scholarly journals The Fisher-Wright model with deterministic seed bank and selection

2015 ◽  
Author(s):  
Bendix Koopmann ◽  
Johannes Müeller ◽  
Aurélien Tellier ◽  
Daniel Živković
Keyword(s):  
Genetic Diversity ◽  
Frequency Spectrum ◽  
Seed Bank ◽  
Seed Banks ◽  
Slowing Down ◽  
Selection Equilibrium ◽  
Site Frequency Spectrum ◽  
The Times ◽  
Combined Impact ◽  
Number Of Seeds

AbstractSeed banks are a common characteristics to many plant species, which allow storage of genetic diversity in the soil as dormant seeds for various periods of time. We investigate an above-ground population following a Fisher-Wright model with selection coupled with a deterministic seed bank assuming the length of the seed bank is kept constant and the number of seeds is large. To assess the combined impact of seed banks and selection on genetic diversity, we derive a general diffusion model. We compute the equilibrium solution of the site-frequency spectrum and derive the times to fixation of an allele with and without selection. Finally, it is demonstrated that seed banks enhance the effect of selection onto the site-frequency spectrum while slowing down the time until the mutation-selection equilibrium is reached.

scholarly journals The effect of strong purifying selection on genetic diversity

2017 ◽  
Author(s):  
Ivana Cvijović ◽  
Benjamin H. Good ◽  
Michael M. Desai
Keyword(s):  
Genetic Diversity ◽  
Frequency Spectrum ◽  
Purifying Selection ◽  
Genomic Diversity ◽  
Small Samples ◽  
Direct Selection ◽  
Background Selection ◽  
Deleterious Mutations ◽  
Site Frequency Spectrum ◽  
Neutral Mutations

Purifying selection reduces genetic diversity, both at sites under direct selection and at linked neutral sites. This process, known as background selection, is thought to play an important role in shaping genomic diversity in natural populations. Yet despite its importance, the effects of background selection are not fully understood. Previous theoretical analyses of this process have taken a backwards-time approach based on the structured coalescent. While they provide some insight, these methods are either limited to very small samples or are computationally prohibitive. Here, we present a new forward-time analysis of the trajectories of both neutral and deleterious mutations at a nonrecombining locus. We find that strong purifying selection leads to remarkably rich dynamics: neutral mutations can exhibit sweep-like behavior, and deleterious mutations can reach substantial frequencies even when they are guaranteed to eventually go extinct. Our analysis of these dynamics allows us to calculate analytical expressions for the full site frequency spectrum. We find that whenever background selection is strong enough to lead to a reduction in genetic diversity, it also results in substantial distortions to the site frequency spectrum, which can mimic the effects of population expansions or positive selection. Because these distortions are most pronounced in the low and high frequency ends of the spectrum, they become particularly important in larger samples, but may have small effects in smaller samples. We also apply our forward-time framework to calculate other quantities, such as the ultimate fates of polymorphisms or the fitnesses of their ancestral backgrounds.

Effect of different treatments on the seed bank of grazed and ungrazed Baltic seashore meadows

1998 ◽  
Vol 76 (7) ◽  
pp. 1188-1197 ◽  
Author(s):  
Heli M. Jutila b. Erkkilä
Keyword(s):  
Seed Bank ◽  
Brackish Water ◽  
Salt Water ◽  
Tap Water ◽  
Cold Treatment ◽  
Abundant Species ◽  
Seed Banks ◽  
The West ◽  
Pesticide Treatment ◽  
Juncus Gerardii

Seed banks of two seashore meadows were studied on the west coast of Finland (latitude 61°30'-61°33'N, longitude 21°28'-21°41'E). Samples were taken in June to a depth of 10 cm in the geolittoral zone of the grazed and ungrazed transects. The grazed samples were halved lengthwise: one half was grown immediately, the other after cold treatment. One third of the all samples was treated as controls, one third was watered with brackish water, and one third was given a pesticide treatment. Altogether, 13 926 seedlings germinated and 25 species were identified (three annuals, two biennials, and the rest perennials). Most seedlings were perennial monocots, with Juncus gerardii Loisel. the most abundant species. The seed bank was significantly larger and richer in the ungrazed site than in the grazed site. Cold treatment reduced the number of germinating species and seedlings. In the grazed and non-cold-treated samples, the numbers of species and seedlings were highest in the pesticide treatment. In ungrazed samples there were no significant differences among treatments. After the cold treatment, the least number of species and seedlings was produced by the salt-water treatment. Changing brackish water to tap water led to a burst of germination, especially of J. gerardii. The seed bank of the upper geolittoral zone was richer than that of the middle geolittoral. The multivariate classification and ordination groupings are based on the abundances of J. gerardii and Glaux maritima L.; different treatments were not distinguishable. There was a low resemblance between the seed bank and the aboveground vegetation.Key words: seed bank, salinity, pesticide, seashore meadow, cold treatment, vegetation.

Seed production and seedling emergence of Giant Parramatta grass on the north coast of New South Wales

1996 ◽  
Vol 36 (3) ◽  
pp. 299 ◽  
Author(s):  
TS Andrews ◽  
RDB Whalley ◽  
CE Jones
Keyword(s):  
Seed Production ◽  
Seed Bank ◽  
New South ◽  
New South Wales ◽  
Seed Banks ◽  
North Coast ◽  
The North ◽  
South Wales ◽  
Seed Fall ◽  
The Impact

Inputs and losses from Giant Parramatta grass [GPG, Sporobolus indicus (L.) R. Br. var. major (Buse) Baaijens] soil seed banks were quantified on the North Coast of New South Wales. Monthly potential seed production and actual seed fall was estimated at Valla during 1991-92. Total potential production was >668 000 seeds/m2 for the season, while seed fall was >146000 seeds/m2. Seed fall >10000 seeds/m2.month was recorded from January until May, with further seed falls recorded in June and July. The impact of seed production on seed banks was assessed by estimating seed banks in the seed production quadrats before and after seed fall. Seed banks in 4 of the 6 sites decreased in year 2, although seed numbers at 1 damp site increased markedly. Defoliation from mid-December until February, April or June prevented seed production, reducing seed banks by 34% over 7 months. Seed banks in undefoliated plots increased by 3300 seeds/m2, although seed fall was estimated at >114 000 seeds/m2. Emergence of GPG seedlings from artificially established and naturally occurring, persistent seed banks was recorded for 3 years from bare and vegetated treatment plots. Sown seeds showed high levels of innate dormancy and only 4% of seeds emerged when sown immediately after collection. Longer storage of seeds after collection resulted in more seedlings emerging. Estimates of persistent seed banks ranged from 1650 to about 21260 seeds/m2. Most seedlings emerged in spring or autumn and this was correlated with rainfall but not with ambient temperatures. Rates of seed bank decline in both bare and vegetated treatment plots was estimated by fitting exponential decay curves to seed bank estimates. Assuming no further seed inputs, it was estimated that it would take about 3 and 5 years, respectively, for seed banks to decline to 150 seeds/m2 in bare and vegetated treatments.

scholarly journals Diversity Assessment of Some Sesame (Sesamum indicum L.) Genotypes Cultivated in Northern Ghana Using Morphological and Simple Sequence Repeat (SSR) Markers

2019 ◽  
Vol 2019 ◽  
pp. 1-10 ◽  
Author(s):  
Raphael Adu-Gyamfi ◽  
Ruth Prempeh ◽  
Issahaku Zakaria
Keyword(s):  
Genetic Diversity ◽  
Plant Height ◽  
Ssr Markers ◽  
Analysis Of Variance ◽  
Morphological Data ◽  
Northern Ghana ◽  
Land Races ◽  
Diversity Assessment ◽  
Parental Lines ◽  
Number Of Seeds

In Ghana, sesame is cultivated in some districts of northern Ghana. Genotypes cultivated are land races that are low yielding leading to decline in production. There is the need for improvement of these land races to generate high yielding cultivars. Characterization of genetic diversity of the sesame land races will be of great value in assisting in parental lines selection for sesame breeding programmes in Ghana. Twenty-five sesame land races were collected from five districts in northern Ghana noted for sesame cultivation. Seeds collected were planted in three replicates in randomized complete block design and were evaluated for a number of morphological characters. Data collected were subjected to Principal Component Analysis (PCA) and a dendrogram showing similarity between the accessions were drawn. Data on number of capsules per plant, number of seeds per capsule, and plant height at flowering were subjected to analysis of variance using GenStat Discovery Edition 4. Molecular genetic diversity was assessed by using thirty eight SSR markers widely distributed across sesame genome to characterize the materials. Twenty-one out of the 38 primers were polymorphic. Cluster analyses using the Euclidean similarity test and a complete link clustering method were used to make a dendrogram out of the morphological data. Analysis of variance showed that capsule number was significantly different; a range of 54.9 and 146.7 was produced. The number of seeds per capsule varied significantly and the variation between highest and lowest accession in seed production was 33%. Plant height was also significantly different ranging from 60.6 to 94.1 cm. Using morphological traits the accessions clustered into two major groups and two minor groups and variation among accessions were 10-61%. On the other hand, SSR marker-based dendrogram revealed five major and two minor groups. It showed that variation among the accessions was low, 10-20%. Heterozygosity was 0.52, total alleles produced were 410, and average allele per locus was 19.52. Six accessions, C3, C4, S5, W1, W3, and W5 fell in five different clusters in the SSR dendrogram and in six clusters in the morphomolecular based dendrogram. These accessions were noted for high capsule number per plant and seeds number per capsule and are recommended for consideration as potential parental lines for breeding programme for high yield.

Buried seed populations in the montane, subalpine, and alpine belts of Mont Jacques-Cartier, Quebec

1988 ◽  
Vol 66 (1) ◽  
pp. 101-107 ◽  
Author(s):  
Hubert Morin ◽  
Serge Payette
Keyword(s):  
Seed Bank ◽  
Linear Correlation ◽  
Altitudinal Gradient ◽  
Number Of Species ◽  
Significant Linear Correlation ◽  
Seed Population ◽  
Close Relationship ◽  
Buried Seed ◽  
Study Sites ◽  
Number Of Seeds

The analysis of the total buried seed population along an altitudinal gradient in the Mont Jacques-Cartier area, southern Quebec, reveals a close relationship between buried seed flora and aboveground vegetation. Eighty-one percent of the species present in the total buried seed population were present in the aboveground vegetation of the study sites. The total number of seeds in the buried seed population, the number of species in the total buried seed population, and the number of seeds and species in the seed bank did not show any significant linear correlation with altitude. A shift from a boreal to an arctic–alpine buried seed population with increasing altitude was observed, instead of a decrease in seed bank size.

scholarly journals Seed Banks Alter the Rate and Direction of Molecular Evolution in Bacillus subtilis

2021 ◽  
Author(s):  
William R. Shoemaker ◽  
Evgeniya Polezhaeva ◽  
Kenzie B. Givens ◽  
Jay T. Lennon
Keyword(s):  
Bacillus Subtilis ◽  
Molecular Evolution ◽  
Seed Bank ◽  
Negative Selection ◽  
Evolutionary Dynamics ◽  
Genetic Manipulation ◽  
Seed Banks ◽  
Rate Of Molecular Evolution ◽  
Over Time ◽  
Growth And Reproduction

Fluctuations in the availability of resources constrains the growth and reproduction of individuals, which in turn effects the evolution of their respective populations. Many organisms are able to respond to fluctuations by entering a reversible state of reduced metabolic activity, a phenomenon known as dormancy. This pool of dormant individuals (i.e., a seed bank) does not reproduce and is expected to act as an evolutionary buffer, though it is difficult to observe this effect directly over an extended evolutionary timescale. Through genetic manipulation, we analyze the molecular evolutionary dynamics of Bacillus subtilis populations in the presence and absence of a seed bank over 700 days. We find that the ability to enter a dormant state increases the accumulation of genetic diversity over time and alters the trajectory of mutations, findings that are recapitulated using simulations based on a simple mathematical model. While the ability to form a seed bank does not alter the degree of negative selection, we find that it consistently alters the direction of molecular evolution across genes. Together, these results show that the ability to form a seed bank affects the direction and rate of molecular evolution over an extended evolutionary timescale.

scholarly journals Similarity between seed bank and herb layer in a natural deciduous temperate lowland forest

2011 ◽  
Vol 79 (2) ◽  
pp. 157-166 ◽  
Author(s):  
Maciej Wódkiewicz ◽  
Anna Justyna Kwiatkowska-Falińska
Keyword(s):  
Seed Bank ◽  
Soil Seed Bank ◽  
Similarity Index ◽  
Seed Banks ◽  
Herb Layer ◽  
Managed Forests ◽  
Lowland Forest ◽  
Soil Seed Banks ◽  
Dominance Structure ◽  
Species Similarity

Forest seed banks mostly studied in managed forests proved to be small, species poor and not reflecting aboveground species composition. Yet studies conducted in undisturbed communities indicate a different seed bank characteristic. Therefore we aimed at describing soil seed bank in an undisturbed forest in a remnant of European lowland temperate forests, the Białowieża Forest. We compared similarity between the herb layer and seed bank, similarity of seed bank between different patches, and dominance structure of species in the herb layer and in the seed bank of two related oak-hornbeam communities. We report relatively high values of Sorensen species similarity index between herb layer and seed bank of both patches. This suggests higher species similarity of the herb layer and soil seed bank in natural, unmanaged forests represented by both plots than in fragmented communities influenced by man. Although there was a set of core seed bank species present at both plots, yielding high Sorensen species similarity index values, considerable differences between plots in seed bank size and dominance structure of species were found, indicating spatial variability of studied seed bank generated by edaphic conditions. Dominance structure of species in the herb layer was not reflected in the underlying seed bank. This stresses, that natural forest regeneration cannot rely only on the seed bank, although some forest species are capable of forming soil seed banks. While forest seed banks may not reflect vegetation composition of past successional stages, they may inform on history and land use of a specific plot.

scholarly journals Non-parametric estimation of population size changes from the site frequency spectrum

2017 ◽  
Author(s):  
Berit Lindum Waltoft ◽  
Asger Hobolth
Keyword(s):  
Population Size ◽  
Frequency Spectrum ◽  
Goodness Of Fit ◽  
Weighted Average ◽  
Cubic Spline ◽  
Parametric Estimation ◽  
New Method ◽  
Eigenvalue Decomposition ◽  
Human Populations ◽  
Site Frequency Spectrum

AbstractThe variability in population size is a key quantity for understanding the evolutionary history of a species. We present a new method, CubSFS, for estimating the changes in population size of a panmictic population from the site frequency spectrum. First, we provide a straightforward proof for the expression of the expected site frequency spectrum depending only on the population size. Our derivation is based on an eigenvalue decomposition of the instantaneous coalescent rate matrix. Second, we solve the inverse problem of determining the variability in population size from an observed SFS. Our solution is based on a cubic spline for the population size. The cubic spline is determined by minimizing the weighted average of two terms, namely (i) the goodness of fit to the SFS, and (ii) a penalty term based on the smoothness of the changes. The weight is determined by cross-validation. The new method is validated on simulated demographic histories and applied on data from nine different human populations.

scholarly journals The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: the effects of sequencing techniques and sampling strategies

2018 ◽  
Author(s):  
Christelle Fraïsse ◽  
Camille Roux ◽  
Pierre-Alexandre Gagnaire ◽  
Jonathan Romiguier ◽  
Nicolas Faivre ◽  
...  
Keyword(s):  
Frequency Spectrum ◽  
Approximate Bayesian Computation ◽  
Exome Capture ◽  
Bayesian Computation ◽  
Sampling Strategies ◽  
Migration Rates ◽  
History Of ◽  
Site Frequency Spectrum ◽  
Approximate Bayesian ◽  
Number Of Individuals

AbstractGenome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymous mutations computed either from exome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the joint site frequency spectrum, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e. periodic connectivity) and across genes (i.e. genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding site frequency spectrum, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed.

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