Data and code from: Geographic isolation after admixture generates a distinct lineage in an Atlantic Forest bird

Although traditionally viewed as opposing divergence, hybridization can have diverse evolutionary outcomes. Yet its role in lineage divergence remains unclear. To investigate this process, we examined the evolutionary history of the Black-cheeked Gnateater (Conopophaga melanops) from the Atlantic Forest of eastern Brazil. The central subspecies, C. m. perspicillata, exhibits plumage traits intermediate to northern and southern populations, raising the question of whether this pattern reflects isolation-by-distance, recent hybridization, or past admixture. Using genome-wide markers from sequencing of ultraconserved elements along with phenotypic data, we assessed genetic structure and trait variation across the species’ range. Our analyses reveal four population genetic clusters, with the two central clusters exhibiting clear signatures of historical admixture. Despite this admixture, central populations are genetically differentiated from northern and southern lineages and sing a distin..., , , This repository contains the genetic, phenotypic, and bioacoustic data, alongside the R scripts, used to investigate the evolutionary history of the Black-cheeked Gnateater (*Conopophaga melanops*) in the following study: > Lima, R. D., *et al*. (2026). Geographic isolation after admixture generates a distinct lineage in an Atlantic Forest bird. *Evolution*, qpag069. The dataset is divided into two compressed directories: * `data.zip` (containing raw and filtered genetic files, phenotypic trait data, and metadata). * `code.zip` (containing R scripts used for all analyses and plots). ## Description of the data files in *data.zip* * `cono_raw.vcf`: The raw, unfiltered variant call format (VCF) file containing 155,803 SNPs generated from the UCE sequence capture. * `cono95MAC2.vcf`: The filtered, linked SNP dataset (758 SNPs) retaining loci with 95% completeness and a Minor Allele Count (MAC) of 2. Used for PCA, Fst, and heterozygosity analyses. * `cono95MAC2_unlinked.vcf`: The filt..., ,尽管传统观点认为杂交与分化相互对立，但杂交实则可产生多样的进化结局。然而其在谱系分化中的作用仍不明晰。为探究这一过程，我们针对巴西东部大西洋森林中的黑颊食蚊鸟（*Conopophaga melanops*）的进化历史展开研究。该物种的中部亚种C. m. perspicillata的羽衣性状介于北部与南部种群之间，这引发了一个核心问题：这一性状模式究竟是源于距离隔离效应、近期杂交事件，还是古代遗传混合？我们借助超保守元件（ultraconserved elements, UCE）测序获得的全基因组标记，并结合表型数据，评估了该物种分布范围内的遗传结构与性状变异。分析结果显示存在四个种群遗传聚类，其中两个中部聚类呈现出明确的历史遗传混合信号。尽管存在遗传混合，中部种群在遗传上仍与北部和南部谱系存在分化，并形成了独特的（原文此处内容截断）…… 本数据集仓库包含用于开展上述研究的遗传、表型与生物声学数据，以及相关R脚本，相关研究成果为： > Lima, R. D. 等（2026）. 杂交后的地理分化造就大西洋森林鸟类的独特谱系. *Evolution*, qpag069. 本数据集分为两个压缩目录： * `data.zip`：包含原始与过滤后的遗传文件、表型性状数据与元数据。 * `code.zip`：包含所有分析与绘图所用的R脚本。 #### data.zip内数据文件说明 * `cono_raw.vcf`：原始未过滤的变异检测格式（Variant Call Format, VCF）文件，包含155,803个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点，由超保守元件序列捕获实验生成。 * `cono95MAC2.vcf`：经过滤的连锁SNP数据集（共758个位点），保留了完整性达95%且最小等位基因计数（Minor Allele Count, MAC）为2的位点，用于主成分分析（Principal Component Analysis, PCA）、遗传分化系数（Fixation Index, Fst）与杂合度分析。 * `cono95MAC2_unlinked.vcf`：经过滤的非连锁SNP数据集（原文此处内容截断）……