The missing link in biogeographic reconstruction: Accounting for lineage extinction rewrites history

Aim
In the most widely used family of methods for ancestral range estimation (ARE), dispersal, speciation and extirpation events are estimated from information on extant lineages. However, this approach fails to consider the geographic distribution of extinct species and their position on the phylogenetic tree, an omission that could compromise reconstruction. Here, we present a method that models the geographic distribution of extinct species and we quantify the potential inaccuracy in ancestral range estimation when extinction rates are above zero.

Location
Global applications, with an example from the Americas.

Taxon
All taxa, with an example from hummingbirds (Amazilia).

Methods
Methods capable of explicitly modelling extinct branches along with their reconstructed geographic information (GeoSSE) have been overlooked in ARE analysis, perhaps due to the inherent complexity of implementation. We develop a user-friendly platform, which we term LEMAD (Lineage Extinction Model of ..., Data were collected from McGuire et al. 2014 and Ornelas et al. 2014. Please see the paper for more details.
I include R scripts to run lemad analysis. Please first install R package LEMAD from: https://github.com/leonelhalsina/lemad,