The evolution of male pregnancy is the most distinctive characteristic of syngnathids, and their specialized life history traits make syngnathid species excellent model species for many issues in biological evolution. However, the origin of syngnathids and the evolutionary divergence time of different syngnathid species remain poorly resolved. Comprehensive phylogenetic studies of the Syngnathidae will provide critical evidence to elucidate their origin, evolution, and dispersal patterns. We sequenced the mitochondrial genomes of eight syngnathid species in this study, and the estimated divergence times suggested that syngnathids diverged from other teleosts approximately 48.8 Mya during the Eocene period. Selection analysis showed that many mitochondrial genes of syngnathids exhibited significantly lower Ka/Ks values than those of other teleosts. The two most frequently used codons in syngnathid fishes were different from those in other teleosts, and a greater proportion of the mitochondrial simple sequence repeats (SSRs) were distributed in non-coding sequences in syngnathids compared with other teleosts. Our study indicated that syngnathid fishes experienced an adaptive radiation process during the early explosion of species. Syngnathid mitochondrial OXPHOS genes appear to exhibit depressed Ka/Ks ratios compared with those of other teleosts, and this may suggest that their mitogenomes have experienced strong selective constraints to eliminate deleterious mutations.

Limbs are a defining characteristic of tetrapods, yet numerous taxa, primarily among amphibians and reptiles, have independently lost limbs as an adaptation to new ecological niches. To elucidate the genetic factors contributing to this convergent limb loss, we present a 12 Gb chromosome-level assembly of the Banna caecilian (Ichthyophis bannanicus), a limbless amphibian. Our comparative analysis, which includes the reconstruction of amphibian karyotype evolution, reveals constrained gene length evolution in a subset of developmental genes across three large genomes. Investigation of limb development genes uncovered the loss of Grem1 in caecilians and Tulp3 in snakes. Interestingly, caecilians and snakes share a significantly larger number of convergent degenerated conserved non-coding elements (dCNEs) than limbless lizards, which have a shorter evolutionary history of limb loss. These convergent dCNEs overlap significantly with active genomic regions during mouse limb development and are conserved in limbed species, suggesting their essential role in limb patterning in the tetrapod common ancestor. While most convergent dCNEs emerged in the jawed vertebrate ancestor, coinciding with the origin of paired appendage, more recent dCNEs also contribute to limb development, as demonstrated through functional experiments. Our study provides novel insights into the regulatory elements associated with limb development and loss, offering an evolutionary perspective on the genetic basis of morphological specialization.

Background The complete mitochondrial genome and phylogenetic relationship of the newly recorded species of sea slug from the South China sea has not been reported. The taxonomic status of sea slug is not clear. Methods and results The whole mitochondrial genome of a newly recorded species of sea slug from the South China sea (Phyllidiella sp) was determined by Illumina Hiseq4000 sequencing and denovo assembly. The mitochondrial genome of Phyllidiella sp was 14,677 bp in length, including 13 protein-coding genes (PCGs), 2 rRNAs, and 22 tRNAs. In the mitochondrial DNA of Phyllidiella sp the base composition of mitogenome is 30.37% for A, 37.30% for T, 15% for C, and 17.33% for G, and the content of AT was 67.67%. Beside the two kinds of tRNA-Ser, the secondary structure of all tRNAs had a typical cloverleaf structure. In comparison with Phyllidiella pustulosa and Phyllidia ocellata from the same family, the mitochondrial genes of Phyllidiella sp. was not rearranged. The phylogenetic results showed that Phyllidiella sp. and Phyllidiella pustulosa from the same genus clustered into one cluster. Moreover, the genus Phyllidiella clade was sister relationship to the Phyllidia clade. Conclusions Our findings demonstrate that Phyllidiella sp. belongs to the family Phyllidiidae, due to the morphological identification. This study provides molecular information for the phylogenetic analysis of the taxonomic status of sea slugs.