Genomic Assessment of Cancer Susceptibility in the Threatened Catalina Island Fox (Urocyon littoralis catalinae).

Small effective population sizes raise the probability of extinction by increasing the frequency of potentially deleterious alleles and reducing fitness. However, the extent to which cancers play a role in the fitness reduction of genetically depauperate wildlife populations is unknown. Santa Catalina island foxes (Urocyon littoralis catalinae) sampled in 2007-2008 have a high prevalence of ceruminous gland tumors, which was not detected in the population prior to a recent bottleneck caused by a canine distemper epidemic. The disease appears to be associated with inflammation from chronic ear mite (Otodectes) infections and secondary elevated levels of Staphyloccus pseudointermedius bacterial infections. However, no other environmental factors to date have been found to be associated with elevated cancer risk in this population. Here, we used whole genome sequencing of the case and control individuals from two islands to identify candidate loci associated with cancer based on genetic divergence, nucleotide diversity, allele frequency spectrum, and runs of homozygosity. We identified several candidate loci based on genomic signatures and putative gene functions, suggesting that cancer susceptibility in this population may be polygenic. Due to the efforts of a recovery program and weak fitness effects of late-onset disease, the population size has increased, which may allow selection to be more effective in removing these presumably slightly deleterious alleles. Long-term monitoring of the disease alleles, as well as overall genetic diversity, will provide crucial information for the long-term persistence of this threatened population.

The role of a mechanistic host in maintaining arctic rabies variant distributions: Assessment of functional genetic diversity in Alaskan red fox (Vulpes vulpes).

Populations are exposed to different types and strains of pathogens across heterogeneous landscapes, where local interactions between host and pathogen may present reciprocal selective forces leading to correlated patterns of spatial genetic structure. Understanding these coevolutionary patterns provides insight into mechanisms of disease spread and maintenance. Arctic rabies (AR) is a lethal disease with viral variants that occupy distinct geographic distributions across North America and Europe. Red fox (Vulpes vulpes) are a highly susceptible AR host, whose range overlaps both geographically distinct AR strains and regions where AR is absent. It is unclear if genetic structure exists among red fox populations relative to the presence/absence of AR or the spatial distribution of AR variants. Acquiring these data may enhance our understanding of the role of red fox in AR maintenance/spread and inform disease control strategies. Using a genotyping-by-sequencing assay targeting 116 genomic regions of immunogenetic relevance, we screened for sequence variation among red fox populations from Alaska and an outgroup from Ontario, including areas with different AR variants, and regions where the disease was absent. Presumed neutral SNP data from the assay found negligible levels of neutral genetic structure among Alaskan populations. The immunogenetically-associated data identified 30 outlier SNPs supporting weak to moderate genetic structure between regions with and without AR in Alaska. The outliers included SNPs with the potential to cause missense mutations within several toll-like receptor genes that have been associated with AR outcome. In contrast, there was a lack of genetic structure between regions with different AR variants. Combined, we interpret these data to suggest red fox populations respond differently to the presence of AR, but not AR variants. This research increases our understanding of AR dynamics in the Arctic, where host/disease patterns are undergoing flux in a rapidly changing Arctic landscape, including the continued northward expansion of red fox into regions previously predominated by the arctic fox (Vulpes lagopus).

Risk aversion affects economic values of blue fox breeding scheme.

The profit and production of an average Finnish blue fox farm was simulated using a deterministic bio-economic farm model. Risk was included using Arrow-Prat absolute risk aversion coefficient and profit variance. Risk-rated economic values were calculated for pregnancy rate, litter loss, litter size, pelt size, pelt quality, pelt colour clarity, feed efficiency and eye infection. With high absolute risk aversion, economic values were lower than with low absolute risk aversion. Economic values were highest for litter loss (18.16 and 26.42 EUR), litter size (13.27 and 19.40 EUR), pregnancy (11.99 and 18.39 EUR) and eye infection (12.39 and 13.81 EUR). Sensitivity analysis showed that selection pressure for improved eye health depended strongly on proportion of culled animals among infected animals and much less on the proportion of infected animals. The economic value of feed efficiency was lower than expected (6.06 and 8.03 EUR). However, it was almost the same magnitude as pelt quality (7.30 and 7.30 EUR) and higher than the economic value of pelt size (3.37 and 5.26 EUR). Risk factors should be considered in blue fox breeding scheme because they change the relative importance of traits.

Kin encounter rate and inbreeding avoidance in canids.

Mating with close kin can lead to inbreeding depression through the expression of recessive deleterious alleles and loss of heterozygosity. Mate selection may be affected by kin encounter rate, and inbreeding avoidance may not be uniform but associated with age and social system. Specifically, selection for kin recognition and inbreeding avoidance may be more developed in species that live in family groups or breed cooperatively. To test this hypothesis, we compared kin encounter rate and the proportion of related breeding pairs in noninbred and highly inbred canid populations. The chance of randomly encountering a full sib ranged between 1-8% and 20-22% in noninbred and inbred canid populations, respectively. We show that regardless of encounter rate, outside natal groups mates were selected independent of relatedness. Within natal groups, there was a significant avoidance of mating with a relative. Lack of discrimination against mating with close relatives outside packs suggests that the rate of inbreeding in canids is related to the proximity of close relatives, which could explain the high degree of inbreeding depression observed in some populations. The idea that kin encounter rate and social organization can explain the lack of inbreeding avoidance in some species is intriguing and may have implications for the management of populations at risk.

[Assessment of population differentiation using DNA fingerprinting and modified Wright's Fst-statistics]. / Otsenka podrazdelennosti populiatsii na osnove dannykh DNK-fingerprintinga i modifitsirovannoi Fst-statistiki Raita.

Using our results and literature data on multilocus DNA fingerprinting, we propose a method of obtaining unbiased estimates of the between--population genetic similarity index and a measure of population subdivision based on modified Wright's FST-statistics. On the basis of multiple comparison T2 Hotelling's test and Holmes' procedure, the FST-statistics was applied to assess differentiation of four (Pacific and Atlantic) subpopulations of humpback whale Megaptera novaeangliae, six populations of California island gray fox Urocyon littoralis, and geographically isolated Ob' and Yakutia populations of Siberian white crane Crus leucogeranus. It was shown that the regional humpback whale subpopulations do not constitute a single panmictic unit (P < 10(-4)). The subdivision index of the Pacific and Atlantic populations expressed in terms of FST-statistics varied from 0.101 to 0.157. The differentiation estimates for the island fox populations, which ranged from 0.2109 to 0.4027, indicate that subdivision of these populations is a function of the distance between the islands, island size, and population size. In particular, the smallest and the greatest differences were found respectively between the populations of the geographically closest northern islands (FST = 0.2157, FST = 0.2109) and between those of the most distant northern and southern islands (FST = 0.4027, FST = 0.3869). Subdivision of the island populations with minimum areas and low population number was intermediate (FST = 0.3789). Mean values of heterozygosity, within-population genetic similarity index, and the number of coinciding fragments for two random individuals of Siberian white crane from the Ob' and Yakutia population were not statistically significantly different (P > or = 0.852, (P > or = 0.491, (P > or = 0.325). However, pairwise comparisons of mean FST values indicated that the differentiation estimates for samples from these populations fall within the limits of population subdivision (P = 0.01). The subdivision estimate (0.108-0.133) of various groups of Siberian white cranes is comparable to interregional subdivision of humpback whale. Based on the results of this study, we recommend the approach based on modified Wright's FST-statistics for studying genetic population structure aimed at detecting population subdivision.

The city-fox phenomenon: genetic consequences of a recent colonization of urban habitat.

The red fox (Vulpes vulpes) is one of the best-documented examples of a species that has successfully occupied cities and their suburbs during the last century. The city of Zurich (Switzerland) was colonized by red foxes 15 years ago and the number of recorded individuals has increased steadily since then. Here, we assessed the hypothesis that the fox population within the city of Zurich is isolated from adjacent rural fox populations against the alternative hypothesis that urban habitat acts as a constant sink for rural dispersers. We examined 11 microsatellite loci in 128 foxes from two urban areas, separated by the main river crossing the city, and three adjacent rural areas from the region of Zurich. Mean observed heterozygosity across individuals and the number of detected alleles were lower for foxes collected within the city as compared with their rural conspecifics. Genetic differentiation was significantly lower between rural than between rural and urban populations, and highest value of pairwise FST was recorded between the two urban areas. Our results indicate that the two urban areas were independently founded by a small number of individuals from adjacent rural areas resulting in genetic drift and genetic differentiation between rural and urban fox populations. Population admixture and immigration analysis revealed that urban-rural gene flow was higher than expected from FST statistics. In the five to seven generations since colonization, fox density has dramatically increased. Currently observed levels of migration between urban and rural populations will probably erode genetic differentiation over time.

Energy expenditure and water flux of Rüppell's foxes in Saudi Arabia.

Scattered populations of Rüppell's foxes (Vulpes rueppelli) occur across the deserts of northern Africa and Arabia. Little is known about the biology of these canids, especially the physiological mechanisms that contribute to their ability to live in such harsh environments. For individuals from Saudi Arabia, we tested the hypotheses that Rüppell's foxes have a reduced basal metabolic rate and total evaporative water loss (TEWL), parameters measured in the laboratory, and a reduced field metabolic rate (FMR) and water flux when free-living. Under basal conditions in the laboratory, males, which averaged 1,858 g in body mass, had an oxygen consumption of 914.9 mL O(2)/h, whereas females, which weighed on average 1,233 g, consumed 682.9 mL O(2)/h; rates of oxygen consumption translated to 441.4 kJ/d and 329.4 kJ/d, respectively. TEWL averaged 52.6 g H(2)O/d for males and 47.5 g H(2)O/d for females. We found no evidence that basal metabolism is reduced in Rüppell's foxes, but their TEWL was remarkably low: 50.9% of allometric prediction for males and 64.5% for females. In the wild during winter, males expended energy at a rate of 1,306.5 kJ/d, whereas females had an expenditure of 722.8 kJ/d. Analysis of covariance with FMR as the dependent variable, sex as a fixed factor, and body mass as a covariate showed no statistical difference in FMR between sexes. Water flux did not differ significantly between sexes and averaged 123 mL H(2)O/d, a value 30% lower than the kit fox from the deserts of southwestern North America. FMR was positively related to nocturnal activity levels as FMR (kJ/d) = -2,900.1+55.5 (% of time moving). The water content of prey items varied between 1.9 and 4.1 g H(2)O/g dry matter consumed. Based on these values and knowledge of their diet, we calculated that foxes captured about one rodent and a variety of anthropods per night of foraging.