MP tree showing evolutionary relationships among 107 haplotypes (AF1–AF107) observed in 214 sub-Saharan Africans (Chen et al. ; present study). The tree is 200 steps in length, has consistency and retention indices (CI and RI) of .745 and .893, respectively, and is one of 3,000 MP trees generated by the TBR algorithm. It was rooted from a chimpanzee haplotype defined by sequence analysis (Horai et al. ) (see text). The RFLPs that define each of the major branches of the MP tree are indicated by the number of the first nucleotide of the respective recognition sites, according to the CR sequence (Anderson et al. ), with the restriction enzymes being indicated by single-letter codes as given in . The length of the horizontal branches is proportional to the number of mutations that separate the haplotypes. The three major haplogroups are denoted by the light-gray shading, whereas the subhaplotype clusters, defined in , are indicated by the smaller unshaded boxes. The “AF”-prefixed numbers at the end of each branch denote the individual haplotypes, and the population(s) in which the individual haplotypes were detected are indicated by symbols as defined in the key. All population-specific lineages are encompassed by dark-gray shading and are also denoted by Greek letters as defined in the key. Haplotypes AF1 and AF2, which are aligned with European haplogroup U, are located in L3d and are indicated by a section symbol (§). Haplotype AF24, which is aligned with Asian macrohaplogroup M, is indicated by a double section symbol (§§). The bootstrap values for the major branches of the MP tree were calculated by use of 100 replicates, with resampling by the TBR algorithm. L1a_{2} cluster AF87–AF90 has a bootstrap value of 92%; subcluster AF88–AF90 has a bootstrap value of 100%. L1a_{2} cluster AF91–AF92 has a bootstrap value of 95%; but AF93 and AF94 were not resolved at bootstrap values >50%. L1a_{1} cluster AF97–AF101 has a bootstrap value of 100%; and subclusters AF99–AF101 and AF60–AF61 have bootstrap values of 52% and 60%, respectively; but AF60 and AF61 were not resolved at bootstrap values >50%. L1b_{1} cluster AF70–AF71/AF77–AF78 has a bootstrap value of 100%, as does subcluster AF71/AF77/AF78. L1b_{2} cluster AF62–AF69 has a bootstrap value of 100%, as do subclusters AF62–AF63 and AF67–AF69, whereas subcluster AF62–AF64/AF66–AF69 has a bootstrap value of 55%. L2 cluster AF26–AF38/AF40–AF50/AF52–AF53/AF55–AF58/AF105–AF107 has a bootstrap value of 52%. L2a cluster AF26–AF38/AF40–AF42 has a bootstrap value of 58%. L2b cluster AF46–AF47 has a bootstrap value of 100%. L2c cluster AF49–AF50/AF52–AF53/AF55–AF58 has a bootstrap value of 100%, and cluster AF106–AF107 has a bootstrap value of 52%. L3a cluster AF22–AF23 has a bootstrap value of 100%, whereas subclusters AF19–AF21/AF24 and AF80–AF84 were not resolved at bootstrap values >50%. L3b cluster AF8/AF85–AF86 has a bootstrap value of 100%, as does subcluster AF85–AF86, but cluster AF4/AF6/AF9/AF11 was not resolved at a bootstrap value of 50%. L3c cluster AF12/AF14–AF18 has a bootstrap value of 100%, as does subcluster AF14–AF18. L3d cluster AF1–AF3 has a bootstrap value of 97%.

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