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 sequenced using ddRadSeq. The most likely clusters ranged from K=2-4, corresponding to categories defined by geographic origins, known phylogenetics, and physical or ecological constraints. Evidence for IBE was weak but stronger for IBD. We observed gradual changes in genetic admixture between C. f. pallescens and C. zonatus along the environmental gradient. Genetic differentiation of the two populations of C. f. pallescens could be driven by a previously undescribed potential physical barrier near the center of western Ecuador. Lowland habitats in this region may be limited due to the proximity of the Andes to the coastline, limiting dispersal and gene flow, particularly among dry-habitat specialists.

Methods
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.