Replicate avian hybrid zones reveal the progression of genetic and trait introgression through time

Replicate hybrid zones between the same pair of taxa provide a unique opportunity to uncover repeatable outcomes of hybridization, which may point to loci and traits under parallel selection and those contributing to reproductive isolation. In addition, replicates allow for the exploration of the factors causing shifts in hybrid zone structure over time. Here we take advantage of a pair of avian taxa that form multiple hybrid zones to assess the predictability of hybridization and explore the progression of trait introgression through evolutionary time. The Lemon-rumped (Ramphocelus flammigerus icteronotus) and Flame-rumped Tanagers (R. f. flammigerus) inhabit the Pacific coast and mid-elevation slopes of the Cauca Valley of Colombia,  hybridizing where they encounter each other in low passes across the Andes. We sampled transects along three such geographically separate passes and found that hybrid zones along these transects were formed independently, show parallel patterns of ph..., , # Replicate avian hybrid zones reveal the progression of genetic and trait introgression through time

Dataset DOI: [10.5061/dryad.zkh1893n9](10.5061/dryad.zkh1893n9)

## Description of the data and file structure

This data repository contains the first genome assembly and homology-based annotation for a female *Ramphocelus flammigerus icteronotus* from Colombia. Additionally, it contains the raw unfiltered vcf files (Variant Call Format) and associated sample table (S1_Table), which is the primary dataset needed to replicate the analyses in the research article “Replicate avian hybrid zones reveal the progression of genetic and trait introgression through time”, Castaño et al. (In review). Details of the methods are in the description of each file. The vcf file includes samples from three hybrid zones between the Flame-rumped Tanager subspecies (*R. f. icteronotus* and *R. f. flammigerus*) in the Western Andes of Colombia, samples from **R. f. icteronotus* populations in Ecuador and P...,

同一类群对之间的重复杂交带（hybrid zone）为揭示杂交的可重复结果提供了独特契机，这些结果可指向经历平行选择的基因座与性状，以及那些参与生殖隔离形成的要素。此外，重复杂交带还可用于探究随时间推移导致杂交带结构发生变化的因素。本研究借助一对可形成多个杂交带的鸟类类群，评估杂交过程的可预测性，并探究性状渐渗随进化时间的演变进程。金腰厚嘴唐纳雀（Ramphocelus flammigerus icteronotus）与红腰厚嘴唐纳雀（R. f. flammigerus）栖息于哥伦比亚考卡山谷的太平洋沿岸与中等海拔坡地，在安第斯山脉的低矮隘口相遇并发生杂交。我们沿三处地理隔离的隘口设置样带进行采样，发现这些样带对应的杂交带独立形成，呈现出相似的ph...

# 重复鸟类杂交带揭示遗传与性状渐渗随时间的演变进程

数据集DOI: 10.5061/dryad.zkh1893n9

## 数据与文件结构说明
本数据集仓库包含首个来自哥伦比亚雌性Ramphocelus flammigerus icteronotus的基因组组装结果与基于同源性的注释信息。此外，仓库还包含未过滤的原始VCF文件（变异识别格式，Variant Call Format）及配套样本表（S1_Table），这是重复该研究论文《重复鸟类杂交带揭示遗传与性状渐渗随时间的演变进程》（Castaño等，已投稿待审）中分析流程的核心数据集。各文件的方法细节已在对应文件的说明中给出。VCF文件涵盖哥伦比亚西部安第斯山脉中红腰厚嘴唐纳雀两个亚种（R. f. icteronotus与R. f. flammigerus）的三处杂交带样本，以及来自厄瓜多尔与P...的R. f. icteronotus种群样本。