The great human expansion.

Genetic and paleoanthropological evidence is in accord that today's human population is the result of a great demic (demographic and geographic) expansion that began approximately 45,000 to 60,000 y ago in Africa and rapidly resulted in human occupation of almost all of the Earth's habitable regions. Genomic data from contemporary humans suggest that this expansion was accompanied by a continuous loss of genetic diversity, a result of what is called the "serial founder effect." In addition to genomic data, the serial founder effect model is now supported by the genetics of human parasites, morphology, and linguistics. This particular population history gave rise to the two defining features of genetic variation in humans: genomes from the substructured populations of Africa retain an exceptional number of unique variants, and there is a dramatic reduction in genetic diversity within populations living outside of Africa. These two patterns are relevant for medical genetic studies mapping genotypes to phenotypes and for inferring the power of natural selection in human history. It should be appreciated that the initial expansion and subsequent serial founder effect were determined by demographic and sociocultural factors associated with hunter-gatherer populations. How do we reconcile this major demic expansion with the population stability that followed for thousands years until the inventions of agriculture? We review advances in understanding the genetic diversity within Africa and the great human expansion out of Africa and offer hypotheses that can help to establish a more synthetic view of modern human evolution.

Genetic evidence for a higher female migration rate in humans.

Mitochondrial DNA and the Y chromosome have been used extensively in the study of modern human origins and other phylogenetic questions, but not in the context of their sex-specific modes of transmission. mtDNA is transmitted exclusively by females, whereas the Y chromosome is passed only among males. As a result, differences in the reproductive output or migration rate of males and females will influence the geographic patterns and relative level of genetic diversity on the Y chromosome, autosomes and mtDNA (ref. 1). We have found that Y chromosome variants tend to be more localized geographically than those of mtDNA and the autosomes. The fraction of variation within human populations for Y chromosome single nucleotide polymorphisms (SNPs) is 35.5%, versus 80-85% for the autosomes and mtDNA (refs 6-8). A higher female than male migration rate (via patrilocality, the tendency for a wife to move into her husband's natal household) explains most of this discrepancy, because diverse Y chromosomes would enter a population at a lower rate than mtDNA or the autosomes. Polygyny may also contribute, but the reduction of variation within populations that we measure for the Y chromosome, relative to the autosomes and mitochondrial DNA, is of such magnitude that differences in the effective population sizes of the sexes alone are insufficient to produce the observation.

Y chromosome sequence variation and the history of human populations.

Binary polymorphisms associated with the non-recombining region of the human Y chromosome (NRY) preserve the paternal genetic legacy of our species that has persisted to the present, permitting inference of human evolution, population affinity and demographic history. We used denaturing high-performance liquid chromatography (DHPLC; ref. 2) to identify 160 of the 166 bi-allelic and 1 tri-allelic site that formed a parsimonious genealogy of 116 haplotypes, several of which display distinct population affinities based on the analysis of 1062 globally representative individuals. A minority of contemporary East Africans and Khoisan represent the descendants of the most ancestral patrilineages of anatomically modern humans that left Africa between 35,000 and 89,000 years ago.

Demic expansions and human evolution.

Geographic expansions are caused by successful innovations, biological or cultural, that favor local growth and movement. They have had a powerful effect in determining the present patterns of human genetic geography. Modern human populations expanded rapidly across the Earth in the last 100,000 years. At the end of the Paleolithic (10,000 years ago) only a few islands and other areas were unoccupied. The number of inhabitants was then about one thousand times smaller than it is now. Population densities were low throughout the Paleolithic, and random genetic drift was therefore especially effective. Major genetic differences between living human groups must have evolved at that time. Population growths that began afterward, especially with the spread of agriculture, progressively reduced the drift in population and the resulting genetic differentiation. Genetic traces of the expansions that these growths determined are still recognizable.

Theory and observation in cultural transmission.

Cultural phenomena may show considerable stability over time and space. Transmission mechanisms responsible for their maintenance are worthy of theoretical and empirical inquiry; they are complex and each possible pathway has different effects on evolutionary stability of traits, as can be shown theoretically. A survey designed to evaluate the importance of some components of cultural transmission on a variety of traits showed that religion and politics are mostly determined in the family, a mode of transmission which guarantees high evolutionary stability and maintenance of high variation between and within groups.

The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perspective.

A genetic perspective of human history in Europe was derived from 22 binary markers of the nonrecombining Y chromosome (NRY). Ten lineages account for >95% of the 1007 European Y chromosomes studied. Geographic distribution and age estimates of alleles are compatible with two Paleolithic and one Neolithic migratory episode that have contributed to the modern European gene pool. A significant correlation between the NRY haplotype data and principal components based on 95 protein markers was observed, indicating the effectiveness of NRY binary polymorphisms in the characterization of human population composition and history.

The DNA revolution in population genetics.

Unprecedental clarity has come to our understanding of genetic variation by the analysis of DNA sequences. It is not surprising that the new DNA technologies are leading to a resurgence of interest in population genetics. In this review, I discuss recent progress and future directions towards reconstructing the history of human populations. There is increasing consensus on a recent 'Out of Africa' origin of modern humans, which explains why the greatest fraction of genetic diversity is found within populations, rather than between them. The comparison of Y chromosome and mitochondrial DNA data shows remarkable sex differences in geographic variation. The analysis of Neanderthal DNA has been a major breakthrough in the study of fossil DNA. Among major hopes for the future are application to polygenic diseases.

Metabolic studies in the African pygmy.

Major metabolic effects of human growth hormone (HGH) were assessed in the African Babinga pygmy. Plasma free fatty acid (FFA) and glucose concentrations were measured in pygmies, HGH-deficient dwarfs, Bantu tribesmen, and Caucasian controls after each received 4 mg of HGH intravenously over a 20 min period. Pygmies had an early decrease of plasma FFA and glucose concentration, but did not exhibit a later lipolytic response. In neighboring Bantu tribesmen, American controls, and HGH-deficient dwarfs, both the early and late responses to intravenous HGH were present. The failure of plasma FFA concentration to increase in the pygmy after intravenous HGH was not due to a generalized defect in lipolysis since a normal lipolytic response was obtained with epinephrine (2 mug/min for 20 min).Pygmies, like HGH-deficient dwarfs, had significantly reduced insulin responses to both oral glucose and arginine. Insulin secretion was significantly reduced when compared with either Bantu tribesmen or American controls and was not altered by 2 wk of a high carbohydrate/high protein diet. HGH treatment in pygmies (5 mg b.i.d. for 5 days) failed to augment either glucose or arginine-induced insulin secretion. Glucagon consistently caused normal insulin secretion in HGH-deficient dwarfs and was, likewise, effective in each pygmy studied. In two offspring from different pygmy mothers and Bantu fathers, insulin responses to glucose were initially normal and increased in a normal manner after HGH treatment. In previous studies, HGH failed to reduce serum urea nitrogen concentration in pygmies. Sulfation factor was found to be normal. A consideration of the data in toto is consistent with a hypothesis that the metabolic findings in the pygmy may result from partial nonresponsiveness to either HGH or to a factor generated by HGH. This defect is not transmitted as either an autosomal or sex-linked dominant trait.

Susceptibility to multiple sclerosis associated with an immunoglobulin gamma 3 restriction fragment length polymorphism.

Susceptibility to multiple sclerosis (MS) has been linked to the immunoglobulin G (Gm) markers as well as HLA-DR genes. We have used a genomic Ig gamma 1 probe which detects polymorphisms in the gamma 1, gamma 2, gamma 3 and pseudogamma genes to identify restriction fragment length polymorphisms associated with MS. A negative association was found between a 5.9-kilobase (kb) Bst EII gamma 3 fragment and MS. Southern blot analysis of genomic DNA revealed the presence of this fragment in 84 of 140 (60.0%) controls, but in only 17 of 59 (28.8%) MS patients. The frequency of the fragment in 47 myasthenia gravis and 16 Graves' disease patients was similar to that in controls, 60.0 and 62.5%, respectively.

The Evolution of Continuous Variation. III. Joint Transmission of Genotype, Phenotype and Environment.

Evolutionary models of continuous traits are developed. The models are based on the ideas that: (1) the phenotype is the result of the interaction between genotype and environment; (2) the phenotype is the object of natural selection; (3) not only the genotype but also environmental variables and even phenotypes can be directly transmitted. The phenotype of an offspring at birth is a linear combination of its genotypic value, the phenotypic values of its parents, and their environmental values, all measured on the phenotypic scale. The genetic effects are additive polygenic, and a mutation contribution to the within family variance is admitted.-The values of the offspring phenotype and environment before selection are each linear combinations of these values at birth, the coefficients defining what we call "development." Selection is mostly stabilizing of the Gaussian type, but directional selection is introduced using a Gaussian fitness function with a large variance and a mean far from the current population.-Assortative mating for both phenotype and environment are considered. The analysis in all cases is made by iteration of the means, variances and covariances of the trivariate random variable (genotype, phenotype, environment) whose changes over time completely specify the evolution. In most cases numerical methods are used. The problems of estimating the relative roles of each of the variates in the parents in determining the variates in the offspring are discussed. The major results concern the relative magnitudes of the variances and correlations of the three variates, genotype, phenotype and environment, in a variety of selective, developmental and assorting situations with complex transmission in which G-(genetic), F-(phenotypic), E-(environment) inheritance mechanisms operate jointly. The transmission rules and development patterns (i.e., interactions between phenotype and environment during development) are of major importance in determining qualitative features of the equilibrium distribution.

An evaluation of genetic distances for use with microsatellite loci.

Mutations of alleles at microsatellite loci tend to result in alleles with repeat scores similar to those of the alleles from which they were derived. Therefore the difference in repeat score between alleles carries information about the amount of time that has passed since they shared a common ancestral allele. This information is ignored by genetic distances based on the infinite alleles model. Here we develop a genetic distance based on the stepwise mutation model that includes allelic repeat score. We adapt earlier treatments of the stepwise mutation model to show analytically that the expectation of this distance is a linear function of time. We then use computer simulations to evaluate the overall reliability of this distance and to compare it with allele sharing and Nei's distance. We find that no distance is uniformly superior for all purposes, but that for phylogenetic reconstruction of taxa that are sufficiently diverged, our new distance is preferable.

Exclusion of linkage between the serotonin2 receptor and schizophrenia in a large Swedish kindred.

Family, twin, and adoption studies suggest that genetic factors play an important role in the etiology of schizophrenia. Detection of single gene(s) involved in a higher susceptibility to a hereditary disease is possible with linkage analysis. The effects of serotonin2-receptor antagonists on symptoms of schizophrenia suggest that a mutation in the gene coding for this receptor subtype might be involved in the pathophysiology of this disease. Recently a copy DNA encoding the serotonin 5-HT2 receptor has been isolated and with a human 5-HT2 receptor copy DNA probe the HTR2 locus has been mapped to chromosome 13. Using multipoint linkage analysis between schizophrenia and genetic markers spanning the region of the HTR2 locus, we were able to exclude linkage between this candidate gene and schizophrenia in a Swedish kindred. Given this result, we conclude that the serotonin 5-HT2 receptor gene itself is not a major susceptibility gene for schizophrenia in this family.

No linkage between D2 dopamine receptor gene region and schizophrenia.

The dopamine hypothesis is one of the major etiological hypotheses of schizophrenia. The well-established role of genetic factors in schizophrenia together with reports of increased D2 dopamine receptor densities in untreated schizophrenic patients support the D2 dopamine receptor gene as a strong candidate gene for schizophrenia. The recent cloning of the D2 dopamine receptor gene made it possible to test the involvement of the D2 dopamine receptor locus (DRD2) in a large Swedish and a smaller Californian schizophrenia pedigree. Using multipoint linkage analysis between schizophrenia and a genetic map that includes the DRD2 locus and assuming a dominant mode of inheritance, we were able to exclude the DRD2 locus with a lod score of -4.14 for the penetrance of 0.72 and with a lod score of -3.05 for the lower bound penetrance of 0.56. The area of exclusion (lod score, less than -2.00) extended 27 centimorgans. These results provide strong evidence against linkage of the D2 dopamine receptor gene region to schizophrenia in the two pedigrees investigated. We conclude that the genetic predisposition to schizophrenia in these pedigrees is not due to aberrations in the DRD2 locus or the porphobilinogen deaminase locus. Our results do not support the D2 dopamine receptor hypothesis of schizophrenia. However, they cannot exclude the possibility that other genes regulating aspects of D2 dopamine expression might be involved in the etiology of schizophrenia, such as the expression of two D2 dopamine receptor subtypes by alternative RNA splicing.

Autism and the X chromosome. Multipoint sib-pair analysis.

BACKGROUND: Genetic factors undoubtedly play a major etiologic role in autism, but how it is inherited remains unanswered. The increased incidence in males suggests possible involvement of the X chromosome. METHODS: Using data from 38 multiplex families with autism (2 or more autistic siblings), we performed a multipoint sib-pair linkage analysis between autism and 35 microsatellite markers located on the X chromosome. The model included a single parameter, the risk ratio lambda xs (i.e., ratio of risk to siblings compared with the population prevalence), owing to an X-linked gene. Different lambda xs values were assumed and regions of exclusion were established. RESULTS: The entire X chromosome could be excluded for a lambda xs value of 4. The ability to exclude an X-linked gene decreased with smaller lambda xs values, and some positive evidence was obtained with smaller values. A maximum lod score of 1.24 was obtained at locus DXS424 with a lambda xs value of 1.5. CONCLUSIONS: We were able to exclude any moderate to strong gene effect causing autism on the X chromosome. Smaller gene effects (lambda xs < 4) could not be excluded, in particular, a gene of small effect located between DXS453 and DXS1001.

Maori origins, Y-chromosome haplotypes and implications for human history in the Pacific.

An assessment of 28 pertinent binary genetic markers on the non-recombining portion of the Y chromosome (NRY) in New Zealand Maori and other relevant populations has revealed a diverse genetic paternal heritage of extant Maori. A maximum parsimony phylogeny was constructed in which nine of the 25 possible binary haplotypes were observed. Although approximately 40% of the samples have haplotypes of unequivocal European origin, an equivalent number of samples have a single binary haplotype that is also observed in Indonesia and New Guinea, indicative of common indigenous Melanesian ancestry. The balance of the lineages has either typical East Asian signatures or alternative compositions consistent with their affinity to Melanesia or New Guinea. Molecular analysis of mtDNA variation confirms the presence of a single predominant characteristic Southeast Asian (9-bp deletion in the Region V) lineage. The Y-chromosome results support a pattern of complex interrelationships between Southeast Asia, Melanesia, and Polynesia, in contrast to mtDNA and linguistic data, which uphold a rapid and homogeneous Austronesian expansion. The Y-chromosome data highlight a distinctive gender-modulated pattern of differential gene flow in the history of Polynesia.

Insulin-like growth factor secretion by human B-lymphocytes: a comparison of cells from normal and pygmy subjects.

Freshly isolated human B-lymphocytes from eight subjects and Epstein-Barr virus-transformed human B-lymphocytes from seven subjects were examined for their capacity to secrete insulin-like growth factor-I (IGF-I) and IGF-II and for their capacity to respond to human GH. Similar studies were conducted with Epstein-Barr virus-transformed lymphocytes collected from six African pygmies. When transformed B-lymphocytes from normal stature subjects were cultured for 3 weeks in RPMI-1640 medium (6 x 10(3) cells/75-cm2 flask at seeding), significant amounts of IGF-I, but no IGF-II, were produced. GH (150 ng/mL) significantly increased for control cells the amount of IGF-I produced at each sampling interval compared to that by unstimulated cultures (P less than 0.05 at 1 week; P = 0.005 at 3 weeks). At 3 weeks, cell counts of cultures compared were 4.13 +/- 0.39 X 10(6)/mL for unstimulated cells and 4.23 +/- 0.87 X 10(6)/mL for GH-stimulated cells. IGF-I production at this time interval by unstimulated cells was 2.8 +/- 2.3 ng/mL, and that by GH-stimulated cells was 12.3 +/- 2.5 ng/mL (P = 0.005). Cell multiplication rates of control cultures were increased in 1 week by GH stimulation [GH stimulated, [16.7 +/- 22.0 X 10(4) cells, unstimulated, 5.73 +/- 4.1 X 10(4) cells; (mean +/- SD); n = 14; P less than 0.01]. Similar results occurred with GH studied at a lower concentration of 10 ng/mL for 3 weeks. Freshly isolated B-lymphocytes did not secrete IGF-I and II after 5 days of culture with GH. Cultures established from cells derived from pygmies produced significantly less IGF-I (4.24 +/- 2.62 ng/mL) when stimulated with 150 ng/mL GH than cultures of cells from normal stature subjects (12.3 +/- 2.5 ng/mL; 0.005 less than P less than 0.01). The cultures compared had a similar cell density. A similar significant difference in IGF-I secretion occurred between cultures of pygmy and control cells stimulated with 10 ng/mL GH. These data are consistent with previous in vivo studies in which pygmies failed to increase IGF-I and exhibit metabolic responses to exogenous GH.

Human genomic diversity in Europe: a summary of recent research and prospects for the future.

Gene frequencies in Europe are intermediate with respect to those of other continents. A phylogenetic tree reconstructed from 95 gene frequencies tested on 26 European samples shows some deviant populations (Lapps, Sardinians, Greeks, Yugoslavs, Basques, Icelanders and Finns) and other weakly structured populations. This behavior may have a simple interpretation: Europeans have not evolved according to a tree of descent probably because of the major role played by migrations in prehistorical and historical times. The leading component of the European genetic landscape is a gradient that originates in the Middle East and is directed to the northwest. According to the hypothesis by Ammerman and Cavalli-Sforza this gradient was generated by a migration of Neolithic farmers from Anatolia followed by continuous, partial admixture of the expanding farmers with local hunter-gatherers. Other leading components of the gene frequencies in Europe show correlations with possible movements of Uralic-speaking people and pastoral nomads from a region north of the Caucasus and Black Sea, which according to Gimbutas is the area of origin of Indo-European speakers. This analysis is based on classical pre-DNA genetic markers. The prospect of future research using DNA polymorphisms is discussed in the context of the Human Genome Project.

The HLA-A,B gene frequencies in the world: migration or selection?

Multivariate methods make it possible to condense much of the information available for a large number of alleles into one or a few synthetic variables. The geographic distribution of synthetic variables can be analyzed and plotted by the same technique used in analyzing and mapping the gene frequency of a single allele. The information contained in 21 HLA-A and HLA-B alleles from 116 world populations is condensed in principal components and discriminant functions which describe the global variation of gene frequencies along longitudes and along latitudes. Most genetic variation is associated with longitude and shows a center of symmetry in Asia. Thus Asia, or some part of it, may have been the center, both geographically and historically, of late Pleistocene migrations. However, latitude also plays a significant role (perhaps 10% of the genetic variation). A remarkable symmetry of the latitude variation in opposite (north and south) hemispheres suggest that climatic factors exercise selective pressure for certain HLA alleles. More specifically A1, A3, B7, B8, and B27 show about equally high correlation coefficients (between 0.45 and 0.55) with distance from equator. This result supports the idea that the well-known linkage disequilibria between A1 and B8, A3 and B7 are probably kept by selective pressure.

Polymorphic markers of human T-cell receptor alpha and beta genes. Family studies and comparison of frequencies in healthy individuals and patients with multiple sclerosis and myasthenia gravis.

Polymorphic markers for the human T-cell receptor (TcR) genes are described. With a TcR beta-chain probe, polymorphic allelic fragments of 5.4 and 1.8 kb were detected in KpnI digests, and fragments of 12.5 and 11.5 kb were seen in the BglII digests. Polymorphism in alpha chain genes was observed in TaqI-digested DNA samples with bands at 10.2 and 6.2-2.1 kb. Mendelian codominant inheritance for all three polymorphisms was confirmed in family studies. The gene frequencies for these alleles were determined in a sample of 70 normal unrelated Caucasian individuals, and were shown to be in Hardy-Weinberg equilibrium. There were no significant differences in the frequency of these polymorphic alpha and beta alleles between patients with multiple sclerosis and patients with myasthenia gravis as compared to a panel of control healthy individuals.

Genetic factors in canine narcolepsy.

The mating of narcopleptic Doberman pinschers yielded 30 puppies in five litters, all of which developed the disease between 1 and 4 months of age. Pedigrees of the Doberman probands are indicative of an autosomal recessive mode of transmission. An analysis of the pedigree of five affected Labrador retriever littermates suggests a similar mode of transmission. Crosses of affected dogs in two other breeds (miniature poodles and beagles) have resulted in all-unaffected F1 generations, thus allowing rejection of the simplest genetic hypothesis of a fully penetrant autosomal or sex-linked dominant or recessive gene.