Abstract We employed non-silica-based dipolar nanoparticle affinity bead technique to extract DNA from sedimentary rocks and successfully obtained aDNA from fossilized Lycoptera fishes from the Early Cretaceous in Beipiao, Liaoning Province, China. After library enrichment, high-throughput sequencing, nucleotide BLAST, and data filtering, 276 highly homologous ray-finned fish sequences were identified from 13,113 matched fragments. Molecular phylogenetic analysis showed that Lycoptera is closely related to Osteoglossiformes. At the same time, matching the 276 sequences to each Order of ray-finned fish showed that the fossil fish is closely related to Cypriniformes, but there are no genetic connections between fish groups geographically isolated from Eurasia. Gene exchange between these lineages has been blocked. In addition, analyzing the genetic connection between Lycoptera aDNA and modern genomes revealed unknown evolutionary relationships: The Cypriniformes genome has inherited many Lycoptera gene sequences. We propose the hypothesis that new transposase genes may arise through genome autonomous evolution mechanisms such as ‘progressive evolution’ and ‘overlapping coding region slippage replication recombination’. Evidence supporting this comes from observing the rapid expansion of gene families associated with transposons in aDNA.

Insights from the Early Cretaceous: The promise of Lycoptera aDNA sequencing