SignificanceThrough the Peruvian Genome Project we generate and analyze the genomes of 280 individuals where the majority have >90% Native American ancestry and explore questions at the interface of evolutionary genetics, history, anthropology, and medicine. This is the most extensive sampling of high-coverage Native American and mestizo whole genomes to date. We estimate an initial peopling of Peru was rapid and began by 12,000 y ago. In addition, the mestizo populations exhibit admixture between Native American groups prior to their Spanish admixture and was likely influenced by the Inca Empire and Spanish conquest. Our results address important Native American population history questions and establish a dataset beneficial to address the underrepresentation of Native American ancestry in sequencing studies.

Western South America was one of the worldwide cradles of civilization. The well-known Inca Empire was the tip of the iceberg of an evolutionary process that started 11,000 to 14,000 years ago. Genetic data from 18 Peruvian populations reveal the following: 1) The between-population homogenization of the central southern Andes and its differentiation with respect to Amazonian populations of similar latitudes do not extend northward. Instead, longitudinal gene flow between the northern coast of Peru, Andes, and Amazonia accompanied cultural and socioeconomic interactions revealed by archeology. This pattern recapitulates the environmental and cultural differentiation between the fertile north, where altitudes are lower, and the arid south, where the Andes are higher, acting as a genetic barrier between the sharply different environments of the Andes and Amazonia. 2) The genetic homogenization between the populations of the arid Andes is not only due to migrations during the Inca Empire or the subsequent colonial period. It started at least during the earlier expansion of the Wari Empire (600 to 1,000 years before present). 3) This demographic history allowed for cases of positive natural selection in the high and arid Andes vs. the low Amazon tropical forest: in the Andes, a putative enhancer inHAND2-AS1(heart and neural crest derivatives expressed 2 antisense RNA1, a noncoding gene related to cardiovascular function) and rs269868-C/Ser1067 inDUOX2(dual oxidase 2, related to thyroid function and innate immunity) genes and, in the Amazon, the gene encoding for the CD45 protein, essential for antigen recognition by T and B lymphocytes in viral–host interaction.

Native Americans from the Amazon, Andes, and coast regions of South America have a rich cultural heritage, but have been genetically understudied leading to gaps in our knowledge of their genomic architecture and demographic history. Here, we sequenced 150 high-coverage and genotyped 130 genomes from Native American and mestizo populations in Peru. A majority of our samples possess greater than 90% Native American ancestry and demographic modeling reveals, consistent with a rapid peopling model of the Americas, that most of Peru was peopled approximately 12,000 years ago. While the Native American populations possessed distinct ancestral divisions, the mestizo groups were admixtures of multiple Native American communities which occurred before and during the Inca Empire. The mestizo communities also show Spanish introgression only after Peruvian Independence. Thus, we present a detailed model of the evolutionary dynamics which impacted the genomes of modern day Peruvians.. CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under aThe copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/219808 doi: bioRxiv preprint first posted online Nov. 16, 2017; 4 Native American ancestry is underrepresented by recent whole genome studies [1][2][3][4] . As a result, there are numerous questions that remain in both Native American genetic architecture and their early history. One such question regards the peopling of the Americas, which began when the genetically diverse Native American ancestral population 5,6 diverged from East Asians ~23,000 years ago (ya) 7 . Following the separation from Asian populations, Native Americans' entered a period of isolation, potentially in Beringia 8 , for as long as 10,000 years 7,9 . Thereafter, they migrated into the New World, likely through a coastal route 10 , and quickly populated both North and South America. This rapid peopling of the Americas is evidenced by Monte Verde, one of the oldest archeological sites in the Americas, being in Southern Chile and is ~14,000 years old 11 . It took Native Americans only 1,000 to 2,000 years after the isolation period to populate the majority of the Americas. While it is widely supported that this was a rapid process, questions still remain regarding the divergence between the Amazon, Andes, and coast regions of South America 9 . Peru contains all three regions within its borders and its population has predominantly Native American ancestry 12 , therefore making it an excellent country to study this process.Peruvian populations have a rich cultural heritage that derives from thousands of years of New World prehistory, that culminated in the last major pre-Columbian civilization, the Inca Empire 13 . The populations of this region have undergone drastic demographic changes that derive from experiences such as forced migration [13][14][15][16][17] and major population size reduction due to the Spanish conquest, during the 16 th century, which introduced mass pandemi...

High incidence rates of tuberculosis in indigenous population have been found, which raises the need of further research in order to guarantee the correct gathering of information in ethnic groups in order to have more and better evidence about the situation of tuberculosis in the indigenous population of Peru.

Objetivos. Identificar a los pobladores indígenas afectados por tuberculosis (TB) en el Perú durante el año 2008. Materiales y métodos. Estudio observacional, descriptivo, realizado de agosto a diciembre de 2009, que incluyó a los pacientes indígenas afectados por tuberculosis que ingresaron al programa durante el año 2008, de las 25 regiones del Perú; los cuales se presentan en tablas y gráficos elaborados en SPSS 16.0 y Excell 2007. Resultados. Se identificó a 702 indígenas con tuberculosis. El grupo étnico que presenta la mayor cantidad de pacientes con TB son los quechuas (417/702; 59,4%), los indígenas amazónicos (201/702; 28,6%) de los cuales los grupos étnicos que presenta más del 60% de indígenas con TB, son los Ashaninka (Campas), Shipibo y Matsiguenga. En tercer lugar se encuentran los indígenas aymaras quienes presentaron (84/702; 11,97% de todos los pacientes diagnosticados con TB). Es importante mencionar que la distribución de los casos de tuberculosis multidrogoresistente involucra a cinco departamentos (nueve casos con TB MDR), siendo mayor el número de casos de TB MDR antes tratado 6/9, encontrándose sólo tres casos de TB MDR nuevos, pertenecientes al grupo indígena quechua. Conclusiones. Se han reportado altas tasas de incidencia en población indígena, lo que hace necesario investigaciones más profundas que garanticen la adecuada recolección de información por grupos étnicos a fin de contar con una evidencia de mayor jerarquía acerca de la situación de la tuberculosis en población indígena del Perú.

Western South America was one of the worldwide cradles of civilization. The well known Inca Empire was the tip of the iceberg of a cultural and biological evolutionary process that started 14-11 thousand years ago. Genetic data from 18 Peruvian populations reveal that: (1) The between-population homogenization of the central-southern Andes and its differentiation with respect to Amazonian populations of similar latitudes do not extend northward. Instead, longitudinal gene flow between the northern coast of Peru, Andes and Amazonia accompanied cultural and socioeconomic interactions revealed by archeological studies. This pattern recapitulates the environmental and cultural differentiation between the fertile north, where altitudes are lower; and the arid south, where the Andes are higher, acting as a genetic barrier between the sharply different environments of the Andes and Amazonia (2). The genetic homogenization between the populations of the arid Andes is not only due to migration during the Inca Empire or the subsequent colonial period. It started at least during the earlier expansion of the pre-Inca Wari Empire (600-1000 YBP) (3) This demographic history allowed for cases of positive natural selection in the high and arid Andes vs. the low Amazon tropical forest: in the Andes, HAND2-AS1 (heart and neural crest derivatives expressed 2 antisense RNA1, related with cardiovascular function) and DUOX2 (dual oxidase 2, related to thyroid function and innate immunity) genes; in the Amazon, the gene encoding for the CD45 protein, essential for antigen recognition by T/B lymphocytes in viral-host interaction, consistent with the host-virus arms race hypothesis.

Objetivo. Conocer el resultado de la vacunación contra la hepatitis B en las comunidades hiperendémicas Kandozi y Chapra de la Amazonia Peruana a partir de la prevalencia de infecciones por los virus de la hepatitis B (VHB) y Delta (VHD), ocho años después de iniciada la vacunación. Material y métodos. Se realizó un estudio transversal en 2 944 pobladores de 67 comunidades indígenas Kandozi y Chapra en abril de 2010. El tamizaje serológico para el antígeno de superficie del VHB (HBsAg), anticuerpos anti-HBc IgM e IgG, anticuerpos anti-HBs y anti-VHD se determinaron mediante pruebas de ELISA. Resultados. Las tasas de prevalencia del HBsAg, anti-HBc IgG, anti-HBs ≥10 mlUI/ml y anti-VHD fueron 2.3, 39.13, 50.95 y 2.11%, respectivamente. La prevalencia del HBsAg en niños <11 años fue cero. Entre los portadores del HBsAg, las tasas de prevalencia de sobreinfeccion por el VHD e infección aguda por el VHB fueron 2.11% (todos fueron >14 años) y 11.94%, respectivamente. Conclusiones. Estos hallazgos muestran la eliminación de portadores de VHB en niños <11 años, ocho años después de iniciada la vacunación contra el VHB.

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