Habitat Reconstruction for Internal Nodes of a Bacterial Phylogenetic Tree

Zhanghan Ni created this dataset on figshare, last updated May 14, 2026. It contains habitat predictions for internal nodes across a bacterial species tree, derived from phylogenetic analysis of 13,637 additional genomes. The data is structured into 16 phylum-specific groups to account for evolutionary rate differences.

Use Cases

• Reconstruct ancestral bacterial habitats based on phylogenetic relationships.
• Analyze habitat transition patterns across different bacterial phyla.
• Validate gene-species tree reconciliation models using habitat trait data.
• Study the correlation between ribosomal protein evolution and environmental adaptation.

Strengths

• Includes habitat predictions for internal nodes across 16 distinct bacterial phyla.
• Based on a substantial genomic expansion, incorporating 13,637 additional genomes.
• Uses a consistent methodological framework with constrained topologies to match a reference 865-leaf species tree.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• Data may reflect taxonomic and genomic sampling bias inherent to the source phylogeny.

Provenance

Source

figshare

Collection Method

Phylogenetic inference using maximum likelihood (IQ-TREE) on ribosomal protein alignments, with ancestral state reconstruction performed using BayesTraits.

Freshness

Last updated 2026-05-14 00:10:10; freshness should be verified.