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

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

Teaching Practicum at Worcester Technical High School

For my Interactive Qualifying Project, I student taught for the 2018 fall semester at Worcester Technical High School. In this report, I extensively demonstrate the connection between the theory of education and the application of this theory in the classroom. After a brief background on the education system in Massachusetts, I analyze the six Candidate Assessment of Performance (CAP) essential elements to explain how my classroom instruction improved to proficiently model each element of CAP. There are six chapters to explore the values and applications of each element. I then evaluate how my education at WPI has prepared me for the classroom. Lastly, I express a professional goal that I would set for myself if I were to begin my own practice

The Creation of an Engineering Standard for Evaluating Fixed Wildfire Fighting Systems For Structures at the Wildland Urban Interface

Fixed wildfire fighting systems for residential structures being developed and currently on the market are neither standardized nor regulated, potentially putting homeowners and their properties at increased risk. This project addresses background information on the nature of wildfires, a methodology outlining the process of creating a standard for evaluating these systems, the development of a proposed standard, and conclusions from the overall process. As part of the project the standard was applied to two commercially available fixed wildfire fighting systems. The project concludes with details on future work for revision and continued development of the standard

Patterns of Admixture and Population Structure in Native Populations of Northwest North America

The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North, Central, and South America. Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendants, reporting on the genomic impact of the history of admixture with colonizing populations of European and African ancestry. However, relatively little genomic research has been conducted on admixture in indigenous North American populations. In this study, we analyze genomic data at 475,109 single-nucleotide polymorphisms sampled in indigenous peoples of the Pacific Northwest in British Columbia and Southeast Alaska, populations with a well-documented history of contact with European and Asian traders, fishermen, and contract laborers. We find that the indigenous populations of the Pacific Northwest have higher gene diversity than Latin American indigenous populations. Among the Pacific Northwest populations, interior groups provide more evidence for East Asian admixture, whereas coastal groups have higher levels of European admixture. In contrast with many Latin American indigenous populations, the variance of admixture is high in each of the Pacific Northwest indigenous populations, as expected for recent and ongoing admixture processes. The results reveal some similarities but notable differences between admixture patterns in the Pacific Northwest and those in Latin America, contributing to a more detailed understanding of the genomic consequences of European colonization events throughout the Americas

Ancient individuals from the North American Northwest Coast reveal 10,000 years of regional genetic continuity

Recent genomic studies of both ancient and modern indigenous people of the Americas have shed light on the demographic processes involved during the first peopling. The Pacific Northwest Coast proves an intriguing focus for these studies because of its association with coastal migration models and genetic ancestral patterns that are difficult to reconcile with modern DNA alone. Here, we report the low-coverage genome sequence of an ancient individual known as "Shuká Káa" ("Man Ahead of Us") recovered from the On Your Knees Cave (OYKC) in southeastern Alaska (archaeological site 49-PET-408). The human remains date to ∼10,300 calendar (cal) y B.P. We also analyze low-coverage genomes of three more recent individuals from the nearby coast of British Columbia dating from ∼6,075 to 1,750 cal y B.P. From the resulting time series of genetic data, we show that the Pacific Northwest Coast exhibits genetic continuity for at least the past 10,300 cal y B.P. We also infer that population structure existed in the late Pleistocene of North America with Shuká Káa on a different ancestral line compared with other North American individuals from the late Pleistocene or early Holocene (i.e., Anzick-1 and Kennewick Man). Despite regional shifts in mtDNA haplogroups, we conclude from individuals sampled through time that people of the northern Northwest Coast belong to an early genetic lineage that may stem from a late Pleistocene coastal migration into the Americas

Time of European and East-Asian admixture in North and Central America estimated using the admixture linkage disequilibrium approach in <i>ALDER</i>[44].

α<p>Populations considered as admixed populations using <i>ALDER</i><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004530#pgen.1004530-Loh1" target="_blank">[44]</a>.</p>β<p>Sets of European populations considered separately in <i>ALDER</i><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004530#pgen.1004530-Loh1" target="_blank">[44]</a> as reference populations for admixture.</p><p><i>EurA</i> : Toscani (TSI); Caucasian (CEU); Russian; Basque; French; Sardinian.</p><p><i>EurB</i> : Toscani (TSI); Basque ; French; Sardinian.</p><p><i>EurC</i> : Toscani (TSI); Caucasian (CEU); Basque; French; Sardinian.</p>γ<p><i>Sets of</i> East Asian populations considered separately in <i>ALDER</i><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004530#pgen.1004530-Loh1" target="_blank">[44]</a> as reference populations for admixture.</p><p><i>na</i>: No significant admixture was found with any of the reference populations considered.</p><p><i>AsA</i> : Japanese (JPT); Japanese.</p><p><i>AsB</i> : Han; Han (CHB); Han (CHD); Japanese (JPT); Japanese.</p><p><i>AsC</i> : Han; Han (CHB); Han (CHD); Japanese (JPT); Japanese; Yakut.</p>δ<p>Mean admixture time in years (25 years for generation time) estimated by <i>ALDER</i><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004530#pgen.1004530-Loh1" target="_blank">[44]</a> across the reference populations considered ± mean of the admixture time standard deviations obtained across the reference populations considered.</p>∈<p>Mean admixture rate estimated by <i>ALDER </i><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004530#pgen.1004530-Loh1" target="_blank">[<i>44</i>]</a> across the reference populations considered ± standard deviation.</p

Worldwide Admixture structure.

<p>Plotted are modes with clustering solutions obtained with 30 replicates at each value of <i>K</i>. Values of <i>K</i> and the number of runs in the mode shown appear on the left. In each plot, each cluster is represented by a different color, and each individual is represented by a vertical line divided into <i>K</i> colored segments with heights proportional to genotype memberships in the clusters. Thin black lines separate individuals from different populations. The same 528 individuals included in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004530#pgen-1004530-g004" target="_blank">Figure 4B</a> are considered in the Admixture analyses. Alternate clustering solutions for values of <i>K</i> from 2 to 12 appear in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004530#pgen.1004530.s003" target="_blank">Figure S3</a>.</p

Individual-level population structure.

<p>(A) Multidimensional scaling plot of pairwise allele-sharing distance (ASD) among 2,140 individuals in the combined dataset. (B) Multidimensional scaling plot of pairwise ASD among 528 individuals from 63 worldwide populations, following the resampling of a maximum of 82 individuals each from 11 different population groups. Group choices for resampling were taken from <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004530#pgen.1004530.s006" target="_blank">Figure S6</a>. Population colors and symbols follow <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004530#pgen-1004530-g001" target="_blank">Figure 1</a>.</p