Disentangling the contemporary and historical effects of landscape on population genomic variation of two bird species restricted to the highland forest enclaves of northeastern Brazil

In this repository, you will find inputs for the main analyses conducted on the article "Disentangling the contemporary and historical effects of landscape on the population genomic variation of two bird species restricted to the highland forest enclaves of northeastern Brazil" by Batalha-Filho et al. 2023 published in Heredity. File types .vcf, .blueprint, .geno, .q, .est, .tpl, .obs, .diffs, .coord, and .outer may be viewed in a standard text viewer. Also, A PDF viewer, such as Adobe Reader, is required for viewing the .pdf figure files. VCF files: This folder includes raw Variant call format files with all SNPs obtained for the sequenced individuals of C. cearae and S. cearensis, considering all samples for each species as well as separated by lineage. PCA and sNMF: This folder contains inputs for the PCA analysis in adegenet and for the sparse non-negative matrix factorization approach (sNMF) of C. cearae and S. cearensis: (1) input files for both analyses (.geno); (2) figures showing PCA eigenvalues for each species; (3) figures with the cross-entropy criterion for each species; and (4) files with the ancestry coefficients (.q) of each individual for the best K value inferred for each species from the sNMF. EEMS folder: This folder contains inputs and outputs of Estimating Effective Migration Surfaces (EEMS) analysis for C. cearae and S. cearensis: inputs (.coord, .diffs, and .outer) and output (figures) files for each species. stairwayplot: This folder contains inputs for stairwayplot analyses for C. cearae and S. cearensis, considering all individuals per species and population cluster: input files (.blueprint) for the lineages of each species. fastsimcoal: This folder includes inputs for simulated demographic scenarios in fastsimcoal for both C. cearae and S. cearensis: input files (.est, .tpl, and .obs) used in the analysis of each model (constant population size, population decline, and population growth) for the lineages of each species.

本数据集仓库收录了发表于《Heredity》期刊、Batalha-Filho等人2023年的论文《厘清巴西东北部高原森林飞地特有两种鸟类的景观对种群基因组变异的当代与历史影响》中核心分析所需的输入文件。其中，.vcf、.blueprint、.geno、.q、.est、.tpl、.obs、.diffs、.coord及.outer格式的文件可通过标准文本查看器打开。此外，查看.pdf格式的配图文件需使用PDF阅读器（如Adobe Reader）。

VCF文件目录：本目录包含塞阿拉唐纳雀（C. cearae）与塞阿拉旋木雀（S. cearensis）测序个体的全部单核苷酸多态性（Single Nucleotide Polymorphism, SNP）原始变异检测格式（Variant Call Format, VCF）文件，涵盖两个物种的全部样本，并按谱系分组。

主成分分析与稀疏非负矩阵分解目录：本目录包含塞阿拉唐纳雀（C. cearae）与塞阿拉旋木雀（S. cearensis）的adegenet包主成分分析（Principal Component Analysis, PCA）以及稀疏非负矩阵分解（sparse non-negative matrix factorization, sNMF）所需输入文件，具体包括：(1) 两类分析共用的输入文件（.geno）；(2) 各物种的PCA特征值配图；(3) 各物种的交叉熵准则配图；(4) 基于sNMF推断的各物种最优K值，对应每个个体的祖先成分文件（.q）。

有效迁移表面估计目录：本目录包含塞阿拉唐纳雀（C. cearae）与塞阿拉旋木雀（S. cearensis）的有效迁移表面估计（Estimating Effective Migration Surfaces, EEMS）分析的输入与输出文件，涵盖各物种的输入文件（.coord、.diffs与.outer）以及输出配图文件。

阶梯图分析目录：本目录包含塞阿拉唐纳雀（C. cearae）与塞阿拉旋木雀（S. cearensis）的stairwayplot分析所需输入文件，涵盖各物种的全部个体与种群分组数据，以及各物种谱系对应的输入文件（.blueprint）。

fastsimcoal模拟目录：本目录包含塞阿拉唐纳雀（C. cearae）与塞阿拉旋木雀（S. cearensis）的fastsimcoal群体历史场景模拟所需输入文件，涵盖针对各物种谱系的三类模型（恒定种群规模、种群衰退与种群扩张）分析所用的输入文件（.est、.tpl与.obs）。