"What Determines Species Diversity?" is one of the top 25 questions from the 125th anniversary issue of Science magazine [Science, July 1, 2005]. The complete reference is ...
Why Do Humans Have So Few Genes?]
The question is poorly phrased because it's really about speciation.
Understanding what shapes diversity will require a major interdisciplinary effort, involving paleontological interpretation, field studies, laboratory experimentation, genomic comparisons, and effective statistical analyses. A few exhaustive inventories, such as the United Nations' Millennium Project and an around-the-world assessment of genes from marine microbes, should improve baseline data, but they will barely scratch the surface. Models that predict when one species will split into two will help. And an emerging discipline called evo-devo is probing how genes involved in development contribute to evolution. Together, these efforts will go a long way toward clarifying the history of life.This question is also related to a more fundamental question; namely, what is a species?
Paleontologists have already made headway in tracking the expansion and contraction of the ranges of various organisms over the millennia. They are finding that geographic distribution plays a key role in speciation. Future studies should continue to reveal large-scale patterns of distribution and perhaps shed more light on the origins of mass extinctions and the effects of these catastrophes on the evolution of new species.
This certainly counts as one of the top questions in biology. If we ask it in the form "What causes speciation?" then it gets us into a discussion about punctuated equilibria, founder effects and all kinds of other controversial problems. It also brings up the issue of the role of natural selection and environment in speciation. While there may not be anything new to discover, there are many open questions concerning the mechanisms of speciation. Does sympatric speciation happen, for example?
There are many who think that natural selection plays only a minor role in most speciation events and there are many who think that environmental change is not correlated with speciation [Adaptation and Accident in PNAS, Evolution of Mammals].