De Novo Assembly and Annotation from Parental and F1 Puma Genomes of the Florida Panther Genetic Restoration Program

Abstract

In the mid-1990s, the population size of Florida panthers became so small that many individuals manifested traits associated with inbreeding depression (e.g., heart defects, cryptorchidism, high pathogen-parasite load). To mitigate these effects, pumas from Texas were introduced into South Florida to augment genetic variation in Florida panthers. In this study, we report a de novo puma genome assembly and annotation after resequencing 10 individual genomes from partial Florida-Texas-F1 trios. The final genome assembly consisted of ∼2.6 Gb and 20,561 functionally annotated protein-coding genes. Foremost, expanded gene families were associated with neuronal and embryological development, whereas contracted gene families were associated with olfactory receptors. Despite the latter, we characterized 17 positively selected genes related to the refinement of multiple sensory perceptions, most notably to visual capabilities. Furthermore, genes under positive selection were enriched for the targeting of proteins to the endoplasmic reticulum, degradation of mRNAs, and transcription of viral genomes. Nearly half (48.5%) of ∼6.2 million SNPs analyzed in the total sample set contained putative unique Texas alleles. Most of these alleles were likely inherited to subsequent F1 Florida panthers, as these individuals manifested a threefold increase in observed heterozygosity with respect to their immediate, canonical Florida panther predecessors. Demographic simulations were consistent with a recent colonization event in North America by a small number of founders from South America during the last glacial period. In conclusion, we provide an extensive set of genomic resources for pumas and elucidate the genomic effects of genetic rescue on this iconic conservation success story.

Inferring the Demographic History of Inbred Species From Genome-Wide SNP Frequency Data

“…2010). Using genomic data from five individuals of Texas pumas and two individuals of ‘canonical’ Florida panthers from Ochoa et al . (2019), we estimated the demographic history of these two populations to investigate their divergence time, changes in population size, and levels of inbreeding (see cartoon in Figure 3).…”

“…Genome-wide variant data from Ochoa et al . (2019) were obtained from the authors for five Texas pumas and two Florida panthers in variant call format (VCF).…”

“…2009). Parameters were converted from estimated ratios of the ancestral population size ( N A ) to real units using a mutation rate of µ = 2.2 × 10 −9 , a generation time of 3 years, and a sequence length of 2,564,692,624 bp Ochoa et al . (2019).…”

Inferring the Demographic History of Inbred Species from Genome-Wide SNP Frequency Data

“…Florida panthers have been the subject of large-scale conservation efforts aimed at ameliorating the adverse effects of small population size, including moving individuals from their closest sister population, the Texas puma, to introduce novel genetic variation (Seal and Lacy 1994;Johnson et al 2010). Using genomic data from five individuals of Texas pumas and two individuals of 'canonical' Florida panthers from Ochoa et al (2019), we estimated the demographic history of these two populations to investigate their divergence time, changes in population size, and levels of inbreeding (see cartoon in Figure 3). More specifically, we fit a model that included an initial change in population size to mimic the colonization of North America by the Texas population (N TX ), the duration of time spent at the new population size (T 1 ), the divergence time between Texas pumas and Florida panthers (T 2 ), and the inbreeding coefficients for both the Texas and Florida populations (F TX and F FL ).…”

A paradigm shift in our view of species drives current trends in biological classification

“…Yet the Florida populations have remained the focus of conservation programs because scientists and managers were well aware that, subspecies or not, these pumas constitute the only surviving population east of the Mississippi and play a key role as top predators in the unique and endangered ecosystem of cypress swamps in southern Florida. They have been working hard to preserve this last population (Culver, 2009) and one of the fundamental measures involved the introduction of pumas from Texas (formerly considered another subspecies, P. c. stanleyana ) to mitigate inbreeding depression manifested through different conditions (Johnson et al ., 2010; Ochoa et al ., 2019).…”