Article Figures & Data
Figures
- Figure 1.—
Geographic location of population samples used in this study. Population samples are identified by the two-letter abbreviations given in Table 1.
- Figure 2.—
Unrooted population distance tree generated by neighbor-joining analysis of FST values. Distance is indicated by the lengths of horizontal branches. Putatively admixed populations (Er, Ga, SA) are excluded.
- Figure 3.—
Population membership in the genetic clusters identified by Structure. In each case, one of the two clusters is arbitrarily shown as shaded, the other as open. (A) Population ancestry for the K = 2 Structure analysis of cosmopolitan and sub-Saharan samples. (B) Population ancestry for the K = 2 Structure analysis of nonadmixed sub-Saharan samples only.
- Figure 4.—
The relationship between interspecific divergence and proportion of singleton polymorphisms for 100-bp sections of the loci studied. The dashed line indicates the proportion of singletons expected in a neutral equilibrium population.
- Figure 5.—
Hypothesized history of D. melanogaster and related species. (A) EOTYMS refers to the common ancestor of D. erecta, D. orena, D. teissieri, D. yakuba, D. melanogaster, and D. simulans, (along with the three known island endemic species), which reached Africa <20 MYA. (B) The split between the ancestor of D. melanogaster and D. simulans (MS) and the ancestor of D. erecta, D. orena, D. teissieri, and D. yakuba (EOTY) occurred ∼10–15 MYA, possibly associated with emergence of the East African Rift. (C) The divergence of D. melanogaster and D. simulans 2–6 MYA may have been initiated by the dispersal of the latter species to Madagascar or other Indian Ocean islands. (D) More recently, D. melanogaster expanded from eastern Africa into western Africa and Eurasia, and D. simulans expanded into continental Africa and Eurasia.
Tables
- TABLE 1
Population samples included in this study
Abbreviation Country Locality na Date collected Collector Ch China Beijing 10 9/1992 X. Huang Fr France Bordeaux 10 7/1998 E. Gravot and M. Hamblin Is Israel 10 Tu Tunisia 9 Gu Guinea Dondé 10 6/2005 B. B. Sow Nr Niger Kareygorou 10 12/2004 D. Ali Bnb Benin Cotonou 9 5/2004 G. Goergen Ng Nigeria Maiduguri 10 9/2004 D. Gwary and B. Sastawa CM, Cam–M Cameroon Maroua 10 3/2004 J. Pool CD, Cam–D Cameroon Mbalang–Djalingo 10 3/2004 P. Konje and J. Pool CW, Cam–W Cameroon Mbengwi 6 4/2004 J. Pool and E. Ajeah CN, Cam–N Cameroon Nkouondja 10 4/2004 J. Pool CO, Cam–O Cameroon Oku 10 4/2004 J. Pool CY, Cam–Y Cameroon Yokadouma 8 4/2004 P. Konje and J. Pool Ga Gabon N'Toum 10 3/2002 B. Ballard and S. Charlat CBc Congo Brazzaville 10 1999 J. David Er Eritrea Asmara 10 7/2004 S. Ghebremeskel Hailu Ug Uganda Namulonge 10 4/2005 J. Ogwang Rw Rwanda Gisakura 8 6/2005 S. Margles KN,d Kenya–N Kenya Naivasha 10 7/1988 R. Woodruff KM, Kenya–M Kenya Malindi 10 7/2002 B. Ballard Mw Malawi Mwanza 10 7/2001 B. Ballard ZK, Zim–K Zimbabwe Lake Kariba 10 5/1994 T. Mutangadura ZS, Zim–S Zimbabwe Sengwa 10 9/1990 R. Ramey SA South Africa Stellenbosch 10 2/1999 J. Lowe ↵a Number of individuals sequenced (from separate isofemale lines).
↵b Sample consists of seven isofemale lines from Benin and two isofemale lines from Kade, Ghana (F. Ansah and E. Okai, 9/2004).
↵c Mass cultured for several generations before separation into isofemale lines.
↵d Sample consists of six isofemale lines from Naivasha and four isofemale lines from North Kinangop, Kenya (sites <50 km apart).
- TABLE 2
Nucleotide-variation summary statistics (average across loci)
Populationa n θwb πb TajDb Var (D)c China 10 0.0036 0.0034 −0.58 3.01 France 10 0.0030 0.0034 0.70 1.43 Israel 10 0.0046 0.0035 −1.01 1.11 Tunisia 9 0.0050 0.0039 −0.64 1.05 Guinea 10 0.0099 0.0089 −0.57 0.25 Niger 10 0.0083 0.0072 −0.55 0.25 Benin 9 0.0099 0.0091 −0.39 0.37 Nigeria 10 0.0130 0.0104 −0.84 0.39 Cam–M 10 0.0090 0.0075 −0.78 0.24 Cam–D 10 0.0107 0.0093 −0.50 0.09 Cam–W 6 0.0106 0.0101 −0.33 0.20 Cam–N 10 0.0106 0.0094 −0.55 0.27 Cam–O 10 0.0115 0.0097 −0.77 0.14 Cam–Y 8 0.0096 0.0084 −0.66 0.08 Gabon 10 0.0095 0.0078 −0.85 0.53 Congo 10 0.0078 0.0086 0.33 2.49 Eritrea 10 0.0086 0.0092 0.33 0.25 Uganda 10 0.0121 0.0102 −0.80 0.03 Rwanda 8 0.0101 0.0103 0.20 0.15 Kenya–N 10 0.0085 0.0086 0.06 0.05 Kenya–M 10 0.0123 0.0101 −0.89 0.15 Malawi 10 0.0114 0.0098 −0.69 0.10 Zim–K 10 0.0122 0.0105 −0.62 0.11 Zim–S 10 0.0112 0.0104 −0.36 0.14 South Africa 10 0.0096 0.0088 −0.42 0.12 ↵a Population abbreviations are listed in Table 1. The four cosmopolitan populations are listed first; then the sub-Saharan populations are listed geographically from northwest to southeast.
↵b Watterson's θ (θw, from the number of segregating sites), nucleotide diversity (π), and Tajima's D (TajD) are averaged across the four loci for each population.
↵c Variance of the four locus-specific values of Tajima's D.
- TABLE 3
Pairwise FST (above diagonal) and P-values (below diagonal)
Population Ch Fr Is Tu Gu Nr Bn Ng CM CD CN CO CY Ga Er Ug Rw KN KM Mw ZK ZS SA China — 0.532 0.524 0.480 0.377 0.396 0.375 0.317 0.387 0.299 0.284 0.310 0.303 0.313 0.346 0.282 0.301 0.346 0.318 0.346 0.321 0.342 0.374 France 0.000 — 0.009 0.023 0.277 0.250 0.262 0.226 0.302 0.259 0.265 0.228 0.275 0.275 0.238 0.214 0.301 0.294 0.337 0.319 0.288 0.337 0.086 Israel 0.000 0.331 — 0.031 0.298 0.259 0.260 0.243 0.324 0.256 0.264 0.231 0.264 0.268 0.247 0.210 0.315 0.292 0.349 0.340 0.290 0.342 0.105 Tunisia 0.000 0.246 0.801 — 0.277 0.254 0.251 0.240 0.306 0.243 0.258 0.219 0.254 0.260 0.239 0.195 0.290 0.276 0.315 0.313 0.260 0.321 0.087 Guinea 0.000 0.000 0.000 0.000 — 0.029 0.020 0.005 0.014 0.030 0.026 0.011 0.003 0.083 0.116 0.019 0.048 0.076 0.047 0.044 0.027 0.065 0.085 Niger 0.000 0.000 0.000 0.000 0.089 — 0.016 0.013 0.018 0.015 0.022 0.011 0.021 0.030 0.102 0.010 0.083 0.104 0.114 0.114 0.081 0.114 0.080 Benin 0.000 0.000 0.000 0.000 0.169 0.188 — 0.007 0.025 0.042 0.027 0.015 0.021 0.055 0.113 0.002 0.052 0.059 0.069 0.059 0.030 0.071 0.064 Nigeria 0.000 0.000 0.000 0.000 0.372 0.225 0.314 — −0.015 −0.001 0.001 −0.005 0.008 0.044 0.077 −0.006 0.042 0.048 0.044 0.031 0.052 0.057 0.066 Cam–M 0.000 0.000 0.000 0.000 0.221 0.161 0.098 0.809 — −0.006 −0.015 0.008 0.026 0.027 0.132 −0.004 0.053 0.063 0.052 0.041 0.052 0.063 0.086 Cam–D 0.000 0.000 0.000 0.000 0.080 0.196 0.027 0.487 0.578 — −0.025 0.002 −0.024 −0.004 0.080 −0.017 0.035 0.074 0.055 0.064 0.038 0.071 0.086 Cam–N 0.000 0.000 0.000 0.000 0.095 0.133 0.097 0.428 0.745 0.895 — 0.003 −0.010 −0.006 0.120 −0.021 0.030 0.069 0.058 0.064 0.051 0.067 0.092 Cam–O 0.000 0.000 0.000 0.000 0.271 0.236 0.199 0.598 0.307 0.413 0.396 — 0.003 0.027 0.090 −0.008 0.049 0.063 0.060 0.055 0.040 0.061 0.076 Cam–Y 0.000 0.000 0.000 0.000 0.384 0.167 0.167 0.322 0.110 0.855 0.637 0.387 — 0.013 0.111 −0.009 0.054 0.066 0.057 0.070 0.047 0.068 0.104 Gabon 0.000 0.000 0.000 0.000 0.001 0.061 0.011 0.010 0.088 0.559 0.572 0.100 0.245 — 0.122 0.017 0.091 0.123 0.131 0.139 0.102 0.131 0.116 Eritrea 0.000 0.000 0.000 0.000 0.003 0.002 0.004 0.012 0.001 0.009 0.000 0.003 0.009 0.001 — 0.087 0.135 0.161 0.174 0.165 0.141 0.180 0.134 Uganda 0.000 0.000 0.000 0.001 0.142 0.253 0.420 0.606 0.553 0.828 0.870 0.672 0.639 0.158 0.004 — 0.013 0.037 0.032 0.030 0.020 0.042 0.042 Rwanda 0.000 0.000 0.000 0.000 0.106 0.016 0.114 0.101 0.089 0.141 0.178 0.096 0.121 0.018 0.003 0.266 — 0.075 0.018 0.015 0.022 0.042 0.103 Kenya–N 0.000 0.000 0.000 0.000 0.011 0.001 0.031 0.041 0.031 0.012 0.013 0.013 0.034 0.001 0.000 0.084 0.048 — 0.029 0.040 0.056 0.068 0.101 Kenya–M 0.000 0.000 0.000 0.000 0.014 0.000 0.001 0.011 0.007 0.008 0.010 0.006 0.012 0.000 0.000 0.048 0.213 0.126 — −0.023 −0.004 −0.007 0.102 Malawi 0.000 0.000 0.000 0.000 0.021 0.000 0.001 0.043 0.015 0.003 0.003 0.006 0.005 0.000 0.000 0.043 0.244 0.065 0.937 — 0.004 −0.012 0.104 Zim–K 0.000 0.000 0.000 0.000 0.094 0.001 0.065 0.004 0.005 0.037 0.009 0.024 0.013 0.000 0.000 0.136 0.204 0.023 0.549 0.381 — 0.009 0.063 Zim–S 0.000 0.000 0.000 0.000 0.004 0.000 0.002 0.001 0.003 0.000 0.003 0.009 0.005 0.000 0.000 0.019 0.104 0.007 0.637 0.751 0.291 — 0.097 South Africa 0.000 0.009 0.002 0.012 0.001 0.016 0.006 0.003 0.002 0.001 0.002 0.003 0.002 0.000 0.001 0.045 0.010 0.005 0.001 0.000 0.010 0.002 — Population abbreviations are listed in Table 1.
- TABLE 4
Summary statistics indicating stable demographic history
Populationa π (rank)b Max. TajD (rank)c ρ/π (rank)b Uganda 0.0102 (5) −0.61 (1) 13.0 (5) Kenya–M 0.0101 (6) −0.40 (3) 15.1 (4) Zim–K 0.0105 (1) −0.25 (7) 10.0 (10) Zim–S 0.0104 (2) 0.06 (14) 15.4 (3) Malawi 0.0098 (7) −0.33 (4) 10.2 (8) Cam–O 0.0097 (8) −0.40 (2) 9.8 (11) Cam–D 0.0093 (10) −0.12 (8) 12.1 (7) Cam–M 0.0075 (18) −0.27 (6) 17.2 (2) Nigeria 0.0104 (3) 0.03 (12) 5.8 (13) Benin 0.0091 (12) 0.42 (17) 17.5 (1) Cam–Y 0.0084 (16) −0.29 (5) 10.0 (9) Cam–N 0.0094 (9) 0.00 (10) 4.6 (14) Niger 0.0072 (19) −0.01 (9) 12.7 (6) Guinea 0.0089 (13) 0.05 (13) 8.6 (12) S.Africa 0.0088 (14) 0.00 (11) 4.2 (15) Rwanda 0.0103 (4) 0.71 (18) 0.9 (19) Eritrea 0.0092 (11) 0.91 (19) 2.7 (17) Gabon 0.0078 (17) 0.12 (15) 3.1 (16) Kenya–N 0.0086 (15) 0.23 (16) 1.3 (18) Population abbreviations are listed in Table 1.
↵a Populations are ordered according to the sum of their ranks for the three statistics presented.
↵b Populations are ranked from highest to lowest values of π (averaged across loci) and ρ/π (composite likelihood for all four loci).
↵c “Max. TajD” refers to the highest value of Tajima's D observed at any locus for the given population. These values are ranked from lowest to highest.
- TABLE 5
Differentiation of sub-Saharan populations from cosmopolitan populations
Populationa FST (rank)b Snn (rank)b Shared polymorphism (rank)c Uganda 0.212 (1) 0.712 (1) 43 (1) Cam–N 0.235 (3) 0.769 (3) 37 (5) Nigeria 0.233 (2) 0.764 (2) 36 (7) Cam–O 0.238 (6) 0.789 (5) 37 (5) Cam–D 0.237 (5) 0.777 (4) 35 (8) Zim–K 0.276 (9) 0.799 (7) 41 (2) Guinea 0.302 (12) 0.811 (10) 39 (3) Kenya–M 0.307 (14) 0.806 (8) 38 (4) Malawi 0.306 (13) 0.799 (6) 34 (9) Niger 0.269 (7) 0.810 (9) 29 (14) Kenya–N 0.279 (10) 0.816 (12) 34 (9) Cam–Y 0.236 (4) 0.822 (13) 29 (14) Benin 0.274 (8) 0.832 (14) 33 (11) Cam–M 0.312 (15) 0.812 (11) 32 (13) Rwanda 0.288 (11) 0.865 (16) 29 (14) Zim–S 0.318 (16) 0.863 (15) 33 (11) Eritread 0.231 0.702 39 Gabond 0.231 0.744 35 South Africad 0.144 0.668 42 Population abbreviations are listed in Table 1.
↵a Populations are ordered according to the sum of their ranks for the three statistics presented.
↵b FST and Snn values are arithmetic means of the four pairwise values from comparisons of the given sub-Saharan population with each of the four cosmopolitan populations. The 17 sub-Saharan populations are ranked starting from the lowest value (closest relationship).
↵c Number of polymorphisms shared between the given sub-Saharan population and one or more of the cosmopolitan populations (total for all four loci).
↵d Not ranked due to apparent cosmopolitan admixture.
- TABLE 6
Simulations showing the effect of population growth on the proportion of singleton polymorphisms observed in a sample of 240
Time of growtha N ratiob Proportion of singletonsc P (sim > obs)d — — 0.1661 0 0.1333 0.1 0.2575 0 0.1333 0.01 0.2726 0 0.1333 0.001 0.2745 0 0.1333 0.0001 0.2748 0 0.1333 0.00001 0.2748 0 0.1333 0.000001 0.2748 0 0.01333 0.1 0.4147 0 0.01333 0.01 0.5159 0.2315 0.01333 0.001 0.5289 0.4084 0.01333 0.0001 0.5301 0.4204 0.01333 0.00001 0.5306 0.4318 0.01333 0.000001 0.5304 0.4327 0.001333 0.1 0.3750 0 0.001333 0.01 0.7466 1 0.001333 0.001 0.8581 1 0.001333 0.0001 0.8721 1 0.001333 0.00001 0.8732 1 0.001333 0.000001 0.8734 1 0.000133 0.1 0.2045 0 0.000133 0.01 0.4496 0.0098 0.000133 0.001 0.8529 1 0.000133 0.0001 0.9692 1 0.000133 0.00001 0.9829 1 0.000133 0.000001 0.9843 1 ↵a The time, in coalescent units before the present, when an instantaneous population-size increase occurred.
↵b The ratio of the preincrease population size to the postincrease population size.
↵c The average proportion of singletons observed across 10,000 simulated replicates.
↵d The proportion of simulated replicates that contained a greater proportion of singletons than the observed data.
Supplement to Pool and Aquadro, 2006
Supporting Information
