datelife

datelife reconstructs phylogenetic chronograms with branch lengths scaled to absolute geological time to synthesize and analyze evolutionary timing across taxa.

Key Features:

• Chronogram Construction: Generates chronograms for user-specified combinations of taxon names using time-scaled branch lengths proportional to absolute geological time.
• Local Database Integration: Uses a local database curated from the Open Tree of Life Phylesystem that integrates phylogenetic data sources including TreeBASE.
• Data Integration and Reanalysis: Retrieves, summarizes, reuses, and reanalyzes expertly curated, peer-reviewed public data on evolutionary timing and synthesizes time data from multiple source chronograms using supertree and congruification algorithms.
• Secondary Calibration: Extracts age data from source chronograms to serve as secondary calibration points and to add branch lengths proportional to absolute time to a given tree topology.
• Implementation and Open Science: Implemented as an R package and exposes curated chronogram data in a programmatic, reusable format to support open science and data sharing.

Scientific Applications:

• Evolutionary biology research: Provides time-calibrated phylogenies for studies of biodiversity, adaptation, and the history of life.
• Comparative phylogenetics: Supplies chronograms for downstream comparative analyses that require absolute timing of branching events.
• Education and science communication: Offers curated chronogram data for teaching and communicating evolutionary timelines.
• Policy and conservation: Informs policy-making and conservation decisions that rely on evolutionary timing and historical context.

Methodology:

Uses a local database curated from the Open Tree of Life Phylesystem (including TreeBASE), retrieves source chronograms, synthesizes time data via supertree and congruification algorithms, extracts ages from source chronograms as secondary calibration points, and adds branch lengths proportional to absolute geological time to tree topologies while enabling retrieval, summarization, reuse, and reanalysis of curated chronogram data.