Detecting frequency-dependent selection through the effects of genotype similarity on fitness components

Frequency-dependent selection (FDS) is an evolutionary regime that can maintain or reduce polymorphisms. Despite the increasing availability of polymorphism data, few effective methods are available for estimating the gradient of FDS from the observed fitness components. We modeled the effects of genotype similarity on individual fitness to develop a selection gradient analysis of FDS. This modeling enabled us to estimate FDS by regressing fitness components on the genotype similarity among individuals. We detected known negative FDS on the visible polymorphism in a wild Arabidopsis and damselfly by applying this analysis to single-locus data. Further, we simulated genome-wide polymorphisms and fitness components to modify the single-locus analysis as a genome-wide association study (GWAS). The simulation showed that negative or positive FDS could be distinguished through the estimated effects of genotype similarity on simulated fitness. Moreover, we conducted the GWAS of the reproducti..., , , # Regression model of frequency-dependent selection

Source codes and data of Sato et al. \"Detecting frequency-dependent selection through the effects of genotype similarity on fitness components\". A vignette-style instruction is available in Rmarkdown and its output HTML as `index.Rmd` and `index.html`, respectively (see also for viewing). A developer version is available at .

## application

This directory includes source codes and/or input data for empirical analyses on *Arabidopsis halleri*, *Ischnura elegans*, and *Arabidopsis thaliana*, proceeding as follows.

### GLMM analysis of *Arabidopsis halleri*

* Ahal_FieldSurvey.R\
Poisson GLMM of the flower number in wild *Arabidopsis halleri* in a natural population. Data are available via Dryad repository ().

### GLMM analysis of *Ischnura elegans*

* damselfly_cage_data.R\
Poisson GLMM of the egg number in *Ischnura elegans* in semi-field cages. The original data are generated by Takahashi et al. (2014) Nature Communic...

频率依赖选择（frequency-dependent selection, FDS）是一种可维持或降低多态性的进化机制。尽管多态性数据的可获取性日益提升，但目前鲜有可通过观测得到的适合度组分估算FDS梯度的有效方法。我们通过构建基因型相似性对个体适合度的影响模型，开发了FDS选择梯度分析方法。该建模框架可通过将适合度组分与个体间的基因型相似性进行回归分析，实现FDS的估算。我们将该分析方法应用于单基因座数据，在野生拟南芥（Arabidopsis）与豆娘（damselfly）的可见多态性中检测到了已知的负向FDS。进一步地，我们模拟了全基因组多态性与适合度组分，将单基因座分析拓展为全基因组关联分析（genome-wide association study, GWAS）。模拟结果显示，通过估算基因型相似性对模拟适合度的影响，可区分负向与正向FDS。此外，我们开展了繁殖相关性状的GWAS分析……
# 频率依赖选择回归模型

佐藤等人的论文"Detecting frequency-dependent selection through the effects of genotype similarity on fitness components"的源代码与数据。本研究提供了R标记文档（Rmarkdown）格式与输出的超文本标记语言（HTML）格式的vignette风格操作指南，分别对应`index.Rmd`与`index.html`文件（可通过对应链接查看）。开发者版本可于对应链接获取。

## 应用说明
本目录包含针对*Arabidopsis halleri*（山脆荠）、*Ischnura elegans*（长叶异痣蟌）与*Arabidopsis thaliana*（拟南芥）开展实证分析的源代码及/或输入数据，具体流程如下：

### *Arabidopsis halleri*的广义线性混合模型（generalized linear mixed model, GLMM）分析
* `Ahal_FieldSurvey.R`：针对自然种群中野生*Arabidopsis halleri*的花数开展泊松广义线性混合模型分析。相关数据可通过Dryad数据仓储获取。

### *Ischnura elegans*的广义线性混合模型分析
* `damselfly_cage_data.R`：针对半野外笼养条件下的*Ischnura elegans*的产卵量开展泊松广义线性混合模型分析。原始数据由Takahashi等人于2014年发表于《Nature Communications》（原文截断）……