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Coat color and pattern are a distinguished feature in mammalian carnivores, shaped by climatic cycles and habitat type. It can be expressed in various ways, such as gradients, polymorphisms, and rare color variants. Although natural selection explains much of the phenotypic variation found in the wild, genetic drift and heterozygote deficiency, as prominent in small and fragmented populations, may also affect phenotypic variability through the fixation of recessive alleles. The aim of this study was to test whether rare color variants in the wild could relate to a deficiency of heterozygotes, resulting from habitat fragmentation and small population size. We present an overview of all rare color variants in the order Carnivora, and compiled demographic and genetic data of the populations where they did and did not occur, to test for significant correlations. We also tested how phylogeny and body weight influenced the presence of color variants with phylogenetic generalized linear mixed models (PGLMMs). We found 40 color-variable species and 59 rare color variants. In 17 variable phenotypic populations for which genetic diversity was available, the average AR was 4.18, HO = 0.59, and HE= 0.66, and FIS= 0.086. We found that variable populations displayed a significant reduction in heterozygosity and allelic richness compared to non-variable populations across species. We also found a significant negative correlation between population size and inbreeding coefficients. Therefore, it is possible that small effective size had phenotypic consequences on the extant populations. The high frequency of the rare color variants (averaging 20%) also implies that genetic drift is locally overruling natural selection in small effective populations. As such, rare color variants could be added to the list of phenotypic consequences of inbreeding in the wild.
The adaptive value of intraspecific phenotypic variability, as well as the extent to which this is balanced by selection and genetic drift, is still relatively poorly explored. An intriguing population of leopard ( Panthera pardus ) occurs in the Cape Floristic Region, South Africa, where body mass is almost half that of leopards occurring in the savanna biome. In this study, we used whole-genome resequencing data of 43 leopards, including 10 from the Western Cape province (WCP). We explored spatial population structure and measured genome-wide diversity, including runs of homozygosity and genetic load. We compared their population demographic history to ‘savanna leopards’ in northern South Africa, and tested for signatures of selection that drive genomic and phenotypic differences. We found that WCP is distinct from other leopards in Africa, and that it diverged 20-24 thousand years ago from northern South Africa, which is in contrast to a lack of genome-wide differentiation found in previous studies. Because we found no obvious signs of genetic drift in WCP, the divergence is likely to have been caused by their population demographic history. We also found enriched genes that may relate to the local phenotype, possibly as an evolutionary response to food-scarce conditions. Leopards in the Cape Floristic Region utilize a unique landscape, which varies biologically in prey availability and vegetation structure, and anthropogenically with the province’s rapidly growing human population. Considering the local adaptation and divergence found in both mitochondrial and nuclear genomes, leopards in the Cape can be considered an evolutionary significant unit (ESU).
