3.2 Demographic parameters
In an attempt to correlate heterozygote deficiency to demographic data,
we have retrieved the population size and level of habitat fragmentation
of colour variable populations (Table 1). The values of 19 variable
populations were statistically compared to similar data of non-variable
populations that were less constrained by population or habitat size (an
overview of all tests and results are available in Table S3). Low
population size generally yielded higher FIS values, but
this relation was non-significant (Kruskal–Wallis; X2= 7.25; P = 0.06). The correlation was tested significant when comparing
threatened populations (<250 individuals) to non-threatened
populations (>250 individuals), in which threatened
populations had higher inbreeding coefficients
(Mann-Whitney; W = 194; P = 0.01;
Figure 3c). Although we found a weak positive correlation, a higher
level of habitat fragmentation did not yield significantly higher
inbreeding coefficients (Kruskal–Wallis; X2 = 4.96; P
= 0.08). We did find that body weight negatively correlates with allelic
richness (Spearman; R = 0.36; P =
0.04; Figure 3d) and expected heterozygosity (Spearman; R = 0.40; P =
0.02). To account for phylogenetic nonindependence of our species data
due to shared ancestry, we used a PGLMM to test the effect of body
weight on the presence of rare colour variants. The results suggests
that variants do not vary in their occurrence in relation to body weight
(PGLMM coefficient: 0.069 ± 0.088 SE, Z = 0.579, P = 0.42). The
intercepts for species were tested significant, meaning that close
relatives had similar values (PGLMM coefficient: 0.93 ± 0.45 SE, Z =
2.04, P = 0.04). Thus, the results imply an overall phylogenetic effect,
and no (or little) body weight effect. The R2 value
suggests that body weight alone explains approximately
15.9% of colour variation in
populations, whereas this is reduced to 11.5% if phylogeny is
incorporated.
Discussion
The aim of our study was to test
whether rare colour variants in the wild may relate to a deficiency of
heterozygotes, possibly resulting from habitat fragmentation and reduced
effective population size. 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
correlation between population size and inbreeding coefficients, in
which small populations suffer from larger heterozygote deficiencies.
This supports the hypothesis that heterozygote deficiency in small
populations might have an influence on the prevalence of rare colour
variants due to the expression of rare recessive alleles. The high
frequency of the rare colour variants in some populations also implies
that genetic drift is occurring in small populations.
In 19 variable populations for which we found genetic data, there was
some indication of a heterozygosity deficiency. This was particularly
evident in charismatic species such as black tigers (Kolipakam et al.,
2019), red leopards (Tensen et al., 2022), and white cougars Puma
concolor (Saranholi et al.,
2017). Non-variable populations
of many species also suffered from heterozygote deficiencies due to
demographic losses, but the difference with non-variable populations was
nonetheless profound in some cases and significant across species. The
direct comparison between variable and non-variable populations remains
challenging, because stochastic events or loss of rare variants will
interact with selective pressures (Caro & Mallarino, 2020).
Furthermore, as our data is based on literature, we were not always able
to include the populations of choice or retrieve historic frequency and
presence / absence data. Studies
with different sample sizes were also compared, which introduces the
risk of bias, and the PGLMM showed an influence of phylogeny on colour
variant presence. Despite these limitations, the loss of genetic
diversity in populations where rare colour variants prevail is
remarkable, and adds to the body of knowledge on the phenotypic effects
of inbreeding in wild populations. The level of habitat fragmentation
did not appear to influence the presence of rare colour variants,
possibly because our dataset did not allow for enough fine-scale detail.
The relationship between habitat fragmentation and genetic diversity
remains indisputable (Templeton et al., 1990; Keyghobadi, 2007; Lino et
al., 2019), and has been linked to rare colour variants before, such as
for Glacier and Spirit bears Ursus americanus in Alaska (Lewis et
al., 2020), where fjords act as barriers to gene flow. Likewise, spatial
variation appears to be the primary driver of colour morph variation in
dragon lizard Ctenophorus decressi in Australia (McLean et al.,
2015).
Another effect of geographic dispersal barriers is that local effective
population sizes are smaller, increasing the effect of genetic drift in
relation to migration and selection as an evolutionary force (Runemark
et al., 2010). A striking example of genetic drift in small populations
is the tiger population in the isolated Similipal tiger reserve, India,
where pseudomelanism reached a frequency of 78%, and in parallel an
exceptionally low heterozygosity was observed (HO =
0.28) (Sagar et al., 2021). It has been revealed that nearly 14% of
homologous alleles, both neutral and damaging, were fixed in small and
isolated tiger populations (Khan et al., 2021). India has a particularly
high degree of habitat fragmentation, and 56 mammalian colour variants
have been recorded between 1886 and 2017 (Mahabal et al., 2019). A
similar situation appears to occur in the highly fragmented Atlantic
rainforest, where melanism in jaguars Panthera onca is
increasing, reaching frequencies of up to 38% (Haag et al., 2010a;b). A
leucistic cougar has been spotted in the same area, which was speculated
to be a sign of inbreeding (Cronemberger et al., 2018). Likewise, in
Eurasian lynx Lynx lynx a wide range of natural coat patterns
exists, associated with geographic location (Darul et al., 2022), which
frequencies have recently altered due to population bottlenecks
resulting from habitat fragmentation (Kubala et al., 2020). In South
Africa, red leopards are spreading in northern provinces, where
effective population sizes are low due to high local population offtake
(Tensen et al., 2022). Even though this population is not isolated, high
population turnover has led to natal philopatry, increasing the overall
relatedness in the population and chances of recessive alleles being
expressed.
We expect this trend to hold true for many other wild carnivores, in
which genetic drift is locally
overruling natural selection in small effective populations. For
instance, phenotypic differences in Arctic foxes Vulpes lagopusreflect distinct selective advantages across their range, however, a
recent increase of blue homozygotes in Arctic foxes Vulpes
lagopus Scandinavia is considered the result of genetic drift (Tietgen
et al., 2021). Furthermore, it appears that melanistic and leucistic
genets Genetta genetta and mongoose Herpestes ichneumonare much more common in Europe, where they have been introduced,
compared to their natural range in Africa (Delibes et al., 2013;
Descalzo et al., 2013). Although it has been suggested that the
phenotypic variation in Spain may relate to a relaxation of selective
pressures (Descalzo et al., 2013), the founder effect has been
overlooked. Likewise, melanistic wolves are common in Yellowstone
National Park, United States, where they were introduced from in and
around Jasper National Park, Canada, where melanism is also common
(Hedrick et al., 2014). Melanism has reached frequencies of
approximately 50% in these areas, which is unlikely to relate to a
concealment advantage (Dekker, 2009) or reproductive fitness (Stahler et
al., 2013), and may instead be the result of genetic drift. The binary
appearance of melanistic wolves, as well as coyote, across their range
(Hinton et al., 2022) supports the notion that neutral, rather than
selective, processes are at play. In European badgers Meles
meles , a population has recently established in central Norway where
leucism now seems abundant, likely as a result of a founder effect
(Hofmeester et al., 2021). The same could be the case for a leucistic
coyote Canis latrans in Costa Rica
(Arroyo-Arce et al., 2019), and
melanistic bobcats at the periphery of their range (McAlpine, 2021),
although this is speculative.
A general trend of an increase in melanistic morphs towards the tropics
and leucistic morphs towards the poles, as predicted by the Gloger’s
rule (Caro & Mallarino, 2020), could not be detected in this study. For
instance, melanistic bobcats Lynx rufus are readily found in the
northern tip of the United States (McAlpine, 2021) and Florida (Regan &
Maehr, 1990), and a melanistic Canada lynx was found in the northern tip
of Alaska (Jung, 2023). Although the Canada lynx appears to be a single
sighting and is likely to suffer a selective disadvantage due to
increased visibility, melanistic bobcats have become fairly common
(McAlpine, 2021). When looking at the map of colour morphs, we can also
see the presence of many leucistic animals in the tropical forests of
Mid-America, such as leucistic coyote Canis latrans , coatiNasua narica , and neotropical otters (Lontra longicaudis ).
Furthermore, leucistic tayra Eira barbara have become abundant in
the Guyana shield in Brazil (Mendes Pontes et al., 2020). This may
further strengthen the theory that rare colour variants are a random,
sometimes maladaptive, occurrence, instead of a selective driver in
response to spatially or temporally variable environments (Svensson,
2017). When not influenced by genetic drift, rare colour variants can
only be maintained through balancing or frequency-dependent selection
(Gray & McKinnon, 2007), which seems unlikely for the before-mentioned
examples. Furthermore, colour variants will only be fixed throughout the
range of a species when they have a selective benefit, at which stage
they are normally referred to as colour polymorphism (Svensson, 2017).
Ecogeographical rules, as such, are more likely to imply to the latter
category, and not to rare colour variants that seems more selectively
neutral or disadvantageous.
It has previously been suggested that leucism mainly prevails in the
Mustelidae, based on the number of published studies (Olson & Allen,
2019), for which we found no evidence during this study. In general, it
appeared that colour variants are most abundant in the Felidae family
(37.5% of cat species), representing 20 out of 59 colour variants
recorded in this study. To compare, the proportion of species that
contain rare colour variants is 23% in Canidae, 15% in Mustelidae,
12.5% in Ursidae, and 3% in Herpestidae and Viverridae (Table S1).
Therefore, the high frequency of variable cats can be considered
somewhat unusual. Furthermore, the PGLMM has illustrated a strong effect
of phylogeny on the presence of colour variants, implying shared
inherited traits among closely related taxa. Because phenotypic
variation is a driver of genetic variation, it is possible that Felidae
species contain more protein polymorphisms associated with pigment-type
switching genes (Andersson & Purugganan, 2022). A similar range of coat
patterns is observed in domestic cats, suggesting it is a conserved
mechanism that can be altered by selection (Kaelin et al., 2012). Wild
cat species exhibit the greatest diversity in colours and spots of all
terrestrial carnivores, likely because they are more reliant on
camouflage compared to for instance canids, which rely more on the chase
(Schneider et al., 2012; Darul et al., 2022). However, it is worth
noting that even though polymorphisms in wild canids are rare, domestic
dogs show more phenotypic variation than any other domesticated animal
(Kaelin & Barsh, 2013). This is due to genome-wide slippage mutations
and pure repetitive sequences in domestic dogs, which occur at a much
greater rate than in other carnivores, likely resulting from strong
population bottlenecks associated with the origin of dog-breeds (Laidlaw
et al., 2007).
Although we found that body size is generally a poor predictor of colour
variation in populations, we did find a correlation between allelic
richness and body weight. Furthermore, a high proportion (33%) of the
colour variants occurred in large carnivore species (>10
kg), even though they have a low species diversity (representing 18% of
all carnivore species). For instance, six of the listed colour variants
were found in large cats (Panthera spp .), of which only five
species exist. The potential bias towards large carnivores could also
partially result from the fact that they are more extensively studied
and more easily observed (Tensen, 2018). They also suffer more from
demographic and genetic deterioration compared to medium-sized and small
predators, based on relatively low effective population sizes (Lino et
al., 2019). Even though we found no significant trend that apex
predators contain more colour variants, this was previously found in
birds. While polymorphisms occur in approximately 3.5% of all bird
species, an estimated 30% of raptorial species are known to be
polymorphic (Hugall & Stuart-Fox, 2012). In birds, colour polymorphism
was associated with accelerated speciation in avian apex predators, due
to a larger niche breath, consistent with theoretical models where
speciation is driven by the fixation of one or more morphs (Hugall &
Stuart-Fox, 2012). Polymorphic bird species also tended to be younger
than monomorphic species, with shorter phylogenetic branches, which can
further increase speciation rates (Gray & McKinnon, 2007; Forsman et
al., 2008). For future research, it would be interesting to test whether
this holds true for polymorphic carnivores as well.
In conclusion, we have collected some compelling evidence that
heterozygote deficiency might contribute to the prevalence of rare
colour variants in the wild, due to the expression of recessive alleles
following reduction in effective population size. As such, it can be
added to the list of phenotypic consequences of population bottlenecks
in the wild, alongside fluctuating asymmetry and bone deformities.
Further investigation of phenotypically variable populations is needed
to determine the genetic basis and the adaptive and evolutionary
significance of rare colour variants to help preserve genetic diversity.
Ideally, a more comprehensive future study should directly sample,
genotype, and compare variable and non-variable populations of species.
With an increase in genomic studies, we may also gain more insights into
random processes versus directional selection in small and fragmented
populations, and their relationship to colour variation in the wild.