 |
||||||||
 |
||||||||
|
||||||||
| Publications in Print | ||||||||
|
Mountain, J.L., Knight, A., Jobin, M., Gignoux, C., Miller, A., Lin, A.A., and Underhill, P.A. (2002) SNPSTRs: Empirically derived, rapidly typed, autosomal haplotypes for inference of population history and mutational processes. Genome Research 12:1766-1772.
Mountain, J.L. Human Evolutionary Genetics. In N. J. Smelser and Paul B. Baltes (editors) 2001 International Encyclopedia of the Social & Behavioral Sciences. Pergamon, Oxford. pp. 6984-6990. www.iesbs.com. Lee, S. S-J., Mountain, J. L., Koenig, B. A. The meanings of "race" in the new genomics: Implications for health disparities research. (2001) Yale Journal of Health Policy and Law I: 33-75. Wiehe, T., Mountain, J.L., Parham, P., and Slatkin, M. Inference of the relative roles of recombination and gene conversion in the generation of HLA class I diversity. (2000), Genetical Research, 75: 61-73. Wagner, T.M., Hirtenlehner, K., Shen, P., Moeslinger, R., Muhr, D., Fleishmann, E., Concin, H., Doeller, W., Haid, A., Lang, A.H., Mayer, P., Petru, E., Ropp, E., Langbauer, G., Kubista, E., Scheiner, O., Underhill, P., Mountain, J., Stierer, M., Zielinski, C., Oefner, P. (1999) Global sequence diversity of BRCA2: analysis of 71 breast cancer families and 95 control individuals of worldwide populations. Human Molecular Genetics, 8:413-423. Rannala, B., and J.L., Mountain. 1997. Detecting immigration by using multilocus genotypes. Proceedings of the National Academy of Sciences USA 94: 9197-9201.
Nielsen, R., Mountain, J.L., Huelsenbeck, J.P. and Slatkin, M. (1998) Maximum likelihood estimation of population divergence times and population phylogenies in models without mutation: applications to human RFLP data. Evolution 52:669-677. Mountain, J.L. (1998) Molecular evolution and modern human origins. Evol. Anthr o. 7:21-37. Mountain, J.L. and Cavalli-Sforza, L.L. (1997) Multilocus genotypes, a tree of individuals, and human evolutionary history. Am. J. Hum. Genet. 61:705-718. Mountain, J.L., Hebert, J.M., Bhattacharyya, S., Underhill, P., Ottolenghi, C., Gadgil, M., Cavalli-Sforza, L.L. (1995) Reply to Govindaraju. Am. J. Hum.Genet., 57:1246-1247. Mountain, J.L., Hebert, J.M., Bhattacharyya, S., Underhill, P., Ottolenghi, C., Gadgil, M., Cavalli-Sforza, L.L. (1995) Demographic history of India and mitochondrial DNA sequence diversity. Am. J. Hum.Genet., 56:979-992. Piazza, A., Rendine, S., Menozzi, P., Mountain, J. and Cavalli-Sforza, L.L. (1995) Genetics and the origin of European languages. Proc. Natl. Acad. Sci., USA, 92:5836-5840. Poloni, E. S., Excoffier, L., Mountain, J. L., Langaney, A., Cavalli-Sforza, L. L. (1995) Nuclear DNA polymorphism in a Mandenka population from Senegal: comparison with eight other human populations. Ann. Hum. Genet., 59: 43-61. Lin, A.A., Hebert, J.M., Mountain, J.L., Cavalli-Sforza, L.L. (1994) Comparison of 79 DNA polymorphisms tested in Australians, Japanese, and Papua New Guineans with those of five other human populations. Gene Geography, 8:191-214. Mountain, J.L. (1994) Inferring human evolutionary history from mitochondrial DNA sequences and nuclear DNA allele frequencies. Ph.D. Thesis, Stanford University. Mountain, J.L. and Cavalli-Sforza, L.L. (1994) Inference of human evolution through cladistic analysis of nuclear DNA restriction polymorphisms. Proc. Natl. Acad.Sci., USA, 91: 6515-6519. Kurth, J.H., Mountain, J.L., Cavalli-Sforza, L.L. (1993). Subclustering of human immunoglobulin k light chain variable region genes. Genomics, 16, 69-77. Mountain, J.L., Lin, A.A., Bowcock, A.M., & Cavalli- Sforza, L.L. (1992). Evolution of modern humans: evidence from nuclear DNA polymorphisms. Phil. Trans. Royal Society, Series B, 337, 159-165. Minch, E., Mountain, J.L., & Cavalli-Sforza, L.L. (1992). Coevolution of genes and languages revisited. Proc. Natl. Acad. Sci., USA, 89, 5620-5624. Mountain, J.L., Wang, W. S.-Y., Du, R., Yuan, Y., & Cavalli-Sforza, L.L. (1992). Congruence of genetic and linguistic evolution in China. J. Chinese Ling., 20, 315-330. Du, R., Yuan, Y., Hwang, J., Mountain, J., & Cavalli- Sforza, L. L. (1992). Chinese surnames and the genetic differences between north and south China. J. Chinese Ling., Monograph no. 5, 1-93. Hallmayer, J., Mountain, J., Ritvo, E., Cavalli-Sforza, L. L., & Ciaranello, R. (1991). A linkage study of familial infantile autism (Abstract). Proceedings of Second World Congress on Psychiatric Genetics, 50-51. Mountain, J.L., & Cavalli-Sforza, L.L. (1991). Relationships among living human populations determined from classical and DNA polymorphisms, in Unity of Evolutionary Biology, College Park, MD: Dioscorides Press, 458-465. Bowcock, A.M., Hebert, J.M., Mountain, J.L., Kidd, J.R., Rogers, J., Kidd, K.K., & Cavalli-Sforza, L.L. (1991). ). Study of an additional 58 DNA markers in five human populations from four continents. Gene Geog., 5, 151-173. Bowcock, A. M., Kidd, J.R., Mountain, J.L., Hebert, J. M., Carotenuto, L., Kidd, K.K., & Cavalli-Sforza, L. L. (1991). ). Drift, admixture, and selection in human evolution: A study with DNA polymorphisms. Proc. Natl. Acad. Sci., USA, 88, 839-843. Cavalli-Sforza, L. L., Piazza, A., Menozzi, P., & Mountain, J. (1988). ). Reconstruction of human evolution: Bringing together genetic, archaeological, and linguistic data. Proc. Natl. Acad. Sci., USA 85, 6002-6006. Updated Nov 2002 Distinguishing recombination and intragenic gene conversion by linkage disequilibrium patterns Thomas Wiehe, Joanna Mountain, Peter Parham* and Montgomery Slatkin Department of Integrative Biology, University of California, Berkeley, California 94720-3140 *Department of Structural Biology, Stanford University, Stanford, CA 94305 Summary Deterministic theory suggests that reciprocal recombination and intragenic, interallelic conversion have different effects on the linkage disequilibrium between a pair of genetic markers. Under a model of reciprocal recombination, the decay rate of linkage disequilibrium depends on the distance between two markers, while under conversion the decay rate is independent of this distance, provided that conversion tracts are short. A population genetic theory locus model provides a function Q of two locus linkage disequilibria. Viewed as a random variable, Q is the basis for a test of the relative impact of conversion and recombination. This test required haplotype frequency data of a sufficiently variable three locus system. One of the yet few available examples are data from the Human Leukocyte Antigen (HLA) class I genes of three Ameridian populaitons. We find that conversion may have played a dominant role in shaping haplotype patterns over short stretches of DNA, whereas reciprocal recombination may have played a greater role over longer stretches of DNA. However, in order to draw firm conclusions more independent data are necessary.
Evolution. 52(3), 1998, pp. 669-677. Maximum-Likelihood Estimation of Population Divergence Times and Population Phylogeny in Models Without Mutation Rasmus Nielsen, Joanna L. Mountain, John P. Huelsenbeck, and Montgomery Slatkin Department of Integrative Biology, University of California, Berkeley, California 94720-3140 Abstract.-- In this paper, we present a method for estimating population divergence times by maximum likelihood in models without mutation. The maximum-likelihood estimator is compared to a commonly applied estimator based on Wright's FST statistic. Simulations suggest that the maximum-likelihood estimator is less biased and has a lower variance than the FST-based estimator. The maximum-likelihood estimator provides a statistical framework for the analysis of population history given genetic data. We demonstrate how maximum-likelihood estimates of the branching pattern of divergence of multiple populations may be obtained. We also describe how the method may be applied to test hypothesis such as whether populations have maintained equal population sizes. We illustrate the method by applying it to two previously published sets of human restriction fragment length polymorphism (RFLP) data. Key words -- FST, maximum likelihood, phylogeny, populations divergence, population history, population size, population subdivision.
Evolutionary Anthropology. 7:21-37 Molecular Evolution and Modern Human Origins Joanna L. Mountain Abstract.-- While molecular evolutionists may be fascinated by the features and history of a particular gene or DNA segment, evolutionary anthropologists are often more interested in the activities and history of groups of people. We may want to know, for instance, when and where humans have migrated, how much exchange between groups has taken place, and how population sized have changes. Population genetic theory provides the hope that through analyses of genetic data we will gain insight into the history of populations. Genetic data from extant human populations are now accruing at a remarkable rate. We might, therefore, expect to have answers in hand. There remains, however, a wide gap between the available theory and data; too often we fail to draw firm conclusions because our interpretation of analytic results required that we make myriad assumptions about our data. In any one instance, these assumptions might include estimated of mutation rate, mutational mechanism, population sizes, the role that natural selection has played, and the rate of migration among groups. Often these assumptions are implicit, invisible to most. How then, are we to make any progress?
Am. J. Hum. Genet. 61:705-718, 1997. Multilocus Genotypes, a Tree of Individuals, and Human Evolutionary History Joanna L. Mountain1 and L. Luca Cavalli-Sforza2 1Department of Integrative Biology, University of California, Berkeley; and 2Department of Genetics, Stanford University, Stanford Summary Our goal is to infer, from human genetic data, general patters as well as details of human evolutionary history. Here we present the results of an analysis of genetic data at the level of the individual. A tree relating 144 individuals from 12 human groups of Africa, Asia, Europe, and Oceania, inferred from an average of 75 DNA polymorphisms/individual, is remarkable in that most individuals cluster with other members of their regional group. In order to interpret this tree, we consider the factors that influence the tree patters, including the number of genetic loci examined, the length of population isolation, the sampling process, and the extent of gene flow among groups. Understanding the impact of these factors enables us to infer details of human evolutionary history that might otherwise remain undetected. Our analyses indicate that some recent ancestor(s) of each of a few of the individuals tested may have immigrated. In general, the populations within regional groups appear to have been isolated from one another for <25,000 years. Regional groups may have been isolated for somewhat longer.
Vol. 94, pp. 9197-9201, August 1997 Genetics Detecting immigration by using multilocus genotypes Bruce Rannala and Joanna L. Mountain Department of Integrative Biology, University of California, Berkeley, California 94720-3140 Abstract.-- Immigration is an important force shaping the social structure, evolution, and genetics of populations. A statistical method is presented that uses multilocus genotypes to identify individuals who are immigrants, or have recent immigrant ancestry. The method is appropriate for use with alloenzymes, micorsatellites, or restriction fragment length polymorphisms (RFLPs) and assumes linkage equilibrium among loci. Potential applications include studies of dispersal among natural populations of animals and plants, human evolutionary studies, and typing zoo animals of unknown origin (for use in captive breeding programs). The method is illustrated by analyzing RFLP genotypes in samples of humans from Australian, Japanese, New Guinean, and Senegalese populations. The test has power to detect immigrant ancestors, for these data, up to two generations in the past even though the overall differentiation of allele frequencies among populations is low.
Am. J. Hum. Genet. 56:979-992, 1995. Demographic History of India and mtDNA-Sequence Diversity Joanna L. Mountain,1 Joan M. Hebert,2 Silanjan Bhattacharyya,2 Peter A. Underhill,1 Chris Ottolenghi,3 Madhav Gadgil,2 L. Luca Cavalli-Sforza1 1Department of Genetics, Stanford University, Stanford; 2Centre for Ecological Sciences, Indian Institute of Science, Bangalore; and 3Villa Saint Michel, Paris Summary The demographic history of India was examined by comparing mtDNA sequences obtained from members of three culturally divergent Indian subpopulations (endogamous caste groups). While an inferred tree revealed some clustering according to caste affiliation, there was no clear separation into three genetically distinct groups along caste lines. Comparison of pairwise nucleotide difference distributions, however, did indicate a difference in growth patterns between two of the castes. The Brahmin population appears to have undergone either a rapid expansion of steady growth. The low-ranking Mukri casts, however, may have either maintained a roughly constant population size of undergone multiple bottlenecks during that period. Comparison of the Indian sequences to those obtained from other populations, using a tree, revealed that the Indian sequences, along with all other non-African samples, form a starlike cluster. This cluster may represent a major expansion, possibly originating in southern Asian, taking place at some point after modern humans initially left Africa.
Vol. 92, pp. 5836-5840, June 1995 Evolution Genetics and the Origin of European Languages Alberto Piazza*, Sabina Rendine*, Eric Minch+ , Paolo Menozzi‡, Joanna Mountain§, and Luigi L. Cavalli-Sforza+ *Dipartmento di Genetica, Biologia e Chimica Medica e Centro Consiglio Nazionale delle Ricerche di Immunogenetica ed Oncologia Sperimentale, Universita di Torino, Italy; ‡Istituto di Ecologia, Univerista di Parma, 43100 Parma, Italy; +Department of Genetics, Stanford University, Stanford, CA, 94305; and §Department of Integrative Biology, University of California at Berkeley, Berkeley, CA 94720. Abstract - A new set of European genetic data has been analyzed to dissect independent patterns of geographic variation. The most important cause of European genetic variation has been confirmed to correspond to the migration of Neolithic farmers from the area of origin of agriculture in the Middle East. The next most important component of genetic variation is apparently associated with a north-south gradient possibly due to adaptation to cold climates but also to the differentiation of the Uralix and the Indo-European language-speaking people; however, the relevant correlations are not significantly different from zero after elimination of the spatial autocorrelation. The third component is highly correlated with the infiltration of the Yamna ("Kurgan") people, who domesticated the horse and who have been claimed to have spread Indo-European languages to Europe; this association, which is statistically significant even when taking spatial autocorrelations into account, does not completely exclude the hypothesis of Indo-European as the language of Neolithic farmers. It is possible that both expansions were responsible for the spread of different subfamilies of Indo-European languages, but our genetic data cannot resolve their relative importance.
Ann. Hum. Genet. (1994) 59, 43-61 Nuclear DNA polymorphisms in a Mandenka population from Senegal: Comparison with eight other human populations E. S. Poloni1, L. Excoffier1, J.L. Mountain2, A. Langaney1, and L.L. Cavalli-Sforza2 1 Laboratoire de Genetique et Biometrie, Department d; Anthropologie et d'Ecologie, Universite de Geneve, 18 route des Acacias, 1227 Carouge/Geneve, Switzerland, and URA 49 C.N.R.S., Musee de l'Homme, 75116 Paris, France 2 Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, U.S.A. SUMMARY A large and ethnically well defined Mandenka sample from Senegal is analyzed for 80 nuclear DNA RFLP's, and compared with eight previously studied human populations. A high level of genetic diversity is found in this sample, comparable to that observed in two African Pygmy samples, but lower than that of a European sample. High population variation is observed for most markers. A neutrality test reveals that the markers used in this study can be considered as neutral. A high correlation is found between genetic and geographic distances (r=0.62), suggesting that geography does also affect long range population genetic relationships and is an important factor behind differentiation among human populations.
Gene Geography 8: 191-214, 1994 Comparison of 79 DNA polymorphisms tested in Australians, Japanese and Paupa New Guineans with those of five other human populations A. A. Lin, J.M. Herbert, J. L. Mountain, L.L. Cavalli-Sforza Department of Genetics, Stanford University, Stanford, California 94309 SUMMARY Seventy-nine DNA polymorphisms from 57 loci (28 genes and 29 anonymous DNA segments) have been typed in eight human populations. Here we present allele frequencies for three populations (Japanese, New Guineans, and Australians) as well as revised frequencies for a Chinese sample: allele frequencies for five additional populations (Biaka and Mbuti Pygmies, Melanesians, Chinese, and Europeans) were described previously [Bowcock et al 1991a]. Evaluation of Hardy-Weinberg equilibrium for these polymorphisms suggested that the New Guinean sample may be from a highly substructured population. Average FST value for the 79 markers 9polymorphisms0 was 0.147 + 0.011 across the eight populations: FST values for some markers changed dramatically with the addition of three populations - in particular, Australians and New Guineans. Average heterozygosity for the eight populations was 0.307 + 0.014. Genetic distances indicated that the Australian sample may have some European ancestry. An average linkage tree inferred from these distances suggested that the first split of modern humans was between Africans and non-Africans, while the second major split was between Australians/ New Guineans and all other non-Africans. The neighbor - joining tress also separated the African populations from all others. European polymorphism ascertainment bias and European admixture appear to have influenced both estimation of population heterozygosity and tree inference.
Vol. 91, pp. 6515-6519, July 1994 Evolution Inference of human evolution through cladistic analysis of nuclear DNA restriction polymorphisms J. L. Mountain and L. L. Cavalli-Sforza Department of Genetics, Stanford University Medical Center, Stanford, CA 94305-5120 Abstract - Testing of nuclear DNA polymorphisms in human populations has been extended to closely related primates. for many polymorphisms, one allele is shared by two or more species: such shared alleles are likely to be ancestral and provide insight not only into the relationships among the primates but also into the evolutionary history of modern humans. Humans from among eight worldwide populations share an allele with chimpanzees for 62 out of 70 polymorphisms examined. Frequencies of these ancestral alleles strengthen the conclusion that the earliest major separation of modern humans was between Africans and non-Africans. The average time since mutation of the ancestral alleles producing the current set of polymorphisms is estimated to be 700,000 years. While differences among ancestral allele frequencies in human populations suggest that natural selection may have played a role in the evolution of a subset of these polymorphisms, simulations indicate that a European bias in the ascertainment of polymorphisms may be at least partially responsible for observed differences. Simulation also suggest that observed heterozygosity levels in African populations, for classical polymorphisms, are artificially low due to the same bias. Observed patterns of mean heterozygosity and mean ancestral allele frequency provide support for the hypothesis that Europeans and northeast Asians are closely related. This work suggests that polymorphisms should be selected by testing a random sample of extant humans.
Subclustering of Human Immunoglobulin Kappa Light Chain Variable Region Genes J. H. Kurth. J. L. Mountain, and L. L. Cavalli-Sforza Department of Genetics, Stanford University, Stanford, California 94305 The human immunoglobulin kappa light chain (IgK) locus includes multiple variable region gene segments (Vk) that can be divided into four subgroups. Oligonucleotide primers were designed to amplify specifically gene segments of the VkI, VkII, and VkIII subgroups using the polymerase chain reaction (PCR). Product sequences were subcloned, sequenced, and compared. Phylogenetic analysis of sequences within each subgroup indicate that some subgroups can be subdivided further into "sub-subgroups." The history of Vk segment duplications apparently includes at least two separate periods, the first giving rise to the subgroups and the second generating further complexity within each subgroup. Duplications of large pieces of DNA (demonstrated by others through pulsed-field gel electrophoresis) also played a role. Rates of synonymous and nonsynonymous base changes between pairs of sequences suggest that natural selection has played a major role in the evolution of the Vk variable gene segments, leading to sequence conservation in some regions and to increased diversity in others.
Phil. Trans. R. Soc. Lond. B (1992) 337, 159-165 Evolution of modern humans: evidence from nuclear DNA polymorphisms Joanna L. Mountain,1 Alice A. Lin,2 Anne M. Bowcock2 and L. Luca Cavalli-Sforza1 1 Department of Genetics, Stanford University, Stanford, California 94305, U. S. A. 2 Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas 75235, U.S.A. SUMMARY Previously we have describes the evolution of modern humans based upon data for classical genetic markers and for nuclear DNA polymorphisms. Such polymorphisms provide a different point of view regarding human evolution than do mitochondrial DNA sequences. Here we compare revised dates for major migrations of anatomically modern humans, estimated from archaeological data, with separations suggested by a genetic tree constructed from classical marker allele frequencies. Analysis of DNA polymorphisms have now been extended and compared with those of classical markers; genetic trees continue to support the hypothesis of an initial African and non-African divergence for modern humans. We have also begun testing non-human primates for a set of human DNA polymorphisms. for most polymorphisms tested so far, humans share a single allele with other primates; such shared alleles are likely to ancestral. Populations living in humid tropical environments have significantly higher frequencies of ancestral alleles than do other populations, supporting the hypothesis that natural selection acts to maintain high frequencies of particular alleles in some environments.
Vol. 89, pp. 5620-5624, June 1992 Evolution Coevolution of genes and languages revisited L.L. Cavalli-Sforza, Eric Minch, and J. L. Mountain Department of Genetics, Stanford University, Stanford, CA 94305 Abstract In an earlier paper it was shown that linguistic families of languages spoken by a set of 38 populations associate rather strongly with an evolutionary tree of the same populations derived from genetic data. While the correlation was clearly high, there was no evaluation of statistical significance; no such test was available at the time. This gap has now been filled by adapting to this aim a procedure based on the consistency index, and the level of significance is found to be much stronger that 10-3. Possible reasons for coevolution of strictly genetic characters and the strictly cultural linguistic system are discussed briefly. Results of this global analysis are compared with those obtained in independent local analysis.
Journal of Chinese Linguistics, 20 (2) Congruence of Genetic and Linguistic Evolution in China Joanna L. Mountain1, William S-Y. Wang2, Du Ruofu3, L. Luca Cavalli-Sforza1 1Stanford University, 2University of California at Berkeley, 3Institute of Genetics, Beijing ABSTRACT We have studies the pattern of similarities among Chinese dialects, analysing lexical and phonological information using two different tree methods (average linkage and neighbor-joining). Agreement between the two methods was better than lexical, or lexical plus phonological data were used. This implies that lexical changes occur at a more regular rate than phonological changes. The pattern of linguistic similarity was compared with the genetic one, as exemplified by the study of surnames in a recent monograph (DU et al. in press). Surname distances are highly correlated with genetic distances, and, like them, reflect migrational history. We found a statistically significant correlation between linguistic distance and surname distance. Both languages and surnames are less correlated with geography or with history, namely chronological information of the major episodes of conquest and settlement in China during the last 3000 years. The observed conguence of genetic and linguistic evolution is a consequence of the similarity of their mechanisms of transmission. Under certain conditions languages are transmitted vertically (from parents to children), as are genes or surnames. Other mechanisms (horizontal or oblique) may also be involved in the case of languages and, to a lesser extent, of surnames; these mechanisms would tend to obscure the correlation.
Journal of Chinese Linguistics Monograph Series Number 5 1992 Chinese Surnames and the Genetic Differences between North and South China Ruofu Du, Yida Yuan, Juliana Hwang, Joanna Mountain, L. Luca Cavalli-Sforza INTRODUCTION Analysis of surnames for genetic purposes has been suggested (1) and widely used (2) as a shortcut for estimating the frequency of cousins, and hence for evaluating the inbreeding coefficients of populations. Surname frequencies have been employed, in lieu of gene frequencies, as a source of information for the study of isolation by distance (3). Our interest here is slightly different, motivated in part by a series of earlier investigations (4,5,6,7,8,9,10) in which the distribution of surnames in a population was equated to that of alleles at a locus. In this respect, surnames offer a very rich source of information that can be tapped to answer specific problems of genetic population structure. In the great majority of populations surnames are transmitted via the male line. Transmission is almost like that of Y-chromosome genes except that surnames are also passed to females, who usually maintain that surname at least until they are married. A notable exception in the Western world is the Icelandic population, which maintains the custom formerly prevalent not only among Scandinavian but also among Celtic populations: the surname is derived from the first name of the father and therefore changes at every generation. In societies where clan names are used, the names are usually transmitted patrilinearly and are therefore essentially equivalent to surnames. There is considerable global variation in the time of first use of surnames. In most of Europe the use of modern surnames began during the late Middle Ages and spread to the whole population by the beginning of the Renaissance. In Japan they were not used until the last century. In China they are probably over 4000 years old, as will be indicated in more detail in section 2. This is the earliest known use of surnames. In this paper we analyze surnames obtained from the stratified random sample sovereign a 1/2000 fraction of the whole Chinese population as censured by the Government of the People's Republic of China in 1982. The sampling units were entire "administrative villages" of parts of cities ("resident' committees"). We pay special attention to the distribution of surnames thus sampled, its interpretation as that of selectively neutral alleles at a single haploid locus under uniparental transmission, and the use of the parameter estimated obtained from this distribution for the analysis of genetic population structure. We compare the distribution with that obtained from genetic data. A related paper, "Congruence between Genetic and Linguistic Evolution in China," had appeared in the Journal of Chinese Linguistics. The article addresses implications of the analysis of Chinese surnames for the study of Chinese linguistics. The main conclusion of the comparison with linguistics is that there is a highly significant statistically correlation between linguistic and surname distances. This correlation probably arose because both linguistic and surname distances reflect migration patterns. Although too few genetic data were available for comparison with linguistic data, they are expected to correlate highly with surname data due to parallels in transmission of genes and surnames. A second major conclusion is that Chinese surnames and language data are more correlated with each other than they are with either geographical or historical information.
College Park, MD: Dioscorides Press, 458-465. Relationships Among Living Human Populations Determined from Classical and DNA Polymorphisms J. L. Mountain and L. L. Cavalli-Sforza Department of Genetics, Stanford University, Stanford, CA 94305, USA. Abstract Frequencies of 120 classical genetic markers (44 loci, including blood groups, and protein and enzyme polymorphisms) in 42 human populations were analyzed previously; the resulting genetic tree correlated well with archaeological and linguistic data. More recently, 99 DNA polymorphisms, primarily restriction fragment polymorphisms (RFLPs) and one polymerase chain reaction (PCRP), have been studied for five populations. While the number of populations included to date is limited, the number of loci is large enough to ensure that the behavior of single genes does not adversely influence the results. The maximum likelihood genetic tree generated from these data supports the hypothesis of an initial African/non African split. This maximum likelihood model had been extended to incorporate admixture, and the hypothesis of a European admixture evaluated.
Gene Geography 5: 151-173, 1991 Study of an additionally 58 DNA markers in five human populations from four continents A. M. Bowcocka, J. M. Heberta, J. L. Mountaina, J. R. Kiddb, J. Rogersb, K.K. Kiddb, L.L. Cavalli-Sforzaa. a Department of Genetics, Stanford University, Stanford, U.S.A. b Department of Human Genetics, Yale University School of Medicine, New Haven, U.S.A. SUMMARY One hundred DNA polymorphisms from 73 loci (42 genes and 31 anonymous DNA segments) were investigated in five populations (Baika and Mbuti Pygmies, Melanesians, Chinese and Caucasoids). Data for 47 polymorphisms, including 42 of those discussed here, were described previously [Bowcock et al 1987]. Here we report statistical quantities of genetic importance for each gene and population. The average FST for the 100 markers is 0.137 and the average heterozygosity in 0.325. When known genes and anonymous segments are compared there is no difference in the average FST values or in the average heterozygosities.
Vol. 88, pp.839-843, February 1991 Evolution Drift, admixture, and selection in human evolution: A study with DNA polymorphisms Anne M. Bowcock1, Judith R Kidd2, Joanna L. Mountain1, Joan M. Hebert1, Luciano Carotenuto3, Denneth K. Kidd2, and L. Luca Cavalli-Sforza1 1 Department of Genetic, Stanford University, Stanford, CA 94305 2 Department of Human Genetics, Yale University, New Haven, CT 06510 3 Dipartmento di Sistemi, Universita della Calabria, 87036 Arcacacata, Cosenza, Italy Abstract - Accuracy of evolutionary analysis of populations within a species requires the testing of a large number of genetic polymorphisms belonging to many loci. We report here a reconstruction of human differentiation based on 100 DNA polymorphisms tested in five populations from four continents. The results agree with earlier conclusions based on other classes of genetic markers but reveal that Europeans do not fit a simple model of independently evolving populations with equal evolutionary rates. Evolutionary models involving early admixture are compatible with the data. Taking one such model into account, we examined through simulation whether random genetic drift alone might explain the variation among gene frequencies across populations and genes. A measure of variation among populations was calculated for each polymorphism, and its distribution for the 100 polymorphisms was compared with that expected for a drift-only hypothesis. At least two-thirds of the polymorphisms appear to be selectively neutral, but there are significant deviations at the two ends of the observed distribution of the measure of variation: a slight excess of polymorphisms with low variation and a greater excess with high variation. This indicated that a few DNA polymorphisms are affected by natural selection, rarely heterozygotic, and more often disruptive, while most are selectively neutral.
Vol. 85, pp. 6002-6006, August 1998 Evolution Reconstruction of human evolution: Bringing together genetic archaeological and linguistic data Luigi Luca Cavalli-Sforza1, Alberto Piazza2, Paolo Menozzi3, and Joanna Moutian1 1 Department of Genetics, Stanford University, Stanford, CA 94305 2 Institute of Medical Genetics, University of Torino, Torino 10126, Italy 3 Institure of Ecology, University of Parma, Parma 4311, Italy Abstract - The genetic information for this work came from a very large collection of gene frequencies for "classical" (non-DNA) polymorphisms of the world aborigines. The data were grouped in 42 populations studies for 120 alleles. the reconstruction of human evolutionary history thus generated was checked with statistical techniques such as "bootstrapping". It changes some earlier conclusion and is in agreement with more recent ones, including published and unpublished DNA-marker results. The first split in the phylogenetic tree separates Africans from non-Africans, and the second separates two major clusters, one corresponding to Caucasoids, East Asians, Arctic populations, and American natives, and the other to Southeast Asians (mainland and insular), Pacific islanders, and New Guineans and Australians. Average genetic distances between the most important clusters are proportional to archaeological separation times. Linguistic families correspond to groups of populations with very few, easily understood overlaps, and their origin can be given a time frame. Linguistic superfamilies show remarkable correspondence with the two major clusters, indicating considerable parallelism between genetic and linguistic evolution. Th latest stop in language development may have been an important factor determining the rapid expansion that followed the appearance of modern humans and the demise of Neanderthals.
Gene Geography 11:15-35, 1997. Seventy-five nuclear DNA polymorphisms in an Italian sample: A comparative worldwide study B. Matulloa, R. M. Griffoa, J. L. Mountainb, F. Calafellc, S. Guarreraa, A. Piazzaa, L. L. Cavalli-Sforzab a Department of Genetica, Biologia e Biochimica, Universita di Torino, Italia. b Department of Genetics, Stanford University, Stanford, CA, USA. c Unitat d'Anthropologia, Facultat de Biologia, Universitat de Barcelona, Spain. SUMMARY A well defined Italian sample from Trino Vercellese (Northern Italy) is analyzed for 75 nuclear DNA RFLPs. It represents the only European sample [Matullo et al 1994] which is unmixed in a comparative study of eight populations from four continents [Bowcock et al 1991a; Lin et al 1994]. Genetic substructure of this sample has been investigated by allele sharing distances and no bias or higher homogeneity is shown. Genetic variability between populations was measured by the FST statistics (average FST was 0.312 + 0.069). Average heterozygosity for eight populations was 0.312 + 0.069. Genetic distances were evaluated between pairs of populations. Phylogenetic trees were reconstructed and principal component analysis performed. Particular attention has been given to the genetic relationship between our sample and the mixed-Caucasoid sample: 14 out of 75 markers show statistically significant frequency differences (P<0.05), 5 of which are significant at a probability level <1%: GH/Bg1II (Lower system), D7S1/HindIII, D17S71/MspI, EPB3/PstI, HLA-DQA. Hypothesis on admixed origin of Europeans has been discussed.
Gene Geography 8: 25-34. 1994 RFLP analysis on a sample from Northern Italy G. Matulloa, R. M. Griffoa, J. L. Mountainb, A. Piazzaa, L. L. Cavalli-Sforzab a Dipartmento do Genetica, Biologia e Chimica Medica, Universita di Torino b Department of Genetics, Stanford University, Stanford, CA, USA SUMMARY We analyzed a sample of 55 unrelated individuals from Trino Vercellese, a village in northern Italy. It represents the only European sample which is unmixed in a comparative study of eight populations from four continents [Bowcock et al 1991a; Lin et al 1994]. RFLP analysis was performed on 32 DNA markers, for a total of 37 independent alleles. Genetic variability between populations was measured by the FST statistics 9average FST is 0.138). Average heterozygosity was calculated for each marker and for each population. Genetic distances were evaluated between pairs of populations. Phylogenetic Trees were reconstructed and principal component analysis performed.
|
||||||||
Design by Adam Miller.