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

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

Genetic structure of First Nation communities in the Pacific Northwest

This study presents genetic data for nine Native American populations from northern North America. Analyses of genetic variation focus on the Pacific Northwest (PNW). Using mitochondrial, Y chromosomal and autosomal DNA variants, we aim to more closely address the relationships of geography and language with present genetic diversity among the regional PNW Native American populations. Patterns of genetic diversity exhibited by the three genetic systems were consistent with our hypotheses, in that we expected genetic variation to be more strongly explained by geographic proximity than linguistic structure. Our findings were corroborated through a variety on analytic approaches, with the unrooted trees for the three genetic systems consistently separating inland from coastal PNW populations. Furthermore, the AMOVA tests support the trends exhibited by the unrooted trees, with geographic partitioning of PNW populations (FCT = 19.43%, p = 0.010 ± 0.009) accounting for over twice as much of the observed genetic variation compared with linguistic partitioning of the same populations (FCT = 9.15%, p = 0.193 ± 0.013). These findings demonstrate a consensus with previous PNW population studies examining the relationships of genome-wide variation, mitochondrial haplogroup frequencies, and skeletal morphology with geography and language

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

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 high through put 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.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

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

Ancient and modern genomics of the Ohlone Indigenous population of California

Traditional knowledge, along with archaeological and linguistic evidence, documents that California supports cultural and linguistically diverse Indigenous populations. Studies that have included ancient genomes in this region, however, have focused primarily on broad-scale migration history of the North American continent, with relatively little attention to local population dynamics. Here, in a partnership involving researchers and the Muwekma Ohlone tribe, we analyze genomic data from ancient and present-day individuals from the San Francisco Bay Area in California: 12 ancient individuals dated to 1905 to 1826 and 601 to 184 calibrated years before the present (cal BP) from two archaeological sites and eight present-day members of the Muwekma Ohlone tribe, whose ancestral lands include these two sites. We find that when compared to other ancient and modern individuals throughout the Americas, the 12 ancient individuals from the San Francisco Bay Area cluster with ancient individuals from Southern California. At a finer scale of analysis, we find that the 12 ancient individuals from the San Francisco Bay Area have distinct ancestry from the other groups and that this ancestry has a component of continuity over time with the eight present-day Muwekma Ohlone individuals. These results add to our understanding of Indigenous population history in the San Francisco Bay Area, in California, and in western North America more broadly

From cheek swabs to consensus sequences : an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes

Background: Next-generation DNA sequencing (NGS) technologies have made huge impacts in many fields of biological research, but especially in evolutionary biology. One area where NGS has shown potential is for high-throughput sequencing of complete mtDNA genomes (of humans and other animals). Despite the increasing use of NGS technologies and a better appreciation of their importance in answering biological questions, there remain significant obstacles to the successful implementation of NGS-based projects, especially for new users. Results: Here we present an ‘A to Z’ protocol for obtaining complete human mitochondrial (mtDNA) genomes – from DNA extraction to consensus sequence. Although designed for use on humans, this protocol could also be used to sequence small, organellar genomes from other species, and also nuclear loci. This protocol includes DNA extraction, PCR amplification, fragmentation of PCR products, barcoding of fragments, sequencing using the 454 GS FLX platform, and a complete bioinformatics pipeline (primer removal, reference-based mapping, output of coverage plots and SNP calling). Conclusions: All steps in this protocol are designed to be straightforward to implement, especially for researchers who are undertaking next-generation sequencing for the first time. The molecular steps are scalable to large numbers (hundreds) of individuals and all steps post-DNA extraction can be carried out in 96-well plate format. Also, the protocol has been assembled so that individual ‘modules’ can be swapped out to suit available resources

Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus

Aligning sequences for phylogenetic analysis (multiple sequence alignment; MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. Much of this sequence data is publicly available, but can be extremely fragmentary (i.e., a combination of full genomes and genomic fragments), which can compound the computational issues related to MSA. Traditionally, alignments are produced with automated algorithms and then checked and/or corrected “by eye” prior to phylogenetic inference. However, this manual curation is inefficient at the data scales required of modern phylogenetics and results in alignments that are not reproducible. Recently, methods have been developed for fully automating alignments of large data sets, but it is unclear if these methods produce alignments that result in compatible phylogenies when compared to more traditional alignment approaches that combined automated and manual methods. Here we use approximately 33,000 publicly available sequences from the hepatitis B virus (HBV), a globally distributed and rapidly evolving virus, to compare different alignment approaches. Using one data set comprised exclusively of whole genomes and a second that also included sequence fragments, we compared three MSA methods: (1) a purely automated approach using traditional software, (2) an automated approach including by eye manual editing, and (3) more recent fully automated approaches. To understand how these methods affect phylogenetic results, we compared resulting tree topologies based on these different alignment methods using multiple metrics. We further determined if the monophyly of existing HBV genotypes was supported in phylogenies estimated from each alignment type and under different statistical support thresholds. Traditional and fully automated alignments produced similar HBV phylogenies. Although there was variability between branch support thresholds, allowing lower support thresholds tended to result in more differences among trees. Therefore, differences between the trees could be best explained by phylogenetic uncertainty unrelated to the MSA method used. Nevertheless, automated alignment approaches did not require human intervention and were therefore considerably less time-intensive than traditional approaches. Because of this, we conclude that fully automated algorithms for MSA are fully compatible with older methods even in extremely difficult to align data sets. Additionally, we found that most HBV diagnostic genotypes did not correspond to evolutionarily-sound groups, regardless of alignment type and support threshold. This suggests there may be errors in genotype classification in the database or that HBV genotypes may need a revision

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy