10 research outputs found
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
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 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 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 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 nelsoni
Fasta file of assembled contigs > than the N50 contig length for Illumina sequencing reads of Ammodramus nelsoni
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
Microsatellite genotypes and locations of New England cottontails in Maine and New Hampshire
Microsatellite genotypes for 11 loci, including a Y chromosome marker, are provided in Excel spreadsheet format. These genotypes are from individual New England cottontails identified from fecal pellet samples collected during field surveys. Location data, in the form of lat/long geographic coordinates, are provided for each sample collected. Column headings and other metadata are found in the spreadsheet