Understanding the evolutionary processes that generate and sustain diversit
y in tropical faunas has challenged biologists for over a century and shoul
d underpin conservation strategies. Molecular studies of diversity within s
pecies and relationships among species, when integrated with more tradition
al approaches of biogeography and paleoecology, have much to contribute to
this challenge. Here we outline the current major hypotheses, develop predi
ctions relevant to integrated molecular approaches, and evaluate the curren
t evidence, focusing on central African, Australian, and South American sys
tems. The available data are sparse relative to the scale of the questions.
However, the following conclusions can be drawn: (a) in most cases, the di
vergence of extant sister taxa predates the Pleistocene; (b) areas with hig
h habitat heterogeneity and recent climatic or geological instability appea
r to harbor more species of recent origin; (c) there is support for both al
lopatric and gradient models of diversification and mon attention should be
given to the role of diversifying selection regardless of geographic conte
xt; and (d) conservation strategies should seek to protect heterogeneous la
ndscapes within and adjacent to large rainforest areas, rather than rainfor
ests alone.