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During California’s Gold Rush of 1849–1855, thousands of miners rushed to San Francisco, Sacramento, and elsewhere throughout northern California, creating a significant demand for food. Here we investigate the role of Atlantic cod (Gadus morhua) and Pacific cod (G. macrocephalus) during the Gold Rush era using historical records, ancient DNA, and vertebral morphology in the cod assemblage recovered from Thompson’s Cove (CA-SFR-186H), a Gold Rush–era site in San Francisco. From the 18 cod bones recovered from Thompson’s Cove, our analysis of five specimens for ancient DNA indicates that Atlantic cod were imported during the 1850s, likely as a (largely) deboned, dried and salted product from the East Coast of the United States. Curiously, while locally available in very deep waters off the California coast, Pacific cod were minimally fished during the 1850s and became abundantly available in the 1860s after an Alaska-based fishery developed.

This study presents the results of ancient DNA analyses of eight snakehead (Channa sp.) bones from the Market Street Chinatown, a nineteenth-century Chinese diaspora archaeological site in San Jose, California. The sequences of a short stretch of the mitochondrial DNA identify the Market Street Chinatown snakeheads as Giant Snakehead (Channa micropeltes), a species native to Southeast Asia. These results provide the first archaeological evidence of the nineteenth-century trade of Asian freshwater fishes to North America, and they reveal that preserved fish products from throughout the Pacific World were readily distributed across the Chinese diaspora. We place our findings within the broader context of nineteenth-century Chinese migration to show how the common Chinese small shareholding business model and access to trade connections facilitated by Chinese-operated import/export firms known as jinshanzhuang allowed Chinese fishers to be successful across the Pacific World. Finally, we suggest avenues for future study by comparing Chinese migration-based, flexible fishing strategies using generalist methods with the highly specialized collection and trade of species like Atlantic Cod (Gadus morhua) in the North Atlantic.

People living in Mesoamerica and what is now the eastern and southwestern United States used turkeys (Meleagris gallopavo) as sources of meat, eggs, bones, and feathers. Turkey husbandry and domestication are confirmed in two of these regions (Mesoamerica and the American Southwest), but human-turkey interactions in Eastern North American (eastern United States and Canada) are not fully explored. We apply stable isotope (δ13C, δ15N) and ancient mitochondrial DNA analyses to archaeofaunal samples from seven sites in the southeastern United States to test whether turkeys were managed or captively reared. These combined data do not support prolonged or intensive captive rearing of turkeys, and evidence for less intensive management is ambiguous. More research is warranted to determine whether people managed turkeys in these areas, and whether this is generalizable. Determining whether turkeys were managed or reared in the southeastern United States helps define cultural and environmental factors related to turkey management or husbandry throughout North America. This inquiry contributes to discussion of the roles of intensified human-animal interactions in animal domestication.

Though chickens (Gallus gallus domesticus) are globally ubiquitous today, the timing, location, and manner of their domestication is contentious. Until recently, archaeologists placed the origin of the domestic chicken in northern China, perhaps as early as 8,000 years ago. Such evidence however complicates our understanding of how the chicken was domesticated because its wild progenitor – the red jungle fowl (Gallus gallus) – lives in tropical ecosystems and does not exist in northern China today or in the recent past. Increasingly, multiple lines of evidence suggest that many of the archaeological bird remains underlying this northern origins hypothesis have been misidentified. Here we analyze the mitochondrial DNA of some of the earliest purported chickens from the Dadiwan site in northern China and conclude that they are pheasants (Phasianus colchicus). Curiously, stable isotope values from the same birds reveal that their diet was heavy in agricultural products (namely millet), meaning that they lived adjacent to or among some of the earliest farming communities in East Asia. We suggest that the exploitation of these baited birds was an important adaptation for early farmers in China’s arid north, and that management practices like these likely played a role in the domestication of animals – including the chicken – in similar contexts throughout the region.

Spanish colonial rule in Peru was marked by dramatic changes to indigenous mortuary customs, bodily practices, and morbidity profiles. However, that era of transformation was not solely shaped by Spanish policies; Native Andeans creatively negotiated with those newcomers, sculpting novel practices that sometimes integrated, and other times challenged, the Spanish agenda. Theoretical perspectives on the constrained agency of indigenous communities under colonial rule and the negotiated outcomes of those colonial encounters are explored through a case study of mummy burials from the cave site of Vinchos in highland Peru and comparisons to other colonial Andean populations. We conduct osteological and stable isotope analyses, molecular assessment of sex chromosomes, and ancient mitochondrial DNA (mtDNA) analysis of the Vinchos mummies and 3,314 other HVR1 sequences from South America (haplotype network analysis). Results show that there are four adults, one child, and one fetus/infant. mtDNA analysis shows three distinct mtDNA lineages. Principal coordinate analysis shows that the Vinchos individuals are near to modern and ancient populations from the Andes; haplotype network analysis shows that one individual shares a haplotype with several geographically dispersed groups in South America, while three individuals exhibit two unique haplotypes. The data show the ongoing practice of cranial modification, the continuation of native mortuary practices, and some continuities in diet and foodways. Despite Spanish colonial attempts to eradicate indigenous practices, these multiple data sets reveal the agential capacities of Native Andeans—though constrained by colonial structures—to continue specific cultural traditions and forge novel practices while subjects of the Spanish Crown. La colonizacion espanola en Peru llevo cambios dramaticos en las costumbres mortuorias indigenas, las practicas corporales y los perfiles de morbilidad. Sin embargo, este periodo de transformacion no fue creado unicamente por las politicas espanolas. Los nativos andinos negociaron creativamente con los espanoles, desarrollando practicas novedosas que a veces integraban, y otras veces desafiaban, la agenda espanola. Las perspectivas teoricas sobre la agencia restringida de las comunidades indigenas y los resultados negociados del gobierno colonial se exploran a traves de un estudio de caso de entierros de momias del sitio de la cueva de Vinchos en las tierras altas de Peru en comparacion con otros poblados andinos. Realizamos analisis de isotopos estables y osteologicos, evaluacion molecular de cromosomas sexuales, analisis de mtADN antiguo de las momias de Vinchos y otras 3,314 secuencias de HVRI de America del Sur (analisis de red de haplotipos). Los resultados muestran que hay cuatro adultos, un nino y un feto/infante. El analisis de mtADN muestra tres linajes de mtADN distintos. El analisis de coordenadas principales muestra que los individuos Vinchos estan cerca de las poblaciones modernas y antiguas de los Andes. El analisis de la red de haplotipos muestra que un individuo comparte un haplotipo con varios grupos geograficamente dispersos en America del Sur, mientras que tres individuos exhiben dos haplotipos unicos. Los datos muestran la practica continua de modificacion craneal, la continuacion de las practicas mortuorias nativas (al menos para algunos) y algunas continuidades en la dieta y los alimentos. A pesar de los intentos coloniales por erradicar las practicas indigenas, estos conjuntos de datos multiples revelan las capacidades agenciales de los andinos nativos, aunque estan limitados por las estructuras coloniales, para continuar con tradiciones culturales especificas y forjar practicas novedosas mientras son sujetos de la Corona espanola.

Understanding a species’ historic range guides contemporary management and habitat restoration. Chinook salmon (Oncorhynchus tshawytscha) are an important commercial and recreational gamefish, but nine Chinook subspecies are federally threatened or endangered due to anthropogenic impacts. Several San Francisco Bay Area streams and rivers currently host spawning Chinook populations, but government agencies consider these non-native hatchery strays. Through the morphology-based analysis of 17,288 fish specimens excavated from Native American middens at Mission Santa Clara (CA-SCL-30H), Santa Clara County, circa 1781–1834 CE, 88 salmonid vertebrae were identified. Ancient DNA sequencing identified three separate individuals as Chinook salmon and the remainder as steelhead/rainbow trout (Oncorhynchus mykiss). These findings comprise the first physical evidence of the nativity of salmon to the Guadalupe River in San Jose, California, extending their documented historic range to include San Francisco Bay’s southernmost tributary watershed.

Understanding a species’ historic range guides contemporary management and habitat restoration. Chinook salmon (Oncorhynchus tshawytscha) are an important commercial and recreational gamefish, but nine Chinook subspecies are federally threatened or endangered due to anthropomorphic impacts. Several San Francisco Bay Area streams and rivers currently host spawning Chinook populations, but government agencies consider these non-native hatchery strays. Using ichthyofaunal analysis of 17,288 fish specimens excavated from Native American middens at Mission Santa Clara circa 1781-1834 CE, 86 salmonid vertebrae were identified. Ancient DNA sequencing identified three of these as from Chinook salmon and the remainder from steelhead trout. These findings comprise the first physical evidence of the nativity of salmon to the Guadalupe River in San Jose, California, extending their historic range to include San Francisco Bay’s southernmost watershed.One Sentence SummaryFirst application of ancient DNA to extend a species’ historic range finds Chinook salmon native to San Jose, California.

Stable isotope analyses show that Ancient Beringian diets were seasonally structured and included substantial summer salmon., The earliest Native Americans have often been portrayed as either megafaunal specialists or generalist foragers, but this debate cannot be resolved by studying the faunal record alone. Stable isotope analysis directly reveals the foods consumed by individuals. We present multi-tissue isotope analyses of two Ancient Beringian infants from the Upward Sun River site (USR), Alaska (~11,500 years ago). Models of fetal bone turnover combined with seasonally-sensitive taxa show that the carbon and nitrogen isotope composition of USR infant bone collagen reflects maternal diets over the summer. Using comparative faunal isotope data, we demonstrate that although terrestrial sources dominated maternal diets, salmon was also important, supported by carbon isotope analysis of essential amino acids and bone bioapatite. Tooth enamel samples indicate increased salmon use between spring and summer. Our results do not support either strictly megafaunal specialists or generalized foragers but indicate that Ancient Beringian diets were complex and seasonally structured.

In this study, we sought to document the efficiency of primer extension capture (PEC) as a method to enrich DNA eluates of targeted DNA molecules and remove nontarget molecules from pools containing both. Efficiency of the method was estimated by comparing number of "copies in" to "copies out" by quantitative polymerase chain reaction. PEC retention of DNA targets ranging 109-288 base pairs (bps) in length was 15.88-2.14% (i.e., loss of 84.12-97.86% of target molecules). Experimental modifications of the PEC method resulted in no significant improvements. However, the benefit of PEC was revealed in its ability to remove most nontarget DNA molecules (99.99%). We also discovered that many (56.69%) of the target molecules are "lost" prior to their immobilization on the streptavidin-coated beads. These estimates of methodological efficiency are directly comparable to previous ones observed following "fishing" for DNA, an alternative method for DNA enrichment.

The bulk storage and mass capture of small forage fish has played a primary role in the cultural traditions and subsistence practices of many ancient and modern indigenous communities throughout the world. Archaeologists are improving their recognition of human interaction with these fisheries through the application of fine-mesh screening techniques and ichthyofaunal analysis of fish bone. Because of the differing life histories of many of these fish, determining their species from archaeological contexts can improve our resolution of past harvesting and consumption patterns. This has remained a challenge for many categories of fish, such as salmon and smelt. Here, we present an improved genetic species identification process that utilizes ancient DNA amplification techniques involving a reagent-rich PCR protocol (i.e., “Rescue PCR”) and a PCR Enhancer Cocktail P (i.e., PEC-P) to identify smelt and other forage fish bone from five archaeological sites located along the northern California (United States) Pacific coast dating to the Late Period (after 1300 cal BP). Through the application of these novel techniques, our species identification success rate increased to 71.2% overall, with some sites having a remarkable 100% success rate. We identified the species of 104 of 146 fish vertebrae, and determined that inhabitants at these sites harvested primarily surf smelt with potentially less emphasis on night smelt. Observations of herring, perch, sculpin and rainbow trout/steelhead were also made. Along with these small surf fish, we found evidence of larger fish such as shark and Pacific hake (common predatory fish in the area). The study demonstrates a significant breakthrough in ancient DNA identification techniques that resulted in information that speak to the long term continuity of use of mass harvested forage fish by indigenous peoples. The results of this project help establish a better understanding of subsistence and cultural traditions of northern California indigenous communities, with the potential to provide a more global understanding of fishing technologies, sustainability, and mass harvesting of small fishes.

This study sought to document the efficiency of DNA bait capture (i.e., "fishing") methods by two measures: (1) its ability to retain targeted DNA molecules, and (2) its ability to remove non-target DNA molecules from a pool containing both. DNA bait capture uses synthetic biotinylated DNA primers to bind target DNA, which are then immobilized onto streptavidin coated magnetic beads and drawn to a magnet. Bound DNA should, therefore, be isolated from non-target DNA and impurities (e.g., PCR inhibitors) and can be later eluted from the beads for downstream applications. Efficiencies were estimated by comparing the number of "copies in" to "copies out" with quantitative polymerase chain reaction (qPCR). Retention of target DNA molecules, ranging from 109 to 288 base pairs (bps) in length, averaged just 9.06–3.53% (i.e., loss of 90.94–96.47%) using the fishing protocol as originally described. Some improvement was achieved by employing a modified protocol (i.e., with a shortened hybridization time, use of twice the amount of M-270 streptavidin-coated beads, and modified bead washing), resulting in average retention of 31.41–12.08% of the same set of targeted molecules. Noted was the lack of efficacy in removing non-target DNA molecules as opposed to targeted molecules. It was also observed that most of the molecules (61.35–69.49%) are "lost" during the essential hybridization step of the fishing protocol, suggesting its suitability for high copy number samples only. While the bait capture method may be useful in the study of polymerase chain reaction (PCR) inhibited DNA samples as previously suggested, it is necessary to carefully weigh this possible advantage against the degree of expected DNA loss and the non-selectivity of the method for targeted over non-targeted DNA.

Minimizing the inadvertent co-extraction of polymerase chain reaction (PCR) inhibitors and/or subduing their influence are two of the most pervasive challenges in the study of ancient DNA (aDNA). Some commonly employed methods to circumvent inhibition include dilution of DNA extracts and/or removal of inhibitors via silica-based treatments. While these methods have been shown to be effective, they may not be useful for all aDNA extracts. Samples with very low copy number, for instance, may not benefit from such methods, as dilutions lower DNA concentration in tandem with the inhibitors, and some DNA loss is expected to follow silica-based treatments. Therefore, the development of additional options to overcome PCR inhibition is at a premium. In this study, we present evidence that a reagent-rich PCR protocol, where all reagents are increased in equal relative proportion can increase amplification success when DNA concentration is reduced relative to inhibitors. The reagent-rich PCR recipe, termed rescue PCR, increased amplification success by 51% for the 112 extracts used in the study. Rescue PCR represents a simple and robust addition to the suite of options currently available to work with DNA in the presence of inhibition, especially ancient, degraded, and low copy number DNA extracts.

The turkey (Meleagris gallopavo) was independently domesticated in Mesoamerica and the Southwest, the latter as the only case of Native American animal domestication north of Mexico. In the upland (non-desert) portion of the American Southwest, distinctive closely related mtDNA lineages belonging to haplogroup H1 (thought to indicate domestication) occur from ca. 1 A.D. (Basketmaker II period) through early historic times. At many sites, low frequencies of lineages belonging to haplogroup H2 also occur, apparently derived from the local Merriam’s subspecies. We report genetic, stable isotope, and coprolite data from turkey remains recovered at three early sites in SE Utah and SW Colorado dating to the Basketmaker II, III, and early Pueblo II periods. Evidence from these and other early sites indicates that both the H1 and H2 turkeys had a predominantly maize-based diet similar to that of humans; prior to late Pueblo II times, the birds were kept primarily to provide feathers for blankets and ritual uses; and ritualized burials indicate turkeys’ symbolic value. We argue that viewing individuals from the H1 and H2 haplogroups as “domestic” versus “wild” is an oversimplification.

The Columbia River and its tributaries provide essential spawning and rearing habitat for many salmonid species, including Chinook salmon (Oncorhynchus tshawytscha). Chinook salmon were historically abundant throughout the basin and Native Americans in the region relied heavily on these fish for thousands of years. Following the arrival of Europeans in the 1800s, salmon in the basin experienced broad declines linked to overfishing, water diversion projects, habitat destruction, connectivity reduction, introgression with hatchery-origin fish, and hydropower development. Despite historical abundance, many native salmonids are now at risk of extinction. Research and management related to Chinook salmon is usually explored under what are termed "the four H's": habitat, harvest, hatcheries, and hydropower; here we explore a fifth H, history. Patterns of prehistoric and contemporary mitochondrial DNA variation from Chinook salmon were analyzed to characterize and compare population genetic diversity prior to recent alterations and, thus, elucidate a deeper history for this species. A total of 346 ancient and 366 contemporary samples were processed during this study. Species was determined for 130 of the ancient samples and control region haplotypes of 84 of these were sequenced. Diversity estimates from these 84 ancient Chinook salmon were compared to 379 contemporary samples. Our analysis provides the first direct measure of reduced genetic diversity for Chinook salmon from the ancient to the contemporary period, as measured both in direct loss of mitochondrial haplotypes and reductions in haplotype and nucleotide diversity. However, these losses do not appear equal across the basin, with higher losses of diversity in the mid-Columbia than in the Snake subbasin. The results are unexpected, as the two groups were predicted to share a common history as parts of the larger Columbia River Basin, and instead indicate that Chinook salmon in these subbasins may have divergent demographic histories.

Significance Fish bones from the 11,500-y-old Upward Sun River site in interior Alaska represent the oldest evidence for salmon fishing in North America. We used ancient DNA analysis to identify the fish specimens as chum salmon ( Oncorhynchus keta ), and stable isotope analysis to confirm that the salmon were anadromous (sea-run). The exploitation of salmon at this early date is noteworthy because Paleoindians are traditionally portrayed as big-game hunting specialists. Furthermore, the presence of salmon at Upward Sun River over 1,400 km upriver from the coast shows that spawning runs had been established by the end of the last Ice Age. The early availability and use of anadromous salmon has important implications for understanding Paleoindian economies and expansion into North America.

Objectives The human population history from Patagonia and Tierra del Fuego has been of great interest in the context of the American peopling. Different sources of evidence have contributed to the characterization of the local populations, but some main questions about their history remain unsolved. Among the native populations, two marine hunter-gatherers groups inhabited the Patagonian channels below the 478S: Kaweskar and Yamana. Regardless of their geographical proximity and cultural resemblance, their languages were mutually unintelligible. In this study we aim to evaluate the genetic diversity of uniparental genetic markers in both groups and to test if there is a high genetic differentiation between them, mirroring their linguistic differences. Material and Methods Ancient DNA was extracted from 37 samples from both populations. We compared their genetic variability of their mitochondrial lineages and Y-STR as well as with other modern native populations from the area and further north. Results and Discussion We observed an important differentiation in their maternal lineages: while Kaweskar shows a high frequency of D (80%), Yamana shows a high frequency of C (90%). The analysis of paternal lineages reveals the presence of only Q1a2a1a1 and little variation was found between individuals. Both groups show very low levels of genetic diversity compared with modern populations. We also notice shared and unique mitochondrial DNA variants between modern and ancient samples of Kaweskar and Yamana. Am J Phys Anthropol 158:719–729, 2015. © 2015 Wiley Periodicals, Inc.

As dogs have traveled with humans to every continent, they can potentially serve as an excellent proxy when studying human migration history. Past genetic studies into the origins of Native American dogs have used portions of the hypervariable region (HVR) of mitochondrial DNA (mtDNA) to indicate that prior to European contact the dogs of Native Americans originated in Eurasia. In this study, we summarize past DNA studies of both humans and dogs to discuss their population histories in the Americas. We then sequenced a portion of the mtDNA HVR of 42 pre-Columbian dogs from three sites located in Illinois, coastal British Columbia, and Colorado, and identify four novel dog mtDNA haplotypes. Next, we analyzed a dataset comprised of all available ancient dog sequences from the Americas to infer the pre-Columbian population history of dogs in the Americas. Interestingly, we found low levels of genetic diversity for some populations consistent with the possibility of deliberate breeding practices. Furthermore, we identified multiple putative founding haplotypes in addition to dog haplotypes that closely resemble those of wolves, suggesting admixture with North American wolves or perhaps a second domestication of canids in the Americas. Notably, initial effective population size estimates suggest at least 1000 female dogs likely existed in the Americas at the time of the first known canid burial, and that population size increased gradually over time before stabilizing roughly 1200 years before present.

Recent genome-wide 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 due to its association with coastal migration models and genetic ancestral patterns that are difficult to reconcile with modern DNA alone. Here we report the genome-wide 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 approximately 10,300 cal years before present (BP). We also analyze low coverage genomes of three more recent individuals from the nearby coast of British Columbia dating from approximately 6075 to 1750 cal years BP. 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 BP. We also infer that population structure existed in the late Pleistocene of North America with Shuká Káa on a different ancestral line compared to other North American individuals (i.e., Anzick-1 and Kennewick Man) from the late Pleistocene or early Holocene. Despite regional shifts in mitochondrial DNA 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.Significance StatementThe peopling of the Americas has been examined on the continental level with the aid of single-nucleotide polymorphism arrays, next generation sequencing, and advancements in ancient DNA, all of which have helped elucidate major population movements. Regional paleogenomic studies, however, have received less attention and may reveal a more nuanced demographic history. Here we present genomewide sequences of individuals from the northern Northwest Coast covering a time span of ~10,000 years and show that continental patterns of demography do not necessarily apply on the regional level. In comparison with existing paleogenomic data, we demonstrate that geographically linked population samples from the Northwest Coast exhibit an early ancestral lineage and find that population structure existed among Native North American groups as early as the late Pleistocene.

We tested a novel hypothesis that recreational use of neurotoxic plants helps defend against parasites. Specifically, we investigated the relationship between smoking and helminthiasis among the Aka, a remote population of Central African foragers who are avid tobacco smokers, suffer high rates of helminthiasis, and have little-to-no access to commercial anthelmintics. Two hundred and six healthy Aka men provided saliva and stool samples. Saliva samples were assayed for cotinine, a nicotine metabolite; a subsample was genotyped for the CYP2A6 enzyme, which metabolizes nicotine. Stool samples were assayed for intestinal helminth eggs as an index of worm burden. After 1year, a subsample of participants was located and provided additional saliva and stool samples. We found (1) an exceptionally high prevalence of tobacco use, (2) a significant negative correlation between cotinine (a nicotine metabolite) and worm burden, (3) that treating helminths with albendazole, a commercial anthelmintic, reduced cotinine concentration two weeks later, compared to placebo controls, (4) among treated participants, higher cotinine concentrations in year 1 predicted less reinfection by year 2, and (5) younger and older participants with slow nicotine-metabolizing CYP2A6 alleles had lower worm burdens compared to those with extensive metabolizing alleles. These results provide the first evidence of a link between helminthiasis and smoking. They also suggest that, in populations where intestinal helminths are endemic, tobacco use might protect against helminth infection and reduce worm burden among infected individuals, and that individuals modulate nicotine exposure in response to infection. The results thus support the hypothesis that substance use helps defend against parasites.

DNA from ancient sources is generally believed to be of low copy number, despite minimal attention towards direct measurement of DNA loss accumulated through the extraction process. We developed synthesized “standards” to measure the efficiency of some common DNA extraction methods for degraded skeletal samples, and used quantitative PCR to estimate a known quantity of DNA subjected to a given extraction method (i.e. “copies in”) versus quantity of DNA retained (i.e. “copies out”). All methods performed poorly in retaining short segments of DNA, giving low copy number results even when pre-extraction copy numbers exceeded those expected of ancient samples. These findings challenge low copy number expectations, suggesting that ancient specimens may contain far more preserved genetic material than previously recognized. Furthermore, they emphasize the importance of optimizing and/or developing specialized extraction methods for retrieving degraded DNA.

American Beauty Modern Native American ancestry traces back to an East Asian migration across Beringia. However, some Native American skeletons from the late Pleistocene show phenotypic characteristics more similar to other, more geographically distant, human populations. Chatters et al. (p. 750 ) describe a skeleton with a Paleoamerican phenotype from the eastern Yucatan, dating to approximately 12 to 13 thousand years ago, with a relatively common extant Native American mitochondrial DNA haplotype. The Paleoamerican phenotype may thus have evolved independently among Native American populations.

This study evaluated techniques that can potentially decrease time, cost, and labor in eliminating, circumventing, and/or inactivating as many polymerase chain reaction (PCR) inhibitors as possible while preserving DNA yield. In order to further explore the role of PCR inhibitors in ancient DNA (aDNA) studies, 140 DNA extractions were conducted on 112 Pacific salmonid vertebrae recovered from two archaeological sites located at Dionisio Point on Galiano Island, in southwestern British Columbia, Canada. These DNA extracts and their dilutions at 1:10 and 1:50 were screened for the presence of a 189 base pair (bp) portion of the 12S mitochondrial gene that is used for species identification of Pacific salmonids and other fish. These extracts and their dilutions were also screened for the presence of PCR inhibitors that can cause negative results for amplification of salmonid mtDNA. Repeat silica extraction was conducted on the full concentration extracts until: (1) they either produced a positive result in the salmonid mtDNA reaction, or (2) were deemed to be free of inhibition, but failed to amplify in the salmonid mtDNA reaction. In the latter case, the samples were concluded to not contain sufficient salmonid mtDNA to permit PCR amplification. In obtaining positive salmonid species identification, repeat silica purified extracts (81/133 successes) statistically outperformed dilutions at 1:10 (55/140, p ¼0.0018), 1:50 (63/140, p ¼0.0312), as well as across all dilutions combined (118/280, p ¼0.0025). We also explored the efficacy of EGTA as a decalcifying agent as compared to EDTA, which is commonly employed in aDNA studies. The only extracts that amplified at full concentration (6/140, 4.3%) were those in which EGTA decalcification was used. However, when diluted there was no statistical difference in the success of obtaining positive species identification from bone decalcified with EGTA or EDTA (1:10 and 1:50 dilutions, p ¼0.7891 and p > 0.9999 respectively). From the results of this study, we recommend that aDNA researchers employ greater flexibility in their methodologies as well as be cognizant of the role that PCR inhibitors may play in their investigations.

Bayesian methods have been adopted by anthropologists for their utility in resolving complex questions about human history based on genetic data. The main advantages of Bayesian methods include simple model comparison, presenting results as a summary of probability distributions, and the explicit inclusion of prior information into analyses. In the field of anthropological genetics, for example, implementing Bayesian skyline plots and approximate Bayesian computation is becoming ubiquitous as means to analyze genetic data for the purpose of demographic or historic inference. Correspondingly, there is a critical need for better understanding of the underlying assumptions, proper applications, and limitations of these two methods by the larger anthropological community. Here we review Bayesian skyline plots and approximate Bayesian computation as applied to human demography and provide examples of the application of these methods to anthropological research questions. We also review the two core components of Bayesian demographic analysis: the coalescent and Bayesian inference. Our goal is to describe their basic mechanics in an attempt to demystify them.

The Tlingit from Southeast Alaska belong to the Northwest Coast cultural tradition, which is defined by regionally shared sociocultural practices. A distinctive feature of Tlingit social organization is the matrilineal exogamous marriage system among clans from two opposite moieties: the Raven/Crow and Eagle/Wolf. Clan and moiety membership are determined by matrilineal descent, and previous genetic studies of Northwest Coast populations have shown a relationship between clan membership and genetic variation of matrilines and patrilines. To further understand this association, in this study mitochondrial DNA sequences from the Tlingit (n = 154) were examined. By comparing mitochondrial DNA with moiety membership information, the authors explore the impact of marriage traditions among the Tlingit with their observable genetic variation. At the genetic level, the results support cultural persistence of Tlingit maternal moiety identity despite the negative impacts of European colonization. This study additionally illustrates the relevance of data derived from Tlingit oral traditions to test hypotheses about population history on the Northwest Coast.

Studies of low copy number (LCN) and degraded DNA are prone to contamination from exogenous DNA sources that in some cases out-compete endogenous DNA in PCR amplification, thus leading to false positives and/or aberrant results. Particularly problematic is contamination that is inadvertently deposited on the surfaces of bones through direct handling. Whereas some previous studies have shown that contamination removal is possible by subjecting samples to sodium hypochlorite prior to DNA extraction, others caution that such treatment can destroy a majority of the molecules endogenous to the sample. To further explore this topic, we experimentally contaminated ancient northern fur seal ( Callorhinus ursinus ) ribs with human DNA and treated them with sodium hypochlorite to remove that contamination. Our findings are consistent with previous studies that found sodium hypochlorite to be highly efficient (∼81–99%) at contamination removal; however, there emerged no treatment capable of removing 100% of the contamination across all of the experiments. Moreover, the ability to estimate the degree of damage to endogenous northern fur seal molecules was compromised due to the inherent variability of preserved mtDNA across the bones, and the presence of co-extracted PCR inhibitors.

A recent study of mitochondrial DNA variation in Native American populations from the American Southwest detected signatures of a population expansion of subhaplogroup B2a, dated to 2,105 years before present (99.5% confidence interval, 1,273–3,773 YBP), following the introduction and intensification of maize agriculture in the region. Only one Yuman group and no Athapaskan speakers were analyzed in previous studies. Here we report mtDNA haplogroup and hypervariable region (HVR I, and II) sequence data from 263 extant Yuman speakers, representing the major branches of the Yuman language family, in addition to the Western Apache (Athapaskan) to further investigate the demographic context and geographic extent of this expansion. Data presented indicate that the expansion of B2a is only slightly older [2,410 YBP (99.5% CI: 1,458–4,320 YBP)] than previously estimated and not significantly. Despite large confidence intervals there are implications for the origin and expansion of the Yuman language family. Cultural transformations due to the inundation and draining of Lake Cahuilla may explain in part the frequencies of this lineage among the Kumeyaay and other Yuman and Takic groups in Southern California. This may have been the result of group fissions and fusions followed by migration and interaction that included expanded trade networks and intermarriage among Yuman speakers. In addition, a series of in-situ genetic bottlenecks is proposed to have occurred among the Western Apache leading to increasing homogeneity within haplogroup A, culminating in an admixture event with the Yavapai. Am J Phys Anthropol 150:618–631, 2013. © 2013 Wiley Periodicals, Inc.

Determining the diversity of salmon species represented in archaeological contexts is critical to understanding patterns of salmon harvesting and consumption, storage practices and seasonal patterns of resource exploitation by precontact peoples of the Northwest Coast. We present species determinations generated for salmon vertebrae from the Dionisio Point site (DgRv-003) in coastal southwestern British Columbia, a well-preserved village site that dates to between 1500 and 1300 cal BP. Molecular species identification was possible for 70 Pacific salmonid vertebral elements recovered from one excavated plankhouse at the site. Coupled with osteometric measures, we determine that residents of the plankhouse fished primarily for chum, sockeye and pink salmon, with a lesser emphasis on chinook, coho and steelhead. These results indicate a diverse fishery that likely occurred between July and December, suggesting a mid summer through winter season of occupation for the village.

In AD 1428, the city-states of Tenochtitlan, Texcoco, and Tlacopan formed the Triple Alliance, laying the foundations of the Aztec empire. Although it is well documented that the Aztecs annexed numerous polities in the Basin of Mexico over the following years, the demographic consequences of this expansion remain unclear. At the city-state capital of Xaltocan, 16th century documents suggest that the site's conquest and subsequent incorporation into the Aztec empire led to a replacement of the original Otomí population, whereas archaeological evidence suggests that some of the original population may have remained at the town under Aztec rule. To help address questions about Xaltocan's demographic history during this period, we analyzed ancient DNA from 25 individuals recovered from three houses rebuilt over time and occupied between AD 1240 and 1521. These individuals were divided into two temporal groups that predate and postdate the site's conquest. We determined the mitochondrial DNA haplogroup of each individual and identified haplotypes based on 372 base pair sequences of first hypervariable region. Our results indicate that the residents of these houses before and after the Aztec conquest have distinct haplotypes that are not closely related, and the mitochondrial compositions of the temporal groups are statistically different. Altogether, these results suggest that the matrilines present in the households were replaced following the Aztec conquest. This study therefore indicates that the Aztec expansion may have been associated with significant demographic and genetic changes within Xaltocan.

They Walked Together Paisley Cave in Oregon provides some of the earliest evidence for humans in North America. Jenkins et al. (p. 223 ) provide a wide variety of additional evidence of early human occupation of this site, including a series of radiocarbon ages extending back to nearly 12,500 radiocarbon years ago (about 14,500 calendar years ago). The find includes examples of projectile points representative of the Western Stemmed Tradition dating to about 11,100 radiocarbon years ago. The Western Stemmed Tradition has been thought to have evolved after the dominant Clovis technology, but the find suggests that the two cultures overlapped in time.

Many well-preserved bones of medium-sized goose have been recovered from the Zeto Point archaeological site (ADK-011) on Adak Island in the central Aleutians, Alaska, that date to ca. 170–415 years before present based on conventional radiometric dates of the deposits. This prehistoric sample includes remains of adults and unfledged goslings that defied confident identification based on osteological criteria. While the presence of newborns indicates that Adak was a breeding ground, which species was doing the nesting remained uncertain. Of the five species of medium-sized goose (order Anseriformes, family Anatidae) known or presumed to visit Adak Island, three are rarely sighted. The only common visitor is the Emperor Goose ( Chen canagica (Sevastianov, 1802)). The Aleutian Cackling Goose ( Branta hutchinsii leucopareia (Brandt, 1836)) breeds elsewhere in the Aleutians but does not currently breed on Adak Island and there are no records of it nesting there in the past. Here DNA sequences from portions of the cytochrome b (cytb) gene and the control region (CR) of the mitochondrial genome were recovered from 28 of 29 Adak prehistoric goose remains. All adult specimens identified to species were either C. canagica or B. h. leuopareia, but all specifically identified juvenile specimens were B. h. leuopareia. The results demonstrate that Adak Island was a breeding ground of the Aleutian Cackling Goose prior to European contact.

To investigate the origin of Koreans, we examined the 12‐locus Y‐chromosome short tandem repeat (Y‐STR) variation in a sample of 310 unrelated males from three localities (Gochang, Andong and Geoje) in Korea and statistically analyzed the previously published four Y‐STR databases (n = 1655) of Korean population. The median joining network of 9‐locus Y‐STR haplotypes inferred as haplogroup O2b‐SRY+465 showed a “star cluster” indicative of a population expansion from a centrally positioned haplotype. The central haplotype in the “star cluster” was the most frequently occurring Y‐STR haplotype among the Korean male gene pool (6%, 127 of 1965, 10,14,12,13,14,16,13,13,23, for loci DYS391, DYS389I, DYS439, DYS438, DYS437, DYS19, DYS392, DYS393, and DYS390), which was shared among all seven datasets. Based on the “star cluster” pattern from both our data (41%, 128 of 310) and those previously published (34%, 563 of 1655), we suggest that the most frequent Y‐STR haplotype among the Korean male gene pool seems to be the Korean modal (ancestral) haplotype. Further study with additional Y‐STR and Y‐SNP data of the east Asian populations as well as Korean

Mitochondrial DNA (mtDNA) was extracted from skeletal remains excavated from three Arikara sites in South Dakota occupied between AD 1600 and 1832. The diagnostic markers of four mtDNA haplogroups to which most Native Americans belong (A, B, C, and D) were successfully identified in the extracts of 55 (87%) of the 63 samples studied. The frequencies of the four haplogroups were 42%, 29%, 22%, and 7%, respectively, and principal coordinates analysis and Fisher's exact tests were conducted to compare these haplogroup frequencies with those from other populations. Both analyses showed closer similarity among the Mohawk, Arikara, and Sioux populations than between any of these three and any other of the comparison populations. Portions of the first hypervariable segment (HVSI) of the mitochondrial genome were successfully amplified and sequenced for 42 of these 55 samples, and haplotype networks were constructed for two of the four haplogroups. The sharing of highly derived lineages suggests that some recent admixture of the Arikara with Algonquian-speaking and Siouan-speaking groups has occurred. The Arikara shared more ancient lineages with both Siouan and Cherokee populations than with any other population, consistent with the Macro-Siouan language hypothesis that Iroquoian, Siouan, and Caddoan languages share a relatively recent common ancestry.

The Farming/Language Dispersal Hypothesis posits that prehistoric population expansions, precipitated by the innovation or early adop-tion of agriculture, played an important role in the uneven distribution of language families recorded across the world. In this case, the most widely spread language families today came to be distributed at the expense of those that have more restricted distributions. In the Americas, Uto-Aztecan is one such language family that may have been spread across Mesoamerica and the American Southwest by ancient farmers. We evaluated this hypothesis with a large-scale study of mitochondrial DNA (mtDNA) and Y-chromosomal DNA vari-ation in indigenous populations from these regions. Partial correlation coefficients, determined with Mantel tests, show that Y-chromosome variation in indigenous populations from the American Southwest and Mesoamerica correlates significantly with linguistic distances ( r = 0.33–0.384; P < 0.02), whereas mtDNA diversity correlates significantly with only geographic distance ( r = 0.619; P = 0.002). The lack of correlation between mtDNA and Y-chromosome diversity is consistent with differing population histories of males and females in these regions. Although unlikely, if groups of Uto-Aztecan speakers were responsible for the northward spread of agriculture and their languages from Mesoamerica to the Southwest, this migration was possibly biased to males. However, a recent in situ population expansion within the American Southwest (2,105 years before present; 99.5% confidence interval = 1,273–3,773 YBP), one that probably followed the introduction and intensification of maize agriculture in the region, may have blurred ancient mtDNA patterns, which might otherwise have revealed a closer genetic relationship between females in the Southwest and Mesoamerica.

Although the cultural and nutritive importance of the turkey ( Meleagris gallopavo ) to precontact Native Americans and contemporary people worldwide is clear, little is known about the domestication of this bird compared to other domesticates. Mitochondrial DNA analysis of 149 turkey bones and 29 coprolites from 38 archaeological sites (200 BC–AD 1800) reveals a unique domesticated breed in the precontact Southwestern United States. Phylogeographic analyses indicate that this domestic breed originated from outside the region, but rules out the South Mexican domestic turkey ( Meleagris gallopavo gallopavo ) as a progenitor. A strong genetic bottleneck within the Southwest turkeys also reflects intensive human selection and breeding. This study points to at least two occurrences of turkey domestication in precontact North America and illuminates the intensity and sophistication of New World animal breeding practices.

We analyzed two mid-Holocene (∼5000 years before present) individuals from North America that belong to mitochondrial DNA (mtDNA) haplogroup M, a common type found in East Asia, but one that has never before been reported in ancient or living indigenous populations in the Americas. This study provides evidence that the founding migrants of the Americas exhibited greater genetic diversity than previously recognized, prompting us to reconsider the widely accepted five-founder model that posits that the Americas were colonized by only five founding mtDNA lineages. Additional genetic studies of prehistoric remains in the Americas are likely to reveal important insights into the early population history of Native Americans. However, the usefulness of this information will be tempered by the ability of researchers to distinguish novel founding lineages from contamination and, as such, we recommend strategies to successfully accomplish this goal.

Mitochondrial and Y-chromosome DNA were analyzed from 10,300-year-old human remains excavated from On Your Knees Cave on Prince of Wales Island, Alaska (Site 49-PET-408). This individual's mitochondrial DNA (mtDNA) represents the founder haplotype of an additional subhaplogroup of haplogroup D that was brought to the Americas, demonstrating that widely held assumptions about the genetic composition of the earliest Americans are incorrect. The amount of diversity that has accumulated in the subhaplogroup over the past 10,300 years suggests that previous calibrations of the mtDNA clock may have underestimated the rate of molecular evolution. If substantiated, the dates of events based on these previous estimates are too old, which may explain the discordance between inferences based on genetic and archaeological evidence regarding the timing of the settlement of the Americas. In addition, this individual's Y-chromosome belongs to haplogroup Q-M3*, placing a minimum date of 10,300 years ago for the emergence of this haplogroup.

The success of ancient DNA (aDNA) studies rests on the preservation of DNA through time, and can be limited by the availability of skeletal samples from particular times and locations. To help overcome this limitation, we sought to extract, amplify, and type human mitochondrial DNA (mtDNA) preserved within 1000- to 2000+-year-old artifacts from the American Southwest. In this study, we successfully typed mtDNA from 21 quids and aprons from Basketmaker II and Mimbres contexts. Recovery and analysis of human DNA from such artifacts will be helpful in confirming and extending genetic characterization of ancient populations for which human remains are scarce or unavailable. To illustrate the potential of these techniques, we tested them as a preliminary and independent line of evidence, relevant to the hypothesis that Western Basketmaker populations in the U S. Southwest were descendants of migrant farmers from central Mexico.

The human population history from Patagonia and Tierra del Fuego has been of great interest in the context of the American peopling. Different sources of evidence have contributed to the characterization of the local populations, but some main questions about their history remain unsolved. Among the native populations, two marine hunter-gatherers groups inhabited the Patagonian channels below the 478S: Kawéskar and Yámana. Regardless of their geographical proximity and cultural resemblance, their languages were mutually unintelligible. In this study we aim to evaluate the genetic diversity of uniparental genetic markers in both groups and to test if there is a high genetic differentiation between them, mirroring their linguistic differences.Ancient DNA was extracted from 37 samples from both populations. We compared their genetic variability of their mitochondrial lineages and Y-STR as well as with other modern native populations from the area and further north.We observed an important differentiation in their maternal lineages: while Kawéskar shows a high frequency of D (80%), Yámana shows a high frequency of C (90%). The analysis of paternal lineages reveals the presence of only Q1a2a1a1 and little variation was found between individuals. Both groups show very low levels of genetic diversity compared with modern populations. We also notice shared and unique mitochondrial DNA variants between modern and ancient samples of Kawéskar and Yámana.

Prüfer and Meyer raise concerns over the mitochondrial DNA (mtDNA) results we reported for the Hoyo Negro individual, citing failure of a portion of these data to conform to their expectations of ancient DNA (aDNA). Because damage patterns in aDNA vary, outright rejection of our findings on this basis is unwarranted, especially in light of our other observations.

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we find that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (KYA), and after no more than 8,000-year isolation period in Beringia. Following their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 KYA, one that is now dispersed across North and South America and the other is restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative ‘Paleoamerican’ relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.