DOI: 10.5061/dryad.ngf1vhj5t
title: Dispersal, isolation and local adaptation promote speciation in South American savannas as indicated by a phylogenomic analysis of a passerine

description: South American savannas are a disjunct biome with an unclear evolutionary
 history. We tested hypotheses about their Quaternary history and evolution
 of savanna cores through fragmentation or dispersal from the Cerrado. We
 used genomic data (genotyping-by-sequencing) and ecological niche models
 of the Burnished-buff Tanager (Stilpnia cayana Linnaeus 1766) to evaluate
 intraspecific differentiation, gene flow, past range shifts, and
 landscape-genomics association. We found clear genomic differences between
 populations on each side of the Amazon basin and high admixture in the
 Marajó Island and Bolivia. Landscape genomics analysis indicated that the
 Amazon River, isolation by distance and temperature predict genomic
 differentiation in this bird. Taken together, the results suggest that a
 combination of dispersal from the Cerrado, isolation due to geographic
 distance and the Amazon River basin, and local adaptation shaped the
 species diversification. We propose that the populations on each side of
 the Amazon River be considered distinct species (S. cayana at the north
 and S. flava at the south) with subspecies huberi representing part of a
 hybrid zone between them, located on Marajó island at the mouth of the
 river.
description: # Dispersal, isolation and local adaptation promote speciation in South
 American savannas as indicated by a phylogenomic analysis of a passerine
 [Access this dataset on Dryad](https://doi.org/10.5061/dryad.ngf1vhj5t) ##
 Overview This dataset includes all the data used in the phylogenomic study
 of *Stilpnia cayana* described in the article referenced above. The
 repository is organized into folders corresponding to each major analysis
 conducted in the study. Within each folder, you will find a `data/`
 subdirectory containing the input files used in that specific analysis.
 Below, we describe the contents of each folder and the associated data
 files. ### Folder: `00_IPYRAD/` **Purpose:** De novo assembly of loci and
 SNP calling using ipyrad ver. 0.9.84 (Eaton & Overcast, 2020).
 **Subfolders:** * `Ingroup_83/`: Contains results from an assembly using
 83 ingroup samples of *Stilpnia cayana*. * `Ingroup-outgroup_84/`:
 Contains results from an assembly using 83 ingroup samples and 1 outgroup
 sample (*Tangara chilensis*). **Contents:** Each subfolder includes: *
 `params-*.txt`: ipyrad configuration file used for the run * `.vcf` files:
 SNP datasets in VCF format * `.phy` files: Full-length GBS loci alignments
 in PHYLIP format * `.stats.txt` Summary statistics and clustering logs
 from ipyrad outputs These datasets were used for variant filtering,
 population genomic, and phylogenetic analyses described in the main
 article. ### Folder: `00_Sampling_sites/` **Purpose:** Contains metadata
 about the geographic origin and population assignment of the samples used
 in the study, along with spatial data representing the distribution range
 of *Stilpnia cayana* subspecies. **Contents:** * `sampling_metadata.csv`:
 A table with the following information for each sample: * Sample ID *
 Specimen ID (Id used in the final publication) * Latitude and longitude
 (in decimal degrees) * Assigned population * `Scay_subsp_range.gpkg`: A
 GeoPackage file containing vector polygons representing the distribution
 ranges of the main *Stilpnia cayana* subspecies. These files were used to
 define sampling structure, visualize geographic context, and support
 spatial analyses throughout the study. ### Folder: `01_Fst/` **Purpose:**
 Contains input and output files used to calculate pairwise
 F<sub>ST</sub> values among populations using the R package
 `hierfstat`. **Contents:** * `Scay_83_maf_mr80_sinMarajo.recode.vcf`: A
 filtered and reduced VCF file containing SNP data for 83 ingroup samples,
 excluding samples from Marajó Island. A filtered VCF file containing SNP
 data from the ingroup dataset, excluding samples from Marajó Island. SNPs
 were filtered by applying a minor allele frequency threshold of 0.05 and
 allowing a maximum of 20% missing data per site. These data were used to
 assess population differentiation across the species’ range. ### Folder:
 `01_PCA_and_PCoA/` **Purpose:** Contains the SNP dataset used to perform
 principal component analysis (PCA) and principal coordinates analysis
 (PCoA) for visualizing patterns of genetic structure among individuals.
 **Contents:** * `Stilpnia_cayana_80_bial_maf_mr80_noIndel.recode.vcf`:
 Three samples (UFG4028, MPEG70537, USNM622381) showed high levels of
 missing data (i.e., fewer than 3,500 loci) and were removed prior to PCA
 and PCoA analyses. A filtered VCF file including 80 ingroup samples. SNPs
 were filtered using a minor allele frequency threshold of 0.05 and a
 maximum of 20% missing data per site. This dataset served as the input for
 multivariate analyses of genetic variation across individuals and
 populations of *Stilpnia cayana*. ### Folder: `02_Admixture/` **Purpose:**
 Contains the SNP dataset used to perform individual ancestry estimation
 using model-based clustering approaches (e.g., ADMIXTURE). **Contents:** *
 `Stilpnia_cayana_80_bial_maf_mr80_noIndel_un.vcf`: A filtered VCF file
 derived from the 83-sample ingroup dataset, with the same filtering
 criteria as used in PCA/PCoA analyses (minor allele frequency &gt; 0.05
 and maximum 20% missing data per site).\ Additionally, to reduce linkage
 among SNPs, only one SNP per RAD locus was retained.\ The three samples
 with high levels of missing data (UFG4028, MPEG70537, USNM622381) were
 excluded from this dataset. This dataset was used to infer population
 structure and individual ancestry proportions across the range of
 *Stilpnia cayana*. ### Folder: `03_RAxML/` **Purpose:** Contains the
 alignment and associated metadata used to perform phylogenetic inference
 using RAxML. **Contents:** * `Stilpnia_cayana_Ingroup-outgroup_84.phy`:
 Phylip-formatted alignment of full-length GBS loci sequences for 84
 samples (83 ingroup samples plus one outgroup: *Tangara chilensis*). This
 dataset was used to infer the phylogenetic relationships among populations
 of *Stilpnia cayana*. * `Features_to_plot.csv`: A metadata file including
 sample IDs, population assignments, subspecies designations, and plumage
 phenotypes. This information was used to map biological traits and
 geographic origin onto the phylogenetic tree. ### Folder: `04_EEMS/`
 **Purpose:** Contains input files used to run the Estimated Effective
 Migration Surfaces (EEMS) analysis to explore patterns of gene flow across
 the landscape. **Contents:** * `Scay_83_SNPRelateDisIBS.txt`: Pairwise
 genetic dissimilarity matrix generated using the SNPRelate package in R,
 based on the VCF file containing 83 ingroup samples and including only
 biallelic SNPs. * `Scay_83.coords`: Text file with geographic coordinates
 (longitude and latitude) for each sample included in the EEMS analysis. *
 `Scay_83.outer`: File containing coordinates that define the outer polygon
 surrounding the study area. This polygon delineates the spatial boundaries
 within which migration surfaces were estimated. ### Folder: `05_GPhoCS/`
 **Purpose:** Contains input files used for demographic inference under a
 coalescent framework using GPhoCS. **Contents:** *
 `Stilpnia_cayana_Ingroup_83.gphocs`: SNP dataset in GPhoCS format,
 generated from the ingroup assembly of 83 samples using ipyrad. *
 `Stilpnia_cayana_Ingroup_83.ctl`: Control file specifying the evolutionary
 model used in the GPhoCS analysis, including population assignments,
 migration bands, and prior distributions for demographic parameters. ###
 Folder: `06_fastsimcoal2/` **Purpose:** Contains input data and
 configuration files used to run demographic inference with fastsimcoal2.
 **Contents:** * `Scay83_full_6pop_5samp.recode.vcf`: VCF file including
 both variant and invariant sites, subsampled to include five samples per
 population (except Marajó, which includes only three). This full VCF was
 generated from the complete loci file exported by ipyrad and converted
 using a Python script provided by Isaac Overcast (see: [ipyrad issue
 #479](https://github.com/dereneaton/ipyrad/issues/479)). *
 `easySFS_6pops_5samp.txt`: File specifying population assignments for each
 sample, used as input in easySFS to generate the multidimensional Site
 Frequency Spectrum (MSFS). * `6pop_Model.tpl` and `6pop_Model.est`:
 Template and estimation files defining the demographic model and prior
 distributions used in fastsimcoal2. * `6pop_Model_MSFS.obs`: Observed
 multidimensional Site Frequency Spectrum used as input in fastsimcoal2
 simulations. ### Folder: `07_ENM/` **Purpose:** Contains data used to
 generate ecological niche models (ENMs) for *Stilpnia cayana*.
 **Contents:** * `occ_stilpnia.txt`: Full set of occurrence records used to
 model the ecological niche of the species. * `M_Stilpnia.gpkg`: Polygon
 vector file (in GeoPackage format) delimiting the accessible area (M) used
 for model calibration. * `.tif` files: Raster files representing habitat
 suitability predictions obtained for each of the studied periods: Present,
 Mid-Holocene (MH), Last Glacial Maximum (LGM), and Last Interglacial
 (LIG). ### Folder: `08_LRDM_CA/` **Purpose:** Contains the matrices used
 in the LRDM (Landscape Resistance Distance Matrix) and causal modeling
 analyses. **Contents:** * `Scay_83_SNPRelateDisIBS.txt`: Genetic
 dissimilarity matrix between individuals, the same used in the EEMS
 analysis. This matrix was generated using the SNPRelate package in R from
 a VCF file including 83 samples and only biallelic SNPs. *
 `Matrix_distgeo.txt`: Euclidean geographic distance matrix between
 individuals, calculated using the `geosphere` R package. *
 `Matrix_ResistPresent_CS.txt`: Landscape resistance matrix between
 individuals, generated using the present-day suitability raster (from ENM
 analyses) as a conductance surface in CircuitScape ver. 4.0 (Anantharaman
 et al., 2020). * `Matrix_ResistHistoric_CS.txt`: Landscape resistance
 matrix between individuals, generated using historical suitability rasters
 (from ENM analyses) as a conductance surface in CircuitScape ver. 4.0. *
 `Matrix_River.txt`: Binary matrix indicating whether individuals are
 located on the same (0) or opposite (1) riverbanks. Individuals from
 Marajó are considered to be on a separate riverbank from both NAS and SAS.
 ### Folder: `09_gradientForest/` **Purpose:** Contains the genetic and
 environmental input data used to perform gradient forest analyses.
 **Contents:** * `Stilpnia_79_unlink_bial_mr0.recode.vcf`: VCF file
 containing unlinked, biallelic SNPs without missing data. Sample
 MZUSP83507 was removed due to high missing data (&gt; 50%). This dataset
 was used to generate the site-by-SNP matrix. *
 `Stilpnia_79_unlink_bial_mr0.gradforest.snp.forR`: Site-by-SNP matrix
 coded as 0, 1, or 2 (genotype dosage) generated using the SNPRelate R
 package. This matrix was used as the genetic input for the gradient forest
 model. * `Stilpnia_preds.csv`: CSV file with environmental predictor
 variables used in the model. Each row corresponds to a sampling locality,
 and each column represents a predictor. The variables included are:
 **Bioclimatic variables (from WorldClim 2):** * **bio1** – Annual Mean
 Temperature (°C × 10) * **bio2** – Mean Diurnal Range (Mean of monthly
 (max temp - min temp)) (°C × 10) * **bio3** – Isothermality (bio2 / bio7)
 × 100 (unitless) * **bio4** – Temperature Seasonality (standard deviation
 × 100) (unitless) * **bio13** – Precipitation of Wettest Month (mm) *
 **bio14** – Precipitation of Driest Month (mm) * **bio15** – Precipitation
 Seasonality (coefficient of variation) (unitless) **Other environmental
 variables:** * **MinGreen** – Minimum Green Vegetation Fraction (unitless,
 range 0–1) * **TreeCover** – Percent Tree Cover (%) * **Elevation** –
 Elevation above sea level (m) **Spatial variables:** * **PCNM1, PCNM2,
 ..., PCNMn** – Principal Coordinates of Neighbor Matrices (unitless
 spatial eigenvectors capturing spatial structure at multiple scales) These
 variables were selected to represent key climatic, ecological, and spatial
 gradients relevant to local adaptation and genetic differentiation across
 the species’ range. ## Folder: `10_mitochondrial_DNA/` **Purpose:**
 Contains the mitochondrial DNA alignment used in the phylogenetic and
 comparative analyses. **Contents:** * `Alignment_ND2_final4.fas`: FASTA
 file containing the DNA alignment of the mitochondrial ND2 gene for the 79
 samples for which sequence data was obtained. ## Folder:
 `11_phylogenetic_network/` **Purpose:** Contains the input files and
 workflow used to generate the phylogenetic network of *Stilpnia cayana*.
 **Contents:** * `Stilpnia_cayana_83_sinN.phy`: Alignment used to construct
 the phylogenetic network. "N" characters were converted to gaps
 (“-”) to avoid being counted in the distance matrix, while still
 preserving ambiguity introduced by heterozygous genotypes. *
 `Stilpnia_cayana_83_sinN.wflow6`: Workflow file exported from SplitsTree
 software, specifying the network construction steps. ## Folder:
 `12_introgression_tests/` **Purpose:** Contains the data used to perform
 ABBA-BABA (D-statistics) tests for introgression between selected
 populations or individuals of *Stilpnia cayana*. **Subdirectories and
 contents:** 1. `01_Marajo_introgression/`: Tests involving the Marajó
 population. 2. `02_WestCerrado_introgression/`: Tests assessing
 introgression in the western Cerrado populations. 3.
 `03_UFG4051_introgression/`: Tests evaluating potential introgression
 involving the individual sample UFG4051. Each subdirectory contains: *
 `pops_*.txt`: Text file with sample IDs and their assigned populations
 used in the respective test. * `tree.nwk`: Newick file specifying the tree
 topology relating the four groups used in the ABBA-BABA test. * `*.vcf`:
 Reduced VCF file with unlinked SNPs used in the analysis. * `*_tree.txt`:
 Output file containing ABBA-BABA (D-statistic) estimates. ## Code The code
 used in these analyses is available in the [GitHub
 repository](https://github.com/aleferreiro/Phylogenomics_Stilpnia_cayana).