Genetic monitoring of the Critically Endangered Araripe Manakin reveals low diversity and declining effective population size

ABSTRACT Genetic information is still underestimated in conservation policies, seldom being monitored or included in management strategies. Monitoring changes in genetic diversity over time in endangered species is useful to anticipate possible risks associated with reduced genetic variation. The Araripe Manakin (Antilophia bokermanni) is a Critically Endangered species, probably with a historically low level of genetic diversity and currently facing demographic population decline. This is the first study to present a fine-scale spatio-temporal genetic monitoring for the Araripe Manakin. Using microsatellite loci, genotyped at two time periods (2003–2004 and 2015–2017), we conclude that genetic diversity has been relatively stable in this short-term assessment, with limited signs of population structure between time frames, and no current population structure within past or present species distribution. However, we also detect signs of genetic bottleneck and evidence that suggest that mating is not presently random. Our results corroborate that the species is a resilient bird, but habitat loss and degradation are jeopardizing Araripe Manakin's persistence. The species comprises a unique small population, and restoration of habitat quality and connectivity should continue to maintain its viability. Nonetheless, given the low genetic diversity observed, we further identify some challenges and recommend solutions for the implementation of genetic information in the current conservation effort of the Araripe Manakin. LAY SUMMARY The Araripe Manakin is restricted to a small area (∼40 km2) of humid forest enclaves in northeastern Brazil. Mostly due to habitat degradation, the species has been severely declining in the last decades. An ongoing action plan has been focusing on habitat quality restoration for the species conservation, but has not yet assessed the genetic consequences of the Araripe Manakin restricted distribution and demographic decline. Such factors can lead to the loss of genetic diversity, which can jeopardize the species survival. Our results show that between 2003 and 2017, the demographic decline has already affected the genetic diversity of the Araripe Manakin, the number of reproducing individuals has declined, and mating is not presently random, further compromising the species genetic diversity stability. The low levels of genetic diversity we report for the Araripe Manakin highlight that the continuous genetic monitoring should be included in the species' conservation plan.