Umbilical Cord: A Non-Invasive DNA Source for Sea Turtle Genomics

High-throughput sequencing has revolutionised conservation genomics by enabling genome-wide information even in non-model species. However, obtaining non-invasive samples for genomics remains challenging in species like sea turtles, which spend most of their lives in the open ocean. In addition, traditional sampling methods are often impractical or unsafe for hatchlings, highlighting the need for alternative approaches. We investigated the potential of umbilical cords (UCs), both from the proximal and distal regions, as a non-invasive sampling method. We assessed the suitability of UC sampling by evaluating prevalence under different incubation conditions, and whether the UC reflected a genetic origin from the mother or offspring. We analysed 76 samples with 2bRAD from five Spanish loggerhead turtle (Caretta caretta) emerging nests, including UCs from 13 hatchlings (both proximal and distal region), 48 hatchling blood samples (four with genotyped UCs) and blood from two breeding females. Using the Percentage of Shared Genotypes (PSG) analysis, we determined that the UC genotype from both sides matched the hatchling blood genotype (97.7%), while PSG were lower between related individuals (73.5%) and even lower between unrelated individuals (56.5%). UC prevalence varied by incubation type, appearing in 100% of artificially incubated nests in Spain, in 25% of Spain's naturally incubated nests, an emergent nesting population, and in only 4.5% of nests naturally incubated in Cape Verde, an established nesting population. Our findings establish UCs as a reliable non-invasive DNA source for hatchlings, particularly in incubator-hatched eggs. This approach advances genomic analysis while minimising disturbance, offering insights into population genetics and conservation strategies.