Primer genoma mitocondrial en restos humanos de la Costa de Santa Cruz, Argentina

En este trabajo se presenta la secuencia completa de ADN mitocondrial, obtenida a partir de restos óseos de un hombre adulto, hallado en el sitio Cañadón Misioneros (provincia de Santa Cruz, Argentina), con una antigüedad de 70 ± 30 años antes del presente. La secuencia corresponde al haplogrupo (hg) D4h3a5, nativo de América y exclusivo del sur de Patagonia, donde ha sido descripto tanto en muestras antiguas como actuales. Esta secuencia constituye el primer dato de ADN mitocondrial en la costa atlántica de Patagonia con la resolución suficiente para definir a nivel de subhaplogrupo. Se discuten las implicancias en cuanto a los vínculos biológicos de las poblaciones que habitaron esa porción del espacio patagónico en el marco de la información genética y arqueológica disponible.We describe the complete mitochondrial genome sequence of an adult male skeleton, discovered at Cañadón Misioneros (Santa Cruz Province, Argentina), and dated 70 ± 30 years before present. The DNA sequence corresponded to haplogroup D4h3a5, native to the Americas and exclusive to the south of Patagonia, where it has been observed both in ancient and present-day individuals. This is the first mitochondrial DNA data of the Atlantic coast of Patagonia of sufficient resolution to permit classification at the subhaplogroup level. The implications for the genetic affinities of populations of this region of Patagonia will be discussed in the context of available genetic and archaeological information

Low Mitochondrial DNA Diversity in an Ancient Population from China: Insight

To gain insight into the social organization of a population associated with the Dawenkou period, ancient DNA analysis of 18 individuals from human remains from Fujia site, Shandong Province, China was completed. Directly radiocarbon dated to 4800–4500 cal BP, the Fujia site is assumed to be associated with a transitional phase from matrilineal clans to patrilineal monogamous families. Our results reveal a low mitochondrial DNA diversity from the site and population. Combined with Y-chromosome data, the pattern observed at the Fujia site is most consistent with a matrilineal community. The patterns also suggest that the bond of marriage were de-emphasized compared to the bonds of descent at Fujia

MamuSNP: A Resource for Rhesus Macaque (Macaca mulatta) Genomics

We developed a novel method for identifying SNPs widely distributed throughout the coding and non-coding regions of a genome. The method uses large-scale parallel pyrosequencing technology in combination with bioinformatics tools. We used this method to generate approximately 23,000 candidate SNPs throughout the Macaca mulatta genome. We estimate that over 60% of the SNPs will be of high frequency and useful for mapping QTLs, genetic management, and studies of individual relatedness, whereas other less frequent SNPs may be useful as population specific markers for ancestry identification. We have created a web resource called MamuSNP to view the SNPs and associated information online. This resource will also be useful for researchers using a wide variety of Macaca species in their research

A time transect of exomes from a Native American population before and after European contact

A major factor for the population decline of Native Americans after European contact has been attributed to infectious disease susceptibility. To investigate whether a pre-existing genetic component contributed to this phenomenon, here we analyse 50 exomes of a continuous population from the Northwest Coast of North America, dating from before and after European contact. We model the population collapse after European contact, inferring a 57% reduction in effective population size. We also identify signatures of positive selection on immune-related genes in the ancient but not the modern group, with the strongest signal deriving from the human leucocyte antigen (HLA) gene HLA-DQA1. The modern individuals show a marked frequency decrease in the same alleles, likely due to the environmental change associated with European colonization, whereby negative selection may have acted on the same gene after contact. The evident shift in selection pressures correlates to the regional European-borne epidemics of the 1800s.Full Tex

Patterns of mtDNA Diversity in Northwestern North America

The mitochondrial DNA (mtDNA) haplogroups of 54 full-blooded modern and 64 ancient Native Americans from northwestern North America were determined. The control regions of 10 modern and 30 ancient individuals were sequenced and compared. Within the Northwest, the frequency distribution for haplogroup A is geographically structured, with haplogroup A decreasing with distance from the Pacific Coast. The haplogroup A distribution suggests that a prehistoric population intrusion from the subarctic and coastal region occurred on the Columbia Plateau in prehistoric times. Overall, the mtDNA pattern in the Northwest suggests significant amounts of gene flow among Northwest Coast, Columbia Plateau, and Great Basin populations

First complete mitochondrial genome sequence from human skeletal remains of the coast of Santa Cruz, Argentina

En este trabajo se presenta la secuencia completa de ADN mitocondrial, obtenida a partir de restos óseos de un hombre adulto, hallado en el sitio Cañadón Misioneros (provincia de Santa Cruz, Argentina), con una antigüedad de 70 ± 30 años antes del presente. La secuencia corresponde al haplogrupo (hg) D4h3a5, nativo de América y exclusivo del sur de Patagonia, donde ha sido descripto tanto en muestras antiguas como actuales. Esta secuencia constituye el primer dato de ADN mitocondrial en la costa atlántica de Patagonia con la resolución suficiente para definir a nivel de subhaplogrupo. Se discuten las implicancias en cuanto a los vínculos biológicos de las poblaciones que habitaron esa porción del espacio patagónico en el marco de la información genética y arqueológica disponible.We describe the complete mitochondrial genome sequence of an adult male skeleton, discovered at Cañadón Misioneros (Santa Cruz Province, Argentina), and dated 70 ± 30 years before present. The DNA sequence corresponded to haplogroup D4h3a5, native to the Americas and exclusive to the south of Patagonia, where it has been observed both in ancient and present-day individuals. This is the first mitochondrial DNA data of the Atlantic coast of Patagonia of sufficient resolution to permit classification at the subhaplogroup level. The implications for the genetic affinities of populations of this region of Patagonia will be discussed in the context of available genetic and archaeological information.Instituto Multidisciplinario de Biología Celula

Análisis del genoma mitocondrial de dos individuos inhumados en el sitio arqueológico CG14E01 “Isla Larga” (Rocha, Uruguay)

CG14E01 “Isla Larga” es un sitio con estructura monticular (“cerrito de indios”) localizado en el departamento de Rocha (Uruguay), con una cronología que se extiende de 3600 años AP al siglo XVII. En este sitio se registran evidencias vinculadas con diversos contactos interétnicos en la forma de dos urnas Tupiguaraní y cuentas de vidrio de origen europeo. Asociados a estas evidencias se recuperaron tres enterramientos primarios, uno masculino y dos femeninos. El objetivo de este trabajo consiste en analizar el mitogenoma completo de los individuos femeninos, que presentan desgaste dental acentuado y que en un caso presenta trauma perimortem. El ADN de los dos individuos fue extraído a partir de piezas dentales y su secuencia genómica mitocondrial fue obtenida mediante secuenciación masiva, verificándose su autenticidad por el análisis de las modificaciones postmortem del ADN en las lecturas mapeadas. Ambos individuos pertenecen a un haplotipo hasta ahora no registrado del haplogrupo fundador americano C1b, compartiendo las mutaciones 185A, 3116T, 3203T y 14502C. En virtud de consideraciones hechas por otros investigadores a propósito del “cerrito” como marcador territorial, la posibilidad de que la estructura haya servido de lugar de inhumación para individuos unidos por lazos de parentesco es sugerente. Por otra parte, los elementos del contexto y la evidencia de trauma añaden una segunda perspectiva, vinculada con las dinámicas interétnicas descriptas en el registro etnohistórico de la región.CG14E01 “Isla Larga” is a site with a moundlike structure (cerrito de indios) located in Rocha (Uruguay), with a chronology spanning the period from 3600 years BP to the 17th century. Evidence of various interethnic interactions has been found at the site, namely, two Tupiguarani urns and some European glass beads. Connected with this evidence, three primary burials, one male and two female, were recovered. The goal of this paper is to analyze the complete mitochondrial genome of the female individuals, one of which shows perimortem trauma. The DNA of both individuals was extracted from teeth, and their mitochondrial genome sequence was obtained by means of highthroughput sequencing. The authenticity of the sequences was verified through the analysis of postmortem DNA damage in the mapped reads. Both individuals were found to belong to a previously unregistered haplotype of the founding American haplogroup C1b, sharing the mutations 185A, 3116T, 3203T, 14397G, and 14502C. In view of the considerations made by other researchers about the mounds as territorial markers, the possibility that this structure could have served as a burial location for individuals related by kinship gains strength. On the other hand, the elements of the context and the evidence of trauma allow a second perspective, related to the interethnic dynamics described in the regional ethnohistorical record.Asociación de Antropología Biológica de la República Argentina (AABRA

Análisis del genoma mitocondrial de dos individuos inhumados en el sitio arqueológico CG14E01 “Isla Larga” (Rocha, Uruguay)

CG14E01 “Isla Larga” es un sitio con estructura monticular (“cerrito de indios”) localizado en el departamento de Rocha (Uruguay), con una cronología que se extiende de 3600 años AP al siglo XVII. En este sitio se registran evidencias vinculadas con diversos contactos interétnicos en la forma de dos urnas Tupiguaraní y cuentas de vidrio de origen europeo. Asociados a estas evidencias se recuperaron tres enterramientos primarios, uno masculino y dos femeninos. El objetivo de este trabajo consiste en analizar el mitogenoma completo de los individuos femeninos, que presentan desgaste dental acentuado y que en un caso presenta trauma perimortem. El ADN de los dos individuos fue extraído a partir de piezas dentales y su secuencia genómica mitocondrial fue obtenida mediante secuenciación masiva, verificándose su autenticidad por el análisis de las modificaciones postmortem del ADN en las lecturas mapeadas. Ambos individuos pertenecen a un haplotipo hasta ahora no registrado del haplogrupo fundador americano C1b, compartiendo las mutaciones 185A, 3116T, 3203T y 14502C. En virtud de consideraciones hechas por otros investigadores a propósito del “cerrito” como marcador territorial, la posibilidad de que la estructura haya servido de lugar de inhumación para individuos unidos por lazos de parentesco es sugerente. Por otra parte, los elementos del contexto y la evidencia de trauma añaden una segunda perspectiva, vinculada con las dinámicas interétnicas descriptas en el registro etnohistórico de la región.CG14E01 “Isla Larga” is a site with a moundlike structure (cerrito de indios) located in Rocha (Uruguay), with a chronology spanning the period from 3600 years BP to the 17th century. Evidence of various interethnic interactions has been found at the site, namely, two Tupiguarani urns and some European glass beads. Connected with this evidence, three primary burials, one male and two female, were recovered. The goal of this paper is to analyze the complete mitochondrial genome of the female individuals, one of which shows perimortem trauma. The DNA of both individuals was extracted from teeth, and their mitochondrial genome sequence was obtained by means of highthroughput sequencing. The authenticity of the sequences was verified through the analysis of postmortem DNA damage in the mapped reads. Both individuals were found to belong to a previously unregistered haplotype of the founding American haplogroup C1b, sharing the mutations 185A, 3116T, 3203T, 14397G, and 14502C. In view of the considerations made by other researchers about the mounds as territorial markers, the possibility that this structure could have served as a burial location for individuals related by kinship gains strength. On the other hand, the elements of the context and the evidence of trauma allow a second perspective, related to the interethnic dynamics described in the regional ethnohistorical record.Asociación de Antropología Biológica de la República Argentina (AABRA

Population Structure Analyses Provide Insight into the Source Populations Underlying Rural Isolated Communities in Illinois

We have previously hypothesized that relatively small and isolated rural communities may experience founder effects, defined as the genetic ramifications of small population sizes at the time of a community’s establishment. To explore this, we used an Illumina Infinium Omni2.5Exome-8 chip to collect data from 157 individuals from four Illinois communities, three rural and one urban. Genetic diversity estimates of 999,259 autosomal markers suggested that the reduction in heterozygosity due to shared ancestry was approximately 0, indicating a randomly mating population. An eigenanalysis, which is similar to a principal component analysis but ran on a genetic coancestry matrix, conducted in the SNPRelate R package revealed that the majority of these individuals formed one cluster with a few putative outliers obscuring population variation. An additional eigenanalysis on the same markers in a combined data set including the 2,504 individuals in the 1000 Genomes database found that most of the 157 Illinois individuals clustered into one group in close proximity to individuals of European descent. A final eigenanalysis of the Illinois individuals with the 503 individuals of European descent (within the 1000 Genomes Project) revealed two clusters of individuals and likely two source populations; one British and one consisting of multiple European subpopulations. We therefore demonstrate the feasibility of examining genetic relatedness across Illinois populations and assessing the number of source populations using publicly available databases. When assessed, it becomes possible for population structure information to contribute to the understanding of genetic history in rural populations