DOI: 10.5061/dryad.w9ghx3frh
title: A comparative phylogenomic analysis of birds reveals heterogeneous differentiation processes among Neotropical Savannas

description: 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.
description: <strong># SNP dataset assembled using
 ipyrad.</strong> <strong>Ahumeralis.vcf
 </strong><em>- Ammodramus humeralis.</em>
 <strong>Ecristata.vcf
 </strong><em>- Elaenia cristata.</em> <strong>Langustirostris.vcf
 </strong><em>- Lepidocolaptes
 angustirostris.</em> <strong>Nfasciata.vcf
 </strong><em>- Neothraupis fasciata.</em>
 <strong># full-length loci dataset for GPhoCS analysis
 assembled using ipyrad</strong> <strong>Ahumeralis.gphocs</strong> -<em> Ammodramus humeralis.</em> <strong>Ecristata.gphocs</strong><em> - Elaenia cristata.</em> <strong>Langustirostris</strong><strong>.gphocs</strong><em> - Lepidocolaptes angustirostris.</em> <strong>Nfasciata.gphocs</strong><em> - Neothraupis fasciata.</em> <strong># Filtered occurrence records.</strong> <strong>Ahumeralis_filtered_occurrence.csv</strong> - <em>Ammodramus humeralis. </em>(GBIF raw data: https://doi.org/10.15468/dl.8k6vqx) <strong>Ecristata_filtered_occurrence.csv</strong> - <em>Elaenia cristata. </em>(GBIF raw data:  https://doi.org/10.15468/dl.2jgujs) <strong>Langustirostris_filtered_occurrence.csv</strong> - <em>Lepidocolaptes angustirostris. </em>(GBIF raw data: https://doi.org/10.15468/dl.6qzxtb) <strong>Nfasciata_filtered_occurrence.csv </strong>- <em>Neothraupis fasciata. </em>(GBIF raw data: https://doi.org/10.15468/dl.sbye7d) <strong># Final species distribution model for the current climate.</strong> <strong>Ahumeralis_Current.asc</strong> - <em>Ammodramus humeralis</em>. <strong>Ecristata_Current.asc</strong> - <em>Elaenia cristata.</em> <strong>Langustirostris_Current.asc</strong> - <em>Lepidocolaptes angustirostris.</em> <strong>Nfasciata_Current.asc</strong> - <em>Neothraupis fasciata.</em> <strong># 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.</strong> <strong>Ahumeralis_Model_PAST.asc</strong> - <em>Ammodramus humeralis.</em> <strong>Ecristata_Model_PAST.asc</strong> - <em>Elaenia cristata.</em> <strong>Langustirostris_Model_PAST.asc</strong> - <em>Lepidocolaptes angustirostris.</em> <strong>Nfasciata_Model_PAST.asc</strong> - <em>Neothraupis fasciata.</em>