DOI: 10.5061/dryad.cvdncjt6g
title: Early stages of speciation with gene flow in the Amazilia Hummingbird (Amazilis amazilia) subspecies complex of Western South America

description: Disentangling the factors underlying the diversification of geographically
 variable species with a wide geographical range is essential to
 understanding the initial stages and drivers of the speciation process.
 The Amazilia Hummingbird, Amazilis amazilia, is found along the Pacific
 coast from northern Ecuador down to the Nazca Valley of Peru, and is
 currently classified as six phenotypically differentiated subspecies. Our
 aims were to resolve the evolutionary relationships of the six subspecies,
 to assess the geographical pattern and extent of evolutionary divergence,
 and to test for introgression using both a mtDNA marker and a
 genome-by-sequencing dataset from 86 individuals from across the species
 range. The consensus phylogenetic tree separated the six subspecies into
 three distinct clades, corresponding with the Ecuador lowlands (A.
 amazilia dumerilii), the Ecuador highlands (A. amazilia alticola and A.
 amazilia azuay), and the Peruvian coast (A. amazilia leucophoea, A.
 amazilia amazilia, and A. amazilia caeruleigularis). However, an
 unresolved mtDNA network suggests that the diversification of the
 subspecies was recent and rapid. We found evidence of gene flow among the
 subspecies A. amazilia dumerilii, A. amazilia alticola, and A. amazilia
 leucophoea, with strong genetic isolation of the subspecies A. amazilia
 azuay in the isolated Yunguilla Valley of Ecuador. Finally, environmental
 data from each subspecies’ capture locations were concordant with the
 three distinct clades. Overall, our results suggest that both expansion
 into new habitats and geographic isolation shaped the present-day
 phylogeny and range of the A. amazilia subspecies, and that A. amazilia
 azuay may be genetically divergent enough to be considered a separate
 species.
description: <strong>Amazilis_filtered_SNPs.vcf</strong>
 This vcf file contains the 34,896 SNPs from GBS used in all of
 the genomic analyses. Please see published article for more information on
 analyses methods.   
 <strong>ND2 sequence files:</strong>
 <strong>-Amazilia amazilia_ND2
 contig.NEX</strong> This file contains
 sequences of the mtDNA gene ND2 for 75 <em>Amazilis
 amazilia</em> samples. Each sequence is 1002 bp in
 length.   
 <strong>-Uranomitra franciae_ND2
 contig.NEX</strong> This file contains
 sequences of the mtDNA gene ND2 for 2 <em>Uranomitra franciae
 </em>samples. Each sequence is 890 bp in length. 
   <strong>-Amazilia tzacatl_ND2
 contig.NEX</strong> This file contains
 sequences of the mtDNA gene ND2 for 5 <em>Amazilia tzacatl
 </em>samples. Each sequence is 1002 bp in length. 
  
 <strong>Cowles_etal_Amazilis_Appendix Table
 1.xlsx</strong> Part of the manuscript
 appendix information, but also provided here. Appendix Table 1 provides
 sample ID, associated species and subspecies, and location data for each
 of the samples collected. Tab 1 has the information for the
 field-collected blood samples (Ecuador, both Amazilis and closely-related
 species), Tab 2 contains the information for the tissue samples from the
 University of New Mexico (Peru).  
 README file also contains instructions.