Integrative Phylogenetic, Genomic, Acoustic, and Geospatial Analyses of U.S. Frog Species Using Mitochondrial COI Sequences

My Abdelmajid Kassem

Authors

My Abdelmajid Kassem Plant Genomics and Bioinformatics Lab, Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA

Keywords:

Amphibian biodiversity, Phylogenetics, COI barcoding, Genome size evolution, Bioacoustics, Species distribution, Frog call analysis, Geospatial mapping, Frog phylogeny, Trait integration

Abstract

Amphibians are critical bioindicators of environmental health, yet integrative frameworks combining genomic, acoustic, and spatial data remain underutilized in regional biodiversity assessments. Here, we present a reproducible bioinformatics workflow that integrates molecular phylogenetics, genome size analysis, acoustic feature extraction, and geospatial occurrence mapping to investigate patterns of amphibian diversity across 30 frog species in the United States. Using mitochondrial cytochrome oxidase I (COI) sequences, we reconstructed a robust maximum-likelihood phylogeny, identifying clear clade-level structuring among Hylidae, Ranidae, and Bufonidae. Genome size data integrated into the phylogenetic context revealed consistent family-level patterns, with Hylidae exhibiting larger genome sizes relative to other families. Acoustic analyses of five focal species demonstrated significant interspecific differences in call duration and dominant frequency, confirmed through principal component analysis (PCA), highlighting the utility of bioacoustics in species discrimination. Geospatial mapping of over 3,000 occurrence records retrieved from GBIF revealed amphibian diversity hotspots in the Southeastern United States, corresponding with known gradients of habitat heterogeneity and climatic suitability. The workflow integrates MAFFT-based sequence alignments, FastTree phylogenetic reconstruction, librosa-based acoustic feature extraction, and GBIF-powered spatial analyses into a single open-source, reproducible pipeline. This integrative informatics framework offers a scalable tool for amphibian biodiversity monitoring, conservation prioritization, and hypothesis-driven ecological research by leveraging computational reproducibility and multi-modal trait data.

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Integrative Phylogenetic, Genomic, Acoustic, and Geospatial Analyses of U.S. Frog Species Using Mitochondrial COI Sequences

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