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

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

Inferring Population Continuity Versus Replacement with aDNA: A Cautionary Tale from the Aleutian Islands

In The Aleutian and Commander Islands and Their Inhabitants (Philadelphia: Wistar Institute of Anatomy and Biology, 1945), Hrdlička proposed a population replacement event in the Aleutian Islands approximately 1,000 years ago based on a perceived temporal shift in cranial morphology. However, the archaeological record indicates cultural, and presumed population, continuity for more than 4,000 years. We use mtDNA haplogroup data in the series of prehistoric eastern Aleutian samples (n = 86) studied craniometrically by Hrdlička to test alternative hypotheses regarding population continuity or replacement in the region. This molecular characterization, in conjunction with direct dating of individual specimens, provided increased resolution for hypothesis testing. Results indicate an apparent shift in mtDNA haplogroup frequencies in the eastern Aleutians approximately 1,000 years ago, in concert with changes in mortuary practices and isotopic signatures reflecting resource acquisition strategies. The earliest Aleut populations were characterized by a high frequency of haplogroup A, as are most modern populations of the North American arctic. Later prehistoric peoples in the Aleutians were characterized by a high frequency of haplogroup D and a correspondingly lower frequency of haplogroup A, a pattern typified by modern Aleut populations

Ancient genomes in South Patagonia reveal population movements associated with technological shifts and geography

Archaeological research documents major technological shifts among people who have lived in the southern tip of South America (South Patagonia) during the last thirteen millennia, including the development of marine-based economies and changes in tools and raw materials. It has been proposed that movements of people spreading culture and technology propelled some of these shifts, but these hypotheses have not been tested with ancient DNA. Here we report genome-wide data from 20 ancient individuals, and co-analyze it with previously reported data. We reveal that immigration does not explain the appearance of marine adaptations in South Patagonia. We describe partial genetic continuity since ~6600 BP and two later gene flows correlated with technological changes: one between 4700–2000 BP that affected primarily marine-based groups, and a later one impacting all <2000 BP groups. From ~2200–1200 BP, mixture among neighbors resulted in a cline correlated to geographic ordering along the coast.Fil: Nakatsuka, Nathan. Harvard Medical School; Estados UnidosFil: Luisi, Pierre. Universidad Nacional de Córdoba. Facultad de Filosofía y Humanidades; ArgentinaFil: Motti, Josefina María Brenda. Universidad Nacional del Centro de la Provincia de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Salemme, Monica Cira. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Austral de Investigaciones Científicas; Argentina. Universidad Nacional de Tierra del Fuego; ArgentinaFil: Santiago, Fernando Carlos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Austral de Investigaciones Científicas; ArgentinaFil: D'angelo del Campo, Manuel Domingo. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Sociales. Grupo de Estudios Interdisciplinarios sobre Poblaciones Humanas de Patagonia Austral; Argentina. Universidad Autónoma de Madrid; EspañaFil: Vecchi, Rodrigo Javier. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional del Sur; ArgentinaFil: Espinosa Parrilla, Yolanda. Consejo Superior de Investigaciones Científicas; EspañaFil: Prieto, Alfredo. Universidad de Magallanes; ChileFil: Adamski, Nicole. Harvard Medical School; Estados UnidosFil: Lawson, Ann Marie. Harvard Medical School; Estados UnidosFil: Harper, Thomas K.. University of Pennsylvania; Estados UnidosFil: Culleton, Brendan J.. University of Pennsylvania; Estados UnidosFil: Kennett, Douglas J.. University of California; Estados UnidosFil: Lalueza Fox, Carles. Consejo Superior de Investigaciones Científicas; EspañaFil: Mallick, Swapan. Harvard Medical School; Estados UnidosFil: Rohland, Nadin. Harvard Medical School; Estados UnidosFil: Guichón, Ricardo A.. Universidad Nacional del Centro de la Provincia de Buenos Aires; ArgentinaFil: Cabana, Graciela S.. University of Tennessee; Estados UnidosFil: Nores, Rodrigo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Antropología de Córdoba. Universidad Nacional de Córdoba. Facultad de Filosofía y Humanidades. Instituto de Antropología de Córdoba; ArgentinaFil: Reich, David. Harvard Medical School. Department Of Medicine; Estados Unido

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

Inferring Population Continuity Versus Replacement with aDNA: A Cautionary Tale from the Aleutian Islands

In The Aleutian and Commander Islands and Their Inhabitants (Philadelphia: Wistar Institute of Anatomy and Biology, 1945), Hrdlicˇka proposed a population replacement event in the Aleutian Islands approximately 1,000 years ago based on a perceived temporal shift in cranial morphology. However, the archaeological record indicates cultural, and presumed population, continuity for more than 4,000 years. We use mtDNA haplogroup data in the series of prehistoric eastern Aleutian samples (n = 86) studied craniometrically by Hrdlicˇka to test alternative hypotheses regarding population continuity or replacement in the region. This molecular characterization, in conjunction with direct dating of individual specimens, provided increased resolution for hypothesis testing. Results indicate an apparent shift in mtDNA haplogroup frequencies in the eastern Aleutians approximately 1,000 years ago, in concert with changes in mortuary practices and isotopic signatures reflecting resource acquisition strategies. The earliest Aleut populations were characterized by a high frequency of haplogroup A, as are most modern populations of the North American arctic. Later prehistoric peoples in the Aleutians were characterized by a high frequency of haplogroup D and a correspondingly lower frequency of haplogroup A, a pattern typified by modern Aleut populations

Linajes mitocondriales en poblaciones del Chaco Argentino: patrones únicos de variación regional

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.Asociación de Antropología Biológica de la República Argentina (AABRA

Linajes mitocondriales en poblaciones del Chaco Argentino: patrones unicos de variacion regional

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

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.Asociación de Antropología Biológica de la República Argentina (AABRA

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