Hypotheses about chimpanzee social behavior, phylogeography, and evolu
tion were evaluated by noninvasive genotyping of free-ranging individu
als from 20 African sites. Degrees of relatedness among individuals in
one community were inferred from allele-sharing at eight nuclear simp
le sequence repeat (SSR) loci. Males are related on the order of half-
siblings, and homozygosity is significantly increased at several SSR l
oci compared to Hardy-Weinberg expectations. These data support the ki
n-selection hypothesis for the evolution of cooperation among males. S
equence variation patterns at two mitochondrial loci indicate historic
ally high long-distance gene flow and clarify the relationships among
three allopatric subspecies. The unexpectedly large genetic distance b
etween the western subspecies, Pan troglodytes verus, and the other tw
o subspecies suggests a divergence time of about 1.58 million years. T
his result, if confirmed at nuclear loci and supported by eco-behavior
al data, implies that P. t. verus should be elevated to full species r
ank.