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Yu J, Zhao H, Niu Y, You Y, Barrett RL, Ranaivoson RM, Rabarijaona RN, Parmar G, Yuan L, Jin X, Li P, Li J, Wen J, Chen Z, Lu L. Distinct hybridization modes in wide- and narrow-ranged lineages of Causonis (Vitaceae). BMC Biol 2023; 21:209. [PMID: 37807051 PMCID: PMC10561429 DOI: 10.1186/s12915-023-01718-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/28/2023] [Indexed: 10/10/2023] Open
Abstract
BACKGROUND Explaining contrasting patterns of distribution between related species is crucial for understanding the dynamics of biodiversity. Despite instances where hybridization and whole genome duplication (WGD) can yield detrimental outcomes, a role in facilitating the expansion of distribution range has been proposed. The Vitaceae genus Causonis exhibits great variations in species' distribution ranges, with most species in the derived lineages having a much wider range than those in the early-diverged lineages. Hybridization and WGD events have been suggested to occur in Causonis based on evidence of phylogenetic discordance. The genus, therefore, provides us with an opportunity to for explore different hybridization and polyploidization modes in lineages with contrasting species' distribution ranges. However, the evolutionary history of Causonis incorporating potential hybridization and WGD events remains to be explored. RESULTS With plastid and nuclear data from dense sampling, this study resolved the phylogenetic relationships within Causonis and revealed significant cyto-nuclear discordance. Nuclear gene tree conflicts were detected across the genus, especially in the japonica-corniculata clade, which were mainly attributed to gene flow. This study also inferred the allopolyploid origin of the core Causonis species, which promoted the accumulation of stress-related genes. Causonis was estimated to have originated in continental Asia in the early Eocene, and experienced glaciation in the early Oligocene, shortly after the divergence of the early-divergent lineages. The japonica-corniculata clade mainly diversified in the Miocene, followed by temperature declines that may have facilitated secondary contact. Species distribution modeling based on current climate change predicted that the widespread C. japonica tends to be more invasive, while the endemic C. ciliifera may be at risk of extinction. CONCLUSIONS This study presents Causonis, a genus with complex reticulate evolutionary history, as a model of how hybridization and WGD modes differ in lineages of contrasting species' geographic ranges. It is important to consider specific evolutionary histories and genetic properties of the focal species within conservation strategies.
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Affiliation(s)
- Jinren Yu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Zhao
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Yanting Niu
- China National Botanical Garden, Beijing, 100093, China
| | - Yichen You
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Russell L Barrett
- National Herbarium of New South Wales, Australian Botanic Garden, Locked Bag 6002, Mount Annan, NSW, 2567, Australia
- School of Biological, Earth and Environmental Sciences, The University of New South Wales Sydney, Kensington, NSW, 2052, Australia
| | - Rindra Manasoa Ranaivoson
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Romer Narindra Rabarijaona
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Langxing Yuan
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Xiaofeng Jin
- Zhejiang Provincial Key Laboratory of Forest Aromatic Plants-Based Healthcare Functions/School of Forestry and Bio-Technology, Zhejiang A&F University, Hangzhou, 311300, China
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jianhua Li
- Biology Department, Hope College, Holland, MI, 49423, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Zhiduan Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Limin Lu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
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The development of SSR markers from the endangered plant Tetracentron sinense Oliv. (Tetracentraceae) based on RAD–seq technique. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01109-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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Dunning LT, Olofsson JK, Papadopulos AST, Hibdige SGS, Hidalgo O, Leitch IJ, Baleeiro PC, Ntshangase S, Barker N, Jobson RW. Hybridisation and chloroplast capture between distinct Themeda triandra lineages in Australia. Mol Ecol 2022; 31:5846-5860. [PMID: 36089907 PMCID: PMC9828686 DOI: 10.1111/mec.16691] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 01/13/2023]
Abstract
Ecotypes are distinct populations within a species that are adapted to specific environmental conditions. Understanding how these ecotypes become established, and how they interact when reunited, is fundamental to elucidating how ecological adaptations are maintained. This study focuses on Themeda triandra, a dominant grassland species across Asia, Africa and Australia. It is the most widespread plant in Australia, where it has distinct ecotypes that are usually restricted to either wetter and cooler coastal regions or the drier and hotter interior. We generate a reference genome for T. triandra and use whole genome sequencing for over 80 Themeda accessions to reconstruct the evolutionary history of T. triandra and related taxa. Organelle phylogenies confirm that Australia was colonized by T. triandra twice, with the division between ecotypes predating their arrival in Australia. The nuclear genome provides evidence of differences in the dominant ploidal level and gene-flow among the ecotypes. In northern Queensland there appears to be a hybrid zone between ecotypes with admixed nuclear genomes and shared chloroplast haplotypes. Conversely, in the cracking claypans of Western Australia, there is cytonuclear discordance with individuals possessing the coastal chloroplast and interior clade nuclear genome. This chloroplast capture is potentially a result of adaptive introgression, with selection detected in the rpoC2 gene which is associated with water use efficiency. The reason that T. triandra is the most widespread plant in Australia appears to be a result of distinct ecotypic genetic variation and genome duplication, with the importance of each depending on the geographic scale considered.
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Affiliation(s)
- Luke T. Dunning
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldSheffieldUK
| | - Jill K. Olofsson
- Section for Forest, Nature and Biomass, Department of Geosciences and Natural Resource ManagementUniversity of CopenhagenFrederiksberg CDenmark
| | | | - Samuel G. S. Hibdige
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldSheffieldUK
| | - Oriane Hidalgo
- Royal Botanic GardensSurreyUK,Institut Botànic de Barcelona (IBB), CSIC‐Ajuntament de BarcelonaBarcelonaSpain
| | | | - Paulo C. Baleeiro
- Department of Biological ScienceThe University of QueenslandSt LuciaQueenslandAustralia
| | | | - Nigel Barker
- Department of Plant and Soil SciencesUniversity of PretoriaHatfieldSouth Africa
| | - Richard W. Jobson
- National Herbarium of New South Wales, Australian Institute of Botanical ScienceSydneyNew South WalesAustralia
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The Evolutionary Dynamics of the Mitochondrial tRNA in the Cichlid Fish Family. BIOLOGY 2022; 11:biology11101522. [PMID: 36290425 PMCID: PMC9598224 DOI: 10.3390/biology11101522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 11/06/2022]
Abstract
Simple Summary Cichlids are a unique example of fish diversity and species richness which have been explained by sympatric speciation at different freshwater sources in Africa. The mitochondria contribute to cell vitality by providing energy. It contains a circular genome with an established translation system that is spatially independent of the cytosolic counterpart. The current study aimed to investigate the evolutionary dynamics of the mitochondrial tRNA and its role in cichlids’ diversity. The available cichlid mitogenomes in the public database were filtered, in addition to newly sequenced accessions from a specific cichlid group known as the haplotilapiine lineage that is widely distributed in the Egyptian sector of the Nile River. Based on the comparative analysis of mitogenomic data, we identified 22 tRNA genes, in which a single gene was D-armless, while the cloverleaf secondary structure subdivided into stem-loop formations was predicted and used to define the levels of genetic divergence for the remained tRNAs. Peculiarly, in cichlids, the formation known as “T-arm” showed the lowest polymorphism levels among other structures in contrast to other organisms (e.g., scorpions). Comparing the whole family to the specific haplotilapiine lineage showed that the tryptophan tRNA was the most conserved tRNA, with signatures of possible purifying selection. Abstract The mitochondrial transfer RNA genes (tRNAs) attract more attention due to their highly dynamic and rapidly evolving nature. The current study aimed to detect and evaluate the dynamics, characteristic patterns, and variations of mitochondrial tRNAs. The study was conducted in two main parts: first, the published mitogenomic sequences of cichlids mt tRNAs have been filtered. Second, the filtered mitochondrial tRNA and additional new mitogenomes representing the most prevalent Egyptian tilapiine were compared and analyzed. Our results revealed that all 22 tRNAs of cichlids folded into a classical cloverleaf secondary structure with four domains, except for trnSGCU, missing the D domain in all cichlids. When consensus tRNAs were compared, most of the mutations were observed in the trnP at nucleotide levels (substitutions and indels), in contrast to trnLUAA. From a structural perspective, the anticodon loop and T-loop formations were the most conserved structures among all parts of the tRNA in contrast to the A-stem and D-loop formations. The trnW was the lowest polymorphic unneutral tRNA among all cichlids (both the family and the haplotilapiine lineage), in contrast with the neutral trnD that was extremely polymorphic among and within the haplotilapiine lineage species compared to other cichlids species. From a phylogenetic perspective, the trnC was extremely hypervariable and neutral tRNA in both haplotilapiine lineage and cichlids but was unable to report correct phylogenetic signal for the cichlids. In contrast to trnI and trnY, less variable neutral tRNAs that were able to cluster the haplotilapiine lineage and cichlids species as previously reported. By observing the DNA polymorphism in the coding DNA sequences (CDS), the highest affected amino acid by non-synonymous mutations was isoleucine and was equally mutated to valine and vice versa; no correlation between mutations in CDS and tRNAs was statistically found. The current study provides an insight into the mitochondrial tRNA evolution and its effect on the cichlid diversity and speciation model at the maternal level.
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5
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Zhang DQ, Ren Y, Zhang JQ. Nonadaptive molecular evolution of plastome during the speciation of Actaea purpurea and its relatives. Ecol Evol 2022; 12:e9321. [PMID: 36177132 PMCID: PMC9482002 DOI: 10.1002/ece3.9321] [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: 02/21/2022] [Revised: 05/02/2022] [Accepted: 08/30/2022] [Indexed: 11/09/2022] Open
Abstract
We have seen an explosive increase of plant plastid genome (plastome) sequences in the last decade, and the view that sequence variation in plastomes is maintained by the mutation-drift balance has been challenged by new evidence. Although comparative genomic and population-level studies provided us with evidence for positive evolution of plastid genes at both the macro- and micro-evolution levels, less studies have systematically investigated how plastomes have evolved during the speciation process. We here sequenced 13 plastomes of Actaea purpurea (P.K. Hsiao) J. Compton, and its closest relatives, and conducted a systematic survey of positive selection in their plastid genes using the McDonald-Kreitman test and codon-based methods using maximum likelihood to estimate the ratio of nonsynonymous to synonymous substitutions (ω) across a phylogeny. We found that during the speciation of A. purpurea and its relatives, all plastid genes evolved neutrally or were under purifying selection. Genome size, gene order, and number were highly conserved. Comparing to A. purpurea, plastomes of Actaea japonica and Actaea biternata had low genetic diversity, consistent with previous studies. Our work not only sheds important light on the evolutionary history of A. purpurea and its kin, but also on the evolution of plastomes during plant speciation.
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Affiliation(s)
- Dan-Qing Zhang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China College of Life Sciences, Shaanxi Normal University Xi'an China.,Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education Shaanxi Normal University Xi'an China
| | - Yi Ren
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China College of Life Sciences, Shaanxi Normal University Xi'an China.,Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education Shaanxi Normal University Xi'an China
| | - Jian-Qiang Zhang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China College of Life Sciences, Shaanxi Normal University Xi'an China.,Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education Shaanxi Normal University Xi'an China
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6
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Yan M, Liu R, Li Y, Hipp AL, Deng M, Xiong Y. Ancient events and climate adaptive capacity shaped distinct chloroplast genetic structure in the oak lineages. BMC Evol Biol 2019; 19:202. [PMID: 31684859 PMCID: PMC6829957 DOI: 10.1186/s12862-019-1523-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 10/01/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Understanding the origin of genetic variation is the key to predict how species will respond to future climate change. The genus Quercus is a species-rich and ecologically diverse woody genus that dominates a wide range of forests and woodland communities of the Northern Hemisphere. Quercus thus offers a unique opportunity to investigate how adaptation to environmental changes has shaped the spatial genetic structure of closely related lineages. Furthermore, Quercus provides a deep insight into how tree species will respond to future climate change. This study investigated whether closely related Quercus lineages have similar spatial genetic structures and moreover, what roles have their geographic distribution, ecological tolerance, and historical environmental changes played in the similar or distinct genetic structures. RESULTS Despite their close relationships, the three main oak lineages (Quercus sections Cyclobalanopsis, Ilex, and Quercus) have different spatial genetic patterns and occupy different climatic niches. The lowest level and most homogeneous pattern of genetic diversity was found in section Cyclobalanopsis, which is restricted to warm and humid climates. The highest genetic diversity and strongest geographic genetic structure were found in section Ilex, which is due to their long-term isolation and strong local adaptation. The widespread section Quercus is distributed across the most heterogeneous range of environments; however, it exhibited moderate haplotype diversity. This is likely due to regional extinction during Quaternary climatic fluctuation in Europe and North America. CONCLUSIONS Genetic variations of sections Ilex and Quercus were significantly predicted by geographic and climate variations, while those of section Cyclobalanopsis were poorly predictable by geographic or climatic diversity. Apart from the different historical environmental changes experienced by different sections, variation of their ecological or climatic tolerances and physiological traits induced varying responses to similar environment changes, resulting in distinct spatial genetic patterns.
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Affiliation(s)
- Mengxiao Yan
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, 05282, Myanmar
| | - Ruibin Liu
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Ying Li
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- The Ecological Technique and Engineering College, Shanghai Institute of Technology, Shanghai, 201418, China
| | - Andrew L Hipp
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL, 60532, USA
- The Field Museum, 1400 S Lake Shore Drive, Chicago, IL, 60605, USA
| | - Min Deng
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, 05282, Myanmar.
| | - Yanshi Xiong
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
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7
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Magdy M, Ou L, Yu H, Chen R, Zhou Y, Hassan H, Feng B, Taitano N, van der Knaap E, Zou X, Li F, Ouyang B. Pan-plastome approach empowers the assessment of genetic variation in cultivated Capsicum species. HORTICULTURE RESEARCH 2019; 6:108. [PMID: 31645963 PMCID: PMC6804749 DOI: 10.1038/s41438-019-0191-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/19/2019] [Accepted: 08/03/2019] [Indexed: 05/19/2023]
Abstract
Pepper species (Capsicum spp.) are widely used as food, spice, decoration, and medicine. Despite the recent old-world culinary impact, more than 50 commercially recognized pod types have been recorded worldwide from three taxonomic complexes (A, B, and P). The current study aimed to apply a pan-plastome approach to resolve the plastomic boundaries among those complexes and identify effective loci for the taxonomical resolution and molecular identification of the studied species/varieties. High-resolution pan-plastomes of five species and two varieties were assembled and compared from 321 accessions. Phyloplastomic and network analyses clarified the taxonomic position of the studied species/varieties and revealed a pronounced number of accessions to be the rare and endemic species, C. galapagoense, that were mistakenly labeled as C. annuum var. glabriusculum among others. Similarly, some NCBI-deposited plastomes were clustered differently from their labels. The rpl23-trnI intergenic spacer contained a 44 bp tandem repeat that, in addition to other InDels, was capable of discriminating the investigated Capsicum species/varieties. The rps16-trnQ/rbcL-accD/ycf3-trnS gene set was determined to be sufficiently polymorphic to retrieve the complete phyloplastomic signal among the studied Capsicum spp. The pan-plastome approach was shown to be useful in resolving the taxonomical complexes, settling the incomplete lineage sorting conflict and developing a molecular marker set for Capsicum spp. identification.
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Affiliation(s)
- Mahmoud Magdy
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, 430070 Wuhan, China
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo, 11241 Egypt
| | - Lijun Ou
- College of Horticulture and Landscape, Hunan Agricultural University, 410128 Changsha, China
| | - Huiyang Yu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, 430070 Wuhan, China
| | - Rong Chen
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, 430070 Wuhan, China
| | - Yuhong Zhou
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, 430070 Wuhan, China
| | - Heba Hassan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, 430070 Wuhan, China
| | - Bihong Feng
- College of Agriculture, Guangxi University, 530004 Nanning, China
| | - Nathan Taitano
- Department of Horticulture, College of Agriculture & Environmental Sciences, University of Georgia, Athens, GA 30602 USA
| | - Esther van der Knaap
- Department of Horticulture, College of Agriculture & Environmental Sciences, University of Georgia, Athens, GA 30602 USA
| | - Xuexiao Zou
- College of Horticulture and Landscape, Hunan Agricultural University, 410128 Changsha, China
| | - Feng Li
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, 430070 Wuhan, China
| | - Bo Ouyang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, 430070 Wuhan, China
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Yan M, Xiong Y, Liu R, Deng M, Song J. The Application and Limitation of Universal Chloroplast Markers in Discriminating East Asian Evergreen Oaks. FRONTIERS IN PLANT SCIENCE 2018; 9:569. [PMID: 29868047 PMCID: PMC5952231 DOI: 10.3389/fpls.2018.00569] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/11/2018] [Indexed: 05/10/2023]
Abstract
The East Asian subtropics mostly occupied by evergreen broad-leaved forests (EBLFs), is one of the global diversity centers for evergreen oaks. Evergreen oaks are keystone canopy trees in EBLFs with important ecosystem function and crucial significance for regional biodiversity conservation. However, the species composition and diversity of Asian evergreen oaks are poorly understood. Here, we test whether the four chloroplast markers atpI-atpH, matK, psbA-trnH, and ycf1, can discriminate the two evergreen oak sections in Asia - Cyclobalanopsis and Ilex. Two hundred and seventy-two individuals representing 57 species were scanned and 17 species from other oaks sections were included for phylogenetic reconstruction. The genetic diversity of the Quercus sections was also compared. Overall, we found that universal chloroplast DNA (cpDNA) barcoding markers could resolve two clades in Quercus, i.e., subgenus Cerris (Old World Clade) and subgenus Quercus (New World Clade). The chloroplast markers distinguished the main sections, with few exceptions. Each cpDNA region showed no barcoding gap and none of them provided good resolution at the species level. The best species resolution (27.78%) was obtained when three or four markers were combined and analyzed using BLAST. The high conservation of the cpDNA and complicated evolutionary patterns, due to incomplete lineage sorting, interspecific hybridization and introgressions may hinder the ability of cpDNA markers to discriminate different species. When comparing diversification pattern across Quercus sections (Cyclobalanopsis, Ilex, Cerris, Quercus, and Protobalanus), we found that section Ilex was the most genetically diverse, and section Cyclobalanopsis was lower genetically diverse. This diversification pattern may have resulted from the interplay of the Eurasia Cenozoic tectonic movements, climate changes and different niches of their ancestral lineages.
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Affiliation(s)
- Mengxiao Yan
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Yanshi Xiong
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Ruibin Liu
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Min Deng
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Jiaojiao Song
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, China
- College of Life Sciences, Shangrao Normal University, Shangrao, China
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9
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Feurtey A, Gladieux P, Hood ME, Snirc A, Cornille A, Rosenthal L, Giraud T. Strong phylogeographic co-structure between the anther-smut fungus and its white campion host. THE NEW PHYTOLOGIST 2016; 212:668-679. [PMID: 27500396 DOI: 10.1111/nph.14125] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 06/18/2016] [Indexed: 06/06/2023]
Abstract
Although congruence between host and pathogen phylogenies has been extensively investigated, the congruence between host and pathogen genetic structures at the within-species level has received little attention. Using an unprecedented and comprehensive collection of associated plant-pathogen samples, we investigated the degree of congruence between the genetic structures across Europe of two evolutionary and ecological model organisms, the anther-smut pathogen Microbotryum lychnidis-dioicae and its host plant Silene latifolia. We demonstrated a significant and particularly strong level of host-pathogen co-structure, with three main genetic clusters displaying highly similar spatial ranges in Western Europe, Eastern Europe and Italy, respectively. Correcting for the geographical component of genetic variation, significant correlations were still found between the genetic distances of anther-smut and host populations. Inoculation experiments suggested plant local adaptation, at the cluster level, for resistance to pathogens. These findings indicate that the pathogen remained isolated in the same fragmented southern refugia as its host plant during the last glaciation, and that little long-distance dispersal has occurred since the recolonization of Europe for either the plant or the pathogen, despite their known ability to travel across continents. This, together with the inoculation results, suggests that coevolutionary and competitive processes may be drivers of host-pathogen co-structure.
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Affiliation(s)
- Alice Feurtey
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, 91400, France
| | - Pierre Gladieux
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, 91400, France
- UMR BGPI, INRA, Montpellier, 34398, France
| | - Michael E Hood
- Department of Biology, Amherst College, Amherst, MA, 01002, USA
| | - Alodie Snirc
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, 91400, France
| | - Amandine Cornille
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, 91400, France
| | - Lisa Rosenthal
- Department of Biology, Amherst College, Amherst, MA, 01002, USA
| | - Tatiana Giraud
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, 91400, France.
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10
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Egamberdiev SS, Saha S, Salakhutdinov I, Jenkins JN, Deng D, Y Abdurakhmonov I. Comparative assessment of genetic diversity in cytoplasmic and nuclear genome of upland cotton. Genetica 2016; 144:289-306. [PMID: 27155886 DOI: 10.1007/s10709-016-9898-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 04/07/2016] [Indexed: 02/05/2023]
Abstract
The importance of the cytoplasmic genome for many economically important traits is well documented in several crop species, including cotton. There is no report on application of cotton chloroplast specific SSR markers as a diagnostic tool to study genetic diversity among improved Upland cotton lines. The complete plastome sequence information in GenBank provided us an opportunity to report on 17 chloroplast specific SSR markers using a cost-effective data mining strategy. Here we report the comparative analysis of genetic diversity among a set of 42 improved Upland cotton lines using SSR markers specific to chloroplast and nuclear genome, respectively. Our results revealed that low to moderate level of genetic diversity existed in both nuclear and cytoplasm genome among this set of cotton lines. However, the specific estimation suggested that genetic diversity is lower in cytoplasmic genome compared to the nuclear genome among this set of Upland cotton lines. In summary, this research is important from several perspectives. We detected a set of cytoplasm genome specific SSR primer pairs by using a cost-effective data mining strategy. We reported for the first time the genetic diversity in the cytoplasmic genome within a set of improved Upland cotton accessions. Results revealed that the genetic diversity in cytoplasmic genome is narrow, compared to the nuclear genome within this set of Upland cotton accessions. Our results suggested that most of these polymorphic chloroplast SSRs would be a valuable complementary tool in addition to the nuclear SSR in the study of evolution, gene flow and genetic diversity in Upland cotton.
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Affiliation(s)
- Sharof S Egamberdiev
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan, 111215
| | - Sukumar Saha
- Crop Science Research Laboratory, Genetics and Sustainable Agriculture Research Unit, USDA-ARS, Mississippi State, MS, 39762, USA.
| | - Ilkhom Salakhutdinov
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan, 111215
| | - Johnie N Jenkins
- Crop Science Research Laboratory, Genetics and Sustainable Agriculture Research Unit, USDA-ARS, Mississippi State, MS, 39762, USA
| | - Dewayne Deng
- Crop Science Research Laboratory, Genetics and Sustainable Agriculture Research Unit, USDA-ARS, Mississippi State, MS, 39762, USA
| | - Ibrokhim Y Abdurakhmonov
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan, 111215
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11
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Hu XS, Filatov DA. The large-X effect in plants: increased species divergence and reduced gene flow on the Silene X-chromosome. Mol Ecol 2016; 25:2609-19. [PMID: 26479725 DOI: 10.1111/mec.13427] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 10/12/2015] [Accepted: 10/15/2015] [Indexed: 12/25/2022]
Abstract
The disproportionately large involvement of the X-chromosome in the isolation of closely related species (the large-X effect) has been reported for many animals, where X-linked genes are mostly hemizygous in the heterogametic sex. The expression of deleterious recessive mutations is thought to drive the frequent involvement of the X-chromosome in hybrid sterility, as well as to reduce interspecific gene flow for X-linked genes. Here, we evaluate the role of the X-chromosome in the speciation of two closely related plant species - the white and red campions (Silene latifolia and S. dioica) - that hybridize widely across Europe. The two species evolved separate sexes and sex chromosomes relatively recently (~10(7) years), and unlike most animal species, most X-linked genes have intact Y-linked homologs. We demonstrate that the X-linked genes show a very small and insignificant amount of interspecific gene flow, while gene flow involving autosomal loci is significant and sufficient to homogenize the gene pools of the two species. These findings are consistent with the hypothesis of the large-X effect in Silene and comprise the first report of this effect in plants. Nonhemizygosity of many X-linked genes in Silene males indicates that exposure of recessive mutations to selection may not be essential for the occurrence of the large-X effect. Several possible causes of the large-X effect in Silene are discussed.
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Affiliation(s)
- Xin-Sheng Hu
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX13RB, UK
| | - Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX13RB, UK
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12
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Genetic and morphological diversity in Cousinia tabrisiana (Asteraceae) populations. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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13
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Twyford AD. Testing evolutionary hypotheses for DNA barcoding failure in willows. Mol Ecol 2014; 23:4674-6. [PMID: 25263402 DOI: 10.1111/mec.12892] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/03/2014] [Accepted: 08/18/2014] [Indexed: 12/26/2022]
Abstract
The goal of DNA barcoding is to enable the rapid identification of taxa from short diagnostic DNA sequence profiles. But how feasible is this objective when many evolutionary processes, such as hybridization and selective sweeps, cause alleles to be shared among related taxa? In this issue of Molecular Ecology, Percy et al. (2014) test the full suite of seven candidate plant barcoding loci in a broad geographic sample of willow species. They show exceptional plastid haplotype sharing between species across continents, with most taxa not possessing a unique barcode sequence. Using population genetic and molecular dating analyses, they implicate hybridization and selective sweeps, but not incomplete lineage sorting, as the historical processes causing widespread haplotype sharing among willow taxa. This study represents an exceptional case of how poorly barcoding can perform, and highlights methodological issues using universal organellar regions for species identification.
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Affiliation(s)
- Alex D Twyford
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA; Institute of Evolutionary Biology, Ashworth Laboratories, The University of Edinburgh, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK
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14
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Bock DG, Andrew RL, Rieseberg LH. On the adaptive value of cytoplasmic genomes in plants. Mol Ecol 2014; 23:4899-911. [PMID: 25223488 DOI: 10.1111/mec.12920] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 09/08/2014] [Accepted: 09/10/2014] [Indexed: 01/30/2023]
Abstract
Is DNA variation maintained in organelle genomes selectively neutral? The answer to this question has important implications for many aspects of ecology and evolution. While traditionally the answer has been 'yes', recent studies in animals have shown that, on the contrary, mitochondrial DNA polymorphism is frequently adaptive. In plants, however, the neutrality assumption has not been strongly challenged. Here, we begin with a critical evaluation of arguments in favour of this long-held view. We then discuss the latest empirical evidence for the opposing prediction that sequence variation in plant cytoplasmic genomes is frequently adaptive. While outstanding research progress is being made towards understanding this fundamental topic, we highlight the need for studies that combine information ranging from field experiments to physiology to molecular evolutionary biology. Such an interdisciplinary approach provides a means for determining the frequency, drivers and evolutionary significance of adaptive organelle DNA variation.
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Affiliation(s)
- Dan G Bock
- Department of Botany, Biodiversity Research Centre, University of British Columbia, 3529-6270 University Blvd., Vancouver, British Columbia, Canada, V6T 1Z4
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15
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Lexer C, Wüest RO, Mangili S, Heuertz M, Stölting KN, Pearman PB, Forest F, Salamin N, Zimmermann NE, Bossolini E. Genomics of the divergence continuum in an African plant biodiversity hotspot, I: drivers of population divergence inRestio capensis(Restionaceae). Mol Ecol 2014; 23:4373-86. [DOI: 10.1111/mec.12870] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 06/18/2014] [Accepted: 07/09/2014] [Indexed: 01/30/2023]
Affiliation(s)
- C. Lexer
- Unit of Ecology & Evolution; Department of Biology; University of Fribourg; Fribourg CH-1700 Switzerland
| | - R. O. Wüest
- Landscape Dynamics Unit; Swiss Federal Research Institute WSL; Birmensdorf CH-8903 Switzerland
- Univ. Grenoble Alpes; LECA; Grenoble F-38000 France
- CNRS; LECA; Grenoble F-38000 France
| | - S. Mangili
- Unit of Ecology & Evolution; Department of Biology; University of Fribourg; Fribourg CH-1700 Switzerland
| | - M. Heuertz
- Unit of Ecology & Evolution; Department of Biology; University of Fribourg; Fribourg CH-1700 Switzerland
- INIA Forest Research Centre; carretera de A Coruña km 7.5 E-28040 Madrid Spain
| | - K. N. Stölting
- Unit of Ecology & Evolution; Department of Biology; University of Fribourg; Fribourg CH-1700 Switzerland
| | - P. B. Pearman
- Landscape Dynamics Unit; Swiss Federal Research Institute WSL; Birmensdorf CH-8903 Switzerland
| | - F. Forest
- Jodrell Laboratory; Royal Botanic Gardens; Kew Richmond Surrey TW 3DS U.K
| | - N. Salamin
- Department of Ecology & Evolution; University of Lausanne; CH-1015 Lausanne Switzerland
- Swiss Institute of Bioinformatics; Quartier Sorge CH-1015 Lausanne Switzerland
| | - N. E. Zimmermann
- Landscape Dynamics Unit; Swiss Federal Research Institute WSL; Birmensdorf CH-8903 Switzerland
| | - E. Bossolini
- Unit of Ecology & Evolution; Department of Biology; University of Fribourg; Fribourg CH-1700 Switzerland
- Bayer CropScience; Technologiepark 38 9052 Gent Belgium
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16
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Percy DM, Argus GW, Cronk QC, Fazekas AJ, Kesanakurti PR, Burgess KS, Husband BC, Newmaster SG, Barrett SC, Graham SW. Understanding the spectacular failure of DNA barcoding in willows (Salix): Does this result from a trans-specific selective sweep? Mol Ecol 2014; 23:4737-56. [DOI: 10.1111/mec.12837] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 05/29/2014] [Accepted: 06/04/2014] [Indexed: 02/04/2023]
Affiliation(s)
- Diana M. Percy
- Department of Botany; University of British Columbia; Vancouver BC Canada V6T 1Z4
- Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada V6T 1Z4
| | - George W. Argus
- Canadian Museum of Nature; PO Box 3443 Stn “D” Ottawa ON Canada K1P 6P4
| | - Quentin C. Cronk
- Department of Botany; University of British Columbia; Vancouver BC Canada V6T 1Z4
- Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada V6T 1Z4
| | - Aron J. Fazekas
- Department of Integrative Biology; University of Guelph; Guelph ON Canada N1G 2W1
| | | | - Kevin S. Burgess
- Department of Biology; Columbus State University; Columbus GA 31907-5645 USA
| | - Brian C. Husband
- Department of Integrative Biology; University of Guelph; Guelph ON Canada N1G 2W1
| | - Steven G. Newmaster
- Department of Integrative Biology; University of Guelph; Guelph ON Canada N1G 2W1
| | - Spencer C.H. Barrett
- Department of Ecology & Evolutionary Biology; University of Toronto; 25 Willcocks Street Toronto ON Canada M5S 3B2
| | - Sean W. Graham
- Department of Botany; University of British Columbia; Vancouver BC Canada V6T 1Z4
- Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada V6T 1Z4
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17
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Herrera-Arroyo ML, Sork VL, González-Rodríguez A, Rocha-Ramírez V, Vega E, Oyama K. Seed-mediated connectivity among fragmented populations of Quercus castanea (Fagaceae) in a Mexican landscape. AMERICAN JOURNAL OF BOTANY 2013; 100:1663-1671. [PMID: 23942083 DOI: 10.3732/ajb.1200396] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
PREMISE OF STUDY Anthropogenic fragmentation is an ongoing process in many forested areas that may create loss of connectivity among tree populations and constitutes a serious threat to ecological and genetic processes. We tested the central hypothesis that seed dispersal mitigates the impact of fragmentation by comparing connectivity and genetic diversity of adult vs. seedling populations in recently fragmented populations of the Mexican red oak Quercus castanea. METHODS Adult individuals, established before fragmentation, and seedlings, established after fragmentation, were sampled at 33 forest fragments of variable size (0.2 to 294 ha) within the Cuitzeo basin, Michoacán state, and genotyped using seven highly polymorphic chloroplast microsatellite markers (cpSSRs). To test whether seed dispersal retains connectivity among fragmented populations, we compared genetic diversity and connectivity networks between adults and progeny and determined the effect of fragment size on these values. KEY RESULTS Seventy haplotypes were identified, 63 in the adults and 60 in the seedlings, with average within-population diversity (hS) values of 0.624 in the adults and 0.630 in the seedlings. A positive correlation of genetic diversity values with fragment size was found in the seedling populations but not in the adult populations. The network connectivity analysis revealed lower connectivity among seedling populations than among adults. The number of connections (edges) as well as other network properties, such as betweenness centrality, node degree and closeness, were significantly lower in the seedlings network. CONCLUSIONS Habitat fragmentation in this landscape is disrupting seed-dispersal-mediated genetic connectivity among extant populations.
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Affiliation(s)
- M Luisa Herrera-Arroyo
- Centro de Investigaciones en Ecosistemas. Universidad Nacional Autónoma de México UNAM, Antigua carretera a Pátzcuaro no. 8701, Col. Ex-hacienda San José de la Huerta, Morelia 58190 Michoacán, México
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18
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Frankham R. How closely does genetic diversity in finite populations conform to predictions of neutral theory? Large deficits in regions of low recombination. Heredity (Edinb) 2012; 108:167-78. [PMID: 21878983 PMCID: PMC3282390 DOI: 10.1038/hdy.2011.66] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2010] [Revised: 06/21/2011] [Accepted: 06/27/2011] [Indexed: 11/09/2022] Open
Abstract
Levels of genetic diversity in finite populations are crucial in conservation and evolutionary biology. Genetic diversity is required for populations to evolve and its loss is related to inbreeding in random mating populations, and thus to reduced population fitness and increased extinction risk. Neutral theory is widely used to predict levels of genetic diversity. I review levels of genetic diversity in finite populations in relation to predictions of neutral theory. Positive associations between genetic diversity and population size, as predicted by neutral theory, are observed for microsatellites, allozymes, quantitative genetic variation and usually for mitochondrial DNA (mtDNA). However, there are frequently significant deviations from neutral theory owing to indirect selection at linked loci caused by balancing selection, selective sweeps and background selection. Substantially lower genetic diversity than predicted under neutrality was found for chromosomes with low recombination rates and high linkage disequilibrium (compared with 'normally' recombining chromosomes within species and adjusted for different copy numbers and mutation rates), including W (median 100% lower) and Y (89% lower) chromosomes, dot fourth chromosomes in Drosophila (94% lower) and mtDNA (67% lower). Further, microsatellite genetic and allelic diversity were lost at 12 and 33% faster rates than expected in populations adapting to captivity, owing to widespread selective sweeps. Overall, neither neutral theory nor most versions of the genetic draft hypothesis are compatible with all empirical results.
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Affiliation(s)
- R Frankham
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia.
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19
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Muir G, Dixon CJ, Harper AL, Filatov DA. Dynamics of drift, gene flow, and selection during speciation in Silene. Evolution 2012; 66:1447-58. [PMID: 22519783 DOI: 10.1111/j.1558-5646.2011.01529.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mechanics of speciation with gene flow are still unclear. Disparity among genes in population differentiation (F(ST)) between diverging species is often interpreted as evidence for semipermeable species boundaries, with selection preventing "key" genes from introgressing despite ongoing gene flow. However, F(ST) can remain high before it reaches equilibrium between the lineage sorting of species divergence and the homogenizing effects of gene flow (via secondary contact). Thus, when interpreting F(ST), the dynamics of drift, gene flow, and selection need to be taken into account. We illustrate this view with a multigenic analyses of gene flow and selection in three closely related Silene species, S. latifolia, S. dioica, and S. diclinis. We report that although S. diclinis appears to have evolved in allopatry, isolation with (bidirectional) gene flow between S. latifolia and S. dioica is likely, perhaps as a result of parapatric speciation followed by more extensive sympatry. Interestingly, we detected the signatures of apparently independent instances of positive selection at the same locus in S. latifolia and S. dioica. Despite gene flow between the species, the adaptive alleles have not crossed the species boundary, suggesting that this gene has independently undergone species-specific (diversifying or parallel) selection.
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Affiliation(s)
- Graham Muir
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, United Kingdom.
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20
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Muir G, Bergero R, Charlesworth D, Filatov DA. Does local adaptation cause high population differentiation of Silene latifolia Y chromosomes? Evolution 2011; 65:3368-80. [PMID: 22133212 DOI: 10.1111/j.1558-5646.2011.01410.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Natural selection can reduce the effective population size of the nonrecombining Y chromosome, whereas local adaptation of Y-linked genes can increase the population divergence and overall intra-species polymorphism of Y-linked sequences. The plant Silene latifolia evolved a Y chromosome relatively recently, and most known X-linked genes have functional Y homologues, making the species interesting for comparisons of X- and Y-linked diversity and subdivision. Y-linked genes show higher population differentiation, compared to X-linked genes, and this might be maintained by local adaptation in Y-linked genes (or low sequence diversity). Here we attempt to test between these causes by investigating DNA polymorphism and population differentiation using a larger set of Y-linked and X-linked S. latifolia genes (than used previously), and show that net sequence divergence for Y-linked sequences (measured by D(a) , also known as δ) is low, and not consistently higher than X-linked genes. This does not support local adaptation, instead, the higher values of differentiation measures for the Y-linked genes probably result largely from reduced total variation on the Y chromosome, which in turn reflect deterministic processes lowering effective population sizes of evolving Y-chromosomes.
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Affiliation(s)
- Graham Muir
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, United Kingdom.
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21
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Marais GAB, Forrest A, Kamau E, Käfer J, Daubin V, Charlesworth D. Multiple nuclear gene phylogenetic analysis of the evolution of dioecy and sex chromosomes in the genus Silene. PLoS One 2011; 6:e21915. [PMID: 21853022 PMCID: PMC3154253 DOI: 10.1371/journal.pone.0021915] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 06/08/2011] [Indexed: 11/18/2022] Open
Abstract
In the plant genus Silene, separate sexes and sex chromosomes are believed to have evolved twice. Silene species that are wholly or largely hermaphroditic are assumed to represent the ancestral state from which dioecy evolved. This assumption is important for choice of outgroup species for inferring the genetic and chromosomal changes involved in the evolution of dioecy, but is mainly based on data from a single locus (ITS). To establish the order of events more clearly, and inform outgroup choice, we therefore carried out (i) multi-nuclear-gene phylogenetic analyses of 14 Silene species (including 7 hermaphrodite or gynodioecious species), representing species from both Silene clades with dioecious members, plus a more distantly related outgroup, and (ii) a BayesTraits character analysis of the evolution of dioecy. We confirm two origins of dioecy within this genus in agreement with recent work on comparing sex chromosomes from both clades with dioecious species. We conclude that sex chromosomes evolved after the origin of Silene and within a clade that includes only S. latifolia and its closest relatives. We estimate that sex chromosomes emerged soon after the split with the ancestor of S. viscosa, the probable closest non-dioecious S. latifolia relative among the species included in our study.
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Affiliation(s)
- Gabriel A B Marais
- Laboratoire de Biométrie et Biologie évolutive, UMR5558, Université Lyon 1, Centre National de la Recherche Scientifique, Villeurbanne, France.
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22
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Rautenberg A, Hathaway L, Oxelman B, Prentice HC. Geographic and phylogenetic patterns in Silene section Melandrium (Caryophyllaceae) as inferred from chloroplast and nuclear DNA sequences. Mol Phylogenet Evol 2010; 57:978-91. [PMID: 20723610 DOI: 10.1016/j.ympev.2010.08.003] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Revised: 07/30/2010] [Accepted: 08/07/2010] [Indexed: 11/28/2022]
Abstract
The phylogenetic relationships between the five dioecious species in Silene section Melandrium (Caryophyllaceae) and their putative hermaphrodite relatives are investigated based on an extensive geographic and taxonomic sample, using DNA sequence data from the chloroplast genome and the nuclear ribosomal ITS region. The hermaphrodite S. noctiflora (the type species of section Elisanthe) is distantly related to the dioecious species. With the exception of chloroplast sequences in one S. latifolia population from Turkey, the dioecious taxa form a strongly supported monophyletic group (Silene section Melandrium). The phylogenetic structure within section Melandrium differs between chloroplast and nuclear sequences. While there is extensive sharing of chloroplast haplotypes among all the dioecious species (the observed patterns reflect geographic structure), the nuclear ITS phylogeny shows a higher degree of taxonomic structure. Chloroplast-sharing by the section Melandrium species is most plausibly explained by a history of hybridization and extensive backcrossing.
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Affiliation(s)
- Anja Rautenberg
- Department of Systematic Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden.
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23
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Ghada B, Ahmed BA, Khaled C, Olfa S, Messaoud M, Mokhtar T, Amel SH. Molecular evolution of chloroplast DNA in fig (Ficus carica L.): Footprints of sweep selection and recent expansion. BIOCHEM SYST ECOL 2010. [DOI: 10.1016/j.bse.2010.06.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Qiu S, Bergero R, Forrest A, Kaiser VB, Charlesworth D. Nucleotide diversity in Silene latifolia autosomal and sex-linked genes. Proc Biol Sci 2010; 277:3283-90. [PMID: 20519224 DOI: 10.1098/rspb.2010.0606] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The plant Silene latifolia has separate sexes and sex chromosomes, and is of interest for studying the early stages of sex chromosome evolution, especially the evolution of non-recombining regions on the Y chromosome. Hitch-hiking processes associated with ongoing genetic degeneration of the non-recombining Y chromosome are predicted to reduce Y-linked genes' effective population sizes, and S. latifolia Y-linked genes indeed have lower diversity than X-linked ones. We tested whether this represents a true diversity reduction on the Y, versus the alternative possibility, elevated diversity at X-linked genes, by collecting new data on nucleotide diversity for autosomal genes, which had previously been little studied. We find clear evidence that Y-linked genes have reduced diversity. However, another alternative explanation for a low Y effective size is a high variance in male reproductive success. Autosomal genes should then also have lower diversity than expected, relative to the X, but this is not found in our loci. Taking into account the higher mutation rate of Y-linked genes, their low sequence diversity indicates a strong effect of within-population hitch-hiking on the Y chromosome.
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Affiliation(s)
- Suo Qiu
- Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, Ashworth Laboratory, West Mains Road, Edinburgh EH9 3JT, UK
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25
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Barluenga M, Austerlitz F, Elzinga JA, Teixeira S, Goudet J, Bernasconi G. Fine-scale spatial genetic structure and gene dispersal in Silene latifolia. Heredity (Edinb) 2010; 106:13-24. [PMID: 20389310 DOI: 10.1038/hdy.2010.38] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Plants are sessile organisms, often characterized by limited dispersal. Seeds and pollen are the critical stages for gene flow. Here we investigate spatial genetic structure, gene dispersal and the relative contribution of pollen vs seed in the movement of genes in a stable metapopulation of the white campion Silene latifolia within its native range. This short-lived perennial plant is dioecious, has gravity-dispersed seeds and moth-mediated pollination. Direct measures of pollen dispersal suggested that large populations receive more pollen than small isolated populations and that most gene flow occurs within tens of meters. However, these studies were performed in the newly colonized range (North America) where the specialist pollinator is absent. In the native range (Europe), gene dispersal could fall on a different spatial scale. We genotyped 258 individuals from large and small (15) subpopulations along a 60 km, elongated metapopulation in Europe using six highly variable microsatellite markers, two X-linked and four autosomal. We found substantial genetic differentiation among subpopulations (global F(ST)=0.11) and a general pattern of isolation by distance over the whole sampled area. Spatial autocorrelation revealed high relatedness among neighboring individuals over hundreds of meters. Estimates of gene dispersal revealed gene flow at the scale of tens of meters (5-30 m), similar to the newly colonized range. Contrary to expectations, estimates of dispersal based on X and autosomal markers showed very similar ranges, suggesting similar levels of pollen and seed dispersal. This may be explained by stochastic events of extensive seed dispersal in this area and limited pollen dispersal.
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Affiliation(s)
- M Barluenga
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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26
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Smith DR, Lee RW. Nucleotide diversity of the Chlamydomonas reinhardtii plastid genome: addressing the mutational-hazard hypothesis. BMC Evol Biol 2009; 9:120. [PMID: 19473533 PMCID: PMC2698885 DOI: 10.1186/1471-2148-9-120] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Accepted: 05/27/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The mutational-hazard hypothesis argues that the noncoding-DNA content of a genome is a consequence of the mutation rate (mu) and the effective number of genes per locus in the population (N(g)). The hypothesis predicts that genomes with a high N(g)mu will be more compact than those with a small N(g)mu. Approximations of N(g)mu can be gained by measuring the nucleotide diversity at silent sites (pi(silent)). We addressed the mutation-hazard hypothesis apropos plastid-genome evolution by measuring pi(silent) of the Chlamydomonas reinhardtii plastid DNA (ptDNA), the most noncoding-DNA-dense plastid genome observed to date. The data presented here in conjunction with previously published values of pi(silent) for the C. reinhardtii mitochondrial and nuclear genomes, which are respectively compact and bloated, allow for a complete analysis of nucleotide diversity and genome compactness in all three genetic compartments of this model organism. RESULTS In C. reinhardtii, the mean estimate of pi(silent) for the ptDNA (14.5 x 10(-3)) is less than that of the nuclear DNA (32 x 10(-3)) and greater than that of the mitochondrial DNA (8.5 x 10(-3)). On average, C. reinhardtii has approximately 4 times more silent-site ptDNA diversity than the mean value reported for land plants, which have more compact plastid genomes. The silent-site nucleotide diversity of the different ptDNA loci that were studied varied significantly: from 0 to 71 x 10(-3) for synonymous sites and from 0 to 42 x 10(-3) for intergenic regions. CONCLUSION Our findings on silent-site ptDNA diversity are inconsistent with what would be expected under the mutational-hazard hypothesis and go against the documented trend in other systems of pi(silent) positively correlating with genome compactness. Overall, we highlight the lack of reliable nucleotide-diversity measurements for ptDNA and hope that the values presented here will act as sound data for future research concerning the mutational-hazard hypothesis and plastid evolution in general.
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Affiliation(s)
- David Roy Smith
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
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27
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Ujvari B, Dowton M, Madsen T. Population genetic structure, gene flow and sex-biased dispersal in frillneck lizards (Chlamydosaurus kingii). Mol Ecol 2009; 17:3557-64. [PMID: 19160482 DOI: 10.1111/j.1365-294x.2008.03849.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
By using both mitochondrial and nuclear multiloci markers, we explored population genetic structure, gene flow and sex-specific dispersal of frillneck lizards (Chlamydosaurus kingii) sampled at three locations, separated by 10 to 50 km, in a homogenous savannah woodland in tropical Australia. Apart from a recombinant lizard, the mitochondrial analyses revealed two nonoverlapping haplotypes/populations, while the nuclear markers showed that the frillneck lizards represented three separate clusters/populations. Due to the small population size of the mtDNA, fixation may occur via founder effects and/or drift. We therefore suggest that either of these two processes, or a combination of the two, are the most likely causes of the discordant results obtained from the mitochondrial and the nuclear markers. In contrast to the nonoverlapping mitochondrial haplotypes, in 12 out of 74 lizards, mixed nuclear genotypes were observed, hence revealing a limited nuclear gene flow. Although gene flow should ultimately result in a blending of the populations, we propose that the distinct nuclear population structure is maintained by frequent fires resulting in local bottlenecks, and concomitant spatial separation of the frillneck lizard populations. Limited mark-recapture data and the difference in distribution of the mitochondrial and nuclear markers suggest that the mixed nuclear genotypes were caused by juvenile male-biased dispersal.
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Affiliation(s)
- Beata Ujvari
- School of Biological Sciences, University of Wollongong, NSW 2522, Australia
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OYAMA RK, VOLZ SM, RENNER SS. A sex-linked SCAR marker in Bryonia dioica (Cucurbitaceae), a dioecious species with XY sex-determination and homomorphic sex chromosomes. J Evol Biol 2009; 22:214-24. [DOI: 10.1111/j.1420-9101.2008.01641.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Recent spread of a retrotransposon in the Silene latifolia genome, apart from the Y chromosome. Genetics 2008; 181:811-7. [PMID: 19064703 DOI: 10.1534/genetics.108.099267] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transposable elements often accumulate in nonrecombining regions, such as Y chromosomes. Contrary to this trend, a new Silene retrotransposon described here, has spread recently all over the genome of plant Silene latifolia, except its Y chromosome. This coincided with the latest steps of sex chromosome evolution in this species.
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