Table 1 Currently published hypotheses supported by a positive correlation between diversification and nucleotide substitution rates.

Extrinsic (Ecological) explanations:

1) Evolutionary rates are causally unrelated to the process of speciation, but are linked to traits or habitats that promote diversification.

1a) Life history. Increased generation time can cause mutations to accumulate faster over absolute time than they do in organisms with a slower life history [7, 20, 34] Shorter generation times are positively correlated with species richness of clades [8], possibly because shortened life cycles and/or enhanced mobility associated with smaller size allow individuals to colonize more extreme habitats.

1b) Environmental energy. High levels of environmental energy such as UV radiation and temperature are mutagenic and tend to speed up development, resulting in increased rates of nucleotide substitution. Environmental energy is linked to both species richness and to rates of molecular evolution, but environmental energy does not appear to affect speciation rates via its effect on mutation rates. Instead, environmental energy directly affects both species-richness and faster evolution [4].

Intrinsic explanations:

2) Faster rates of molecular evolution in speciose clades are caused by rapid bursts of evolution during speciation events.

2a) Rapid evolution due to drift during speciation: If speciation commonly occurs in small, peripheral populations [e.g., founder event speciation, [10, 35], then speciose clades will be more likely to have experienced reduced population sizes throughout their evolutionary history. Under conditions of reduced population sizes, selection is relaxed and slightly deleterious mutations may accumulate, contributing to enhanced substitution rates throughout the genome [9].

2b) Rapid evolution due to increased selection pressure during speciation: Speciation involving adaptation to a new niche or geographic range will involve strong selection favoring traits adaptive in the new environment. In this process of adaptation, average population fitness may decline, reducing population sizes [19]. Selection is also more likely to favor mutations of large effect early in the process of adaptation [36]. The combined effects of smaller population sizes and selection for mutations of large effect might allow slightly deleterious and neutral mutations to hitchhike to fixation, causing rapid turnover of alleles throughout the genome during speciation.

3) Faster rates of molecular evolution may cause speciation, by:

3a) Increasing the rate at which reproductive isolation develops between isolated populations [37].

3b) Increasing the rate of production of new adaptations via increased mutational genetic variation [17].

Statistical artifact explanation:

4) Finally, the relationship between diversification and molecular evolution may be a statistical artifact.

When multiple substitutions have occurred at the same nucleotide position, this is undetectable on unbranched clades. However, if branching events have occurred between these 'multiple hits', then multiple substitutions at the same site are detectable. It will therefore appear as though the more speciose clade has undergone more substitutions (i.e., evolved faster) than its species-poor counterpart. This artifact is known as the node density effect [12, 38].