Data from: Becoming pure: identifying generational classes of admixed individuals within lesser and greater scaup populations ...

• Main Authors: Lavretsky, Philip, Peters, Jeffrey, Winker, Kevin, Bahn, Volker, Kulikova, Irina, Zhuravlev, Yuri, Wilson, Robert, Barger, Christopher, Gurney, Kirsty, McCracken, Kevin, Peters, Jeffrey L., Barger, Chris, McCracken, Kevin G.
• Format: Dataset
• Language: English
• Published: Dryad 2015
• Subjects: Diving Duck; greater scaup
• Online Access: https://dx.doi.org/10.5061/dryad.g3g65; https://datadryad.org/stash/dataset/doi:10.5061/dryad.g3g65

Estimating the frequency of hybridization is important to understand its evolutionary consequences and its effects on conservation efforts. In this study, we examined the extent of hybridization in two sister species of ducks that hybridize. We used mitochondrial control region sequences and 3,589 double-digest restriction-associated DNA sequences (ddRADseq) to identify admixture between wild lesser scaup (Aythya affinis) and greater scaup (A. marila). Among 111 individuals, we found one introgressed mitochondrial DNA haplotype in lesser scaup and four in greater scaup. Likewise, based on the site-frequency spectrum from autosomal DNA, gene flow was asymmetrical, with higher rates from lesser into greater scaup. However, using ddRADseq nuclear DNA all individuals were assigned to their respective species with > 0.95 posterior assignment probability. To examine the power for detecting admixture, we simulated a breeding experiment in which empirical data were used to create F1 hybrids and nine generations ... : DADI.INPUT.FILESReady-run dadi files for 3 models that includes isolation-with-migration (IM), neutral-no-divergence (neutral.model), and split with secondary contact (Split.Mig) using the folded frequency spectrum of only minor alleles for greater (N = 64) and lesser (N = 47) scaup. The site-frequency spectrum is based on bi-allelic single nucleotide polymorphisms from 3448 autosomal ddRAD-seq markers.INIDIVIDUAL & CONCATENATED FASTA FILESIndividual and concatenated fasta files for 3448 Autosomal and 140 Z linked markers identified using ddRAD-seq protocols for greater (N = 64) and lesser (N = 47) scaup. A fasta file with mitochondrial sequences is also provided.FASTA.FILES.zipPCA & ADMIXTURE FILESRun-ready input files of 140 Z-linked and 3448 autosomal ddRAD-seq markers for PCA (*.4.PCA.stru) and ADMIXTURE (*.map & *.ped) analyses for greater (N = 64) and lesser (N = 47) scaup.PCA&ADMIXTURE.FILES.zipR Code for SimulationsR Code ("R.code.4.hybrid.Simulations.r") is provided to run ...