High MHC diversity maintained by balancing selection in an otherwise genetically monomorphic mammal

Abstract

The San Nicolas Island fox (Urocyon littoralis dickeyi) is genetically the most monomorphic sexually reproducing animal population yet reported and has no variation in hypervariable genetic markers. Such low levels of variation imply lower resistance to pathogens, reduced fitness, and problems in distinguishing kin from non-kin. In vertebrates, the MHC contains genes that influence disease resistance and kin recognition and may be under intense balancing selection in some populations. Hence, genetic variation at the MHC might persist despite the extreme monomorphism shown by neutral markers. We examine variation of five loci within the MHC of San Nicolas Island foxes and find remarkably high levels of variation. Further, we show by simulation that genetic monomorphism at neutral loci and high MHC variation could arise only through an extreme population bottleneck of <10 individuals, Ϸ10 -20 generations ago, accompanied by unprecedented selection coefficients of >0.5 on MHC loci. These results support the importance of balancing selection as a mechanism to maintain variation in natural populations and expose the difficulty of using neutral markers as surrogates for variation in fitness-related loci.T he island fox (Urocyon littoralis) is an endemic North American canid that inhabits six of the eight Channel Islands off the coast of southern California (Fig. 1). As suggested by the archeological record and molecular genetic data, foxes colonized the three northern Channel Islands (San Miguel, Santa Rosa, and Santa Cruz) Ϸ16,000 years ago and, subsequently, were transported by Native Americans to the three southern Channel Islands (San Nicolas, Santa Catalina, and San Clemente) 800 to 4,300 years ago (1-4) ( Fig. 1). Effective population size varies with island area and ranges from Ͻ200 to Ϸ1,000 individuals (Table 1). Levels of genetic variation reflect population size and colonization history, with the San Nicolas Island population having the second smallest effective population size and a recent colonization history (4) ( Fig. 1 and Table 1). No variation has been discovered for any of four independent genetic marker classes in the San Nicolas Island population, including supposedly neutral hypervariable microsatellite loci (5) and multilocus fingerprints (2), for which the probability of genetic identity is commonly Ͻ1 in several million (6). Recently, because of dramatic declines, populations on the three Northern Islands and Santa Catalina Island have been proposed for listing under the U.S. Endangered Species Act (7).The MHC contains the most variable set of coding genes in vertebrates, with as many as 349 alleles described for a single locus (8) and heterozygosity values that generally exceed those predicted by neutrality (9). Class I and II MHC molecules are responsible for the presentation to T cells of intracellular (endogenous) and extracellular (exogenous) peptides, respectively (10). High levels of heterozygosity at the MHC may be maintained by balancing selection through pathogen-mediated selection, ...

MHC-based patterns of social and extra-pair mate choice in the Seychelles warbler

“…Indeed, strong pathogen-mediated balancing selection is thought to be responsible for maintaining the remarkably high levels of variation observed at several MHC loci in the otherwise genetically monomorphic endemic San Nicolas Island fox, Urocyon littoralis dickeyi (Aguilar et al 2004). In small, bottlenecked populations where MHC diversity may be reduced-as is the case in the Seychelles warbler (Richardson & Westerdahl 2003)-behavioural strategies maximizing the MHC diversity may be especially important (Aeschlimann et al 2003).…”

Balancing selection and heterogeneity across the classical human leukocyte antigen loci: A meta-analytic review of 497 population studies

“…Population bottlenecks may be responsible for the elevated F nd values seen at some loci in isolated populations, even while those same populations maintain a large part of their ancestral diversity at other HLA loci, presumably as a result of the influence of balancing selection, linkage disequilibrium, or a combination of these two forces. The ability of balancing selection to maintain diversity in MHC genes despite the loss of genetic diversity in other genes during a population bottleneck has been described in another mammalian species [233].…”

High MHC DQB Variation and Asymmetric Allelic Distribution in the Endangered Yangtze Finless Porpoise, Neophocaena phocaenoides asiaeorientalis

“…Thus, population size does not explain the high DQB diversity in Yangtze finless porpoises. An intriguing alternative explanation is that high diversity in MHC genes is driven by balancing selection against diverse pathogens (Slade 1992;Hughes and Yeager 1998;Aguilar et al 2004;Yang et al 2005), suggesting that Yangtze finless porpoises encounter more infectious pathogens than their marine counterparts do. This exposure would then drive diversity at the DQB locus in terms of sequence.…”

“…In contrast, the MHC locus did not evolve neutrally. Instead, novel MHC alleles were created by mutation, duplication, and microrecombination, and this diversity was maintained by balancing selection (Edwards and Hedrick 1998;Aguilar et al 2004;Sommer 2005). According to balancing selection, DQB would have evolved faster than neutral genetic markers, such as mtDNA and microsatellite DNA (Martínez-Agüero et al 2006).…”