Simulation code for: Clones on the run - the genomics of a recently expanded partially clonal species

Why species that in their core areas mainly reproduce sexually become enriched with clones in marginal populations (\"geographic parthenogenesis\") remains unclear. Earlier hypotheses have emphasised that selection might promote clonality because it protects locally adapted genotypes. On the other hand, it also hampers recombination and adaptation to changing conditions. The aim of the present study was to investigate the early stages of range expansion in a partially clonal species and what drives an increase in cloning during such expansion. We used genome-wide sequencing to investigate the origin and evolution of large clones formed in a macroalgal species (Fucus vesiculosus) during a recent expansion into the postglacial Baltic Sea. We found low but persistent clonality in core populations, while at range margins, large dominant clonal lineages had evolved repeatedly from different sexual populations. A range expansion model showed that even when asexual recruitment is less favourable..., This dataset consists of a custom-made simulation code of the mathematical model employed in the study (written in Matlab; .m file), and the simulation outputs (.mat files). Matlab was used to run the simulations and analyze the simulation outputs., Files can be accessed using MATLAB., # Simulation code for: Clones on the run - the genomics of a recently expanded partially clonal species

The simulations used in “Clones on the run - the genomics of a recently expanded partially clonal species” by R.T. Pereyra, M. Rafajlović, P. De Wit, M. Pinder, A. Kinnby, M. Töpel and K. Johannesson are written and executed in Matlab. This Matlab code (.m file) is named here ‘main_fixedMaxN.m’. The explanations of the notations used, and of the main steps in the model are explained in the comments in this .m file.

## Description of the data and file structure

The raw simulation outputs for the model with both short- and long-range dispersal are contained in .mat files with names starting with ‘YesLong_’. Each filename further specifies parameter values for the corresponding simulation, i.e., MaxN, mean long-range dispersal distance (dist), death rate d, per-individual total dispersal probability (mT), probability that a migrant disperses by long-range dispersal (pL), and per-clo...

为何在核心区域主要以有性繁殖的物种，在边缘种群中克隆繁殖占比更高（即"地理孤雌生殖（geographic parthenogenesis）"），这一科学问题至今尚未阐明。此前的相关假说强调，自然选择或许会促进克隆繁殖，因为它能够保护局部适应的基因型；但另一方面，克隆繁殖也会阻碍基因重组与物种对环境变化的适应能力。本研究旨在探究部分克隆繁殖物种的范围扩张早期阶段，以及何种驱动因素会在扩张过程中提升克隆繁殖的占比。我们采用全基因组测序技术，研究了近期从冰期后海域扩张至波罗的海的大型褐藻——囊岩藻（Fucus vesiculosus）中形成的大型克隆的起源与演化历程。研究发现，核心种群中克隆繁殖比例较低但持续存在，而在分布范围的边缘地带，大型优势克隆谱系反复从不同的有性种群中演化而来。一项范围扩张模型显示，即使无性补充的适应性较差…… 本数据集包含本研究中所使用数学模型的定制化模拟代码（采用Matlab编写，格式为.m文件）以及模拟输出结果（.mat格式文件）。模拟运行与结果分析均通过Matlab完成，文件需使用Matlab软件打开。

# 用于"Clones on the run - the genomics of a recently expanded partially clonal species"的模拟代码
本数据集对应论文《Clones on the run - the genomics of a recently expanded partially clonal species》的作者为R.T. Pereyra、M. Rafajlović、P. De Wit、M. Pinder、A. Kinnby、M. Töpel与K. Johannesson，其模拟代码采用Matlab编写并运行，代码文件名为main_fixedMaxN.m。该.m文件中的注释已对所用符号及模型的主要步骤进行了详细解释说明。

## 数据与文件结构说明
同时包含短距离与长距离扩散的模型的原始模拟输出结果，存放在文件名以"YesLong_"开头的.mat格式文件中。每个文件名进一步标注了对应模拟的参数值，包括MaxN、平均长距离扩散距离（dist）、死亡率d、个体总扩散概率（mT）、移民通过长距离扩散的概率（pL）以及每克隆……