Genomic signatures of isolation, hybridization, and selection during speciation of island finches

Data associated to the study Genomic signatures of isolation, hybridization, and selection during speciation of island finches

Contents

Table_S9_samples_accession_nos.xlsx: Editable Excel matrix with sample names and accession numbers.

RAD_SNPs_stacks_42424_loci.vcf.tar.gz: VCF file (gzip-compressed tarball) containing SNPs in 42,424 loci, based on analyses of restriction site-associated DNA (RAD) sequencing using Stacks.

RAD_SNPs_standard_variant_calling.vcf.tar.gz: VCF file (gzip-compressed tarball) containing 131,661 SNPs from standard variant calling pipelines.

mitochondrial_markers_full_data.nex: Nexus file containing mitochondrial (mt) sequences used for mt-phylogeny. Partitioned for COX2, tRNA-Lys, ATP8, and ATP6. 

sequences_nuclear_genotype_with_zebra_finch_TG.tar.gz: Directory (gzip-compressed tarball) containing genotype sequence (heterozygous sites with IUPAC codes) alignments of nuclear markers in nexus files. In addition to the study species, the sequence for zebra finch Taeniopygia guttata is included with sample code TG.

sequences_nuclear_phased_and_mitochondrial_haplotypes_matching.tar.gz: Directory (gzip-compressed tarball) containing phased sequence (haplotype) alignments of nuclear markers in nexus files. These include only those individuals that match individuals sequenced for mitochondrial markers (also included here). In case of recombining loci, both the full locus and the largest non-recombining block are represented.

sequences_nuclear_phased_haplotypes_all.tar.gz: Directory (gzip-compressed tarball) containing phased sequence (haplotype) alignments of nuclear markers in nexus files. These include all individuals. In case of recombining loci, both the full locus and the largest non-recombining block are represented.

microsatellite_dataset.xlsx: Microsatellite datasets for the study species and additional outgroups.

Sequences and short read datasets available from NCBI; accession numbers in Table S9 (Table_S9_samples_accession_nos.xlsx).

Study summary

Sister species occurring sympatrically on islands are rare and offer unique opportunities to understand how speciation can proceed in the face of gene flow. The São Tomé grosbeak is a massive-billed, ‘giant’ finch endemic to the island of São Tomé in the Gulf of Guinea, where it has diverged from its co-occurring sister species the Príncipe seedeater, an average-sized finch that also inhabits two neighbouring islands. Here, we show that the grosbeak carries a large number of unique alleles different from all three Príncipe seedeater populations, but also shares many alleles with the sympatric São Tomé population of the seedeater, a genomic signature signifying divergence in isolation as well as subsequent introgressive hybridization. Furthermore, genomic segments that remain unique to the grosbeak are situated close to genes, including genes that determine bill morphology, suggesting the preservation of adaptive variation through natural selection during divergence with gene flow. This study reveals a complex speciation process whereby genetic drift, introgression, and selection during periods of isolation and secondary contact all have shaped the diverging genomes of these sympatric island endemic finches.

本数据集关联一项研究：《岛屿雀鸟物种形成过程中的隔离、杂交与选择的基因组特征》（Genomic signatures of isolation, hybridization, and selection during speciation of island finches）

### 数据集内容
1. Table_S9_samples_accession_nos.xlsx：可编辑Excel矩阵表，包含样本名称与登录号。
2. RAD_SNPs_stacks_42424_loci.vcf.tar.gz：VCF格式文件（gzip压缩打包文件），基于Stacks软件对限制性酶切位点相关DNA（Restriction site-associated DNA, RAD）测序数据的分析得到，包含42424个基因座的单核苷酸多态性位点。
3. RAD_SNPs_standard_variant_calling.vcf.tar.gz：VCF格式文件（gzip压缩打包文件），基于标准变异检测流程得到，包含131661个单核苷酸多态性位点。
4. mitochondrial_markers_full_data.nex：Nexus格式文件，包含用于构建线粒体系统发育树的线粒体（mt）序列数据，已按COX2、tRNA-Lys、ATP8及ATP6基因进行分区。
5. sequences_nuclear_genotype_with_zebra_finch_TG.tar.gz：gzip压缩打包目录，包含以Nexus格式存储的核标记基因分型序列比对文件（杂合位点采用IUPAC编码标注）。除本研究涉及的物种外，还包含以样本代号TG标注的斑胸草雀（Taeniopygia guttata）序列。
6. sequences_nuclear_phased_and_mitochondrial_haplotypes_matching.tar.gz：gzip压缩打包目录，包含以Nexus格式存储的核标记基因的单倍型序列比对文件。仅包含与线粒体标记测序个体相匹配的样本；若存在重组基因座，则同时保留完整基因座与最大非重组区块的比对结果。
7. sequences_nuclear_phased_haplotypes_all.tar.gz：gzip压缩打包目录，包含以Nexus格式存储的核标记基因的单倍型序列比对文件，涵盖所有研究个体；若存在重组基因座，则同时保留完整基因座与最大非重组区块的比对结果。
8. microsatellite_dataset.xlsx：本研究物种及外类群的微卫星数据集。

此外，序列与短读长测序数据集可从NCBI获取，登录号详见表S9（Table_S9_samples_accession_nos.xlsx）。

### 研究摘要
同域分布的姊妹物种在岛屿上极为罕见，为解析存在基因流时的物种形成过程提供了独特研究契机。圣多美蜡嘴雀是几内亚湾圣多美岛特有的“巨型”雀鸟，喙部硕大，由其同域分布的姊妹物种普林西比食籽雀分化而来；普林西比食籽雀为体型中等的雀类，同时栖息于两座邻近岛屿。

本研究显示，圣多美蜡嘴雀拥有大量区别于三个普林西比食籽雀种群的独有等位基因，但同时也与该食籽雀在圣多美岛的同域种群共享诸多等位基因，这一基因组特征表明其经历了隔离分化与后续的渐渗杂交过程。进一步分析发现，蜡嘴雀的独有基因组区段紧邻功能基因（包括决定喙部形态的相关基因），提示在存在基因流的分化过程中，自然选择保留了适应性遗传变异。本研究揭示了一种复杂的物种形成模式：隔离与二次接触阶段的遗传漂变、渐渗杂交以及自然选择共同塑造了这些同域分布的岛屿特有雀鸟的分化基因组。