***********Genotype data_extended 3***********
Description: 
2009_Ben_ext_out_f (.bim, .fam) correspond to 50k SNP genotype data in .bed format (PLINK binary biallelic genotype table) after quality control in PLINK (Purcell et al., 2007)
The genotype data include current (own) and historical genotype from Beninese cattle, genotype data from African taurine, African hybrids, African zebu, European taurine and Asian Indicine Asian Indicine, as well as the genotype of Gayal (Bos frontalis). Except our own dataset, the other genotype were retrieved from the WIDDE database (Sempéré et al., 2015) 

Number of variant 32,228 SNP 

Number of animals: 1,118 cattle

Breeds:
1)African taurines (AFT): 
Dahomey: DAH_cur (30); 
Lagune: LA_cur (110); LA_out(25); LA_hist (44); 
Somba: SO_cur (57); SO_hist (44); 
Baoulé (28); N’dama (25);
2) African Hybrids
BO_cur (135); Adm_cur (98); BO_hist (45);
Kuri (30)
3) African zebu (AFZ)
Zebu White Fulani (43); Zebu Bororo (23); 
4)European taurine (EUT)
Angus (62), Holstein (30), Charolais (20), Shorthorn (35); Salers (22);
5)Asian Indicine/Zebu (AID)
Gir (24); Brahman (25); Ongole (20); Nellore (24); 
6)Outgroup: 
Gayal (21)


Analyses
This data set was used to estimate admixture proportion in the Beninese cattle population through the calculation of f4 ratio with the Admixtools software (Patterson et al., 2012). Before the analyses, the genotype data was pruned in PLINK (Purcell et al., 2007) and converted to eigenstrat format using the convertf program as described in the Admixtools guideline. 

References:
Patterson, N., Moorjani, P., Luo, Y., Mallick, S., Rohland, N., Zhan, Y., et al. (2012). Ancient admixture in human history. Genetics 192, 1065–1093. doi: 10.1534/genetics.112.145037
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., et al. (2007). PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses. Am J Hum Genet 81, 559–575.
Sempéré, G., Moazami-Goudarzi, K., Eggen, A., Laloë, D., Gautier, M., and Flori, L. (2015). WIDDE: a Web-Interfaced next generation database for genetic diversity exploration, with a first application in cattle. BMC Genomics 16, 940. doi: 10.1186/s12864-015-2181-1