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Herrera CM, Bazaga P, Pérez R, Alonso C. Lifetime genealogical divergence within plants leads to epigenetic mosaicism in the shrub Lavandula latifolia (Lamiaceae). THE NEW PHYTOLOGIST 2021; 231:2065-2076. [PMID: 33634863 DOI: 10.1111/nph.17257] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Epigenetic mosaicism is a possible source of within-plant phenotypic heterogeneity, yet its frequency and developmental origin remain unexplored. This study examines whether extant epigenetic heterogeneity within Lavandula latifolia (Lamiaceae) shrubs reflects recent epigenetic modifications experienced independently by different plant parts or, alternatively, it is the cumulative outcome of a steady lifetime process. Leaf samples from different architectural modules (branch tips) were collected from three L. latifolia plants and characterized epigenetically by global DNA cytosine methylation and methylation state of methylation-sensitive amplified fragment-length polymorphism (MS-AFLP) markers. Epigenetic characteristics of modules were then assembled with information on the branching history of plants. Methods borrowed from phylogenetic research were used to assess genealogical signal of extant epigenetic variation and reconstruct within-plant genealogical trajectory of epigenetic traits. Plants were epigenetically heterogeneous, as shown by differences among modules in global DNA methylation and variation in the methylation states of 6 to 8% of MS-AFLP markers. All epigenetic features exhibited significant genealogical signal within plants. Events of epigenetic divergence occurred throughout the lifespan of individuals and were subsequently propagated by branch divisions. Internal epigenetic diversification of L. latifolia individuals took place steadily during their development, a process which eventually led to persistent epigenetic mosaicism.
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Affiliation(s)
- Carlos M Herrera
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio 26, Sevilla, E-41092, Spain
| | - Pilar Bazaga
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio 26, Sevilla, E-41092, Spain
| | - Ricardo Pérez
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de La Cartuja, CSIC-US, Avda. Américo Vespucio 49, Sevilla, E-41092, Spain
| | - Conchita Alonso
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio 26, Sevilla, E-41092, Spain
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2
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Major EI, Höhn M, Avanzi C, Fady B, Heer K, Opgenoorth L, Piotti A, Popescu F, Postolache D, Vendramin GG, Csilléry K. Fine-scale spatial genetic structure across the species range reflects recent colonization of high elevation habitats in silver fir (Abies alba Mill.). Mol Ecol 2021; 30:5247-5265. [PMID: 34365696 PMCID: PMC9291806 DOI: 10.1111/mec.16107] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 07/07/2021] [Accepted: 07/16/2021] [Indexed: 12/03/2022]
Abstract
Variation in genetic diversity across species ranges has long been recognized as highly informative for assessing populations’ resilience and adaptive potential. The spatial distribution of genetic diversity within populations, referred to as fine‐scale spatial genetic structure (FSGS), also carries information about recent demographic changes, yet it has rarely been connected to range scale processes. We studied eight silver fir (Abies alba Mill.) population pairs (sites), growing at high and low elevations, representative of the main genetic lineages of the species. A total of 1,368 adult trees and 540 seedlings were genotyped using 137 and 116 single nucleotide polymorphisms (SNPs), respectively. Sites revealed a clear east‐west isolation‐by‐distance pattern consistent with the post‐glacial colonization history of the species. Genetic differentiation among sites (FCT = 0.148) was an order of magnitude greater than between elevations within sites (FSC = 0.031), nevertheless high elevation populations consistently exhibited a stronger FSGS. Structural equation modelling revealed that elevation and, to a lesser extent, post‐glacial colonization history, but not climatic and habitat variables, were the best predictors of FSGS across populations. These results suggest that high elevation habitats have been colonized more recently across the species range. Additionally, paternity analysis revealed a high reproductive skew among adults and a stronger FSGS in seedlings than in adults, suggesting that FSGS may conserve the signature of demographic changes for several generations. Our results emphasize that spatial patterns of genetic diversity within populations provide information about demographic history complementary to non‐spatial statistics, and could be used for genetic diversity monitoring, especially in forest trees.
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Affiliation(s)
- Enikő I Major
- Department of Botany, Hungarian University of Agronomy and Life Sciences, Budapest, Hungary
| | - Mária Höhn
- Department of Botany, Hungarian University of Agronomy and Life Sciences, Budapest, Hungary
| | - Camilla Avanzi
- Institute of Biosciences and Bioresources, National Research Council of Italy (IBBR-CNR), Sesto Fiorentino (Firenze), Italy
| | - Bruno Fady
- Ecology of Mediterranean Forests (URFM), INRAE, UR629, Avignon, France
| | - Katrin Heer
- Conservation Biology, Philipps Universität Marburg, Marburg, Germany
| | - Lars Opgenoorth
- Plant Ecology and Geobotany, Philipps Universität Marburg, Marburg, Germany.,Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Andrea Piotti
- Institute of Biosciences and Bioresources, National Research Council of Italy (IBBR-CNR), Sesto Fiorentino (Firenze), Italy
| | - Flaviu Popescu
- National Institute for Research and Development in Forestry "Marin Drăcea", Ilfov County, Romania
| | - Dragos Postolache
- National Institute for Research and Development in Forestry "Marin Drăcea", Ilfov County, Romania
| | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, National Research Council of Italy (IBBR-CNR), Sesto Fiorentino (Firenze), Italy
| | - Katalin Csilléry
- Land Change Science, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
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Bogdziewicz M, Szymkowiak J, Calama R, Crone EE, Espelta JM, Lesica P, Marino S, Steele MA, Tenhumberg B, Tyre A, Żywiec M, Kelly D. Does masting scale with plant size? High reproductive variability and low synchrony in small and unproductive individuals. ANNALS OF BOTANY 2020; 126:971-979. [PMID: 32574370 PMCID: PMC7539353 DOI: 10.1093/aob/mcaa118] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/18/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND AND AIMS In a range of plant species, the distribution of individual mean fecundity is skewed and dominated by a few highly fecund individuals. Larger plants produce greater seed crops, but the exact nature of the relationship between size and reproductive patterns is poorly understood. This is especially clear in plants that reproduce by exhibiting synchronized quasi-periodic variation in fruit production, a process called masting. METHODS We investigated covariation of plant size and fecundity with individual-plant-level masting patterns and seed predation in 12 mast-seeding species: Pinus pinea, Astragalus scaphoides, Sorbus aucuparia, Quercus ilex, Q. humilis, Q. rubra, Q. alba, Q. montana, Chionochloa pallens, C. macra, Celmisia lyallii and Phormium tenax. KEY RESULTS Fecundity was non-linearly related to masting patterns. Small and unproductive plants frequently failed to produce any seeds, which elevated their annual variation and decreased synchrony. Above a low fecundity threshold, plants had similar variability and synchrony, regardless of their size and productivity. CONCLUSIONS Our study shows that within-species variation in masting patterns is correlated with variation in fecundity, which in turn is related to plant size. Low synchrony of low-fertility plants shows that the failure years were idiosyncratic to each small plant, which in turn implies that the small plants fail to reproduce because of plant-specific factors (e.g. internal resource limits). Thus, the behaviour of these sub-producers is apparently the result of trade-offs in resource allocation and environmental limits with which the small plants cannot cope. Plant size and especially fecundity and propensity for mast failure years play a major role in determining the variability and synchrony of reproduction in plants.
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Affiliation(s)
- Michał Bogdziewicz
- Department of Systematic Zoology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Jakub Szymkowiak
- Population Ecology Laboratory, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Rafael Calama
- Department of Forest Dynamics and Management, INIA-CIFOR, Ctra A CoruñaMadrid, Spain
| | | | | | - Peter Lesica
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Shealyn Marino
- Department of Biology, Wilkes University, Wilkes-Barre, PA, USA
| | | | - Brigitte Tenhumberg
- School of Biological Sciences and Department of Mathematics, University of Nebraska, Lincoln, NE, USA
| | - Andrew Tyre
- School of Natural Resources, University of Nebraska, Lincoln, NE, USA
| | - Magdalena Żywiec
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz, Kraków, Poland
| | - Dave Kelly
- Centre for Integrative Ecology, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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Minor DM, Kobe RK. Fruit production is influenced by tree size and size-asymmetric crowding in a wet tropical forest. Ecol Evol 2019; 9:1458-1472. [PMID: 30805174 PMCID: PMC6374663 DOI: 10.1002/ece3.4867] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 09/28/2018] [Accepted: 11/23/2018] [Indexed: 11/08/2022] Open
Abstract
In tropical forest communities, seedling recruitment can be limited by the number of fruit produced by adults. Fruit production tends to be highly unequal among trees of the same species, which may be due to environmental factors. We observed fruit production for ~2,000 trees of 17 species across 3 years in a wet tropical forest in Costa Rica. Fruit production was modeled as a function of tree size, nutrient availability, and neighborhood crowding. Following model selection, tree size and neighborhood crowding predicted both the probability of reproduction and the number of fruit produced. Nutrient availability only predicted only the probability of reproduction. In all species, larger trees were more likely to be reproductive and produce more fruit. In addition, number of fruit was strongly negatively related to presence of larger neighboring trees in 13 species; presence of all neighboring trees had a weak-to-moderate negative influence on reproductive status in 16 species. Among various metrics of soil nutrient availability, only sum of base cations was positively associated with reproductive status, and for only four species. Synthesis Overall, these results suggest that direct influences on fruit production tend to be mediated through tree size and crowding from neighboring trees, rather than soil nutrients. However, we found variation in the effects of neighbors and nutrients among species; mechanistic studies of allocation to fruit production are needed to explain these differences.
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Affiliation(s)
- David M. Minor
- Department of Plant Biology, Program in Ecology, Evolutionary Biology, and BehaviorMichigan State UniversityEast LansingMichigan
| | - Richard K. Kobe
- Department of Plant Biology, Program in Ecology, Evolutionary Biology, and BehaviorMichigan State UniversityEast LansingMichigan
- Department of ForestryMichigan State UniversityEast LansingMichigan
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5
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Oddou-Muratorio S, Gauzere J, Bontemps A, Rey JF, Klein EK. Tree, sex and size: Ecological determinants of male vs. female fecundity in three Fagus sylvatica
stands. Mol Ecol 2018; 27:3131-3145. [DOI: 10.1111/mec.14770] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Revised: 05/29/2018] [Accepted: 06/07/2018] [Indexed: 12/25/2022]
Affiliation(s)
| | - Julie Gauzere
- URFM; INRA; Avignon France
- BioSP; INRA; Avignon France
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6
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Alonso C, Pérez R, Bazaga P, Medrano M, Herrera CM. Within-plant variation in seed size and inflorescence fecundity is associated with epigenetic mosaicism in the shrub Lavandula latifolia (Lamiaceae). ANNALS OF BOTANY 2018; 121:153-160. [PMID: 29186299 PMCID: PMC5786237 DOI: 10.1093/aob/mcx140] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 11/02/2017] [Indexed: 05/30/2023]
Abstract
BACKGROUND AND AIMS Sub-individual variation in traits of homologous structures has multiple ecological consequences for individuals and populations. Assessing the evolutionary significance of such effects requires an improved knowledge of the mechanisms underlying within-plant phenotypic heterogeneity. The hypothesis that continuous within-plant variation in some phenotypic traits can be associated with epigenetic mosaicism was examined. METHODS Fifteen individuals of the long-lived, evergreen Mediterranean shrub Lavandula latifolia were studied. Five widely spaced 'modules', each consisting of a single inflorescence plus all its subtending basal leaves, were collected from each shrub. Genomic DNA was extracted from leaf samples and genome-wide cytosine methylation determined by reversed phase high-performance liquid chromatography (HPLC) with spectrofluorimetric detection. The number and mean mass of seeds produced were determined for each inflorescence. An assessment was made of whether (1) leaves from different modules in the same plant differed significantly in global DNA cytosine methylation, and (2) mosaicism in cytosine methylation contributed to explain variation across modules in number and size of seeds. KEY RESULTS Leaves from different modules in the same plant differed in global DNA cytosine methylation. The magnitude of epigenetic mosaicism was substantial, as the variance in DNA methylation among modules of the same shrub was greater than the variance between individuals. Number and mean mass of seeds produced by individual inflorescences varied within plants and were quadratically related to cytosine methylation of subtending leaves, with an optimum at an intermediate methylation level (approx. 25 %). CONCLUSIONS The results support a causal link between global cytosine methylation of leaves in a module and the size and numbers of seeds produced by the associated inflorescence. It is proposed that variation in global DNA methylation within L. latifolia shrubs may result from the concerted action of plant sectoriality and differential exposure of different plant parts to some environmental factor(s) with a capacity to induce durable epigenetic changes.
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Affiliation(s)
- Conchita Alonso
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio, Sevilla, Spain
| | - Ricardo Pérez
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de La Cartuja, CSIC-US, Avda. Américo Vespucio, Sevilla, Spain
| | - Pilar Bazaga
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio, Sevilla, Spain
| | - Mónica Medrano
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio, Sevilla, Spain
| | - Carlos M Herrera
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio, Sevilla, Spain
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7
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Wang B, Ives AR. Tree-to-tree variation in seed size and its consequences for seed dispersal versus predation by rodents. Oecologia 2016; 183:751-762. [DOI: 10.1007/s00442-016-3793-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 12/04/2016] [Indexed: 10/20/2022]
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Herrera CM, Bazaga P. Genetic and epigenetic divergence between disturbed and undisturbed subpopulations of a Mediterranean shrub: a 20-year field experiment. Ecol Evol 2016; 6:3832-3847. [PMID: 28725357 PMCID: PMC5513313 DOI: 10.1002/ece3.2161] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/11/2016] [Accepted: 04/13/2016] [Indexed: 01/19/2023] Open
Abstract
Little is known on the potential of ecological disturbance to cause genetic and epigenetic changes in plant populations. We take advantage of a long‐term field experiment initiated in 1986 to study the demography of the shrub Lavandula latifolia, and compare genetic and epigenetic characteristics of plants in two adjacent subplots, one experimentally disturbed and one left undisturbed, 20 years after disturbance. Experimental setup was comparable to an unreplicated ‘Before‐After‐Control‐Impact’ (BACI) design where a single pair of perturbed and control areas were compared. When sampled in 2005, plants in the two subplots had roughly similar ages, but they had established in contrasting environments: dense conspecific population (‘Undisturbed’ subpopulation) versus open area with all conspecifics removed (‘Disturbed’ subpopulation). Plants were characterized genetically and epigenetically using amplified fragment length polymorphism (AFLP) and two classes of methylation‐sensitive AFLP (MSAP) markers. Subpopulations were similar in genetic diversity but differed in epigenetic diversity and multilocus genetic and epigenetic characteristics. Epigenetic divergence between subpopulations was statistically unrelated to genetic divergence. Bayesian clustering revealed an abrupt linear boundary between subpopulations closely coincident with the arbitrary demarcation line between subplots drawn 20 years back, which supports that genetic and epigenetic divergence between subpopulations was caused by artificial disturbance. There was significant fine‐scale spatial structuring of MSAP markers in both subpopulations, which in the Undisturbed one was indistinguishable from that of AFLP markers. Genetic differences between subpopulations could be explained by divergent selection alone, while the concerted action of divergent selection and disturbance‐driven appearance of new methylation variants in the Disturbed subpopulation is proposed to explain epigenetic differences. This study provides the first empirical evidence to date suggesting that relatively mild disturbances could leave genetic and epigenetic signatures on the next adult generation of long‐lived plants.
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Affiliation(s)
- Carlos M Herrera
- Estación Biológica de Doñana Consejo Superior de Investigaciones Científicas (CSIC) Avenida Américo Vespucio s/n Isla de La Cartuja Sevilla 41092 Spain
| | - Pilar Bazaga
- Estación Biológica de Doñana Consejo Superior de Investigaciones Científicas (CSIC) Avenida Américo Vespucio s/n Isla de La Cartuja Sevilla 41092 Spain
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9
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Oexle K. Evaluation of the evenness score in next-generation sequencing. J Hum Genet 2016; 61:627-32. [PMID: 27074764 DOI: 10.1038/jhg.2016.21] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 02/21/2016] [Accepted: 02/21/2016] [Indexed: 12/12/2022]
Abstract
The evenness score (E) in next-generation sequencing (NGS) quantifies the homogeneity in coverage of the NGS targets. Here I clarify the mathematical description of E, which is 1 minus the integral from 0 to 1 over the cumulative distribution function F(x) of the normalized coverage x, where normalization means division by the mean, and derive a computationally more efficient formula; that is, 1 minus the integral from 0 to 1 over the probability density distribution f(x) times 1-x. An analogous formula for empirical coverage data is provided as well as fast R command line scripts. This new formula allows for a general comparison of E with the coefficient of variation (=standard deviation σ of normalized data) which is the conventional measure of the relative width of a distribution. For symmetrical distributions, including the Gaussian, E can be predicted closely as 1-σ(2)/2⩾E⩾1-σ/2 with σ⩽1 owing to normalization and symmetry. In case of the log-normal distribution as a typical representative of positively skewed biological data, the analysis yields E≈exp(-σ*/2) with σ*(2)=ln(σ(2)+1) up to large σ (⩽3), and E≈1-F(exp(-1)) for very large σ (⩾2.5). In the latter kind of rather uneven coverage, E can provide direct information on the fraction of well-covered targets that is not immediately delivered by the normalized σ. Otherwise, E does not appear to have major advantages over σ or over a simple score exp(-σ) based on it. Actually, exp(-σ) exploits a much larger part of its range for the evaluation of realistic NGS outputs.
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Affiliation(s)
- Konrad Oexle
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland
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10
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Wenk EH, Falster DS. Quantifying and understanding reproductive allocation schedules in plants. Ecol Evol 2015; 5:5521-38. [PMID: 27069603 PMCID: PMC4813122 DOI: 10.1002/ece3.1802] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/13/2015] [Accepted: 09/20/2015] [Indexed: 11/15/2022] Open
Abstract
A plant's reproductive allocation (RA) schedule describes the fraction of surplus energy allocated to reproduction as it increases in size. While theorists use RA schedules as the connection between life history and energy allocation, little is known about RA schedules in real vegetation. Here we review what is known about RA schedules for perennial plants using studies either directly quantifying RA or that collected data from which the shape of an RA schedule can be inferred. We also briefly review theoretical models describing factors by which variation in RA may arise. We identified 34 studies from which aspects of an RA schedule could be inferred. Within those, RA schedules varied considerably across species: some species abruptly shift all resources from growth to reproduction; most others gradually shift resources into reproduction, but under a variety of graded schedules. Available data indicate the maximum fraction of energy allocated to production ranges from 0.1 to 1 and that shorter lived species tend to have higher initial RA and increase their RA more quickly than do longer-lived species. Overall, our findings indicate, little data exist about RA schedules in perennial plants. Available data suggest a wide range of schedules across species. Collection of more data on RA schedules would enable a tighter integration between observation and a variety of models predicting optimal energy allocation, plant growth rates, and biogeochemical cycles.
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Riday H, Smith MA, Peel MD. A simple model for pollen-parent fecundity distributions in bee-pollinated forage legume polycrosses. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1865-1879. [PMID: 26105686 DOI: 10.1007/s00122-015-2553-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 06/05/2015] [Indexed: 06/04/2023]
Abstract
A simple Weibull distribution based empirical model that predicts pollen-parent fecundity distributions based on polycross size alone has been developed in outbred forage legume species for incorporation into quantitative genetic theory. Random mating or panmixis is a fundamental assumption in quantitative genetic theory. Random mating is sometimes thought to occur in actual fact, although a large body of empirical work shows that this is often not the case in nature. Models have been developed to explain many non-random mating phenomena. This paper measured pollen-parent fecundity distributions among outbred perennial forage legume species [autotetraploid alfalfa (Medicago sativa L.), autohexaploid kura clover (Trifolium ambiguum M. Bieb.), and diploid red clover (Trifolium pratense L.)] in ten polycrosses ranging in size (N) from 9 to 94 pollinated with bee pollinators [Bumble Bees (Bombus impatiens Cr.) and leafcutter bees (Megachile rotundata F.)]. A Weibull distribution best fit the observed pollen-parent fecundity distributions. After standardizing data among the 10 polycrosses, a single Weibull distribution-based model was obtained with an R (2) of 0.978. The model is able to predict pollen-parent fecundity distributions based on polycross size alone. The model predicts that the effective polycross size will be approximately 9 % smaller than under random mating (i.e., N e/N ~ 0.91). The model is simple and can easily be incorporated into other models or simulations requiring a pollen-parent fecundity distribution. Further work is needed to determine how widely applicable the model is.
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Affiliation(s)
- Heathcliffe Riday
- U.S. Dairy Forage Research Center, USDA-ARS, Madison, WI, 53706, USA,
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12
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Broadhurst L. Pollen dispersal in fragmented populations of the dioecious wind-pollinated tree, Allocasuarina verticillata (drooping sheoak, drooping she-oak; Allocasuarinaceae). PLoS One 2015; 10:e0119498. [PMID: 25742183 PMCID: PMC4350918 DOI: 10.1371/journal.pone.0119498] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 01/21/2015] [Indexed: 11/28/2022] Open
Abstract
Vegetation clearing, land modification and agricultural intensification have impacted on many ecological communities around the world. Understanding how species respond to fragmentation and the scales over which functionality is retained, can be critical for managing biodiversity in agricultural landscapes. Allocasuarina verticillata (drooping sheoak, drooping she-oak) is a dioecious, wind-pollinated and -dispersed species with key conservation values across southeastern Australia. But vegetation clearing associated with agricultural expansion has reduced the abundance and spatial distribution of this species in many regions. Spatial genetic structure, relatedness among trees, pollen dispersal and mating patterns were examined in fragmented A. verticillata populations selected to represent the types of remnants that now characterise this species. Short scale spatial genetic structure (5-25 m) and relatedness among trees were observed in most populations. Unexpectedly, the two male trees closest to each female did not have a reproductive advantage accounting for only 4-15% of the seed produced in larger populations. Biparental inbreeding was also generally low (<4%) with limited evidence of seed crop domination by some male trees. More male trees contributed to seed crops in linear remnants (mean 17) compared to those from patch remnants (mean 11.3) which may reflect differences in pollen dispersal within the two remnant types. On average, pollen travels ~100 m irrespective of remnant type but was also detected to have dispersed as far as 1 km in open landscapes. Low biparental inbreeding, limited reproductive assurance for near-neighbour and probably related males and variability in the distances over which females sample pollen pools suggest that some mechanism to prevent matings between relatives exists in this species.
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Affiliation(s)
- Linda Broadhurst
- Centre for Australian National Biodiversity Research, National Research Collections, CSIRO, Canberra, Australia
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13
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Barks PM, Laird RA. Senescence in duckweed: age‐related declines in survival, reproduction and offspring quality. Funct Ecol 2014. [DOI: 10.1111/1365-2435.12359] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Patrick M. Barks
- Department of Biological Sciences University of Lethbridge Lethbridge AlbertaT1K 3M4 Canada
| | - Robert A. Laird
- Department of Biological Sciences University of Lethbridge Lethbridge AlbertaT1K 3M4 Canada
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Müller M, Siles L, Cela J, Munné-Bosch S. Perennially young: seed production and quality in controlled and natural populations of Cistus albidus reveal compensatory mechanisms that prevent senescence in terms of seed yield and viability. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:287-97. [PMID: 24218328 PMCID: PMC3883297 DOI: 10.1093/jxb/ert372] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The question of whether or not perennial plants senesce at the organism level remains unresolved. The aim of this study was to unravel whether or not plant age can influence the production and composition of seeds. Flower and seed production was examined in 3-, 8-, and 13-year-old Cistus albidus plants growing in experimental plots corresponding to the F2, F1, and F0 generations of the same population. Furthermore, the phytohormone, fatty acid, and vitamin E content of the seeds was evaluated, and their viability was examined. Whether or not age-related differences in seed quality were observed in a natural population in the Montserrat Mountains (NE Spain) was also tested. The results indicate that under controlled conditions, the oldest plants not only produced fewer flowers, but also had higher rates of embryo abortion in mature seeds. However, germination capacity was not negatively affected by plant ageing. Seeds of the oldest plants contained significantly higher salicylic acid, jasmonic acid, and vitamin E levels compared with those from younger plants. Despite vigour (in terms of plant growth) being severely reduced due to harsh environmental conditions in the natural population, the oldest individuals produced seeds with no decline in viability. Seed biomass was instead positively correlated with seed viability. In conclusion, increased plant size may explain the loss of seed viability in the experimental field, but older smaller individuals in natural populations can escape senescence in terms of seed viability loss.
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Affiliation(s)
- Maren Müller
- * These authors contributed equally to this work
| | - Laura Siles
- * These authors contributed equally to this work
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Moran EV, Clark JS. Causes and consequences of unequal seedling production in forest trees: a case study in red oaks. Ecology 2012; 93:1082-94. [PMID: 22764494 DOI: 10.1890/11-1428.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Inequality in reproductive success has important implications for ecological and evolutionary dynamics, but lifetime reproductive success is challenging to measure in long-lived species such as forest trees. While seed production is often used as a proxy for overall reproductive success, high mortality of seeds and the potential for trade-offs between seed number and quality draw this assumption into question. Parentage analyses of established seedlings can bring us one step closer to understanding the causes and consequences of variation in reproductive success. In this paper we demonstrate a new method for estimating individual seedling production and average percentage germination, using data from two mixed-species populations of red oaks (Quercus rubra, Q. velutina, Q. falcata, and Q. coccinea). We use these estimates to examine the distribution of female reproductive success and to test the relationship between seedling number and individual seed production, age, and growth rate. We show that both seed and seedling production are highly skewed, roughly conforming to zero-inflated lognormal distributions, rather than to the Poisson or negative-binomial distributions often assumed by population genetics analyses. While the number of established offspring is positively associated with mean annual seed production, a lower proportion of seeds from highly fecund individuals become seedlings. Our red oak populations also show evidence of trade-offs between growth rate and reproductive success. The high degree of inequality in seedling production shown here for red oaks, and by previous studies in other species, suggests that many trees may be more vulnerable to genetic drift than previously thought, if immigration in limited by fragmentation or other environmental changes.
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Affiliation(s)
- Emily V Moran
- National Institute for Mathematical and Biological Synthesis, 1534 White Avenue, University of Tennessee, Knoxville, Tennessee 37996, USA.
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Moran EV, Clark JS. Between-site differences in the scale of dispersal and gene flow in red oak. PLoS One 2012; 7:e36492. [PMID: 22563504 PMCID: PMC3341347 DOI: 10.1371/journal.pone.0036492] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 04/09/2012] [Indexed: 11/18/2022] Open
Abstract
Background Nut-bearing trees, including oaks (Quercus spp.), are considered to be highly dispersal limited, leading to concerns about their ability to colonize new sites or migrate in response to climate change. However, estimating seed dispersal is challenging in species that are secondarily dispersed by animals, and differences in disperser abundance or behavior could lead to large spatio-temporal variation in dispersal ability. Parentage and dispersal analyses combining genetic and ecological data provide accurate estimates of current dispersal, while spatial genetic structure (SGS) can shed light on past patterns of dispersal and establishment. Methodology and Principal Findings In this study, we estimate seed and pollen dispersal and parentage for two mixed-species red oak populations using a hierarchical Bayesian approach. We compare these results to those of a genetic ML parentage model. We also test whether observed patterns of SGS in three size cohorts are consistent with known site history and current dispersal patterns. We find that, while pollen dispersal is extensive at both sites, the scale of seed dispersal differs substantially. Parentage results differ between models due to additional data included in Bayesian model and differing genotyping error assumptions, but both indicate between-site dispersal differences. Patterns of SGS in large adults, small adults, and seedlings are consistent with known site history (farmed vs. selectively harvested), and with long-term differences in seed dispersal. This difference is consistent with predator/disperser satiation due to higher acorn production at the low-dispersal site. While this site-to-site variation results in substantial differences in asymptotic spread rates, dispersal for both sites is substantially lower than required to track latitudinal temperature shifts. Conclusions Animal-dispersed trees can exhibit considerable spatial variation in seed dispersal, although patterns may be surprisingly constant over time. However, even under favorable conditions, migration in heavy-seeded species is likely to lag contemporary climate change.
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Affiliation(s)
- Emily V Moran
- National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, Tennessee, United States of America.
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Haymes KL, Fox GA. Variation among individuals in cone production in Pinus palustris (Pinaceae). AMERICAN JOURNAL OF BOTANY 2012; 99:640-645. [PMID: 22434774 DOI: 10.3732/ajb.1100339] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY Reproductive output varies considerably among individuals within plant populations, and this is especially so in cone production of conifers. While this variation can have substantial effects on populations, little is known about its magnitude or causes. METHODS We studied variation in cone production for 2 years within a population of Pinus palustris Mill. (longleaf pine; Pinaceae). Using hurdle models, we evaluated the importance of burn treatments, tree size (dbh), canopy status (open, dominant, subordinate), and number of conspecific neighbors within 4 m (N(4)). KEY RESULTS Cone production of individuals-even after accounting for other variables-was strongly correlated between years. Trees in plots burned every 1, 2, or 5 years produced more cones than those burned every 7 years, or unburned. Larger trees tend to produce more cones, but the large effects of the other factors studied caused substantial scatter in the dbh-cone number relationship. Among trees in the open, dbh had little explanatory power. Subordinate trees with three neighbors produced no cones. CONCLUSIONS Tree size alone was a weak predictor of cone production. Interactions with neighbors play an important role in generating reproductive heterogeneity, and must be accounted for when relating cone production to size. The strong between-year correlation, together with the large variance in cone production among trees without neighbors, suggests that still more of the variance may be explainable, but requires factors outside of our study.
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Affiliation(s)
- Kelly L Haymes
- Department of Integrative Biology, University of South Florida, Tampa, Florida 33620, USA
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Oñate M, García MB, Munné-Bosch S. Age and sex-related changes in cytokinins, auxins and abscisic acid in a centenarian relict herbaceous perennial. PLANTA 2012; 235:349-358. [PMID: 21909759 DOI: 10.1007/s00425-011-1513-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 08/24/2011] [Indexed: 05/27/2023]
Abstract
It is still an unsolved question of fundamental biology if, and how, perennial plants senesce. Here, age- and sex-related changes in phytohormones were tested in Borderea pyrenaica, a small dioecious geophyte relict of the Tertiary with one of the longest lifespan ever recorded for any non-clonal herb (more than 300 years). Biomass allocation, together with levels of cytokinins, auxins and absicisic acid, and other indicators of leaf physiology (chlorophylls, lipid peroxidation and F (v)/F (m) ratio) were measured in juvenile and mature plants, including both males and females of three age classes (up to 50 years, 50-100 years, and over 100 years). Plants maintained intact capacity of their vegetative growth and reproductive potential. Cytokinin levels decreased with age, but only in females. Such sex-related differences, however, were not associated with symptoms of physiological deterioration in leaves, but with an increased reproductive effort in females. It is concluded that B. pyrenaica does not show clear signs of senescence at the organism level. Altered cytokinin levels in females were associated with their reproductive effort, rather than to a degenerative process. The alternate use of five meristematic points in the tuber could explain the extraordinary longevity of this species.
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Affiliation(s)
- Marta Oñate
- Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal 645, 08028 Barcelona, Spain
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Herrera CM, Bazaga P. Untangling individual variation in natural populations: ecological, genetic and epigenetic correlates of long-term inequality in herbivory. Mol Ecol 2011; 20:1675-88. [PMID: 21466603 DOI: 10.1111/j.1365-294x.2011.05026.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Individual variation in ecologically important features of organisms is a crucial element in ecology and evolution, yet disentangling its underlying causes is difficult in natural populations. We applied a genomic scan approach using amplified fragment length polymorphism (AFLP) markers to quantify the genetic basis of long-term individual differences in herbivory by mammals at a wild population of the violet Viola cazorlensis monitored for two decades. In addition, methylation-sensitive amplified polymorphism (MSAP) analyses were used to investigate the association between browsing damage and epigenetic characteristics of individuals, an aspect that has been not previously explored for any wild plant. Structural equation modelling was used to identify likely causal structures linking genotypes, epigenotypes and herbivory. Individuals of V. cazorlensis differed widely in the incidence of browsing mammals over the 20-year study period. Six AFLP markers (1.6% of total) were significantly related to herbivory, accounting altogether for 44% of population-wide variance in herbivory levels. MSAP analyses revealed considerable epigenetic variation among individuals, and differential browsing damage was significantly related to variation in multilocus epigenotypes. In addition, variation across plants in epigenetic characteristics was related to variation in several herbivory-related AFLP markers. Statistical comparison of alternative causal models suggested that individual differences in herbivory are the outcome of a complex causal structure where genotypes and epigenotypes are interconnected and have direct and indirect effects on herbivory. Insofar as methylation states of MSAP markers influential on herbivory are transgenerationally heritable, herbivore-driven evolutionary changes at the study population will involve correlated changes in genotypic and epigenotypic distributions.
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Affiliation(s)
- C M Herrera
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas, Avenida Américo Vespucio s/n, Isla de La Cartuja, Sevilla 41092, Spain.
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Aragón CF, Méndez M, Escudero A. Linkages among life-history components through time: Carryover effects on the demography of a short-lived polycarpic plant. AMERICAN JOURNAL OF BOTANY 2010; 97:1492-7. [PMID: 21616903 DOI: 10.3732/ajb.1000072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
PREMISE OF THE STUDY Current reproduction in polycarpic plants may be affected by a wide variety of factors, including carryover or "historical" effects derived from environments experienced early in life and from previous investments in organ preformation or other life functions, such as growth or reproduction. Historical effects as determinants of plant reproductive success in a specific season have received considerably less attention than events during the current reproductive episode, especially for short-lived plants. • METHODS We used structural equation modeling to assess direct and indirect relations between past reproduction and both subsequent reproduction and growth in Helianthemum squamatum, a short-lived polycarpic plant. Additionally, we explored the effects of current reproduction on future survival (binomial variable) by using logistic regression. • KEY RESULTS Historical effects derived from previous growth positively affected current reproduction, suggesting the existence of a reproductive hierarchy in the population, in which some individuals are consistently better growers and seeders. The lack of effects of current reproduction on future reproduction, together with the existence of a negative effect on future survival, suggests that to invest maximally in reproduction at the expense of a short life span may be the optimal strategy for H. squamatum, a species inhabiting very unpredictable ecosystems. • CONCLUSIONS Historical effects derived from past investments in growth or reproduction may have important consequences for current plant performance and may play an essential role in shaping life histories.
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Affiliation(s)
- Cristina F Aragón
- Área de Biodiversidad y Conservación, Departamento de Biología y Geología, Universidad Rey Juan Carlos, C/Tulipán s/n 28933 Móstoles, Madrid, Spain
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Espeland EK, O'Farrell MR. Small variance in growth rates in annual plants has large effects on genetic drift. AMERICAN JOURNAL OF BOTANY 2010; 97:1407-1411. [PMID: 21616892 DOI: 10.3732/ajb.1000006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
PREMISE OF THE STUDY Effective population size (N(e)) is a critical index of the evolutionary capacity of populations. Low N(e) indicates that standing genetic diversity is susceptible to loss via stochastic processes (and inbreeding) and is, therefore, unavailable for natural selection to act upon. Reported N(e) in plant populations is often quite low. What biological and ecological factors might produce such low N(e) • METHODS We conducted a simulation model to test the effect of randomly assigned and autocorrelated growth rates of annual plants on plant-size distributions at the end of the growing season. Because plant size is directly correlated with reproductive output in annual plants, variation in plant size reflects variation in reproduction, and thus our modeled size distributions can be used to estimate N(e). • KEY RESULTS Randomly assigned growth rates had a negligble effect on N(e)/N. Autocorrelated growth rates decreased N(e)/N as the length of the growing season increased. This was the case even when the variance in growth rates was as low as 0.1% of the mean. • CONCLUSIONS While intrinsic plant biology can affect the degree of growth autocorrelation, ecological factors such as competition, herbivory, and abiotic stress can increase or decrease levels of growth autocorrelation. Ecological factors that increase growth autocorrelation can have significant effects on genetic drift within populations.
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Affiliation(s)
- Erin K Espeland
- Graduate Group in Ecology, University of California, Davis, California 95616, USA
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