Genetic diversity of the California sea lion assessed by pedigree analysis

Dissertação de Mestrado Integrado em Medicina Veterinária ; The genetic diversity and population structure of the California sea lion (Zalophus californianus) were assessed based on the pedigree information registered in the European studbook, currently under the management of the Lisbon Zoo, as an EEP programme. Records collected from 1930 until 2020 were used for this analysis, including a total of 1998 individuals, 477 of which represent the current living population. To our knowledge, this is the most comprehensive and up-to-date analysis for this species, assessing the evolution of genetic diversity, inbreeding and relationships, and the genetic contribution of founders, using conventional pedigree analysis procedures and additional software tools commonly used in domestic species, such as ENDOG. The average equivalent complete generations were 1.54 (±1.20) per animal for the overall population. However, there has been an increase in pedigree depth throughout the years, with the reference population reaching 3.37 (±0.76) complete generations, where all animals had maternal grandparents known and nearly 85% to 90% had paternal grandparents known. The whole population had a generation interval of 11.52 (±4.70) years, however the mean ages at which individuals had their progeny has been increasing, particularly in the last decade. Regarding the number of offspring for each parent, dams had an average of 4.05 (±3.16) pups and sires 7.97 (±8.57) pups. The overall mean inbreeding was 2.03% (±5.92), though throughout the years, this has been increasing, with the reference population reaching 3.34% (±6.08). The rate of increase in inbreeding was around 1.6% per generation. The number of inbred animals has also been growing, representing 16.87% and 52.94% of the total and reference populations, respectively. However, the average inbreeding coefficient, of the inbred individuals has shown a significant decrease, with the value for the reference population being nearly half that of the overall population. The mean ...