Novel microsatellite markers reveal low genetic diversity and evidence of heterospecific introgression in the critically endangered Chinese Crested Tern (Thalasseus bernsteini)

Abstract The Chinese Crested Tern, Thalasseus bernsteini, is one of the most endangered seabird species in the world, with only small breeding populations of around 100 individuals. To profile the genetic properties of this population, we screened 200 short tandem repeat sequences from a de novo assembled genome of the Great Crested Tern, T. bergii, which is the sister species of T. bernsteini. We designed a panel of 12 novel microsatellites, and genotyped nine and 23 individuals of T. bernsteini and T. bergii, respectively. The results showed that T. bernsteini genetic diversity was lower than that of T. bergii, and no inbreeding was detected. There was no sign of recent bottleneck events in the two species, but T. bernsteini showed signals of a post-bottleneck population expansion. Gene flow analysis indicated introgression between the two species, but the magnitude from T. bernsteini to T. bergii was higher than the opposite. This could be explained by Hubb’s principle, which states that there is a propensity of rarer species to reproduce with abundant congeners. Overall, our efforts provide useful genetic tools for conservation genetic studies of T. bernsteini and potentially other crested terns which face several natural and anthropogenic threats. The findings of this study further highlight that introgression may be a neglected factor in species conservation that needs to be seriously considered for conservation management. Availability of data and materials The dataset of all microsatellite are available from the corresponding author upon request.