Challenges in estimating species' age from phylogenetic trees.

Area of Science:

• Evolutionary biology
• Phylogenetics
• Paleontology

Background:

• Species age, the time since origination, is crucial for understanding eco-evolutionary dynamics and extinction risk.
• Traditionally, species ages are estimated from fossil records.
• Phylogenetic branch lengths are increasingly used to estimate species ages, but this method has limitations.

Purpose of the Study:

• To investigate the accuracy of using phylogenetic branch lengths for species age estimation.
• To identify factors that introduce errors in phylogenetic age estimation.
• To develop a more accurate method for estimating species ages.

Main Methods:

• Analysis of the relationship between true species age and phylogenetic branch lengths.
• Modeling the impact of incomplete taxon sampling, extinction, and speciation modes on age estimation.
• Development and application of a probabilistic birth-death process model for species age estimation.

Main Results:

• Phylogenetic branch lengths can significantly deviate from true species ages due to incomplete sampling, extinction, and speciation assumptions.
• Biases in phylogenetic age estimation can lead to erroneous conclusions about eco-evolutionary patterns and extinction risk.
• The proposed birth-death process model reduces estimation error by an order of magnitude, especially with high extinction and unsampled species.

Conclusions:

• Caution is advised when interpreting relationships between phylogenetic ages and eco-evolutionary traits.
• The novel birth-death process approach, combined with branch lengths, provides unbiased approximations of species age under bifurcating speciation.
• This method offers a more reliable way to estimate species ages, improving ecological and evolutionary inference.