How important is it to consider lineage diversification heterogeneity in macroevolutionary studies: lessons from the lizard family Liolaemidae

Macroevolutionary studies commonly apply multiple models to test state-dependent diversification. These models track the association between states of interest along a phylogeny, but they do not consider whether independent shifts in character states are associated with shifts in diversification rates. This potentially problematic issue has received little theoretical attention, while macroevolutionary studies implementing such models in increasing larger scale studies continue growing. A recent macroevolutionary study has found that Andean orogeny has acted as a species pump driving diversification of the family Liolaemidae, a highly species-rich lizard family native to temperate southern South America. This study approaches a distribution-dependent hypothesis using the Geographic State Speciation and Extinction model (GeoSSE). However, more recent analyses have shown that there is a clear heterogeneous diversification pattern in the Liolaemidae, which likely biased the GeoSSE analysis. Specifically, we show here that there are two shifts to accelered speciation rates involving species groups that were classified as "Andean" in their distributions. We demonstrate that this GeoSSE result is meaningless when heterogeneous diversification rates are included. We use the lizard family Liolaemidae to demonstrate potential risks of ignoring clade-specific differences in diversification rates in macroevolutionary studies.