, most of which were related to basic metabolism, and a few might be involved in expression regulation of gene and response to environmental stress. In addition, 375 primer pairs were randomly selected and synthesized for the amplification and validation of microsatellite markers. Seventy-seven primer pairs were successfully amplified and 40 primer pairs were found to be polymorphic. Finally, 20 pairs of primers with high polymorphism were selected to assess the genetic diversity in four P. chienii populations. In addition, the newly developed microsatellite markers exhibited high transferability (70%) in Amentotaxus argotaenia. Our study could enable further genetic diversity analysis and functional gene mining on Taxaceae.
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Affiliation(s)
- Ruixiang Xu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhen Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, China
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, China
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Bolte CE, Eckert AJ. Determining the when, where and how of conifer speciation: a challenge arising from the study 'Evolutionary history of a relict conifer Pseudotaxus chienii'. ANNALS OF BOTANY 2020; 125:v-vii. [PMID: 31913458 PMCID: PMC6948208 DOI: 10.1093/aob/mcz201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/11/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Constance E Bolte
- Integrative Life Sciences Doctoral Program, Virginia Commonwealth University, Richmond, VA, USA
| | - Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, VA, USA
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