The sequencing of complete puma genomes provides insights into the genetic consequences of isolation and inbreeding and gives ideas of how to reverse these and apply that framework to the conservation of many other species.
Today pumas are the most widely distributed mammal in the entire western hemisphere, ranging from Canada all the way to the southern tip of South America. However, in the 19th and 20th centuries hunting caused the puma population to be forced to the North America West and the South of Florida. Towards the end of the 20th century hunting bans allowed puma population to regrow and take back some land, resulting in them once again being distributed throughout the country. This has been somewhat hampered by the expansion of highways, agriculture, and residential development causing encroachment on their habitat, and resulting in continued small and isolated populations that are susceptible to loss of genetic diversity and predisposed to inbreeding. Recent advances in sequencing technologies made it possible for the researchers in this study to sequence 10 whole Puma genomes from different isolated populations across North America in order to compare the genomes to determine changes over time and the impacts of inbreeding. Their goal in doing this was to answer two important questions which could have impacts on conservation biology as a whole. First, they wanted to use shared tracts of homozygosity to predict the effectiveness of assisted gene flow in restoring lost genetic diversity. Second, they hoped to assess the long- term efficacy of inter-population mixture as a means to rescue small and isolated populations from the deleterious effects of inbreeding. These questions could assist conservation biologists in not only saving the North American Puma, but also many other isolated species.
This project shed a light on the negative consequences of societal development on species ability to roam between populations and therefore their genetic diversity. The researchers first used nuclear genomic data to perform PCA in order to establish the general genetic structure among puma populations. They found that 52% of the genetic variance between the species was geographic, the separation of North and South America as well as a trend in relatedness from East to West across North America. This genetic variance caused by geographic separation is largely the result of highway expansion and inability of populations to interact with each other because the development causes forced separation. This idea is further emphasized by the data the researchers found which showed that the puma species in South America had increased amounts of genetic diversity, where habitat loss and forced isolation is significantly less widespread.
After establishing the overall population and genetic structure of the Puma populations across North and South America the researchers looked more closely at the extent of inbreeding within these populations in order to establish differences in genetic variation between the populations and the impact inbreeding has on these. In order to do this they found and analyzed runs of homozygosity (ROH) in each of the sequenced pumas and compared these. They found that all of the pumas that they sequenced in North America had low heterozygosity and high proportion of their genomes in ROH, whereas the in the pumas from Brazil they saw the opposite impact. They then compared the ROH levels and heterozygosity of a puma from before and after the introduction of a different puma population as a method of interpopulation mixture to decrease the impacts of inbreeding. They found that there was increased heterozygosity and the levels of ROH decreased, however they did not decrease as much as expected showing that this is not necessarily an effective method of genetic rescue.
This study shows that genetic rescue is possible, giving conservationists a new template with which to study and assist isolated populations. By studying the impacts of inbreeding on levels of genetic variation in different populations the researchers were able to establish that the isolation of these populations is causing a decrease in variation which could cause reproductive failure and phenotypic defects resulting in extinction. Additionally, their study of inbreeding provided knowledge of shared ROH, which is critical when designing plans for genetic rescue, because it predicts whether enhancing connectivity would restore lost genetic diversity and helps identify candidates for translocation. By also studying generally puma genomes from a variety of locations they found that it is human behavior that is resulting in this isolation. Human land use has reduced the connectivity that is critical to recovery and maintenance of healthy populations, however, gene flow among neighboring populations can be facilitated by enhancing landscape connectivity through coordinated land use planning and by adding bridges or underpasses across freeways. This study gave us the knowledge that this change in land use is what is needed to improve the genetic variation of pumas in North America, and this is extremely important because it can serve as a template for future conservation genomic research targeting species living in small, isolated populations. For example, the pumas in South America currently experience less habitat degradation than pumas in North America which has allowed them to retain their genetic diversity. However, they will likely face further habitat loss and fragmentation as rapid human population growth and land development continues on the continent. Therefore the conservation efforts and findings taken from isolated populations in North America may need to be applied to other parts of the puma range in the future, as well as to other species which are suffering from becoming increasingly isolated. This study opens the door for conservationists to help restore a vast array of species who have been gradually becoming less and less diverse, and hopefully, as a result prevent the extinction of more species on our planet.
Nedda F. Saremi et al. 2019. Puma genomes from North and South America provide insights into the genomic consequences of inbreeding. Nature Communications 10: 4769. https://www.nature.com/articles/s41467-019-12741-1