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Background  It is believed that natural selection acts on the phenotypical changes caused by mutations. Phenotypically, from fishes to amphibians to reptiles, the emergence of limbs greatly facilitates the landing of ancient vertebrates, but the causal mutations and evolutionary trajectory of this process remain unclear.    Results  We serendipitously obtained a pig of limbless phenotype. Mutations specific to this handicapped pig were identified using genome re-sequencing and comparative genomic analysis. We narrowed down the causal mutations to particular chromosomes and even several candidate genes and sites, such like a mutation-containing codon in gene  BMP7  (bone morphogenetic protein) which was conserved in mammals but variable in lower vertebrates.    Conclusions  We parsed the limbless-related mutations in the light of evolution. The limbless pig shows phenocopy of the clades before legs were evolved. Our findings might help deduce the emergence of limbs during vertebrate evolution and should be appealing to the broad community of human genetics and evolutionary biology.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07925-3.

Comparative genomic analysis of a naturally born serpentized pig reveals putative mutations related to limb and bone development