Paleogenomics in the Americas: demography, adaptations, and resilience

This work covers the evolutionary history of an indigenous population from the Americas through the lens of ancient DNA. In recent years, major advances in DNA sequencing have allowed for the utilization of ancient DNA on a grand scale. We now have the ability to examine the whole genomes of ancient individuals and examine the forces of evolution though space and time. Through these advances, this project addresses questions that would have otherwise been difficult to address with modern DNA alone. These questions span a period of 10,000 years and broach both local and continental demographic histories. In doing so, a comprehensive genetic picture of an indigenous population, with a history characteristic of other native groups, emerges so as to explain nuanced migration patterns, the historical experiences of Native Americans with European-borne pathogens, and the long-lasting genomic effects of European contact. This work was made possible through the collaborative efforts of Northwest Coast First Nations. The first topic presented here focuses on the highly debated processes behind the initial peopling of the Americas and, more specifically, the Northwest Coast. Over the past decades, this region has received a great deal of a attention due to the Northwest Coast’s proximity to Beringia and its prime location with respect to the coastal migration model, which holds that the first migration wave into the Americas occurred along the Pacific coast. Recent research, utilizing genome-wide data of both ancient and modern native individuals, has pointed to a primary migration that extends an ancestral lineage to most indigenous groups living today. Previous research, however, utilizing paternal and maternal genetic lineages, have found distributions of genetic markers that are difficult to reconcile into a single migration event. To address this discrepancy, the genomes of three ancient individuals from the Northwest Coast, ranging in age from 10,000 to 1,500 years Before Present (BP), were sequenced and compared to previously described ancient individuals from the Americas. The results suggest that the Northwest Coast was populated by two sources, which may represent two separate migrations into the region. I present analyses suggesting that the first source was part of a primary migration that led to the peopling of both continents. The second source may have been a result of a migration that occurred during the Holocene, which further diversified the gene pool and directly links to the current indigenous populations of the Northwest Coast. This analysis reconciles modern distributions of genetic markers, which are missing from North America but are prevalent on the southern continent. These markers, which are evident in the most ancient individuals of the region, are gradually replaced through time, which may be indicative of additional gene flow that entered the area after the primary migration wave made its way southward. The next period of inquiry moves forward to the era of European colonization and addresses its consequences on the indigenous populations of the Americas. A common notion holds that Native Americans were especially susceptible to European borne pathogens at the time of first contact. This has generated a variety of theories from a variety of fields to explain this epidemiological pattern. The most fundamental of these is immunological naiveté, which posits that Native Americans were more susceptible to these diseases simply because they had never encountered them. Others have tried to find a genetic component by exploring the diversity of immune markers in extant indigenous populations. These hypotheses, however, either fail to articulate the exact genetic mechanism or fail to incorporate the genetic diversity of indigenous peoples before the massive population declines associated with European contact. In order to address these issues, I examined the genomes of a Northwest Coast First Nation from two different time frames: before and after European contact. This population, from present day British Columbia, suffered extensive population declines in the mid-Nineteenth Century, mainly due to smallpox epidemics. By comparing the DNA sequences (covering all coding regions) of the contemporary individuals to that of their ancestors, I was able to examine the pre-existing genetic diversity and scan the ancient and living individuals for signals of natural selection. My initial hypothesis held that the ancient individuals would exhibit signs of adaptations to the ancient environments of the Americas, which occurred over several thousand years before the era of European colonization. Remarkably, the gene that showed the strongest signal for selection was indeed an immune gene (HLA-DQA1), which is involved in the detection of pathogens and in launching targeted immune responses. Furthermore, components of the ancient version of the gene are now in very low frequency in the living members of this population. This pattern suggests the occurrence of two selection events: the first in ancient times, respective to the ancient environment, followed by the second event occurring after European contact, which favored the present version of the gene. These findings are consistent with the hypothesis that the ancient population was adapted to a distinct and local epidemiological prehistory. European-borne pathogens like smallpox may have been able to take advantage of this ancient immune configuration, thus leading to increased virulence. My research suggests that the full explanation for Native American disease susceptibility appears to involve local adaptations to distinct and ancient immunological scenarios. These adaptations may have been advantageous in the ancient environment but proved deleterious once the environment was radically changed upon the onset of European contact. The final period of indigenous evolutionary history explored here extends into modern times. From a general perspective, the genomic patterns of a population are molded by a variety of evolutionary factors, ranging from demographic to cultural. The indigenous peoples of the Americas have a particularly nuanced evolutionary history—involving founder effects, migrations, severe bottlenecks, and gene flow with non-native populations. While all of these events lend to the shaping of genomic patterns, theoretical expectations suggests that the severe population decline suffered after European contact will have left an equally severe deleterious mark on the indigenous populations of the Americas. This expectation is mainly based on the loss of genetic diversity, which would increase the appearance of genomic features that could prove harmful in terms of both disease and the ability to adapt. Upon comparing the genomic patterns of the ancient and contemporary individuals from a Northwest Coast First Nation, however, I found a resilience that belayed expectations. I show that in less than 7 generations since the bottleneck due to European-borne epidemics in the 19th Century, the contemporary population’s genetic pool shows reduced levels of rare variants, lower homozygosity, and lower overall potentially damaging variants with respect to the ancient individuals. This can be explained by gene flow from non-native populations, which has increased genetic diversity and broken-up potentially damaging stretches of homozygous regions. This demographic process has mitigated, in a rapid fashion, the predicted deleterious effects of the population declines suffered after European contact. This feature not only demonstrates the resilience of Native Americans but also, in a broader sense, the beneficial effects of gene flow between populations as cultural and political boundaries begin to fade in the modern age of globalization

Correlation of reservoir sedimentation and watershed factors, Springfield Plain, Illinois

Bibliography: p. 21.A cooperative study by Illinois State Water Survey, U.S. Department of Agriculture Soil Conservation Service and Agricultural Research Service, and Illinois Agricultural Experiment Station.Enumeration continues through succeeding title

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

Unique Cryptosporidium Population in HIV-Infected Persons, Jamaica

A cryptosporidiosis survey showed the presence of Cryptosporidium hominis, C. parvum, C. canis, and C. felis in 25, 7, 1, and 1 HIV-positive persons from Jamaica, respectively; 1 person had both C. hominis and C. felis. Multilocus sequence typing indicated the presence of a homogeneous but geographically distinct C. hominis population in Jamaica

The Business Model as a technique for problem identification and scoping: a case study of Brazilian drinking water quality assessment sector

In this case study, a Business Model Canvas (BMC) was used as a technique for problem identification and scoping for the introduction of a new technology or methodology for water quality assessment. Therefore, information about the Brazilian water supply sector was used for the application of a BMC based on technological innovations for coliform analysis. The innovations proposed in the study include faster results, internet connection, and portability. To populate the model, data regarding the drinking water quality from Brazil were used from public data banks and reports. Also, a group of accountable representatives from diverse water supply systems and water quality laboratories reported their experience with the new coliform analysis and their perception of its technological improvement. The major gaps identified in this study were simplicity and faster results. These may be associated with technological improvements such as portability and internet connection. It was possible to conclude that the segment is diverse, and the BMC highlighted that value might differ for different niches. The results emphasized that the application of a BMC may be more than a business tool. It can also be used by developers or scientists to understand and improve both technology concepts and applications. HIGHLIGHTS A Business Model was applied to structure coliform analysis in drinking water.; Characteristics of water supply systems influence value proposition priorities.; Legal demands have influences in different levels and applications.; Technological innovation and advantages alone may not fit customer needs.; Information gathered reveals a technological gap in coliform analysis.

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

The genetic prehistory of the Andean highlands 7000 years BP though European contact

The peopling of the Andean highlands above 2500 m in elevation was a complex process that included cultural, biological, and genetic adaptations. Here, we present a time series of ancient whole genomes from the Andes of Peru, dating back to 7000 calendar years before the present (BP), and compare them to 42 new genome-wide genetic variation datasets from both highland and lowland populations. We infer three significant features: A split between low- And high-elevation populations that occurred between 9200 and 8200 BP; a population collapse after European contact that is significantly more severe in South American lowlanders than in highland populations; and evidence for positive selection at genetic loci related to starch digestion and plausibly pathogen resistance after European contact. We do not find selective sweep signals related to known components of the human hypoxia response, which may suggest more complex modes of genetic adaptation to high altitude