The global pattern of gene identity variation reveals a history of long-range migrations, bottlenecks, and local mate exchange: Implications for biological race

Several recent studies have argued that human genetic variation conforms to a model of isolation by distance, whereas others see a predominant role for long-range migrations and bottlenecks. It is unclear whether either of these views fully describes the global pattern of human genetic variation. In this article, we use a coalescent-based simulation approach to compare the pattern of neutral genetic variation predicted by these views to the observed pattern estimated from neutral autosomal microsatellites assayed in 1,032 individuals from 53 globally-distributed populations. We find that neither view predicts every aspect of the observed pattern of variation on its own, but that a combination of the two does. Specifically, we demonstrate that the observed pattern of global gene identity variation is consistent with a history of serial population fissions, bottlenecks and long-range migrations associated with the peopling of major geographic regions, and gene flow between local populations. This history has produced a nested pattern of genetic structure that is inconsistent with the existence of independently evolving biological races. We consider the implications of our findings for methods that apportion variation into within- and between-group components and for medical genetics. Am J Phys Anthropol 2009. © 2009 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62159/1/20932_ftp.pd

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

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

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

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

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 repeated founder effects, growth, and isolation. However, this serial founder effect (SFE) process has not yet been adequately vetted against other evolutionary processes that may also affect geospatial patterns of diversity. Additionally, studies of the SFE process have been largely based on a limited 52-population sample. In this modestly updated article, originally published in Human Biology in 2016 (vol. 88, no. 3, pp. 219–231), we assess the effects of founder effect, admixture, and localized gene flow processes on patterns of global and regional diversity using a published data set of 645 autosomal microsatellite genotypes from 5,415 individuals in 248 widespread populations. We used a formal tree-fitting approach to explore the role of founder effects. 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 versus waypoint geographic distances from Africa. We tested the role of localized gene flow using partial Mantel correlograms of gene diversity versus geographic distance controlling for the confounding effects of treelike genetic structure. 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. Here, patterns of diversity have been largely shaped by recent interregional admixture and secondary range expansions. Our 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. Our new foreword situates these findings in a long line of anthropological research that categorically rejects racial interpretations of analyses of human diversity

Linajes mitocondriales en poblaciones del Chaco argentino: patrones únicos de variación regional / Mitochondrial lineages in populations of the Argentine Chaco: unique patterns of regional variation

En este estudio se revisa la hipótesis sobre la supuesta singularidad genética de las poblaciones del Chaco argentino (alta diversidad intragrupal y baja diferenciación intergrupal) a partir del estudio de secuencias de la RHV-I del ADN mitocondrial. El análisis de 204 individuos del Chaco argentino y más de 2000 de diversas poblaciones y regiones de Centro y Sudamérica corrobora y refina los resultados derivados del estudio de haplogrupos mitocondriales: A diferencia de lo observado en otras regiones, las poblaciones del Chaco argentino presentan una gran diversidad genética, conjuntamente con una baja distancia genética entre poblaciones. Estos rasgos configuran un patrón único, que puede ser explicado por la forma de vida de sus habitantes antes del contacto con los europeos y las características de transición geográfica de la región chaqueña. Sin embargo, no pueden excluirse como explicaciones igualmente plausibles un posible error de muestreo o bien la ruptura post contacto de las formas tradicionales de parentesco. En otro orden, la alta variación genética encontrada en la región, geográficamente intermedia dentro de Sudamérica, no se ajusta al modelo que propone la existencia de dos patrones de diversidad genética nítidamente diferentes para las poblaciones nativas del Este y del Oeste del Continente, sostenido por otros autores

Linajes mitocondriales en poblaciones del Chaco argentino: patrones únicos de variación regional / Mitochondrial lineages in populations of the Argentine Chaco: unique patterns of regional variation

En este estudio se revisa la hipótesis sobre la supuesta singularidad genética de las poblaciones del Chaco argentino (alta diversidad intragrupal y baja diferenciación intergrupal) a partir del estudio de secuencias de la RHV-I del ADN mitocondrial. El análisis de 204 individuos del Chaco argentino y más de 2000 de diversas poblaciones y regiones de Centro y Sudamérica corrobora y refina los resultados derivados del estudio de haplogrupos mitocondriales: A diferencia de lo observado en otras regiones, las poblaciones del Chaco argentino presentan una gran diversidad genética, conjuntamente con una baja distancia genética entre poblaciones. Estos rasgos configuran un patrón único, que puede ser explicado por la forma de vida de sus habitantes antes del contacto con los europeos y las características de transición geográfica de la región chaqueña. Sin embargo, no pueden excluirse como explicaciones igualmente plausibles un posible error de muestreo o bien la ruptura post contacto de las formas tradicionales de parentesco. En otro orden, la alta variación genética encontrada en la región, geográficamente intermedia dentro de Sudamérica, no se ajusta al modelo que propone la existencia de dos patrones de diversidad genética nítidamente diferentes para las poblaciones nativas del Este y del Oeste del Continente, sostenido por otros autores

Linajes mitocondriales en poblaciones del Chaco argentino: patrones únicos de variación regional / Mitochondrial lineages in populations of the Argentine Chaco: unique patterns of regional variation

En este estudio se revisa la hipótesis sobre la supuesta singularidad genética de las poblaciones del Chaco argentino (alta diversidad intragrupal y baja diferenciación intergrupal) a partir del estudio de secuencias de la RHV-I del ADN mitocondrial. El análisis de 204 individuos del Chaco argentino y más de 2000 de diversas poblaciones y regiones de Centro y Sudamérica corrobora y refina los resultados derivados del estudio de haplogrupos mitocondriales: A diferencia de lo observado en otras regiones, las poblaciones del Chaco argentino presentan una gran diversidad genética, conjuntamente con una baja distancia genética entre poblaciones. Estos rasgos configuran un patrón único, que puede ser explicado por la forma de vida de sus habitantes antes del contacto con los europeos y las características de transición geográfica de la región chaqueña. Sin embargo, no pueden excluirse como explicaciones igualmente plausibles un posible error de muestreo o bien la ruptura post contacto de las formas tradicionales de parentesco. En otro orden, la alta variación genética encontrada en la región, geográficamente intermedia dentro de Sudamérica, no se ajusta al modelo que propone la existencia de dos patrones de diversidad genética nítidamente diferentes para las poblaciones nativas del Este y del Oeste del Continente, sostenido por otros autores

The effects of socioeconomic status, clinical factors, and genetic ancestry on pulmonary tuberculosis disease in northeastern Mexico.

Diverse socioeconomic and clinical factors influence susceptibility to tuberculosis (TB) disease in Mexico. The role of genetic factors, particularly those that differ between the parental groups that admixed in Mexico, is unclear. The objectives of this study are to identify the socioeconomic and clinical predictors of the transition from latent TB infection (LTBI) to pulmonary TB disease in an urban population in northeastern Mexico, and to examine whether genetic ancestry plays an independent role in this transition. We recruited 97 pulmonary TB disease patients and 97 LTBI individuals from a public hospital in Monterrey, Nuevo León. Socioeconomic and clinical variables were collected from interviews and medical records, and genetic ancestry was estimated for a subset of 142 study participants from 291,917 single nucleotide polymorphisms (SNPs). We examined crude associations between the variables and TB disease status. Significant predictors from crude association tests were analyzed using multivariable logistic regression. We also compared genetic ancestry between LTBI individuals and TB disease patients at 1,314 SNPs in 273 genes from the TB biosystem in the NCBI BioSystems database. In crude association tests, 12 socioeconomic and clinical variables were associated with TB disease. Multivariable logistic regression analyses indicated that marital status, diabetes, and smoking were independently associated with TB status. Genetic ancestry was not associated with TB disease in either crude or multivariable analyses. Separate analyses showed that LTBI individuals recruited from hospital staff had significantly higher European genetic ancestry than LTBI individuals recruited from the clinics and waiting rooms. Genetic ancestry differed between individuals with LTBI and TB disease at SNPs located in two genes in the TB biosystem. These results indicate that Monterrey may be structured with respect to genetic ancestry, and that genetic differences in TB susceptibility in parental populations may contribute to variation in disease susceptibility in the region