Parallel shifts in differential gene expression reveal convergent miniaturization in fishes

Body size variation in vertebrates is a complex polygenic trait, tightly
correlated with numerous aspects of a species biology, ecology, and
physiology. Miniaturization, the extreme reduction of adult body size, is
a common phenomenon across the Tree of Life, yet the mechanisms underlying
this process are poorly understood. Here, we investigate the molecular
basis of body size evolution in goby fishes, a clade encompassing some of
the smallest vertebrates on Earth.  We generate a new genome-wide
phylogeny for 162 Gobioidei species and perform comparative
transcriptomics across three clades with repeated instances of
miniaturization and large-bodied forms. We identified 54 differentially
expressed one-to-one orthologs between miniature and large-bodied species.
These genes reveal distinct functional profiles, suggesting that
regulation of cell numbers is a key mechanism governing body size control.
Miniature species consistently overexpress growth inhibitors like CDKN1B
and ING2, associated with tighter cell cycle regulation and decreased
proliferation rates, while large-bodied species upregulate
growth-promoting genes such as TGFB3, linked to tissue development and
growth signaling. These enriched functional pathways, conserved since the
Eocene (50 Ma), suggest macroevolutionary convergence in size regulation
over deep time. Our findings provide insights into how size determination
is governed at a genetic level and highlights the importance of exploring
these factors in non-model organisms to uncover the fundamental processes
regulating vertebrate body size evolution.