We used the results of phylogenetic analyses of relationships among spider
monkeys (Ateles) based on mitochondrial and nuclear DNA to investigate ques
tions of their evolutionary origins and speciation mechanisms. We employed
the concept of a local molecular clock to date nodes of interest (correspon
ding to hypothesized species and subspecies) in the various phylograms for
comparison to hypothesized biogeographical events that might have affected
speciation. We considered various mechanisms-Pleistocene refuge formation,
riverine barriers, geological fluctuations, and ecological changes associat
ed with these mechanisms-for their contribution to speciation in Ateles. Mo
st speciation among the various species of Ateles occurred during the middl
e to late Pliocene, suggesting that Pleistocene refuge formation was not a
key speciation mechanism. However, it is likely that the genetic structure
of populations of Ateles was modified to some extent by refuge formation. A
dditionally, riverine barriers do not seem to interrupt gene flow significa
ntly among Ateles. No river formed a barrier among species of Ateles, with
the exception of the lower Amazon and possibly some of the black-water rive
rs draining the Guianan highlands. Large-scale geographic changes associate
d with the continued rise of the eastern and western cordilleras of the nor
thern Alines and associated changes in habitat were the most important caus
es of speciation in Ateles. The various factors that modify genetic structu
re in ateles are important to consider in order to protect endangered prima
te genera in the Neotropics.