Building megaphylogenies for macroecology: taking up the challenge

Area of Science:

• Ecology
• Evolutionary Biology
• Bioinformatics

Background:

• Ecological studies increasingly integrate phylogenetic information, assuming shared ancestry influences ecological traits due to niche conservatism.
• Methods range from simple taxonomy to complex molecular phylogenetics, with the latter being more informative but underutilized in ecology.
• Reliable ecological analyses incorporating evolutionary aspects necessitate robust phylogenetic hypotheses.

Purpose of the Study:

• To clarify concepts and methodological challenges in reconstructing dated megaphylogenies.
• To demonstrate the feasibility of obtaining accurate, well-sampled megaphylogenies with informative branch lengths for large species datasets.
• To provide a practical workflow for ecologists to build such phylogenies.

Main Methods:

• Utilizing vast molecular data from public databases (e.g., GenBank).
• Employing improved phylogenetic inference methods and consensus on deep evolutionary relationships.
• Developing a step-by-step workflow pipeline in the R environment, incorporating free web servers.

Main Results:

• Demonstrated the possibility of generating accurate, dated megaphylogenies with informative branch lengths for extensive species samples.
• Successfully applied the workflow to reconstruct a species-level phylogeny for European breeding birds.
• Highlighted the accessibility of advanced phylogenetic methods for ecologists.

Conclusions:

• Accurate and well-sampled megaphylogenies are now achievable for large-scale ecological studies.
• Improved phylogenetic methods and data availability facilitate the integration of evolutionary history into ecological research.
• The provided workflow pipeline empowers ecologists to utilize advanced phylogenetic tools effectively.