1
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Long Z, Rieseberg LH. Documenting homoploid hybrid speciation. Mol Ecol 2024:e17412. [PMID: 38780141 DOI: 10.1111/mec.17412] [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: 01/29/2024] [Revised: 04/11/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
Homoploid hybrid speciation is challenging to document because hybridization can lead to outcomes other than speciation. Thus, some authors have argued that establishment of homoploid hybrid speciation should include evidence that reproductive barriers isolating the hybrid neo-species from its parental species were derived from hybridization. While this criterion is difficult to satisfy, several recent papers have successfully employed a common pipeline to identify candidate genes underlying such barriers and (in one case) to validate their function. We describe this pipeline, its application to several plant and animal species and what we have learned about homoploid hybrid speciation as a consequence. We argue that - given the ubiquity of admixture and the polygenic basis of reproductive isolation - homoploid hybrid speciation could be much more common and more protracted than suggested by earlier conceptual arguments and theoretical studies.
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Affiliation(s)
- Zhiqin Long
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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2
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Fu PC, Guo QQ, Chang D, Gao QB, Sun SS. Cryptic diversity and rampant hybridization in annual gentians on the Qinghai-Tibet Plateau revealed by population genomic analysis. PLANT DIVERSITY 2024; 46:194-205. [PMID: 38807911 PMCID: PMC11128845 DOI: 10.1016/j.pld.2023.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 05/30/2024]
Abstract
Understanding the evolutionary and ecological processes involved in population differentiation and speciation provides critical insights into biodiversity formation. In this study, we employed 29,865 single nucleotide polymorphisms (SNPs) and complete plastomes to examine genomic divergence and hybridization in Gentiana aristata, which is endemic to the Qinghai-Tibet Plateau (QTP) region. Genetic clustering revealed that G. aristata is characterized by geographic genetic structures with five clusters (West, East, Central, South and North). The West cluster has a specific morphological character (i.e., blue corolla) and higher values of FST compared to the remaining clusters, likely the result of the geological barrier formed by the Yangtze River. The West cluster diverged from the other clusters in the Early Pliocene; these remaining clusters diverged from one another in the Early Quaternary. Phylogenetic reconstructions based on SNPs and plastid data revealed substantial cyto-nuclear conflicts. Genetic clustering and D-statistics demonstrated rampant hybridization between the Central and North clusters, along the Bayankala Mountains, which form the geological barrier between the Central and North clusters. Species distribution modeling demonstrated the range of G. aristata expanded since the Last Interglacial period. Our findings provide genetic and morphological evidence of cryptic diversity in G. aristata, and identified rampant hybridization between genetic clusters along a geological barrier. These findings suggest that geological barriers and climatic fluctuations have an important role in triggering diversification as well as hybridization, indicating that cryptic diversity and hybridization are essential factors in biodiversity formation within the QTP region.
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Affiliation(s)
- Peng-Cheng Fu
- School of Life Science, Luoyang Normal University, Luoyang 471934, PR China
| | - Qiao-Qiao Guo
- School of Life Science, Luoyang Normal University, Luoyang 471934, PR China
| | - Di Chang
- School of Life Science, Luoyang Normal University, Luoyang 471934, PR China
| | - Qing-Bo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, PR China
| | - Shan-Shan Sun
- School of Life Science, Luoyang Normal University, Luoyang 471934, PR China
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3
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Hu H, Wang Q, Hao G, Zhou R, Luo D, Cao K, Yan Z, Wang X. Insights into the phylogenetic relationships and species boundaries of the Myricaria squamosa complex (Tamaricaceae) based on the complete chloroplast genome. PeerJ 2023; 11:e16642. [PMID: 38099308 PMCID: PMC10720482 DOI: 10.7717/peerj.16642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 11/19/2023] [Indexed: 12/17/2023] Open
Abstract
Myricaria plants are widely distributed in Eurasia and are helpful for windbreak and embankment protection. Current molecular evidence has led to controversy regarding species boundaries within the Myricaria genus and interspecific phylogenetic relationships between three specific species-M. bracteata, M. paniculata and M. squamosa-which have remained unresolved. This study treated these three unresolved taxa as a species complex, named the M. squamosa complex. The genome skimming approach was used to determine 35 complete plastome sequences and nuclear ribosomal DNA sequences for the said complex and other closely related species, followed by de novo assembly. Comparative analyses were conducted across Myricaria to identify the genome size, gene content, repeat type and number, SSR (simple sequence repeat) abundance, and codon usage bias of chloroplast genomes. Tree-based species delimitation results indicated that M. bracteata, M. paniculata and M. squamosa could not be distinguished and formed two monophyletic lineages (P1 and P2) that were clustered together. Compared to plastome-based species delimitation, the standard nuclear DNA barcode had the lowest species resolution, and the standard chloroplast DNA barcode and group-specific barcodes delimitated a maximum of four out of the five species. Plastid phylogenomics analyses indicated that the monophyletic M. squamosa complex is comprised of two evolutionarily significant units: one in the western Tarim Basin and the other in the eastern Qinghai-Tibet Plateau. This finding contradicts previous species discrimination and promotes the urgent need for taxonomic revision of the threatened genus Myricaria. Dense sampling and plastid genomes will be essential in this effort. The super-barcodes and specific barcode candidates outlined in this study will aid in further studies of evolutionary history.
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Affiliation(s)
- Huan Hu
- Microbial Resources and Drug Development Key Laboratory of Guizhou Tertiary Institution, Zunyi Medical University, Zunyi, China
| | - Qian Wang
- Microbial Resources and Drug Development Key Laboratory of Guizhou Tertiary Institution, Zunyi Medical University, Zunyi, China
| | - Guoqian Hao
- School of Life Science and Food Engineering, Yibin University, Yibin, China
| | - Ruitao Zhou
- School of Preclinical Medicine, Zunyi Medical University, Zunyi, China
| | - Dousheng Luo
- School of Preclinical Medicine, Zunyi Medical University, Zunyi, China
| | - Kejun Cao
- School of Preclinical Medicine, Zunyi Medical University, Zunyi, China
| | - Zhimeng Yan
- School of Medical Information Engineering, Zunyi Medical University, Zunyi, China
| | - Xinyu Wang
- Key Laboratory of Medical Electrophysiology, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
- Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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4
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Qin HT, Mӧller M, Milne R, Luo YH, Zhu GF, Li DZ, Liu J, Gao LM. Multiple paternally inherited chloroplast capture events associated with Taxus speciation in the Hengduan Mountains. Mol Phylogenet Evol 2023; 189:107915. [PMID: 37666379 DOI: 10.1016/j.ympev.2023.107915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 06/16/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
Mountainous regions provide a multitude of habitats and opportunities for complex speciation scenarios. Hybridization leading to chloroplast capture, which can be revealed by incongruent phylogenetic trees, is one possible outcome. Four allopatric Taxus lineages (three species and an undescribed lineage) from the Hengduan Mountains, southwest China, exhibit conflicting phylogenetic relationships between nuclear and chloroplast phylogenies. Here, we use multi-omic data at the population level to investigate their historical speciation processes. Population genomic analysis based on ddRAD-seq data revealed limited contemporary inter-specific gene flow involving only populations located close to another species. In a historical context, chloroplast and nuclear data (transcriptome) consistently showed conflicting phylogenetic relationships for T. florinii and the Emei type lineage. ILS and chloroplast recombination were excluded as possible causes, and transcriptome and ddRAD-seq data revealed an absence of the mosaic nuclear genomes that characterize hybrid origin scenarios. Therefore, T. florinii appears to have originated when a lineage of T. florinii captured the T. chinensis plastid type, whereas plastid introgression in the opposite direction generated the Emei Type. All four species have distinct ecological niche based on community investigations and ecological niche analyses. We propose that the origins of both species represent very rare examples of chloroplast capture events despite the paternal cpDNA inheritance of gymnosperms. Specifically, allopatrically and/or ecologically diverged parental species experienced a rare secondary contact, subsequent hybridization and reciprocal chloroplast capture, generating two new lineages, each of which acquired a unique ecological niche. These events might have been triggered by orogenic activities of the Hengduan Mountains and an intensification of the Asian monsoon in the late Miocene, and may represent a scenario more common in these mountains than presently known.
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Affiliation(s)
- Han-Tao Qin
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Michael Mӧller
- Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, United Kingdom
| | - Richard Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, United Kingdom
| | - Ya-Huang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang 674100, Yunnan, China
| | - Guang-Fu Zhu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - De-Zhu Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; University of Chinese Academy of Sciences, Beijing 100049, China; Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang 674100, Yunnan, China.
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China.
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang 674100, Yunnan, China.
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5
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Liu G, Xue G, Zhao T, Li Y, Yue L, Song H, Liu Q. Population structure and phylogeography of three closely related tree peonies. Ecol Evol 2023; 13:e10073. [PMID: 37274151 PMCID: PMC10234759 DOI: 10.1002/ece3.10073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/23/2023] [Accepted: 04/25/2023] [Indexed: 06/06/2023] Open
Abstract
Paeonia decomposita, Paeonia rotundiloba, and Paeonia rockii are three closely related species of Sect. Moutan is distributed in the montane area of the Eastern Hengduan Mountain region. Understanding the population history of these three tree peony species could contribute to unraveling the evolutionary patterns of undergrowth species in this hotspot area. We used one nuclear DNA marker (internal transcribed spacer region, ITS) and two chloroplast DNA markers (matK, ycf1) to reconstruct the phylogeographic pattern of the populations. In total, 228 individuals from 17 populations of the three species were analyzed in this study. Three nuclear clades (Clade I - Clade III) and four maternal clades (Clade A - Clade D) were reconstructed. Molecular dating suggested that young lineages diverged during the late Pliocene and early Pleistocene, younger than the uplift of the Hengduan Mountains but older than the last glacial maximum (LGM). Significant population and phylogeographic structures were detected at both markers. Furthermore, the populations of these tree peonies were overall at equilibrium during the climatic oscillations of the Pleistocene. The simulated palaeoranges of the three species during the LGM period mostly overlapped, which could have led to cross-breeding events. We propose an evolutionary scenario in which mountain orogenesis around the Hengduan Mountain area triggered parapatric isolation between maternal lineages of tree peonies. Subsequent climatic fluctuations drove migration and range recontact of these populations along the valleys. This detailed evolutionary history provides new insights into the phylogeographic pattern of species from mountain-valley systems.
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Affiliation(s)
- Guangli Liu
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
| | - Ge Xue
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
| | - Tingting Zhao
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
| | - Yang Li
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
| | - Liangliang Yue
- National Plateau Wetlands Research Center, College of WetlandsSouthwest Forestry UniversityKunmingChina
| | - Huixing Song
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
| | - Qinglin Liu
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
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Yang Z, Ma W, Yang X, Wang L, Zhao T, Liang L, Wang G, Ma Q. Plastome phylogenomics provide new perspective into the phylogeny and evolution of Betulaceae (Fagales). BMC PLANT BIOLOGY 2022; 22:611. [PMID: 36566190 PMCID: PMC9789603 DOI: 10.1186/s12870-022-03991-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Betulaceae is a relatively small but morphologically diverse family, with many species having important economic and ecological values. Although plastome structure of Betulaceae has been reported sporadically, a comprehensive exploration for plastome evolution is still lacking. Besides, previous phylogenies had been constructed based on limited gene fragments, generating unrobust phylogenetic framework and hindering further studies on divergence ages, biogeography and character evolution. Here, 109 plastomes (sixteen newly assembled and 93 previously published) were subject to comparative genomic and phylogenomic analyses to reconstruct a robust phylogeny and trace the diversification history of Betulaceae. RESULTS All Betulaceae plastomes were highly conserved in genome size, gene order, and structure, although specific variations such as gene loss and IR boundary shifts were revealed. Ten divergent hotspots, including five coding regions (Pi > 0.02) and five noncoding regions (Pi > 0.035), were identified as candidate DNA barcodes for phylogenetic analysis and species delimitation. Phylogenomic analyses yielded high-resolution topology that supported reciprocal monophyly between Betula and Alnus within Betuloideae, and successive divergence of Corylus, Ostryopsis, and Carpinus-Ostrya within Coryloideae. Incomplete lineage sorting and hybridization may be responsible for the mutual paraphyly between Ostrya and Carpinus. Betulaceae ancestors originated from East Asia during the upper Cretaceous; dispersals and subsequent vicariance accompanied by historical environment changes contributed to its diversification and intercontinental disjunction. Ancestral state reconstruction indicated the acquisition of many taxonomic characters was actually the results of parallel or reversal evolution. CONCLUSIONS Our research represents the most comprehensive taxon-sampled and plastome-level phylogenetic inference for Betulaceae to date. The results clearly document global patterns of plastome structural evolution, and established a well-supported phylogeny of Betulaceae. The robust phylogenetic framework not only provides new insights into the intergeneric relationships, but also contributes to a perspective on the diversification history and evolution of the family.
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Affiliation(s)
- Zhen Yang
- State Key Laboratory of Tree Genetics and Breeding, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- National Innovation Alliance of Hazelnut Industry, Beijing, 100091, China
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Wenxu Ma
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Forest Botany and Tree Physiology, University of Goettingen, 37077, Goettingen, Germany
| | | | - Lujun Wang
- Anhui Academy of Forestry, Hefei, 230031, China
| | - Tiantian Zhao
- State Key Laboratory of Tree Genetics and Breeding, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- National Innovation Alliance of Hazelnut Industry, Beijing, 100091, China
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Lisong Liang
- State Key Laboratory of Tree Genetics and Breeding, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- National Innovation Alliance of Hazelnut Industry, Beijing, 100091, China
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Guixi Wang
- State Key Laboratory of Tree Genetics and Breeding, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- National Innovation Alliance of Hazelnut Industry, Beijing, 100091, China
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Qinghua Ma
- State Key Laboratory of Tree Genetics and Breeding, Beijing, 100091, China.
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
- National Innovation Alliance of Hazelnut Industry, Beijing, 100091, China.
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China.
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Zhang J, Zhang S, Zheng Z, Lu Z, Yang Y. Genomic divergence between two sister Ostrya species through linked selection and recombination. Ecol Evol 2022; 12:e9611. [PMID: 36540075 PMCID: PMC9754895 DOI: 10.1002/ece3.9611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/16/2022] [Accepted: 11/22/2022] [Indexed: 12/23/2022] Open
Abstract
Studying the evolution of genomic divergence between lineages is a topical issue in evolutionary biology. However, the evolutionary forces that shape the heterogeneous divergence of the genomic landscape are still poorly understood. Here, two wind-pollinated sister-species (Ostrya japonica and O. chinensis) are used to explore what these potential forces might be. A total of 40 individuals from 16 populations across their main distribution areas in China were sampled for genome-wide resequencing. Population demography analyses revealed that these two sister-species diverged at 3.06-4.43 Mya. Both population contraction and increased gene flow were detected during glacial periods, suggesting secondary contact at those times. All three parameters (D XY, π, and ρ) decreased in those regions showing high levels of differentiation (F ST). These findings indicate that linked selection and recombination played a key role in the genomic heterogeneous differentiation between the two Ostrya species. Genotype-environment association analyses showed that precipitation was the most important ecological factor for speciation. Such environmentally related genes and positive selection genes may have contributed to local adaptation and the maintenance of species boundaries.
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Affiliation(s)
- Jin Zhang
- State Key Laboratory of Grassland Agro‐Ecosystems, College of EcologyLanzhou UniversityLanzhouChina
| | - Shangzhe Zhang
- State Key Laboratory of Grassland Agro‐Ecosystems, College of EcologyLanzhou UniversityLanzhouChina
| | - Zeyu Zheng
- State Key Laboratory of Grassland Agro‐Ecosystems, College of EcologyLanzhou UniversityLanzhouChina
| | - Zhiqiang Lu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglaChina
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro‐Ecosystems, College of EcologyLanzhou UniversityLanzhouChina
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8
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Wu X, Wang M, Li X, Yan Y, Dai M, Xie W, Zhou X, Zhang D, Wen Y. Response of distribution patterns of two closely related species in Taxus genus to climate change since last inter-glacial. Ecol Evol 2022; 12:e9302. [PMID: 36177121 PMCID: PMC9475124 DOI: 10.1002/ece3.9302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 07/05/2022] [Accepted: 08/26/2022] [Indexed: 02/02/2023] Open
Abstract
Climate change affects the species spatio-temporal distribution deeply. However, how climate affects the spatio-temporal distribution pattern of related species on the large scale remains largely unclear. Here, we selected two closely related species in Taxus genus Taxus chinensis and Taxus mairei to explore their distribution pattern. Four environmental variables were employed to simulate the distribution patterns using the optimized Maxent model. The results showed that the highly suitable area of T. chinensis and T. mairei in current period was 1.616 × 105 km2 and 3.093 × 105 km2, respectively. The distribution area of T. chinensis was smaller than that of T. mairei in different periods. Comparison of different periods shown that the distribution area of the two species was almost in stasis from LIG to the future periods. Temperature and precipitation were the main climate factors that determined the potential distribution of the two species. The centroids of T. chinensis and T. mairei were in Sichuan and Hunan provinces in current period, respectively. In the future, the centroid migration direction of the two species would shift towards northeast. Our results revealed that the average elevation distribution of T. chinensis was higher than that of T. mairei. This study sheds new insights into the habitat preference and limiting environment factors of the two related species and provides a valuable reference for the conservation of these two threatened species.
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Affiliation(s)
- Xingtong Wu
- Central South University of Forestry and TechnologyHunanChina
| | - Minqiu Wang
- Central South University of Forestry and TechnologyHunanChina
| | - Xinyu Li
- Central South University of Forestry and TechnologyHunanChina
| | - Yadan Yan
- Central South University of Forestry and TechnologyHunanChina
| | | | - Wanyu Xie
- Central South University of Forestry and TechnologyHunanChina
| | - Xiaofen Zhou
- Central South University of Forestry and TechnologyHunanChina
| | | | - Yafeng Wen
- Central South University of Forestry and TechnologyHunanChina
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Wang Z, Jiang Y, Yang X, Bi H, Li J, Mao X, Ma Y, Ru D, Zhang C, Hao G, Wang J, Abbott RJ, Liu J. Molecular signatures of parallel adaptive divergence causing reproductive isolation and speciation across two genera. Innovation (N Y) 2022; 3:100247. [PMID: 35519515 PMCID: PMC9065898 DOI: 10.1016/j.xinn.2022.100247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 04/16/2022] [Indexed: 11/18/2022] Open
Abstract
Parallel evolution of reproductive isolation (PERI) provides strong evidence for natural selection playing a fundamental role in the origin of species. However, PERI has been rarely demonstrated for well established species drawn from different genera. In particular, parallel molecular signatures for the same genes in response to similar habitat divergence in such different lineages is lacking. Here, based on whole-genome sequencing data, we first explore the speciation process in two sister species of Carpinus (Betulaceae) in response to divergence for temperature and soil-iron concentration in habitats they occupy in northern and southwestern China, respectively. We then determine whether parallel molecular mutations occur during speciation in this pair of species and also in another sister-species pair of the related genus, Ostryopsis, which occupy similarly divergent habitats in China. We show that gene flow occurred during the origin of both pairs of sister species since approximately 9.8 or approximately 2 million years ago, implying strong natural selection during divergence. Also, in both species pairs we detected concurrent positive selection in a gene (LHY) for flowering time and in two paralogous genes (FRO4 and FRO7) of a gene family known to be important for iron tolerance. These changes were in addition to changes in other major genes related to these two traits. The different alleles of these particular candidate genes possessed by the sister species of Carpinus were functionally tested and indicated likely to alter flowering time and iron tolerance as previously demonstrated in the pair of Ostryopsis sister species. Allelic changes in these genes may have effectively resulted in high levels of prezygotic reproductive isolation to evolve between sister species of each pair. Our results show that PERI can occur in different genera at different timescales and involve similar signatures of molecular evolution at genes or paralogues of the same gene family, causing reproductive isolation as a consequence of adaptation to similarly divergent habitats. PERI provides strong evidence for natural selection playing a fundamental role in the origin of species PERI is rarely demonstrated for well-established species drawn from different genera We detected PERI across two genera (Carpinus and Ostryopsis) in the family Betulaceae PERI can occur in different genera at different timescales and involve molecular signatures at similar pathways
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Affiliation(s)
- Zefu Wang
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yuanzhong Jiang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xiaoyue Yang
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Hao Bi
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jialiang Li
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xingxing Mao
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yazhen Ma
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Dafu Ru
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Cheng Zhang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Guoqian Hao
- Sichuan Tea College, Yibin University, Yibin 644000, China
| | - Jing Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | | | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- Corresponding author
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10
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Hanes MM, Shell S, Shimu T, Crist C, Machkour‐M’Rabet S. The phylogeographic history of Megistostegium (Malvaceae) in the dry, spiny thickets of southwestern Madagascar using RAD-seq data and ecological niche modeling. Ecol Evol 2022; 12:e8632. [PMID: 35222982 PMCID: PMC8848458 DOI: 10.1002/ece3.8632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 12/21/2021] [Accepted: 01/15/2022] [Indexed: 11/09/2022] Open
Abstract
The spiny thicket of southwestern Madagascar represents an extreme and ancient landscape with extraordinary levels of biodiversity and endemism. Few hypotheses exist for explaining speciation in the region and few plant studies have explored hypotheses for species diversification. Here, we investigate three species in the endemic genus Megistostegium (Malvaceae) to evaluate phylogeographic structure and explore the roles of climate, soil, and paleoclimate oscillations on population divergence and speciation throughout the region. We combine phylogenetic and phylogeographic inference of RADseq data with ecological niche modeling across space and time. Population structure is concurrent with major rivers in the region and we identify a new, potentially important biogeographic break coincident with several landscape features. Our data further suggests that niches occupied by species and populations differ substantially across their distribution. Paleodistribution modeling provide evidence that past climatic change could be responsible for the current distribution, population structure, and maintenance of species in Megistostegium.
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Affiliation(s)
- Margaret M. Hanes
- Department of BiologyEastern Michigan UniversityYpsilantiMichiganUSA
| | - Susan Shell
- Department of BiologyEastern Michigan UniversityYpsilantiMichiganUSA
| | - Tahsina Shimu
- Department of BiologyEastern Michigan UniversityYpsilantiMichiganUSA
| | - Clarissa Crist
- Department of BiologyEastern Michigan UniversityYpsilantiMichiganUSA
| | - Salima Machkour‐M’Rabet
- Departamento de Conservación de la BiodiversiadadEl Colegio de la Frontera SurChetumalMexico
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11
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You J, Lougheed SC, Zhao Y, Zhang G, Liu W, Lu F, Wang Y, Zhang W, Yang J, Qiong L, Song Z. Comparative phylogeography study reveals introgression and incomplete lineage sorting during rapid diversification of Rhodiola. ANNALS OF BOTANY 2022; 129:185-200. [PMID: 34718397 PMCID: PMC8796671 DOI: 10.1093/aob/mcab133] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND AIMS Many plant taxa in the Qinghai-Tibetan Plateau (QTP) and the Hengduan Mountains (HM) radiated rapidly during the Quaternary but with frequent secondary contact between diverging populations. Incomplete lineage sorting and introgressive hybridization might be involved during the rapid radiation, but their effects on phylogeography have not been fully determined. METHODS We investigated the chloroplast DNA (cpDNA)/internal transcribed spacer (ITS) sequence variations of 611 samples of Rhodiola bupleuroides, R. discolor, R. fastigiata and R. chrysanthemifolia from the QTP and HM to compare the phylogeographic patterns between the four species with different evolutionary histories, geographic ranges and reproductive modes. KEY RESULTS The divergence times of these species were consistent with the last peak of in situ speciation in the HM. While closely related species exhibited different phylogeographic patterns, they shared several ribotypes and haplotypes in sympatric populations, suggesting introgressive hybridization. A significant phylogenetic discordance between ribotypes and haplotypes was detected in three species, implying incomplete lineage sorting. Rhodiola discolor houses an extraordinary richness of cpDNA haplotypes, and this finding may be attributed to adaptive radiation. CONCLUSION In addition to geographic isolation and climate oscillations during the Quaternary, both introgressive hybridization and incomplete lineage sorting play important roles in species that experienced rapid diversification in the QTP and HM.
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Affiliation(s)
- Jianling You
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Botany, Tibet University–Fudan University Joint Laboratory for Biodiversity and Global Change, Fudan University, Shanghai, China
- BGI-Yunnan, BGI-Shenzhen, Kunming, China
| | | | - Yao Zhao
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Guojie Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Wensheng Liu
- College of Life Science and Technology, Central South University of Forestry and Techonology, Changsha, China
| | - Fan Lu
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Botany, Tibet University–Fudan University Joint Laboratory for Biodiversity and Global Change, Fudan University, Shanghai, China
| | - Yuguo Wang
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Botany, Tibet University–Fudan University Joint Laboratory for Biodiversity and Global Change, Fudan University, Shanghai, China
| | - Wenju Zhang
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Botany, Tibet University–Fudan University Joint Laboratory for Biodiversity and Global Change, Fudan University, Shanghai, China
| | - Ji Yang
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Botany, Tibet University–Fudan University Joint Laboratory for Biodiversity and Global Change, Fudan University, Shanghai, China
| | - La Qiong
- Tibet University–Fudan University Joint Laboratory for Biodiversity and Global Change, Tibet University, Thasa, China
| | - Zhiping Song
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Botany, Tibet University–Fudan University Joint Laboratory for Biodiversity and Global Change, Fudan University, Shanghai, China
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12
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Can Ecological Farming Systems Positively Affect Household Income from Agriculture? A Case Study of the Suburban Area of Hanoi, Vietnam. SUSTAINABILITY 2022. [DOI: 10.3390/su14031466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
From 1995, Vietnam started building safety standards for agricultural products divided into three labels, “safe”, “VietGAP”, and “organic” to deal with environmental problems and health issues resulting from the intensification of farming methods and increasing awareness of food safety. This research examines the reasons for government support of agricultural production according to those standards instead of conventional methods. To this end, we characterised the current farming systems, identified factors affecting the generation of cash income from agriculture, and investigated the influence of the farming system on farm income in the suburban area of Hanoi. Data collection involved a survey based on a structured questionnaire, key informants’ interviews, and focus group discussions conducted in 2015 with a sample size of 312 respondents. Three forms of farming systems: conventional, safe, and organic were identified. Literature suggested that ecological farming systems that are safe and organic are supported by stakeholders in Vietnam to maintain agricultural sustainability. A multiple linear regression model was applied to identify factors that affect cash incomes from agricultural activities. This research found a direct correlation between the ecological factor of farming systems and respondents’ cash income from agricultural activities. Additionally, the amount of family labour and respondents’ higher-level education and farm experiences appeared to positively influence the cash incomes from agriculture. On the other hand, farm size and membership in a farmers’ association were identified as the major factors that negatively affect agricultural cash income in the study area.
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13
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Yang Z, Ma W, He X, Zhao T, Yang X, Wang L, Ma Q, Liang L, Wang G. Species divergence and phylogeography of Corylus heterophylla Fisch complex (Betulaceae): Inferred from molecular, climatic and morphological data. Mol Phylogenet Evol 2022; 168:107413. [PMID: 35031460 DOI: 10.1016/j.ympev.2022.107413] [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: 06/22/2021] [Revised: 11/04/2021] [Accepted: 11/29/2021] [Indexed: 10/19/2022]
Abstract
Historical geo-climatic changes have shaped the geographical distributions and genetic diversity of numerous plant taxa in East Asia, which promote species divergence and ultimately speciation. Here, we integrated multiple approaches, including molecular phylogeography, ecological niche modeling, and morphological traits to examine the nucleotide diversity and interspecific divergence within Corylus heterophylla complex (C. heterophylla, C. kweichowensis, and C. yunnanensis). These three sibling taxa harbored similar high levels of nucleotide diversity at the species level. The molecular data (SCNG and cpDNA) unanimously supported the division of C. heterophylla complex into two major clades, with C. yunnanensis diverged earlier from the complex, whereas C. heterophylla and C. kweichowensis could hardly be separated. The split between the two clades (c. 12.89 Ma) coincided with the formation of Sichuan Basin in the middle Miocene, while the divergence among and within the five subclades (YUN1-YUN3, HK1-HK2) occurred from the late Miocene to the Pleistocene. C. heterophylla of northern China experienced glacial contraction and interglacial expansion during the Quaternary, whereas C. kweichowensis and C. yunnanensis of southern China presented population expansion even during the last glacial maximum. Despite of high levels of genetic admixture between C. heterophylla and C. kweichowensis, significant ecological and morphological discrepancy as well as incomplete geographic isolation indicated that adaptive evolution triggered by divergent selection may have played important roles in incipient ecological speciation.
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Affiliation(s)
- Zhen Yang
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China; National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing, 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Wenxu Ma
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China; National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing, 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Xin He
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China; National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing, 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Tiantian Zhao
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China; National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing, 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | | | - Lujun Wang
- Anhui Academy of Forestry, Hefei, 230031, China
| | - Qinghua Ma
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China; National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing, 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Lisong Liang
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China; National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing, 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China
| | - Guixi Wang
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China; National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing, 100091, China; Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing, 100091, China.
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14
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Chen S, Milne R, Zhou R, Meng K, Yin Q, Guo W, Ma Y, Mao K, Xu K, Kim YD, Do TV, Liao W, Fan Q. When tropical and subtropical congeners met: Multiple ancient hybridization events within Eriobotrya in the Yunnan-Guizhou Plateau, a tropical-subtropical transition area in China. Mol Ecol 2021; 31:1543-1561. [PMID: 34910340 DOI: 10.1111/mec.16325] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 01/09/2023]
Abstract
Global climate changes during the Miocene may have created ample opportunities for hybridization between members of tropical and subtropical biomes at the boundary between these zones. Yet, very few studies have explored this possibility. The Yunnan-Guizhou Plateau (YGP) in Southwest China is a biodiversity hotspot for vascular plants, located in a transitional area between the floristic regions of tropical Southeast Asia and subtropical East Asia. The genus Eriobotrya (Rosaceae) comprises both tropical and subtropical taxa, with 12 species recorded in the YGP, making it a suitable basis for testing the hypothesis of between-biome hybridization. Therefore, we surveyed the evolutionary history of Eriobotrya by examining three chloroplast regions and five nuclear genes for 817 individuals (47 populations) of 23 Eriobotrya species (including 19 populations of 12 species in the YGP), plus genome re-sequencing of 33 representative samples. We concluded that: (1) phylogenetic positions for 16 species exhibited strong cytonuclear conflicts, most probably due to ancient hybridization; (2) the YGP is a hotspot for hybridization, with 11 species showing clear evidence of chloroplast capture; and (3) Eriobotrya probably originated in tropical Asia during the Eocene. From the Miocene onwards, the intensification of the Eastern Asia monsoon and global cooling may have shifted the tropical-subtropical boundary and caused secondary contact between species, thus providing ample opportunity for hybridization and diversification of Eriobotrya, especially in the YGP. Our study highlights the significant role that paleoclimate changes probably played in driving hybridization and generating rich species diversity in climate transition zones.
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Affiliation(s)
- Sufang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Richard Milne
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, UK
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Kaikai Meng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Qianyi Yin
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Wei Guo
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yongpeng Ma
- Kunming Botanical Garden, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Kangshan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Kewang Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Young-Dong Kim
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon City, South Korea
| | - Truong Van Do
- Vietnam National Museum of Nature, Vietnam Academy of Science & Technology, Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science & Technology, Hanoi, Vietnam
| | - Wenbo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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15
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Zheng W, Yan LJ, Burgess KS, Luo YH, Zou JY, Qin HT, Wang JH, Gao LM. Natural hybridization among three Rhododendron species (Ericaceae) revealed by morphological and genomic evidence. BMC PLANT BIOLOGY 2021; 21:529. [PMID: 34763662 PMCID: PMC8582147 DOI: 10.1186/s12870-021-03312-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 11/02/2021] [Indexed: 06/08/2023]
Abstract
BACKGROUND Natural hybridization can influence the adaptive response to selection and accelerate species diversification. Understanding the composition and structure of hybrid zones may elucidate patterns of hybridization processes that are important to the formation and maintenance of species, especially for taxa that have experienced rapidly adaptive radiation. Here, we used morphological traits, ddRAD-seq and plastid DNA sequence data to investigate the structure of a Rhododendron hybrid zone and uncover the hybridization patterns among three sympatric and closely related species. RESULTS Our results show that the hybrid zone is complex, where bi-directional hybridization takes place among the three sympatric parental species: R. spinuliferum, R. scabrifolium, and R. spiciferum. Hybrids between R. spinuliferum and R. spiciferum (R. ×duclouxii) comprise multiple hybrid classes and a high proportion of F1 generation hybrids, while a novel hybrid taxon between R. spinuliferum and R. scabrifolium dominated the F2 generation, but no backcross individuals were detected. The hybrid zone showed basically coincident patterns of population structure between genomic and morphological data. CONCLUSIONS Natural hybridization exists among the three Rhododendron species in the hybrid zone, although patterns of hybrid formation vary between hybrid taxa, which may result in different evolutionary outcomes. This study represents a unique opportunity to dissect the ecological and evolutionary mechanisms associated with adaptive radiation of Rhododendron species in a biodiversity hotspot.
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Affiliation(s)
- Wei Zheng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, 10049, Beijing, China
| | - Li-Jun Yan
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, 10049, Beijing, China
- College of Vocational and Technical Education, Yunnan Normal University, 650092, Kunming, Yunnan, China
| | - Kevin S Burgess
- Department of Biology, Columbus State University, University System of Georgia, 31907-5645, Columbus, GA, USA
| | - Ya-Huang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
| | - Jia-Yun Zou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, 10049, Beijing, China
| | - Han-Tao Qin
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, 10049, Beijing, China
| | - Ji-Hua Wang
- The Flower Research Institute, Yunnan Academy of Agricultural Sciences, 650205, Kunming, China.
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China.
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, 674100, Lijiang, Yunnan, China.
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16
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Lyu R, He J, Luo Y, Lin L, Yao M, Cheng J, Xie L, Pei L, Yan S, Li L. Natural Hybrid Origin of the Controversial "Species" Clematis × pinnata (Ranunculaceae) Based on Multidisciplinary Evidence. FRONTIERS IN PLANT SCIENCE 2021; 12:745988. [PMID: 34712260 PMCID: PMC8545901 DOI: 10.3389/fpls.2021.745988] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/22/2021] [Indexed: 05/23/2023]
Abstract
Interspecific hybridization is common and has often been viewed as a driving force of plant diversity. However, it raises taxonomic problems and thus impacts biodiversity estimation and biological conservation. Although previous molecular phylogenetic studies suggested that interspecific hybridization may be rather common in Clematis, and artificial hybridization has been widely applied to produce new Clematis cultivars for nearly two centuries, the issue of natural hybridization of Clematis has never been addressed in detail. In this study, we tested the hybrid origin of a mesophytic and cold-adapted vine species, Clematis pinnata, which is a rare and taxonomically controversial taxon endemic to northern China. Using field investigations, flow cytometry (FCM), phylogenomic analysis, morphological statistics, and niche modeling, we tested hybrid origin and species status of C. pinnata. The FCM results showed that all the tested species were homoploid (2n = 16). Phylonet and HyDe analyses based on transcriptome data showed the hybrid origins of C. × pinnata from either C. brevicaudata × C. heracleifolia or C. brevicaudata × C. tubulosa. The plastome phylogeny depicted that C. × pinnata in different sampling sites originated by different hybridization events. Morphological analysis showed intermediacy of C. × pinnata between its putative parental species in many qualitative and quantitative characters. Niche modeling results suggested that C. × pinnata had not been adapted to a novel ecological niche independent of its putative parents. These findings demonstrated that plants of C. × pinnata did not formed a self-evolved clade and should not be treated as a species. The present study also suggests that interspecific hybridization is a common mechanism in Clematis to generate diversity and variation, and it may play an important role in the evolution and diversification of this genus. Our study implies that morphological diversity caused by natural hybridization may overstate the real species diversity in Clematis.
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Affiliation(s)
- Rudan Lyu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jian He
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yike Luo
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Lele Lin
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Min Yao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jin Cheng
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Lei Xie
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Linying Pei
- Beijing Engineering Research Center for Landscape Plant, Beijing Forestry University Forest Science Co. Ltd., Beijing, China
| | - Shuangxi Yan
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou, China
| | - Liangqian Li
- Institute of Botany, The Chinese Academy of Sciences, Beijing, China
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17
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Fu PC, Twyford AD, Sun SS, Wang HY, Xia MZ, Tan CX, Zhou XJ, Chen SL. Recurrent hybridization underlies the evolution of novelty in Gentiana (Gentianaceae) in the Qinghai-Tibetan Plateau. AOB PLANTS 2021; 13:plaa068. [PMID: 33510891 PMCID: PMC7821390 DOI: 10.1093/aobpla/plaa068] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 11/30/2020] [Indexed: 05/31/2023]
Abstract
The Qinghai-Tibetan Plateau (QTP) and adjacent areas are centres of diversity for several alpine groups. Although it is known that the QTP acted as a source area for diversification of the alpine genus Gentiana, the evolutionary processes underlying diversity in this genus, especially the formation of narrow endemics, are still poorly understood. Hybridization has been proposed as a driver of plant endemism in the QTP but few cases have been documented with genetic data. Here, we describe a new endemic species in Gentiana section Cruciata as G. hoae sp. nov., and explore its evolutionary history with complete plastid genomes and nuclear ribosomal internal transcribed spacer sequence data. Genetic divergence within G. hoae ~3 million years ago was followed by postglacial expansion on the QTP, suggesting Pleistocene glaciations as a key factor shaping the population history of G. hoae. Furthermore, a mismatch between plastid and nuclear data suggest that G. hoae participated in historical hybridization, while population sequencing show this species continues to hybridize with the co-occurring congener G. straminea in three locations. Our results indicate that hybridization may be a common process in the evolution of Gentiana and may be widespread among recently diverged taxa of the QTP.
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Affiliation(s)
- Peng-Cheng Fu
- School of Life Science, Luoyang Normal University, Luoyang, P.R. China
| | - Alex D Twyford
- Ashworth Laboratories, Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, UK
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, UK
| | - Shan-Shan Sun
- School of Life Science, Luoyang Normal University, Luoyang, P.R. China
| | - Hong-Yu Wang
- School of Life Science, Luoyang Normal University, Luoyang, P.R. China
| | - Ming-Ze Xia
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, P.R. China
- University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Cheng-Xi Tan
- School of Life Science, Luoyang Normal University, Luoyang, P.R. China
| | - Xiao-Jun Zhou
- School of Life Science, Luoyang Normal University, Luoyang, P.R. China
| | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, P.R. China
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18
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Wang Z, Jiang Y, Bi H, Lu Z, Ma Y, Yang X, Chen N, Tian B, Liu B, Mao X, Ma T, DiFazio SP, Hu Q, Abbott RJ, Liu J. Hybrid speciation via inheritance of alternate alleles of parental isolating genes. MOLECULAR PLANT 2021; 14:208-222. [PMID: 33220509 DOI: 10.1016/j.molp.2020.11.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/11/2020] [Accepted: 11/13/2020] [Indexed: 05/21/2023]
Abstract
It is increasingly realized that homoploid hybrid speciation (HHS), which involves no change in chromosome number, is an important mechanism of speciation. HHS will likely increase in frequency as ecological and geographical barriers between species are continuing to be disrupted by human activities. HHS requires the establishment of reproductive isolation between a hybrid and its parents, but the underlying genes and genetic mechanisms remain largely unknown. In this study, we reveal by integrated approaches that reproductive isolation originates in one homoploid hybrid plant species through the inheritance of alternate alleles at genes that determine parental premating isolation. The parent species of this hybrid species are reproductively isolated by differences in flowering time and survivorship on soils containing high concentrations of iron. We found that the hybrid species inherits alleles of parental isolating major genes related to flowering time from one parent and alleles of major genes related to iron tolerance from the other parent. In this way, it became reproductively isolated from one parent by the difference in flowering time and from the other by habitat adaptation (iron tolerance). These findings and further modeling results suggest that HHS may occur relatively easily via the inheritance of alternate parental premating isolating genes and barriers.
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Affiliation(s)
- Zefu Wang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Yuanzhong Jiang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Hao Bi
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Zhiqiang Lu
- State Key Laboratory of Grassland Agro-Ecosystem, Innovation Institute of Ecology and Life Sciences, Lanzhou University, Lanzhou 730000, China; CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | - Yazhen Ma
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Xiaoyue Yang
- State Key Laboratory of Grassland Agro-Ecosystem, Innovation Institute of Ecology and Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Ningning Chen
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Bin Tian
- State Key Laboratory of Grassland Agro-Ecosystem, Innovation Institute of Ecology and Life Sciences, Lanzhou University, Lanzhou 730000, China; Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry and Grassland Administration, Southwest Forestry University, Kunming 650224, China
| | - Bingbing Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan 030006, China
| | - Xingxing Mao
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Tao Ma
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV 25606, USA
| | - Quanjun Hu
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China.
| | - Richard J Abbott
- School of Biology, University of St Andrews, St Andrews KY16 9TH, UK.
| | - Jianquan Liu
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China; State Key Laboratory of Grassland Agro-Ecosystem, Innovation Institute of Ecology and Life Sciences, Lanzhou University, Lanzhou 730000, China.
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19
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Mao X, Wang J, Shrestha N, Ma Y, Liu J. Species Identification in the Rhododendron vernicosum- R. decorum Species Complex (Ericaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:608964. [PMID: 33584768 PMCID: PMC7876077 DOI: 10.3389/fpls.2021.608964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Delimitating species boundaries is the primary aim of biological classification and could be critical for evaluating the evolving process of species and conserving biodiversity. Rhododendron is an iconic group with an extraordinary diversity in southwest China. However, it remains unknown whether the recorded species therein comprise independently evolving lineages or artificially delimitated morphological entities. In this study, we carried out species delimitation of four Rhododendron species in the R. vernicosum-R. decorum species complex based on morphological analyses and population genetic data from nuclear simple sequence repeats (SSR) markers. We randomly selected a total of 105 specimens of different individuals identified as four species across their distributional ranges to examine the statistically distinct phenotypic clusters based on 19 morphological traits. Similarly, we genotyped 55 individuals of four species from 21 populations using 15 SSR markers. The morphological analyses sorted R. decorum and the other three species into two different phenotypic clusters. The genetic clusters were consistent with the morphological clusters. However, we also recovered the third genetic cluster, comprising six R. vernicosum populations and containing the admixed genetic compositions of the other two distinct genetic clusters. This hybrid group was morphologically similar to the typical R. vernicosum (including the samples from its type specimen locality and both R. verruciferum and R. gonggashanense) but with more genetic ancestry from R. decorum. Based on our findings, we identify two distinct species and one putative hybrid group due to introgression in the R. vernicosum-R. decorum species complex. We propose to merge R. verruciferum and R. gonggashanense into R. vernicosum based on genetic compositions and our morphological analyses. The hybrid group inferred from our findings, however, needs further investigations.
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Affiliation(s)
- Xingxing Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Lab of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Ji Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Lab of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Yazhen Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Lab of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Lab of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
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20
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Meng KK, Chen SF, Xu KW, Zhou RC, Li MW, Dhamala MK, Liao WB, Fan Q. Phylogenomic analyses based on genome-skimming data reveal cyto-nuclear discordance in the evolutionary history of Cotoneaster (Rosaceae). Mol Phylogenet Evol 2021; 158:107083. [PMID: 33516804 DOI: 10.1016/j.ympev.2021.107083] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 12/16/2020] [Accepted: 01/12/2021] [Indexed: 11/19/2022]
Abstract
As a consequence of hybridization, polyploidization, and apomixis, the genus Cotoneaster (Rosaceae) represents one of the most complicated and controversial lineages in Rosaceae, with ca. 370 species which have been classified into two subgenera and several sections, and is notorious for its taxonomic difficulty. The infrageneric relationships and taxonomy of Cotoneaster have remained poorly understood. Previous studies have focused mainly on natural hybridization involving only several species, and phylogeny based on very limited markers. In the present study, the sequences of complete chloroplast genomes and 204 low-copy nuclear genes of 72 accessions, representing 69 species as ingroups, were used to conduct the most comprehensive phylogenetic analysis so far for Cotoneaster. Based on the sequences of complete chloroplast genomes and many nuclear genes, our analyses yield two robust phylogenetic trees respectively. Chloroplast genome and nuclear data confidently resolved relationships of this genus into two major clades which largely supported current classification based on morphological evidence. However, conflicts between the chloroplast genome and low-copy nuclear phylogenies were observed in both the species level and clade level. Cyto-nuclear discordance in the phylogeny could be caused by frequent hybridization events and incomplete sorting lineage (ILS). In addition, our divergence-time analysis revealed an evolutionary radiation of the genus from late Miocene to date.
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Affiliation(s)
- Kai-Kai Meng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Su-Fang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ke-Wang Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Ren-Chao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ming-Wan Li
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China
| | - Man Kumar Dhamala
- Central Department of Environmental Science, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Wen-Bo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
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21
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Abdelaziz M, Muñoz-Pajares AJ, Berbel M, García-Muñoz A, Gómez JM, Perfectti F. Asymmetric Reproductive Barriers and Gene Flow Promote the Rise of a Stable Hybrid Zone in the Mediterranean High Mountain. FRONTIERS IN PLANT SCIENCE 2021; 12:687094. [PMID: 34512685 PMCID: PMC8424041 DOI: 10.3389/fpls.2021.687094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 07/15/2021] [Indexed: 05/13/2023]
Abstract
Hybrid zones have the potential to shed light on evolutionary processes driving adaptation and speciation. Secondary contact hybrid zones are particularly powerful natural systems for studying the interaction between divergent genomes to understand the mode and rate at which reproductive isolation accumulates during speciation. We have studied a total of 720 plants belonging to five populations from two Erysimum (Brassicaceae) species presenting a contact zone in the Sierra Nevada mountains (SE Spain). The plants were phenotyped in 2007 and 2017, and most of them were genotyped the first year using 10 microsatellite markers. Plants coming from natural populations were grown in a common garden to evaluate the reproductive barriers between both species by means of controlled crosses. All the plants used for the field and greenhouse study were characterized by measuring traits related to plant size and flower size. We estimated the genetic molecular variances, the genetic differentiation, and the genetic structure by means of the F-statistic and Bayesian inference. We also estimated the amount of recent gene flow between populations. We found a narrow unimodal hybrid zone where the hybrid genotypes appear to have been maintained by significant levels of a unidirectional gene flow coming from parental populations and from weak reproductive isolation between them. Hybrid plants exhibited intermediate or vigorous phenotypes depending on the analyzed trait. The phenotypic differences between the hybrid and the parental plants were highly coherent between the field and controlled cross experiments and through time. The highly coherent results obtained by combining field, experimental, and genetic data demonstrate the existence of a stable and narrow unimodal hybrid zone between Erysimum mediohispanicum and Erysimum nevadense at the high elevation of the Sierra Nevada mountains.
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Affiliation(s)
- Mohamed Abdelaziz
- Departamento de Genética, Facultad de Ciencias, Campus Fuentenueva, Universidad de Granada, Granada, Spain
- *Correspondence: Mohamed Abdelaziz
| | - A. Jesús Muñoz-Pajares
- Departamento de Genética, Facultad de Ciencias, Campus Fuentenueva, Universidad de Granada, Granada, Spain
- Laboratório Associado, Plant Biology, Research Centre in Biodiversity and Genetic Resources, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade Do Porto, Campus Agrário de Vairão, Fornelo e Vairão, Portugal
- Research Unit Modeling Nature, Universidad de Granada, Granada, Spain
| | - Modesto Berbel
- Departamento de Genética, Facultad de Ciencias, Campus Fuentenueva, Universidad de Granada, Granada, Spain
| | - Ana García-Muñoz
- Departamento de Genética, Facultad de Ciencias, Campus Fuentenueva, Universidad de Granada, Granada, Spain
| | - José M. Gómez
- Research Unit Modeling Nature, Universidad de Granada, Granada, Spain
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas, Consejo Superior de Investigaciones Científicas, Almeria, Spain
| | - Francisco Perfectti
- Departamento de Genética, Facultad de Ciencias, Campus Fuentenueva, Universidad de Granada, Granada, Spain
- Research Unit Modeling Nature, Universidad de Granada, Granada, Spain
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22
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Linan AG, Lowry PP, Miller AJ, Schatz GE, Sevathian JC, Edwards CE. RAD-sequencing reveals patterns of diversification and hybridization, and the accumulation of reproductive isolation in a clade of partially sympatric, tropical island trees. Mol Ecol 2020; 30:4520-4537. [PMID: 33210759 DOI: 10.1111/mec.15736] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/04/2020] [Accepted: 11/11/2020] [Indexed: 12/31/2022]
Abstract
A common pattern observed in temperate tree clades is that species are often morphologically distinct and partially interfertile but maintain species cohesion despite ongoing hybridization where ranges overlap. Although closely related species commonly occur in sympatry in tropical ecosystems, little is known about patterns of hybridization within a clade over time, and the implications of this hybridization for the maintenance of species boundaries. In this study, we focused on a clade of sympatric trees in the genus Diospyros in the Mascarene islands and investigated whether species are genetically distinct, whether they hybridize, and how patterns of hybridization are related to the time since divergence among species. We sampled multiple populations from each of 12 Mascarene Diospyros species, generated genome-wide single nucleotide polymorphism data using 2bRADseq, and conducted population genomic and phylogenomic analyses. We found that Mascarene Diospyros species diverged millions of years ago and are today largely genetically distinct from one another. Although hybridization was observed between closely related species belonging to the same subclade, more distantly related species showed little evidence of interspecific hybridization. Phylogenomic analyses also suggested that introgression has occurred during the evolutionary history of the clade. This suggests that, as diversification progressed, interspecific hybridization occurred among species, but became infrequent as lineages diverged from one another and evolved reproductive barriers. Species now coexist in partial sympatry, and experience limited hybridization between close relatives. Additional research is needed to better understand the role that introgression may have played in adaptation and diversification of Mascarene Diospyros, and its relevance for conservation.
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Affiliation(s)
- Alexander G Linan
- Department of Biology, Saint Louis University, St. Louis, MO, USA.,Center for Conservation and Sustainable Development, Missouri Botanical Garden, St. Louis, MO, USA
| | - Porter P Lowry
- Africa and Madagascar Program, Missouri Botanical Garden, St. Louis, MO, USA.,Institut de Systématique, Évolution et Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, École Pratique des Hautes Études, Université des Antilles, Paris, France
| | - Allison J Miller
- Department of Biology, Saint Louis University, St. Louis, MO, USA.,Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - George E Schatz
- Africa and Madagascar Program, Missouri Botanical Garden, St. Louis, MO, USA
| | - Jean-Claude Sevathian
- Botanist, Sustainability Consultant and Landscape Care and Maintenance Service, Beau Bassin-Rose Hill, Mauritius
| | - Christine E Edwards
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St. Louis, MO, USA
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23
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Arteaga MC, Bello-Bedoy R, Gasca-Pineda J. Hybridization Between Yuccas From Baja California: Genomic and Environmental Patterns. FRONTIERS IN PLANT SCIENCE 2020; 11:685. [PMID: 32733491 PMCID: PMC7358647 DOI: 10.3389/fpls.2020.00685] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/30/2020] [Indexed: 06/11/2023]
Abstract
Hybridization can occur when two geographically isolated species are reproductively compatible and have come into sympatry due to range shifts. Yucca and yucca moths exhibit obligate pollination mutualism; yucca moths are responsible for the gene flow mediated by pollen among yucca populations. In the Baja California Peninsula, there are two yucca sister species, Y. capensis and Y. valida, that have coevolved with the same pollinator, Tegeticula baja. Both yucca species are endemic to the peninsula, and their current distributions are allopatric. Based on their morphological characteristics, it has been suggested that some plants growing in the southern part of the Magdalena flatland, a spatially disjunct part of Yucca valida's range, have hybrid origins. We conducted genomic and climatic analyses of the two yucca species as well as the putative hybrid populations. We genotyped 3,423 single nucleotide polymorphisms in 120 individuals sampled from 35 localities. We applied Bayesian tests and geographic cline analyses to the genomic data. Using climatic information from the occurrence sites, we projected species distribution models in different periods to assess changes in the distributional range, and we performed a statistical test to define the niche divergence between the paternal species and the putative hybrid populations. Structure analysis revealed mixed ancestry in the genome of hybrid populations, and the Bayesian models supported a scenario of post-divergence gene flow between the yucca species. Our species distribution models reveal that the geographical ranges of the parental species overlapped mainly during the Last Glacial Maximum, which could facilitate genetic admixture between those species. Finally, we found that most of the assessed environmental axes between the parents and hybrid populations are divergent, indicating that the climatic niche of the hybrid populations is shifting from that of the populations' progenitors. Our results show that the populations in the southern part of the Magdalena flatland are the result of combination of the genetic components of two species. Hybrid individuals with this novel genomic combination arose in a different habitat than their parental species, and they exhibit ecological divergence, which contributes to reproductive isolation through spatial and temporal barriers.
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Affiliation(s)
- Maria Clara Arteaga
- Departamento de Biología de la Conservación, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Mexico
| | - Rafael Bello-Bedoy
- Facultad de Ciencias, Universidad Autónoma de Baja California, Ensenada, Mexico
| | - Jaime Gasca-Pineda
- Departamento de Biología de la Conservación, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Mexico
- Unidad de Biotecnología y Prototipos (UBIPRO), Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Mexico City, Mexico
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24
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Li J, Milne RI, Ru D, Miao J, Tao W, Zhang L, Xu J, Liu J, Mao K. Allopatric divergence and hybridization withinCupressus chengiana(Cupressaceae), a threatened conifer in the northern Hengduan Mountains of western China. Mol Ecol 2020; 29:1250-1266. [DOI: 10.1111/mec.15407] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 02/21/2020] [Accepted: 02/26/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Jialiang Li
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
| | - Richard I. Milne
- Institute of Molecular Plant Sciences The University of Edinburgh Edinburgh UK
| | - Dafu Ru
- State Key Laboratory of Grassland Agro‐Ecosystem Institute of Innovation Ecology Lanzhou University Lanzhou China
| | - Jibin Miao
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
| | - Wenjing Tao
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
| | - Lei Zhang
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
| | - Jingjing Xu
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
| | - Jianquan Liu
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
| | - Kangshan Mao
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
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25
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Fu PC, Sun SS, Khan G, Dong XX, Tan JZ, Favre A, Zhang FQ, Chen SL. Population subdivision and hybridization in a species complex of Gentiana in the Qinghai-Tibetan Plateau. ANNALS OF BOTANY 2020; 125:677-690. [PMID: 31922527 PMCID: PMC7103000 DOI: 10.1093/aob/mcaa003] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 01/08/2020] [Indexed: 05/31/2023]
Abstract
BACKGROUND AND AIMS Hosting several global biodiversity hotspots, the region of the Qinghai-Tibetan Plateau (QTP) is exceptionally species-rich and harbours a remarkable level of endemism. Yet, despite a growing number of studies, factors fostering divergence, speciation and ultimately diversity remain poorly understood for QTP alpine plants. This is particularly the case for the role of hybridization. Here, we explored the evolutionary history of three closely related Gentiana endemic species, and tested whether our results supported the mountain geo-biodiversity hypothesis (MGH). METHODS We genotyped 69 populations across the QTP with one chloroplast marker and 12 nuclear microsatellite loci. We performed phylogeographical analysis, Bayesian clustering, approximate Bayesian computation and principal components analysis to explore their genetic relationship and evolutionary history. In addition, we modelled their distribution under different climates. KEY RESULTS Each species was composed of two geographically distinct clades, corresponding to the south-eastern and north-western parts of their distribution. Thus Gentiana veitchiorum and G. lawrencei var. farreri, which diverged recently, appear to have shared at least refugia in the past, from which their range expanded later on. Indeed, climatic niche modelling showed that both species went through continuous expansion from the Last Interglacial Maximum to the present day. Moreover, we have evidence of hybridization in the northwest clade of G. lawrencei var. farreri, which probably occurred in the refugium located on the plateau platform. Furthermore, phylogenetic and population genetic analyses suggested that G. dolichocalyx should be a geographically limited distinct species with low genetic differentiation from G. lawrencei var. farreri. CONCLUSIONS Climatic fluctuations in the region of the QTP have played an important role in shaping the current genetic structure of G. lawrencei var. farreri and G. veitchiorum. We argue that a species pump effect did occur prior to the Last Interglacial Maximum, thus lending support to the MGH. However, our results do depart from expectations as suggested in the MGH for more recent distribution range and hybridization dynamics.
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Affiliation(s)
- Peng-Cheng Fu
- School of Life Science, Luoyang Normal University, Luoyang, P. R. China
| | - Shan-Shan Sun
- School of Life Science, Luoyang Normal University, Luoyang, P. R. China
| | - Gulzar Khan
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Carl von Ossietzky Strasse, Oldenburg, Germany
| | - Xiao-Xia Dong
- School of Life Science, Luoyang Normal University, Luoyang, P. R. China
| | - Jin-Zhou Tan
- School of Life Science, Luoyang Normal University, Luoyang, P. R. China
| | - Adrien Favre
- Senckenberg Research Institute and Natural History Museum, Senckenberganlage, Frankfurt am Main, Germany
| | - Fa-Qi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, P. R. China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, P. R. China
| | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, P. R. China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, P. R. China
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26
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Yamamoto M, Takahashi D, Horita K, Setoguchi H. Speciation and subsequent secondary contact in two edaphic endemic primroses driven by Pleistocene climatic oscillation. Heredity (Edinb) 2020; 124:93-107. [PMID: 31253956 PMCID: PMC6906382 DOI: 10.1038/s41437-019-0245-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/11/2019] [Accepted: 06/15/2019] [Indexed: 11/09/2022] Open
Abstract
Climatic perturbation during the Pleistocene era has played a major role in plant evolutionary history by altering species distribution range. However, the relative roles of climatic and geographic factors in the distribution dynamics remain poorly understood; in particular, the edaphic endemics. In this paper, we examine the evolutionary history of two ultramafic primroses, Primula hidakana and Primula takedana. These species are ecologically and morphologically distinct with disjunct distributions on Hokkaido Island, Japan. Primula hidakana is found on various rocks in southern Hokkaido and P. takedana in serpentine areas in northern Hokkaido. We performed population genetics analyses on nuclear and chloroplast data sets and tested alternative phylogenetic models of divergence using approximate Bayesian computation (ABC) analyses. Nuclear microsatellite loci clearly distinguished the two sister taxa. In contrast, chloroplast sequence variations were shared between P. takedana and P. hidakana. ABC analyses based on nuclear data supported a secondary contact scenario involving asymmetrical gene flow from P. hidakana to P. takedana. Paleodistribution modeling also supported the divergence model, and predicted their latitudinal range shifts leading to past secondary contact. Our findings highlight the importance of the distribution dynamics during the Pleistocene climatic oscillations in the evolution of serpentine plants, and demonstrate that tight species cohesion between serpentine and nonserpentine sister taxa has been maintained despite past interspecific gene flow across soil boundaries.
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Affiliation(s)
- Masaya Yamamoto
- Hyogo University of Teacher Education, 942-1 Shimokume, Kato-city, Hyogo, 673-1494, Japan.
| | - Daiki Takahashi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Kiyoshi Horita
- Medical Plant Garden & Northern Ecological Garden, Faculty of Pharmaceutical Science, Health Sciences University of Hokkaido, 1757 Kanazawa, Tobetsu-cho, Ishikari-gun, Hokkaido, 061-0293, Japan
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu, Sakyo-ku, Kyoto, 606-8501, Japan
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27
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Molecular and morphological evidence for hybrid origin and matroclinal inheritance of an endangered wild rose, Rosa × pseudobanksiae (Rosaceae) from China. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01227-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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28
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Distinctiveness, speciation and demographic history of the rare endemic conifer Juniperus erectopatens in the eastern Qinghai-Tibet Plateau. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01211-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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29
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Yang R, Folk R, Zhang N, Gong X. Homoploid hybridization of plants in the Hengduan mountains region. Ecol Evol 2019; 9:8399-8410. [PMID: 31380098 PMCID: PMC6662326 DOI: 10.1002/ece3.5393] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 04/24/2019] [Accepted: 05/30/2019] [Indexed: 12/24/2022] Open
Abstract
The Hengduan Mountains Region (HMR) is a major global biodiversity hotspot. Complex tectonic and historical climatic conditions created opportunities for natural interspecific hybridization. Likewise, anthropogenic disturbance potentially raises the frequency of hybridization. Among species studies to date, the frequency of homoploid hybridization appears in the HMR. Of nine taxa in which natural hybridization has been detected, three groups are involved in homoploid hybrid speciation, and species pairs from the remaining six genera suggest that continuous gene flow occurs in hybrid zones. Reproductive isolation may greatly affect the dynamic and architecture of hybrid zones in the HMR. Asymmetrical hybridization and introgression can primarily be attributed to both prezygotic and postzygotic barriers. The frequent observation of such asymmetry may imply that reproductive barrier contributes to maintaining species boundaries in the alpine region. Ecological isolations with environmental disturbance may promote breeding barriers between parental species and hybrids. Hybrid zones may be an important phase for homoploid hybrid speciation. Hybrid zones potentially provided abundant genetic resources for the diversification of the HMR flora. The ecological and molecular mechanisms of control and mediation for natural hybridization will help biologists to understand the formation of biodiversity in the HMR. More researches from ecological and molecular aspects were required in future studies.
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Affiliation(s)
- Rui Yang
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
- Key Laboratory of Economic Plants and BiotechnologyKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ryan Folk
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFloridaUSA
| | - Ningning Zhang
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
- Key Laboratory of Economic Plants and BiotechnologyKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
- Key Laboratory of Economic Plants and BiotechnologyKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
- Yunnan Key Laboratory for Wild Plant ResourcesKunmingChina
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Li Y, Song F, Zhang XN, Lv GH. Phylogeography suggest the Yili Valley being the glacial refuge of the genus Ixiolirion (Amaryllidaceae) in China. SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1612966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yan Li
- Institute of Arid Ecology and Environment, Xinjiang University, Urumqi, 830046, China
- Key Laboratory of Oasis Ecology, Xinjiang University, Urumqi, 830046, China
| | - Feng Song
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Xue-Ni Zhang
- Institute of Arid Ecology and Environment, Xinjiang University, Urumqi, 830046, China
- Key Laboratory of Oasis Ecology, Xinjiang University, Urumqi, 830046, China
| | - Guang-Hui Lv
- Institute of Arid Ecology and Environment, Xinjiang University, Urumqi, 830046, China
- Key Laboratory of Oasis Ecology, Xinjiang University, Urumqi, 830046, China
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31
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Takahashi D, Teramine T, Sakaguchi S, Setoguchi H. Genetic data reveals a complex history of multiple admixture events in presently allopatric wild gingers (Asarum spp.) showing intertaxonomic clinal variation in calyx lobe length. Mol Phylogenet Evol 2019; 137:146-155. [PMID: 31075504 DOI: 10.1016/j.ympev.2019.05.003] [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: 12/14/2018] [Revised: 05/06/2019] [Accepted: 05/06/2019] [Indexed: 10/26/2022]
Abstract
Clinal variation is a major pattern of observed phenotypic diversity and identifying underlying demographic processes is a necessary step to understand the establishment of clinal variation. The wild ginger series Sakawanum (genus Asarum) comprises four taxa, which exhibit intertaxonomic clinal variation in calyx lobe length across two continental islands isolated by a sea strait. To test alternative hypotheses of the evolutionary history and to determine the implications for the formation of clinal variation, we conducted approximate Bayesian computation (ABC) analysis and ecological niche modeling (ENM). ABC analysis indicated that the scenario assuming multiple admixture events was strongly supported. This scenario assumed two admixture events occurred between morphologically distinct taxa, likely leading to the generation of intermediate taxa. One of the admixture events was estimated to have occurred during the last glacial maximum (LGM), during which the taxa were estimated to have formed a common refugia in southern areas by ENM analysis. Although four taxa are currently distributed allopatrically on different islands and trans-oceanic dispersal appears unlikely, the formation of a land bridge and the geographic range shift to refugia would have allowed secondary contact between previously isolated taxa. This study suggests that clinal variation can be shaped by demographic history including multiple admixtures due to climatic oscillations.
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Affiliation(s)
- Daiki Takahashi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-Nihonmatsu, Sakyo-ku, Kyoto 606-8501, Japan.
| | | | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-Nihonmatsu, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-Nihonmatsu, Sakyo-ku, Kyoto 606-8501, Japan
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Manish K, Pandit MK. Geophysical upheavals and evolutionary diversification of plant species in the Himalaya. PeerJ 2018; 6:e5919. [PMID: 30425898 PMCID: PMC6228543 DOI: 10.7717/peerj.5919] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 10/11/2018] [Indexed: 11/20/2022] Open
Abstract
The Himalaya is one of the youngest and the loftiest mountain chains of the world; it is also referred to as the water tower of Asia. The Himalayan region harbors nearly 10,000 plant species constituting approximately 2.5% of the global angiosperm diversity of which over 4,000 are endemics. The present-day Himalayan flora consists of an admixture of immigrant taxa and diversified species over the last 40 million years. The interesting questions about the Himalayan flora discussed here are: how did the Himalaya achieve high endemic plant diversity starting with immigrant taxa and what were the main drivers of this diversity? This contribution aims to answer these questions and raise some more. We review and analyze existing information from diverse areas of earth and climate sciences, palaeobiology and phytogeography to evolve a bio-chronological record of plant species divergence and evolution in the Himalaya. From the analysis we infer the effects of major environmental upheavals on plant diversity in the region. The understanding developed in the following discussion is based on the idea that Himalaya experienced at least five phases of major geophysical upheavals, namely: (i) mega-collision between India and Eurasian plates, (ii) tectonic uplift in phases and progressive landform elevation, (iii) onset of southwest (SW) Indian monsoon, (iv) spurring of arid conditions in Central Asia, and (v) cyclic phases of cooling and warming in the Quaternary. The geophysical upheavals that were potentially disrupting for the ecosystem stability had a key role in providing impetus for biological diversification. The upheavals produced new geophysical environments, new ecological niches, imposed physical and physiological isolation barriers, acted as natural selection sieves and led to the formation of new species. This contribution aims to develop a comprehensive understanding of the plant biodiversity profile of the Himalaya in the context of complex, interconnected and dynamic relationship between earth system processes, climate and plant diversity.
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Affiliation(s)
- Kumar Manish
- Department of Environmental Studies, University of Delhi, Delhi, India.,Department of Environmental Studies, Dr. Bhim Rao Ambedkar College, University of Delhi, Delhi, India.,Centre for Interdisciplinary Studies of Mountain and Hill Environment, University of Delhi, Delhi, India
| | - Maharaj K Pandit
- Department of Environmental Studies, University of Delhi, Delhi, India.,Centre for Interdisciplinary Studies of Mountain and Hill Environment, University of Delhi, Delhi, India
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White OW, Reyes-Betancort A, Chapman MA, Carine MA. Independent homoploid hybrid speciation events in the Macaronesian endemic genus Argyranthemum. Mol Ecol 2018; 27:4856-4874. [DOI: 10.1111/mec.14889] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 08/29/2018] [Accepted: 09/26/2018] [Indexed: 01/03/2023]
Affiliation(s)
- Oliver W. White
- Algae, Fungi and Plants Division; Department of Life Sciences; The Natural History Museum; London UK
- Biological Sciences; University of Southampton; Southampton UK
| | | | - Mark A. Chapman
- Biological Sciences; University of Southampton; Southampton UK
| | - Mark A. Carine
- Algae, Fungi and Plants Division; Department of Life Sciences; The Natural History Museum; London UK
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Approximate Bayesian computation analysis of EST-associated microsatellites indicates that the broadleaved evergreen tree Castanopsis sieboldii survived the Last Glacial Maximum in multiple refugia in Japan. Heredity (Edinb) 2018; 122:326-340. [PMID: 30072800 DOI: 10.1038/s41437-018-0123-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 06/10/2018] [Accepted: 06/19/2018] [Indexed: 11/09/2022] Open
Abstract
Climatic changes have played major roles in plants' evolutionary history. Glacial oscillations have been particularly important, but some of their effects on plants' populations are poorly understood, including the numbers and locations of refugia in Asian warm temperate zones. In the present study, we investigated the demographic history of the broadleaved evergreen tree species Castanopsis sieboldii (Fagaceae) during the last glacial period in Japan. We used approximate Bayesian computation (ABC) for model comparison and parameter estimation for the demographic modeling using 27 EST-associated microsatellites. We also performed the species distribution modeling (SDM). The results strongly support a demographic scenario that the Ryukyu Islands and the western parts in the main islands (Kyushu and western Shikoku) were derived from separate refugia and the eastern parts in the main islands and the Japan Sea groups were diverged from the western parts prior to the coldest stage of the Last Glacial Maximum (LGM). Our data indicate that multiple refugia survived at least one in the Ryukyu Islands, and the other three regions of the western and eastern parts and around the Japan Sea of the main islands of Japan during the LGM. The SDM analysis also suggests the potential habitats under LGM climate conditions were mainly located along the Pacific Ocean side of the coastal region. Our ABC-based study helps efforts resolve the demographic history of a dominant species in warm temperate broadleaved forests during and after the last glacial period, which provides a basic model for future phylogeographical studies using this approach.
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Schumer M, Rosenthal GG, Andolfatto P. What do we mean when we talk about hybrid speciation? Heredity (Edinb) 2018; 120:379-382. [PMID: 29302049 PMCID: PMC5842215 DOI: 10.1038/s41437-017-0036-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 11/10/2017] [Accepted: 11/11/2017] [Indexed: 01/01/2023] Open
Affiliation(s)
- Molly Schumer
- Hanna Gray Fellow, Howard Hughes Medical Institute, Cambridge, MA, USA.
- Harvard Society of Fellows, Harvard University, Boston, MA, USA.
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", Calnali, Hidalgo, Mexico.
| | - Gil G Rosenthal
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", Calnali, Hidalgo, Mexico
- Department of Biology and Interdisciplinary Faculty of Ecology & Evolutionary Biology, Texas A&M University, College Station, TX, USA
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
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Ma XG, Sun WG, Sun H. Historical introgression among the species of Rodgersia (Saxifragaceae) in mountainous forests of southwest China. Mol Phylogenet Evol 2018. [PMID: 29526806 DOI: 10.1016/j.ympev.2018.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
In the present study, we used genetic data and ecological niche modelling to explore possible historical introgressions among the species of Rodgersia (Saxifragaceae) in central-southwest China. Markedly differentiated chloroplast haplotypes were found in R. aesculifolia, R. sambucifolia and the Lijiang (LJ) population of R. pinnata, respectively, and differentiated chloroplast haplotypes within each of them showed the closest relationships with haplotypes from different species. ITS cloning did not reveal any shared ribotype between R. aesculifolia and the remaining species. Historical introgression between R. aesculifolia and R. sambucifolia (or R. pinnata) seems to be the most plausible explanation according to the geographical pattern and derivative status of putative introgressed chloroplast haplotypes, and also from morphological evidence. Introgressions were also found among R. sambucifolia, R. pinnata, and R. henricii from Yunnan. Frequent gene exchanges may have promoted the diversity of leaf shapes in this genus. Ecological niche modelling indicated that past secondary contact following range shifts during Pleistocene cold periods may have provided opportunities for ancient introgression between R. aesculifolia and adjacent species.
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Affiliation(s)
- Xiang-Guang Ma
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132, Lanhei Road, Kunming, Yunnan 650201, China
| | - Wen-Guang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132, Lanhei Road, Kunming, Yunnan 650201, China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132, Lanhei Road, Kunming, Yunnan 650201, China.
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37
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Liu Y, Li D, Zhang Q, Song C, Zhong C, Zhang X, Wang Y, Yao X, Wang Z, Zeng S, Wang Y, Guo Y, Wang S, Li X, Li L, Liu C, McCann HC, He W, Niu Y, Chen M, Du L, Gong J, Datson PM, Hilario E, Huang H. Rapid radiations of both kiwifruit hybrid lineages and their parents shed light on a two-layer mode of species diversification. THE NEW PHYTOLOGIST 2017; 215:877-890. [PMID: 28543189 DOI: 10.1111/nph.14607] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 04/04/2017] [Indexed: 05/20/2023]
Abstract
Reticulate speciation caused by interspecific hybridization is now recognized as an important mechanism in the creation of biological diversity. However, depicting the patterns of phylogenetic networks for lineages that have undergone interspecific gene flow is challenging. Here we sequenced 25 taxa representing natural diversity in the genus Actinidia with an average mapping depth of 26× on the reference genome to reconstruct their reticulate history. We found evidence, including significant gene tree discordance, cytonuclear conflicts, and changes in genome-wide heterozygosity across taxa, collectively supporting extensive reticulation in the genus. Furthermore, at least two separate parental species pairs were involved in the repeated origin of the hybrid lineages, in some of which a further phase of syngameon was triggered. On the basis of the elucidated hybridization relationships, we obtained a highly resolved backbone phylogeny consisting of taxa exhibiting no evidence of hybrid origin. The backbone taxa have distinct demographic histories and are the product of recent rounds of rapid radiations via sorting of ancestral variation under variable climatic and ecological conditions. Our results suggest a mode for consecutive plant diversification through two layers of radiations, consisting of the rapid evolution of backbone lineages and the formation of hybrid swarms derived from these lineages.
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Affiliation(s)
- Yifei Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
| | - Dawei Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Qiong Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Chi Song
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, Hubei, 430070, China
| | - Caihong Zhong
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Xudong Zhang
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, Hubei, 430070, China
| | - Ying Wang
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, Hubei, 430070, China
| | - Xiaohong Yao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Zupeng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
| | - Shaohua Zeng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
| | - Ying Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
| | - Yangtao Guo
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
| | - Shuaibin Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
| | - Xinwei Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Li Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Chunyan Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Honour C McCann
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
- New Zealand Institute for Advanced Study, Massey University, Auckland, 0745, New Zealand
| | - Weiming He
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
| | - Yan Niu
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, Hubei, 430070, China
| | - Min Chen
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, Hubei, 430070, China
| | - Liuwen Du
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Junjie Gong
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Paul M Datson
- The New Zealand Institute for Plant and Food Research Limited, Mt Albert Research Centre, Auckland, 1142, New Zealand
| | - Elena Hilario
- The New Zealand Institute for Plant and Food Research Limited, Mt Albert Research Centre, Auckland, 1142, New Zealand
| | - Hongwen Huang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
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Yan LJ, Burgess KS, Milne R, Fu CN, Li DZ, Gao LM. Asymmetrical natural hybridization varies among hybrid swarms between two diploid Rhododendron species. ANNALS OF BOTANY 2017; 120:51-61. [PMID: 28444136 PMCID: PMC5737508 DOI: 10.1093/aob/mcx039] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/14/2017] [Indexed: 05/23/2023]
Abstract
Background and Aims The extent to which hybridization leads to gene flow between plant species depends on the structure of hybrid populations. However, if this varies between locations, species barriers might prove permeable in some locations but not in others. To assess possible variation in hybrid population structure, the magnitude and direction of natural hybridization between two Chinese endemic species, Rhododendron spiciferum and Rhododendron spinuliferum , were evaluated. Methods Thirteen nuclear microsatellite markers were employed to characterize 566 individuals collected from 15 non-allopatric populations and nine allopatric parental populations. Chloroplast DNA (cpDNA) sequences were obtained from a subset of samples. Genetic structure and direction of gene flow was determined using a combination of STRUCTURE and NEWHYBRIDS analysis. Key Results Nuclear analysis revealed that parental taxa formed two genetically distinct clusters and hybrids shared the genetic background of both parents and did not form a separate genetic lineage. Overall, hybrid swarms were dominated by early- and later-generation hybrids, with a significantly higher proportion of hybrids (59·6 %) possessing >50 % R. spiciferum-like nuclear germplasm. The cpDNA analysis further indicated that a significantly greater proportion of hybrids (61·1 %) possessed the R. spiciferum cpDNA haplotype. Conclusions Gene flow between R. spiciferum and R. spinuliferum was found to be bidirectional in 14 of the 15 hybrid swarms and asymmetrical in six hybrid swarms. Asymmetrical gene flow was evident for only nuclear DNA (nDNA) in two populations, for only cpDNA in three populations, and for both nDNA and cpDNA in one population. Collectively, the variation in genetic structure found among the 15 hybrid swarms suggests that introgression rather than hybrid speciation is a more likely outcome of hybridization between these hybridizing taxa.
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Affiliation(s)
- Li-Jun Yan
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- College of Vocational and Technical Education, Yunnan Normal University, Kunming 650092, China
| | - Kevin S. Burgess
- Department of Biology, College of Letters & Sciences, Columbus State University, University System of Georgia, 163A LeNoir Hall, Columbus, GA 31907-5645, USA
| | - Richard Milne
- Institute of Molecular Plant Sciences, University of Edinburgh, King’s Buildings, Edinburgh EH9 3JH, UK
| | - Chao-Nan Fu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - De-Zhu Li
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lian-Ming Gao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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Worth JRP, Larcombe MJ, Sakaguchi S, Marthick JR, Bowman DMJS, Ito M, Jordan GJ. Transient hybridization, not homoploid hybrid speciation, between ancient and deeply divergent conifers. AMERICAN JOURNAL OF BOTANY 2016; 103:246-259. [PMID: 26872492 DOI: 10.3732/ajb.1500433] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 01/04/2016] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Homoploid hybrid speciation is receiving growing attention due the increasing recognition of its role in speciation. We investigate if individuals intermediate in morphology between the two species of the conifer genus Athrotaxis represent a homoploid hybrid species, A. laxifolia, or are spontaneous F1 hybrids. METHODS A total of 1055 individuals of Athrotaxis cupressoides and A. selaginoides, morphologically intermediate individuals, and two putative hybrid swarms were sampled across the range of the genus and genotyped with 13 microsatellites. We used simulations to test the power of our data to identify the pure species, F1s, F2s, and backcross generations. KEY RESULTS We found that Athrotaxis cupressoides and A. selaginoides are likely the most divergent congeneric conifers known, but the intermediates are F1 hybrids, sharing one allele each from A. cupressoides and A. selaginoides at six loci with completely species specific alleles. The hybrid swarms contain wide genetic variation with stronger affinities to the locally dominant species, A. selaginoides and A. selaginoides backcrosses outnumbering A. cupressoides backcrosses. In addition, we observed evidence for isolated advanced generation backcrosses within the range of the pure species. CONCLUSIONS We conclude that, even though they can be large and long-lived, Athrotaxis hybrid swarms are on a trajectory of decline and will eventually be reabsorbed by the parental species. However, this process may take millennia and fossil evidence suggests that such events have occurred repeatedly since the early Quaternary. Given this timeline, our study highlights the many obstacles to homoploid hybrid speciation.
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Affiliation(s)
- James R P Worth
- Department of Forest Genetics, Forestry and Forest Products Research Institute, 1 Matsunosato, Ibaraki 305-8687, Japan +81 29 829 8261
| | - Matthew J Larcombe
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia +61 3 6226 1943
| | - Shota Sakaguchi
- Laboratory of Plant Evolution and Biodiversity, Department of General Systems Studies, Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan +81 35 454 6368
| | - James R Marthick
- Menzies Institute for Medical Research, University of Tasmania, Private Bag 24, Hobart, Tasmania 7001, Australia +61 3 6226 4636
| | - David M J S Bowman
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia +61 3 6226 1943
| | - Motomi Ito
- Laboratory of Plant Evolution and Biodiversity, Department of General Systems Studies, Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan +81 35 454 6368
| | - Gregory J Jordan
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia +61 3 6226 1943
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Jia DR, Wang YJ, Liu TL, Wu GL, Kou YX, Cheng K, Liu JQ. Diploid hybrid origin ofHippophaë gyantsensis(Elaeagnaceae) in the western Qinghai-Tibet Plateau. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12707] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dong-Rui Jia
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
- School of Ecology and Environmental Science; Yunnan University; Kunming 650091 China
| | - Yu-Jin Wang
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - Teng-Liang Liu
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - Gui-Li Wu
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - Yi-Xuan Kou
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - Kai Cheng
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - Jian-Quan Liu
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
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Su X, Wu G, Li L, Liu J. Species delimitation in plants using the Qinghai-Tibet Plateau endemic Orinus (Poaceae: Tridentinae) as an example. ANNALS OF BOTANY 2015; 116:35-48. [PMID: 25987712 PMCID: PMC4479750 DOI: 10.1093/aob/mcv062] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 11/27/2014] [Accepted: 03/31/2015] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Accurate identification of species is essential for the majority of biological studies. However, defining species objectively and consistently remains a challenge, especially for plants distributed in remote regions where there is often a lack of sufficient previous specimens. In this study, multiple approaches and lines of evidence were used to determine species boundaries for plants occurring in the Qinghai-Tibet Plateau, using the genus Orinus (Poaceae) as a model system for an integrative approach to delimiting species. METHODS A total of 786 individuals from 102 populations of six previously recognized species were collected for niche, morphological and genetic analyses. Three plastid DNA regions (matK, rbcL and trnH-psbA) and one nuclear DNA region [internal transcribed space (ITS)] were sequenced. KEY RESULTS Whereas six species had been previously recognized, statistical analyses based on character variation, molecular data and niche differentiation identified only two well-delimited clusters, together with a third possibly originating from relatively recent hybridization between, or historical introgression from, the other two. CONCLUSIONS Based on a principle of integrative species delimitation to reconcile different sources of data, the results provide compelling evidence that the six previously recognized species of the genus Orinus that were examined should be reduced to two, with new circumscriptions, and a third, identified in this study, should be described as a new species. This empirical study highlights the value of applying genetic differentiation, morphometric statistics and ecological niche modelling in an integrative approach to re-circumscribing species boundaries. The results produce relatively objective, operational and unbiased taxonomic classifications of plants occurring in remote regions.
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Affiliation(s)
- Xu Su
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou 730000, PR China and Key Laboratory of Education Ministry of Environments and Resources in the Qinghai-Tibet Plateau, School of Geography and Life Science, Qinghai Normal University, Xining 810008, PR China State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou 730000, PR China and Key Laboratory of Education Ministry of Environments and Resources in the Qinghai-Tibet Plateau, School of Geography and Life Science, Qinghai Normal University, Xining 810008, PR China
| | - Guili Wu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou 730000, PR China and Key Laboratory of Education Ministry of Environments and Resources in the Qinghai-Tibet Plateau, School of Geography and Life Science, Qinghai Normal University, Xining 810008, PR China
| | - Lili Li
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou 730000, PR China and Key Laboratory of Education Ministry of Environments and Resources in the Qinghai-Tibet Plateau, School of Geography and Life Science, Qinghai Normal University, Xining 810008, PR China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou 730000, PR China and Key Laboratory of Education Ministry of Environments and Resources in the Qinghai-Tibet Plateau, School of Geography and Life Science, Qinghai Normal University, Xining 810008, PR China
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Yan HF, Liu YJ, Xie XF, Zhang CY, Hu CM, Hao G, Ge XJ. DNA barcoding evaluation and its taxonomic implications in the species-rich genus Primula L. in China. PLoS One 2015; 10:e0122903. [PMID: 25875620 PMCID: PMC4395239 DOI: 10.1371/journal.pone.0122903] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 02/24/2015] [Indexed: 11/19/2022] Open
Abstract
The genus Primula is extremely diverse in the east Himalaya-Hengduan Mountains (HHM) in China as a result of rapid radiation. In order to overcome the difficulty of morphological classification of this genus, we surveyed three plastid regions (rbcL, matK, and trnH-psbA) and two nuclear markers (ITS and ITS2) from 227 accessions representing 66 Primula species across 18 sections, to assess their discriminatory power as barcodes. We found that ITS alone or combined with plastid regions showed the best discrimination across different infrageneric ranks and at species level. We suggest rbcL + matK + ITS as the first choice at present to barcode Primula plants. Although the present barcoding combination performed poorly in many closely related species of Primula, it still provided many new insights into current Primula taxonomy, such as the underlying presence of cryptic species, and several potential improper taxonomic treatments. DNA barcoding is one useful technique in the integrative taxonomy of the genus Primula, but it still requires further efforts to improve its effectiveness in some taxonomically challenging groups.
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Affiliation(s)
- Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yun-Jiao Liu
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Xiu-Feng Xie
- Tropical Agriculture department, Guangdong Agriculture Industry Business Polytechnic College, Guangzhou, China
| | - Cai-Yun Zhang
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Chi-Ming Hu
- 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
- * E-mail: (GH); (XJG)
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- * E-mail: (GH); (XJG)
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Husson C, Aguayo J, Revellin C, Frey P, Ioos R, Marçais B. Evidence for homoploid speciation in Phytophthora alni supports taxonomic reclassification in this species complex. Fungal Genet Biol 2015; 77:12-21. [DOI: 10.1016/j.fgb.2015.02.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 02/18/2015] [Accepted: 02/19/2015] [Indexed: 01/25/2023]
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