1
|
Liu T, Liu H, Yang Y. Uncovering the determinants of biodiversity hotspots in China: Evidence from the drivers of multiple diversity metrics on insect assemblages and implications for conservation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 880:163287. [PMID: 37028670 DOI: 10.1016/j.scitotenv.2023.163287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/31/2023] [Accepted: 03/31/2023] [Indexed: 05/27/2023]
Abstract
Understanding large-scale biodiversity patterns and underlying mechanisms during the formation process is essential for guiding conservation efforts. However, previous studies on the identification and formation mechanism of diversity hotspots in China were often limited to a single (alpha) diversity metric, while multiple (beta or zeta) diversity has rarely been used for exploring drivers and conservation actions. Here, a comprehensive species distribution dataset consisting of representative families of three insect orders was compiled to explore biodiversity hotspots based on different algorithms. Furthermore, to assess the effects of environmental factors on hotspots, we fitted generalized additive mixed-effects models (GAMMs) for species richness, generalized dissimilarity models (GDMs) and multi-site generalized dissimilarity modeling (MS-GDM) for the total beta and zeta diversity. Our results showed that biodiversity hotspots were mainly concentrated in central and southern China, especially in mountainous areas with complex topography, which indicated the insects' affinity to montane environments. Further analyses based on multiple models showed that water-energy factors exerted the strongest explanatory power for the insect assemblage diversity in hotspots of both alpha and beta (or zeta) levels. Additionally, anthropogenic factors also exerted a significant effect on hotspots, and this effect was higher for beta diversity than for alpha diversity. Overall, our study elucidates a comprehensive analysis of the identification and underlying mechanism of biodiversity hotspots in China. Despite several limitations, we still believe that our findings can provide some new insights for conservation efforts in Chinese hotspots.
Collapse
Affiliation(s)
- Tong Liu
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Haoyu Liu
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China.
| | - Yuxia Yang
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China.
| |
Collapse
|
2
|
Zhou J, He W, Wang J, Liao X, Xiang K, Ma M, Liu Z, Li Y, Tembrock LR, Wu Z, Liu L. The pan-plastome of tartary buckwheat (fagopyrum tataricum): key insights into genetic diversity and the history of lineage divergence. BMC PLANT BIOLOGY 2023; 23:212. [PMID: 37088810 PMCID: PMC10123988 DOI: 10.1186/s12870-023-04218-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/06/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Tartary buckwheat (Fagopyrum tataricum) is an important food and medicine crop plant, which has been cultivated for 4000 years. A nuclear genome has been generated for this species, while an intraspecific pan-plastome has yet to be produced. As such a detailed understanding of the maternal genealogy of Tartary buckwheat has not been thoroughly investigated. RESULTS In this study, we de novo assembled 513 complete plastomes of Fagopyrum and compared with 8 complete plastomes of Fagopyrum downloaded from the NCBI database to construct a pan-plastome for F. tartaricum and resolve genomic variation. The complete plastomes of the 513 newly assembled Fagopyrum plastome sizes ranged from 159,253 bp to 159,576 bp with total GC contents ranged from 37.76 to 37.97%. These plastomes all maintained the typical quadripartite structure, consisting of a pair of inverted repeat regions (IRA and IRB) separated by a large single copy region (LSC) and a small single copy region (SSC). Although the structure and gene content of the Fagopyrum plastomes are conserved, numerous nucleotide variations were detected from which population structure could be resolved. The nucleotide variants were most abundant in the non-coding regions of the genome and of those the intergenic regions had the most. Mutational hotspots were primarily found in the LSC regions. The complete 521 Fagopyrum plastomes were divided into five genetic clusters, among which 509 Tartary buckwheat plastomes were divided into three genetic clusters (Ft-I/Ft-II/Ft-III). The genetic diversity in the Tartary buckwheat genetic clusters was the greatest in Ft-III, and the genetic distance between Ft-I and Ft-II was the largest. Based on the results of population structure and genetic diversity analysis, Ft-III was further subdivided into three subgroups Ft-IIIa, Ft-IIIb, and Ft-IIIc. Divergence time estimation indicated that the genera Fagopyrum and Rheum (rhubarb) shared a common ancestor about 48 million years ago (mya) and that intraspecies divergence in Tartary buckwheat began around 0.42 mya. CONCLUSIONS The resolution of pan-plastome diversity in Tartary buckwheat provides an important resource for future projects such as marker-assisted breeding and germplasm preservation.
Collapse
Affiliation(s)
- Jiawei Zhou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Wenchuang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- College of Science, Health, Engineering and Education, Murdoch University, Western Australia, Perth, 6150, Australia
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Kunli Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Mingchuan Ma
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, China
- Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Taiyuan, 030031, China
| | - Zhang Liu
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, China
- Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Taiyuan, 030031, China
| | - Yongyao Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Zhiqiang Wu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China.
- College of Horticulture, Shanxi Agricultural University, Shanxi, 030801, China.
| | - Longlong Liu
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, China.
- Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Taiyuan, 030031, China.
| |
Collapse
|
3
|
Du S, Hu X, Guo Y, Wang S, Yang X, Wu Z, Huang Y. A comparative plastomic analysis of Ziziphus jujuba var. spinosa (Bunge) Hu ex H. F. Chow and implication of the origin of Chinese jujube. AOB PLANTS 2023; 15:plad006. [PMID: 37025103 PMCID: PMC10071050 DOI: 10.1093/aobpla/plad006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 02/17/2023] [Indexed: 06/19/2023]
Abstract
Comparative plastomics can be used to explicitly dissect various types of plastome variation. In the present study, the plastome variation pattern of Ziziphus jujuba var. spinosa (also called sour jujube) and its phylogenomic relationship with Chinese jujube were investigated. Plastomes of 21 sour jujube individuals were sequenced and assembled. The length of the sour jujube plastomes ranged between 159399 and 161279 bp. The plastomes exhibited collinearity of structure, gene order and content. The most divergent regions were located in the intergenic spacers, such as trnR-UCU-atpA and psbZ-trnG-UCC. Sliding window analysis demonstrated that the sequence variation among the sour jujube plastomes was relatively low. Sixty-two to 76 SSRs with 4 motif types were identified in the sour jujube plastomes with a predominant motif type of A/T. Three protein-coding genes exhibited higher nonsynonymous/synonymous substitution ratios, indicating that these genes may undergo positive selection. A total of 80 SNPs were detected and 1266 potential RNA editing sites of 23 protein-coding genes were predicted. In the phylogenomic tree constructed, sour jujube has a sister relationship to Chinese jujube, which indicates that Chinese jujube may have originated or been domesticated from sour jujube. The present study explicitly investigated the individual-level plastome variation of sour jujube and provides potential valuable molecular markers for future genetic-related study of this lineage.
Collapse
Affiliation(s)
- Shuhui Du
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Xiaoyan Hu
- College of Food Science and Technology, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Yuanting Guo
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Shengji Wang
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
| | | | - Zhenzhen Wu
- Taian Dushihuaxiang Agricultural Technology Co., Ltd, Taian, Shandong, China
| | - Yuyin Huang
- Shandong Huinongtianxia Science and Technology Information Consulting Co., Ltd, Taian, Shandong, China
| |
Collapse
|
4
|
Han M, Zhang J, Li D, Sun S, Zhang C, Zhang C, Yan L, Guan Y, Chen L, Guo Y, You M, Gou W, Li X, Yan J, Bai S, Yan X. Phylogeographical Pattern and Population Evolution History of Indigenous Elymus sibiricus L. on Qinghai-Tibetan Plateau. FRONTIERS IN PLANT SCIENCE 2022; 13:882601. [PMID: 35845670 PMCID: PMC9277506 DOI: 10.3389/fpls.2022.882601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
Elymus sibiricus L. is a perennial allotetraploid belonging to Triticeae of Poaceae, Elymus L., as the type species of genus Elymus L. The existing geographical distribution pattern and genetic spatial structure of E. sibiricus on Qinghai-Tibetan Plateau (QTP) are not yet clear. In this study, population genetic structure and demography history of 216 individuals from 44 E. sibiricus populations on QTP were studied used specific-locus amplified fragment sequencing (SLAF-seq). The result of genetic diversity showed that there was no single genetic diversity center was observed across all E. sibiricus populations. The results of genetic variation showed that 44 populations were clearly divided into the following three groups: Qinghai Plateau (Group I), South Tibet (Group II), and Hengduan Mountains (Group III). From the three analyses of AMOVA, Mantel test and Treemix, strong genetic differentiation across all populations and low genetic differentiation among populations within three groups. Molecular dating indicated that E. sibiricus diverged at 16.08 Ma (during the early Miocene) can be linked to the Himalayan Motion stage of QTP uplift. It is speculated that the reasons affecting the current phylogeographical pattern are as follows: (1) The environmental changes due to the uplift of the QTP; (2) The geographic distance between the populations (Groups I and III are close in geographic distance, and gene flow are frequent); (3) Geographical barriers (the Tanggula and Bayangela Mountains between Groups I and II). This study provides new evidence and historical perspective to the future exploration of the evolution and geographic distribution pattern of Elymus L.
Collapse
Affiliation(s)
- Mengli Han
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jingxue Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Daxu Li
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Shengnan Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | | | - Chuanjie Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Lijun Yan
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Yongzhuo Guan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Lili Chen
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Yuxia Guo
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Minghong You
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Wenlong Gou
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Xinrui Li
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Jiajun Yan
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Xuebing Yan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| |
Collapse
|
5
|
Mondal S, Moktan S. Study on the morpho-anatomy of Lepisorus species through light microscopy and scanning electron microscopy and its systematic implications. Microsc Res Tech 2022; 85:3165-3180. [PMID: 35678524 DOI: 10.1002/jemt.24174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/29/2022] [Accepted: 05/25/2022] [Indexed: 11/05/2022]
Abstract
The genus Lepisorus is often associated with complex lineages in Polypodiaceae, which leads to difficulty in understanding taxonomic relationships among the species. The taxa is mostly epiphytic with some distinct features like rhizomes covered with clathrate scales, simple fronds, sori in a single row, intermixed with peltate paraphyses. In this study, we precisely focus on the Lepisorus species and seek a broader understanding of the taxonomic relationships that prevail in this genus. The morpho-anatomical traits of rhizomes, stipe, lamina, and sporangia were explored in nine species with the aid of light microscopy and scanning electron microscopy techniques for gathering the qualitative and quantitative data sets. These character traits were resolved into groups based on degree of similarity and principal component analysis to comprehend the covariance among the variables. The data were then employed to prepare an artificial dichotomous key and hierarchical cluster analysis was established that revealed five related clades with eight members whereas one member emerged as outgroup. The results correspond with other recent phylogenetic studies of the concerned genus hence confirming immense reliability and thrust of light microscopy, scanning electron microscopy, and morphology-based studies that are being less utilized in fern taxonomy.
Collapse
Affiliation(s)
- Sinjini Mondal
- Department of Botany, University of Calcutta, Kolkata, West Bengal, India
| | - Saurav Moktan
- Department of Botany, University of Calcutta, Kolkata, West Bengal, India
| |
Collapse
|
6
|
Chao YS, Ebihara A, Chiou WL, Tsai JM, Huang YW, Ranker TA. Reticulate evolution in the Pteris fauriei group (Pteridaceae). Sci Rep 2022; 12:9145. [PMID: 35650209 PMCID: PMC9159987 DOI: 10.1038/s41598-022-11390-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 04/14/2022] [Indexed: 11/10/2022] Open
Abstract
The Pteris fauriei group (Pteridaceae) has a wide distribution in Eastern Asia and includes 18 species with similar but varied morphology. We collected more than 300 specimens of the P. fauriei group and determined ploidy by flow cytometry and inferred phylogenies by molecular analyses of chloroplast and nuclear DNA markers. Our results reveal a complicated reticulate evolution, consisting of seven parental taxa and 58 hybrids. The large number of hybrid taxa have added significant morphological complexity to the group leading to difficult taxonomic issues. The hybrids generally had broader ranges and more populations than their parental taxa. Genetic combination of different pairs of parental species created divergent phenotypes of hybrids, exhibited by both morphological characteristics and ecological fidelities. Niche novelty could facilitate hybrid speciation. Apogamy is common in this group and potentially contributes to the sustainability of the whole group. We propose that frequent hybridizations among members of the P. fauriei group generate and maintain genetic diversity, via novel genetic combinations, niche differentiation, and apogamy.
Collapse
Affiliation(s)
- Yi-Shan Chao
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, 100, Shih-Chuan 1st Rd., Kaohsiung, 80708, Taiwan.
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, 4-1-1, Amakubo, Tsukuba-shi, Ibaraki, 305-0005, Japan
| | - Wen-Liang Chiou
- Taiwan Forestry Research Institute, 53 Nan-Hai Rd., Taipei, 100051, Taiwan
| | - Jer-Min Tsai
- Department of Information and Communication, Kun Shan University, 195, Kunda Rd., Tainan, 710303, Taiwan
| | - Yu-Wen Huang
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, 100, Shih-Chuan 1st Rd., Kaohsiung, 80708, Taiwan
| | - Tom A Ranker
- University of Hawai'i at Mānoa, School of Life Sciences, Honolulu, HI, 96822, USA
| |
Collapse
|
7
|
Liu K, Qi M, Du FK. Population and Landscape Genetics Provide Insights Into Species Conservation of Two Evergreen Oaks in Qinghai-Tibet Plateau and Adjacent Regions. FRONTIERS IN PLANT SCIENCE 2022; 13:858526. [PMID: 35665182 PMCID: PMC9161217 DOI: 10.3389/fpls.2022.858526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
The combination of population and landscape genetics can facilitate the understanding of conservation strategy under the changing climate. Here, we focused on the two most diverse and ecologically important evergreen oaks: Quercus aquifolioides and Quercus spinosa in Qinghai-Tibetan Plateau (QTP), which is considered as world's biodiversity hotspot. We genotyped 1,657 individuals of 106 populations at 15 nuclear microsatellite loci throughout the species distribution range. Spatial patterns of genetic diversity were identified by mapping the allelic richness (AR) and locally common alleles (LCA) according to the circular neighborhood methodology. Migration routes from QTP were detected by historical gene flow estimation. The response pattern of genetic variation to environmental gradient was assessed by the genotype-environment association (GEA) analysis. The overall genetic structure showed a high level of intra-species genetic divergence of a strong west-east pattern. The West-to-East migration route indicated the complex demographic history of two oak species. We found evidence of isolation by the environment in Q. aqu-East and Q. spi-West lineage but not in Q. aqu-West and Q. spi-East lineage. Furthermore, priority for conservation should be given to populations that retain higher spatial genetic diversity or isolated at the edge of the distribution range. Our findings indicate that knowledge of spatial diversity and migration route can provide valuable information for the conservation of existing populations. This study provides an important guide for species conservation for two oak species by the integration of population and landscape genetic methods.
Collapse
Affiliation(s)
| | | | - Fang K. Du
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| |
Collapse
|
8
|
Comparative Analyses of 35 Complete Chloroplast Genomes from the Genus Dalbergia (Fabaceae) and the Identification of DNA Barcodes for Tracking Illegal Logging and Counterfeit Rosewood. FORESTS 2022. [DOI: 10.3390/f13040626] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The genus Dalbergia contains more than 200 species, several of which are trees that produce traditional medicines and extremely high-value timber commonly referred to as rosewood. Due to the rarity of these species in the wild, the high value of the timber, and a growing international illicit trade, CITES (Convention on International Trade in Endangered Species of Wild Fauna and Flora) has listed the entire genus in appendix II and the species Dalbergia nigra in appendix I because species in this genus are considered at risk of extinction. Given this, and the fact that species or even genus level determination is nearly impossible from cut timber morphology, alternative molecular methods are needed to identify and track intercepted rosewood. To better identify rosewood using molecular methods, we sequenced and assembled eight chloroplast genomes including D. nigra as well as conducted comparative analyses with all other available chloroplast genomes in Dalbergia and closely related lineages. From these analyses, numerous repeats including simple sequence repeats (SSR) and conserved nucleotide polymorphisms unique to subclades within the genus were detected. From phylogenetic analysis based on the CDS from 77 chloroplast genes, the groups Siam rosewood and scented rosewood resolved as monophyletic, supporting the morphological traits used to delimit these species. In addition, several instances of paraphyly and polyphyly resulting from mismatches between taxonomic determinations and phylogenetic tree topology were identified. Ultimately, the highly variable regions in the chloroplast genomes will provide useful plastid markers for further studies regarding the identification, phylogeny, and population genetics of Dalbergia species, including those frequently intercepted in illegal trade.
Collapse
|
9
|
Phylogeographical Analyses of a Relict Fern of Palaeotropical Flora (Vandenboschia speciosa): Distribution and Diversity Model in Relation to the Geological and Climate Events of the Late Miocene and Early Pliocene. PLANTS 2022; 11:plants11070839. [PMID: 35406819 PMCID: PMC9002575 DOI: 10.3390/plants11070839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/24/2022] [Accepted: 03/08/2022] [Indexed: 11/19/2022]
Abstract
Fern phylogeographic studies have mostly focused on the influence of the Pleistocene climate on fern distributions and the prevalence of long-distance dispersal. The effect of pre-Pleistocene events on the distributions of fern species is largely unexplored. Here, we elucidate a hypothetical scenario for the evolutionary history of Vandenboschia speciosa, hypothesised to be of Tertiary palaeotropical flora with a peculiar perennial gametophyte. We sequenced 40 populations across the species range in one plastid region and two variants of the nuclear gapCp gene and conducted time-calibrated phylogenetic, phylogeographical, and species distribution modelling analyses. Vandenboschia speciosa is an allopolyploid and had a Tertiary origin. Late Miocene aridification possibly caused the long persistence in independent refugia on the Eurosiberian Atlantic and Mediterranean coasts, with the independent evolution of gene pools resulting in two evolutionary units. The Cantabrian Cornice, a major refugium, could also be a secondary contact zone during Quaternary glacial cycles. Central European populations resulted from multiple post-glacial, long-distance dispersals. Vandenboschia speciosa reached Macaronesia during the Pliocene–Pleistocene, with a phylogeographical link between the Canary Islands, Madeira, and southern Iberia, and between the Azores and northwestern Europe. Our results support the idea that the geological and climate events of the Late Miocene/Early Pliocene shifted Tertiary fern distribution patterns in Europe.
Collapse
|
10
|
Ben-Menni Schuler S, Picazo-Aragonés J, Rumsey FJ, Romero-García AT, Suárez-Santiago VN. Macaronesia Acts as a Museum of Genetic Diversity of Relict Ferns: The Case of Diplazium caudatum (Athyriaceae). PLANTS 2021; 10:plants10112425. [PMID: 34834788 PMCID: PMC8623695 DOI: 10.3390/plants10112425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 12/05/2022]
Abstract
Macaronesia has been considered a refuge region of the formerly widespread subtropical lauroid flora that lived in Southern Europe during the Tertiary. The study of relict angiosperms has shown that Macaronesian relict taxa preserve genetic variation and revealed general patterns of colonization and dispersal. However, information on the conservation of genetic diversity and range dynamics rapidly diminishes when referring to pteridophytes, despite their dominance of the herbaceous stratum in the European tropical palaeoflora. Here we aim to elucidate the pattern of genetic diversity and phylogeography of Diplazium caudatum, a hypothesized species of the Tertiary Palaeotropical flora and currently with its populations restricted across Macaronesia and disjunctly in the Sierras de Algeciras (Andalusia, southern Iberian Peninsula). We analysed 12 populations across the species range using eight microsatellite loci, sequences of a region of plastid DNA, and carry out species-distribution modelling analyses. Our dating results confirm the Tertiary origin of this species. The Macaronesian archipelagos served as a refuge during at least the Quaternary glacial cycles, where populations of D. caudatum preserved higher levels of genetic variation than mainland populations. Our data suggest the disappearance of the species in the continent and the subsequent recolonization from Macaronesia. The results of the AMOVA analysis and the indices of clonal diversity and linkage disequilibrium suggest that D. caudatum is a species in which inter-gametophytic outcrossing predominates, and that in the Andalusian populations there was a shift in mating system toward increased inbreeding and/or clonality. The model that best explains the genetic diversity distribution pattern observed in Macaronesia is, the initial and recurrent colonization between islands and archipelagos and the relatively recent diversification of restricted area lineages, probably due to the decrease of favorable habitats and competition with lineages previously established. This study extends to ferns the concept of Macaronesia archipelagos as refugia for genetic variation.
Collapse
Affiliation(s)
- Samira Ben-Menni Schuler
- Department of Botany, Faculty of Sciences, University of Granada, 18071 Granada, Spain; (S.B.-M.S.); (J.P.-A.); (A.T.R.-G.)
| | - Jesús Picazo-Aragonés
- Department of Botany, Faculty of Sciences, University of Granada, 18071 Granada, Spain; (S.B.-M.S.); (J.P.-A.); (A.T.R.-G.)
| | - Fred J. Rumsey
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK;
| | - Ana Teresa Romero-García
- Department of Botany, Faculty of Sciences, University of Granada, 18071 Granada, Spain; (S.B.-M.S.); (J.P.-A.); (A.T.R.-G.)
| | - Víctor N. Suárez-Santiago
- Department of Botany, Faculty of Sciences, University of Granada, 18071 Granada, Spain; (S.B.-M.S.); (J.P.-A.); (A.T.R.-G.)
- Correspondence: ; Tel.: +34-958-248814
| |
Collapse
|
11
|
Zhang Y, Qian L, Spalink D, Sun L, Chen J, Sun H. Spatial phylogenetics of two topographic extremes of the Hengduan Mountains in southwestern China and its implications for biodiversity conservation. PLANT DIVERSITY 2021; 43:181-191. [PMID: 34195502 PMCID: PMC8233532 DOI: 10.1016/j.pld.2020.09.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/30/2020] [Accepted: 09/01/2020] [Indexed: 05/15/2023]
Abstract
Previous attempts to elucidate the drivers of speciation mechanisms and spatial distribution patterns of biodiversity in mountain regions have treated different floras within a single geological region as one flora, ignoring the potential contributions of high habitat/ecosystem heterogeneity. Furthermore, current conservation strategies largely focus on forest ecosystems and/or specific flagship species, ignoring marginal ecosystems, leaving species in these ecosystems at risk. Here, we compared the spatial patterns of biodiversity and the potential drivers of these patterns in the river valley and subnival ecosystems of the Hengduan Mountains region (HDM) in southwestern China. Specifically, we compared spatial patterns of diversity, endemism, and threatened species in these ecosystems based on both traditional measurements and recent phylogenetic approaches. We then examined how those patterns were related to environmental factors and human activity in these same regions. We found that the middle-southern HDM supports the highest diversity and endemism for the river valley and subnival ecosystems; however, the distribution patterns of neo- and paleo-endemism in these two ecosystems differ. Regression models indicate that habitat diversity and paleo-climatic fluctuation are important drivers of diversity and endemism for these two ecosystems. Temperature and precipitation, however, showed different influences on the spatial patterns in different ecosystems. Categorical analysis of neo- and paleo-endemism (CANAPE) indicated that most endemism centers are not covered by current nature reserves. Moreover, the intensity of human activity is highest in the southern and southeastern HDM, which coincides with the distribution patterns of diversity, mixed-endemism and high-priority (and threatened) species. These findings suggest that different floras within a single geographic/floristic region respond differently to environmental factors and show different spatial phylogenetic patterns. We, therefore, recommend that future research into the drivers of biodiversity consider the contributions of various ecosystem types within a single geological region. This study also provides a theoretical basis for protecting habitat diversity. Our work confirms that current conservation efforts are insufficient to protect ecosystem diversity in the river valley and subnival ecosystems of the Hengduan Mountains. Therefore, we recommend the establishment of nature reserves in the regions identified in this study; furthermore, we strongly recommend improving current and establishing new management policies for biodiversity conservation in this region.
Collapse
Affiliation(s)
- Yazhou Zhang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Lishen Qian
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Daniel Spalink
- Department of Ecology and Conservation Biology, Texas A&M University, College Station 77843-2138, TX, USA
| | - Lu Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jianguo Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, PR China
| |
Collapse
|
12
|
Zhou J, Zhang S, Wang J, Shen H, Ai B, Gao W, Zhang C, Fei Q, Yuan D, Wu Z, Tembrock LR, Li S, Gu C, Liao X. Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution. Sci Rep 2021; 11:9471. [PMID: 33947883 PMCID: PMC8096831 DOI: 10.1038/s41598-021-88160-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/06/2021] [Indexed: 02/02/2023] Open
Abstract
The chloroplast is one of two organelles containing a separate genome that codes for essential and distinct cellular functions such as photosynthesis. Given the importance of chloroplasts in plant metabolism, the genomic architecture and gene content have been strongly conserved through long periods of time and as such are useful molecular tools for evolutionary inferences. At present, complete chloroplast genomes from over 4000 species have been deposited into publicly accessible databases. Despite the large number of complete chloroplast genomes, comprehensive analyses regarding genome architecture and gene content have not been conducted for many lineages with complete species sampling. In this study, we employed the genus Populus to assess how more comprehensively sampled chloroplast genome analyses can be used in understanding chloroplast evolution in a broadly studied lineage of angiosperms. We conducted comparative analyses across Populus in order to elucidate variation in key genome features such as genome size, gene number, gene content, repeat type and number, SSR (Simple Sequence Repeat) abundance, and boundary positioning between the four main units of the genome. We found that some genome annotations were variable across the genus owing in part from errors in assembly or data checking and from this provided corrected annotations. We also employed complete chloroplast genomes for phylogenetic analyses including the dating of divergence times throughout the genus. Lastly, we utilized re-sequencing data to describe the variations of pan-chloroplast genomes at the population level for P. euphratica. The analyses used in this paper provide a blueprint for the types of analyses that can be conducted with publicly available chloroplast genomes as well as methods for building upon existing datasets to improve evolutionary inference.
Collapse
Affiliation(s)
- Jiawei Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Shuo Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- School of Landscape and Architecture, Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
| | - Hongmei Shen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- The Second Peoples's Hospital of Nantong, Nantong, 226000, Jiangsu, China
| | - Bin Ai
- Foshan Green Development Innovation Research Institute, Foshan, 528000, Guangdong, China
| | - Wei Gao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Cuijun Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Qili Fei
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhiqiang Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- The College of Horticulture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Sen Li
- The College of Horticulture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
| | - Cuihua Gu
- School of Landscape and Architecture, Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China.
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
| |
Collapse
|
13
|
Kuo LY, Chang YH, Huang YH, Testo W, Ebihara A, Rouhan G, Quintanilla LG, Watkins JE, Huang YM, Li FW. A global phylogeny of Stegnogramma ferns (Thelypteridaceae): generic and sectional revision, historical biogeography and evolution of leaf architecture. Cladistics 2020; 36:164-183. [PMID: 34618958 DOI: 10.1111/cla.12399] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2019] [Indexed: 10/26/2022] Open
Abstract
The thelypteroid fern genus Stegnogramma s.l. contains around 18-35 species and has a global, cross-continental distribution ranging from tropical to temperate regions. Several genera and infrageneric sections have been recognized previously in Stegnogramma s.l., but their phylogenetic relationships are still unclear. In this study, we present a global phylogeny of Stegnogramma s.l. with the most comprehensive sampling to date and aim to pinpoint the phylogenetic positions of biogeographically and taxonomically important taxa. Based on the reconstructed historical biogeography and character evolution, we propose a new (infra)generic classification and discuss the diversification of Stegnogramma s.l. in a biogeographical context. New names or combinations are made for 12 (infra)species, including transferring the monotypic species of Craspedosorus to Leptogramma. Finally, we discuss a possible link between leaf architecture and ecological adaptation, and hypothesize that the increase in leaf dissection and free-vein proportion is an adaptive feature to cool climates in Stegnogramma s.l.
Collapse
Affiliation(s)
- Li-Yaung Kuo
- Boyce Thompson Institute, Ithaca, NY, 14853, USA.,Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
| | - Yi-Hang Chang
- Taiwan Forestry Research Institute, Taipei, 10066, Taiwan
| | - Yu-Hsuan Huang
- Taiwan Forestry Research Institute, Taipei, 10066, Taiwan
| | - Weston Testo
- Biology Department, University of Florida, Gainesville, FL, 32611, USA
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, Amakubo 4-1-1, Tsukuba, Ibaraki, 305-0005, Japan
| | - Germinal Rouhan
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, EPHE, Sorbonne Université, 16 rue Buffon CP39, F-75005, Paris, France
| | - Luis G Quintanilla
- School of Environmental Sciences and Technology, Rey Juan Carlos University, Móstoles, Spain
| | - James E Watkins
- Department of Biology, Colgate University, Hamilton, NY, 13346, USA
| | - Yao-Moan Huang
- Taiwan Forestry Research Institute, Taipei, 10066, Taiwan
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, 14853, USA.,Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
| |
Collapse
|
14
|
Exploring phylogeny of the microsoroid ferns (Polypodiaceae) based on six plastid DNA markers. Mol Phylogenet Evol 2020; 143:106665. [DOI: 10.1016/j.ympev.2019.106665] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 10/25/2019] [Accepted: 10/25/2019] [Indexed: 01/11/2023]
|
15
|
Zhao C, Wei R, Zhang X, Xiang Q. Backbone phylogeny of
Lepisorus
(Polypodiaceae) and a novel infrageneric classification based on the total evidence from plastid and morphological data. Cladistics 2019; 36:235-258. [DOI: 10.1111/cla.12403] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2019] [Indexed: 01/20/2023] Open
Affiliation(s)
- Cun‐Feng Zhao
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences Beijing100093China
- University of Chinese Academy of Sciences Beijing100049China
| | - Ran Wei
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences Beijing100093China
| | - Xian‐Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences Beijing100093China
| | - Qiao‐Ping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences Beijing100093China
| |
Collapse
|
16
|
Testo WL, Sessa E, Barrington DS. The rise of the Andes promoted rapid diversification in Neotropical Phlegmariurus (Lycopodiaceae). THE NEW PHYTOLOGIST 2019; 222:604-613. [PMID: 30326543 DOI: 10.1111/nph.15544] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 10/10/2018] [Indexed: 06/08/2023]
Abstract
Tropical mountains are disproportionately biodiverse relative to their surface area, but the processes underlying their exceptional diversity require further study. Here, we use comparative phylogenetic methods to examine the impact of the Andean orogeny on the diversification of Neotropical Phlegmariurus, a species-rich lycophyte clade. We generated a time-calibrated phylogeny of 105 species of Neotropical Phlegmariurus and estimated lineage diversification rates. We tested for correlations between lineage diversification rates and species range size, niche breadth, elevational range amplitude, and mean elevation of occurrence. A recently developed macroevolutionary model was used to incorporate geological data and test for an association between diversification rates and the Andean uplift. Diversification rates of Neotropical Phlegmariurus are negatively correlated with species range size and positively correlated with mean elevation of species occurrence. The rise of the Andes is strongly associated with increased rates of diversification in Neotropical Phlegmariurus during the last 10 Myr. Our study demonstrates the importance of mountain-building events and geographical isolation of alpine populations as drivers of rapid diversification, even in spore-dispersed plants. This work also highlights the usefulness of combined phylogenetic, geological and ecological datasets, and the promise of comparative environment-dependent diversification models in better understanding the evolutionary origins of biodiversity.
Collapse
Affiliation(s)
- Weston L Testo
- Department of Biology, University of Florida, Box 118525, Gainesville, FL, 32611, USA
| | - Emily Sessa
- Department of Biology, University of Florida, Box 118525, Gainesville, FL, 32611, USA
| | - David S Barrington
- Department of Plant Biology, University of Vermont, 63 Carrigan Drive, Burlington, VT, 05405, USA
| |
Collapse
|
17
|
Wang YR, Zhao CF, Yu XD, Zhang XC. The complete chloroplast genome sequence of a typical alpine fern Lepisorus waltonii (Ching) S. L. Yu in Polypodiaceae. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1574631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Ya-Rong Wang
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany Chinese Academy of Sciences, Beijing, China
| | - Cun-Feng Zhao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xu-Dong Yu
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
18
|
Gu C, Dong B, Xu L, Tembrock LR, Zheng S, Wu Z. The Complete Chloroplast Genome of Heimia myrtifolia and Comparative Analysis within Myrtales. Molecules 2018; 23:E846. [PMID: 29642470 PMCID: PMC6017443 DOI: 10.3390/molecules23040846] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 12/18/2022] Open
Abstract
Heimia myrtifolia is an important medicinal plant with several pharmacologically active alkaloids and is also used as an ornamental landscape plant. The purpose of this study is to complete and characterize the chloroplast (cp) genome of H. myrtifolia and compare genomic features to other Myrtales species' cp genomes. The analysis showed that H. myrtifolia has a total length of 159,219 bp with a typical quadripartite structure containing two identical inverted repeats (IRs) of 25,643 bp isolated by one large single copy (LSC) of 88,571 bp and one small single copy (SSC) of 18,822 bp. The H. myrtifolia cp genome contains 129 genes with eight ribosomal RNAs, 30 transfer RNAs, and 78 protein coding genes, in which 17 genes are duplicated in two IR regions. The genome organization including gene type and number and guanine-cytosine (GC) content is analyzed among the 12 cp genomes in this study. Approximately 255 simple sequence repeats (SSRs) and 16 forward, two reverses, and two palindromic repeats were identified in the H. myrtifolia cp genome. By comparing the whole H. myrtifolia cp genome with 11 other Myrtales species, the results showed that the sequence similarity was high between coding regions while sequence divergence was high between intergenic regions. By employing the full cp genomes for phylogenetic analysis, structural and sequence differences were characterized between H. myrtifolia and 11 Myrtales species illustrating what patterns are common in the evolution of cp genomes within the Myrtales. The first entire cp genome in the genus Heimia provides a valuable resource for further studies in these medicinally and ornamentally important taxa.
Collapse
Affiliation(s)
- Cuihua Gu
- School of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China.
| | - Bin Dong
- School of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China.
| | - Liang Xu
- Zhejiang Academy of Forestry, Hangzhou 310023, China.
| | - Luke R Tembrock
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA.
| | - Shaoyu Zheng
- School of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China.
| | - Zhiqiang Wu
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA.
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 5011, USA.
| |
Collapse
|
19
|
Abstract
According to the present taxonomical treatment, Paeonia subsect. Delavayanae consists of only two species (P. delavayi and P. ludlowii) endemic to the Himalayan-Hengduan Mountains. Although P. ludlowii can be distinguished from P. delavayi on the basis of a series of morphological characters, the species delimitation remains controversial because the more widespread one, P. delavayi, exhibits considerable morphological diversity. Both chloroplast DNA markers and nuclear microsatellites or simple sequence repeats (nSSR) are used herein to reveal genetic diversity and relationships of the two taxa included in this subsection, and ecological niche modeling (ENM) is employed to get insights into their paleodistribution. Our results show that genetic boundaries between the two currently recognized species are unclear, probably due to recent divergence. Paeonia ludlowii is budding from P. delavayi, probably by genetic isolation but also by shifting its niche to the harsher upland Tibetan conditions. Paeonia delavayi itself would be, however, under active speciation, showing significant genetic differentiation and morphological diversity. Whereas P. ludlowii would have endured the Pleistocene glacial periods by in situ persistence in local, small refugia, a 'dual' model seems to apply for P. delavayi (in situ persistence and retreat to refugia). The rarity of P. ludlowii and high evolutionary potential of P. delavayi imply high priority for in situ conservation of both taxa. The Himalayan-Hengduan Mountains are an ideal arena for differentiation within subsect. Delavayanae of Paeonia, by means of expansions/contractions/displacements, vertical migrations, and local survival/extinctions in response to the Neogene climate fluctuations and geological changes.
Collapse
|
20
|
Wu Z, Gu C, Tembrock LR, Zhang D, Ge S. Characterization of the whole chloroplast genome of Chikusichloa mutica and its comparison with other rice tribe (Oryzeae) species. PLoS One 2017; 12:e0177553. [PMID: 28542519 PMCID: PMC5443529 DOI: 10.1371/journal.pone.0177553] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 04/28/2017] [Indexed: 11/19/2022] Open
Abstract
Chloroplast genomes are a significant genomic resource in plant species and have been used in many research areas. The complete genomic information from wild crop species could supply a valuable genetic reservoir for breeding. Chikusichloa mutica is one of the most important wild distant relatives of cultivated rice. In this study, we sequenced and characterized its complete chloroplast (cp) genome and compared it with other species in the same tribe. The whole cp genome sequence is 136,603 bp in size and exhibits a typical quadripartite structure with large and small single-copy regions (LSC, 82,327 bp; SSC, 12,598 bp) separated by a pair of 20,839-bp inverted repeats (IRA, B). A total of 110 unique genes are annotated, including 76 protein-coding genes, 4 ribosomal RNA genes and 30 tRNA genes. The genome structure, gene order, GC content, and other features are similar to those of other angiosperm cp genomes. When comparing the cp genomes between Oryzinae and Zizaniinae subtribes, the main differences were found between the junction regions and distribution of simple sequence repeats (SSRs). In comparing the two Chikusichloa species, the genomes were only 40 bp different in length and 108 polymorphic sites, including 83 single nucleotide substitutions (SNPs) and 25 insertion-deletions (Indels), were found between the whole cp genomes. The complete cp genome of C. mutica will be an important genetic tool for future breeding programs and understanding the evolution of wild rice relatives.
Collapse
Affiliation(s)
- Zhiqiang Wu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- * E-mail:
| | - Cuihua Gu
- School of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Luke R. Tembrock
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Dong Zhang
- Department of Statistics, Iowa State University, Ames, Iowa, United States of America
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
21
|
Singh AP, Johari D, Khare PB. Studies on ontogeny and reproductive behaviour of Lepisorus nudus (Hook.) Ching (Polypodiaceae). JOURNAL OF PLANT RESEARCH 2017; 130:281-290. [PMID: 28012124 DOI: 10.1007/s10265-016-0891-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 10/26/2016] [Indexed: 06/06/2023]
Abstract
In-vitro studies of the ontogeny and mating system of the gametophytes of Lepisorus nudus were carried out through multispore and isolate cultures lasting 23 weeks. Spore germination begins early, on day 5-6. Spore germination pattern was Vittaria type and the germination percentage reached 82.69% (± 3.20%). Filamentous gametophyte did not branch and never produce separate prothalli. Occasionally the branching and separate prothalli were produced from mature and cordate gametophytes. Prothallial development was Drynaria type (cordate gametophytes with notched apex) contrary to other known species of Lepisorus, where gametophyte development was Kaulinia type (strap gametophytes without apical notch). Gametophyte production in multispore cultures reached up-to 75.6% (± 18.85%). All isolates initially produced archegonia and antheridia only after a prolonged cessation of production in archegonia. In contrast, only 37.2% (±12.63%) of individuals in multispore culture exhibited the same pattern with 29.8% (±7.56%) developing as males that did not produce archegonia by the end of the study. Only 37.2% (±12.63%) of archegoniate gametophytes developed antheridia by the end of the study and only once archegonia had degenerated; i.e., a temporal gap existed in expression of female and male gametangia. In multispore culture, only 26.21% (±5.70%) sporophytes developed on 160th day by fusion of female and male gametes that were derived from matings between sib gametophytes. In contrast, isolated gametophytes did not produce sporophytes. In isolate gametophytes, mature archegonia could not take delivery of male gametangia because antheridia were produced sequentially. This study suggests that the sequential expression of gametangia and absence of the intragametophytic selfing may also be a possible cause of reproductive barriers. Lepisorus nudus promotes inter-gametophytic selfing as an adaptive mechanism for reproductive success in multispore culture. This study presents a detailed account on reproductive biology of the taxa whose population is decreasing at distressing rate.
Collapse
Affiliation(s)
- Ajit Pratap Singh
- Pteridology Laboratory, CSIR-National Botanical Research Institute, 2-Rana Pratap Marg, Lucknow, U.P, 226 001, India.
| | - Deepali Johari
- Pteridology Laboratory, CSIR-National Botanical Research Institute, 2-Rana Pratap Marg, Lucknow, U.P, 226 001, India
| | - Prem Behari Khare
- Pteridology Laboratory, CSIR-National Botanical Research Institute, 2-Rana Pratap Marg, Lucknow, U.P, 226 001, India
| |
Collapse
|
22
|
Against all odds: reconstructing the evolutionary history of Scrophularia (Scrophulariaceae) despite high levels of incongruence and reticulate evolution. ORG DIVERS EVOL 2017. [DOI: 10.1007/s13127-016-0316-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
23
|
Zhou W, Jin J, Wu J, Chen H, Yang J, Murphy RW, Che J. Mountains too high and valleys too deep drive population structuring and demographics in a Qinghai-Tibetan Plateau frog Nanorana pleskei (Dicroglossidae). Ecol Evol 2016; 7:240-252. [PMID: 28070287 PMCID: PMC5214757 DOI: 10.1002/ece3.2646] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/09/2016] [Accepted: 11/13/2016] [Indexed: 12/31/2022] Open
Abstract
Pleistocene glacial–interglacial climatic oscillations greatly shaped the current genetic structure of many species. However, geographic features may influence the impact of climatic cycling. Distinct geographic and environmental characters between northern and southern parts of the eastern Qinghai–Tibetan Plateau (EQTP) facilitate explorations into the impacts of geographic features on species. The northern parts of EQTP contain large areas of marsh, and the environment is rather homogeneous. In contrast, the southern EQTP harbors complex alpine valleys and a much more heterogeneous setting. We evaluate DNA sequence variation from both the mitochondrial and nuclear genomes in Nanorana pleskei, a species endemic to the EQTP. Hypothesis testing on the evolutionary history of N. pleskei indicates that northern populations can disperse freely, but alpine valleys isolate southern populations. Demographic histories between northern and southern populations also differ. Northern populations appear to have experienced population expansions, while southern frogs exhibit a far more stable demographic history. By combining climatic analyses and species' distribution models, our study suggests that geographic and environmental features drive the differences between the northern and southern EQTP.
Collapse
Affiliation(s)
- Weiwei Zhou
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Jieqiong Jin
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Jun Wu
- Nanjing Institute of Environmental Sciences Ministry of Environmental Protection Nanjing China
| | - Hongman Chen
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Junxiao Yang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China; Kunming College of Life Science University of Chinese Academy of Sciences Kunming China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China; Centre for Biodiversity and Conservation Biology Royal Ontario Museum Toronto ON Canada
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| |
Collapse
|
24
|
Transverse Alpine Speciation Driven by Glaciation. Trends Ecol Evol 2016; 31:916-926. [DOI: 10.1016/j.tree.2016.08.009] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 08/26/2016] [Accepted: 08/26/2016] [Indexed: 01/19/2023]
|
25
|
Li WJ, Sui XL, Kuss P, Liu YY, Li AR, Guan KY. Long-Distance Dispersal after the Last Glacial Maximum (LGM) Led to the Disjunctive Distribution of Pedicularis kansuensis (Orobanchaceae) between the Qinghai-Tibetan Plateau and Tianshan Region. PLoS One 2016; 11:e0165700. [PMID: 27806090 PMCID: PMC5091882 DOI: 10.1371/journal.pone.0165700] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 10/17/2016] [Indexed: 11/19/2022] Open
Abstract
Quaternary climate fluctuations have profoundly affected the current distribution patterns and genetic structures of many plant and animal species in the Qinghai-Tibetan Plateau (QTP) and adjacent mountain ranges, e.g. Tianshan (TSR), Altay, etc. In this greater area disjunct distributions are prominent but have nevertheless received little attention with respect to the historical processes involved. Here, we focus on Pedicularis kansuensis to test whether the current QTP and TSR disjunction is the result of a recent Holocene range expansion involving dispersal across arid land bridge(s) or a Pleistocene range fragmentation involving persistence in refugia. Two chloroplast DNA spacers were sequenced for 319 individuals from 34 populations covering the entire distribution range of this species in China. We found a total of 17 haplotypes of which all occurred in the QTP, and only five in the TSR. Overall genetic diversity was high (HT = 0.882, HS = 0.559) and higher in the QTP than in the TSR. Genetic differentiation among regions and populations was relatively low (GST = 0.366) and little evidence for a phylogeographic pattern emerged. The divergence times for the four main lineages could be dated to the early Pleistocene. Surprisingly, the two ubiquitous haplotypes diverged just before or around the Last Glacial Maximum (LGM) and were found in different phylogenetic lineages. The Species Distribution Model suggested a disappearance of P. kansuensis from the TSR during the LGM in contrast to a relatively constant potential distribution in the QTP. We conclude that P. kansuensis colonized the TSR after the LGM. The improbable long-distance dispersal by wind or water across arid land seed flow may well have had birds or men as vector.
Collapse
Affiliation(s)
- Wen-Jun Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Lin Sui
- Yunnan Key Laboratory for Research and Development of Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Patrick Kuss
- Institute of Systematic and Evolutionary Botany, University of Zurich, 8008 Zurich, Switzerland
| | - Yan-Yan Liu
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Ai-Rong Li
- Yunnan Key Laboratory for Research and Development of Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- * E-mail: (ARL); (KYG)
| | - Kai-Yun Guan
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Yunnan Key Laboratory for Research and Development of Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- * E-mail: (ARL); (KYG)
| |
Collapse
|
26
|
Zhao CF, Kwak M, Xiang QP. Isolation and characterization of microsatellite markers in the Lepisorus clathratus complex (Polypodiaceae). APPLICATIONS IN PLANT SCIENCES 2016; 4:apps1600069. [PMID: 27785385 PMCID: PMC5077284 DOI: 10.3732/apps.1600069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 07/05/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Microsatellites were designed and characterized in the Sino-Himalayan fern Lepisorus clathratus complex (Polypodiaceae) to further study the phylogeography and reproductive ecology of this species. METHODS AND RESULTS From a genomic library obtained by next-generation sequencing, 10 polymorphic and six monomorphic microsatellite loci were developed. In one population of L. clathratus from Taibaishan in central China, the number of alleles observed for these microsatellites ranged from seven to 29, and observed and expected heterozygosity ranged from 0.463 to 0.919 and from 0.797 to 0.947, respectively. Cross-amplification in other taxa within this complex was successful, but cross-amplification was poor for other congeneric species. CONCLUSIONS This set of newly developed microsatellite markers will be useful for assessing genetic diversity, population structure, and mating system, and to infer polyploid origin in the L. clathratus complex.
Collapse
Affiliation(s)
- Cun-Feng Zhao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Myounghai Kwak
- Plant Resources Division, National Institute of Biological Resources, Incheon 404-708, Republic of Korea
| | - Qiao-Ping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People’s Republic of China
| |
Collapse
|
27
|
Gu C, Tembrock LR, Li Y, Lu X, Wu Z. The complete chloroplast genome of queen's crape-myrtle( Lagerstroemia macrocarpa). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:408-409. [PMID: 33473500 PMCID: PMC7799958 DOI: 10.1080/23802359.2016.1176879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The whole complete chloroplast genome of Lagerstroemia macrocarpa was assembled in this study. Total genome is 152,472 bp in length consisting of two inverted repeats of 17,562 bp separated by a large single-copy region and a small single-copy region of 84,050 bp and 33,295 bp, respectively. This genome contains 112 unique genes including 78 protein-coding genes, 4 ribosomal RNA genes and 30 transfer RNA genes. In 78 protein-coding genes, 8 genes (atpF, ndhA, ndhB, petB, petD, rpl16, rpoC1, rps16) contain one intron and three genes with two introns each (clpP, rps12 and ycf3). This newly sequenced chloroplast genome supply highly variable information of polymorphisms within Lagerstroemia species.
Collapse
Affiliation(s)
- Cuihua Gu
- School of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, People's Republic of China
| | - Luke R Tembrock
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Yunlong Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden Mem.Sun Yat-Sen, Nanjing, People's Republic of China
| | - Xiaoqing Lu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden Mem.Sun Yat-Sen, Nanjing, People's Republic of China
| | - Zhiqiang Wu
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| |
Collapse
|
28
|
Wu Z, Gu C, Tembrock LR, Sun C. The complete chloroplast genome of Arabidopsis lyrata. MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:291-292. [PMID: 33644362 PMCID: PMC7871834 DOI: 10.1080/23802359.2016.1166082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We report the complete chloroplast DNA (cpDNA) of Arabidopsis lyrata (Brassicaceae), a less studied relative of A. thaliana, by employing next-generation sequencing reads and de novo assembly. The length of the closed circular cpDNA is 154,604 bp with a typical quadripartite structure. The genome is composed of one large single copy and one small single copy regions of 84,209 bp and 17,871 bp, respectively, and separated by a pair of inverted repeats of 26,262 bp in length. The overall GC content is 36.35% and the GC content of the LSC, IRs and SSC regions are 34.12%, 42.30% and 29.38%, separately. The gene content and the number for A. lyrata are the same as other published species in Brassicaceae with 112 annotated known unique genes including 78 protein-coding genes, 30 tRNA genes and four rRNA genes. The complete cpDNA of A. lyrata will provide valuable molecular resources for further phylogenetic and evolutionary analysis in the model Arabidopsis genus.
Collapse
Affiliation(s)
- Zhiqiang Wu
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Cuihua Gu
- School of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, PR China
| | - Luke R Tembrock
- School of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, PR China
| | - Cheng Sun
- Key Laboratory of Pollinating Insect Biology of the Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
29
|
Liu F, Tembrock LR, Sun C, Han G, Guo C, Wu Z. The complete plastid genome of the wild rice species Oryza brachyantha (Poaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:218-219. [PMID: 33644346 PMCID: PMC7871827 DOI: 10.1080/23802359.2016.1155093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The whole plastid genome of wild rice (Oryza brachyantha) is characterized in this study. The genome is 134 604 bp in length and is arranged in a typical circular structure, including a pair of inverted repeats (IRs) of 20 832 bp in size separated by a large single-copy region (LSC) of 80 411 bp in length and a small single-copy region (SSC) of 12 529 bp in length. The overall GC content of the genome is 38.98%. One hundred and ten unique genes were annotated from the chloroplast genome, including 76 protein-coding genes, 4 ribosomal RNA genes and 30 tRNA genes. A total of 20 of these genes are duplicated in the IR regions, 13 genes contain 1 intron and 2 genes (rps12 and ycf3) have 2 introns.
Collapse
Affiliation(s)
- Fengqi Liu
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, China.,Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Science, Harbin, China
| | - Luke R Tembrock
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Cheng Sun
- Key Laboratory of Pollinating Insect Biology of the Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guiqing Han
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, China.,Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Science, Harbin, China
| | - Changhong Guo
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Zhiqiang Wu
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| |
Collapse
|
30
|
Wu Z, Tembrock LR. Two complete chloroplast genomes of white campion (Silene latifolia) from male and female individuals. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:375-376. [PMID: 26714215 DOI: 10.3109/19401736.2015.1126829] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, we assembled two individuals' complete chloroplast genomes with one male and one female from the dioecious plant species white campion (Silene latifolia). The two chloroplast genomes have an identical composition with each other as a circular molecule of 150 931 bp in length, with an overall GC content of 36.4%. The genomes consist of a pair of inverted repeats (IRs) of 25 503 bp, separated by a large single-copy (LSC) region and a small single-copy (SSC) region of 82 708 and 17 217 bp, respectively. The genomes contain 111 single copy genes, including 77 protein-coding genes, 4 ribosomal RNA genes and 30 transfer RNA genes. In these protein-coding genes, eight genes (rpl16, rpoC1, rps16, petD, petB, ndhB, ndhA and atpF) contain a single intron and three genes (rps12, clpP and ycf3) contain two introns. The two newly sequenced chloroplast genomes provide valuable information for detecting polymorphisms within species and between sexes.
Collapse
Affiliation(s)
- Zhiqiang Wu
- a Department of Biology , Colorado State University , Fort Collins , CO , USA
| | - Luke R Tembrock
- a Department of Biology , Colorado State University , Fort Collins , CO , USA
| |
Collapse
|
31
|
Wu Z, Ma Q. Limited variation across two chloroplast genomes with finishing chloroplast genome of Capsella grandiflora. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3460-1. [PMID: 26186303 DOI: 10.3109/19401736.2015.1066347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete chloroplast genome of Capsella grandiflora is finished in this study, which consists of 154 638 base pairs (bp) in size containing a pair of inverted repeats (IRa and IRb) of 26 462 bp each and a small and large single-copies (SSC and LSC) of 17 835 and 83 879 bp, respectively. The overall GC content is 36.54% and the GC contents of LSC, IRs, and SSC are 34.34%, 42.38%, and 29.61% separately. The gene contents and numbers are the same with other two published species in genus Capsella with 112 annotated unique genes including 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. Among these, 16 are duplicated in the inverted repeat regions, 15 genes contained one intron, and three genes (rps12, clpP, and ycf3) comprising two introns. Based on the whole genome comparison, only 28 SNPs and 16 Indels (insertion and deletion) are detected between two closed relatives' chloroplast genomes.
Collapse
Affiliation(s)
- Zhiqiang Wu
- a Department of Biological Sciences , Texas Tech University , Lubbock , TX , USA and
| | - Qiumao Ma
- b Department of Computer Science , Iowa State University , Ames , IA , USA
| |
Collapse
|
32
|
An M, Zeng L, Zhang T, Zhong Y. Phylogeography of Thlaspi arvense (Brassicaceae) in China Inferred from Chloroplast and Nuclear DNA Sequences and Ecological Niche Modeling. Int J Mol Sci 2015; 16:13339-55. [PMID: 26110380 PMCID: PMC4490498 DOI: 10.3390/ijms160613339] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 05/11/2015] [Accepted: 05/11/2015] [Indexed: 11/17/2022] Open
Abstract
Thlaspi arvense is a well-known annual farmland weed with worldwide distribution, which can be found from sea level to above 4000 m high on the Qinghai-Tibetan Plateau (QTP). In this paper, a phylogeographic history of T. arvense including 19 populations from China was inferred by using three chloroplast (cp) DNA segments (trnL-trnF, rpl32-trnL and rps16) and one nuclear (n) DNA segment (Fe-regulated transporter-like protein, ZIP). A total of 11 chloroplast haplotypes and six nuclear alleles were identified, and haplotypes unique to the QTP were recognized (C4, C5, C7 and N4). On the basis of molecular dating, haplotypes C4, C5 and C7 have separated from others around 1.58 Ma for cpDNA, which corresponds to the QTP uplift. In addition, this article suggests that the T. arvense populations in China are a mixture of diverged subpopulations as inferred by hT/vT test (hT ≤ vT, cpDNA) and positive Tajima's D values (1.87, 0.05 < p < 0.10 for cpDNA and 3.37, p < 0.01 for nDNA). Multimodality mismatch distribution curves and a relatively large shared area of suitable environmental conditions between the Last Glacial Maximum (LGM) as well as the present time recognized by MaxEnt software reject the sudden expansion population model.
Collapse
Affiliation(s)
- Miao An
- School of Life Sciences, Fudan University, Shanghai 200433, China.
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences/ Shanghai Chenshan Botanical Garden, Shanghai 201602, China.
| | - Liyan Zeng
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China.
| | - Ticao Zhang
- School of Life Sciences, Fudan University, Shanghai 200433, China.
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, CAS, Kunming 650201, China.
| | - Yang Zhong
- School of Life Sciences, Fudan University, Shanghai 200433, China.
- Institute of Biodiversity Science and Geobiology, Tibet University, Lhasa 850000, China.
| |
Collapse
|
33
|
Abstract
The whole nucleotide sequence of the chloroplast genome from Capsella rubella is determined in this study using short Illumina sequence data from public database. The circular double-stranded DNA, which consists of 154,601 base pairs (bp) in size, contains a pair of inverted repeats (IRa and IRb) of 26,462 bp each, which are separated by a small and large single-copies (SSC and LSC) of 17,855 and 83,822 bp, respectively. The overall GC content of the chloroplast genome is 36.54% and the GC contents of LSC, IRs and SSC are 34.33%, 42.38% and 29.61% separately. One hundred and twelve unique genes were annotated, including 78 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Among these, 16 are duplicated in the inverted repeat regions, 15 genes contained 1 intron, and 3 genes (rps12, clpP and ycf3) comprised of 2 introns. Two protein genes (rps19 and ycf1) span in the boundaries of LSC-IR and IR-SSC to produce two partial pseudogenes.
Collapse
Affiliation(s)
- Zhiqiang Wu
- a Department of Biology , Colorado State University , Fort Collins , CO , USA
| |
Collapse
|
34
|
Zhang X, Chen G, Ma YP, Ge J, Sun WB. Genetic diversity and population structure of Buddleja crispa Bentham in the Himalaya-Hengduan Mountains region revealed by AFLP. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2014.10.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
35
|
Wu Z. The completed eight chloroplast genomes of tomato from Solanum genus. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4155-4157. [DOI: 10.3109/19401736.2014.1003890] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Zhiqiang Wu
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| |
Collapse
|
36
|
Wu Z. The whole chloroplast genome of shrub willows (Salix suchowensis). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:2153-4. [PMID: 25418623 DOI: 10.3109/19401736.2014.982602] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The whole chloroplast genome of Salix suchowensis was determined in this study using next generation sequencing data. The total genome size was 155,214 bp in length, containing a pair of inverted repeats (IRs) of 27,459 bp, which were separated by large single copy (LSC) and small single copy (SSC) of 84,077 bp and 16,219 bp, respectively. The overall GC contents of the chloroplast genome were 36.73%. One hundred and ten unique genes were annotated, including 76 protein coding genes, 30 tRNA genes and 4 rRNA genes. Among these, 18 are duplicated in the inverted repeat regions, 14 genes contained 1 intron, and 3 genes (rps12, clpP and ycf3) comprised of 2 introns.
Collapse
Affiliation(s)
- Zhiqiang Wu
- a Department of Biology , Colorado State University , Fort Collins , CO , USA
| |
Collapse
|
37
|
Zhou WW, Zhang BL, Chen HM, Jin JQ, Yang JX, Wang YY, Jiang K, Murphy RW, Zhang YP, Che J. DNA barcodes and species distribution models evaluate threats of global climate changes to genetic diversity: a case study from Nanorana parkeri (Anura: Dicroglossidae). PLoS One 2014; 9:e103899. [PMID: 25093586 PMCID: PMC4122371 DOI: 10.1371/journal.pone.0103899] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Accepted: 07/07/2014] [Indexed: 11/25/2022] Open
Abstract
Anthropogenic global climate changes are one of the greatest threats to biodiversity. Distribution modeling can predict the effects of climate changes and potentially their effects on genetic diversity. DNA barcoding quickly identifies patterns of genetic diversity. As a case study, we use DNA barcodes and distribution models to predict threats under climate changes in the frog Nanorana parkeri, which is endemic to the Qinghai-Tibetan Plateau. Barcoding identifies major lineages W and E. Lineage W has a single origin in a refugium and Lineage E derives from three refugia. All refugia locate in river valleys and each greatly contributes to the current level of intraspecific genetic diversity. Species distribution models suggest that global climate changes will greatly influence N. parkeri, especially in the level of genetic diversity, because two former refugia will fail to provide suitable habitat. Our pipeline provides a novel application of DNA barcoding and has important implications for the conservation of biodiversity in southern areas of the Qinghai-Tibetan Plateau.
Collapse
Affiliation(s)
- Wei-wei Zhou
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Bao-lin Zhang
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, China
| | - Hong-man Chen
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jie-qiong Jin
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jun-xiao Yang
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yun-yu Wang
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ke Jiang
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Robert W. Murphy
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Ya-ping Zhang
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, China
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| |
Collapse
|
38
|
Wen J, Zhang JQ, Nie ZL, Zhong Y, Sun H. Evolutionary diversifications of plants on the Qinghai-Tibetan Plateau. Front Genet 2014; 5:4. [PMID: 24575120 PMCID: PMC3921583 DOI: 10.3389/fgene.2014.00004] [Citation(s) in RCA: 227] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 01/06/2014] [Indexed: 11/13/2022] Open
Abstract
The Qinghai-Tibetan Plateau (QTP) is the highest and one of the most extensive plateaus in the world. Phylogenetic, phylogeographic, and ecological studies support plant diversifications on the QTP through multiple mechanisms such as allopatric speciation via geographic isolation, climatic oscillations and divergences, pollinator-mediated isolation, diploid hybridization and introgression, and allopolyploidy. These mechanisms have driven spectacular radiations and/or species diversifications in various groups of plants such as Pedicularis L., Saussurea DC., Rhododendron L., Primula L., Meconopsis Vig., Rhodiola L., and many lineages of gymnosperms. Nevertheless, much work is needed toward understanding the evolutionary mechanisms of plant diversifications on the QTP. Well-sampled biogeographic analyses of the QTP plants in the broad framework of the Northern Hemisphere as well as the Southern Hemisphere are still relatively few and should be encouraged in the next decade. This paper reviews recent evidence from phylogenetic and biogeographic studies in plants, in the context of rapid radiations, mechanisms of species diversifications on the QTP, and the biogeographic significance of the QTP in the broader context of both the Northern and Southern Hemisphere biogeography. Integrative multidimensional analyses of phylogeny, morphological innovations, geography, ecology, development, species interactions and diversifications, and geology are needed and should shed insights into the patterns of evolutionary assembly and radiations in this fascinating region.
Collapse
Affiliation(s)
- Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution Washington, DC, USA
| | | | - Ze-Long Nie
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences Kunming, China
| | - Yang Zhong
- Institute of Biodiversity Science and Geobiology, Tibet University Lhasa, China ; School of Life Sciences, Fudan University Shanghai, China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences Kunming, China
| |
Collapse
|
39
|
Bystriakova N, Ansell SW, Russell SJ, Grundmann M, Vogel JC, Schneider H. Present, past and future of the European rock fern Asplenium fontanum: combining distribution modelling and population genetics to study the effect of climate change on geographic range and genetic diversity. ANNALS OF BOTANY 2014; 113:453-465. [PMID: 24284816 PMCID: PMC3906967 DOI: 10.1093/aob/mct274] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 10/10/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND AND AIMS Climate change is expected to alter the geographic range of many plant species dramatically. Predicting this response will be critical to managing the conservation of plant resources and the effects of invasive species. The aim of this study was to predict the response of temperate homosporous ferns to climate change. METHODS Genetic diversity and changes in distribution range were inferred for the diploid rock fern Asplenium fontanum along a South-North transect, extending from its putative last glacial maximum (LGM) refugia in southern France towards southern Germany and eastern-central France. This study reconciles observations from distribution models and phylogeographic analyses derived from plastid and nuclear diversity. KEY RESULTS Genetic diversity distribution and niche modelling propose that genetic diversity accumulates in the LGM climate refugium in southern France with the formation of a diversity gradient reflecting a slow, post-LGM range expansion towards the current distribution range. Evidence supports the fern's preference for outcrossing, contradicting the expectation that homosporous ferns would populate new sites by single-spore colonization. Prediction of climate and distribution range change suggests that a dramatic loss of range and genetic diversity in this fern is possible. The observed migration is best described by the phalanx expansion model. CONCLUSIONS The results suggest that homosporous ferns reproducing preferentially by outcrossing accumulate genetic diversity primarily in LGM climate refugia and may be threatened if these areas disappear due to global climate change.
Collapse
Affiliation(s)
- Nadia Bystriakova
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Stephen W. Ansell
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Stephen J. Russell
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Michael Grundmann
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Johannes C. Vogel
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Harald Schneider
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| |
Collapse
|
40
|
Chen JM, Du ZY, Sun SS, Gituru RW, Wang QF. Chloroplast DNA phylogeography reveals repeated range expansion in a widespread aquatic herb Hippuris vulgaris in the Qinghai-Tibetan Plateau and adjacent areas. PLoS One 2013; 8:e60948. [PMID: 23565290 PMCID: PMC3614902 DOI: 10.1371/journal.pone.0060948] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 03/06/2013] [Indexed: 11/18/2022] Open
Abstract
Background The Qinghai-Tibetan Plateau (QTP) is one of the most extensive habitats for alpine plants in the world. Climatic oscillations during the Quaternary ice age had a dramatic effect on species ranges on the QTP and the adjacent areas. However, how the distribution ranges of aquatic plant species shifted on the QTP in response to Quaternary climatic changes remains almost unknown. Methodology and Principal Findings We studied the phylogeography and demographic history of the widespread aquatic herb Hippuris vulgaris from the QTP and adjacent areas. Our sampling included 385 individuals from 47 natural populations of H. vulgaris. Using sequences from four chloroplast DNA (cpDNA) non-coding regions, we distinguished eight different cpDNA haplotypes. From the cpDNA variation in H. vulgaris, we found a very high level of population differentiation (GST = 0.819) but the phylogeographical structure remained obscure (NST = 0.853>GST = 0.819, P>0.05). Phylogenetic analyses revealed two main cpDNA haplotype lineages. The split between these two haplotype groups can be dated back to the mid-to-late Pleistocene (ca. 0.480 Myr). Mismatch distribution analyses showed that each of these had experienced a recent range expansion. These two expansions (ca. 0.12 and 0.17 Myr) might have begun from the different refugees before the Last Glacial Maximum (LGM). Conclusions/Significance This study initiates a research on the phylogeography of aquatic herbs in the QTP and for the first time sheds light on the response of an alpine aquatic seed plant species in the QTP to Quaternary climate oscillations.
Collapse
Affiliation(s)
- Jin-Ming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, China
| | | | | | | | | |
Collapse
|
41
|
Wang L, Schneider H, Zhang XC, Xiang QP. The rise of the Himalaya enforced the diversification of SE Asian ferns by altering the monsoon regimes. BMC PLANT BIOLOGY 2012; 12:210. [PMID: 23140168 PMCID: PMC3508991 DOI: 10.1186/1471-2229-12-210] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 11/06/2012] [Indexed: 05/24/2023]
Abstract
BACKGROUND The rise of high mountain chains is widely seen as one of the factors driving rapid diversification of land plants and the formation of biodiversity hotspots. Supporting evidence was reported for the impact of the rapid rise of the Andean mountains but this hypothesis has so far been less explored for the impact of the "roof of the world". The formation of the Himalaya, and especially the rise of the Qinghai-Tibetan Plateau in the recent 20 million years, altered the monsoon regimes that dominate the current climates of South East Asia. Here, we infer the hypothesis that the rise of Himalaya had a strong impact on the plant diversity in the biodiversity hotspot of the Southwest Chinese Mountains. RESULTS Our analyses of the diversification pattern of the derived fern genus Lepisorus recovered evidence for changes in plant diversity that correlated with the strengthening of South East Asian monsoon. Southwest China or Southwest China and Japan was recovered as the putative area of origin of Lepisorus and enhancing monsoon regime were found to shape the early diversification of the genus as well as subsequent radiations during the late Miocene and Pliocene. CONCLUSIONS We report new evidence for a coincidence of plant diversification and changes of the climate caused by the uplift of the Himalaya. These results are discussed in the context of the impact of incomplete taxon sampling, uncertainty of divergence time estimates, and limitations of current methods used to assess diversification rates.
Collapse
Affiliation(s)
- Li Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Harald Schneider
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- Department of Botany, The Natural History Museum London, London, SW7 5BD, UK
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Qiao-Ping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| |
Collapse
|
42
|
Yan HF, Zhang CY, Wang FY, Hu CM, Ge XJ, Hao G. Population expanding with the phalanx model and lineages split by environmental heterogeneity: a case study of Primula obconica in subtropical China. PLoS One 2012; 7:e41315. [PMID: 23028425 PMCID: PMC3446961 DOI: 10.1371/journal.pone.0041315] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 06/25/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Current and historical events have both affected the current distribution patterns and intraspecific divergence of plants. While numerous studies have focused on the Qinghai-Tibetan Plateau (QTP), the impacts of such events on the flora of subtropical China remain poorly understood. Subtropical China is famous for its highly complex topography and the limited impact from glaciation during the Pleistocene; this may have resulted in a different genetic legacy for species in this region compared to fully glaciated areas. METHODOLOGY/PRINCIPAL FINDINGS We used plastid and nuclear DNA sequence data and distribution modeling to analyze the divergence patterns and demographic history of Primula obconica Hance, a widespread herbaceous montane species in subtropical China. The phylogenetic analysis revealed two major lineages (lineage A and lineage B), representing a west-east split into the Yunnan and Eastern groups, and the Sichuan and Central groups, respectively. The Eastern and Central groups comprised relatively new derived haplotypes. Nested Clade Analysis and Bayesian Skyline Plot analyses both indicated that P. obconica mainly experienced a gradual expansion of populations. In addition, the simulated distribution of P. obconica during the Last Glacial Maximum was slightly larger than its present-day distribution. CONCLUSION/SIGNIFICANCE Our results are the first to identify a west-east migration of P. obconica. The gradual expansion pattern and a larger potential distribution range in cold periods detected for P. obconica indicate that the population expansion of this species is consistent with the phalanx model. In addition, the current patterns of genetic differentiation have persisted as a result of the extensive environmental heterogeneity that exists in subtropical China.
Collapse
Affiliation(s)
- Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Cai-Yun Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Graduate University of the Chinese Academy of Sciences, Beijing, China
| | - Feng-Ying Wang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Chi-Ming Hu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Gang Hao
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| |
Collapse
|
43
|
Wang L, Schneider H, Wu Z, He L, Zhang X, Xiang Q. Indehiscent sporangia enable the accumulation of local fern diversity at the Qinghai-Tibetan Plateau. BMC Evol Biol 2012; 12:158. [PMID: 22929005 PMCID: PMC3560248 DOI: 10.1186/1471-2148-12-158] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 08/27/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Indehiscent sporangia are reported for only a few of derived leptosporangiate ferns. Their evolution has been likely caused by conditions in which promotion of self-fertilization is an evolutionary advantageous strategy such as the colonization of isolated regions and responds to stressful habitat conditions. The Lepisorus clathratus complex provides the opportunity to test this hypothesis because these derived ferns include specimens with regular dehiscent and irregular indehiscent sporangia. The latter occurs preferably in well-defined regions in the Himalaya. Previous studies have shown evidence for multiple origins of indehiscent sporangia and the persistence of populations with indehiscent sporangia at extreme altitudinal ranges of the Qinghai-Tibetan Plateau (QTP). RESULTS Independent phylogenetic relationships reconstructed using DNA sequences of the uniparentally inherited chloroplast genome and two low-copy nuclear genes confirmed the hypothesis of multiple origins of indehiscent sporangia and the restriction of particular haplotypes to indehiscent sporangia populations in the Lhasa and Nyingchi regions of the QTP. In contrast, the Hengduan Mountains were characterized by high haplotype diversity and the occurrence of accessions with and without indehiscent sporangia. Evidence was found for polyploidy and reticulate evolution in this complex. The putative case of chloroplast capture in the Nyingchi populations provided further evidence for the promotion of isolated but persistent populations by indehiscent sporangia. CONCLUSIONS The presented results confirmed the hypothesis that indehiscent sporangia promote the establishment of persistent population in different regions of the QTP. These results are consistent with the expectations of reproductive reassurance by promotion of self-fertilization that played a critical role in the assembly of populations in isolated locations and/or extreme habitats.
Collapse
Affiliation(s)
- Li Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- Department of Botany, Natural History Museum, London, United Kingdom
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Harald Schneider
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- Department of Botany, Natural History Museum, London, United Kingdom
| | - Zhiqiang Wu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Lijuan He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Xianchun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Qiaoping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| |
Collapse
|
44
|
Yang FS, Qin AL, Li YF, Wang XQ. Great genetic differentiation among populations of Meconopsis integrifolia and its implication for plant speciation in the Qinghai-Tibetan Plateau. PLoS One 2012; 7:e37196. [PMID: 22590654 PMCID: PMC3349641 DOI: 10.1371/journal.pone.0037196] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 04/18/2012] [Indexed: 11/26/2022] Open
Abstract
The complex tectonic events and climatic oscillations in the Qinghai-Tibetan Plateau (QTP), the largest and highest plateau in the world, are thought to have had great effects on the evolutionary history of the native plants. Of great interest is to investigate plant population genetic divergence in the QTP and its correlation with the geologic and climatic changes. We conducted a range-wide phylogeographical analysis of M. integrifolia based on the chloroplast DNA (cpDNA) trnL-trnF and trnfM-trnS regions, and defined 26 haplotypes that were phylogenetically divided into six clades dated to the late Tertiary. The six clades correspond, respectively, to highly differentiated population groups that do not overlap in geographic distribution, implying that the mountain ranges acting as corridors or barriers greatly affected the evolutionary history of the QTP plants. The older clade of M. integrifolia only occurs in the southwest of the species' range, whereas the distributions of younger clades extend northeastward in the eastern QTP, suggesting that climatic divergence resulting from the uplift of the QTP triggered the initial divergence of M. integrifolia native to the plateau. Also, the nrDNA ITS region was used to clarify the unexpected phylogenetic relationships of cpDNA haplotypes between M. integrifolia and M. betonicifolia. The topological incongruence between the two phylogenies suggests an ancestral hybridization between the two species. Our study indicates that geographic isolation and hybridization are two important mechanisms responsible for the population differentiation and speciation of Meconopsis, a species-rich genus with complex polyploids.
Collapse
Affiliation(s)
- Fu-Sheng Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Ai-Li Qin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Yu-Fei Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| |
Collapse
|