Disentangling the contemporary and historical effects of landscape on population genomic variation of two bird species restricted to the highland forest enclaves of northeastern Brazil

Investigating the impact of landscape features on patterns of genetic variation is crucial to understand spatially dependent evolutionary processes. Here, we assess the population genomic variation of two bird species (Conopophaga cearae and Sclerurus cearensis) through the Caatinga moist forest enclaves in northeastern Brazil. To infer the evolutionary dynamics of bird populations through the Late Quaternary, we used genome-wide polymorphism data obtained from double-digestion restriction-site-associated DNA sequencing (ddRADseq), and integrated population structure analyses, historical demography models, paleodistribution modeling, and landscape genetics analyses. We found the population differentiation among enclaves to be significantly related to the geographic distance and historical resistance across the rugged landscape. The climate changes at the end of the Pleistocene to the Holocene likely triggered synchronic population decline in all enclaves for both species. Our findings r..., , , In this repository, you will find inputs for the main analyses conducted on the article \"Disentangling the contemporary and historical effects of landscape on the population genomic variation of two bird species restricted to the highland forest enclaves of northeastern Brazil\" by Batalha-Filho et al. 2023 published in Heredity.

File types .vcf, .blueprint, .geno, .q, .est, .tpl, .obs, .diffs, .coord, and .outer may be viewed in a standard text viewer. Also, A PDF viewer, such as Adobe Reader, is required for viewing the .pdf figure files.

VCF files: This folder includes raw Variant call format files with all SNPs obtained for the sequenced individuals of C. cearae and S. cearensis, considering all samples for each species as well as separated by lineage.

PCA and sNMF: This folder contains inputs for the PCA analysis in adegenet and for the sparse non-negative matrix factorization approach (sNMF) of C. cearae and S. cearensis: (1) input files for both analyses (.geno); (2) figures sh...