Using UCEs to track the influence of sea-level change on leafy seadragon populations

Data and code used in bioinformatic processing, bathymetry calculations, population genetic analyses and their output files. Ultraconserved Elements (UCEs) were sequenced in 68 individuals of leafy seadragons (Phycodurus eques, Syngnathidae) sampled across their range along the southern Australian coast.

The repository contains

A) Scripts to process the sequence data and the resulting

BAM read mapping files

VCF files with SNPs before and after filtering

B) Scripts, input files, and output files for the analyses to

reconstruct shallow water areas at different sea levels

estimate population structure (PCA, DAPC, Structure, SVDquartets), and spatial genetic patterns (IBD plots, EEMS)

calculate genetic diversity (individual-level heterozygosity, population-level heterozygosity, Tajima's D)

perform phylogeographic modeling (DIYABC).

本数据集包含用于生物信息学处理、水深计算、群体遗传学分析及其对应输出文件的相关数据与代码。研究针对澳大利亚南部沿岸全域分布的68尾叶海龙（*Phycodurus eques*，海龙科Syngnathidae）个体开展了超保守元件（Ultraconserved Elements, UCEs）测序。

本数据仓库包含如下内容：
A) 用于处理序列数据的脚本，以及由此生成的如下文件：
- BAM读取比对文件
- 过滤前后均包含单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）的VCF文件

B) 用于以下各类分析的脚本、输入文件与输出文件：
1. 重建不同海平面情境下的浅水区范围
2. 估算群体遗传结构（主成分分析（PCA）、判别分析主成分（DAPC）、Structure、SVDquartets）与空间遗传模式（IBD绘图、EEMS分析）
3. 计算遗传多样性指标（个体水平杂合度、群体水平杂合度、Tajima's D检验）
4. 开展系统地理建模（DIYABC分析）