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
Data files
Nov 28, 2023 version files 43.38 MB
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EEMS.zip
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fastsimcoal.zip
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PCA_and_sNMF.zip
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README.md
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stairwayplot.zip
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VCF_files.zip
Abstract
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.
README
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.