Speciation with gene flow in an island endemic hummingbird

We find evidence for speciation in streamertail hummingbirds (Trochilus polytmus and T. scitulus), Jamaican endemic taxa thought to represent an exception to the rule that, for birds, speciation cannot progress in situ on small islands. Our analysis shows that divergent selection acting on male bill color, a sexual ornament that is red in polytmus and black in scitulus, plays a pivotal role as a reproductive barrier. We sequenced 6,451 single nucleotide polymorphisms (SNPs) and the mitochondrial control region. Low genomic divergence was detected across the two datasets, consistent with a demographic history of recent speciation or extensive gene flow between previously diverged taxa. Such low background divergence offers little support for the presence of post-mating reproductive incompatibilities. Yet, a geographic cline analysis reveals narrow clines in a handful of traits likely to be under selection. In particular, the cline width for male bill color is only 2.3 km, marking it as o..., Laboratory Methods and Bioinformatics Processing: 
Genotyping-by-sequencing
SNPs were generated using a genotyping-by-sequencing method by the Cornell Institute of Genomic Diversity (IGD). Briefly, DNA extracts for 160 Trochilus individuals was digested with PstI (CTGCAG), and the resulting fragments were ligated to sample-specific adapters and common adapters. Fragments were then pooled, cleaned, and amplified using an 18-cycle PCR. Final libraries were sequenced as single-end, 100-base pairs reads in one lane of an Illumina HiSeq 2000 (Illumina, San Diego, CA, USA).
SNP calling was performed using UNEAK, a reference-free SNP calling pipeline specific to GBS data that is an extension of the Java program TASSEL. UNEAK filters to remove reads that lack barcodes, cut sites, or that have ‘N’s present in the first part of the sequence following the barcode. High quality reads were then clustered into tags. Unique tags were merged and their counts in the whole sample of individuals were..., , # Data from: Speciation with gene flow in an island endemic hummingbird

## Authors of the Dataset:

Caroline D. Judy, PhD, Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution
[[e-mail]](mailto:[e-mail])

Gary R. Graves, John McCormack, Katherine Faust Stryjewski, Robb T. Brumfield

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## Description of the data files

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Three genomic data tables are archived in this repository (.csv, .fasta).

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### museumID\_raw\.analysis.SNPs.csv

A data matrix containing 6,451 individual SNPs in 145 individuals.

Variable names and descriptions:

* Column1: MuseumID - a unique identifier associated with each vouchered specimen that can be cross referenced in Table S1.
* Column2: phenotype - description of bill color based on morphological assessement
Row1[,3:6453] labels for individual SNP IDs.

### SNP\_Loci.fasta

A fasta file containing SNP loci.

Variable names and descri...,