关键词: 软骨鱼类, 比较基因组学, 表型多样性, 适应性演化, 遗传多样性

Abstract

Background: Cartilaginous fishes (Chondrichthyes) represent one of the earliest diverging lineages of extant jawed vertebrates (gnathostomes). Retaining numerous ancestral gnathostome features, they serve as a crucial comparative model for elucidating the mechanisms underlying early gnathostome evolution and adaptation. The group comprises approximately 1,267 extant species across 14 orders, exhibiting remarkable diversity in morphology, sensory systems, and reproductive modes. However, their large and highly repetitive genomes have long constrained progress in understanding phenotypic evolution and genetic diversity in this clade. This review aims to synthesize recent advances in chondrichthyan genomics, with emphasis on how adaptive innovations have arisen against a conserved genomic background and how genomic data can inform the conservation of threatened chondrichthyans. 

Progress: In recent years, advances in long-read sequencing and chromatin conformation capture technologies have substantially improved the contiguity and completeness of chondrichthyan genome assemblies. We summarize the core features of chondrichthyan genomes and the molecular basis of their distinctive traits, including a lifelong unossified endoskeleton, continuous tooth replacement, the specialized Ampullae of Lorenzini for detecting weak electric fields, and a urea-based osmoregulatory strategy for maintaining hypertonicity. We further outline the applications of population genomics in reconstructing demographic history, assessing genetic diversity and delineating conservation units. Current evidence indicates that cartilaginous fishes exhibit an exceptionally low germline mutation rate together with highly conserved large-scale synteny and coding gene sequences. Their diverse morphological, physiological, and life-history traits are associated largely with gene family expansion and loss, altered gene regulation, and chromosomal rearrangement. Overall, chondrichthyan genomes preserve essential ancestral genetic footprints of early gnathostomes while also recording diverse genomic innovations acquired during long-term adaptation to marine environments. 

Prospects: Future efforts should prioritize telomere-to-telomere assemblies across the major chondrichthyan lineages, establish cell culture and gene-editing systems to functionally validate candidate genes, and expand reference genome and population resequencing for highly threatened groups such as Rhinopristiformes and Squatiniformes. These efforts will provide a comparative framework for understanding the origin and evolution of key gnathostome traits and a genomic basis for the conservation of threatened chondrichthyan species diversity and the management of their genetic resources.

Key words: Chondrichthyes, comparative genomics, phenotypic diversity, adaptive evolution, genetic diversity