Cris E. Hughes

Ancient DNA analysis of mid-Holocene individuals from the Northwest Coast of North America reveals different evolutionary paths for mitogenomes

To gain a better understanding of North American population history, complete mitochondrial genomes (mitogenomes) were generated from four ancient and three living individuals of the northern Northwest Coast of North America, specifically the north coast of British Columbia, Canada, current home to the indigenous Tsimshian, Haida, and Nisga’a. The mitogenomes of all individuals were previously unknown and assigned to new sub-haplogroup designations D4h3a7, A2ag and A2ah. The analysis of mitogenomes allows for more detailed analyses of presumed ancestor–descendant relationships than sequencing only the HVSI region of the mitochondrial genome, a more traditional approach in local population studies. The results of this study provide contrasting examples of the evolution of Native American mitogenomes. Those belonging to sub-haplogroups A2ag and A2ah exhibit temporal continuity in this region for 5000 years up until the present day. Of possible associative significance is that archaeologically identified house structures in this region maintain similar characteristics for this same period of time, demonstrating cultural continuity in residence patterns. The individual dated to 6000 years before present (BP) exhibited a mitogenome belonging to sub-haplogroup D4h3a. This sub-haplogroup was earlier identified in the same general area at 10300 years BP on Prince of Wales Island, Alaska, and may have gone extinct, as it has not been observed in any living individuals of the Northwest Coast. The presented case studies demonstrate the different evolutionary paths of mitogenomes over time on the Northwest Coast.

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.

Investigating the case of human nose shape and climate adaptation

The evolutionary reasons for variation in nose shape across human populations have been subject to continuing debate. An import function of the nose and nasal cavity is to condition inspired air before it reaches the lower respiratory tract. For this reason, it is thought the observed differences in nose shape among populations are not simply the result of genetic drift, but may be adaptations to climate. To address the question of whether local adaptation to climate is responsible for nose shape divergence across populations, we use Qst–Fst comparisons to show that nares width and alar base width are more differentiated across populations than expected under genetic drift alone. To test whether this differentiation is due to climate adaptation, we compared the spatial distribution of these variables with the global distribution of temperature, absolute humidity, and relative humidity. We find that width of the nares is correlated with temperature and absolute humidity, but not with relative humidity. We conclude that some aspects of nose shape may indeed have been driven by local adaptation to climate. However, we think that this is a simplified explanation of a very complex evolutionary history, which possibly also involved other non-neutral forces such as sexual selection.

A South American Prehistoric Mitogenome: Context, Continuity, and the Origin of Haplogroup C1d

Based on mitochondrial DNA (mtDNA), it has been estimated that at least 15 founder haplogroups peopled the Americas. Subhaplogroup C1d3 was defined based on the mitogenome of a living individual from Uruguay that carried a lineage previously identified in hypervariable region I sequences from ancient and modern Uruguayan individuals. When complete mitogenomes were studied, additional substitutions were found in the coding region of the mitochondrial genome. Using a complete ancient mitogenome and three modern mitogenomes, we aim to clarify the ancestral state of subhaplogroup C1d3 and to better understand the peopling of the region of the Río de la Plata basin, as well as of the builders of the mounds from which the ancient individuals were recovered. The ancient mitogenome, belonging to a female dated to 1,610±46 years before present, was identical to the mitogenome of one of the modern individuals. All individuals share the mutations defining subhaplogroup C1d3. We estimated an age of 8,974 (5,748–12,261) years for the most recent common ancestor of C1d3, in agreement with the initial peopling of the geographic region. No individuals belonging to the defined lineage were found outside of Uruguay, which raises questions regarding the mobility of the prehistoric inhabitants of the country. Moreover, the present study shows the continuity of Native lineages over at least 6,000 years.

Development and Assessment of Postcranial Sex Estimation Methods for a Guatemalan Population

This study tests whether postcranial sex estimation methods generated from Hispanic, and mainly Mexican samples, can be successfully applied to other increasingly common migrant populations from Central America. We use a sample of postcranial data from a modern (1980s) Guatemalan Maya sample (n = 219). Results indicate a decrease in classification accuracies for previously established univariate methods when applied to the Guatemalan study sample, specifically for males whose accuracies ranged from 30 to 84%. This bias toward inaccuracies for Guatemalan males is associated with the smaller skeletal sizes for the Guatemalan sample as compared to the samples used in the tested sex estimation methods. In contrast, the tested multivariate discriminant function classification yielded less sex bias and improved classification accuracies ranging from 82 to 89%. Our results highlight which of the tested univariate and multivariate methods reach acceptable levels for accuracy for sex estimation of cases where the region of origin may include Guatemala.

Correction: Investigating the case of human nose shape and climate adaptation

[This corrects the article DOI: 10.1371/journal.pgen.1006616.].

Understanding (Mis)classification Trends of Latin Americans in Fordisc 3.1: Incorporating Cranial Morphology, Microgeographic Origin, and Admixture Proportions for Interpretation

Assigning correct population affinity to a skeleton can contribute important information to an investigation—yet recent work highlights high error rates when classifying Latinos with a traditional tool, Fordisc 3.1 (FD3). Our study examines whether misclassification trends exist, and whether these can be used to infer population affinity. We examine the relationships among ancestry, geography, and FD3 misclassifications of Latinos using canonical variate analysis and unsupervised model‐based clustering of craniometrics. Northern Mexicans appear more strongly associated with FD3 references samples with elevated amounts of European ancestry (e.g., American Blacks and Whites), while Southern Mexicans are more strongly associated with FD3 reference samples with reduced amounts of European ancestry (e.g., Guatemalans and Native Americans). FD3 classifications revealed that Latinos exhibited lower posterior probabilities when compared to other common case demographics (Whites and African Americas), even when the classification was “correct.” We make recommendations for practitioner interpretation of FD3 reports for casework.

Thinking Computationally about Forensics: Anthropological Perspectives on Advancements in Technologies, Data, and Algorithms

2Department of Scientifijic Computing, Florida State University, Tallahassee, Florida, USA. 3Department of Anthropology, University of Illinois at Urbana–Champaign, Champaign, Illinois, USA. *Correspondence to: Jieun Kim, Department of Scientifijic Computing, Florida State University, 400 Dirac Science Library, Tallahassee, FL 32306-4120 USA. E-mail: jkim17@fsu.edu.

Genetic Structure of First Nation Communities in the Pacific Northwest

ABSTRACT 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 aimed 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: genetic variation was more strongly explained by geographic proximity than by 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, analyses of molecular variance 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 as 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.