Analyzing Genetic Admixture Patterns in Gorilla Populations
This content discusses the use of ADMIXTURE software to analyze genetic admixture in various Gorilla populations. The analyses include clusters, admixture proportions, ancestral allele frequencies, and sample variants. Different scenarios with varying cluster numbers are explored, providing insights into the genetic diversity and relationships among the studied Gorilla groups.
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Lets run ADMIXTURE ourselves! Sorry, there is only a Mac and Linux version Get the tar ball Unpack it E.g. tar- xzf Day2_PM_2_Admixture.tar.gz Move to the directory Day2_PM_2_Admixture E.g. cd Day2_PM_2_Admixture Move (mv) either admixtureLinux or admixtureMAC to admixture E.g. mv admixtureMAC admixture
Running basic Admixture ./admixture 1KG.A.5K.bed 2
ADMIXTURE (Alexander et al. 2009) p11 p12 p1K p21 p22 p2K g11 g21 g12 g22 g1N g2N Samples Variants G = Genotypes gM1 gM2 gMN q11 q21 q12 q22 q1N q2N Samples Admixture Proportions Clusters Q= qK1 qK2 qKN Clusters Ancestral Allele Frequencies Variants P = pM1 pM2 pMK
Admixture analyses Cross River K == 3 G.beringei Cameroon Captive Congo 1.0 0.8 0.6 K=3 0.4 0.2 K == 4 0.0 1.0 Gorilla_beringei_graueri A929_Kaisi Gorilla_gorilla_gorilla 9750_Azizi Gorilla_gorilla_gorilla A934_Delphi Gorilla_gorilla_gorilla B647_Anthal Gorilla_gorilla_gorilla B644_Paki Gorilla_gorilla_gorilla A932_Mimi Gorilla_gorilla_gorilla A962_Amani Gorilla_gorilla_gorilla B642_Akiba_Beri Gorilla_gorilla_gorilla B642_Akiba_Beri Gorilla_beringei_graueri 9732_Mkubwa Gorilla_beringei_graueri 9732_Mkubwa Gorilla_beringei_graueri Victoria Gorilla_gorilla_dielhi B646_Nyango Gorilla_gorilla_gorilla 9753_Kokomo Gorilla_gorilla_gorilla KB5792_Carolyn Gorilla_gorilla_gorilla KB5792_Carolyn Gorilla_gorilla_gorilla KB7973_Porta Gorilla_gorilla_gorilla KB7973_Porta Gorilla_gorilla_gorilla X00109_Tzambo Gorilla_gorilla_gorilla X00109_Tzambo Gorilla_gorilla_gorilla KB3784_Dolly Gorilla_gorilla_gorilla KB3782_Vila Gorilla_gorilla_gorilla KB5852_Helen Gorilla_gorilla_gorilla KB5852_Helen Gorilla_gorilla_gorilla A936_Coco Gorilla_gorilla_gorilla A933_Dian Gorilla_gorilla_gorilla X00108_Abe Gorilla_gorilla_gorilla A931_Banjo Gorilla_gorilla_gorilla A930_Sandra Gorilla_gorilla_gorilla A937_Kolo Gorilla_gorilla_gorilla B643_Choomba Gorilla_gorilla_gorilla B643_Choomba 0.8 0.6 K=4 0.4 0.2 K == 5 0.0 1.0 Gorilla_beringei_graueri A929_Kaisi Gorilla_gorilla_gorilla 9750_Azizi Gorilla_gorilla_gorilla A934_Delphi Gorilla_gorilla_gorilla B647_Anthal Gorilla_gorilla_gorilla B644_Paki Gorilla_gorilla_gorilla A932_Mimi Gorilla_gorilla_gorilla A962_Amani Gorilla_gorilla_gorilla B642_Akiba_Beri Akiba Beri Gorilla_beringei_graueri 9732_Mkubwa Mkubwa Gorilla_beringei_graueri Victoria Gorilla_gorilla_dielhi B646_Nyango Gorilla_gorilla_gorilla 9753_Kokomo Gorilla_gorilla_gorilla KB5792_Carolyn Carolyn Gorilla_gorilla_gorilla KB7973_Porta Gorilla_gorilla_gorilla X00109_Tzambo Tzambo Gorilla_gorilla_gorilla KB3782_Vila Gorilla_gorilla_gorilla KB5852_Helen Helen Gorilla_gorilla_gorilla A936_Coco Gorilla_gorilla_gorilla A933_Dian Gorilla_gorilla_gorilla X00108_Abe Gorilla_gorilla_gorilla A931_Banjo Gorilla_gorilla_gorilla A930_Sandra Gorilla_gorilla_gorilla A937_Kolo Gorilla_gorilla_gorilla B643_Choomba Choomba Gorilla_gorilla_gorilla KB3784_Dolly 0.8 K=5 0.6 0.4 0.2 K == 6 0.0 1.0 Gorilla_beringei_graueri A929_Kaisi Gorilla_gorilla_gorilla 9750_Azizi Gorilla_gorilla_gorilla A934_Delphi Gorilla_gorilla_gorilla B647_Anthal Gorilla_gorilla_gorilla B644_Paki Gorilla_gorilla_gorilla A932_Mimi Gorilla_gorilla_gorilla A962_Amani Gorilla_beringei_graueri Victoria Gorilla_gorilla_dielhi B646_Nyango Gorilla_gorilla_gorilla 9753_Kokomo Gorilla_gorilla_gorilla KB3782_Vila Gorilla_gorilla_gorilla A936_Coco Gorilla_gorilla_gorilla A933_Dian Gorilla_gorilla_gorilla X00108_Abe Gorilla_gorilla_gorilla A931_Banjo Gorilla_gorilla_gorilla A930_Sandra Gorilla_gorilla_gorilla A937_Kolo Gorilla_gorilla_gorilla KB3784_Dolly Prado-Martinez et al. (2013) Nature 0.8 K=6 0.6 0.4 0.2 0.0 Kaisi Azizi Delphi Anthal Paki Mimi Amani Victoria Nyango Kokomo Porta Dolly Vila Coco Dian Abe Banjo Sandra Kolo
Admixture analyses: when is the K correct? Cross River Congo G.beringei K == 3 Cameroon Captive 1.0 0.8 0.6 K=3 0.4 0.2 K == 4 0.0 1.0 Gorilla_beringei_graueri A929_Kaisi Gorilla_gorilla_gorilla 9750_Azizi Gorilla_gorilla_gorilla A934_Delphi Gorilla_gorilla_gorilla B647_Anthal Gorilla_gorilla_gorilla B644_Paki Gorilla_gorilla_gorilla A932_Mimi Gorilla_gorilla_gorilla A962_Amani Gorilla_gorilla_gorilla B642_Akiba_Beri Gorilla_gorilla_gorilla B642_Akiba_Beri Gorilla_beringei_graueri 9732_Mkubwa Gorilla_beringei_graueri 9732_Mkubwa Gorilla_beringei_graueri Victoria Gorilla_gorilla_dielhi B646_Nyango Gorilla_gorilla_gorilla 9753_Kokomo Gorilla_gorilla_gorilla KB5792_Carolyn Gorilla_gorilla_gorilla KB5792_Carolyn Gorilla_gorilla_gorilla KB7973_Porta Gorilla_gorilla_gorilla KB7973_Porta Gorilla_gorilla_gorilla X00109_Tzambo Gorilla_gorilla_gorilla X00109_Tzambo Gorilla_gorilla_gorilla KB3784_Dolly Gorilla_gorilla_gorilla KB3782_Vila Gorilla_gorilla_gorilla KB5852_Helen Gorilla_gorilla_gorilla KB5852_Helen Gorilla_gorilla_gorilla A936_Coco Gorilla_gorilla_gorilla A933_Dian Gorilla_gorilla_gorilla X00108_Abe Gorilla_gorilla_gorilla A931_Banjo Gorilla_gorilla_gorilla A930_Sandra Gorilla_gorilla_gorilla A937_Kolo Gorilla_gorilla_gorilla B643_Choomba Gorilla_gorilla_gorilla B643_Choomba 0.8 0.6 K=4 0.4 0.2 K == 5 0.0 1.0 Gorilla_beringei_graueri A929_Kaisi Gorilla_gorilla_gorilla 9750_Azizi Gorilla_gorilla_gorilla A934_Delphi Gorilla_gorilla_gorilla B647_Anthal Gorilla_gorilla_gorilla B644_Paki Gorilla_gorilla_gorilla A932_Mimi Gorilla_gorilla_gorilla A962_Amani Gorilla_gorilla_gorilla B642_Akiba_Beri Akiba Beri Gorilla_beringei_graueri 9732_Mkubwa Mkubwa Gorilla_beringei_graueri Victoria Gorilla_gorilla_dielhi B646_Nyango Gorilla_gorilla_gorilla 9753_Kokomo Gorilla_gorilla_gorilla KB5792_Carolyn Carolyn Gorilla_gorilla_gorilla KB7973_Porta Gorilla_gorilla_gorilla X00109_Tzambo Tzambo Gorilla_gorilla_gorilla KB3782_Vila Gorilla_gorilla_gorilla KB5852_Helen Helen Gorilla_gorilla_gorilla A936_Coco Gorilla_gorilla_gorilla A933_Dian Gorilla_gorilla_gorilla X00108_Abe Gorilla_gorilla_gorilla A931_Banjo Gorilla_gorilla_gorilla A930_Sandra Gorilla_gorilla_gorilla A937_Kolo Gorilla_gorilla_gorilla B643_Choomba Choomba Gorilla_gorilla_gorilla KB3784_Dolly 0.8 K=5 0.6 0.4 0.2 K == 6 0.0 1.0 Gorilla_beringei_graueri A929_Kaisi Gorilla_gorilla_gorilla 9750_Azizi Gorilla_gorilla_gorilla A934_Delphi Gorilla_gorilla_gorilla B647_Anthal Gorilla_gorilla_gorilla B644_Paki Gorilla_gorilla_gorilla A932_Mimi Gorilla_gorilla_gorilla A962_Amani Gorilla_beringei_graueri Victoria Gorilla_gorilla_dielhi B646_Nyango Gorilla_gorilla_gorilla 9753_Kokomo Gorilla_gorilla_gorilla KB3782_Vila Gorilla_gorilla_gorilla A936_Coco Gorilla_gorilla_gorilla A933_Dian Gorilla_gorilla_gorilla X00108_Abe Gorilla_gorilla_gorilla A931_Banjo Gorilla_gorilla_gorilla A930_Sandra Gorilla_gorilla_gorilla A937_Kolo Gorilla_gorilla_gorilla KB3784_Dolly 0.8 K=6 0.6 0.4 0.2 0.0 Kaisi Azizi Delphi Anthal Paki Mimi Amani Victoria Nyango Kokomo Porta Dolly Vila Coco Dian Abe Banjo Sandra Kolo Prado-Martinez et al. (2013) Nature
TheK Problem In practice, people often try different K, and choose the K that makes most biological sense. -Frappe Manual
ADMIXTURE: using cross validation to identify the best K g11 g12 g21 g22 g1N g2N G = gM1 gM 2 gMN K gli= 2 qki plk k=1 Alexander and Lange (2011) BMC Bioinformatics
ADMIXTURE: using cross validation to identify the best K ./admixture --cv=10 1KG.A.5K.bed 2
ADMIXTURE: using cross validation to identify the best K ./admixture --cv=10 1KG.A.5K.bed 2 K Alexander and Lange (2011) BMC Bioinformatics gli= 2 qki plk k=1 across all masked entries over all folds.
To compare run across multiple K One way: ./admixture --cv=10 1KG.A.5K.bed 1 ./admixture --cv=10 1KG.A.5K.bed 2 [3,4,5] ./admixture --cv=10 1KG.A.5K.bed 6
To compare run across multiple K Another way for today: bash run5K.sh A Which does: for i in $(seq 1 6); do for j in $(ls -1 *.$1.5K.bed); do ./admixture --cv=10 $j $i | tee $(basename $j .bed).$i.log; done; done grep -h CV 1KG.$1.5K.*.log
How well X-validation performs CEU CEU+ASW+YRI CEU+ASW+YRI+MEX Cross validation error 0.54 0.52 0.50 0.48 0.46 1 2 3 4 5 1 2 3 4 5 1 2 3 4 5 K Alexander and Lange (2011) BMC Bioinformatics
Samples to define clusters CEU (European) NA12878 YRI (African) NA18499 JPT (East Asian) NA19000 PEL (Lima/Latino) HG01565
