SimulatedGenotypes

Genotypes, simulated in HYBRIDLAB, at 12 diagnostics microsatellite loci for six genotypic classes of Ammodramus sparrows: pure caudacutus, backcrossed caudacutus, F1, F2, backcrossed nelsoni, and pure nelsoni

SparrowGenotypes

Genotypes at 12 diagnostic microsatellite loci of 96 Ammodramus caudacutus and A. nelsoni. Sparrows were sampled from sympatric and allopatric populations

Additional file 2: Figure S2. of Differential introgression and the maintenance of species boundaries in an advanced generation avian hybrid zone

Determination of the number of genetic clusters (K) for nelsoni and caudacutus individuals sampled from 32 marshes using the ΔK (left) and LnPD (right) methods. (PDF 64 kb

Additional file 6: Table S1. of Differential introgression and the maintenance of species boundaries in an advanced generation avian hybrid zone

Primer information for the markers used in this study. Table includes locus name, annealing temperatures, fragment length, the number of individuals with haplotype data (either from sequencing or restriction fragment length polymorphism assays), primer sequences, and original reference for each primer. (PDF 67 kb

Additional file 7: Table S2. of Differential introgression and the maintenance of species boundaries in an advanced generation avian hybrid zone

Restriction Fragment Length Polymorphism (RFLP) assay information for ND2, SLC30A-5, and RAG-1. Table includes the restriction enzyme used for each assay and the approximate sizes of bands produced for each species. Conditions for the restriction digests followed manufacturer protocols. (PDF 71 kb

Assembled N50 contigs Ammodramus caudacutus

Fasta file of assembled contigs that were > the N50contig size of assembled Ammodramus caudacutus reads from Illumina sequencing

Additional file 5: Figure S5. of Differential introgression and the maintenance of species boundaries in an advanced generation avian hybrid zone

Genomic clines estimated in introgress for A. caudacutus and A. nelsoni. Each plot represents a marker and includes the name of each locus and a P value from the analysis. Solid color lines represent genomic clines for caudacutus homozygote genotypes, dashed lines represent genomic clines for heterozygote genotypes. Shaded areas represent 95 % confidence intervals. (PDF 1572 kb

Additional file 4: Figure S4. of Differential introgression and the maintenance of species boundaries in an advanced generation avian hybrid zone

Plot of introgression patterns for 29 markers (24 microsatellites, 1 nuclear gene, 2 mitochondrial genes, and 2 z-linked genes). Each column represents a marker and each row represents an individual (allopatric individuals are not included). Colors correspond to parental alleles: 2 nelsoni alleles (white), 2 caudacutus alleles (black), and 1 allele from each parental population (grey). (PDF 74 kb

Assembled N50 contigs Ammodramus nelsoni

Fasta file of assembled contigs > than the N50 contig length for Illumina sequencing reads of Ammodramus nelsoni

Sparrow Genotypes/Haplotypes

Genotypes at 24 microsatellite loci and haplotype information at 5 genes for 292 Ammodramus caudacutus and A. nelsoni. Sparrows were sampled from 34 sites along a geographic transect, including allopatric and sympatric populations