Genomic diversity in felids correlates with range and density, not census size

By: Michaël Meeus, Jonas Lescroart & Hannes Svardal

Genetic diversity is an important resource inherent to wild populations, allowing species to adapt to novel circumstances in an ever-changing environment. In an era of rapid anthropogenic climate change, pandemics, and the 6th global mass extinction, this importance becomes increasingly pronounced. Understanding the differences in genetic diversity between species and populations, as well as how genetic diversity relates to other key parameters such as population density, may be key to preserving many of the species we know today.

In this study, we investigated how and why genetic diversity differed among different species of the cat family (Felidae). With around 40 extant species spread across the world, wild cats offer a cohesive group of related species, while presenting sufficient variation in ecological traits (geographic range, population density…) and life history (litter size, body size…) that could potentially explain the differences in genetic diversity. Some cats have been well documented as suffering from low genetic diversity, but no study has truly compared genetic diversity across nearly the whole family using a singular methodology.

We took advantage of publicly available genome data of 100 individuals derived from 39 different felid species and mapped this data to two top-quality reference genomes, a domestic cat and a tiger, to uncover differences between the genomes of each individual and the reference genomes in order to ascertain the genetic diversity of all samples. The total volume of raw data amounted to 9.5 TB, which needed to be processed simultaneously with our custom bioinformatic pipeline. This feat was only possible thanks to the computational infrastructure and resources provided by the Flemish Supercomputer Centre (VSC), allowing for massively parallel steps in quality control and data filtering to take place, often lasting for days or even weeks of elapsed real time.

We found that levels of genetic diversity can vary wildly even among closely related species. Those species with a large distribution or high population density typically harbour the highest levels of diversity, like the ocelot (0.32%), serval (0.29%) and African wildcat (0.27%), while notoriously rare felids such as the snow leopard (0.017%), Andean cat (0.015%) and Asiatic lion (0.005%) trail at the extreme of the low end (Figure 1). A similar trend was seen regarding the species’ conservation status according to the IUCN Red List: species with low genetic diversity were more likely to be considered threatened than those with high genetic diversity.

Figure 1: Genetic diversity varies wildly across cat species, even when they are closely related, such as different species of lynx.

Contrary to geographic range and population density, and rather unexpectedly, census size did not show a significant relationship with genetic diversity. This discrepancy is likely explained by the fact that available census size data is global, whereas geographic range and population density offer better approximations on a smaller scale. Estimates of body size, i.e., average body length and mass, exhibited a nonsignificant but noticeable negative relationship with genetic diversity, suggesting that larger species have lower levels of genetic diversity on average. This makes sense given the finding of a positive relationship between genetic diversity and population density, as larger species tend to live at lower population densities.

Figure 2: The Asiatic lion and ocelot, representing the lowest and highest estimates of genetic diversity found in this study. Photo credits: Thomas Galewski (ocelot, CC-BY) & Pramod CL (Asiatic lion, CC-BY).

Our results are congruent with a growing consensus in conservation circles that genetic diversity as a metric of conservation is severely underutilised in formal assessments, despite its known importance in evolutionary potential, general health, and, as we have shown, the relationship with dominant indicators of threat status, including Red List assessments themselves. Going forward, we hope that our study may add to an appreciation for the relation between genetic diversity, population size, and threat status.

Publication: Meeus, M.P., Lescroart, J. & Svardal, H. Genomic diversity in felids correlates with range and density, not census size. Conserv Genet (2025). https://doi.org/10.1007/s10592-025-01709-y

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