***********FIRST EXTENDED GENOTYPE DATA***********
Description: 
2009_Ben_ext_f_pr (.bim, .fam) corresponds 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, and genotype data from other African taurine, African hybrids, African zebu, European taurine and Asian Indicine Asian Indicine. Except for our own dataset, the other genotypes were retrieved from the WIDDE database (Sempéré et al., 2015).


Number of variants: 30,637 SNP 

Number of animals: 997 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); 


Analyses
This dataset was used to perform diversity analyses (principal component analysis, unsupervised k-means clustering), admixture tests  and the estimation of admixture dates.
For the unsupervised k-means clustering with the “adegenet” software (Jombart, 2008; Jombart and Ahmed, 2011), the dataset was first pruned for LD and converted in Structure format in PLINK (Purcell et al., 2007) as required by “adegenet”.
For the admixture tests in Admixtools (Patterson et al., 2012) and the estimation of admixture dates in ALDER (Loh et al., 2013), the dataset was converted to eigenstrat format using the convertf program as described in the guideline of Admixtools.

References:
Jombart, T. (2008). adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24, 1403–1405. doi: 10.1093/bioinformatics/btn129
Jombart, T., and Ahmed, I. (2011). adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics 27, 3070–3071. doi: 10.1093/bioinformatics/btr521
Loh, P.-R., Lipson, M., Patterson, N., Moorjani, P., Pickrell, J. K., Reich, D., et al. (2013). Inferring admixture histories of human populations using linkage disequilibrium. Genetics 193, 1233–1254. doi: 10.1534/genetics.112.147330
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