Allelic genealogy under overdominant and frequency-dependent selection and polymorphism of major histocompatibility complex loci

Recombination within the human MHC

Recombination (crossing over) in the human MHC is thought to have played a role in generation of novel alleles at various HLA loci. It is also responsible for the diversity observed at the haplotype level, although the functional consequences of this activity are not clear. Historic and family studies of recombination have provided estimations of recombination fractions across the MHC and identified potential hotspots for recombination in the class II region. Other characteristics of recombination in the human MHC such as haplotype specificity in recombination frequency and localized sequence motifs involved in recombination have been considered, but have been difficult to address given the constraints of human population studies. Single-sperm typing holds promise in overcoming some of the limitations inherent in the study of recombination in human populations. Both family-based and sperm typing analyses of recombination, along with our knowledge of linkage disequilibrium patterns in the MHC, may provide novel information regarding the evolution of HLA haplotypes that will be difficult to obtain by other means.

Allelic genealogies in sporophytic self-incompatibility systems in plants

Expectations for the time scale and structure of allelic genealogies in finite populations are formed under three models of sporophytic self-incompatibility. The models differ in the dominance interactions among the alleles that determine the self-incompatibility phenotype: In the SSIcod model, alleles act codominantly in both pollen and style, in the SSIdom model, alleles form a dominance hierarchy, and in SSIdomcod, alleles are codominant in the style and show a dominance hierarchy in the pollen. Coalescence times of alleles rarely differ more than threefold from those under gametophytic self-incompatibility, and transspecific polymorphism is therefore expected to be equally common. The previously reported directional turnover process of alleles in the SSIdomcod model results in coalescence times lower and substitution rates higher than those in the other models. The SSIdom model assumes strong asymmetries in allelic action, and the most recessive extant allele is likely to be the most recent common ancestor. Despite these asymmetries, the expected shape of the allele genealogies does not deviate markedly from the shape of a neutral gene genealogy. The application of the results to sequence surveys of alleles, including interspecific comparisons, is discussed.

Evidence for balancing selection operating at the het-c heterokaryon incompatibility locus in a group of filamentous fungi

In filamentous fungi, het loci (for heterokaryon incompatibility) are believed to regulate self/nonself-recognition during vegetative growth. As filamentous fungi grow, hyphal fusion occurs within an individual colony to form a network. Hyphal fusion can occur also between different individuals to form a heterokaryon, in which genetically distinct nuclei occupy a common cytoplasm. However, heterokaryotic cells are viable only if the individuals involved have identical alleles at all het loci. One het locus, het-c, has been characterized at the molecular level in Neurospora crassa and encodes a glycine-rich protein. In an effort to understand the role of this locus in filamentous fungi, we chose to study its evolution by analyzing het-c sequence variability in species within Neurospora and related genera. We determined that the het-c locus was polymorphic in a field population of N. crassa with close to equal frequency of each of the three allelic types. Different species and even genera within the Sordariaceae shared het-c polymorphisms, indicating that these polymorphisms originated in an ancestral species. Finally, an analysis of the het-c specificity region shows a high occurrence of nonsynonymous substitution. The persistence of allelic lineages, the nearly equal allelic distribution within populations, and the high frequency of nonsynonymous substitutions in the het-c specificity region suggest that balancing selection has operated to maintain allelic diversity at het-c. Het-c shares this particular evolutionary characteristic of departing from neutrality with other self/nonself-recognition systems such as major histocompatibility complex loci in mammals and the S (self-incompatibility) locus in angiosperms.

The number of self-incompatibility alleles in a finite, subdivided population

The actual and effective number of gametophytic self-incompatibility alleles maintained at mutation-drift-selection equilibrium in a finite population subdivided as in the island model is investigated by stochastic simulations. The existing theory founded by Wright predicts that for a given population size the number of alleles maintained increases monotonically with decreasing migration as is the case for neutral alleles. The simulation results here show that this is not true. At migration rates above Nm = 0.01-0.1, the actual and effective number of alleles is lower than for an undivided population with the same number of individuals, and, contrary to Wright's theoretical expectation, the number of alleles is not much higher than for an undivided population unless Nm < 0.001. The same pattern is observed in a model where the alleles display symmetrical overdominant selection. This broadens the applicability of the results to include proposed models for the major histocompatibility (MHC) loci. For a subdivided population over a large range of migration rates, it appears that the number of self-incompatibility alleles (or MHC-alleles) observed can provide a rough estimate of the total number of individuals in the population but it underestimates the neutral effective size of the subdivided population.

Analysis of intron sequences at the class II HLA-DRB1 locus: implications for the age of allelic diversity

Analyses of the coding sequences of HLA class II alleles have revealed high similarity between species, indicating that much of the polymorphism predates the separation of human (Homo) and chimpanzee (Pan), 4-7.4 million years ago. Recent studies of the intron sequences of alleles provide support for a much more recent origin and rapid generation of HLA alleles. At the DRB1 locus, intron analysis indicates that most of the allelic lineages have diverged from each other before the separation of Homo and Pan, consistent with the exon analysis. However, the intron sequences of alleles within lineages are almost identical, indicating that many of the alleles have been generated after the divergence of the Homo and Pan lineages.

Effects of intra-locus recombination of HLA polymorphism

The observed number of alleles (n(a)) at some human major histocompatibility complex (HLA) loci is more than twice as large as the pairwise mean number (KB) of nonsynonymous nucleotide substitutions in the peptide-binding region (PBR), although the KB is about the same as that predicted by a model of balancing selection. In order to assess the joint effect of intra-locus recombination and balancing selection on the HLA polymorphism, large scale computer simulation is conducted. It reveals that (1) both rate and location of break points of recombination are crucial factors to determine n(a), (2) intra-locus recombination tends to decrease KB, and (3) the rate of PBR nonsynonymous substitutions is insensitive to the recombination rate. Although a large number of alleles can be generated by intra-locus recombination, this fact alone is insufficient to account for the HLA polymorphism. It is argued that even patchwork patterns of PBR motifs, presumably owing to intra-locus recombination, must be maintained primarily by balancing selection.

Genealogical structure among alleles regulating self-incompatibility in natural populations of flowering plants

A method is proposed for characterizing the structure of genealogies among alleles that regulate self-incompatibility in flowering plants. Expected distributions of ratios of divergence times among alleles, scaled by functions of allele number, were generated by numerical simulation. These distributions appeared relatively insensitive to the particular parameter values assigned in the simulations over a fourfold range in effective population size and a 100-fold range in mutation rate. Generalized least-squares estimates of the scaled indices were obtained from genealogies reconstructed from nucleotide sequences of self-incompatibility alleles from natural populations of two solanaceous species. Comparison of the observed indices to the expected distributions generated by numerical simulation indicated that the allelic genealogy of one species appeared consistent with the symmetric balancing selection generated by self-incompatibility. However, the allelic genealogy of the second species showed unusually long terminal branches, suggesting the operation of additional evolutionary processes.

Dissimilar evolution of B-locus versus A-locus and class II loci of the HLA region in South American Indian tribes

Native American populations have a limited HLA polymorphism compared with other ethnic groups. In spite of this, many novel HLA-B locus alleles, not observed in other populations, have been identified in South American tribes, and rapid evolution of this locus has been suggested. We have studied unrelated subjects of the Toba (TOB n = 116), Wichi (WIC n = 46) and Pilaga (PIL n = 14) tribes from northeastern Argentina to investigate the extent of the HLA polymorphism and obtain clues of selective forces that may have acted in these populations. In these tribes the number of HLA alleles is small at all loci except HLA-B, which presents 22 alleles. Seven novel alleles were characterized including 5 of HLA-B (B*35092, B*3518, B*3519, B*4009, B*4803) 1 at HLA-A (A*0219) and 1 at DRB1 (DRB1*0417). All these variants may have arisen by gene conversion events. Some of the novel variants represent the most frequent alleles of these populations (B*4803 in TOB and PIL; B*3519 in WIC) or are the most frequent subtypes in their lineages. HLA-A, B, DRB1,DQA1 and DQB1, but not DPB1, display relatively similar gene frequencies. This results in high heterozygosity in all the tribes for all the loci studied except HLA-DPB1. The larger polymorphism and the generation and maintenance of novel alleles at the HLA-B locus suggests a more specialized response of this locus to evolutionary forces. These effects may be related to the nature of the polymorphism, to the number of founder alleles and to the functional characteristics of the individual alleles.

Phylogenetics and the origin of species

A recent criticism that the biological species concept (BSC) unduly neglects phylogeny is examined under a novel modification of coalescent theory that considers multiple, sex-defined genealogical pathways through sexual organismal pedigrees. A competing phylogenetic species concept (PSC) also is evaluated from this vantage. Two analytical approaches are employed to capture the composite phylogenetic information contained within the braided assemblages of hereditary pathways of a pedigree: (i) consensus phylogenetic trees across allelic transmission routes and (ii) composite phenograms from quantitative values of organismal coancestry. Outcomes from both approaches demonstrate that the supposed sharp distinction between biological and phylogenetic species concepts is illusory. Historical descent and reproductive ties are related aspects of phylogeny and jointly illuminate biotic discontinuity.

Neutral behavior of shared polymorphism

Several cases have been described in the literature where genetic polymorphism appears to be shared between a pair of species. Here we examine the distribution of times to random loss of shared polymorphism in the context of the neutral Wright-Fisher model. Order statistics are used to obtain the distribution of times to loss of a shared polymorphism based on Kimura's solution to the diffusion approximation of the Wright-Fisher model. In a single species, the expected absorption time for a neutral allele having an initial allele frequency of 1/2 is 2.77 N generations. If two species initially share a polymorphism, that shared polymorphism is lost as soon as either of two species undergoes fixation. The loss of a shared polymorphism thus occurs sooner than loss of polymorphism in a single species and has an expected time of 1.7 N generations. Molecular sequences of genes with shared polymorphism may be characterized by the count of the number of sites that segregate in both species for the same nucleotides (or amino acids). The distribution of the expected numbers of these shared polymorphic sites also is obtained. Shared polymorphism appears to be more likely at genetic loci that have an unusually large number of segregating alleles, and the neutral coalescent proves to be very useful in determining the probability of shared allelic lineages expected by chance. These results are related to examples of shared polymorphism in the literature.

How large was the founding population of Darwin's finches?

A key assumption of many allopatric speciation models is that evolution in peripheral or isolated populations is facilitated by drastic reductions in population size. Population bottlenecks are believed to lead to rapid changes in gene frequencies through genetic drift, to facilitate rapid emergence of novel phenotypes, and to enhance reproductive isolation via genetic revolutions. For such effects to occur, founding populations must be very small, and remain small for some time after founding. This assumption has, however, rarely been tested in nature. One approach is to exploit the polymorphism of the major histocompatibility complex (Mhc ) to obtain information about the founding population. Here, we use the Mhc polymorphism to estimate the size of the founding population of Darwin's finches in the Galápagos Archipelago. The results indicate that the population could not have been smaller than 30 individuals.

Inferring frequency dependent selection from the molecular evolution of a rapidly evolving virus: a theoretical investigation

Hypotheses have been put forward suggesting that immune selection generates much of the intra-patient genetic diversity of rapidly evolving viruses. A Monte Carlo simulation is presented which models sequence evolution in an HIV-like virus under selection from the immune system. Measurements of evolutionary change are then made from the resulting sequences, generating predicted outcomes for each scenario. Frequency dependent immune selection is shown by two statistical measurements to have a significant effect on viral sequence evolution. The use of drawing inferences about underlying evolutionary processes from samples of viral diversity in infected individuals is discussed.

Allelic diversity and gene genealogy at the self-incompatibility locus in the Solanaceae

The self-incompatibility (S) locus of flowering plants offers an example of extreme polymorphism maintained by balancing selection. Estimates of recent and long-term effective population size (Ne) were determined for two solanaceous species by examination of S-allele diversity. Estimates of recent Ne in two solanaceous species differed by an order of magnitude, consistent with differences in the species' ecology. In one species, the evidence was consistent with historical population restriction despite a large recent Ne. In the other, no severe bottleneck was indicated over millions of years. Bottlenecks are integral to founder-event speciation, and loci that are subject to balancing selection can be used to evaluate the frequency of this mode of speciation.

Variation and evolution of class I Mhc in sexual and parthenogenetic geckos

We present the first Mhc class I sequences in geckos. We compared Mhc variation in gekkonid species that reproduce sexually (Hemidactylus frenatus, Lepidodactylus aureolineatus, L. moestus, L. sp. Arno, L. sp. Takapoto) to others reproducing parthenogenetically (H. garnotii, L. lugubris). These comparisons include the known maternal (L. moestus) and paternal (L. sp. Arno) ancestors of the asexual L. lugubris. Sequences similar to other vertebrate species were obtained from both nuclear and cDNA templates indicating that these sequences are derived from expressed class I Mhc loci. Southern blot analysis using gecko class I probes, revealed that parthenogenetic clonal lineages of independent evolutionary origin have no within-clone band variation at class I loci and that no detectable recombination between restriction sites had taken place. Variability in the sexual species was similar to mammalian taxa, i.e. class I genes are highly variable in outbreeding sexual populations. Sequence analysis of the alpha-2 domain of class I genes identified point mutations in a clonal lineage of L. lugubris which led to amino acid substitutions. Potential transspecific allelic lineages were also observed. The persistence of asexual lineages with little or no class I diversification over thousands of generations seems to argue against strong selection for Mhc multi-allelism caused by pathogen-Mhc allele specificity. On the other hand, the high level of heterozygosity in the parthenogenetic species (a consequence of their hybrid origin) may provide clonal lineages with adequate antigen presenting diversity to survive and compete with sexual relatives.

Evolutionary relationship of HLA-DRB genes inferred from intron sequences

The major histocompatibility complex (Mhc) consists of class I and class II genes. In the human Mhc (HLA) class II genes, nine DRB loci have been identified. To elucidate the origin of these duplicated loci and allelic divergences at the most polymorphic DRB1 locus, introns 4 and 5 as well as the 3' untranslated region (altogether approximately 1,000 base pairs) of seven HLA-DRB loci, three HLA-DRB1 alleles, and nine nonhuman primate DRB genes were examined. It is shown that there were two major diversification events in HLA-DRB genes, each involving gene duplications and allelic divergences. Approximately 50 million years (my) ago, DRB1*04 and an ancestor of the DRB1*03 cluster (DRB1*03, DRB1*15, and DRB3) diverged from each other and DRB5, DRB7, DRB8, and an ancestor of the DRB2 cluster (DRB2, DRB4, and DRB6) arose by gene duplication. Later, about 25 my ago, DRB1*15 diverged from DRB1*03, and DRB3 was duplicated from DRB1*03. Then, some 20 my ago, the lineage leading to the DRB2 cluster produced two new loci, DRB4 and DRB6. The DRB1*03 and DRB1*04 allelic lineages are extraordinarily old and have persisted longer than some duplicated genes. The orthologous relationships of DRB genes between human and Old World monkeys are apparent, but those between Catarrhini and New World monkeys are equivocal because of a rather rapid expansion and contraction of primate DRB genes by duplication and deletion.

Genetic susceptibility to malaria and other infectious diseases: from the MHC to the whole genome

There is substantial evidence that host genetic factors play a major role in determining the outcome of infection with many pathogens. Detailed analysis of malaria has identified twelve genes that affect susceptibility in various human populations. However, less attention has been paid to other major infectious diseases where twin studies have identified an important host genetic component to susceptibility. Recent progress in the analysis of the human genome offers exciting prospects for the mapping and identification of new susceptibility and resistance genes for common infectious diseases. Screening of the whole genome in affected sibling pair studies is now feasible by employing highly informative microsatellite markers. In addition, many polymorphic candidate genes have become available for analysis in case-control studies. It is proposed that these new genetic tools offer a powerful approach to the epidemiological analysis of many infectious diseases in humans and supersede traditional genetic approaches to identifying susceptibility genes in mouse models. Progress in characterizing the role of major histocompatibility genes in susceptibility to malaria and other infectious diseases is reviewed before outlining the methodologies for and progress in identifying non-MHC susceptibility genes.

HLA-B alleles of the Navajo: no evidence for rapid evolution in the Nadene

New HLA-B locus alleles have been found in South American Amerindian populations but were largely absent in North American Amerindian tribes also descended from this first Paleo-Indian migration. We have now extended these studies to the Navajo, descendants of the second Nadene migration. No new functional alleles were found at the B locus of this tribe. This limited study supports the notion that while new B locus variants are common in South American Amerindians, it is more difficult to find new B locus alleles in North American native peoples. Whether this dichotomy is due to differences in pathogen environment and/or population structures between North and South America remains a subject of speculation.

The myth of Eve: molecular biology and human origins

It has been proposed that modern humans descended from a single woman, the "mitochondrial Eve" who lived in Africa 100,000 to 200,000 years ago. The human immune system DRB1 genes are extremely polymorphic, with gene lineages that coalesce into an ancestor who lived around 60 million years ago, a time before the divergence of the apes from the Old World monkeys. The theory of gene coalescence suggests that, throughout the last 60 million years, human ancestral populations had an effective size of 100,000 individuals or greater. Molecular evolution data favor the African origin of modern humans, but the weight of the evidence is against a population bottleneck before their emergence. The mitochondrial Eve hypothesis emanates from a confusion between gene genealogies and individual genealogies.

An evolutionary perspective on signaling in behavior and immunology

Signaling and communication are important at different levels of biological organization. Signals exchanged between cells of the immune system initiate and coordinate the immune response; signals exchanged between individuals often coordinate social behavior. Behavioral ecologists interested in the evolution and functional design of signals exchanged between individuals have produced a theory of signaling and communication that stresses the importance of cooperation and conflict; if a conflict of interest between signaler and receiver is great enough, signals evolve towards greater reliability. We suggest that the application of signaling system theory to signals exchanged between cells within an individual will allow for a better understanding of immunity and intra-individual communication in general, with potential for novel approaches to the treatment of disease.

Adaptive evolution of color vision genes in higher primates

The intron 4 sequences of the three polymorphic alleles at the X-linked color photo-pigment locus in the squirrel monkey and the marmoset reveal that the alleles in each species are exceptionally divergent. The data further suggest either that each triallelic system has arisen independently in these two New World monkey lineages, or that in each species at least seven deletions and insertions (14 in the two species) in intron 4 have been transferred and homogenized among the alleles by gene conversion or recombination. In either case, the alleles in each species apparently have persisted more than 5 million years and probably have been maintained by overdominant selection.

Extensive MHC class II DRB3 diversity in African and European cattle

Genetic diversity at the highly polymorphic BoLA-DRB3 locus was investigated by DNA sequence analyses of 18 African cattle from two breeds representing the two subspecies of cattle, Bos primigenius indicus and Bos primigenius taurus. The polymorphism was compared with that found in a sample of 32 European cattle from four breeds, all classified as B. p. taurus. Particularly extensive genetic diversity was found among African cattle, in which as many as 18 alleles were recognized in this small random sample of animals from two breeds. The observed similarity in allele frequency distribution between the two African populations, N'Dama and Zebu cattle, is consistent with the recent recognition of gene flow between B. p. indicus and B. p. taurus cattle in Africa. A total of 30 DRB3 alleles were documented and as many as 26 of these were classified as major allelic types showing at least five amino acid substitutions compared with other major types. The observation of extensive genetic diversity at MHC loci in cattle, as well as in other farm animals, provides a compelling argument against mating-type preferences as a primary cause in maintaining major histocompatibility complex diversity, since the reproduction of these animals has been controlled by humans for many generations.

Linkage and the limits to natural selection

The probability of fixation of a favorable mutation is reduced if selection at other loci causes inherited variation in fitness. A general method for calculating the fixation probability of an allele that can find itself in a variety of genetic backgrounds is applied to find the effect of substitutions, fluctuating polymorphisms, and deleterious mutations in a large population. With loose linkage, r, the effects depend on the additive genetic variance in relative fitness, var(W), and act by reducing effective population size by (N/Ne) = 1 + var(W)/2r2. However, tightly linked loci can have a substantial effect not predictable from Ne. Linked deleterious mutations reduce the fixation probability of weakly favored alleles by exp (-2U/R), where U is the total mutation rate and R is the map length in Morgans. Substitutions can cause a greater reduction: an allele with advantage s < scrit = (pi 2/6) loge (S/s) [var(W)/R] is very unlikely to be fixed. (S is the advantage of the substitution impeding fixation.) Fluctuating polymorphisms at many (n) linked loci can also have a substantial effect, reducing fixation probability by exp [square root of 2Kn var(W)/R] [K = -1/E((u-u)2/uv) depending on the frequencies (u,v) at the selected polymorphisms]. Hitchhiking due to all three kinds of selection may substantially impede adaptation that depends on weakly favored alleles.

Low major histocompatibility complex class II diversity in European and North American moose

Major histocompatibility complex (MHC) genes encode cell surface proteins whose function is to bind and present intracellularly processed peptides to T lymphocytes of the immune system. Extensive MHC diversity has been documented in many species and is maintained by some form of balancing selection. We report here that both European and North American populations of moose (Alces alces) exhibit very low levels of genetic diversity at an expressed MHC class II DRB locus. The observed polymorphism was restricted to six amino acid substitutions, all in the peptide binding site, and four of these were shared between continents. The data imply that the moose have lost MHC diversity in a population bottleneck, prior to the divergence of the Old and New World subspecies. Sequence analysis of mtDNA showed that the two subspecies diverged at least 100,000 years ago. Thus, viable moose populations with very restricted MHC diversity have been maintained for a long period of time. Both positive selection for polymorphism and intraexonic recombination have contributed to the generation of MHC diversity after the putative bottleneck.

HLA-B alleles of the Cayapa of Ecuador: new B39 and B15 alleles

Recent data suggest that HLA-B locus alleles can evolve quickly in native South American populations. To investigate further this phenomenon of new HLA-B variants among Amerindians, we studied samples from another South American tribe, the Cayapa from Ecuador. We selected individuals for HLA-B molecular typing based upon their HLA class II typing results. Three new variants of HLA-B39 and one new variant of HLA-B15 were found in the Cayapa: HLA-B*3905, HLA-B*3906, HLA-B*3907, and HLA-B*1522. A total of thirteen new HLA-B alleles have now been found in the four South American tribes studied. Each of these four tribes studied, including the Cayapa, had novel alleles that were not found in any of the other tribes, suggesting that many of these new HLA-B alleles may have evolved since the Paleo-Indians originally populated South America. Each of these 13 new alleles contained predicted amino acid replacements that were located in the peptide binding site. These amino acid replacements may affect the sequence motif of the bound peptides, suggesting that these new alleles have been maintained by selection. New allelic variants have been found for all common HLA-B locus antigenic groups present in South American tribes with the exception of B48. In spite of its high frequency in South American tribes, no evidence for variants of B48 has been found in all the Amerindians studied, suggesting that B48 may have unique characteristics among the B locus alleles.

Pathogen-based models favoring MHC genetic diversity

We present six models that are currently the most likely ways that pathogens might favor the evolution of MHC genetic diversity. Although each model makes one or more unique predictions, the current lack of crucial data prevents distinguishing the relative importance of each model. However, this first-time organization of these models should contribute to the design of critical experiments. This synthetic review yields at least three essentially new ideas. First, MHC-dependent immune recognition may be sufficiently redundant to render it essentially escape-proof by pathogens. Second, the four models based on pathogen escape do not work (or work weakly) for diversifying class II genes, unless class II-restricted cytotoxic T-cells are important, an idea that is controversial. Third, pathogen-escape events have traditionally been thought to result in only frequency-dependent selection but here we show that heterozygote advantage is an inevitable consequence of such pathogen evasion. Therefore, the controversy over the relative importance of these two forms of balancing selection is largely a false dichotomy.

The role of infectious disease, inbreeding and mating preferences in maintaining MHC genetic diversity: an experimental test

In house mice, and probably most mammals, major histocompatibility complex (MHC) gene products influence both immune recognition and individual odours in an allele-specific fashion. Although it is generally assumed that some form of pathogen-driven balancing selection is responsible for the unprecedented genetic diversity of MHC genes, the MHC-based mating preferences observed in house mice are sufficient to account for the genetic diversity of MHC genes found in this and other vertebrates. These MHC disassortative mating preferences are completely consistent with the conventional view that pathogen-driven MHC heterozygote advantage operates on MHC genes. This is because such matings preferentially produce MHC-heterozygours progeny, which could enjoy enhanced disease resistance. However, such matings could also function to avoid genome-wide inbreeding. To discriminate between these two hypotheses we measured the fitness consequences of both experimentally manipulated levels of inbreeding and MHC homozygosity and heterozygosity in semi-natural populations of wild-derived house mice. We were able to measure a fitness decline associated with inbreeding, but were unable to detect fitness declines associated with MHC homozygosity. These data suggest that inbreeding avoidance may be the most important function of MHC-based mating preferences and therefore the fundamental selective force diversifying MHC genes in species with such mating patterns. Although controversial, this conclusion is consistent with the majority of the data from the inbreeding and immunological literature.

Human leukocyte antigens and natural selection by malaria

The extraordinary polymorphism of human leukocyte antigens (HLA) poses a question as to how this remarkable diversity arose and is maintained. The explanation that infectious pathogens are largely responsible is theoretically attractive but clear and consistent associations between HLA alleles and major infectious diseases have rarely been identified. Large case-control studies of HLA types in African children with severe malaria indicate that HLA associations with this parasitic infection do exist and it is becoming possible to investigate the underlying mechanisms by identification of peptide epitopes in parasite antigens. Such analysis reveals how the magnitude and detectability of HLA associations may be influenced by numerous genetic and environmental factors. These complex interactions will give rise to variation over time and space in the selective pressures exerted by infectious diseases and this fluctuation may, in itself, contribute to the maintenance of HLA polymorphism.

Natural selection at the class II major histocompatibility complex loci of mammals

The role of natural selection at major histocompatibility complex (MHC) loci was studied by analysis of molecular sequence data from mammalian class II MHC loci. As found previously for the class I MHC molecule and a hypothetical model of the class II molecule, the rate of non-synonymous nucleotide substitution exceeded that of synonymous substitution in the codons encoding the antigen recognition site of polymorphic class II molecules. This pattern is evidence that the polymorphism at these loci is maintained by a form of balancing selection, such as overdominant selection. By contrast, in the case of monomorphic class II loci, no such enhancement of the rate of non-synonymous substitution was observed. Phylogenetic analysis indicates that, in contrast to monomorphic ('non-classical') class I MHC loci, some monomorphic class II loci of mammals are quite ancient. The DMA and DMB loci, for example, diverged before all other known mammalian class II loci, possibly before the divergence of tetrapods from bony fishes. Analysis of the patterns of sharing of polymorphic residues at class II MHC loci by mammals of different species revealed that extensive convergent evolution has occurred at these loci; but no support was found for the hypothesis that MHC polymorphisms have been maintained since before the divergence of orders of eutherian mammals.

Molecular genetics of speciation and human origins

The major histocompatibility complex (MHC) plays a cardinal role in the defense of vertebrates against parasites and other pathogens. In some genes there are extensive and ancient polymorphisms that have passed from ancestral to descendant species and are shared among contemporary species. The polymorphism at the DRB1 locus, represented by 58 known alleles in humans, has existed for at least 30 million years and is shared by humans, apes, and other primates. The coalescence theory of populations genetics leads to the conclusion that the DRB1 polymorphism requires that the population ancestral to modern humans has maintained a mean effective size of 100,000 individuals over the 30-million-year persistence of this polymorphism. We explore the possibility of occasional population bottlenecks and conclude that the ancestral population could not have at any time consisted of fewer than several thousand individuals. The MHC polymorphisms exclude the theory claiming, on the basis of mitochondrial DNA polymorphisms, that a constriction down to one or few women occurred in Africa, at the transition from archaic to anatomically modern humans, some 200,000 years ago. The data are consistent with, but do not provide specific support for, the claim that human populations throughout the World were at that time replaced by populations migrating from Africa. The MHC and other molecular polymorphisms are consistent with a "multiregional" theory of Pleistocene human evolution that proposes regional continuity of human populations since the time of migrations of Homo erectus to the present, with distinctive regional selective pressures and occasional migrations between populations.

Structure, function, and evolution of mouse TL genes, nonclassical class I genes of the major histocompatibility complex

In contrast to well-studied "classical" class I genes of the major histocompatibility complex (MHC), the biology of nonclassical class I genes remains largely unexamined. The mouse TL genes constitute one of the best defined systems among nonclassical class I genes in the T region of the MHC. To elucidate the function and the evolution of TL genes and their relationship to classical class I genes, seven TL DNA sequences, including one from a Japanese wild mouse, were examined and compared with those of several mouse and human classical class I genes. The TL genes differ from either classical class I genes or pseudogenes in the extent and pattern of nucleotide substitutions. Natural selection appears to have operated so as to preserve the function of TL, which might have been acquired in an early stage of its evolution. In a putative peptide-binding region encoded by TL genes, the rate of nonsynonymous (amino acid replacing) substitution is considerably lower than that of synonymous substitution. This conservation is completely opposite that in classical class I genes, in which the peptide-binding region has evolved to diversify amino acid sequences so as to recognize a variety of antigens. Thus, it is suggested that the function of TL antigens is distinct from that of classical class I antigens and is related to the recognition of a relatively restricted repertoire of antigens and their presentation to T-cell receptors.

Notes on individual sequence variation in humans: immunoglobulin kappa light chain

Little is known concerning the magnitude of variability in the nucleic acid sequence of DNA at the individual level. We have collected a large set of sequence data from the human immunoglobulin kappa light-chain-locus constant region (10,444 bp) and subgroup IV variable region (18,580 bp). For the constant region, absolute conservation of sequence was observed, even in intron and coding-region silent sites, with the exception of one previously defined polymorphic site. For the variable region, 12 heterozygous positions were identified, giving a heterozygosity of 6 x 10(-4) per nucleotide site. The amount of nucleic acid sequence variation differs significantly (chi 2 = 4.88) between these two regions, and the observed variation is two orders of magnitude lower than that reported for two Drosophila melanogaster loci. These data suggest that, for at least some regions of the human genome, nucleic acid sequence may be less variable than previously estimated.

Statistical analysis of DNA polymorphism

A large amount of genetic variation can be maintained in natural populations. In order to understand the mechanism maintaining genetic variation, we must first estimate the amount of genetic variation. There are two measures for estimating the amount of DNA polymorphism, i.e., the average number of pairwise nucleotide differences and the number of segregating sites among a sample of DNA sequences. Using these two measures, we can test the neutral mutation-random drift hypothesis (the neutral theory). The expectation of the amount of DNA polymorphism has been studied under several models, including population subdivision, change in population size, and natural selection. When a population is subdivided, a large amount of DNA polymorphism can be maintained in the population if the migration rates among subpopulations are small. In this case the amount of DNA polymorphism in the subpopulation with lower migration rate is expected to be smaller than that of higher migration rate. When the population size changes, the number of segregating sites changes more rapidly than does the average number of nucleotide differences. When purifying selection is operating, the number of segregating sites is more strongly affected by the existence of deleterious mutants than is the average number of nucleotide differences. On the other hand, when balancing selection is operating, the effect of the selection on the average number of nucleotide differences is larger than that on the number of segregating sites. A mutant under natural selection affects the amount of DNA polymorphism at linked sites (hitchhiking effect). DNA sequences are not random sequences and there may be conservative and variable regions in them. A statistical method for determining the window size and for finding nonrandom regions in the sequence is also presented.

Major histocompatibility complex monomorphism and low levels of DNA fingerprinting variability in a reintroduced and rapidly expanding population of beavers

Loss of genetic variation due to population bottlenecks may be a severe threat for the survival of endangered species. Assessment and maintenance of genetic variability are thus crucial for conservation programs related to endangered populations. Scandinavian beavers went through an extensive bottleneck during the last century due to overhunting. In Sweden the species became extirpated but in Norway extinction was avoided by legal protection. Following reintroductions of small numbers of remaining Norwegian animals in 1922-1939, the Swedish population has increased tremendously, now harboring 100,000 animals. We show here that this viable population of beavers possesses extremely low levels of genetic variability at DNA fingerprinting loci and monomorphism at major histocompatibility complex (MHC) class I and class II loci. A similar pattern was also evident among Norwegian beavers but low levels of genetic variability were not a characteristic of the species since Russian conspecifics displayed substantial DNA fingerprinting polymorphism. However, the Russian animals were monomorphic at MHC loci, indicating that the European beaver is exceptional in its low level of MHC variability. The results demonstrate that a conservation program can be successful despite low levels of genetic variation in the founder population.

The HLA polymorphism of two distinctive South-American Indian tribes: the Kaingang and the Guarani

The HLA-A, B, C, DR and DQ antigens of 240 Kaingang and 98 Guarani individuals have been characterized. The most frequent antigens found among the Kaingang are A31, 2, 24; B35, 51, 39, 48; Cw4, 7, 3, 1; DR8, 4, 2; DQ blank, 3. In the Guarani, they are A2, 28, 31; B40, 62, "53G"; Cw3, 4; DR2, 4, 8, 6; DQ3, blank. B " 53G" is an unusual antigen of the B5 cross-reactive group. DQ blank possibly corresponds to DQ4, not tested in this study. The reaction patterns of B35, B40 and DR4 indicate intra-tribal (of B35 and B40), and inter-tribal (DR4, B40 and B35) heterogeneity of these antigens. 408 Kaingang and 141 Guarani haplotypes were defined by segregation analysis. Of the commonest 10 Guarani and 9 Kaingang haplotypes, only one is shared by both tribes. Significant, positive linkage disequilibrium values for HLA-A,B; HLA-A,C; HLA-B,DR and most HLA-B,C antigen pairs were also different for the two populations. Genetic distance estimates between these two and another seven South-American Indian populations, and relative to the major human races (negroids, caucasoids, and mongoloids) reveal a comparatively high degree of divergence between the Kaingang and the Guarani, which is uncommon for Amerindian populations living close one to another.

Contrasting roles of interallelic recombination at the HLA-A and HLA-B loci

A statistical study of DNA sequences of alleles at the highly polymorphic class I MHC loci of humans, HLA-A and HLA-B, showed evidence of both large-scale recombination events (involving recombination of exons 1-2 of one allele with exons 3-8 of another) and small-scale recombination events (involving apparent exchange of short DNA segments). The latter events occurred disproportionately in the region of the gene encoding the antigen recognition site (ARS) of the class I molecule. Furthermore, they involved the ARS codons which are under the strongest selection favoring allelic diversity at the amino acid level. Thus, the frequency of recombinant alleles appears to have been increased by some form of balancing selection (such as overdominant selection) favoring heterozygosity in the ARS. These analyses also revealed a striking difference between the A and B loci. Recombination events appear to have occurred about twice as frequently at the B locus, and recombinants at the B locus were significantly more likely to affect polymorphic sites in the ARS. At the A locus, there are well-defined allelic lineages that have persisted since prior to the human-chimpanzee divergence; but at the B locus, there is no evidence for such long-lasting allelic lineages. Thus, relatively frequent interallelic recombination has apparently been a feature of the long-term evolution of the B locus but not of the A locus.

The prospects for polymorphisms shared between species

Recent molecular evidence has shown that many MHC polymorphisms are not only shared between species but are in fact identical at the molecular level. Species that share these polymorphisms may be very distantly related and often diverged millions of generations ago. It is now known that this phenomenon is very unlikely to occur if the alleles are selectively neutral. A large number of other studies suggest, however, that this phenomenon of shared polymorphisms is very common and extends to many other loci beyond just the MHC/HLA complexes. These studies also suggest that some polymorphisms may be older than the MHC/HLA polymorphisms. The maintenance of these polymorphisms via overdominant and frequency-dependent selection is discussed. Strong levels of selection are required for overdominance to maintain shared polymorphisms but most studies of effective population size produce long-term estimates that are very small and would not permit the level of overdominant selection required to maintain these polymorphisms. Frequency-dependent selection can maintain them for longer with less 'apparent' equilibrium selection and might permit smaller effective sizes. The variance of allele frequencies is suggested to be one way to distinguish between these two selection models.

Gene duplications and sequence polymorphism of bovine class II DQB genes

The genetic diversity of bovine class II DQB genes was investigated by polymerase chain reaction amplification and DNA sequencing. The first domain exon was amplified from genomic DNA samples representing 14 class II haplotypes, defined by restriction fragment length polymorphism (RFLP) analysis. The presence of a polymorphism in the copy number of DQB genes was confirmed since two DQB sequences were isolated from certain haplotypes. Four subtypes of bovine DQB genes were found. DQB1 is the major type and was found in almost all haplotypes. DQB2 is very similar to DQB1 but was found only in the duplicated haplotypes DQ9 to 12. DQB3 and DQB4 are two quite divergent genes only present in certain duplicated haplotypes. The bovine DQB complexity thus resembles that in the human DRB region. Bovine DQB genes were found to be highly polymorphic as ten DQB1 alleles and four DQB2 alleles were identified. The observed sequence polymorphism correlated well with previously defined DQB RFLPs. Bovine and human DQB alleles show striking similarities at the amino acid level. In contrast, the frequency of silent substitutions is much higher in comparisons of DQB alleles between species than within species ruling out the possibility that any of the contemporary DQB alleles have been maintained since the divergence of humans and cattle. The frequency of silent substitutions between DQB alleles was markedly lower in cattle than in humans, in agreement with a previous comparison of human and bovine DRB alleles.