Spread of an Inactive Form of Caspase-12 in Humans Is Due to Recent Positive Selection Yali Xue, Allan Daly, Bryndis Yngvadottir, Mengning Liu, Graham.

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Spread of an Inactive Form of Caspase-12 in Humans Is Due to Recent Positive Selection Yali Xue, Allan Daly, Bryndis Yngvadottir, Mengning Liu, Graham.

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Spread of an Inactive Form of Caspase-12 in Humans Is Due to Recent Positive Selection Yali Xue, Allan Daly, Bryndis Yngvadottir, Mengning Liu, Graham Coop, Yuseob Kim, Pardis Sabeti, Yuan Chen, Jim Stalker, Elizabeth Huckle, John Burton, Steven Leonard, Jane Rogers, Chris Tyler-Smith The American Journal of Human Genetics Volume 78, Issue 4, Pages 659-670 (April 2006) DOI: 10.1086/503116 Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 1 Worldwide distribution of the active and inactive forms of the caspase-12 gene in the HGDP-CEPH diversity panel. Circle area is proportional to sample size, up to a maximum of 50 individuals. The American Journal of Human Genetics 2006 78, 659-670DOI: (10.1086/503116) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 2 Structure of the caspase-12 gene. The exon-intron structure—including exon 3, which is present only in some transcripts—is shown at the top, as is the whole sequenced region and the location of the 8.6-kb LD block. The lower part of the figure shows the LD block identified using Haploview. Each square represents a pairwise value of D′, with the standard color coding (red indicates LOD⩾2 and D′=1; pink indicates LOD⩾2 and D′<1; blue indicates LOD<2 and D′=1; white indicates LOD<2 and D′<1). The American Journal of Human Genetics 2006 78, 659-670DOI: (10.1086/503116) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 3 Inferred caspase-12 haplotypes. Only positions that are variable in humans are shown, coded according to whether they carry the same allele as chimpanzee (white) or not (yellow), except that the stop-codon polymorphism is shown in blue or red, respectively. The low diversity and high frequency of derived alleles can be seen in the inactive genes. The American Journal of Human Genetics 2006 78, 659-670DOI: (10.1086/503116) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 4 Median-joining network of inferred caspase-12 haplotypes from the 8.6-kb LD block. Roots 1, 2, and 3 are discussed in the text. Circle area is proportional to haplotype frequency, and circles are coded according to population. The American Journal of Human Genetics 2006 78, 659-670DOI: (10.1086/503116) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 5 Top, EHH as a function of genetic distance in the CEU. Bottom, Corresponding haplotype bifurcation diagram. The American Journal of Human Genetics 2006 78, 659-670DOI: (10.1086/503116) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 6 Likelihood surface for the selection parameter 4Nes The American Journal of Human Genetics 2006 78, 659-670DOI: (10.1086/503116) Copyright © 2006 The American Society of Human Genetics Terms and Conditions