A likelihood framework for inferring the evolution of geographic range on phylogenetic trees

Area of Science:

• Ecology and Evolutionary Biology
• Historical Biogeography
• Phylogenetics

Background:

• Historical biogeography is expanding its scope beyond area relationships.
• Existing methods for ancestral area estimation have limitations.
• New inference methods are needed to incorporate diverse data types.

Purpose of the Study:

• To introduce a novel likelihood framework for inferring geographic range evolution on phylogenies.
• To model lineage dispersal and local extinction as continuous-time stochastic events.
• To address questions about ancestral geographic ranges and their inheritance during cladogenesis.

Main Methods:

• Developed a likelihood framework incorporating lineage dispersal and local extinction.
• Modeled geographic range evolution as stochastic events in continuous time.
• Utilized Monte Carlo methods to estimate transition probabilities and evaluate data likelihood for phylogenies and paleogeographic models.

Main Results:

• The framework successfully infers ancestral geographic ranges on phylogenies.
• It quantifies the impact of speciation and inheritance on ancestral ranges.
• Demonstrated application using hypothetical data and a Northern Hemisphere plant clade (Cercis).

Conclusions:

• The developed framework offers a flexible approach to historical biogeography.
• It integrates lineage divergence timing and dispersal route availability.
• The framework can be extended to incorporate additional data and address broader biogeographic questions.