DOI: 10.5061/dryad.7d7wm37w1
title: 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

description: 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 revealed that both geographic distance and
 historical connectivity through highlands are important factors that can
 explain the current patterns of genetic variation. Our results further
 suggest that levels of population differentiation and connectivity cannot
 be explained purely on the basis of contemporary environmental conditions.
 By combining historical demographic analyses and niche modeling
 predictions in a historical framework, we provide strong evidence that
 climate fluctuations of the Quaternary promoted population differentiation
 and a high degree of temporal synchrony among population size changes in
 both species.
description: 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
 showing PCA eigenvalues for each species; (3) figures with the
 cross-entropy criterion for each species; and (4) files with the ancestry
 coefficients (.q) of each individual for the best K value inferred for
 each species from the sNMF. EEMS folder: This folder contains inputs and
 outputs of Estimating Effective Migration Surfaces (EEMS) analysis for C.
 cearae and S. cearensis: inputs (.coord, .diffs, and .outer) and output
 (figures) files for each species. stairwayplot: This folder contains
 inputs for stairwayplot analyses for C. cearae and S. cearensis,
 considering all individuals per species and population cluster: input
 files (.blueprint) for the lineages of each species. fastsimcoal: This
 folder includes inputs for simulated demographic scenarios in fastsimcoal
 for both C. cearae and S. cearensis: input files (.est, .tpl, and .obs)
 used in the analysis of each model (constant population size, population
 decline, and population growth) for the lineages of each species.