Beyond Serial Founder Effects: The Impact of Admixture and Localized Gene Flow on Patterns of Regional Genetic Diversity

Objectives. Geneticists have argued that the linear decay in within-population genetic diversity with increasing geographic distance from East Africa is best explained by a phylogenetic process of founder effects, growth, and isolation termed serial founder effects (SFE). However, the SFE process has not yet been adequately vetted against other evolutionary processes that may also affect geospatial patterns of diversity. Additionally, studies of SFE have been largely based on a limited 52 population sample from the HGDP-CEPH. Here, we assess the effects of SFE, admixture, and localized gene flow processes on patterns of global and regional diversity using a published dataset consisting of 645 autosomal microsatellite genotypes from 5,415 individuals in 248 widespread populations. Materials and Methods. Because SFE is a phylogenetic process, we used a formal tree-fitting approach to explore the role of the process in shaping patterns of global and regional diversity. The approach involved fitting global and regional population trees to extant patterns of gene diversity and then systematically examining the deviations in fit. We also informally tested the SFE process using linear models of gene diversity vs. waypoint geographic distances from Africa. Because gene flow and phylogenetic processes can both shape geospatial patterns of diversity, we tested the role of localized gene flow using partial Mantel correlograms of gene diversity vs. geographic distance controlling for the confounding effects of tree-like genetic structure. Results. We corroborate previous findings that global patterns of diversity, both within and between populations, are the product of an out-of-Africa SFE process. Within regions, however, diversity within populations is uncorrelated with geographic distance from Africa. Instead, deviations in the fit of regional population trees are largely the product of recent inter-regional admixture. Additionally, in several regions, we found that positive correlations between pairwise gene diversity and geographic distance, frequently attributed to localized gene flow, were instead the product of phylogenetic processes associated with initial peopling or subsequent range expansions. Conclusions. Detailed analyses of the pattern of diversity within and between populations reveal that the signatures of different evolutionary processes dominate at different geographic scales. These findings have important implications for recent publications on the biology of race

The birth of NASA: The diary of T. Keith Glennan

In this book, part diary and recollection, T. Keith Glennan--the first administrator of NASA--relates the story of how he and others both inside and outside of the agency worked within the circumstances created by the Sputnik crisis to plan and organize a viable space program that ultimately put 12 Americans on the Moon. In the process, Glennan also reveals a great deal about Eisenhower as a human

A formal test of linguistic and genetic coevolution in native Central and South America

This paper investigates a mechanism of linguistic and genetic coevolution in Native Central and South America. This mechanism proposes that a process of population fissions, expansions into new territories, and isolation of ancestral and descendant groups will produce congruent language and gene trees. To evaluate this population fissions mechanism, we collected published mtDNA sequences for 1,381 individuals from 17 Native Central and South American populations. We then tested the hypothesis that three well-known language classifications also represented the genetic structure of these populations. We rejected the hypothesis for each language classification. Our tests revealed linguistic and genetic correspondence in several shallow branches common to each classification, but no linguistic and genetic correspondence in the deeper branches contained in two of the language classifications. We discuss the possible causes for the lack of congruence between linguistic and genetic structure in the region, and describe alternative mechanisms of linguistic and genetic correspondence and their predictions. Am J Phys Anthropol, 2007. © 2007 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/55923/1/20542_ftp.pd

Social Identity in New Mexicans of Spanish-Speaking Descent Highlights Limitations of Using Standardized Ethnic Terminology in Research

In this study, we evaluated the extent to which regional history has shaped the social identity nomenclature in New Mexicans of Spanish-speaking descent (NMSD). We asked 507 NMSD to list the social-identity terms they used to describe themselves and their parents, and we examined the correspondence between these choices and family ties to the region, birthplace, and continental ancestry. NMSD frequently identified using the regional terms “Nuevomexicano/a” (15%) and “Spanish” (12%). These individuals reported family ties to the region that predate New Mexican statehood. They and their parents were frequently born in New Mexico, frequently chose the other of the two terms as a secondary descriptor, and frequently ascribed one of the two terms to their parents. About 10% of NMSD identified as “Mexican American” and “Mexican.” About 25% of these individuals, and more than half of their parents, were born in Mexico. They also frequently chose the other of the two terms as a secondary descriptor and frequently ascribed one of the two terms to their parents. Compared to NMSD who identified as “Mexican” and “Mexican American,” individuals who identified as “Nuevomexicano/a” and “Spanish” had higher European ancestry and lower Native American and African ancestry. Our results also suggest that the term “Hispanic,” frequently chosen as both a primary and secondary social identity term by NMSD, may, as it continues to rise in prominence, mask more deeply rooted and potential socially relevant aspects of social identity in New Mexico. More broadly, these results indicate that regional history influences social identity nomenclatures in ways that are potentially incompatible with US Office of Management and Budget standards. This incompatibility may adversely affect the ability of researchers in the social sciences to assess the causes of social inequality and health disparities in individuals of Spanish-speaking descent in different regions of the United States. We argue that future studies would benefit from more fine-grained, region-specific analyses of social identity

Identifying artificially deformed crania

In this paper we report on a new discriminant function for the identification of artificially deformed crania. Development of the function, based on a sample of deformed and undeformed crania from the Philippines, required visual classification of the sample into deformed and undeformed groups. Working from the observation that deformed crania display flattened frontal and occipital regions, the sample was seriated based on degree of flattening; classification was based on the results of this seriation. The discriminant function, calculated using curvature indices, required only six simple measurements: arc and chord measurements for the frontal (glabella to bregma), parietals (bregma to lambda) and occipital (lambda to opisthion). The function was designed to be conservative, in that a deformed cranium may be classified as undeformed, but the opposite should not occur. Our function classified the undeformed crania with 100% accuracy and deformed crania with 76.9% accuracy, for a total of 91.9% agreement with visual classification. In order to evaluate whether the function is applicable for samples from outside the Philippines, a double blind test was conducted with a large sample of deformed and undeformed crania from a broad geographical and temporal range. For this sample, the function agreed with visual classification in 89.7% of cases; 98.8% of undeformed crania were correctly classified, while deformed crania were identified with 73.7% accuracy. These results demonstrate the utility of the new discriminant function for the classification of artificially deformed crania from diverse contexts. Copyright © 2007 John Wiley & Sons, Ltd.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/57385/1/910_ftp.pd

Genetic and Linguistic Coevolution in Northern Island Melanesia

Recent studies have detailed a remarkable degree of genetic and linguistic diversity in Northern Island Melanesia. Here we utilize that diversity to examine two models of genetic and linguistic coevolution. The first model predicts that genetic and linguistic correspondences formed following population splits and isolation at the time of early range expansions into the region. The second is analogous to the genetic model of isolation by distance, and it predicts that genetic and linguistic correspondences formed through continuing genetic and linguistic exchange between neighboring populations. We tested the predictions of the two models by comparing observed and simulated patterns of genetic variation, genetic and linguistic trees, and matrices of genetic, linguistic, and geographic distances. The data consist of 751 autosomal microsatellites and 108 structural linguistic features collected from 33 Northern Island Melanesian populations. The results of the tests indicate that linguistic and genetic exchange have erased any evidence of a splitting and isolation process that might have occurred early in the settlement history of the region. The correlation patterns are also inconsistent with the predictions of the isolation by distance coevolutionary process in the larger Northern Island Melanesian region, but there is strong evidence for the process in the rugged interior of the largest island in the region (New Britain). There we found some of the strongest recorded correlations between genetic, linguistic, and geographic distances. We also found that, throughout the region, linguistic features have generally been less likely to diffuse across population boundaries than genes. The results from our study, based on exceptionally fine-grained data, show that local genetic and linguistic exchange are likely to obscure evidence of the early history of a region, and that language barriers do not particularly hinder genetic exchange. In contrast, global patterns may emphasize more ancient demographic events, including population splits associated with the early colonization of major world regions

Brief communication Social and clinical predictors of drug-resistant tuberculosis in a public hospital, Monterrey, Mexico

a b s t r a c t Purpose: Drug-resistant tuberculosis (DRTB) is steadily increasing in Mexico, but little is known of patient risk factors in the MexicoeUnited States border region. This preliminary case-control study included 95 patients with active pulmonary TB with drug susceptibility results attending the José E. González University Hospital in the urban hub of Nuevo Leóndthe Monterrey Metropolitan Area. We report potential social and clinical risk factors of DRTB among this hospital-based sample. Methods: We collected data through face-to-face interviews and medical record reviews from 25 cases with DRTB and 70 drug-sensitive controls. DNA was collected to assess an effect of genetic ancestry on DRTB by using a panel of 291,917 genomic markers. We calculated crude and multivariate logistic regression. Results: After adjusting for potential confounding factors, we found that prior TB treatment (odds ratio, 4.5; 95% confidence interval, 0.9e21.1) and use of crack cocaine (odds ratio, 4.6; 95% confidence interval, 1.1e18.7) were associated with DRTB. No other variables, including genetic ancestry and comorbidities, were predictive. Conclusions: Health care providers may benefit from recognizing predictors of DRTB in regions where routine drug susceptibility testing is limited. Prior TB treatment and illicit drug use, specifically crack cocaine, may be important risk factors for DRTB in this region

Does Lateral Transmission Obscure Inheritance in Hunter-Gatherer Languages?

In recent years, linguists have begun to increasingly rely on quantitative phylogenetic approaches to examine language evolution. Some linguists have questioned the suitability of phylogenetic approaches on the grounds that linguistic evolution is largely reticulate due to extensive lateral transmission, or borrowing, among languages. The problem may be particularly pronounced in hunter-gatherer languages, where the conventional wisdom among many linguists is that lexical borrowing rates are so high that tree building approaches cannot provide meaningful insights into evolutionary processes. However, this claim has never been systematically evaluated, in large part because suitable data were unavailable. In addition, little is known about the subsistence, demographic, ecological, and social factors that might mediate variation in rates of borrowing among languages. Here, we evaluate these claims with a large sample of hunter-gatherer languages from three regions around the world. In this study, a list of 204 basic vocabulary items was collected for 122 hunter-gatherer and small-scale cultivator languages from three ecologically diverse case study areas: northern Australia, northwest Amazonia, and California and the Great Basin. Words were rigorously coded for etymological (inheritance) status, and loan rates were calculated. Loan rate variability was examined with respect to language area, subsistence mode, and population size, density, and mobility; these results were then compared to the sample of 41 primarily agriculturalist languages in [1]. Though loan levels varied both within and among regions, they were generally low in all regions (mean 5.06%, median 2.49%, and SD 7.56), despite substantial demographic, ecological, and social variation. Amazonian levels were uniformly very low, with no language exhibiting more than 4%. Rates were low but more variable in the other two study regions, in part because of several outlier languages where rates of borrowing were especially high. High mobility, prestige asymmetries, and language shift may contribute to the high rates in these outliers. No support was found for claims that hunter-gatherer languages borrow more than agriculturalist languages. These results debunk the myth of high borrowing in hunter-gatherer languages and suggest that the evolution of these languages is governed by the same type of rules as those operating in large-scale agriculturalist speech communities. The results also show that local factors are likely to be more critical than general processes in determining high (or low) loan rates

The anthropological utility of genetic data in small -scale populations: Migration rates and patterns among the Yanomamo.

Anthropological questions are difficult to address using conventional population genetic approaches. In this thesis, I illustrate this problem using F statistics to estimate migration rates and patterns among the Yanomamo, an indigenous South America population. I show that Fst fails to produce meaningful estimates of migration parameters because this statistic fails to consider the complex ways that individual and group-level human behaviors affect genetic diversity. Given this problem, I utilize three alternative non-conventional methods to estimate migration parameters from genetic and related data. The first two, one pedigree-based and the other multilocus genetic, are relatively insensitive to the effects of human behavior. They produce migration rate estimates between 3--29% per generation and indicate that both males and females move frequently between villages. However, both methods still ignore important aspects of behavior and produce only short-term estimates of migration. I therefore develop a third, computer simulation method that is capable of incorporating unlimited behavioral complexity at any time depth. I implement this approach by simulating, over multiple generations, the effects of fixed demographic and varying reproductive behavior on the estimation of male and female migration rates. I show that, for ethnographically documented demographic conditions, and for the observed pattern of genetic variation, migration rate estimates increase as a function of increased variance in reproductive success for both males and females. Depending on the degree of reproductive variance, I estimate migration rates between 0.3--37% per generation. I show that it is impossible to determine whether male or female migration is higher unless the degree of reproductive variance is known. This thesis thus demonstrates that human behaviors affect genetic variation in important ways. Because it incorporates realistic behavioral complexity over any time depth, I conclude that the simulation approach is optimal for measuring migration rates and patterns from genetic data. Though different behaviors may be important at other levels of population structure, I argue that this conclusion holds for any parameter measured from genetic data at any level of population structure.Ph.D.Physical anthropologySocial SciencesUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/132089/2/3057969.pd