The main objective of this study is to evaluate biogeographic hypotheses of diversification and connection between isolated savannas north (Amazonian savannas) and south (Cerrado core) of the Amazon River. To achieve our goal, we employed genomic markers (genotyping by sequencing) to evaluate the genetic structure, population phylogenetic relationships, and historical range shifts of four Neotropical passerines with peri-Atlantic distributions: the Narrow-billed Woodcreeper (Lepidocolaptes angustirostris), the Plain-crested Elaenia (Elaenia cristata), the Grassland Sparrow (Ammodramus humeralis), and the White-banded Tanager (Neothraupis fasciata). The population genetic analyses indicated that landscape (e.g., geographic distance, landscape resistance, and percentage of tree cover) and climate metrics explained divergence among populations in most species, but without indicating a differential role between current and historical factors. Our results did not fully support the hypothesis that isolated populations at Amazonian savannas have been recently derived from the Cerrado core domain. Intraspecific phylogenies and gene flow analyses supported multiple routes of connection between the Cerrado and Amazonian savannas, rejecting the hypothesis that the Atlantic corridor explains the peri-Atlantic distribution. Our results reveal that the biogeographic history of the region is complex and cannot be explained by simple vicariant models.

# SNP dataset assembled using ipyrad.

Ahumeralis.vcf - Ammodramus humeralis.

Ecristata.vcf - Elaenia cristata.

Langustirostris.vcf - Lepidocolaptes angustirostris.

Nfasciata.vcf - Neothraupis fasciata.

# full-length loci dataset for GPhoCS analysis assembled using ipyrad

Ahumeralis.gphocs - Ammodramus humeralis.

Ecristata.gphocs - Elaenia cristata.

Langustirostris.gphocs - Lepidocolaptes angustirostris.

Nfasciata.gphocs - Neothraupis fasciata.

# Filtered occurrence records.

Ahumeralis_filtered_occurrence.csv - Ammodramus humeralis. (GBIF raw data: https://doi.org/10.15468/dl.8k6vqx)

Ecristata_filtered_occurrence.csv - Elaenia cristata. (GBIF raw data:  https://doi.org/10.15468/dl.2jgujs)

Langustirostris_filtered_occurrence.csv - Lepidocolaptes angustirostris. (GBIF raw data: https://doi.org/10.15468/dl.6qzxtb)

Nfasciata_filtered_occurrence.csv - Neothraupis fasciata. (GBIF raw data: https://doi.org/10.15468/dl.sbye7d)

# Final species distribution model for the current climate.

Ahumeralis_Current.asc - Ammodramus humeralis.

Ecristata_Current.asc - Elaenia cristata.

Langustirostris_Current.asc - Lepidocolaptes angustirostris.

Nfasciata_Current.asc - Neothraupis fasciata.

# Historical prediction based on the average of projections to the mid-Holocene (~ 6 kya), Last Glacial Maximum (~ 21 kya), and Last Interglacial (~ 120 – 140 kya) periods.

Ahumeralis_Model_PAST.asc - Ammodramus humeralis.

Ecristata_Model_PAST.asc - Elaenia cristata.

Langustirostris_Model_PAST.asc - Lepidocolaptes angustirostris.

Nfasciata_Model_PAST.asc - Neothraupis fasciata.