Integrating fossils samples with heterogeneous diversification rates: a combined Multi-Type Fossilized Birth-Death...

Area of Science:

• Evolutionary biology
• Paleontology
• Computational phylogenetics

Background:

• Birth-death models are fundamental for understanding species diversification and phylogenetic inference.
• Existing models often focus on extant species or lack lineage-specific rate variation.
• Integrating fossil data and lineage-specific rates can improve phylogenetic and diversification analyses.

Purpose of the Study:

• To introduce and implement a novel multi-type fossilized birth-death (MTFBD) process within the BEAST2 framework.
• To jointly infer phylogenies, diversification rates, and fossil sampling rates, accommodating both extinct and extant species.
• To evaluate the performance of the MTFBD model against existing methods using simulated and empirical data.

Main Methods:

• Development of the multi-type fossilized birth-death (MTFBD) model.
• Implementation of the MTFBD model in the BEAST2 phylogenetic inference software.
• Validation using simulated datasets and empirical fossil data, comparing results with and without detailed morphological information.

Main Results:

• The MTFBD model accurately estimates phylogenies and diversification rates, particularly extinction rates, when detailed morphological data for fossils are available.
• Including fossil data significantly improves accuracy compared to models using only extant species.
• When morphological information is lacking, MTFBD model estimates become heavily influenced by prior assumptions.

Conclusions:

• The MTFBD model offers a powerful tool for joint phylogenetic and diversification inference, especially with informative fossil data.
• Accurate placement of fossils using morphological characters is crucial for reliable MTFBD model performance.
• The model provides precise characterization of how speciation, extinction, and fossil sampling rates vary throughout diversification.