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Wang MZ, Wu J, Zhang SL, Mao LM, Ohi-Toma T, Takano A, Zhang YH, Cameron KM, Li P. Species delimitation in Amana (Liliaceae): transcriptomes battle with evolutionary complexity. Cladistics 2024; 40:135-156. [PMID: 37983640 DOI: 10.1111/cla.12565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 10/10/2023] [Accepted: 10/18/2023] [Indexed: 11/22/2023] Open
Abstract
Species delimitation has long been a subject of controversy, and there are many alternative concepts and approaches used to define species in plants. The genus Amana (Liliaceae), known as "East Asian tulips" has a number of cryptic species and a huge genome size (1C = 21.48-57.35 pg). It also is intriguing how such a spring ephemeral genus thrives in subtropical areas. However, phylogenetic relationships and species delimitation within Amana are challenging. Here we included all species and 84 populations of Amana, which are collected throughout its distribution range. A variety of methods were used to clarify its species relationships based on a combination of morphological, ecological, genetic, evolutionary and phylogenetic species concepts. This evidence supports the recognition of at least 12 species in Amana. Moreover, we explored the complex evolutionary history within the genus and detected several historical hybridization and introgression events based on phylogenetic trees (transcriptomic and plastid), phylonetworks, admixture and ABBA-BABA analyses. Morphological traits have undergone parallel evolution in the genus. This spring ephemeral genus might have originated from a temperate region, yet finally thrives in subtropical areas, and three hypotheses about its adaptive evolution are proposed for future testing. In addition, we propose a new species, Amana polymorpha, from eastern Zhejiang Province, China. This research also demonstrates that molecular evidence at the genome level (such as transcriptomes) has greatly improved the accuracy and reasonability of species delimitation and taxon classification.
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Affiliation(s)
- Mei-Zhen Wang
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Jing Wu
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Sheng-Lu Zhang
- Plant Quarantine Station of Lin'an District, Hangzhou, 311300, Zhejiang, China
| | - Li-Mi Mao
- Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu, China
| | - Tetsuo Ohi-Toma
- Nature Fieldwork Center, Okayama University of Science, Okayama, 700-0005, Japan
| | - Atsuko Takano
- Museum of Nature and Human Activities, Hyogo 6 chome, Yayoigaoka, Sanda, Hyogo, 669-1546, Japan
| | - Yong-Hua Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Kenneth M Cameron
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
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Tensen L, Fischer K. Evaluating hybrid speciation and swamping in wild carnivores with a decision-tree approach. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2024; 38:e14197. [PMID: 37811741 DOI: 10.1111/cobi.14197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/12/2023] [Accepted: 06/28/2023] [Indexed: 10/10/2023]
Abstract
Hybridization is an important evolutionary force with a principal role in the origin of new species, known as hybrid speciation. However, ongoing hybridization can create hybrid swamping, in which parental genomes are completely lost. This can become a biodiversity threat if it involves species that have adapted to certain environmental conditions and occur nowhere else. Because conservation scientists commonly have a negative attitude toward hybrids, it is important to improve understanding of the influence of interspecific gene flow on the persistence of species. We reviewed the literature on species hybridization to build a list of all known cases in the order Carnivora. To examine the relative impact, we also noted level of introgression, whether fertile offspring were produced, and whether there was mention of negative or positive evolutionary effects (hybrid speciation and swamping). To evaluate the conservation implications of hybrids, we developed a decision-making tree with which to determine which actions should be taken to manage hybrid species. We found 53 hybrids involving 68 unique taxa, which is roughly 23% of all carnivore species. They mainly involved monophyletic (83%) and sympatric species (75%). For 2 species, the outcome of the assessment was to eliminate or restrict the hybrids: Ethiopian wolf (Canis simensis) and Scottish wildcat (Felis silvestris silvestris). Both species hybridize with their domestic conspecifics. For all other cases, we suggest hybrids be protected in the same manner as native species. We found no evidence of genomic extinction in Carnivora. To the contrary, some species appear to be of hybrid origin, such as the Asiatic black bear (Ursus thibetanus) and African golden wolf (Canis lupaster). Other positive outcomes of hybridization are novel genetic diversity, adaptation to extreme environments, and increased reproductive fitness. These outcomes are particularly valuable for counterbalancing genetic drift and enabling adaptive introgression in a human-dominated world.
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Affiliation(s)
- Laura Tensen
- Institute for Integrated Natural Sciences, Department of Zoology, University of Koblenz, Koblenz, Germany
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Johannesburg, South Africa
| | - Klaus Fischer
- Institute for Integrated Natural Sciences, Department of Zoology, University of Koblenz, Koblenz, Germany
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Suetsugu K, Hirota SK, Shitara T, Ishida K, Nakato N, Hayakawa H, Suyama Y. The absence of bumblebees on an oceanic island blurs the species boundary of two closely related orchids. THE NEW PHYTOLOGIST 2024; 241:1321-1333. [PMID: 37847353 DOI: 10.1111/nph.19325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/26/2023] [Indexed: 10/18/2023]
Abstract
Oceanic islands offer valuable natural laboratories for studying evolution. The Izu Islands, with their recent geological origin, provide an exceptional opportunity to explore the initial evolution on oceanic islands. Another noteworthy aspect is the absence of bumblebee species on most Izu Islands. We used ecological, morphological, and molecular data to investigate the impact of bumblebee absence on the evolution of two closely related orchid species, Goodyera henryi and Goodyera similis, focusing on Kozu Island, the Izu Islands. Our investigation revealed that while G. henryi exclusively relies on a bumblebee species for pollination on the mainland, G. similis is pollinated by scoliid wasps on both the mainland and the island. Intriguingly, all specimens initially categorized as G. henryi on Kozu Island are hybrids of G. henryi and G. similis, leading to the absence of pure G. henryi distribution on the island. These hybrids are pollinated by the scoliid wasp species that also pollinates G. similis on the island. The absence of bumblebees might result in sporadic and inefficient pollination of G. henryi by scoliid wasps, consequently promoting hybrid proliferation on the island. Our findings suggest that the absence of bumblebees can blur plant species boundaries.
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Affiliation(s)
- Kenji Suetsugu
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Hyogo, 657-8501, Japan
- Institute for Advanced Research, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Shun K Hirota
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi, 989-6711, Japan
- Botanical Gardens, Osaka Metropolitan University, 2000 Kisaichi, Katano City, Osaka, 576-0004, Japan
| | - Takuto Shitara
- Tama Forest Science Garden, Forestry and Forest Products Research Institute, 1833-81 Todori-machi, Hachioji, Tokyo, 193-0843, Japan
| | | | - Narumi Nakato
- Narahashi 1-363, Higashiyamato-shi, Tokyo, 207-0031, Japan
| | - Hiroshi Hayakawa
- Museum of Natural and Environmental History, Shizuoka, 5762 Oya, Suruga, Shizuoka, Shizuoka, 422-8017, Japan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi, 989-6711, Japan
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4
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Lan Z, Song Z, Wang Z, Li L, Liu Y, Zhi S, Wang R, Wang J, Li Q, Bleckmann A, Zhang L, Dresselhaus T, Dong J, Gu H, Zhong S, Qu LJ. Antagonistic RALF peptides control an intergeneric hybridization barrier on Brassicaceae stigmas. Cell 2023; 186:4773-4787.e12. [PMID: 37806310 PMCID: PMC10615786 DOI: 10.1016/j.cell.2023.09.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 05/24/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023]
Abstract
Pollen-pistil interactions establish interspecific/intergeneric pre-zygotic hybridization barriers in plants. The rejection of undesired pollen at the stigma is crucial to avoid outcrossing but can be overcome with the support of mentor pollen. The mechanisms underlying this hybridization barrier are largely unknown. Here, in Arabidopsis, we demonstrate that receptor-like kinases FERONIA/CURVY1/ANJEA/HERCULES RECEPTOR KINASE 1 and cell wall proteins LRX3/4/5 interact on papilla cell surfaces with autocrine stigmatic RALF1/22/23/33 peptide ligands (sRALFs) to establish a lock that blocks the penetration of undesired pollen tubes. Compatible pollen-derived RALF10/11/12/13/25/26/30 peptides (pRALFs) act as a key, outcompeting sRALFs and enabling pollen tube penetration. By treating Arabidopsis stigmas with synthetic pRALFs, we unlock the barrier, facilitating pollen tube penetration from distantly related Brassicaceae species and resulting in interspecific/intergeneric hybrid embryo formation. Therefore, we uncover a "lock-and-key" system governing the hybridization breadth of interspecific/intergeneric crosses in Brassicaceae. Manipulating this system holds promise for facilitating broad hybridization in crops.
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Affiliation(s)
- Zijun Lan
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, New Cornerstone Science Laboratory, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Zihan Song
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, New Cornerstone Science Laboratory, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Zhijuan Wang
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, New Cornerstone Science Laboratory, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Ling Li
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, New Cornerstone Science Laboratory, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Yiqun Liu
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, New Cornerstone Science Laboratory, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Shuaihua Zhi
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, New Cornerstone Science Laboratory, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Ruihan Wang
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Jizong Wang
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Qiyun Li
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, New Cornerstone Science Laboratory, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Andrea Bleckmann
- Cell Biology and Plant Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Li Zhang
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, New Cornerstone Science Laboratory, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Juan Dong
- The Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Hongya Gu
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, New Cornerstone Science Laboratory, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Sheng Zhong
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, New Cornerstone Science Laboratory, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China.
| | - Li-Jia Qu
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, New Cornerstone Science Laboratory, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China.
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Gawrońska B, Marszałek M, Kosiński P, Podsiedlik M, Bednorz L, Zeyland J. No wonder, it is a hybrid. Natural hybridization between Jacobaea vulgaris and J. erucifolia revealed by molecular marker systems and its potential ecological impact. Ecol Evol 2023; 13:e10467. [PMID: 37664498 PMCID: PMC10468328 DOI: 10.1002/ece3.10467] [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: 03/07/2023] [Revised: 08/09/2023] [Accepted: 08/18/2023] [Indexed: 09/05/2023] Open
Abstract
Progressive changes in the environment are related to modifications of the habitat. Introducing exotic species, and interbreeding between species can lead to processes that in the case of rare species or small populations threatens their integrity. Given the declining trends of many populations due to increased hybridization, early recognition of hybrids becomes important in conservation management. Natural hybridization is prevalent in Jacobaea. There are many naturally occurring interspecific hybrids in this genus, including those between Jacobaea vulgaris and its relatives. Although Jacobaea erucifolia and J. vulgaris often co-occur and are considered closely related, apart from the few reports of German botanists on the existence of such hybrids, there is no information on research confirming hybridization between them. Morphologically intermediate individuals, found in the sympatric distributions of J. vulgaris and J. erucifolia, were hypothesized to be their hybrids. Two molecular marker systems (nuclear and chloroplast DNA markers) were employed to test this hypothesis and characterize putative hybrids. Nuclear and chloroplast DNA sequencing results and taxon-specific amplified fragment length polymorphism (AFLP) fragment distribution analysis confirmed the hybrid nature of all 25 putative hybrids. The AFLP patterns of most hybrids demonstrated a closer relationship to J. erucifolia, suggesting frequent backcrossing. Moreover, they showed that several individuals previously described as pure were probably also of hybrid origin, backcrosses to J. erucifolia and J. vulgaris. This study provides the first molecular confirmation that natural hybrids between J. vulgaris and J. erucifolia occur in Poland. Hybridization appeared to be bidirectional but asymmetrical with J. vulgaris as the usual maternal parent.
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Affiliation(s)
- Barbara Gawrońska
- Department of Biochemistry and Biotechnology, Faculty of Agronomy, Horticulture and BioengineeringPoznań University of Life SciencesPoznańPoland
| | - Małgorzata Marszałek
- Department of Biochemistry and Biotechnology, Faculty of Agronomy, Horticulture and BioengineeringPoznań University of Life SciencesPoznańPoland
| | - Piotr Kosiński
- Department of Botany, Faculty of Agronomy, Horticulture and BioengineeringPoznań University of Life SciencesPoznańPoland
- Institute of DendrologyPolish Academy of SciencesKórnikPoland
| | - Marek Podsiedlik
- Natural History Collections, Faculty of BiologyAdam Mickiewicz University in PoznańPoznańPoland
| | - Leszek Bednorz
- Department of Botany, Faculty of Agronomy, Horticulture and BioengineeringPoznań University of Life SciencesPoznańPoland
| | - Joanna Zeyland
- Department of Biochemistry and Biotechnology, Faculty of Agronomy, Horticulture and BioengineeringPoznań University of Life SciencesPoznańPoland
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6
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Zhuo J, Vasupalli N, Wang Y, Zhou G, Gao H, Zheng Y, Li B, Hou D, Lin X. Molecular identification of Bambusa changningensis is the natural bamboo hybrid of B. rigida × Dendrocalamus farinosus. FRONTIERS IN PLANT SCIENCE 2023; 14:1231940. [PMID: 37727859 PMCID: PMC10505617 DOI: 10.3389/fpls.2023.1231940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/09/2023] [Indexed: 09/21/2023]
Abstract
Bamboo is one of the fastest-growing plants commonly used in food, fibre, paper, biofuel, ornamental and medicinal industries. Natural hybridization in bamboo is rare due to its long vegetative period followed by gregarious flowering and death of the entire population. In the current study, a new bamboo species, Bambusa changningensis, shows intermediate characteristics of Dendrocalamus farinosus and B. rigida morphologically, but it is unknown whether B. changningensis is a natural hybrid. Moreover, B. changningensis has been identified as a superior variety of Sichuan Province with high pulping yield, fibre length and width. Therefore, we analyzed the morphological characteristics, DNA markers, DNA barcoding and chloroplast genomes to identify the hybrid origin of B. changningensis and possible maternal parent. We have developed the transcriptomic data for B. changningensis and mined the SSR loci. The putative parental lines and hybrid were screened for 64 SSR makers and identified that SSR14, SSR28, SSR31 and SSR34 markers showed both alleles of the parental species in B. changningensis, proving heterozygosity. Sequencing nuclear gene GBSSI partial regions and phylogenetic analysis also confirm the hybrid nature of B. changningensis. Further, we have generated the complete chloroplast genome sequence (139505 bp) of B. changningensis. By analyzing the cp genomes of both parents and B. changningensis, we identified that B. rigida might be the female parent. In conclusion, our study identified that B. changningensis is a natural hybrid, providing evidence for bamboo's natural hybridization. This is the first report on confirming a natural bamboo hybrid and its parents through SSR and chloroplast genome sequence.
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Affiliation(s)
- Juan Zhuo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’An, Zhejiang, China
| | - Naresh Vasupalli
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’An, Zhejiang, China
| | - Yong Wang
- Forest and Bamboo Resources Conservation and Cultivation Institute, Yibin Forestry and Bamboo Industry Research Institute, Yibin, Sichuan, China
| | - Guoqiang Zhou
- Forest and Bamboo Resources Conservation and Cultivation Institute, Yibin Forestry and Bamboo Industry Research Institute, Yibin, Sichuan, China
| | - Huibin Gao
- Forest and Bamboo Resources Conservation and Cultivation Institute, Yibin Forestry and Bamboo Industry Research Institute, Yibin, Sichuan, China
| | - Ying Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’An, Zhejiang, China
| | - Benxiang Li
- Sichuan Changning Century Bamboo Garden, Yibin, Sichuan, China
| | - Dan Hou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’An, Zhejiang, China
| | - Xinchun Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’An, Zhejiang, China
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Yu X, Qin M, Qu M, Jiang Q, Guo S, Chen Z, Shen Y, Fu G, Fei Z, Huang H, Gao L, Yao X. Genomic analyses reveal dead-end hybridization between two deeply divergent kiwifruit species rather than homoploid hybrid speciation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1528-1543. [PMID: 37258460 DOI: 10.1111/tpj.16336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/02/2023]
Abstract
Despite the importance of hybridization in evolution, the evolutionary consequence of homoploid hybridizations in plants remains poorly understood. Specially, homoploid hybridization events have been rarely documented due to a lack of genomic resources and methodological limitations. Actinidia zhejiangensis was suspected to have arisen from hybridization of Actinidia eriantha and Actinidia hemsleyana or Actinidia rufa. However, this species was very rare in nature and exhibited sympatric distribution with its potential parent species, which implied it might be a spontaneous hybrid of ongoing homoploid hybridization. Here, we illustrate the dead-end homoploid hybridization and genomic basis of isolating barriers between A. eriantha and A. hemsleyana through whole genome sequencing and population genomic analyses. Chromosome-scale genome assemblies of A. zhejiangensis and A. hemsleyana were generated. The chromosomes of A. zhejiangensis are confidently assigned to the two haplomes, and one of them originates from A. eriantha and the other originates from A. hemsleyana. Whole genome resequencing data reveal that A. zhejiangensis are mainly F1 hybrids of A. hemsleyana and A. eriantha and gene flow initiated about 0.98 million years ago, implying both strong genetic barriers and ongoing hybridization between these two deeply divergent kiwifruit species. Five inversions containing genes involved in pollen germination and pollen tube growth might account for the fertility breakdown of hybrids between A. hemsleyana and A. eriantha. Despite its distinct morphological traits and long recurrent hybrid origination, A. zhejiangensis does not initiate speciation. Collectively, our study provides new insights into homoploid hybridization in plants and provides genomic resources for evolutionary and functional genomic studies of kiwifruit.
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Affiliation(s)
- Xiaofen Yu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, 430070, China
| | - Mengyun Qin
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Minghao Qu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Quan Jiang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sumin Guo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Zhenghai Chen
- Forest Resources Monitoring Center of Zhejiang Province, Hangzhou, Zhejiang, 310020, China
| | - Yufang Shen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Guodong Fu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, 14853, USA
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, 14853, USA
| | - Hongwen Huang
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, 332900, China
| | - Lei Gao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, 430070, China
| | - Xiaohong Yao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
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8
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Kinneberg VB, Lü DS, Peris D, Ravinet M, Skrede I. Introgression between highly divergent fungal sister species. J Evol Biol 2023; 36:1133-1149. [PMID: 37363874 DOI: 10.1111/jeb.14190] [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: 11/24/2022] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 06/28/2023]
Abstract
To understand how species evolve and adapt to changing environments, it is important to study gene flow and introgression due to their influence on speciation and radiation events. Here, we apply a novel experimental system for investigating these mechanisms using natural populations. The system is based on two fungal sister species with morphological and ecological similarities occurring in overlapping habitats. We examined introgression between these species by conducting whole genome sequencing of individuals from populations in North America and Europe. We assessed genome-wide nucleotide divergence and performed crossing experiments to study reproductive barriers. We further used ABBA-BABA statistics together with a network analysis to investigate introgression, and conducted demographic modelling to gain insight into divergence times and introgression events. The results revealed that the species are highly divergent and incompatible in vitro. Despite this, small regions of introgression were scattered throughout the genomes and one introgression event likely involves a ghost population (extant or extinct). This study demonstrates that introgression can be found among divergent species and that population histories can be studied without collections of all the populations involved. Moreover, the experimental system is shown to be a useful tool for research on reproductive isolation in natural populations.
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Affiliation(s)
- Vilde Bruhn Kinneberg
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Evolution and Paleobiology, Natural History Museum, University of Oslo, Oslo, Norway
| | - Dabao Sun Lü
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - David Peris
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Spain
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Inger Skrede
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
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9
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Brown MR, Becher H, Williams S, Twyford AD. Is there hybridization between diploid and tetraploid Euphrasia in a secondary contact zone? AMERICAN JOURNAL OF BOTANY 2023; 110:e16100. [PMID: 36371731 PMCID: PMC10107515 DOI: 10.1002/ajb2.16100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
PREMISE Strong postzygotic reproductive isolating barriers are usually expected to limit the extent of natural hybridization between species with contrasting ploidy. However, genomic sequencing has revealed previously overlooked examples of natural cross-ploidy hybridization in some flowering plant genera, suggesting that the phenomenon may be more common than once thought. We investigated potential cross-ploidy hybridization in British eyebrights (Euphrasia, Orobanchaceae), a group from which 13 putative cross-ploidy hybrid combinations have been reported based on morphology. METHODS We analyzed a contact zone between diploid Euphrasia rostkoviana and tetraploid E. arctica in Wales. We sequenced part of the internal transcribed spacer (ITS) of nuclear ribosomal DNA and used genotyping by sequencing (GBS) to look for evidence of cross-ploidy hybridization and introgression. RESULTS Common variant sites in the ITS region were fixed between diploids and tetraploids, indicating a strong barrier to hybridization. Clustering analyses of 356 single-nucleotide polymorphisms (SNPs) generated using GBS clearly separated samples by ploidy and revealed strong genetic structure (FST = 0.44). However, the FST distribution across all SNPs was bimodal, indicating potential differential selection on loci between diploids and tetraploids. Demographic inference suggested potential gene flow, limited to around one or fewer migrants per generation. CONCLUSIONS Our results suggest that recent cross-ploidy hybridization is rare or absent in a site of secondary contact in Euphrasia. While a strong ploidy barrier prevents hybridization over ecological timescales, such hybrids may form in stable populations over evolutionary timescales, potentially allowing cross-ploidy introgression to take place.
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Affiliation(s)
- Max R. Brown
- Institute of Ecology and EvolutionUniversity of Edinburgh, Ashworth Laboratories, Charlotte Auerbach RoadEdinburghEH9 3FLUK
- Wellcome Sanger InstituteWellcome Genome Campus, HinxtonCambridgeCB10 1SAUK
| | - Hannes Becher
- Institute of Ecology and EvolutionUniversity of Edinburgh, Ashworth Laboratories, Charlotte Auerbach RoadEdinburghEH9 3FLUK
| | - Sebastian Williams
- Institute of Ecology and EvolutionUniversity of Edinburgh, Ashworth Laboratories, Charlotte Auerbach RoadEdinburghEH9 3FLUK
| | - Alex D. Twyford
- Institute of Ecology and EvolutionUniversity of Edinburgh, Ashworth Laboratories, Charlotte Auerbach RoadEdinburghEH9 3FLUK
- Royal Botanic Garden Edinburgh, 20a Inverleith RowEdinburghEH3 5LRUK
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10
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Kolarčik V, Kocová V, Mikoláš V, Mártonfiová L, Hajdučeková N, Mártonfi P. Variability of Reproduction Pathways in the Central-European Populations of Hawthorns with Emphasis on Triploids. PLANTS (BASEL, SWITZERLAND) 2022; 11:3497. [PMID: 36559608 PMCID: PMC9786806 DOI: 10.3390/plants11243497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/21/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
The role of apomeiosis, parthenogenesis, and pseudogamy in the asexual reproduction of some plant groups has not been fully elucidated in relation to species diversification. Quantitative analyses of seed origin may help in gaining better understanding of intercytotypic interactions. Asexual reproduction associated with polyploidy and frequent hybridization plays a crucial role in the evolutionary history of the genus Crataegus in North America. In Europe, the genus represents a taxonomically complex and very difficult species group not often studied using a modern biosystematic approach. We investigated the reproduction pathways in mixed-cytotype populations of selected taxa of Crataegus in eastern Slovakia, Central Europe. The investigated accessions were characterized by seed production data and the ploidy level of mature plants as well as the embryo and endosperm tissues of their seeds determined via flow cytometry. Diploid and polyploid hawthorns reproduce successfully; they also produce high numbers of seeds. An exception is represented by an almost sterile triploid. Diploids reproduce sexually. Polyploids shift to asexual reproduction, but pseudogamy seems to be essential for regular seed development. In rare cases, fertilization of unreduced gametes occurs, which offers opportunity for the establishment of new polyploid cytotypes between diploid sexuals and polyploid asexuals. Opposite to sexual diploids, triploids are obligate, and tetraploids almost obligate apomicts. Apomixis is considered to help stabilize individual weakly differentiated polyploid microspecies. Pseudogamy is a common feature and usually leads to unbalanced maternal to paternal contribution in the endosperm of triploid accessions. Parental contribution to endosperm gene dosage is somehow relaxed in triploids. Our Crataegus plant system resembles reproduction in the diploids and polyploids of North American hawthorns. Our data provide support for the hypothesis that polyploidization, shifts in reproduction modes, and hybridization shape the genus diversity also in Central Europe.
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Affiliation(s)
- Vladislav Kolarčik
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University, Mánesova 23, SK-041 54 Košice, Slovakia
| | - Valéria Kocová
- Botanical Garden, Pavol Jozef Šafárik University, Mánesova 23, SK-043 52 Košice, Slovakia
| | | | - Lenka Mártonfiová
- Botanical Garden, Pavol Jozef Šafárik University, Mánesova 23, SK-043 52 Košice, Slovakia
| | | | - Pavol Mártonfi
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University, Mánesova 23, SK-041 54 Košice, Slovakia
- Botanical Garden, Pavol Jozef Šafárik University, Mánesova 23, SK-043 52 Košice, Slovakia
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11
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Wu S, Wang Y, Wang Z, Shrestha N, Liu J. Species divergence with gene flow and hybrid speciation on the Qinghai-Tibet Plateau. THE NEW PHYTOLOGIST 2022; 234:392-404. [PMID: 35020198 DOI: 10.1111/nph.17956] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
The Qinghai-Tibet Plateau (QTP) sensu lato (sl), comprising the platform, the Himalaya and the Hengduan Mountains, is characterized by a large number of endemic plant species. This evolutionary cradle may have arisen from explosive species diversification because of geographic isolation. However, gene flow has been widely detected during the speciation processes of all groups examined, suggesting that natural selection may have also played an important role during species divergence in this region. In addition, natural hybrids have been recovered in almost all species-rich genera. This suggests that numerous species in this region are still 'on the speciation pathway to complete reproductive isolation (RI)'. Such hybrids could directly develop into new species through hybrid polyploidization and homoploid hybrid speciation (HHS). HHS may take place more easily than previously thought through alternate inheritance of alleles of parents at multiple RI loci. Therefore, isolation, selection and hybridization could together have promoted species diversification of numerous plant genera on the QTP sl. We emphasize the need for identification and functional analysis of alleles of major genes for speciation, and especially encourage investigations of parallel adaptive divergence causing RI across different lineages within similar but specific habitats in this region.
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Affiliation(s)
- Shengdan Wu
- State Key Laboratory of Grassland Agro-Ecosystems and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Yi Wang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Zefu Wang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystems and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystems and 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
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12
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Hinojosa JC, Dapporto L, Pitteloud C, Koubínová D, Hernández-Roldán J, Vicente JC, Alvarez N, Vila R. Hybridization fuelled diversification in Spialia butterflies. Mol Ecol 2022; 31:2951-2967. [PMID: 35263484 PMCID: PMC9310813 DOI: 10.1111/mec.16426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 01/17/2022] [Accepted: 02/28/2022] [Indexed: 12/02/2022]
Abstract
The importance of hybridization and introgression is well documented in the evolution of plants but, in insects, their role is not fully understood. Given the fact that insects are the most diverse group of organisms, assessing the impact of reticulation events on their evolution may be key to comprehend the emergence of such remarkable diversity. Here, we used an insect model, the Spialia butterflies, to gather genomic evidence of hybridization as a promoter of novel diversity. By using double‐digest RADseq (ddRADseq), we explored the phylogenetic relationships between Spialia orbifer, S. rosae and S. sertorius, and documented two independent events of interspecific gene flow. Our data support that the Iberian endemism S. rosae probably received genetic material from S. orbifer in both mitochondrial and nuclear DNA, which could have contributed to a shift in the ecological preferences of S. rosae. We also show that admixture between S. sertorius and S. orbifer probably occurred in Italy. As a result, the admixed Sicilian populations of S. orbifer are differentiated from the rest of populations both genetically and morphologically, and display signatures of reproductive character displacement in the male genitalia. Additionally, our analyses indicated that genetic material from S. orbifer is present in S. sertorius along the Italian Peninsula. Our findings add to the view that hybridization is a pervasive phenomenon in nature and in butterflies in particular, with important consequences for evolution due to the emergence of novel phenotypes.
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Affiliation(s)
- Joan C Hinojosa
- Institut de Biologia Evolutiva (CSIC-UPF), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Leonardo Dapporto
- ZEN lab, Biology Department, Università degli Studi di Firenze, 50019, Sesto Fiorentino, Italy
| | - Camille Pitteloud
- Geneva Natural History Museum, Route de Malagnou 1, 1208, Geneva, Switzerland
| | - Darina Koubínová
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
| | - Juan Hernández-Roldán
- Departamento de Biología, Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Calle Darwin 2, 28049, Madrid, Spain
| | - Juan Carlos Vicente
- Asociación Española para la Protección de las Mariposas y su Medio (ZERYNTHIA), Madrid, Spain
| | - Nadir Alvarez
- Geneva Natural History Museum, Route de Malagnou 1, 1208, Geneva, Switzerland.,Department of Genetics and Evolution, University of Geneva, Boulevard d'Ivoy 4, 1205, Geneva, Switzerland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
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13
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Wong ELY, Hiscock SJ, Filatov DA. The Role of Interspecific Hybridisation in Adaptation and Speciation: Insights From Studies in Senecio. FRONTIERS IN PLANT SCIENCE 2022; 13:907363. [PMID: 35812981 PMCID: PMC9260247 DOI: 10.3389/fpls.2022.907363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/03/2022] [Indexed: 05/08/2023]
Abstract
Hybridisation is well documented in many species, especially plants. Although hybrid populations might be short-lived and do not evolve into new lineages, hybridisaiton could lead to evolutionary novelty, promoting adaptation and speciation. The genus Senecio (Asteraceae) has been actively used to unravel the role of hybridisation in adaptation and speciation. In this article, we first briefly describe the process of hybridisation and the state of hybridisation research over the years. We then discuss various roles of hybridisation in plant adaptation and speciation illustrated with examples from different Senecio species, but also mention other groups of organisms whenever necessary. In particular, we focus on the genomic and transcriptomic consequences of hybridisation, as well as the ecological and physiological aspects from the hybrids' point of view. Overall, this article aims to showcase the roles of hybridisation in speciation and adaptation, and the research potential of Senecio, which is part of the ecologically and economically important family, Asteraceae.
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Affiliation(s)
- Edgar L. Y. Wong
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
- *Correspondence: Edgar L. Y. Wong,
| | - Simon J. Hiscock
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
- Oxford Botanic Garden and Arboretum, Oxford, United Kingdom
| | - Dmitry A. Filatov
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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14
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Jamal A, Wen J, Ma ZY, Ahmed I, Abdullah, Chen LQ, Nie ZL, Liu XQ. Comparative Chloroplast Genome Analyses of the Winter-Blooming Eastern Asian Endemic Genus Chimonanthus (Calycanthaceae) With Implications For Its Phylogeny and Diversification. Front Genet 2021; 12:709996. [PMID: 34917123 PMCID: PMC8670589 DOI: 10.3389/fgene.2021.709996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Chimonanthus of Calycanthaceae is a small endemic genus in China, with unusual winter-blooming sweet flowers widely cultivated for ornamentals and medicinal uses. The evolution of Chimonanthus plastomes and its phylogenetic relationships remain unresolved due to limited availability of genetic resources. Here, we report fully assembled and annotated chloroplast genomes of five Chimonanthus species. The chloroplast genomes of the genus (size range 153,010 – 153,299 bp) reveal high similarities in gene content, gene order, GC content, codon usage, amino acid frequency, simple sequence repeats, oligonucleotide repeats, synonymous and non-synonymous substitutions, and transition and transversion substitutions. Signatures of positive selection are detected in atpF and rpoB genes in C. campanulatus. The correlations among substitutions, InDels, and oligonucleotide repeats reveal weak to strong correlations in distantly related species at the intergeneric levels, and very weak to weak correlations among closely related Chimonanthus species. Chloroplast genomes are used to reconstruct a well-resolved phylogenetic tree, which supports the monophyly of Chimonanthus. Within Chimonanthus, C. praecox and C. campanulatus form one clade, while C. grammatus, C. salicifolius, C. zhejiangensis, and C. nitens constitute another clade. Chimonanthus nitens appears paraphyletic and is closely related to C. salicifolius and C. zhejiangensis, suggesting the need to reevaluate the species delimitation of C. nitens. Chimonanthus and Calycanthus diverged in mid-Oligocene; the radiation of extant Chimonanthus species was dated to the mid-Miocene, while C. grammatus diverged from other Chimonanthus species in the late Miocene. C. salicifolius, C. nitens(a), and C. zhejiangensis are inferred to have diverged in the Pleistocene of the Quaternary period, suggesting recent speciation of a relict lineage in the subtropical forest regions in eastern China. This study provides important insights into the chloroplast genome features and evolutionary history of Chimonanthus and family Calycanthaceae.
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Affiliation(s)
- Abbas Jamal
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC, United States
| | - Zhi-Yao Ma
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC, United States
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad, Pakistan
| | - Abdullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Long-Qing Chen
- Southwest Engineering Technology and Research Center of Landscape Architecture, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou, China
| | - Xiu-Qun Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
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15
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Lukjanová E, Řepková J. Chromosome and Genome Diversity in the Genus Trifolium (Fabaceae). PLANTS (BASEL, SWITZERLAND) 2021; 10:2518. [PMID: 34834880 PMCID: PMC8621578 DOI: 10.3390/plants10112518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Trifolium L. is an economically important genus that is characterized by variable karyotypes relating to its ploidy level and basic chromosome numbers. The advent of genomic resources combined with molecular cytogenetics provides an opportunity to develop our understanding of plant genomes in general. Here, we summarize the current state of knowledge on Trifolium genomes and chromosomes and review methodologies using molecular markers that have contributed to Trifolium research. We discuss possible future applications of cytogenetic methods in research on the Trifolium genome and chromosomes.
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Affiliation(s)
| | - Jana Řepková
- Department of Experimental Biology, Faculty of Sciences, Masaryk University, 611 37 Brno, Czech Republic;
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16
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Baiakhmetov E, Ryzhakova D, Gudkova PD, Nobis M. Evidence for extensive hybridisation and past introgression events in feather grasses using genome-wide SNP genotyping. BMC PLANT BIOLOGY 2021; 21:505. [PMID: 34724894 PMCID: PMC8559405 DOI: 10.1186/s12870-021-03287-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/20/2021] [Indexed: 06/03/2023]
Abstract
BACKGROUND The proper identification of feather grasses in nature is often limited due to phenotypic variability and high morphological similarity between many species. Among plausible factors influencing this issue are hybridisation and introgression recently detected in the genus. Nonetheless, to date, only a bounded set of taxa have been investigated using integrative taxonomy combining morphological and molecular data. Here, we report the first large-scale study on five feather grass species across several hybrid zones in Russia and Central Asia. In total, 302 specimens were sampled in the field and classified based on the current descriptions of these taxa. They were then genotyped with high density genome-wide markers and measured based on a set of morphological characters to delimitate species and assess levels of hybridisation and introgression. Moreover, we tested species for past introgression and estimated divergence times between them. RESULTS Our findings demonstrated that 250 specimens represent five distinct species: S. baicalensis, S. capillata, S. glareosa, S. grandis and S. krylovii. The remaining 52 individuals provided evidence for extensive hybridisation between S. capillata and S. baicalensis, S. capillata and S. krylovii, S. baicalensis and S. krylovii, as well as to a lesser extent between S. grandis and S. krylovii, S. grandis and S. baicalensis. We detected past reticulation events between S. baicalensis, S. krylovii, S. grandis and inferred that diversification within species S. capillata, S. baicalensis, S. krylovii and S. grandis started ca. 130-96 kya. In addition, the assessment of genetic population structure revealed signs of contemporary gene flow between populations across species from the section Leiostipa, despite significant geographical distances between some of them. Lastly, we concluded that only 5 out of 52 hybrid taxa were properly identified solely based on morphology. CONCLUSIONS Our results support the hypothesis that hybridisation is an important mechanism driving evolution in Stipa. As an outcome, this phenomenon complicates identification of hybrid taxa in the field using morphological characters alone. Thus, integrative taxonomy seems to be the only reliable way to properly resolve the phylogenetic issue of Stipa. Moreover, we believe that feather grasses may be a suitable genus to study hybridisation and introgression events in nature.
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Affiliation(s)
- Evgenii Baiakhmetov
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland.
- Research laboratory 'Herbarium', National Research Tomsk State University, Lenin 36 Ave., 634050, Tomsk, Russia.
| | - Daria Ryzhakova
- Research laboratory 'Herbarium', National Research Tomsk State University, Lenin 36 Ave., 634050, Tomsk, Russia
- Department of Biology, Altai State University, Lenin 61 Ave., 656049, Barnaul, Russia
| | - Polina D Gudkova
- Research laboratory 'Herbarium', National Research Tomsk State University, Lenin 36 Ave., 634050, Tomsk, Russia
- Department of Biology, Altai State University, Lenin 61 Ave., 656049, Barnaul, Russia
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland.
- Research laboratory 'Herbarium', National Research Tomsk State University, Lenin 36 Ave., 634050, Tomsk, Russia.
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17
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Karunarathne P, Hojsgaard D. Single Independent Autopolyploidization Events From Distinct Diploid Gene Pools and Residual Sexuality Support Range Expansion of Locally Adapted Tetraploid Genotypes in a South American Grass. Front Genet 2021; 12:736088. [PMID: 34671384 PMCID: PMC8520906 DOI: 10.3389/fgene.2021.736088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 09/07/2021] [Indexed: 12/02/2022] Open
Abstract
Polyploidy plays a major role in plant evolution. The establishment of new polyploids is often a consequence of a single or few successful polyploidization events occurring within a species’ evolutionary trajectory. New polyploid lineages can play different roles in plant diversification and go through several evolutionary stages influenced by biotic and abiotic constraints and characterized by extensive genetic changes. The study of such changes has been crucial for understanding polyploid evolution. Here, we use the multiploid-species Paspalum intermedium to study population-level genetic and morphological variation and ecological differentiation in polyploids. Using flow cytometry, amplified fragment length polymorphism (AFLP) genetic markers, environmental variables, and morphological data, we assessed variations in ploidy, reproductive modes, and the genetic composition in 35 natural populations of P. intermedium along a latitudinal gradient in South America. Our analyses show that apomictic auto-tetraploids are of multiple independent origin. While overall genetic variation was higher in diploids, both diploids and tetraploids showed significant variation within and among populations. The spatial distribution of genetic variation provides evidence for a primary origin of the contact zone between diploids and tetraploids and further supports the hypothesis of geographic displacement between cytotypes. In addition, a strong link between the ecological differentiation of cytotypes and spatial distribution of genetic variation was observed. Overall, the results indicate that polyploidization in P. intermedium is a recurrent phenomenon associated to a shift in reproductive mode and that multiple polyploid lineages from genetically divergent diploids contributed to the successful establishment of local polyploid populations and dispersal into new environments.
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Affiliation(s)
- Piyal Karunarathne
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute for Plant Sciences, University of Goettingen, Goettingen, Germany.,Georg-August University School of Science, University of Goettingen, Goettingen, Germany.,Evolutionary Biology Center, Uppsala University, Uppsala, Sweden
| | - Diego Hojsgaard
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute for Plant Sciences, University of Goettingen, Goettingen, Germany.,Taxonomy & Evolutionary Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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18
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Suissa JS, Kinosian SP, Schafran PW, Bolin JF, Taylor WC, Zimmer EA. Homoploid hybrids, allopolyploids, and high ploidy levels characterize the evolutionary history of a western North American quillwort (Isoëtes) complex. Mol Phylogenet Evol 2021; 166:107332. [PMID: 34687842 DOI: 10.1016/j.ympev.2021.107332] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 10/05/2021] [Accepted: 10/18/2021] [Indexed: 12/26/2022]
Abstract
Polyploidy and hybridization are important processes in seed-free plant evolution. However, a major gap lies in our understanding of how these processes affect the evolutionary history of high-ploidy systems. The heterosporous lycophyte genus Isoëtes is a lineage with many putative hybrids and high-level polyploid taxa (ranging from tetraploid to dodecaploid). Here, we use a complex of western North American Isoëtes, to understand the role of hybridization and high-level polyploidy in generating and maintaining novel diversity. To uncover these processes, we use restriction-site associated DNA sequencing (RADseq), multiple alleles of a single low-copy nuclear marker, whole plastomes, cytology (genome size estimates and chromosome counts), and reproductive status (fertile or sterile). With this dataset, we show that hybridization occurs easily between species in this complex and is bidirectional between identical, but not different, cytotypes. Furthermore, we show that fertile allopolyploids appear to have formed repeatedly from sterile homoploid and interploid hybrids. We propose that low prezygotic reproductive barriers and a high frequency of whole-genome duplication allow for high-level polyploid systems to generate novel lineages, and that these mechanisms may be important in shaping extant Isoëtes diversity.
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Affiliation(s)
- Jacob S Suissa
- The Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA; The Arnold Arboretum of Harvard University, Boston, MA, USA; Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
| | - Sylvia P Kinosian
- Department of Biology & Ecology Center, Utah State University, Logan, UT, USA
| | - Peter W Schafran
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA; Boyce Thompson Institute, Ithaca, NY, USA
| | - Jay F Bolin
- Department of Biology, Catawba College, Salisbury, NC, USA
| | - W Carl Taylor
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Elizabeth A Zimmer
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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19
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Köhler M, Oakley LJ, Font F, Peñas MLL, Majure LC. On the continuum of evolution: a putative new hybrid speciation event in Opuntia (Cactaceae) between a native and an introduced species in southern South America. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1967510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Matias Köhler
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- University of Florida Herbarium (FLAS), Florida Museum of Natural History, Gainesville, FL, USA
| | - Luis J. Oakley
- Cátedra de Botánica, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Santa Fe, Argentina
- Red List Authority Coordinator for the Temperate South American Plant Specialist Groups – International Union for Conservation of Nature (IUCN), Gland, Switzerland
| | - Fabián Font
- Herbario Museo de Farmacobotánica “Juan A. Domínguez” (BAF), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - M. Laura Las Peñas
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Facultas de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba – CONICET, Córdoba, Argentina
| | - Lucas C. Majure
- University of Florida Herbarium (FLAS), Florida Museum of Natural History, Gainesville, FL, USA
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20
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Qiao L, Liu S, Li J, Li S, Yu Z, Liu C, Li X, Liu J, Ren Y, Zhang P, Zhang X, Yang Z, Chang Z. Development of Sequence-Tagged Site Marker Set for Identification of J, J S, and St Sub-genomes of Thinopyrum intermedium in Wheat Background. FRONTIERS IN PLANT SCIENCE 2021; 12:685216. [PMID: 34249056 PMCID: PMC8261300 DOI: 10.3389/fpls.2021.685216] [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: 03/24/2021] [Accepted: 05/14/2021] [Indexed: 06/13/2023]
Abstract
Thinopyrum intermedium (2n = 6x = 42, JJJSJSStSt) is one of the important resources for the wheat improvement. So far, a few Th. intermedium (Thi)-specific molecular markers have been reported, but the number is far from enough to meet the need of identifying alien fragments in wheat-Th. intermedium hybrids. In this study, 5,877,409 contigs were assembled using the Th. intermedium genotyping-by-sequencing (GBS) data. We obtained 5,452 non-redundant contigs containing mapped Thi-GBS markers with less than 20% similarity to the wheat genome and developed 2,019 sequence-tagged site (STS) molecular markers. Among the markers designed, 745 Thi-specific markers with amplification products in Th. intermedium but not in eight wheat landraces were further selected. The distribution of these markers in different homologous groups of Th. intermedium varied from 47 (7/12/28 on 6J/6St/6JS) to 183 (54/62/67 on 7J/7St/7JS). Furthermore, the effectiveness of these Thi-specific markers was verified using wheat-Th. intermedium partial amphidiploids, addition lines, substitution lines, and translocation lines. Markers developed in this study provide a convenient, rapid, reliable, and economical method for identifying Th. intermedium chromosomes in wheat. In addition, this set of Thi-specific markers can also be used to estimate genetic and physical locations of Th. intermedium chromatin in the introgression lines, thus providing valuable information for follow-up studies such as alien gene mining.
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Affiliation(s)
- Linyi Qiao
- College of Agriculture, Shanxi Agricultural University, Taiyuan, China
| | - Shujuan Liu
- Department of Plant Science, College of Agronomy, Northwest Agriculture & Forestry University, Yangling, China
| | - Jianbo Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
- School of Life and Environmental Sciences, Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, Australia
| | - Shijiao Li
- Department of Botany, College of Life Science, Shanxi University, Taiyuan, China
| | - Zhihui Yu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Cheng Liu
- School of Life and Environmental Sciences, Plant Breeding Institute, The University of Sydney, Sydney, NSW, Australia
| | - Xin Li
- College of Agriculture, Shanxi Agricultural University, Taiyuan, China
| | - Jing Liu
- Department of Botany, College of Life Science, Shanxi University, Taiyuan, China
| | - Yongkang Ren
- College of Agriculture, Shanxi Agricultural University, Taiyuan, China
| | - Peng Zhang
- School of Life and Environmental Sciences, Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, Australia
| | - Xiaojun Zhang
- College of Agriculture, Shanxi Agricultural University, Taiyuan, China
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhijian Chang
- College of Agriculture, Shanxi Agricultural University, Taiyuan, China
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21
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Rossetto M, Yap JYS, Lemmon J, Bain D, Bragg J, Hogbin P, Gallagher R, Rutherford S, Summerell B, Wilson TC. A conservation genomics workflow to guide practical management actions. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01492] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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Hernández-Hernández T, Miller EC, Román-Palacios C, Wiens JJ. Speciation across the Tree of Life. Biol Rev Camb Philos Soc 2021; 96:1205-1242. [PMID: 33768723 DOI: 10.1111/brv.12698] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 01/04/2023]
Abstract
Much of what we know about speciation comes from detailed studies of well-known model systems. Although there have been several important syntheses on speciation, few (if any) have explicitly compared speciation among major groups across the Tree of Life. Here, we synthesize and compare what is known about key aspects of speciation across taxa, including bacteria, protists, fungi, plants, and major animal groups. We focus on three main questions. Is allopatric speciation predominant across groups? How common is ecological divergence of sister species (a requirement for ecological speciation), and on what niche axes do species diverge in each group? What are the reproductive isolating barriers in each group? Our review suggests the following patterns. (i) Based on our survey and projected species numbers, the most frequent speciation process across the Tree of Life may be co-speciation between endosymbiotic bacteria and their insect hosts. (ii) Allopatric speciation appears to be present in all major groups, and may be the most common mode in both animals and plants, based on non-overlapping ranges of sister species. (iii) Full sympatry of sister species is also widespread, and may be more common in fungi than allopatry. (iv) Full sympatry of sister species is more common in some marine animals than in terrestrial and freshwater ones. (v) Ecological divergence of sister species is widespread in all groups, including ~70% of surveyed species pairs of plants and insects. (vi) Major axes of ecological divergence involve species interactions (e.g. host-switching) and habitat divergence. (vii) Prezygotic isolation appears to be generally more widespread and important than postzygotic isolation. (viii) Rates of diversification (and presumably speciation) are strikingly different across groups, with the fastest rates in plants, and successively slower rates in animals, fungi, and protists, with the slowest rates in prokaryotes. Overall, our study represents an initial step towards understanding general patterns in speciation across all organisms.
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Affiliation(s)
- Tania Hernández-Hernández
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A.,Catedrática CONACYT asignada a LANGEBIO-UGA Cinvestav, Libramiento Norte Carretera León Km 9.6, 36821, Irapuato, Guanajuato, Mexico
| | - Elizabeth C Miller
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| | - Cristian Román-Palacios
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
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23
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Mizeriene G, Cerny K, Zyka V, Bakonyi J, Nagy ZÁ, Oliva J, Redondo MA, Corcobado T, Martín-García J, Prospero S. Patterns of Genetic Diversification in the Invasive Hybrid Plant Pathogen Phytophthora × alni and Its Parental Species P. uniformis. PHYTOPATHOLOGY 2020; 110:1959-1969. [PMID: 32633698 DOI: 10.1094/phyto-12-19-0475-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In pathogenic fungi and oomycetes, interspecific hybridization may lead to the formation of new species having a greater impact on natural ecosystems than the parental species. From the early 1990s, a severe alder (Alnus spp.) decline due to an unknown Phytophthora species was observed in several European countries. Genetic analyses revealed that the disease was caused by the triploid hybrid P. × alni, which originated in Europe from the hybridization of P. uniformis and P. × multiformis. Here, we investigated the population structure of P. × alni (158 isolates) and P. uniformis (85 isolates) in several European countries using microsatellite markers. Our analyses confirmed the genetic structure previously observed in other European populations, with P. uniformis populations consisting of at most two multilocus genotypes (MLGs) and P. × alni populations dominated by MLG Pxa-1. The genetic structure of P. × alni populations in the Czech Republic, Hungary and Sweden seemed to reflect the physical isolation of river systems. Most rare P. × alni MLGs showed a loss of heterozygosity (LOH) at one or a few microsatellite loci compared with other MLGs. This LOH may allow a stabilization within the P. × alni genome or a rapid adaptation to stress situations. Alternatively, alleles may be lost because of random genetic drift in small, isolated populations, with no effect on fitness of P. × alni. Additional studies would be necessary to confirm these patterns of population diversification and to better understand the factors driving it.
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Affiliation(s)
- Goda Mizeriene
- Swiss Federal Research Institute WSL, Zuercherstrasse 111, CH-8903 Birmensdorf, Switzerland
- Institute of Botany at The Lithuanian State Research Institute Nature Research Centre, Žaliųjų Ežerų Str. 49, LT-08406 Vilnius, Lithuania
| | - Karel Cerny
- The Silva Tarouca Research Institute for Landscape and Ornamental Gardening (RILOG), Květnové náměstí 391, Průhonice 252 43, The Czech Republic
| | - Vladimir Zyka
- The Silva Tarouca Research Institute for Landscape and Ornamental Gardening (RILOG), Květnové náměstí 391, Průhonice 252 43, The Czech Republic
| | - József Bakonyi
- Plant Protection Institute, Centre for Agricultural Research, Herman Ottó Str. 15, H-1022 Budapest, Hungary
| | - Zoltán Árpád Nagy
- Phytophthora Research Centre, Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 61300 Brno, Czech Republic
| | - Jonas Oliva
- Department Crop and Forest Sciences, University of Lleida, Alcalde Rovira Roure 191, 25198, Lleida, Spain
- Joint Research Unit CTFC-Agrotecnio, Alcalde Rovira Roure 191 Lleida, 25198, Spain
| | - Miguel Angel Redondo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 07 Uppsala, Sweden
| | - Tamara Corcobado
- Phytophthora Research Centre, Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 61300 Brno, Czech Republic
- Federal Research and Training Centre for Forests, Natural Hazards and Landscape (BFW), Seckendorff-Gudent-Weg 8, 1131 Vienna, Austria
| | - Jorge Martín-García
- Department of Biology, CESAM (Centre for Environmental and Marine Studies), University of Aveiro, Campus Universitario de Santiago, 3810-193 Aveiro, Portugal
- Department of Plant Production and Forest Resources, University of Valladolid, Avenida de Madrid 44, 34071 Palencia, Spain
| | - Simone Prospero
- Swiss Federal Research Institute WSL, Zuercherstrasse 111, CH-8903 Birmensdorf, Switzerland
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24
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Meeus S, Šemberová K, De Storme N, Geelen D, Vallejo-Marín M. Effect of Whole-Genome Duplication on the Evolutionary Rescue of Sterile Hybrid Monkeyflowers. PLANT COMMUNICATIONS 2020; 1:100093. [PMID: 33367262 PMCID: PMC7747968 DOI: 10.1016/j.xplc.2020.100093] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/08/2020] [Accepted: 07/01/2020] [Indexed: 05/15/2023]
Abstract
Hybridization is a creative evolutionary force, increasing genomic diversity and facilitating adaptation and even speciation. Hybrids often face significant challenges to establishment, including reduced fertility that arises from genomic incompatibilities between their parents. Whole-genome duplication in hybrids (allopolyploidy) can restore fertility, cause immediate phenotypic changes, and generate reproductive isolation. Yet the survival of polyploid lineages is uncertain, and few studies have compared the performance of recently formed allopolyploids and their parents under field conditions. Here, we use natural and synthetically produced hybrid and polyploid monkeyflowers (Mimulus spp.) to study how polyploidy contributes to the fertility, reproductive isolation, phenotype, and performance of hybrids in the field. We find that polyploidization restores fertility and that allopolyploids are reproductively isolated from their parents. The phenotype of allopolyploids displays the classic gigas effect of whole-genome duplication, in which plants have larger organs and are slower to flower. Field experiments indicate that survival of synthetic hybrids before and after polyploidization is intermediate between that of the parents, whereas natural hybrids have higher survival than all other taxa. We conclude that hybridization and polyploidy can act as sources of genomic novelty, but adaptive evolution is key in mediating the establishment of young allopolyploid lineages.
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Affiliation(s)
- Sofie Meeus
- Department of Biological and Environmental Sciences. University of Stirling, Stirling FK9 4LA, UK
| | - Kristýna Šemberová
- Department of Botany, Charles University, 128 43 Prague 2, Czech Republic
| | - Nico De Storme
- Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium
| | - Danny Geelen
- Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium
| | - Mario Vallejo-Marín
- Department of Biological and Environmental Sciences. University of Stirling, Stirling FK9 4LA, UK
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25
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Contreras R, van den Brink L, Burgos B, González M, Gacitúa S. Genetic Characterization of an Endangered Chilean Endemic Species, Prosopis burkartii Muñoz, Reveals its Hybrids Parentage. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9060744. [PMID: 32545703 PMCID: PMC7355918 DOI: 10.3390/plants9060744] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/31/2020] [Accepted: 06/11/2020] [Indexed: 05/25/2023]
Abstract
The hybridization of Prosopis burkartii, a critically endangered endemic species, and the identification of its paternal species has not been genetically studied before. In this study we aimed to genetically confirm the origin of this species. To resolve the parental status of P. burkartii, inter-simple sequence repeat (ISSR), simple sequence repeats (SSR) and intron trnL molecular markers were used, and compared with Chilean species from the Algarobia and Strombocarpa sections. Out of seven ISSRs, a total of 70 polymorphic bands were produced in four species of the Strombocarpa section. An Multi-dimensional scaling (MDS) and Bayasian (STRUCTURE) analysis showed signs of introgression of genetic material in P. burkartii. Unweighted pair group method with arithmetic average (UPGMA) cluster analysis showed three clusters, and placed the P. burkartii cluster nested within the P. tamarugo group. Sequencing of the trnL intron showed a fragment of 535 bp and 529 bp in the species of the Algarobia and Strombocarpa sections, respectively. Using maximum parsimony (MP) and maximum likelihood (ML) trees with the trnL intron, revealed four clusters. A species-specific diagnostic method was performed, using the trnL intron Single Nucleotide Polymorphism (SNP). This method identified if individuals of P. burkartii inherited their maternal DNA from P. tamarugo or from P. strombulifera. We deduced that P. tamarugo and P. strombulifera are involved in the formation of P. burkartii.
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Affiliation(s)
- Roberto Contreras
- Centro Regional de Investigación y Desarrollo Sustentable de Atacama (CRIDESAT), Universidad de Atacama, Av. Copayapu 485, 1530000 Copiapó, Chile
| | - Liesbeth van den Brink
- Department of Evolution and Ecology, Plant Ecology Group, Universität Tübingen, 72076 Tübingen, Germany;
| | - Boris Burgos
- Corporación Nacional Forestal (CONAF), Región de Atacama, Juan Martínez 55, 1530000 Copiapó, Chile;
| | - Marlene González
- Instituto Nacional Forestal (INFOR), Sede Metropolitana y Sede Diaguita, 1760000 Diaguitas, Chile; (M.G.); (S.G.)
| | - Sandra Gacitúa
- Instituto Nacional Forestal (INFOR), Sede Metropolitana y Sede Diaguita, 1760000 Diaguitas, Chile; (M.G.); (S.G.)
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26
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Zhou Y, Li WW, Zhang YQ, Xing XC, Zhang JQ, Ren Y. Extensive reticulate evolution within Fargesia (s.l.) (Bambusoideae: Poaceae) and its allies: Evidence from multiple nuclear markers. Mol Phylogenet Evol 2020; 149:106842. [PMID: 32305509 DOI: 10.1016/j.ympev.2020.106842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 04/10/2020] [Accepted: 04/13/2020] [Indexed: 11/16/2022]
Abstract
Reticulate evolution resulting from hybridization and introgression has been recognized as a creative source of species and diversification in bamboos. Previous phylogenetic studies revealed that Fargesia (s.l.) (Fargesia and Yushania) was divided into the Fargesia spathe clade and the non-spathe clade. Interestingly, the Fargesia spathe clade may have originated from hybridization among other clades within Fargesia (s.l.). Understanding the hybrid origin of this clade requires a robust phylogenetic framework in which major clades within Fargesia (s.l.) are resolved. Here, we used three nuclear genes to reconstruct the evolutionary history of Fargesia (s.l.) and its allies to identify putative patterns in the origin of the Fargesia spathe clade and to examine the extent to which reticulate evolution has occurred at the interspecific level in bamboos. Bashania species form a clade with Fargesia (s.l.), which is further divided into Group I and Group II. The Fargesia spathe clade, the Alpine Bashania clade, and Fargesia yajiangensis comprise Group I, while the Bashania fargesii clade and the remaining Fargesia (s.l.) species form Group II. Incongruence between the current nuclear-based and previous plastid phylogenies demonstrate several possible hybridization events among Fargesia (s.l.) species and related taxa, which have given rise to the Fargesia spathe clade, the Phyllostachys clade, and the Ampelocalamus clade. We also detected several putative hybrid species of Fargesia (s.l.). Our results show that reticulate evolution has played a prominent role in Fargesia (s.l.) evolution, which could, in part, account for the taxonomic difficulty associated with Fargesia (s.l.) and the alpine bamboos. The study also underscores the importance of hybridization in the evolution of bamboos, at both intergeneric and intrageneric levels.
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Affiliation(s)
- Yun Zhou
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Wan-Wan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Yu-Qu Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Xiao-Cheng Xing
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Jian-Qiang Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
| | - Yi Ren
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
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What nature separated, and human joined together: About a spontaneous hybridization between two allopatric dogwood species (Cornus controversa and C. alternifolia). PLoS One 2019; 14:e0226985. [PMID: 31869386 PMCID: PMC6927628 DOI: 10.1371/journal.pone.0226985] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/09/2019] [Indexed: 11/19/2022] Open
Abstract
In this study, possible hybridization between two allopatric species, Cornus controversa and Cornus alternifolia, was explored using molecular and morphological approaches. Scanning electron microscope analyses of the adaxial and the abaxial leaf surfaces yielded a few new not yet described characters typical for the particular species and intermediate for hybrids. With the use of 14 Random Amplified Polymorphic DNA and 5 Amplified Fragment Length Polymorphism primer combinations, 44 fragments species specific to C. controversa and 51 species specific to C. alternifolia were obtained. Most of these bands were also found in putative hybrids. All clustering analyses based on binary data combined from both methods confirmed a separate and intermediate status of the hybrids. Hybrid index estimates for hybrids C1-C5 indicated that all were the first generation of offspring (F1). Chloroplast intergenic spacers (trnF-trnL and psbC-trnS) were used to infer the hybridization direction. Based on the assumption of maternal inheritance of chloroplast DNA, C. controversa seems to be the maternal parent of the hybrid. Internal transcribed spacer sequences of the five hybrids analyzed here indicated higher similarity with the sequences of C. controversa (all shared the majority of its single nucleotide polymorphisms). Sequence analysis of PI-like genes fully confirmed the hybrid origin of C1-C5 hybrids. Our results also showed that two specimens in the C. alternifolia group, A1 and A3, are not free of introgression. They are probably repeated backcrosses toward C. alternifolia. Furthermore, molecular data seem to point not only to unidirectional introgression toward C. controversa (the presence of hybrids) but to bidirectional introgression as well, since the presence of markers specific for C. controversa in the profiles of C. alternifolia specimen A3 was observed.
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Maxwell SJ, Bordon AV, Rymer TL, Congdon BC. The birth of a species and the validity of hybrid nomenclature demonstrated with a revision of hybrid taxa within Strombidae (Neostromboidae). P BIOL SOC WASH 2019. [DOI: 10.2988/19-00007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Stephen J. Maxwell
- (SJM, TLR, BCC) College of Science and Engineering, James Cook University, Cairns Qld 4870 Australia
| | - Anton V. Bordon
- (AVB) Snezhnaya, 17-2-459, Moscow, 129323, The Russian Federation
| | - Tasmin L. Rymer
- (SJM, TLR, BCC) College of Science and Engineering, James Cook University, Cairns Qld 4870 Australia
| | - Bradley C. Congdon
- (SJM, TLR, BCC) College of Science and Engineering, James Cook University, Cairns Qld 4870 Australia
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Melichárková A, Španiel S, Marhold K, Hurdu BI, Drescher A, Zozomová-Lihová J. Diversification and independent polyploid origins in the disjunct species Alyssum repens from the Southeastern Alps and the Carpathians. AMERICAN JOURNAL OF BOTANY 2019; 106:1499-1518. [PMID: 31639199 DOI: 10.1002/ajb2.1370] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/30/2019] [Indexed: 05/20/2023]
Abstract
PREMISE Disjunct distributions have been commonly observed in mountain plant species and have stimulated phylogeographic and phylogenetic research. Here we studied Alyssum repens, a member of the polyploid species complex A. montanum-A. repens, which exhibits SE Alpine-Carpathian disjunctions with a large elevational span and consists of diploid and tetraploid populations. We aimed to investigate the species' genetic and cytotype structure in the context of its distribution patterns, to elucidate the polyploid origins and to propose an appropriate taxonomic treatment. METHODS We combined AFLP fingerprinting markers, sequence variation of the highly repetitive ITS region of rDNA and the low-copy DET1 nuclear gene, genome size, and morphometric data. RESULTS We identified four geographically structured genetic lineages. One consisted of diploid populations from the foothills of the Southeastern Alps and neighboring regions, and the three others were allopatric montane to alpine groups comprising diploids and tetraploids growing in the Southeastern Carpathians and the Apuseni Mts. in Romania. CONCLUSIONS We inferred a vicariance scenario associated with Quaternary climatic oscillations, accompanied by one auto- and two allopolyploidization events most likely involving a northern Balkan relative. Whereas genetic differentiation and allopatric distribution would favor the taxonomic splitting of this species, the genetic lineages largely lack morphological distinguishability, and their ecological, cytotype and genome size divergence is only partial. Even though we probably face here a case of incipient speciation, we propose to maintain the current taxonomic treatment of Alyssum repens as a single, albeit variable, species.
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Affiliation(s)
- Andrea Melichárková
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23, Bratislava, Slovakia
| | - Stanislav Španiel
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23, Bratislava, Slovakia
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-128 01, Prague, Czech Republic
| | - Karol Marhold
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23, Bratislava, Slovakia
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-128 01, Prague, Czech Republic
| | - Bogdan-Iuliu Hurdu
- Institute of Biological Research, National Institute of Research and Development for Biological Sciences, 48 Republicii Street, 400015, Cluj-Napoca, Romania
| | - Anton Drescher
- Institut für Pflanzenwissenschaften der Universität Graz - Herbarium GZU, Holteigasse 6, A-8010, Graz, Austria
| | - Judita Zozomová-Lihová
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23, Bratislava, Slovakia
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30
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Mandáková T, Zozomová-Lihová J, Kudoh H, Zhao Y, Lysak MA, Marhold K. The story of promiscuous crucifers: origin and genome evolution of an invasive species, Cardamine occulta (Brassicaceae), and its relatives. ANNALS OF BOTANY 2019; 124:209-220. [PMID: 30868165 PMCID: PMC6758578 DOI: 10.1093/aob/mcz019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 01/24/2019] [Indexed: 05/16/2023]
Abstract
BACKGROUND AND AIMS Cardamine occulta (Brassicaceae) is an octoploid weedy species (2n = 8x = 64) originated in Eastern Asia. It has been introduced to other continents including Europe and considered to be an invasive species. Despite its wide distribution, the polyploid origin of C. occulta remained unexplored. The feasibility of comparative chromosome painting (CCP) in crucifers allowed us to elucidate the origin and genome evolution in Cardamine species. We aimed to investigate the genome structure of C. occulta in comparison with its tetraploid (2n = 4x = 32, C. kokaiensis and C. scutata) and octoploid (2n = 8x = 64, C. dentipetala) relatives. METHODS Genomic in situ hybridization (GISH) and large-scale CCP were applied to uncover the parental genomes and chromosome composition of the investigated Cardamine species. KEY RESULTS All investigated species descended from a common ancestral Cardamine genome (n = 8), structurally resembling the Ancestral Crucifer Karyotype (n = 8), but differentiated by a translocation between chromosomes AK6 and AK8. Allotetraploid C. scutata originated by hybridization between two diploid species, C. parviflora and C. amara (2n = 2x = 16). By contrast, C. kokaiensis has an autotetraploid origin from a parental genome related to C. parviflora. Interestingly, octoploid C. occulta probably originated through hybridization between the tetraploids C. scutata and C. kokaiensis. The octoploid genome of C. dentipetala probably originated from C. scutata via autopolyploidization. Except for five species-specific centromere repositionings and one pericentric inversion post-dating the polyploidization events, the parental subgenomes remained stable in the tetra- and octoploids. CONCLUSIONS Comparative genome structure, origin and evolutionary history was reconstructed in C. occulta and related species. For the first time, whole-genome cytogenomic maps were established for octoploid plants. Post-polyploid evolution in Asian Cardamine polyploids has not been associated with descending dysploidy and intergenomic rearrangements. The combination of different parental (sub)genomes adapted to distinct habitats provides an evolutionary advantage to newly formed polyploids by occupying new ecological niches.
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Affiliation(s)
- Terezie Mandáková
- Plant Cytogenomics research group, CEITEC – Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Czech Republic
| | - Judita Zozomová-Lihová
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano, Japan
| | - Yunpeng Zhao
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, China
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, Institute of Ecology and Conservation Centre for Gene Resources of Endangered Wildlife, Zhejiang University, Hangzhou, China
| | - Martin A Lysak
- Plant Cytogenomics research group, CEITEC – Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Czech Republic
| | - Karol Marhold
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovak Republic
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
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Banjanac T, Đurović S, Jelić M, Dragićević M, Mišić D, Skorić M, Nestorović Živković J, Šiler B. Phenotypic and Genetic Variation of an Interspecific Centaurium Hybrid ( Gentianaceae) and Its Parental Species. PLANTS 2019; 8:plants8070224. [PMID: 31337143 PMCID: PMC6681202 DOI: 10.3390/plants8070224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 11/16/2022]
Abstract
Interspecific hybridization is one of the major actuators of evolutionary changes in plants. As the result of allopolyploid hybridization, offspring may gain different ploidy levels in comparison to parental species, which can provide them instant reproductive isolation. Two tetraploid sister species, Centaurium erythraea and C. littorale, readily cross-fertilize, resulting in hybrids of various ploidy. In northern Serbia, two stable populations of a hexaploid taxon C. pannonicum have been documented. It has been proposed previously that this taxon emerged after an interspecific hybridization event between two tetraploid sister-species: C. erythraea and C. littorale subsp. compressum. The existing populations of the hybridogenic taxon, as well as neighboring populations of the two parental taxa were here characterized by both morphometrics and molecular markers (EST-SSR and trnL-F). Three leaf and two flower characteristics were found to be informative in delimitation of the parental taxa and in their discernment from hybrid individuals, the latter having intermediate values. Eight microsatellite markers were found to have good ability to distinguish studied taxa, placing C. pannonicum in closer relationship with C. erythraea. Conversely, trnL-F plastid marker nominated C. littorale subsp. compressum to be the donor of the C. pannonicum plastid DNA. Reproductive isolation of the hexaploid hybrid individuals from the parental species should be examined as the next logical step in describing the new species.
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Affiliation(s)
- Tijana Banjanac
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060 Belgrade, Serbia.
| | - Sanja Đurović
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia
| | - Mihailo Jelić
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia
| | - Milan Dragićević
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060 Belgrade, Serbia
| | - Danijela Mišić
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060 Belgrade, Serbia
| | - Marijana Skorić
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060 Belgrade, Serbia
| | - Jasmina Nestorović Živković
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060 Belgrade, Serbia
| | - Branislav Šiler
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060 Belgrade, Serbia
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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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33
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Biodiversity and apomixis: Insights from the East-Asian holly ferns in Polystichum section Xiphopolystichum. Mol Phylogenet Evol 2018; 127:345-355. [PMID: 29763663 DOI: 10.1016/j.ympev.2018.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 04/30/2018] [Accepted: 05/03/2018] [Indexed: 11/24/2022]
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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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Comeault AA. The genomic and ecological context of hybridization affects the probability that symmetrical incompatibilities drive hybrid speciation. Ecol Evol 2018; 8:2926-2937. [PMID: 29531706 PMCID: PMC5838063 DOI: 10.1002/ece3.3872] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 12/21/2017] [Accepted: 12/22/2017] [Indexed: 01/03/2023] Open
Abstract
Despite examples of homoploid hybrid species, theoretical work describing when, where, and how we expect homoploid hybrid speciation to occur remains relatively rare. Here, I explore the probability of homoploid hybrid speciation due to "symmetrical incompatibilities" under different selective and genetic scenarios. Through simulation, I test how genetic architecture and selection acting on traits that do not themselves generate incompatibilities interact to affect the probability that hybrids evolve symmetrical incompatibilities with their parent species. Unsurprisingly, selection against admixture at "adaptive" loci that are linked to loci that generate incompatibilities tends to reduce the probability of evolving symmetrical incompatibilities. By contrast, selection that favors admixed genotypes at adaptive loci can promote the evolution of symmetrical incompatibilities. The magnitude of these outcomes is affected by the strength of selection, aspects of genetic architecture such as linkage relationships and the linear arrangement of loci along a chromosome, and the amount of hybridization following the formation of a hybrid zone. These results highlight how understanding the nature of selection, aspects of the genetics of traits affecting fitness, and the strength of reproductive isolation between hybridizing taxa can all be used to inform when we expect to observe homoploid hybrid speciation due to symmetrical incompatibilities.
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Rita J, Capó M, Moragues E, Bota J, Cursach J. Hybridization processes in an introduced subpopulation of an endangered plant: Management strategies to guarantee the conservation of Helosciadium bermejoi (Apiaceae). J Nat Conserv 2018. [DOI: 10.1016/j.jnc.2017.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Zhang R, Gong X, Folk R. Evidence for continual hybridization rather than hybrid speciation between Ligularia duciformis and L. paradoxa (Asteraceae). PeerJ 2017; 5:e3884. [PMID: 29038755 PMCID: PMC5640982 DOI: 10.7717/peerj.3884] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 09/13/2017] [Indexed: 11/20/2022] Open
Abstract
Background Hybrids possess phenotypic traits that are often intermediate between their parental taxa, which commonly serves as evidence of hybridization in morphological analyses. Natural hybridization has been shown to occur frequently in Ligularia (Asteraceae). In a previous study, Ligularia ×maoniushanensis was demonstrated as a natural hybrid species between L. duciformis and L. paradoxa based on morphological and reproductive traits. Methods We used three chloroplast (cpDNA) fragments (psbA-trnH, trnL-rpl32 and trnQ-5′rps16), the nuclear ribosomal internal transcribed spacer (nrITS), and co-dominant SSR and dominant ISSR markers to study natural hybridization between L. duciformis and L. paradoxa growing sympatrically in two locations. Parental taxa were inferred using network analyses of cpDNA and nrITS haplotypes. Admixture among individuals was examined using the Bayesian clustering programs STRUCTURE and NewHybrids based on the SSR and ISSR data; and potential introgression in the SSR loci was assessed using the INTROGRESS package. Results The putative parental species were clearly distinguished from other sympatric Ligularia species by nrITS data, and L. ×maoniushanensis individuals were confirmed to be the hybrid offspring of L. duciformis and L. paradoxa. Moreover, introgression was detected among several individuals morphologically identified as L. duciformis or L. paradoxa. Analyses of the cpDNA data revealed primarily unidirectional hybridization between L. duciformis and L. paradoxa, with L. paradoxa as the maternal parent in Mt. Maoniu, whereas bidirectional but asymmetrical hybridization was inferred to occur in Heihai Lake. The STRUCTURE analyses based on the SSR data detected two distinct clusters among the three taxa. The NewHybrids analyses showed that individuals circumscribed as L. ×maoniushanensis were dominated by early- and later-generation and backcrossing hybrids. The NewHybrids results based on the ISSR data were congruent with SSR results. In addition, introgression was detected in some SSR loci, and heterogeneity among loci was found in terms of detected patterns of introgression. Conclusions Our data provide strong evidence for hybridization and introgression between L. duciformis and L. paradoxa. Ligularia ×maoniushanensis was demonstrated to be of hybrid origin. Since no evident reproductive isolation was found between the two parental species, detected hybrids appear to be part of hybrid swarms resulting from frequent and ongoing gene flow, which might impede the formation of a new hybrid species.
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Affiliation(s)
- Rong Zhang
- Key Laboratory of Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.,Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.,Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xun Gong
- Key Laboratory of Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.,Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Ryan Folk
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
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Banjanac T, Dragićević M, Šiler B, Gašić U, Bohanec B, Nestorović Živković J, Trifunović S, Mišić D. Chemodiversity of two closely related tetraploid Centaurium species and their hexaploid hybrid: Metabolomic search for high-resolution taxonomic classifiers. PHYTOCHEMISTRY 2017; 140:27-44. [PMID: 28448798 DOI: 10.1016/j.phytochem.2017.04.005] [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: 12/13/2016] [Revised: 04/07/2017] [Accepted: 04/11/2017] [Indexed: 06/07/2023]
Abstract
Species within the genus Centaurium readily hybridize and polyploid complexes are often seen in natural populations. We describe phytochemical profiles of newly discovered allohexaploid hybrid, here named Centaurium pannonicum, and its parental tetraploid species C. erythraea and rare C. littorale ssp. compressum. Our aim was to examine chemodiversity of these taxa in the area of Vojvodina (North Serbia) and to perform metabolomics search for chemical classifiers which would provide high resolution discrimination of parental and hybrid individuals. In sum, UHPLC-MS/MS Orbitrap metabolomics fingerprinting revealed seventy compounds in methanol extracts. Despite the lack of qualitative chemical novelty in hybrid plants, UHPLC-qqqMS targeted metabolomics approach, aimed at three secoiridoid compounds and seventeen phenolics, pointed to considerable differences in quantitative composition of these dominant compounds among the plant taxa studied. In addition to the difference in the ploidy levels, the hybrid taxon was well distinguished from both parental species based on metabolite profiles, and, for most individuals, positioned intermediately to the parental taxa in both PCA and hierarchical clustering. After optimizing and comparing several statistical learning methods, it was possible to narrow the number of taxonomic classifiers to five (three xanthones, one secoiridoid glycoside, and one phenolic acid), while increasing the differentiation resolution. The presented metabolomics approach will certainly, along with morphometrics and molecular genetics studies, have high impact on further elucidation of complex relationships among taxa within the genus Centaurium.
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Affiliation(s)
- Tijana Banjanac
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060, Belgrade, Serbia
| | - Milan Dragićević
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060, Belgrade, Serbia
| | - Branislav Šiler
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060, Belgrade, Serbia.
| | - Uroš Gašić
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, 11000, Belgrade, Serbia
| | - Borut Bohanec
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Jasmina Nestorović Živković
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060, Belgrade, Serbia
| | - Snežana Trifunović
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, 11000, Belgrade, Serbia
| | - Danijela Mišić
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060, Belgrade, Serbia
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Jarvis KJ, Allan GJ, Craig AJ, Beresic-Perrins RK, Wimp G, Gehring CA, Whitham TG. Arthropod communities on hybrid and parental cottonwoods are phylogenetically structured by tree type: Implications for conservation of biodiversity in plant hybrid zones. Ecol Evol 2017; 7:5909-5921. [PMID: 28808554 PMCID: PMC5551273 DOI: 10.1002/ece3.3146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/17/2017] [Indexed: 02/03/2023] Open
Abstract
Although hybridization in plants has been recognized as an important pathway in plant speciation, it may also affect the ecology and evolution of associated communities. Cottonwood species (Populus angustifolia and P. fremontii) and their naturally occurring hybrids are known to support different plant, animal, and microbial communities, but no studies have examined community structure within the context of phylogenetic history. Using a community composed of 199 arthropod species, we tested for differences in arthropod phylogenetic patterns within and among hybrid and parental tree types in a common garden. Three major patterns emerged. (1) Phylogenetic diversity (PD) was significantly different between arthropod communities on hybrids and Fremont cottonwood when pooled by tree type. (2) Mean phylogenetic distance (MPD) and net relatedness index (NRI) indicated that communities on hybrid trees were significantly more phylogenetically overdispersed than communities on either parental tree type. (3) Community distance (Dpw) indicated that communities on hybrids were significantly different than parental species. Our results show that arthropod communities on parental and hybrid cottonwoods exhibit significantly different patterns of phylogenetic structure. This suggests that arthropod community assembly is driven, in part, by plant-arthropod interactions at the level of cottonwood tree type. We discuss potential hypotheses to explain the effect of plant genetic dissimilarity on arthropod phylogenetic community structure, including the role of competition and environmental filtering. Our findings suggest that cottonwood species and their hybrids function as evolutionarily significant units (ESUs) that affect the assembly and composition of associated arthropod communities and deserve high priority for conservation.
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Affiliation(s)
- Karl J Jarvis
- School of Forestry Northern Arizona University Flagstaff AZ USA.,Biology Department Southern Utah University Cedar City UT USA
| | - Gerard J Allan
- Department of Biological Sciences Northern Arizona University Flagstaff AZ USA.,Merriam-Powell Center for Environmental Research Flagstaff AZ USA
| | - Ashley J Craig
- Department of Biological Sciences Northern Arizona University Flagstaff AZ USA
| | | | - Gina Wimp
- Department of Biology Georgetown University Washington DC USA
| | - Catherine A Gehring
- Department of Biological Sciences Northern Arizona University Flagstaff AZ USA.,Merriam-Powell Center for Environmental Research Flagstaff AZ USA
| | - Thomas G Whitham
- Department of Biological Sciences Northern Arizona University Flagstaff AZ USA.,Merriam-Powell Center for Environmental Research Flagstaff AZ USA
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Zhuang Y, Tripp EA. Genome-scale transcriptional study of hybrid effects and regulatory divergence in an F 1 hybrid Ruellia (Wild Petunias: Acanthaceae) and its parents. BMC PLANT BIOLOGY 2017; 17:15. [PMID: 28095782 PMCID: PMC5240417 DOI: 10.1186/s12870-016-0962-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 12/22/2016] [Indexed: 05/30/2023]
Abstract
BACKGROUND New combinations of divergent genomes can give rise to novel genetic functions in resulting hybrid progeny. Such functions may yield opportunities for ecological divergence, contributing ultimately to reproductive isolation and evolutionary longevity of nascent hybrid lineages. In plants, the degree to which transgressive genotypes contribute to floral novelty remains a question of key interest. Here, we generated an F1 hybrid plant between the red-flowered Ruellia elegans and yellow flowered R. speciosa. RNA-seq technology was used to explore differential gene expression between the hybrid and its two parents, with emphasis on genetic elements involved in the production of floral anthocyanin pigments. RESULTS The hybrid was purple flowered and produced novel floral delphinidin pigments not manufactured by either parent. We found that nearly a fifth of all 86,475 unigenes expressed were unique to the hybrid. The majority of hybrid unigenes (80.97%) showed a pattern of complete dominance to one parent or the other although this ratio was uneven, suggesting asymmetrical influence of parental genomes on the progeny transcriptome. However, 8.87% of all transcripts within the hybrid were expressed at significantly higher or lower mean levels than observed for either parent. A total of 28 unigenes coding putatively for eight core enzymes in the anthocyanin pathway were recovered, along with three candidate MYBs involved in anthocyanin regulation. CONCLUSION Our results suggest that models of gene evolution that explain phenotypic novelty and hybrid establishment in plants may need to include transgressive effects. Additionally, our results lend insight into the potential for floral novelty that derives from unions of divergent genomes. These findings serve as a starting point to further investigate molecular mechanisms involved in flower color transitions in Ruellia.
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Affiliation(s)
- Yongbin Zhuang
- Department of Ecology and Evolutionary Biology, University of Colorado, UCB 334, Boulder, CO 80309 USA
- Museum of Natural History, University of Colorado, UCB 350, Boulder, CO 80309 USA
| | - Erin A. Tripp
- Department of Ecology and Evolutionary Biology, University of Colorado, UCB 334, Boulder, CO 80309 USA
- Museum of Natural History, University of Colorado, UCB 350, Boulder, CO 80309 USA
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Marczewski T, Ma YP, Zhang XM, Sun WB, Marczewski AJ. Why is population information crucial for taxonomy? A case study involving a hybrid swarm and related varieties. AOB PLANTS 2016; 8:plw070. [PMID: 27758764 PMCID: PMC5142052 DOI: 10.1093/aobpla/plw070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 09/14/2016] [Indexed: 05/14/2023]
Abstract
Hybridization has become a focal topic in evolutionary biology, and many taxonomists are aware that the process occurs more frequently than previously assumed. Nonetheless many species and varieties are still described without explicitly considering the possibility of hybridization, especially in countries that have relatively short scientific histories, but which often possess the highest species diversities. Furthermore, new taxa are often described based only on herbarium specimens, not taking into account information from wild populations, significantly decreasing the potential to detect morphologies arising from hybridization at this crucial descriptive stage. We used morphological data from a hybrid swarm involving two Rhododendron species to showcase possible character combinations in intermediates. Certain characters used to distinguish taxa were more variable within the same individual than between species, emphasizing the importance of population information for an adequate choice of characters. Most described varieties of the two species fell within the spectrum of hybrid morphology, suggesting that these taxa would be unlikely to have merited formal description if contemporary standards had been employed. In all investigated cases the hybrid nature of described varieties seems to have been detectable with adequate morphological data alone, if populations had been assessed. A post hoc assessment of taxa is often complicated, especially if certain types of information are not provided. To avoid accumulation of such invalid taxa, careful scrutiny should be employed for new descriptions. Hybrids (not hybrid species) described as taxa obscure valuable information about natural processes and impact negatively on further research that depends on taxonomic data.
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Affiliation(s)
- Tobias Marczewski
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan 650201, China
| | - Yong-Peng Ma
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan 650201, China
| | - Xue-Mei Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan 650201, China
| | - Wei-Bang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan 650201, China
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Zhao L, Jiang XW, Zuo YJ, Liu XL, Chin SW, Haberle R, Potter D, Chang ZY, Wen J. Multiple Events of Allopolyploidy in the Evolution of the Racemose Lineages in Prunus (Rosaceae) Based on Integrated Evidence from Nuclear and Plastid Data. PLoS One 2016; 11:e0157123. [PMID: 27294529 PMCID: PMC4905661 DOI: 10.1371/journal.pone.0157123] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 05/25/2016] [Indexed: 01/01/2023] Open
Abstract
Prunus is an economically important genus well-known for cherries, plums, almonds, and peaches. The genus can be divided into three major groups based on inflorescence structure and ploidy levels: (1) the diploid solitary-flower group (subg. Prunus, Amygdalus and Emplectocladus); (2) the diploid corymbose group (subg. Cerasus); and (3) the polyploid racemose group (subg. Padus, subg. Laurocerasus, and the Maddenia group). The plastid phylogeny suggests three major clades within Prunus: Prunus-Amygdalus-Emplectocladus, Cerasus, and Laurocerasus-Padus-Maddenia, while nuclear ITS trees resolve Laurocerasus-Padus-Maddenia as a paraphyletic group. In this study, we employed sequences of the nuclear loci At103, ITS and s6pdh to explore the origins and evolution of the racemose group. Two copies of the At103 gene were identified in Prunus. One copy is found in Prunus species with solitary and corymbose inflorescences as well as those with racemose inflorescences, while the second copy (II) is present only in taxa with racemose inflorescences. The copy I sequences suggest that all racemose species form a paraphyletic group composed of four clades, each of which is definable by morphology and geography. The tree from the combined At103 and ITS sequences and the tree based on the single gene s6pdh had similar general topologies to the tree based on the copy I sequences of At103, with the combined At103-ITS tree showing stronger support in most clades. The nuclear At103, ITS and s6pdh data in conjunction with the plastid data are consistent with the hypothesis that multiple independent allopolyploidy events contributed to the origins of the racemose group. A widespread species or lineage may have served as the maternal parent for multiple hybridizations involving several paternal lineages. This hypothesis of the complex evolutionary history of the racemose group in Prunus reflects a major step forward in our understanding of diversification of the genus and has important implications for the interpretation of its phylogeny, evolution, and classification.
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Affiliation(s)
- Liang Zhao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xi-Wang Jiang
- College of Life Sciences, Jianghan University, Wuhan, Hubei, 430056, China
| | - Yun-juan Zuo
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences / Shanghai Chenshan Botanical Garden, 3888 Chenhua Road, Songjiang, Shanghai, 201602, China
| | - Xiao-Lin Liu
- School of Applied Chemistry and Biological Engineering, Weifang Engineering Vocational College, Qingzhou, Shandong, 262500, China
| | - Siew-Wai Chin
- Department of Plant Sciences, MS2, University of California Davis, Davis, California, 95616, United States of America
| | - Rosemarie Haberle
- Department of Biology, Pacific Lutheran University, Tacoma, Washington, 98447, United States of America
| | - Daniel Potter
- Department of Plant Sciences, MS2, University of California Davis, Davis, California, 95616, United States of America
| | - Zhao-Yang Chang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013–7012, United States of America
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Meeus S, Janssens S, Helsen K, Jacquemyn H. Evolutionary trends in the distylous genus Pulmonaria (Boraginaceae): Evidence of ancient hybridization and current interspecific gene flow. Mol Phylogenet Evol 2016; 98:63-73. [DOI: 10.1016/j.ympev.2015.11.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 11/28/2015] [Accepted: 11/30/2015] [Indexed: 10/22/2022]
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Gorafi YSA, Eltayeb AE, Tsujimoto H. Alteration of wheat vernalization requirement by alien chromosome-mediated transposition of MITE. BREEDING SCIENCE 2016; 66:181-90. [PMID: 27162490 PMCID: PMC4784996 DOI: 10.1270/jsbbs.66.181] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/29/2015] [Indexed: 05/27/2023]
Abstract
Under the changing climate, early flowering is advantageous to escape terminal heat and drought. Previously during evaluation of 14 chromosome introgression lines (ILs), we found three ILs that flowered a month earlier than their wheat background Chinese Spring (CS). This paper describes the cause of the early flowering in the ILs and provides insight into the evolution of spring wheat from the winter wheat. We used specific molecular markers for Vrn genes to determine its allelic composition. Phenotypic evaluations carried out under field conditions and in a growth chamber. Unlike the winter vrn-A1 allele of CS, the spring Vrn-A1 allele of the ILs had insertions of 222 and 131-bp miniature inverted-repeat transposable element (MITE) in the promoter region. Sequence analysis indicated that the 222-bp insertion is similar to an insertion in the spring genotype, Triple Dirk D. Our results ruled out any possibility of outcrossing or contamination. Without vernalization, Vrn-A1 is highly expressed in the ILs compared to CS. We attribute the early flowering of the ILs to the insertion of the MITE in the promoter of Vrn-A1. The alien chromosome might mediate this insertion.
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Affiliation(s)
- Yasir Serag Alnor Gorafi
- Arid Land Research Center, Tottori University,
1390 Hamasaka, Tottori 680-0001,
Japan
- Agricultural Research Corporation,
Wad Medani, PO Box 126,
Sudan
| | - Amin Elsadig Eltayeb
- Arid Land Research Center, Tottori University,
1390 Hamasaka, Tottori 680-0001,
Japan
| | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University,
1390 Hamasaka, Tottori 680-0001,
Japan
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Soltani A, Kumar A, Mergoum M, Pirseyedi SM, Hegstad JB, Mazaheri M, Kianian SF. Novel nuclear-cytoplasmic interaction in wheat (Triticum aestivum) induces vigorous plants. Funct Integr Genomics 2016; 16:171-82. [PMID: 26860316 DOI: 10.1007/s10142-016-0475-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 01/03/2016] [Accepted: 01/10/2016] [Indexed: 10/22/2022]
Abstract
Interspecific hybridization can be considered an accelerator of evolution, otherwise a slow process, solely dependent on mutation and recombination. Upon interspecific hybridization, several novel interactions between nuclear and cytoplasmic genomes emerge which provide additional sources of diversity. The magnitude and essence of intergenomic interactions between nuclear and cytoplasmic genomes remain unknown due to the direction of many crosses. This study was conducted to address the role of nuclear-cytoplasmic interactions as a source of variation upon hybridization. Wheat (Triticum aestivum) alloplasmic lines carrying the cytoplasm of Aegilops mutica along with an integrated approach utilizing comparative quantitative trait locus (QTL) and epigenome analysis were used to dissect this interaction. The results indicate that cytoplasmic genomes can modify the magnitude of QTL controlling certain physiological traits such as dry matter weight. Furthermore, methylation profiling analysis detected eight polymorphic regions affected by the cytoplasm type. In general, these results indicate that novel nuclear-cytoplasmic interactions can potentially trigger an epigenetic modification cascade in nuclear genes which eventually change the genetic network controlling physiological traits. These modified genetic networks can serve as new sources of variation to accelerate the evolutionary process. Furthermore, this variation can synthetically be produced by breeders in their programs to develop epigenomic-segregating lines.
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Affiliation(s)
- Ali Soltani
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Mohamed Mergoum
- Department of Crop and Soil, University of Georgia, 1109 Experiment St, Griffin, GA, 30223, USA
| | | | - Justin B Hegstad
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Mona Mazaheri
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Shahryar F Kianian
- USDA-ARS Cereal Disease Laboratory, University of Minnesota, Saint Paul, MN, 55108, USA.
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Videvall E, Sletvold N, Hagenblad J, Ågren J, Hansson B. Strong Maternal Effects on Gene Expression inArabidopsis lyrataHybrids. Mol Biol Evol 2015; 33:984-94. [DOI: 10.1093/molbev/msv342] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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47
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Fogelqvist J, Verkhozina AV, Katyshev AI, Pucholt P, Dixelius C, Rönnberg-Wästljung AC, Lascoux M, Berlin S. Genetic and morphological evidence for introgression between three species of willows. BMC Evol Biol 2015; 15:193. [PMID: 26376815 PMCID: PMC4574262 DOI: 10.1186/s12862-015-0461-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 08/20/2015] [Indexed: 01/16/2023] Open
Abstract
Background Hybridization and introgression are said to occur relatively frequently in plants, and in particular among different species of willows. However, data on the actual frequency of natural hybridization and introgression is rare. Here, we report the first fine-scale genetic analysis of a contact zone shared between the three basket willow species, Salix dasyclados, S. schwerinii and S. viminalis in the vicinity of the Lake Baikal in Southern Siberia. Individuals were sampled in fourteen populations and classified as pure species or hybrids based on a set of morphological characters. They were then genotyped at 384 nuclear SNP and four chloroplast SSR loci. The STRUCTURE and NewHybrids softwares were used to estimate the frequency and direction of hybridization using genotypic data at the nuclear SNP loci. Results As many as 19 % of the genotyped individuals were classified as introgressed individuals and these were mainly encountered in the centre of the contact zone. All introgressed individuals were backcrosses to S. viminalis or S. schwerinii and no F1 or F2 hybrids were found. The rest of the genotyped individuals were classified as pure species and formed two clusters, one with S. schwerinii individuals and the other with S. viminalis and S. dasyclados individuals. The two clusters were significantly genetically differentiated, with FST = 0.333 (0.282–0.382, p < 0.001). In contrast, for the chloroplast haplotypes, no genetic differentiation was observed as they were completely shared between the species. Based on morphological classification only 5 % of the individuals were classified as introgressed individuals, which was much less than what was detected using genotypic data. Conclusions We have discovered a new willow hybrid zone with relatively high frequency of introgressed individuals. The low frequency of F1 hybrids indicates that ongoing hybridization is limited, which could be because of the presence of reproductive barriers or simply because the conditions are not favorable for hybridization. We further conclude that in order to get a complete picture of the species composition of a hybrid zone it is necessary to use a combination of morphological characters and genetic data from both nuclear and chloroplast markers. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0461-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Johan Fogelqvist
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, P.O. Box 7080, SE-75007, Uppsala, Sweden.
| | - Alla V Verkhozina
- Siberian Institute of Plant Physiology & Biochemistry, Irkutsk-33, P.O. Box 317, 664033, Irkutsk, Russia.
| | - Alexander I Katyshev
- Siberian Institute of Plant Physiology & Biochemistry, Irkutsk-33, P.O. Box 317, 664033, Irkutsk, Russia.
| | - Pascal Pucholt
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, P.O. Box 7080, SE-75007, Uppsala, Sweden.
| | - Christina Dixelius
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, P.O. Box 7080, SE-75007, Uppsala, Sweden.
| | - Ann Christin Rönnberg-Wästljung
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, P.O. Box 7080, SE-75007, Uppsala, Sweden.
| | - Martin Lascoux
- Uppsala University, Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Norbyvägen 18D, 752 36, Uppsala, Sweden.
| | - Sofia Berlin
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, P.O. Box 7080, SE-75007, Uppsala, Sweden.
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Evren ÖH, Yüzbaştoğlu E, Dadandi MY. Determination of intra-specific genetic variation of Phlomis kurdica and Phlomis oppositiflora and investigation for the hybridity of P. × melitenense (Lamiaceae) by means of molecular markers. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Novakazi F, Inderbitzin P, Sandoya G, Hayes RJ, von Tiedemann A, Subbarao KV. The Three Lineages of the Diploid Hybrid Verticillium longisporum Differ in Virulence and Pathogenicity. PHYTOPATHOLOGY 2015; 105:662-673. [PMID: 25585057 DOI: 10.1094/phyto-10-14-0265-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Verticillium longisporum is an economically important vascular pathogen of Brassicaceae crops in different parts of the world. V. longisporum is a diploid hybrid that consists of three different lineages, each of which originated from a separate hybridization event between two different sets of parental species. We used 20 isolates representing the three V. longisporum lineages and the relative V. dahliae, and performed pathogenicity tests on 11 different hosts, including artichoke, cabbage, cauliflower, cotton, eggplant, horseradish, lettuce, linseed, oilseed rape (canola), tomato, and watermelon. V. longisporum was overall more virulent on the Brassicaceae crops than V. dahliae, which was more virulent than V. longisporum across the non-Brassicaceae crops. There were differences in virulence between the three V. longisporum lineages. V. longisporum lineage A1/D1 was the most virulent lineage on oilseed rape, and V. longisporum lineage A1/D2 was the most virulent lineage on cabbage and horseradish. We also found that on the non-Brassicaceae hosts eggplant, tomato, lettuce, and watermelon, V. longisporum was more or equally virulent than V. dahliae. This suggests that V. longisporum may have a wider potential host range than currently appreciated.
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Affiliation(s)
- Fluturë Novakazi
- First and fifth authors: Plant Pathology and Crop Protection Division, Department of Crop Sciences, Faculty of Agriculture, Georg-August University of Göttingen, Grisebachstraße 6, D-37077 Göttingen, Germany; second and seventh authors: Department of Plant Pathology, and third author: Genome Center and Department of Plant Sciences, University of California, Davis; and fourth author: United States Department of Agriculture-Agricultural Research Service, 1636 E. Alisal Street, Salinas, CA 93905
| | - Patrik Inderbitzin
- First and fifth authors: Plant Pathology and Crop Protection Division, Department of Crop Sciences, Faculty of Agriculture, Georg-August University of Göttingen, Grisebachstraße 6, D-37077 Göttingen, Germany; second and seventh authors: Department of Plant Pathology, and third author: Genome Center and Department of Plant Sciences, University of California, Davis; and fourth author: United States Department of Agriculture-Agricultural Research Service, 1636 E. Alisal Street, Salinas, CA 93905
| | - German Sandoya
- First and fifth authors: Plant Pathology and Crop Protection Division, Department of Crop Sciences, Faculty of Agriculture, Georg-August University of Göttingen, Grisebachstraße 6, D-37077 Göttingen, Germany; second and seventh authors: Department of Plant Pathology, and third author: Genome Center and Department of Plant Sciences, University of California, Davis; and fourth author: United States Department of Agriculture-Agricultural Research Service, 1636 E. Alisal Street, Salinas, CA 93905
| | - Ryan J Hayes
- First and fifth authors: Plant Pathology and Crop Protection Division, Department of Crop Sciences, Faculty of Agriculture, Georg-August University of Göttingen, Grisebachstraße 6, D-37077 Göttingen, Germany; second and seventh authors: Department of Plant Pathology, and third author: Genome Center and Department of Plant Sciences, University of California, Davis; and fourth author: United States Department of Agriculture-Agricultural Research Service, 1636 E. Alisal Street, Salinas, CA 93905
| | - Andreas von Tiedemann
- First and fifth authors: Plant Pathology and Crop Protection Division, Department of Crop Sciences, Faculty of Agriculture, Georg-August University of Göttingen, Grisebachstraße 6, D-37077 Göttingen, Germany; second and seventh authors: Department of Plant Pathology, and third author: Genome Center and Department of Plant Sciences, University of California, Davis; and fourth author: United States Department of Agriculture-Agricultural Research Service, 1636 E. Alisal Street, Salinas, CA 93905
| | - Krishna V Subbarao
- First and fifth authors: Plant Pathology and Crop Protection Division, Department of Crop Sciences, Faculty of Agriculture, Georg-August University of Göttingen, Grisebachstraße 6, D-37077 Göttingen, Germany; second and seventh authors: Department of Plant Pathology, and third author: Genome Center and Department of Plant Sciences, University of California, Davis; and fourth author: United States Department of Agriculture-Agricultural Research Service, 1636 E. Alisal Street, Salinas, CA 93905
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50
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Renaut S, Rowe HC, Ungerer MC, Rieseberg LH. Genomics of homoploid hybrid speciation: diversity and transcriptional activity of long terminal repeat retrotransposons in hybrid sunflowers. Philos Trans R Soc Lond B Biol Sci 2015; 369:rstb.2013.0345. [PMID: 24958919 DOI: 10.1098/rstb.2013.0345] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Hybridization is thought to play an important role in plant evolution by introducing novel genetic combinations and promoting genome restructuring. However, surprisingly little is known about the impact of hybridization on transposable element (TE) proliferation and the genomic response to TE activity. In this paper, we first review the mechanisms by which homoploid hybrid species may arise in nature. We then present hybrid sunflowers as a case study to examine transcriptional activity of long terminal repeat retrotransposons in the annual sunflowers Helianthus annuus, Helianthus petiolaris and their homoploid hybrid derivatives (H. paradoxus, H. anomalus and H. deserticola) using high-throughput transcriptome sequencing technologies (RNAseq). Sampling homoploid hybrid sunflower taxa revealed abundant variation in TE transcript accumulation. In addition, genetic diversity for several candidate genes hypothesized to regulate TE activity was characterized. Specifically, we highlight one candidate chromatin remodelling factor gene with a direct role in repressing TE activity in a hybrid species. This paper shows that TE amplification in hybrid lineages is more idiosyncratic than previously believed and provides a first step towards identifying the mechanisms responsible for regulating and repressing TE expansions.
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Affiliation(s)
- Sebastien Renaut
- Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Heather C Rowe
- Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Mark C Ungerer
- Division of Biology, Kansas State University, 426 Ackert Hall, Manhattan, KS 66506, USA
| | - Loren H Rieseberg
- Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 Department of Biology, Indiana University, 1001 East Third St., Bloomington, IN 47405, USA
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