Historical shifts and ecological patterns: rethinking genome size evolution in Coffea L

Although genome size (GS) is decoupled from organismal complexity, a phenomenon known as the C-value paradox, some authors have proposed that GS may play an adaptive role when correlated with ecologically relevant traits. Among diploid Coffea, GS variation is modest but measurable, offering an opportunity to test this hypothesis. Using a well-resolved phylogeny and phylogenetic comparative methods, we evaluated whether GS is phylogenetically correlated with ecological traits including latitudinal range, elevational distribution, thermal tolerance, and caffeine content (CAF). GS showed substantial phylogenetic signal and correlated positively with CAF, but no phylogenetic association was detected with the other variables. Notably, this association traces to a single, lineage-specific shift at the base of a clade comprising the species with the largest genomes and highest CAF, occurring in West and Central Africa. Comparisons between two sequenced genomes, Coffea canephora and C. eugenioides, which differ in caffeine production, revealed that gene copy number does not correlate with CAF levels, suggesting that increases in caffeine production are more likely driven by regulatory change rather than gene duplication. Overall, these findings do not support a generalized adaptive model for GS evolution in Coffea, but instead indicate that the observed associations reflect lineage-specific historical events rather than direct adaptive responses.