Fixation and effective size in a haploid–diploid population with asexual reproduction

Bessho, Kazuhiro; Otto, Sarah P.

doi:10.1016/j.tpb.2021.11.002

Cited by 6 publications

(10 citation statements)

References 35 publications

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“…Our fixation probability results deviate drastically from these classical expectations, a disparity that is consistent with the findings of other studies. In models of haploid–diploid populations (populations with a mixture of haploid and diploid individuals, with asexual reproduction), Bessho and Otto ( 2022 ) found that the presence and degree of asexual reproduction (i.e., cloning) is expected to alter fixation probability and that the relative reproductive output of haploid versus diploid life stages greatly affects the strength of natural selection versus genetic drift. Of course, our models also violate many assumptions of these classical models, including variable N (and therefore, variable N e ), and the alternation‐of‐generations life cycle itself, in addition to the presence of cloning in our realistic parameter simulations.…”

Section: Discussionmentioning

confidence: 99%

“…The latter can also be an important mediator of maternal effects (Jesson et al, 2012 ; Chettoor et al, 2016 ). Despite the many potential effects of the gametophyte life stage on patterns of genome evolution, we lack a model‐based framework for predicting these effects, and studies exploring the impact of alternation of generations on evolutionary processes are few (Hoban et al, 2012 ; Bessho and Otto, 2022 ).…”

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confidence: 99%

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Selection on the gametophyte: Modeling alternation of generations in plants

et al. 2022

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Premise The degree of gametophyte dependence on the sporophyte life stage is a major feature that differentiates the life cycles of land plants, yet the evolutionary consequences of this difference remain poorly understood. Most evolutionary models assume organisms are either haploid or diploid for their entire lifespan, which is not appropriate for simulating plant life cycles. Here, we introduce shadie ( S imulating Ha ploid– Di ploid E volution), a new, simple Python program for implementing simulations with biphasic life cycles and analyzing their results, using SLiM 3 as a simulation back end. Methods We implemented evolutionary simulations under three realistic plant life cycle models supported in shadie , using either standardized or biologically realistic parameter settings to test how variation in plant life cycles and sexual systems affects patterns of genome diversity. Results The dynamics of single beneficial mutation fixation did not vary dramatically between different models, but the patterns of spatial variation did differ, demonstrating that different life histories and model parameters affect both genetic diversity and linkage disequilibrium. The rate of linkage disequilibrium decay away from selected sites varied depending on model parameters such as cloning and selfing rates, through their impact on effective population sizes. Discussion Evolutionary simulations are an exciting, underutilized approach in evolutionary research and education. shadie can aid plant researchers in developing null hypotheses, examining theory, and designing empirical studies, in order to investigate the role of the gametophyte life stage, and the effects of variation in plant life cycles, on plant genome evolution.

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

Selection on the gametophyte: Modeling alternation of generations in plants

et al. 2022

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“…During the burn‐in period, the pathogen population only evolves on S. To reach the genetic drift and mutation equilibrium from the initial state, the burn‐in period is set to

2 N

generations. For a diploid organism with frequent sexual reproduction,

2 N

generations are sufficient to reach a steady state (Bessho & Otto, 2022; Hartfield, 2021; Reichel et al, 2016). We build a random simulation design of 150,000 simulations, with input parameter values drawn randomly from defined prior distributions (Table 1).…”

Section: Methodsmentioning

confidence: 99%

Approximate Bayesian Computation applied to time series of population genetic data disentangles rapid genetic changes and demographic variations in a pathogen population

et al. 2023

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Adaptation can occur at remarkably short timescales in natural populations, leading to drastic changes in phenotypes and genotype frequencies over a few generations only. The inference of demographic parameters can allow understanding how evolutionary forces interact and shape the genetic trajectories of populations during rapid adaptation. Here we propose a new Approximate Bayesian Computation (ABC) framework that couples a forward and individual‐based model with temporal genetic data to disentangle genetic changes and demographic variations in a case of rapid adaptation. We test the accuracy of our inferential framework and evaluate the benefit of considering a dense versus sparse sampling. Theoretical investigations demonstrate high accuracy in both model and parameter estimations, even if a strong thinning is applied to time series data. Then, we apply our ABC inferential framework to empirical data describing the population genetic changes of the poplar rust pathogen following a major event of resistance overcoming. We successfully estimate key demographic and genetic parameters, including the proportion of resistant hosts deployed in the landscape and the level of standing genetic variation from which selection occurred. Inferred values are in accordance with our empirical knowledge of this biological system. This new inferential framework, which contrasts with coalescent‐based ABC analyses, is promising for a better understanding of evolutionary trajectories of populations subjected to rapid adaptation.

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“…The genetic material of most organisms in nature, including humans, contains two sets of chromosomes, one from the mother and the other from the father, called diploid organisms. Diploidy has many advantages, such as effectively preventing the elimination of organisms due to recessive deleterious mutations and maintaining the relative stability of genetics and the biosphere [ 1 , 2 ]. It also increases genetic diversity through interspecific hybridization, which promotes biological evolution and the creation of new species.…”

Section: Introductionmentioning

confidence: 99%

Development and application of haploid embryonic stem cells

Wang,

Ma,

Guo

2024

Stem Cell Res Ther

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Haploid cells are a kind of cells with only one set of chromosomes. Compared with traditional diploid cells, haploid cells have unique advantages in gene screening and drug-targeted therapy, due to their phenotype being equal to the genotype. Embryonic stem cells are a kind of cells with strong differentiation potential that can differentiate into various types of cells under specific conditions in vitro. Therefore, haploid embryonic stem cells have the characteristics of both haploid cells and embryonic stem cells, which makes them have significant advantages in many aspects, such as reproductive developmental mechanism research, genetic screening, and drug-targeted therapy. Consequently, establishing haploid embryonic stem cell lines is of great significance. This paper reviews the progress of haploid embryonic stem cell research and briefly discusses the applications of haploid embryonic stem cells.

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Fixation and effective size in a haploid–diploid population with asexual reproduction

Cited by 6 publications

References 35 publications

Selection on the gametophyte: Modeling alternation of generations in plants

Selection on the gametophyte: Modeling alternation of generations in plants

Approximate Bayesian Computation applied to time series of population genetic data disentangles rapid genetic changes and demographic variations in a pathogen population

Development and application of haploid embryonic stem cells

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