Abstract:
The blackchin guitarfish (Glaucostegus cemiculus) is a critically endangered ray species that in the last 45 years has undergone a steep population decline and has already gone locally extinct in some parts of its former range. Here, Illumina-based whole-genome sequencing data from two separate populations of blackchin gui-
tarfish were analysed to confirm earlier work based on microsatellites which showed severe inbreeding in a population from the Cabo Verde Archipelago. That population was sampled close to two different islands of the Cabo Verde Archipelago. The other population, originally from the coast of Spain, was sampled from formerly wild-caught specimens, which are now part of a European Association of Zoos and Aquaria (EAZA) Ex situ Programme and are held at the Nausica´a aquarium in France.
Significant differences between the two populations were observed, with the Cabo Verde population showing at least a 55% reduction in heterozygosity and 67% lower nucleotide diversity in comparison to the population from Nausica´a. Almost no intra-population stratification between the two islands was detected. Runs of homozygosity were also analysed for the 7 total samples (n = 4 Cabo Verde, n= 3 Nausica´a), with, depending on the computation method used, up to 4 times the total length of short (>100 kbp) runs of homozygosity and up to 5 times the total length of very long runs (>2 Mbp) in the Cabo Verde population compared with the Nausica´a population, also confirming lower diversity in Cabo Verde. The lower diversity in the Cabo Verde population was previously assumed based on
microsatellite genotyping data, which was successfully confirmed here. These results were also put into context with other vulnerable marine species, several of which are among the most endangered species known, like the vaquita (Phocoena sinus). To improve diversity retention in the ex situ breeding programme, 52 specimens that are currently part of that programme were genotyped at 12 microsatellite loci to enable paternity testing and, through this, retain as much genetic diversity as possible.