Supplementary Information for:

Ancestry, admixture and selection in Colombian genomes Lavanya Rishishwar1,2,3,†, Andrew B. Conley1,†, Charles H. Wigington1, Lu Wang1, Augusto Valderrama-Aguirre2,4,5 and I. King Jordan1,2,3,* 1School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA 2PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia 3BIOS Center de Bioinformática y Biología Computacional, Manizales, Caldas, Colombia 4Biomedical Research Institute, Universidad Libre, Cali, Valle del Cauca, Colombia 5Regenerar - Center of Excellence for Regenerative and Personalized Medicine, Valle del Cauca, Colombia

Ancestral Populations from Around the WorldName Color Ancestral Origin

CEU Northern & Western Europe 85 23128226 Whole genome sequencing

CHB Beijing, China 92 23128226 Whole genome sequencing

Totonac & Bolivian Mexico & Bolivia 45 22606979 SNP microarray

YRI Nigeria 87 23128226 Whole genome sequencing

Admixed Populations from the Americas

CLM Medellin, Colombia 60 23128226 Whole genome sequencing

Colombian Colombia 26 20445096 Illumina 610K array

Dominican Republican Dominican Republic 27 20445096 Illumina 610K array

Ecuador Ecuador 20 20445096 Illumina 610K array

Mexican Mexico 112 20445096 Affymetrix GeneChip 500K Array Set

Puerto Rican Puerto Rico 27 20445096 Illumina 610K array

n Source (PMID) Platform

Name Color Country n Source (PMID) Platform

S1 Figure. World-wide source of genome sequence and genotype data analyzed in this study. The global locations of putative ancestral populations are shown – African (blue), Asian (red), European (orange) and Native American (purple) – along with the locations of admixed American populations (green). Information on the source populations, number of samples, supporting publication and genome characterization platform is provided. Note: The global map shown here was modified from http://commons.wikimedia.org/wiki/File:World_Map_Blank_-_with_blue_sea.svg, which has been released into the public domain and thus free to be used by anyone for any purpose.

PC1 (81.07%)

PC2

(10.

54%

)

−15 −10 −5 0 5 10 15 20 25 30

−10

−50

510

European

East Asian

African

Medellin

Totonac &Bolivian

PC3 (3.79%)

PC4

(0.3

0%)

−15 −10 −5 0 5 10 15 20 25 30

−10

−50

510

European

East Asian

African

Medellin

Totonac &Bolivian

PC5 (0.11%)

PC6

(0.0

9%)

−15 −10 −5 0 5 10 15 20 25 30

−10

−50

510

European

African

Medellin

Totonac &Bolivian

PC7 (0.06%)

PC8

(0.0

6%)

−15 −10 −5 0 5 10 15 20 25 30

−10

−50

510

European

African

Medellin

Totonac &Bolivian

(A) (B)

(C) (D)

S2 Figure. PCA of pairwise allele sharing distances among admixed Colombian genomes from Medellin compared to putative ancestral populations from Africa, the Americas, Asia and Europe. The panels have comparisons of the successive principal components (PCs): (A) PC1-PC2, (B) PC3-PC4, (C) PC5-PC6 and (D) PC7-PC8.

Ancestry-specific Segment Size

Fre

quen

cy

0 5000 10000 15000

0

5000

10000

15000

20000

S3 Figure. Size distribution of the ancestry-specific chromosomal segments used for the ancestry enrichment analysis.

Scalechr2:

1 Mb hg19108,500,000 109,000,000 109,500,000 110,000,000 110,500,000

RefSeq Genes

Num

ber o

fC

hrom

osom

esLo

g Fo

ldEn

richm

ent

0.85

-1.57

0

86

7

Scalechr2:

2 Mb hg19107,000,000 108,000,000 109,000,000 110,000,000 111,000,000 112,000,000 113,000,000

RefSeq Genes

95

71.48

-1.87

0

Num

ber o

fC

hrom

osom

esLo

g Fo

ldEn

richm

ent

EuropeanAfrican Native American

EDAR

S4 Figure. Example of an Asian (American)-depleted region found at the EDAR locus. Population-wide chromosome counts from the three ancestry-components are shown above the genomic axis and log-fold enrichment values (observed counts/genomic average counts) for the ancestry components are shown below the axis. The upper panel shows a ~7Mb region surrounding the locus on chromosome 2, and the lower panel shows a zoomed in view centered on the Asian (American) ancestry-depleted gene EDAR.