Independent Histories of Human Y Chromosomes from Melanesia and Australia Manfred Kayser, Silke Brauer, Gunter Weiss, Wulf Schiefenhövel, Peter A. Underhill,

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Independent Histories of Human Y Chromosomes from Melanesia and Australia Manfred Kayser, Silke Brauer, Gunter Weiss, Wulf Schiefenhövel, Peter A. Underhill, Mark Stoneking The American Journal of Human Genetics Volume 68, Issue 1, Pages 173-190 (January 2001) DOI: 10.1086/316949 Copyright © 2001 The American Society of Human Genetics Terms and Conditions

Figure 1 Y-chromosome haplotypes, as defined by six Y-chromosome SNPs and two specific deletions at the Y-chromosome STR locus DYS390, and their frequency distribution in human populations from eastern/southeastern Asia, Melanesia, Polynesia, and Australia. Color codings are as follows: black, complete ancestral haplotype (with respect to the markers analyzed); gray, M9G; red, M4G/M5T/M9G; yellow, M119C/M9G; orange, M122C/M9G; green, RPS4Y711T; dark blue, DYS390.1del/RPS4Y711T; purple, DYS390.3del/M9G; and light blue, DYS390.3del/RPS4Y711T. Abbreviations are as follows: Aus1 = Australia, Arnhem Land; Aus2 = Australia, Sandy Desert; Bor = southern Borneo; Chi = China; Coo = Cook Islands; Jav = Java; Kor = Korea; Mal = Malaysia; Mol = Moluccas; Phi = Philippines; PNC = PNG coast; PNH = PNG highlands; TaC = Taiwan Chinese; Tai = Taiwan aborigines; Ten = Nusa Tenggara; TNB = Tolai New Britain; Tro = Trobriand Islands; Vie = Vietnam. The American Journal of Human Genetics 2001 68, 173-190DOI: (10.1086/316949) Copyright © 2001 The American Society of Human Genetics Terms and Conditions

Figure 2 Y-chromosome haplotypes, based on six Y-chromosome SNPs and two specific deletions at the Y-chromosome STR locus DYS390, and their phylogenetic relationship. The superscript “a” denotes a recurrent mutation event. The American Journal of Human Genetics 2001 68, 173-190DOI: (10.1086/316949) Copyright © 2001 The American Society of Human Genetics Terms and Conditions

Figure 3 Structure of the Y-chromosome STR locus DYS390, and proposed mutational events leading to the DYS390.1 deletion and the DYS390.3 deletion. The American Journal of Human Genetics 2001 68, 173-190DOI: (10.1086/316949) Copyright © 2001 The American Society of Human Genetics Terms and Conditions

Figure 4 Median-joining network of 41 Y-chromosome STR haplotypes found in 51 individuals carrying the M4G/M5T/M9G haplotype. Circles denote the Y-chromosome STR haplotypes, with the area of the circle being proportional to the number of individuals. Lines denote mutation steps (one-step distance is indicated); parallel lines represent identical mutations. Color coding is as follows: red, highland PNG; blue, coastal PNG/New Britain; green, Trobriand Islands; yellow, eastern Indonesia. The American Journal of Human Genetics 2001 68, 173-190DOI: (10.1086/316949) Copyright © 2001 The American Society of Human Genetics Terms and Conditions

Figure 5 Bayesian-based demographic inference of associated Y-chromosome STR variation concerning the DYS390.1del/RPS4Y711T haplotype (a and b), the M119C/M9G haplotype (c and d), and the M4G/M5T/M9G haplotype (e and f). Prior probabilities (dashed lines) and posterior-probability distributions (continuous lines) are shown for the time when population expansion began (a, c, and e) and for the TMRCA (b, d, and f). The American Journal of Human Genetics 2001 68, 173-190DOI: (10.1086/316949) Copyright © 2001 The American Society of Human Genetics Terms and Conditions

Figure 6 PC plot of Y-chromosome haplotype frequencies for 18 populations from eastern/southeastern Asia, Melanesia, Polynesia, and Australia (for abbreviations, see the legend to figure 1). Geographic regions are highlighted. The American Journal of Human Genetics 2001 68, 173-190DOI: (10.1086/316949) Copyright © 2001 The American Society of Human Genetics Terms and Conditions

Figure 7 Correlation analysis of genetic distance (FST based on SNP markers) and geographic distance (km), for 12 populations from eastern/southeastern Asia, Melanesia, and Australia (for particular populations, see the text), for mtDNA (triangles, dashed trendline) and Y-chromosome DNA (squares, continuous trendline). The American Journal of Human Genetics 2001 68, 173-190DOI: (10.1086/316949) Copyright © 2001 The American Society of Human Genetics Terms and Conditions