Y. Liang, B. Zuo, Y.-B. Sun
The Mutational Hazard Hypothesis (MHH) predicts that reduced effective population size weakens purifying selection and promotes transposable element (TE) accumulation. Because effective population size is difficult to estimate across broad taxonomic scales, body mass, generation time, and dN/dS are often used as proxies. We analyzed TE landscapes across 167 sauropsid genomes to test whether these proxies predict genomic TE proportion consistently across phylogenetic scales. All three showed strong scale dependence. Body mass was positively associated with TE proportion across clades, but this relationship broke down within clades: only snakes retained a significant negative Pearson correlation after multiple-testing correction, whereas the corresponding phylogenetically corrected slopes were not significant. Generation time showed a strong pooled association that disappeared within every major clade in both Pearson and PGLS analyses. The pooled dN/dS-TE relationship also disappeared after accounting for body mass and generation time in a structural equation model, with a robust within-clade association retained only in turtles. Lineage-specific TE dynamics, including LTR expansion in sea snakes, were not captured by these proxies. These results show that commonly used MHH proxies mainly reflect clade-level structure rather than consistent within-lineage mechanisms.