Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas

The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages

Violencia interpersonal y violencia contra la mujer durante el Horizonte Medio (550-1000 d.c) en Huaca Pucllana, valle bajo del Rímac: una aproximación desde la bioarqueología

Se analizaron los restos de 135 de estos individuos recuperados de 47 tumbas, intentando un abordaje con perspectiva de género, con el fin de conocer las posibles formas de violencia que pudieron haber afectado al pueblo Wari enterrado en Pucllana, incluyendo la violencia contra la mujer, así como la violencia interpersonal, como consecuencia de la jerarquización derivada de una estructura de tipo imperial, y su impacto en los pobladores. La premisa inicial es que la expansión y consolidación del imperio influyó en la forma en que se establecieron las relaciones de género, como sociedad jerarquizada y como tal, socialmente estratificada. Si bien es cierto, las mujeres jugaron roles importantes como parte de las élites en sociedades pasadas, la evidencia sugiere que también habrían estado sujetas a las estructuras jerárquicas atravesadas por los modelos patriarcales de dominación, que afectarían tanto a hombres y mujeres como a sub adultos, pero en mayor proporción a estos dos últimos grupos. La evidencia de violencia física para este sitio es relativamente baja, solo el 30% de la población se vería afectada por ella. El análisis realizado, muestra una mayor mortalidad infantil, seguida de la mortalidad femenina, con indicadores de muertes violentas, así como la presencia de osteopatologías, donde predominaron las de tipo traumático. También se encontraron lesiones traumáticas ante mortem y peri mortem en individuos masculinos, aunque en menor proporción que en mujeres. Junto con los hallazgos funerarios, pudimos establecer las formas de violencia estructural existentes, lo que sugiere que el impacto de la jerarquización imperial, en efecto, condujo a esta situación en contra de algunos de los pobladores, lo cual puede haber tenido un componente en razón del género

AmericaPlex26: a SNaPshot multiplex system for genotyping the main human mitochondrial founder lineages of the Americas.

Phylogeographic studies have described a reduced genetic diversity in Native American populations, indicative of one or more bottleneck events during the peopling and prehistory of the Americas. Classical sequencing approaches targeting the mitochondrial diversity have reported the presence of five major haplogroups, namely A, B, C, D and X, whereas the advent of complete mitochondrial genome sequencing has recently refined the number of founder lineages within the given diversity to 15 sub-haplogroups. We developed and optimized a SNaPshot assay to study the mitochondrial diversity in pre-Columbian Native American populations by simultaneous typing of 26 single nucleotide polymorphisms (SNPs) characterising Native American sub-haplogroups. Our assay proved to be highly sensitive with respect to starting concentrations of target DNA and could be applied successfully to a range of ancient human skeletal material from South America from various time periods. The AmericaPlex26 is a powerful assay with enhanced phylogenetic resolution that allows time- and cost-efficient mitochondrial DNA sub-typing from valuable ancient specimens. It can be applied in addition or alternative to standard sequencing of the D-loop region in forensics, ancestry testing, and population studies, or where full-resolution mitochondrial genome sequencing is not feasible

AmericaPlex26: a SNaPshot multiplex system for genotyping the main human mitochondrial founder lineages of the Americas.

Phylogeographic studies have described a reduced genetic diversity in Native American populations, indicative of one or more bottleneck events during the peopling and prehistory of the Americas. Classical sequencing approaches targeting the mitochondrial diversity have reported the presence of five major haplogroups, namely A, B, C, D and X, whereas the advent of complete mitochondrial genome sequencing has recently refined the number of founder lineages within the given diversity to 15 sub-haplogroups. We developed and optimized a SNaPshot assay to study the mitochondrial diversity in pre-Columbian Native American populations by simultaneous typing of 26 single nucleotide polymorphisms (SNPs) characterising Native American sub-haplogroups. Our assay proved to be highly sensitive with respect to starting concentrations of target DNA and could be applied successfully to a range of ancient human skeletal material from South America from various time periods. The AmericaPlex26 is a powerful assay with enhanced phylogenetic resolution that allows time- and cost-efficient mitochondrial DNA sub-typing from valuable ancient specimens. It can be applied in addition or alternative to standard sequencing of the D-loop region in forensics, ancestry testing, and population studies, or where full-resolution mitochondrial genome sequencing is not feasible

Table showing the details of multiplex primers and SBE probes used in the AmericaPlex26 assay.

<p>SBE probes in reverse direction are shown in Italics.</p><p>hg haplogroup; conc. concentration; bp base pairs; nt nucleotides.</p

Details of primers used for standard HVR-I amplification and sequencing.

<p>Details of primers used for standard HVR-I amplification and sequencing.</p

Electropherograms of two ancient examples representing the optimized AmericaPlex26.

<p>Panel A shows a South American sample and panel B an ancient European sample illustrating the ancestral state of all 26-haplogroups B2a (16483), B2b (6755), B2c (7241), B2d (8875), B2e (6119) and B2f (10535).</p

Direct comparison of results for HVR-I sequencing and AmericaPlex26 SNP typing assay for samples unambiguously typed using the AmericaPlex26 assay.

<p>Consensus haplogroups were called based on last common SNP from both replicates from independent extractions, and minimum peak size >50 rfu. (?)/(−): Insufficient or no sequence information; EI: Early Intermediate; MH: Middle Horizon; LI: Late Intermediate.</p

Simplified phylogeny in related to the Reconstructed Sapiens Reference Sequence (RSRS [52]) and typing scheme of the 26 SNPs targeted in the AmericaPlex26.

<p>Sub-haplogroups, which can be unambiguously assigned, are shown in blue (blue). Basal hgs, which cannot be unambiguously assigned, are also shown (black) in order to illustrate the phylogenetic relationship, but also the inherent limitations of our assay. The phylogenetic position of the revised Cambridge Reference Sequence (rCRS <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0093292#pone.0093292-Andrews1" target="_blank">[53]</a>) is indicated within macro-hg N. SNPs with a SBE primer in reverse direction targeting the opposite strand are given in Italics.</p

Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas.

The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages