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Supplemental Material for Heikkinen et al., 2020

dataset
posted on 01.07.2020 by Marja Heikkinen, Minna Ruokonen, Thomas A. White, Michelle Alexander, İslam Gündüz, Keith M. Dobney, Jouni Aspi, Jeremy B. Searle, Tanja Pyhäjärvi
These supplemental files include:

Supplementary File 1. Supplemental materials and methods and results.

Figure S5. Neighbor-joining tree based on genetic distances between all samples of geese analyzed in this study including the reference genome A. cygnoid domesticus breed Zhedong that was used as a reference in SNP calling. Branches leading to graylags are blue, to European domestic geese green and to Chinese domestic geese red. Branches that lead to breeds which are crosses between European and Chinese domestic geese are colored purple. Branches are labelled with a population identifier followed by the graylag, European and Chinese domestic goose admixture proportions from STRUCTURE.

Table S2. Pairwise FST values for each population analyzed in this study.

Table S3. The ƒ3 analysis results for the Netherlands and Turkey. Significant negative Z-scores are in bold.

Table S4. The ƒ3 analysis results for domestic geese. Significant negative Z-scores are in bold.

Table S6. The ƒ3 analysis results for the graylags.

Table S7. The ƒ3 analysis results for domestic geese with Chinese domestic as a source. Significant negative Z-scores are in bold.

Supplementary file 2. Commands for Tassel-GBS pipeline and vcftools.

Scaffold_name_conversion_key.txt. The reference genome's scaffold names were changed to continuous numbering for the analyses. This file explains the conversion that was made.

Filtered_Goose_SNPs.vcf. The file contains the filtered genotypes.

History

Article title

Long-term reciprocal gene flow in wild and domestic geese reveals complex domestication history

Manuscript #

G3/2019/400886

Article DOI

10.1534/g3.120.400886

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