DOI: 10.5061/dryad.g3g65
title: Data from: Becoming pure: identifying generational classes of admixed individuals within lesser and greater scaup populations

description: 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 &gt; 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 (F2-F10) of backcrossing. F1 hybrids and F2, F3, and most F4
 backcrosses were clearly distinguishable from pure individuals, but
 evidence of admixed histories was effectively lost after the fourth
 generation. Thus, we conclude that low interspecific assignment
 probabilities (0.011 – 0.043) for two lesser and nineteen greater scaup
 were consistent with admixed histories beyond the F3 generation. These
 results indicate that the propensity of these species to hybridize in the
 wild is low and largely asymmetric. When applied to species-specific
 cases, our approach offers powerful utility for examining concerns of
 hybridization in conservation efforts, especially for determining the
 generational time until admixed histories are effectively lost through
 backcrossing.
description: 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 simulations from ADMIXTURE style .ped files. Missing data across individuals is first replaced with a randomly chosen allele from their respective population ("impute.gen"), and then hybridization and X backcrossing events are simulated ("sim.hybrid").R.code.4.hybrid.Simulations.r