Fish genomes and their evolution under the influence of ecology

Abstract

Environmental interactions and the effects of such interactions on the evolution of genome attributes is an intriguing area of ongoing research. Several earlier studies have delved into how the genome size (GS) and the guanine-cytosine content (GC) of genomes are shaped by species’ ecology while largely disregarding other genome attributes, such as number of chromosomes (CR), number of genes (GE), and protein count (PC) from such comparisons. The present study was designed at understanding the influence of ecology––climate, habitat, and depth––on genome attributes by using the most current data on 579 whole fish genomes available at NCBI. Given the diverse and intricate roles of GS and GC in species adaptations to temperature, salinity, and hydrostatic pressure, the focus was on finding if and how the genomes responded to these stressors and if any common patterns existed in the genome-level responses. Our analyses exhibited some significant and intriguing trends for fishes as a whole while indicating strong effects of ecology on GS, GC, CR, and PC. Also, some very unique trends were observed on regressing GS and GC values across temperature, salinity, and depth clines. Accordingly, a very strong decline in the GS and a concomitant increase in GC were observed in species through the tropics/sub tropics to the temperate/poles, from freshwater to the marine habitats, and from the pelagic to bathydemersal depths. Observed patterns strongly support the notion that smaller GS and larger GC are associated with species inhabiting more stable environments and vice versa. The results also signify the effect of these patterns on protein flexibility and its role in tolerating stressful conditions. Observed patterns are discussed in the light of latitudinal biodiversity gradient, habitat complexity, and energy and metabolic expenditure hypothesis.