Data and Code for: Reproductive strategies and their consequences for divergence, gene flow, and genetic diversity in three taxa of Clarkia

Differences in reproductive strategies can have important implications for macro- and micro-evolutionary processes. We used a comparative approach through a population genetics lens to evaluate how three distinct reproductive strategies shape patterns of divergence among as well as gene flow and genetic diversity within three closely related taxa in the genus Clarkia. One taxon is a predominantly autonomous self-fertilizer and the other two taxa are predominantly outcrossing but vary in the primary pollinator they attract. In genotyping populations using genotyping-by-sequencing and comparing loci shared across taxa, our results suggest that differences in reproductive strategies in part promote evolutionary divergence among these closely related taxa. Contrary to expectations, we found that the selfing taxon had the highest levels of heterozygosity but a low rate of polymorphism. The high levels of fixed heterozygosity for a subset of loci suggests this pattern is driven by the presenc..., DNA extraction and sequencing
We extracted genomic DNA following a modified cetyltrimethylammonium (CTAB) developed by Doyle and Doyle (1987). We used single nucleotide polymorphisms (SNPs) generated from genotyping-by-sequencing libraries which were prepared following Elshire et al. (2011) and using the restriction enzyme ApeKI to fragment the genome. To avoid any batch effect, half the individuals from each population were split between the two genomic libraries of 96. Each polymerase chain reaction (PCR) was carried out independently for all samples, and each library was then quantified using High sensitivity QubitTM (dsDNA HS Assay Kit, Thermo Fisher Scientific) and then pooled in the final step before sequencing to assure an equivalent amount of each sample was present in the final genomic library. Sequencing was performed using Illumina HiSeq, 150bp Paired-End reads at the Center for Genetic Medicine at Northwestern Medicine.
Calling single nucleotide polymorphisms (SNPs)
We used..., See README file. , This README file was generated on 2023-09-06 by Zoe Diaz-Martin.

GENERAL INFORMATION

1. Title of Dataset: Reproductive strategies and their consequences for divergence, gene flow, and genetic diversity in three taxa of Clarkia
2. Author Information
A. Corresponding Author Contact Information
Name: Zoe Diaz-Martin
Institution: Spelman College
Address: Atlanta, GA USA
Email: [e-mail]

SHARING/ACCESS INFORMATION

1. Licenses/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0) Public Domain
2. Links to publications that cite or use the data:

Diaz-Martin, Zoe et al. Reproductive strategies and their consequences for divergence, gene flow, and genetic diversity in three taxa of Clarkia. Heredity.

3. Links to other publicly accessible locations of the data: None
4. Links/relationships to ancillary data sets: None
5. Was data derived from another source? No
A. If yes, list source(s): NA
6. Recommended citation for this dataset:

Diaz-Martin...

生殖策略差异对宏观进化与微观进化过程均具有重要意义。本研究以群体遗传学视角采用比较分析方法，探究三种不同生殖策略如何塑造克拉克拉属（Clarkia）三个近缘类群间的分化模式，以及类群内的基因流与遗传多样性水平。其中一个类群以自主自交为主，另外两个类群以异交为主，但二者所吸引的主要传粉者存在差异。

本研究通过测序分型（genotyping-by-sequencing）对种群进行基因分型，并比对类群间共享的基因座，结果显示生殖策略差异在一定程度上推动了这些近缘类群的进化分化。与预期相悖的是，自交类群的杂合度水平最高，但多态性比率较低。部分基因座呈现高水平的固定杂合性，表明该模式由……驱动。

[DNA提取与测序]
本研究参照Doyle与Doyle（1987）开发的改良十六烷基三甲基溴化铵（cetyltrimethylammonium, CTAB）法提取基因组DNA。本研究利用基于测序分型文库获得的单核苷酸多态性（single nucleotide polymorphisms, SNPs）位点，该文库参照Elshire等（2011）的方法构建，并使用限制性内切酶ApeKI对基因组进行酶切片段化。
为避免批次效应，每个种群的半数个体被分配至两个96孔基因组文库中。所有样本均独立进行聚合酶链式反应（polymerase chain reaction, PCR）扩增，随后分别采用高灵敏度QubitTM（双链DNA高灵敏度检测试剂盒，赛默飞世尔科技）对文库进行定量，测序前最终混合所有文库以确保每个样本在最终文库中含量一致。测序工作在西北医学遗传医学中心完成，采用Illumina HiSeq平台进行150bp双端读长测序。

[单核苷酸多态性位点识别]
本研究采用……方法，详见README文件。本README文件由Zoe Diaz-Martin于2023年9月6日生成。

### 数据集基本信息
1. 数据集名称：克拉克拉属三个类群的生殖策略及其对分化、基因流与遗传多样性的影响
2. 作者信息
A. 通讯作者联系方式
姓名：Zoe Diaz-Martin
所属机构：斯贝尔曼学院
地址：美国佐治亚州亚特兰大
电子邮箱：[e-mail]

### 数据共享与获取信息
1. 数据使用许可/限制条款：CC0 1.0 通用公共领域授权（CC0 1.0 Universal Public Domain）
2. 引用该数据集的已发表文献链接：
Diaz-Martin, Zoe等. 克拉克拉属三个类群的生殖策略及其对分化、基因流与遗传多样性的影响. 遗传(Heredity).
3. 该数据的其他公开访问链接：无
4. 附属数据集的链接/关联关系：无
5. 本数据集是否源自其他数据源？否
A. 若是，请列出数据源：无
6. 本数据集推荐引用格式：
Diaz-Martin...