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Zhang H, Liu H, Han X. Traits-based approach: leveraging genome size in plant-microbe interactions. Trends Microbiol 2024; 32:333-341. [PMID: 37925351 DOI: 10.1016/j.tim.2023.10.004] [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: 06/21/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 11/06/2023]
Abstract
Trait-based approaches have gained growing interest in studying plant-microbe interactions. However, current traits normally considered (e.g., morphological, physiological, or chemical traits) are biased towards those showing large intraspecific variations, necessitating the identification of fewer plastic traits that differ between species. Here, we propose using genome size (the amount of DNA in the nucleus of a cell) as a suitable trait for studying plant-microbiome interactions due to its relatively stable nature, minimally affected by external environmental variations. Emerging evidence suggests that plant genome size affects the plant-associated microbial community, and tissue-specific environments select microbes based on their genome size. These findings pinpoint environmental selection in genome size as an emerging driver of plant-microbiome interactions, potentially impacting ecosystem functions and productivity.
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Affiliation(s)
- Haiyang Zhang
- College of Life Sciences, Hebei University, Baoding, China.
| | - Hongwei Liu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2753, Australia
| | - Xingguo Han
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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2
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Saha A, Bellucci A, Fratini S, Cannicci S, Ciofi C, Iannucci A. Ecological factors and parity mode correlate with genome size variation in squamate reptiles. BMC Ecol Evol 2023; 23:69. [PMID: 38053023 PMCID: PMC10696768 DOI: 10.1186/s12862-023-02180-4] [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: 05/16/2023] [Accepted: 11/25/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Evidence of correlation between genome size, the nuclear haploid DNA content of a cell, environmental factors and life-history traits have been reported in many animal species. Genome size, however, spans over three orders of magnitude across taxa and such a correlation does not seem to follow a universal pattern. In squamate reptiles, the second most species-rich order of vertebrates, there are currently no studies investigating drivers of genome size variability. We run a series of phylogenetic generalized least-squares models on 227 species of squamates to test for possible relationships between genome size and ecological factors including latitudinal distribution, bioclimatic variables and microhabitat use. We also tested whether genome size variation can be associated with parity mode, a highly variable life history trait in this order of reptiles. RESULTS The best-fitting model showed that the interaction between microhabitat use and parity mode mainly accounted for genome size variation. Larger genome sizes were found in live-bearing species that live in rock/sand ecosystems and in egg-laying arboreal taxa. On the other hand, smaller genomes were found in fossorial live-bearing species. CONCLUSIONS Environmental factors and species parity mode appear to be among the main parameters explaining genome size variation in squamates. Our results suggest that genome size may favour adaptation of some species to certain environments or could otherwise result from the interaction between environmental factors and parity mode. Integration of genome size and genome sequencing data could help understand the role of differential genome content in the evolutionary process of genome size variation in squamates.
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Affiliation(s)
- Anik Saha
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Arianna Bellucci
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Sara Fratini
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- National Biodiversity Future Center, 90133, Palermo, Italy
| | - Stefano Cannicci
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- National Biodiversity Future Center, 90133, Palermo, Italy
| | - Claudio Ciofi
- Department of Biology, University of Florence, Sesto Fiorentino, Italy.
| | - Alessio Iannucci
- Department of Biology, University of Florence, Sesto Fiorentino, Italy.
- National Biodiversity Future Center, 90133, Palermo, Italy.
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Zhang HY, Lü XT, Wei CZ, Powell JR, Wang XB, Xing DL, Xu ZW, Li HL, Han XG. β-diversity in temperate grasslands is driven by stronger environmental filtering of plant species with large genomes. Ecology 2023; 104:e3941. [PMID: 36469035 DOI: 10.1002/ecy.3941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 10/27/2022] [Accepted: 10/31/2022] [Indexed: 12/12/2022]
Abstract
Elucidating mechanisms underlying community assembly and biodiversity patterns is central to ecology and evolution. Genome size (GS) has long been hypothesized to potentially affect species' capacity to tolerate environmental stress and might therefore help drive community assembly. However, its role in driving β-diversity (i.e., spatial variability in species composition) remains unclear. We measured GS for 161 plant species and community composition across 52 sites spanning a 3200-km transect in the temperate grasslands of China. By correlating the turnover of species composition with environmental dissimilarity, we found that resource filtering (i.e., environmental dissimilarity that includes precipitation, and soil nitrogen and phosphorus concentrations) affected β-diversity patterns of large-GS species more than small-GS species. By contrast, geographical distance explained more variation of β-diversity for small-GS than for large-GS species. In a 10-year experiment manipulating levels of water, nitrogen, and phosphorus, adding resources increased plant biomass in species with large GS, suggesting that large-GS species are more sensitive to the changes in resource availability. These findings highlight the role of GS in driving community assembly and predicting species responses to global change.
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Affiliation(s)
- Hai-Yang Zhang
- College of Life Sciences, Hebei University, Baoding, China.,Erguna Forest-Steppe Ecotone Research Station, CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China.,Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Xiao-Tao Lü
- Erguna Forest-Steppe Ecotone Research Station, CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Cun-Zheng Wei
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jeff R Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Xiao-Bo Wang
- Erguna Forest-Steppe Ecotone Research Station, CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China.,Center for Grassland Microbiome, State Key Laboratory of Grassland Agroecosystems, and College of Pastoral, Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Ding-Liang Xing
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Zhu-Wen Xu
- Department of Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Huan-Long Li
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xing-Guo Han
- Erguna Forest-Steppe Ecotone Research Station, CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China.,State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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4
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Phylogenomics and genome size evolution in Amomum s. s. (Zingiberaceae): Comparison of traditional and modern sequencing methods. Mol Phylogenet Evol 2023; 178:107666. [PMID: 36384185 DOI: 10.1016/j.ympev.2022.107666] [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: 04/15/2021] [Revised: 11/05/2022] [Accepted: 11/08/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND AIMS A targeted enrichment NGS approach was used to construct the phylogeny of Amomum Roxb. (Zingiberaceae). Phylogenies based on hundreds of nuclear genes, the whole plastome and the rDNA cistron were compared with an ITS-based phylogeny. Trends in genome size (GS) evolution were examined, chromosomes were counted and the geographical distribution of phylogenetic lineages was evaluated. METHODS In total, 92 accessions of 54 species were analysed. ITS was obtained for 79 accessions, 37 accessions were processed with Hyb-Seq and sequences from 449 nuclear genes, the whole cpDNA, and the rDNA cistron were analysed using concatenation, coalescence and supertree approaches. The evolution of absolute GS was analysed in a phylogenetic and geographical context. The chromosome numbers of 12 accessions were counted. KEY RESULTS Four groups were recognised in all datasets though their mutual relationships differ among datasets. While group A (A. subulatum and A. petaloideum) is basal to the remaining groups in the nuclear gene phylogeny, in the cpDNA topology it is sister to group B (A. repoeense and related species) and, in the ITS topology, it is sister to group D (the Elettariopsis lineage). The former Elettariopsis makes a monophyletic group. There is an increasing trend in GS during evolution. The largest GS values were found in group D in two tetraploid taxa, A. cinnamomeum and A. aff. biphyllum (both 2n = 96 chromosomes). The rest varied in GS (2C = 3.54-8.78 pg) with a constant chromosome number 2n = 48. There is a weak connection between phylogeny, GS and geography in Amomum. CONCLUSIONS Amomum consists of four groups, and the former Elettariopsis is monophyletic. Species in this group have the largest GS. Two polyploids were found and GS greatly varied in the rest of Amomum.
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Becker FW, Oberlander KC, Trávníček P, Dreyer LL. Inconsistent expression of the gigas effect in polyploid Oxalis. AMERICAN JOURNAL OF BOTANY 2022; 109:1607-1621. [PMID: 36193941 DOI: 10.1002/ajb2.16077] [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: 03/31/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
PREMISE It is well-known that whole genome duplication (WGD) has played a significant role in the evolution of plants. The best-known phenotypic effect of WGD is the gigas effect, or the enlargement of polyploid plant traits. WGD is often linked with increased weediness, which could be a result of fitness advantages conferred by the gigas effect. As a result, the gigas effect could potentially explain polyploid persistence and abundance. We test whether a gigas effect is present in the polyploid-rich geophyte Oxalis, at both organ and cellular scales. METHODS We measured traits in conspecific diploid and polyploid accessions of 24 species across the genus. In addition, we measured the same and additional traits in 20 populations of the weedy and highly ploidy-variable species Oxalis purpurea L., including measures of clonality and selfing as a proxy for weediness. Ploidy level was determined using flow cytometry. RESULTS We found substantial variation and no consistent ploidy-related size difference, both between and within species, and across traits. Oxalis purpurea polyploids did, however, produce significantly more underground biomass and more bulbils than diploids, consistent with a potential role of WGD in the weediness of this species. CONCLUSIONS Our results suggest a more nuanced role for the gigas effect, at least in Oxalis. It may be temporary, short-lived, and inconsistently expressed and retained on evolutionary time scales, but in the short term can contribute to lineage success via increased vegetative reproduction.
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Affiliation(s)
- Frederik W Becker
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Kenneth C Oberlander
- H. G. W. J. Schweickerdt Herbarium, Department of Plant and Soil Sciences, Plant Sciences Complex, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Pavel Trávníček
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic, and Department of Botany, Charles University, Praha, Czech Republic
| | - Léanne L Dreyer
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
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Iannucci A, Saha A, Cannicci S, Bellucci A, Cheng CLY, Ng KH, Fratini S. Ecological, physiological and life-history traits correlate with genome sizes in decapod crustaceans. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.930888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Crustaceans are characterized by some of the most variable genome sizes among animals. Significant relationships between genome size and specific eco-physiological and morphological features have been described in many crustacean taxa, such as Amphipoda, Ostracoda, Cladocera, and Copepoda. A consistent pattern of genome size variation is yet to be found, however, in one of the most specious order of crustaceans, the Decapoda. We investigated how genome size is related to selected eco-physiological and life-history traits in species belonging to this order. We analyzed the respiratory, excretory, and developmental adaptations of 179 decapod species inhabiting shallow marine, deep marine, freshwater, intertidal, and terrestrial habitats. Our results show that the genome size is significantly larger in decapods that have a direct development. Moreover, in Anomura, Astacidea, and Brachyura we found larger genome sizes in species (i) living in freshwater habitats, (ii) using gills as a strictly water-breathing organs, and (iii) presenting a direct development. While species that (i) live in shallow waters, and intertidal and terrestrial habitats, (ii) have some degrees of air-breathing adaptations, namely gills that can exchange oxygen with air if wet or branchiostegal lungs, and (iii) possess an indirect or extended development are characterized by significantly smaller genomes. Our analyses show that developmental complexity affects genome size in decapods, and that multiple eco-physiological and life-history traits correlate with genome size in Anomura, Astacidea, and Brachyura.
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Faizullah L, Morton JA, Hersch-Green EI, Walczyk AM, Leitch AR, Leitch IJ. Exploring environmental selection on genome size in angiosperms. TRENDS IN PLANT SCIENCE 2021; 26:1039-1049. [PMID: 34219022 DOI: 10.1016/j.tplants.2021.06.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 05/22/2023]
Abstract
Angiosperms show a remarkable range in genome size (GS), yet most species have small genomes, despite the frequency of polyploidy and repeat amplification in the ancestries of most lineages. It has been suggested that larger genomes incur costs that have driven selection for GS reduction, although the nature of these costs and how they might impact selection remain unclear. We explore potential costs of increased GS encompassing impacts on minimum cell size with consequences for photosynthesis and water-use efficiency and effects of greater nitrogen and phosphorus demands of the nucleus leading to more severe trade-offs with photosynthesis. We suggest that nutrient-, water-, and/or CO2-stressed conditions might favour species with smaller genomes, with implications for species' ecological and evolutionary dynamics.
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Affiliation(s)
- Lubna Faizullah
- Character Evolution Team, Royal Botanic Gardens, Kew, Richmond, Surrey, UK; School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, UK
| | - Joseph A Morton
- Character Evolution Team, Royal Botanic Gardens, Kew, Richmond, Surrey, UK; School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, UK
| | - Erika I Hersch-Green
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Angela M Walczyk
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, UK.
| | - Ilia J Leitch
- Character Evolution Team, Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
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Wang X, Morton JA, Pellicer J, Leitch IJ, Leitch AR. Genome downsizing after polyploidy: mechanisms, rates and selection pressures. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1003-1015. [PMID: 34077584 DOI: 10.1111/tpj.15363] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 05/20/2023]
Abstract
An analysis of over 10 000 plant genome sizes (GSs) indicates that most species have smaller genomes than expected given the incidence of polyploidy in their ancestries, suggesting selection for genome downsizing. However, comparing ancestral GS with the incidence of ancestral polyploidy suggests that the rate of DNA loss following polyploidy is likely to have been very low (4-70 Mb/million years, 4-482 bp/generation). This poses a problem. How might such small DNA losses be visible to selection, overcome the power of genetic drift and drive genome downsizing? Here we explore that problem, focussing on the role that double-strand break (DSB) repair pathways (non-homologous end joining and homologous recombination) may have played. We also explore two hypotheses that could explain how selection might favour genome downsizing following polyploidy: to reduce (i) nitrogen (N) and phosphate (P) costs associated with nucleic acid synthesis in the nucleus and the transcriptome and (ii) the impact of scaling effects of GS on cell size, which influences CO2 uptake and water loss. We explore the hypothesis that losses of DNA must be fastest in early polyploid generations. Alternatively, if DNA loss is a more continuous process over evolutionary time, then we propose it is a byproduct of selection elsewhere, such as limiting the damaging activity of repetitive DNA. If so, then the impact of GS on photosynthesis, water use efficiency and/or nutrient costs at the nucleus level may be emergent properties, which have advantages, but not ones that could have been selected for over generational timescales.
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Affiliation(s)
- Xiaotong Wang
- Royal Botanic Gardens, Kew, Surrey, TW9 3AB, UK
- Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Joseph A Morton
- Royal Botanic Gardens, Kew, Surrey, TW9 3AB, UK
- Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Surrey, TW9 3AB, UK
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia sn, Barcelona, 08038, Spain
| | | | - Andrew R Leitch
- Queen Mary University of London, Mile End Road, London, E1 4NS, UK
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Glazier DS. Genome Size Covaries More Positively with Propagule Size than Adult Size: New Insights into an Old Problem. BIOLOGY 2021; 10:270. [PMID: 33810583 PMCID: PMC8067107 DOI: 10.3390/biology10040270] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 12/17/2022]
Abstract
The body size and (or) complexity of organisms is not uniformly related to the amount of genetic material (DNA) contained in each of their cell nuclei ('genome size'). This surprising mismatch between the physical structure of organisms and their underlying genetic information appears to relate to variable accumulation of repetitive DNA sequences, but why this variation has evolved is little understood. Here, I show that genome size correlates more positively with egg size than adult size in crustaceans. I explain this and comparable patterns observed in other kinds of animals and plants as resulting from genome size relating strongly to cell size in most organisms, which should also apply to single-celled eggs and other reproductive propagules with relatively few cells that are pivotal first steps in their lives. However, since body size results from growth in cell size or number or both, it relates to genome size in diverse ways. Relationships between genome size and body size should be especially weak in large organisms whose size relates more to cell multiplication than to cell enlargement, as is generally observed. The ubiquitous single-cell 'bottleneck' of life cycles may affect both genome size and composition, and via both informational (genotypic) and non-informational (nucleotypic) effects, many other properties of multicellular organisms (e.g., rates of growth and metabolism) that have both theoretical and practical significance.
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10
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Genome Size Unaffected by Variation in Morphological Traits, Temperature, and Precipitation in Turnip. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9020253] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Genome size (GS) was proposed as proxy for gross phenotypic and environmental changes in plants. GS organismal complexity is an enigma in evolutionary biology. While studies pertaining to intraspecific GS variation are abundant, literatures reporting the adaptive significance of GS are largelymissing. During food shortage, Brassica rapa var. rapa (turnip) is used as food and fodder for sustaining the livelihood of residents in the Qinghai Tibetan Plateau (QTP), which is also known as “the roof of the world”. Thus, climatic extremities make this region a natural environment to test adaptive significance of GS variation in turnip landraces. Therefore, from the QTP and its adjacent regions (the Hengduanshan and the Himalayas), we investigated adaptive evolution of GS in turnip landraces. Tuber diameter of turnip landraces was found to be significantly correlated with most of the environmental factors. GS was also shown not to be associated with morphological traits, temperature, and precipitation. Moreover, principal component analyses based on the whole dataset trisected the landraces into three distinct populations based on landrace usage—Hengduanshan, QTP, and the Himalayas. Nonetheless, our cumulative dataset showed evidence of adaptation of turnip landrace to different environments throughnonassociated genomic and phenomic plasticity.
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Affiliation(s)
- Julia M. Kreiner
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Stephen I. Wright
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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Gaynor ML, Ng J, Laport RG. Phylogenetic Structure of Plant Communities: Are Polyploids Distantly Related to Co-occurring Diploids? Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Pellicer J, Hidalgo O, Dodsworth S, Leitch IJ. Genome Size Diversity and Its Impact on the Evolution of Land Plants. Genes (Basel) 2018; 9:E88. [PMID: 29443885 PMCID: PMC5852584 DOI: 10.3390/genes9020088] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/02/2018] [Accepted: 02/05/2018] [Indexed: 01/09/2023] Open
Abstract
Genome size is a biodiversity trait that shows staggering diversity across eukaryotes, varying over 64,000-fold. Of all major taxonomic groups, land plants stand out due to their staggering genome size diversity, ranging ca. 2400-fold. As our understanding of the implications and significance of this remarkable genome size diversity in land plants grows, it is becoming increasingly evident that this trait plays not only an important role in shaping the evolution of plant genomes, but also in influencing plant community assemblages at the ecosystem level. Recent advances and improvements in novel sequencing technologies, as well as analytical tools, make it possible to gain critical insights into the genomic and epigenetic mechanisms underpinning genome size changes. In this review we provide an overview of our current understanding of genome size diversity across the different land plant groups, its implications on the biology of the genome and what future directions need to be addressed to fill key knowledge gaps.
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Affiliation(s)
- Jaume Pellicer
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew TW9 3DS, UK.
| | - Oriane Hidalgo
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew TW9 3DS, UK.
| | - Steven Dodsworth
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew TW9 3DS, UK.
| | - Ilia J Leitch
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew TW9 3DS, UK.
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Schmidt JP, Drake JM, Stephens P. Residence time, native range size, and genome size predict naturalization among angiosperms introduced to Australia. Ecol Evol 2017; 7:10289-10300. [PMID: 29238555 PMCID: PMC5723587 DOI: 10.1002/ece3.3505] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/30/2017] [Accepted: 09/01/2017] [Indexed: 11/11/2022] Open
Abstract
Although critical to progress in understanding (i) if, and (ii) at what rate, introduced plants will naturalize and potentially become invasive, establishing causal links between traits and invasion success is complicated by data gaps, phylogenetic nonindependence of species, the inability to control for differences between species in residence time and propagule pressure, and covariance among traits. Here, we focus on statistical relationships between genomic factors, life history traits, native range size, and naturalization status of angiosperms introduced to Australia. In a series of analyses, we alternately investigate the role of phylogeny, incorporate introduction history, and use graphical models to explore the network of conditional probabilities linking traits and introduction history to naturalization status. Applying this ensemble of methods to the largest publicly available data set on plant introductions and their fates, we found that, overall, residence time and native range size best predicted probability of naturalization. Yet, importantly, probability of naturalization consistently increased as genome size decreased, even when the effects of shared ancestry and residence time in Australia were accounted for, and that this pattern was stronger in species without a history of cultivation, but present across annual-biennials, and herbaceous and woody perennials. Thus, despite introduction biases and indirect effects of traits via introduction history, across analyses, reduced genome size was nevertheless consistently associated with a tendency to naturalize.
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Affiliation(s)
| | - John M. Drake
- Odum School of EcologyUniversity of GeorgiaAthensGAUSA
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15
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Segraves KA. The effects of genome duplications in a community context. THE NEW PHYTOLOGIST 2017; 215:57-69. [PMID: 28418074 DOI: 10.1111/nph.14564] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/16/2017] [Indexed: 06/07/2023]
Abstract
Contents 57 I. 57 II. 59 III. 59 IV. 63 V. 64 VI. 64 VII. 66 66 References 66 SUMMARY: Whole-genome duplication (WGD), or polyploidy, has important effects on the genotype and phenotype of plants, potentially altering ecological interactions with other organisms. Even though the connections between polyploidy and species interactions have been recognized for some time, we are only just beginning to test whether WGD affects community context. Here I review the sparse information on polyploidy and community context and then present a set of hypotheses for future work. Thus far, community-level studies of polyploids suggest an array of outcomes, from no changes in community context to shifts in the abundance and composition of interacting species. I propose a number of mechanisms for how WGD could alter community context and how the emergence of polyploids in populations could also alter the community context of parental diploids and other plant species. Resolving how and when these changes are expected to occur will require a deeper understanding of the connections among WGD, phenotypic changes, and the direct and indirect effects of species interactions.
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Affiliation(s)
- Kari A Segraves
- Department of Biology, Syracuse University, Syracuse, NY, 13244, USA
- Archbold Biological Station, Venus, FL, 33960, USA
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Hidalgo O, Pellicer J, Christenhusz M, Schneider H, Leitch AR, Leitch IJ. Is There an Upper Limit to Genome Size? TRENDS IN PLANT SCIENCE 2017; 22:567-573. [PMID: 28506667 DOI: 10.1016/j.tplants.2017.04.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/03/2017] [Accepted: 04/05/2017] [Indexed: 05/08/2023]
Abstract
At 50-fold the size of the human genome (3 Gb), the staggeringly huge genome of 147.3 Gb recently discovered in the fern Tmesipteris obliqua is comparable in size to those of the other plant and animal record-holders (i.e., Paris japonica, a flowering plant with a genome size of 148.8 Gb, and Protopterus aethiopicus, a lungfish with a genome of 130 Gb). The synthesis of available information on giant genomes suggests that the biological limit to genome size expansion in eukaryotes may have been reached. We propose several explanations for why the genomes of ferns, flowering plants, and lungfish, all of which have independently undergone dramatic increases in genome size through a variety of mechanisms, do not exceed 150 Gb.
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Affiliation(s)
| | | | | | - Harald Schneider
- Department of Life Sciences, Natural History Museum, London W7 5BD, UK; Xishuangbanna Tropical Botanical Garden, Centre for Integrative Conservation, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, PR China
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
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John GP, Scoffoni C, Buckley TN, Villar R, Poorter H, Sack L. The anatomical and compositional basis of leaf mass per area. Ecol Lett 2017; 20:412-425. [DOI: 10.1111/ele.12739] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/12/2016] [Accepted: 12/21/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Grace P. John
- Department of Ecology and Evolutionary Biology University of California Los Angeles 621 Charles E. Young Drive South Los Angeles CA90095 USA
| | - Christine Scoffoni
- Department of Ecology and Evolutionary Biology University of California Los Angeles 621 Charles E. Young Drive South Los Angeles CA90095 USA
| | - Thomas N. Buckley
- Plant Breeding Institute Sydney Institute of Agriculture The University of Sydney 12656, Newell Hwy Narrabri NSW2390 Australia
| | - Rafael Villar
- Área de Ecología Universidad de Córdoba Edificio Celestino Mutis Campus de Rabanales 14071 Córdoba Spain
| | - Hendrik Poorter
- Plant Sciences (IBG2), Forschungszentrum Jülich GmbH D‐52425 Jülich Germany
| | - Lawren Sack
- Department of Ecology and Evolutionary Biology University of California Los Angeles 621 Charles E. Young Drive South Los Angeles CA90095 USA
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Bromham L, Hua X, Lanfear R, Cowman PF. Exploring the Relationships between Mutation Rates, Life History, Genome Size, Environment, and Species Richness in Flowering Plants. Am Nat 2015; 185:507-24. [PMID: 25811085 DOI: 10.1086/680052] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A new view is emerging of the interplay between mutation at the genomic level, substitution at the population level, and diversification at the lineage level. Many studies have suggested that rate of molecular evolution is linked to rate of diversification, but few have evaluated competing hypotheses. By analyzing sequences from 130 families of angiosperms, we show that variation in the synonymous substitution rate is correlated among genes from the mitochondrial, chloroplast, and nuclear genomes and linked to differences in traits among families (average height and genome size). Within each genome, synonymous rates are correlated to nonsynonymous substitution rates, suggesting that increasing the mutation rate results in a faster rate of genome evolution. Substitution rates are correlated with species richness in protein-coding sequences from the chloroplast and nuclear genomes. These data suggest that species traits contribute to lineage-specific differences in the mutation rate that drive both synonymous and nonsynonymous rates of change across all three genomes, which in turn contribute to greater rates of divergence between populations, generating higher rates of diversification. These observations link mutation in individuals to population-level processes and to patterns of lineage divergence.
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Affiliation(s)
- Lindell Bromham
- Centre for Macroevolution and Macroecology, Division of Evolution, Ecology and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 0200, Australia
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Abstract
BACKGROUND AND AIMS Both regional and local plant abundances are driven by species' dispersal capacities and their abilities to exploit new habitats and persist there. These processes are affected by clonal growth, which is difficult to evaluate and compare across large numbers of species. This study assessed the influence of clonal reproduction on local and regional abundances of a large set of species and compared the predictive power of morphologically defined traits of clonal growth with data on actual clonal growth from a botanical garden. The role of clonal growth was compared with the effects of seed reproduction, habitat requirements and growth, proxied both by LHS (leaf-height-seed) traits and by actual performance in the botanical garden. METHODS Morphological parameters of clonal growth, actual clonal reproduction in the garden and LHS traits (leaf-specific area - height - seed mass) were used as predictors of species abundance, both regional (number of species records in the Czech Republic) and local (mean species cover in vegetation records) for 836 perennial herbaceous species. Species differences in habitat requirements were accounted for by classifying the dataset by habitat type and also by using Ellenberg indicator values as covariates. KEY RESULTS After habitat differences were accounted for, clonal growth parameters explained an important part of variation in species abundance, both at regional and at local levels. At both levels, both greater vegetative growth in cultivation and greater lateral expansion trait values were correlated with higher abundance. Seed reproduction had weaker effects, being positive at the regional level and negative at the local level. CONCLUSIONS Morphologically defined traits are predictive of species abundance, and it is concluded that simultaneous investigation of several such traits can help develop hypotheses on specific processes (e.g. avoidance of self-competition, support of offspring) potentially underlying clonal growth effects on abundance. Garden performance parameters provide a practical approach to assessing the roles of clonal growth morphological traits (and LHS traits) for large sets of species.
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Affiliation(s)
- Tomáš Herben
- Institute of Botany, Academy of Science of the Czech Republic, CZ-252 43 Průhonice, Czech Republic Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 01 Praha 2, Czech Republic
| | - Zuzana Nováková
- Botanical Garden of the Charles University, Na Slupi 16, CZ-128 01 Praha 2, Czech Republic
| | - Jitka Klimešová
- Institute of Botany, Academy of Sciences of the Czech Republic, CZ-379 82 Třeboň, Czech Republic
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Kang M, Tao J, Wang J, Ren C, Qi Q, Xiang QY, Huang H. Adaptive and nonadaptive genome size evolution in Karst endemic flora of China. THE NEW PHYTOLOGIST 2014; 202:1371-1381. [PMID: 24533910 DOI: 10.1111/nph.12726] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 01/16/2014] [Indexed: 05/03/2023]
Abstract
Genome size variation is of fundamental biological importance and has been a longstanding puzzle in evolutionary biology. Several hypotheses for genome size evolution including neutral, maladaptive, and adaptive models have been proposed, but the relative importance of these models remains controversial. Primulina is a genus that is highly diversified in the Karst region of southern China, where genome size variation and the underlying evolutionary mechanisms are poorly understood. We reconstructed the phylogeny of Primulina using DNA sequences for 104 species and determined the genome sizes of 101 species. We examined the phylogenetic signal in genome size variation, and tested the fit to different evolutionary models and for correlations with variation in latitude and specific leaf area (SLA). The results showed that genome size, SLA and latitudinal variation all displayed strong phylogenetic signals, but were best explained by different evolutionary models. Furthermore, significant positive relationships were detected between genome size and SLA and between genome size and latitude. Our study is the first to investigate genome size evolution on such a comprehensive scale and in the Karst region flora. We conclude that genome size in Primulina is phylogenetically conserved but its variation among species is a combined outcome of both neutral and adaptive evolution.
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Affiliation(s)
- Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Junjie Tao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Chen Ren
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Qingwen Qi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiu-Yun Xiang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695-7612, USA
| | - Hongwen Huang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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Poulíčková A, Poulíèková A, Mazalová P, Vašut RJ, Šarhanová P, Neustupa J, Neustupa J, Škaloud P. DNA content variation and its significance in the evolution of the genus Micrasterias (Desmidiales, Streptophyta). PLoS One 2014; 9:e86247. [PMID: 24465986 PMCID: PMC3897674 DOI: 10.1371/journal.pone.0086247] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 12/12/2013] [Indexed: 01/06/2023] Open
Abstract
It is now clear that whole genome duplications have occurred in all eukaryotic evolutionary lineages, and that the vast majority of flowering plants have experienced polyploidisation in their evolutionary history. However, study of genome size variation in microalgae lags behind that of higher plants and seaweeds. In this study, we have addressed the question whether microalgal phylogeny is associated with DNA content variation in order to evaluate the evolutionary significance of polyploidy in the model genus Micrasterias. We applied flow-cytometric techniques of DNA quantification to microalgae and mapped the estimated DNA content along the phylogenetic tree. Correlations between DNA content and cell morphometric parameters were also tested using geometric morphometrics. In total, DNA content was successfully determined for 34 strains of the genus Micrasterias. The estimated absolute 2C nuclear DNA amount ranged from 2.1 to 64.7 pg; intraspecific variation being 17.4–30.7 pg in M. truncata and 32.0–64.7 pg in M. rotata. There were significant differences between DNA contents of related species. We found strong correlation between the absolute nuclear DNA content and chromosome numbers and significant positive correlation between the DNA content and both cell size and number of terminal lobes. Moreover, the results showed the importance of cell/life cycle studies for interpretation of DNA content measurements in microalgae.
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Affiliation(s)
| | - Aloisie Poulíèková
- Department of Botany, Faculty of Science, Palacký University in Olomouc, Olomouc, Czech Republic
| | - Petra Mazalová
- Department of Botany, Faculty of Science, Palacký University in Olomouc, Olomouc, Czech Republic ; Department of Biology, Faculty of Science, University of Hradec Králové, Hradec Králové, Czech Republic
| | - Radim J Vašut
- Department of Botany, Faculty of Science, Palacký University in Olomouc, Olomouc, Czech Republic
| | - Petra Šarhanová
- Department of Botany, Faculty of Science, Palacký University in Olomouc, Olomouc, Czech Republic
| | | | - Jiøí Neustupa
- Department of Botany, Charles University in Prague, Prague, Czech Republic
| | - Pavel Škaloud
- Department of Botany, Charles University in Prague, Prague, Czech Republic
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23
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Ashman TL, Kwok A, Husband BC. Revisiting the dioecy-polyploidy association: alternate pathways and research opportunities. Cytogenet Genome Res 2013; 140:241-55. [PMID: 23838528 DOI: 10.1159/000353306] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The evolutionary transition from hermaphroditism (combined sexes) to dioecy (separate sexes) is associated with whole genome duplication (polyploidy) in several flowering plant genera. Moreover, there is evidence for transitions in the opposite direction, i.e. a loss of dioecy with an increase in ploidy. Here, we review evidence for these associations, synthesize previous ideas on the mechanism underlying the patterns and explore alternative pathways. Specifically, we examine potential ecological and genetic mechanisms, differentiated by whether ploidy or gender (functional sex expression of the plant) changes are the primary cause and whether the effect is direct or indirect. An analysis of 22 genera variable for both ploidy and gender indicates that gender monomorphism (hermaphroditism, monoecy) is more common among diploid than polyploid species, whereas gender dimorphism (dioecy, gynodioecy, subdioecy) is more frequent among polyploid species. The transition from diploid hermaphroditic to polyploid gender-dimorphic taxa may arise directly through changes in gender as a result of genome duplication through genomic rearrangements or homeologous recombination, or changes in gender may result in increased unreduced gamete production leading to polyploid formation. Alternatively, the transition may occur through the indirect effects of genome duplication on mating system and inbreeding depression, which favor selection for unisexuality, or habitat shifts associated with unisexuality may simultaneously cause increased unreduced gamete production. Novel mechanisms for transitions in the opposite direction (from dioecy to hermaphroditism with increase in ploidy) include disruption of genetic sex determination and the benefits of reproductive assurance. We highlight key questions requiring further attention and promising approaches for answering them and better clarifying the genesis of sexual system polyploidy associations. See also the sister article focusing on animals by Wertheim et al. in this themed issue.
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Affiliation(s)
- T-L Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260-3929, USA. tia1 @ pitt.edu
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24
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Díez CM, Gaut BS, Meca E, Scheinvar E, Montes-Hernandez S, Eguiarte LE, Tenaillon MI. Genome size variation in wild and cultivated maize along altitudinal gradients. THE NEW PHYTOLOGIST 2013; 199:264-276. [PMID: 23550586 PMCID: PMC4119021 DOI: 10.1111/nph.12247] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 02/20/2013] [Indexed: 05/18/2023]
Abstract
It is still an open question as to whether genome size (GS) variation is shaped by natural selection. One approach to address this question is a population-level survey that assesses both the variation in GS and the relationship of GS to ecological variants. We assessed GS in Zea mays, a species that includes the cultivated crop, maize, and its closest wild relatives, the teosintes. We measured GS in five plants of each of 22 maize landraces and 21 teosinte populations from Mexico sampled from parallel altitudinal gradients. GS was significantly smaller in landraces than in teosintes, but the largest component of GS variation was among landraces and among populations. In maize, GS correlated negatively with altitude; more generally, the best GS predictors were linked to geography. By contrast, GS variation in teosintes was best explained by temperature and precipitation. Overall, our results further document the size flexibility of the Zea genome, but also point to a drastic shift in patterns of GS variation since domestication. We argue that such patterns may reflect the indirect action of selection on GS, through a multiplicity of phenotypes and life-history traits.
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Affiliation(s)
- Concepción M Díez
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, 92697, USA
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, 92697, USA
| | - Esteban Meca
- Department of Mathematics, UC Irvine, Irvine, CA, 92607, USA
| | - Enrique Scheinvar
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CP 04510, Mexico City, Mexico
| | - Salvador Montes-Hernandez
- Campo Experimental Bajío, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, CP 38110, Celaya, Guanajuato, Mexico
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CP 04510, Mexico City, Mexico
| | - Maud I Tenaillon
- CNRS, UMR de Génétique Végétale, INRA/CNRS/Univ Paris-Sud/AgroParisTech, Ferme du Moulon, Gif-sur-Yvette, France
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Pannell JR. The ecology of plant populations: their dynamics, interactions and evolution. ANNALS OF BOTANY 2012; 110:1351-5. [PMID: 24734260 PMCID: PMC3489153 DOI: 10.1093/aob/mcs224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Affiliation(s)
- John R Pannell
- Department of Ecology and Evolution, University of Lausanne, Switzerland.
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