FishPhyloMaker

FishPhyloMaker generates reproducible phylogenetic hypotheses for ray-finned fishes (Actinopterygii) to support evolutionary and ecological analyses.

Key Features:

• Automated Species Verification: Verifies species names against FishBase using the rfishbase R package, identifies synonyms, and flags taxa not found in FishBase for manual Family and Order input.
• Phylogenetic Tree Construction: Builds phylogenetic trees by inserting taxa according to cladistic rules of insertion while preserving key phylogenetic distance properties.
• Sensitivity Analysis: Evaluates the insertion algorithm through sensitivity analyses to assess preservation of phylogenetic relationships.
• Interactive Insertion Procedure: Implements an insertion procedure that enables iterative placement of taxa at different hierarchical levels to handle highly speciose groups.
• Calculation of Darwinian Shortfalls: Computes Darwinian shortfalls to quantify absence of species from phylogenetic hypotheses and supports mapping these shortfalls across freshwater drainages.

Scientific Applications:

• Community Phylogenetics: Enables community-level phylogenetic analyses of ray-finned fishes.
• Trait Evolution: Supports investigations of trait evolution within Actinopterygii.
• Evolutionary Diversity and Ecosystem Functioning: Facilitates analyses of relationships between evolutionary diversity and ecosystem functioning, including studies in freshwater ecoregions.
• Biodiversity Pattern Mapping: Allows mapping of Darwinian shortfalls across major freshwater drainages to inform biodiversity and conservation analyses.

Methodology:

Species names are checked against FishBase via the rfishbase package; missing taxa are inserted into a backbone using cladistic rules of insertion to assemble phylogenetic trees; the insertion algorithm is assessed with sensitivity analyses; Darwinian shortfalls are calculated from the resulting phylogenies.