Assisted gene flow is used to counteract genetic erosion in small populations of endangered species, yet an evaluation of genetic compatibility of potential donor populations and recipient populations is rare. We developed new metrics for assessing genetic impact of genetic augmentation based on genotype identity of functional variants between donor and recipient genomes and used these metrics to evaluate options for assisted gene flow in Eastern Massasauaga rattlesnake (Sistrutus catenatus) populations in Ohio, USA. We used putatively deleterious variants, and genetic variants likely under positive selection (termed “adaptive” variants) as the two components of functional variation. For potential donor and recipient populations, we estimated three key aspects of genetic compatibility – (a) introduction of novel variants, (b) masking or unmasking of existing deleterious variants, and (c) potential for outbreeding depression through disruption of local adaptation. The main impact of augmentation from diverse donor populations was to introduce novel deleterious variants and to a lesser extent novel adaptive variants into each recipient population. Both donor populations had a similar minor impact in terms of masking existing deleterious variants. Finally, only ~ 7% of adaptive variants show evidence for local adaptation arguing that the negative effect of outbreeding depression would be small. These results draw attention to the importance of considering the potential impact of both deleterious and adaptive genetic variants in augmentation efforts and suggest that in case of these endangered rattlesnakes, the net effect of proposed assisted gene flow may lead to an increase in absolute levels of mutation load.

The Inyo County population of California towhee, now recognized as Melozone crissalis, was officially listed as Threatened under the U.S. Endangered Species Act in 1987. This isolated population in the Argus Mountains was then estimated to consist of less than 175 individuals. Its major threats were habitat destruction caused by grazing, mining, water exporting, and human recreational activities but stakeholders eventually developed a recovery plan to mitigate habitat damage. Due to the demographic success of the recovery plan, the U.S. Fish and Wildlife Service (USFWS) proposed to remove the California towhee from their formal list of threatened and endangered species in 2013. Herein, we generated a high-quality reference genome assembly for a typical representative of the California towhee (N50 = 22 Mb among 627 contigs, max contig size 89.1Mb), then conducted whole genome resequencing on birds sampled from geographic sites across much of the species’ range. Our findings indicate that the California towhee gene pool is relatively deep (i.e., diverse; mean individual heterozygosity = 0.0021, range = 0.0013-0.0026) and that moderately low levels of autozygosity in isolated populations are due to a combination of historic and contemporary inbreeding. Our population, landscape, and phylogeographic analyses indicate that the shallower (less diverse) regions of the gene pool are likely due to a combination of natural geography, anthropogenic impacts, and demographic histories associated with isolated habitats. None of our findings are inconsistent with the 2013 USFWS proposal and we see no reason to protest the delisting petition based exclusively on genetic/genomic data.