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

Lavretsky P, Peters J, Winker K, Bahn V, Kulikova I, Zhuravlev Y, Wilson R, Barger C, Gurney K, McCracken K

Date Published: November 19, 2015

DOI: http://dx.doi.org/10.5061/dryad.g3g65

 

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Title DADI.INPUT.FILES
Downloaded 14 times
Description Ready-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.
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Title INIDIVIDUAL & CONCATENATED FASTA FILES
Downloaded 5 times
Description Individual 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.
Download FASTA.FILES.zip (31.78 Mb)
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Title PCA & ADMIXTURE FILES
Downloaded 7 times
Description Run-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.
Download PCA&ADMIXTURE.FILES.zip (1.224 Mb)
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Title R Code for Simulations
Downloaded 10 times
Description R 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").
Download R.code.4.hybrid.Simulations.r (7.064 Kb)
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When using this data, please cite the original publication:

Lavretsky P, Peters J, Winker K, Bahn V, Kulikova I, Zhuravlev Y, Wilson R, Barger C, Gurney K, McCracken K (2015)Becoming pure: identifying generational classes of admixed individuals within lesser and greater scaup populations.Molecular Ecology, 25(3):661–674 http://dx.doi.org/ 10.1111/mec.13487

Additionally, please cite the Dryad data package:

Lavretsky P, Peters J, Winker K, Bahn V, Kulikova I, Zhuravlev Y, Wilson R, Barger C, Gurney K, McCracken K (2015) Data from: Becoming pure: identifying generational classes of admixed individuals within lesser and greater scaup populations. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.g3g65
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