Macroevolutionary patterns of chromosomal rearrangements in Siluriformes

Abstract Chromosomal rearrangement is a primary driver of speciation. The macroevolutionary forces governing diversification, however, remain poorly understood. This study aimed to elucidate the mechanisms of karyotypic evolution across Siluriformes (catfish), with an emphasis on the genomic plasticity of Clarias. Using a dataset of 88 species, we integrated continuous and discrete evolutionary models to evaluate the ancestral chromosomal states and tempo of karyotypic diversification. Our results revealed a basal Siluriform karyotype of n = 27, followed by 13 phylogenetic rate shifts that caused saltational transitions in diploid chromosome numbers (24 to 100) and fundamental chromosome numbers (NF = 40 to 136). Phylogenetic generalized least squares and Ornstein–Uhlenbeck modeling indicated that karyotypic trait evolution in Siluriformes is better described by an Ornstein–Uhlenbeck process than by neutral Brownian motion, indicating a tendency toward a model-inferred optimum. We identified a transition of haploid chromosome numbers from 27 to 28 in the African Clarias root, consistent with the hypothesis that chromosomal rearrangements may act as a recombination suppressor and facilitate semipermeable reproductive barriers in Clarias. This result indicates that fertile interspecific hybrid occurs between species with different karyotypes in Clarias, supporting a model of speciation with gene flow. By reconciling speciational bursts with selective constraints, this study provides a robust framework for understanding the complex genomic landscapes of teleosts and highlights the ecological role of karyotypic diversity in shaping catfish diversification.