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Genome evolution and long-term demographic history in true crocodiles
Ana M Saldarriaga-Gómez1,2,3, Agusto Luzuriaga-Neira4, Mario Vargas-Ramírez3
1Department of Biological Sciences, Fordham University, Bronx, NY 10458, United States.
G3 (Bethesda, Md.)
|August 5, 2026
Summary
New crocodile genomes reveal distinct population histories and molecular evolution patterns. Crocodylus intermedius shows low effective population size (Ne), while C. niloticus has higher Ne, impacting molecular evolution across crocodilians.
Area of Science:
- Genomics
- Evolutionary Biology
- Molecular Evolution
Background:
- Reference-quality genomes for true crocodiles (Crocodylus) are limited, hindering comparative genomic and evolutionary studies.
- Understanding genome architecture and demographic history is crucial for crocodilian conservation and evolutionary insights.
Purpose of the Study:
- To generate and analyze high-quality genomes for Crocodylus intermedius and Crocodylus niloticus.
- To investigate genome structure, historical effective population size (Ne), and molecular evolution across crocodilians.
- To explore the relationship between demographic history and genome-wide evolutionary patterns.
Main Methods:
- Generated two long-read genomes for C. intermedius and C. niloticus.
- Performed comparative genomic analyses, including repeat landscapes and macro-synteny.
- Utilized phased diploid assemblies and MSMC2 to reconstruct historical Ne trajectories.
- Conducted genome-wide codon-based analyses (dN/dS) and branch-site tests for positive selection.
Main Results:
- Demonstrated strong structural conservation across crocodilian genomes with extensive macro-synteny.
- Revealed contrasting historical Ne trajectories: C. intermedius had persistently low Ne, while C. niloticus had substantially larger Ne.
- Identified significant heterogeneity in dN/dS (ω) across lineages, with lower ω in C. niloticus.
- Found evidence of reduced purifying selection efficacy in species with smaller historical population sizes.
- Identified candidate genes under positive selection in both species, involved in ion transport, endocrine regulation, and signaling.
Conclusions:
- Provided valuable genomic resources for the genus Crocodylus.
- Supported a strong association between long-term demographic history (Ne) and genome-wide molecular evolution patterns in crocodilians.
- Highlighted species-specific evolutionary trajectories influencing genome evolution and selection pressures.
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