Biogeographic dependent diversification analyses
To test if the Andean uplift or closure of the Panama Isthmus influenced
Preponini diversification rates we used a similar likelihood approach as
for time dependent diversification analyses implemented in RPANDA. In
this case, we evaluated the fit of six models allowing speciation and
extinction rates to be dependent on the paleo-elevation of the Andes
(three models) or the degree of connectivity between Central and South
America (three models; Morlon, 2014;
Morlon et al., 2011; see Table 1).
We used Andean paleo-elevation from present time until 32 Ma based on
the database provided by Lagomarsino et al.
(2016) and information from Garzione
et al. (2008). The closure of the
Panama Isthmus was estimated using reports of migration rates for
several groups of organisms by Bacon et al (2015). In the latter study
they reported that migration rates between the two continents increased
sequentially at four points in time, 41.1, 23.7, 8.7 and 5.2 Ma. We used
these migration rate estimates to compute the probability of observing
at least one migration event in each time period (i.e. 50 – 41.1, 41.1
– 23.7, 23.7 – 8.7, 8.7 – 5.2, 5.2 - present). We then used the
cumulative probability through time to observe at least one migration
event per million years as a proxy of the degree of connectivity between
land masses (Table S3).