De novo assembly of SNPs in VCF format for 112 individualss of Campylorhynchus in western Ecuador

Climate variability has a significant impact on the evolution of biodiversity, which results in genetic and phenotypic diversity within species. A balance between gene flow and selection maintains changes in the frequency of genetic and phenotypic variants that occur along an environmental gradient. Here, we investigate a hybrid zone in western Ecuador involving C. zonatus, C. fasciatus, and admixed populations. We hypothesized that different ecological preferences and geographical distances result in limited dispersal between populations along the precipitation gradient in western Ecuador.
In the context of testing IBE and IBD shaping distributions of C. zonatus, C. fasciatus, and potential hybrids, we asked (1) Is there evidence of genetic admixture and introgression between these taxa in Western Ecuador? And (2) What is the relative contribution of IBE and IBD on patterns of genetic differentiation and admixture patterns? We analyzed 4409 SNPs from the blood of 112 individuals sequen..., We collected blood samples from the brachial vein of 112 individuals of Campylorhynchus along Western Ecuador. Most samples were collected between July and December 2018. We also obtained 27 tissue samples of C. fasciatus from Peru at the Florida Museum of Natural History (FLMNH). DNA for all samples was extracted using Qiagen DNeasy blood & tissue kits (Qiagen, Maryland USA). We followed the ddRAD-seq protocol by Peterson et al. (2012) and modified by Thrasher et al. (2018). We trimmed all sequences to 147bp using fastX_trimmer (FASTX-Toolkit) to exclude low-quality calls near the 3’ of the reads. We removed reads containing at least a single base with a Phred quality score of less than 10 (using fastq_quality_filter). We removed sequences if more than 5% of the bases had a Phred quality score of less than 20. Using the process_radtags module from the STACKS version 2.3 (Catchen et al., 2013), we demultiplexed the reads to obtain files with specific sequences for each individual., , # De novo assembly of SNPs in VCF format for 112 individuals of Campylorhynchus in Western Ecuador.

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We have submitted the resulting populations.snps.vcf (Variant Call Format) file from the de novo assembly performed using the STACK software. This file is the primary dataset utilized for the various analyses described in our article, \"Unraveling the Genomic Landscape of Campylorhynchus Wrens along Western Ecuador's Precipitation Gradient: Insights into Hybridization, Isolation by Distance, and Isolation by Environment.\" The article investigates the population structure and hybridization patterns between Campylorhynchus zonatus and C. fasciatus across western Ecuador. Additionally, we have included the file DeNovoAssemblyStack.bash, which contains the Unix code used to perform the de novo assembly with STACK, this code uses as input the raw FASTA files deposited at NCBI Sequence Read Archive under Bioproject accession number PRJNA925654.

## Description of the data and file structur...