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Prior to their extirpation around 1900 CE, Lake Ontario hosted the world’s largest freshwater Atlantic salmon (Salmo salar) fishery. Due to their early disappearance, questions remained about fundamental aspects of the species’ biology, such as whether they belonged to sea-run (anadromous) or freshwater resident (potamodromous) ecotypes. Recent isotopic analyses have demonstrated that the complex of Atlantic salmon populations spawning in tributaries emptying along Lake Ontario’s northern shores were potamodromous. However, no evidence has yet been gathered for Atlantic salmon migratory behaviour from Lake Ontario’s southeastern region, where historical observations suggest both anadromous and potamodromous populations may have spawned. Here, we provide the first results for isotopic analyses of bone collagen from seven fish bones from archaeological sites (c. 1427 to 1600 CE) identified as Atlantic salmon through ancient DNA and zooarchaeological analyses. The results of the isotopic analyses confirm that at least some of the salmon spawning in tributaries emptying into Lake Ontario’s southeastern shores were also potamodromous. Although further analyses are needed, this suggests anadromy may have been completely absent in Lake Ontario’s complex of Atlantic salmon populations in recent centuries.

Ancient DNA was extracted from 12 500 to 10 500 year old ground squirrel bones from Tse’K’wa, an archaeological site in the Peace River region of northeastern British Columbia, Canada. Analysis of mitochondrial DNA from seven individuals demonstrates that all are Urocitellus richardsonii (Richardson’s ground squirrel), a species not found in the region today. Phylogenetic and sequence analyses indicate these individuals share a previously undocumented mitochondrial control region haplotype that is most closely related to haplotypes observed in modern specimens from Saskatchewan and Montana. At the end of the Pleistocene these ground squirrels extended their range north and west into open vegetation communities that developed when ice sheets melted and glacial lakes drained. They were subsequently extirpated from the Peace River region when forests replaced earlier pioneering vegetation communities.

Wild specimens are often collected in challenging field conditions, where samples may be contaminated with the DNA of conspecific individuals. This contamination can result in false genotype calls, which are difficult to detect, but may also cause inaccurate estimates of heterozygosity, allele frequencies and genetic differentiation. Marine broadcast spawners are especially problematic, because population genetic differentiation is low and samples are often collected in bulk and sometimes from active spawning aggregations. Here, we used contaminated and clean Pacific herring (Clupea pallasi) samples to test (a) the efficacy of bleach decontamination, (b) the effect of decontamination on RAD genotypes and (c) the consequences of contaminated samples on population genetic analyses. We collected fin tissue samples from actively spawning (and thus contaminated) wild herring and nonspawning (uncontaminated) herring. Samples were soaked for 10 min in bleach or left untreated, and extracted DNA was used to prepare DNA libraries using a restriction site-associated DNA (RAD) approach. Our results demonstrate that intraspecific DNA contamination affects patterns of individual and population variability, causes an excess of heterozygotes and biases estimates of population structure. Bleach decontamination was effective at removing intraspecific DNA contamination and compatible with RAD sequencing, producing high-quality sequences, reproducible genotypes and low levels of missing data. Although sperm contamination may be specific to broadcast spawners, intraspecific contamination of samples may be common and difficult to detect from high-throughput sequencing data and can impact downstream analyses.

The timing of reproduction influences key evolutionary and ecological processes in wild populations. Variation in reproductive timing may be an especially important evolutionary driver in the marine environment, where the high mobility of many species and few physical barriers to migration provide limited opportunities for spatial divergence to arise. Using genomic data collected from spawning aggregations of Pacific herring (Clupea pallasii) across 1600 km of coastline, we show that reproductive timing drives population structure in these pelagic fish. Within a specific spawning season, we observed isolation by distance, indicating that gene flow is also geographically limited over our study area. These results emphasize the importance of considering both seasonal and spatial variation in spawning when delineating management units for herring. On several chromosomes, we detected linkage disequilibrium extending over multiple Mb, suggesting the presence of chromosomal rearrangements. Spawning phenology was highly correlated with polymorphisms in several genes, in particularSYNE2, which influences the development of retinal photoreceptors in vertebrates.SYNE2is probably within a chromosomal rearrangement in Pacific herring and is also associated with spawn timing in Atlantic herring (Clupea harengus). The observed genetic diversity probably underlies resource waves provided by spawning herring. Given the ecological, economic and cultural significance of herring, our results support that conserving intraspecific genetic diversity is important for maintaining current and future ecosystem processes.

Many Indigenous People value dogs as hunting aides, draft animals, sources of fiber and food, protectors, and as companions. To better understand the close human-dog relationship among the Northern Coast Salish Tla'amin, we bring together several lines of evidence, including ethnographic information, interviews, and ancient DNA of archaeological dog burials. All indicate that dogs were an important part of ancestral Tla'amin culture and society. Local knowledge, including oral traditions, reflects the long-term social importance of dogs in mundane and ritual spheres. Tla'amindog relationships were focused on special breeding and training practices that enhanced the hunting skill of dogs and reinforced the bond between dog and owner. Ancient DNA analysis of 17 skeletal dog remains (3500–430 BP) from six archaeological sites confirmed that domestic dogs have a long and continuous history in Tla'amin territory, culture, and identity. DNA analysis of the D-loop region of mitochondrial DNA revealed haplotypes that were shared across broad regions and others that were unique to more localized culture areas, reflecting gene flow between dog populations via ancient social networks. Our study highlights the value of integrating archaeological data, genetic studies, and local knowledge to achieve a fuller understanding of the close relationship between dogs and humans.

The ability to distinguish between different migratory behaviours (e.g., anadromy and potamodromy) in fish can provide important insights into the ecology, evolution, and conservation of many aquatic species. We present a simple stable carbon isotope (δ13C) approach for distinguishing between sockeye (anadromous ocean migrants) and kokanee (potamodromous freshwater residents), two migratory ecotypes of Oncorhynchus nerka (Salmonidae) that is applicable throughout most of their range across coastal regions of the North Pacific Ocean. Analyses of kokanee (n = 239) and sockeye (n = 417) from 87 sites spanning the North Pacific (Russia to California) show that anadromous and potamodromous ecotypes are broadly distinguishable on the basis of the δ13C values of their scale and bone collagen. We present three case studies demonstrating how this approach can address questions in archaeology, archival, and conservation research. Relative to conventional methods for determining migratory status, which typically apply chemical analyses to otoliths or involve genetic analyses of tissues, the δ13C approach outlined here has the benefit of being non-lethal (when applied to scales), cost-effective, widely available commercially, and should be much more broadly accessible for addressing archaeological questions since the recovery of otoliths at archaeological sites is rare.

The decline of passenger pigeons (Ectopistes migratorius) during the late nineteenth century continues to draw substantial public and scientific attention as perhaps the most (in-)famous extinction event in North America’s recent history. While humans undeniably caused the extinction, the relative importance of indirect (habitat destruction) versus direct (overhunting) impacts has remained a mystery, in part, due to a lack of scientific evidence for critical aspects of the species’ dietary ecology. One key factor in explaining why passenger pigeons went extinct is that their highly specialized diet and foraging strategy, focusing on mast (tree nuts), were no longer feasible as the forested habitats that they depended on became depleted by deforestation. We used stable isotope (δ13C and δ15N, n = 94) and ancient DNA (n = 9) analyses of archaeological specimens to demonstrate that, during the later Holocene, passenger pigeons had a substantial degree of dietary plasticity (including some individuals specializing in consumption of agricultural crops) that could have allowed them to take advantage of other food opportunities when mast became scarce. Dietary variation is not linked with either biological age (juveniles versus adults) or haplogroup. These results suggest that habitat destruction was less important for the passenger pigeon’s extinction than the impacts of hunting and trapping and highlight the tremendous potential of the archaeological record for exploring the factors that led to this species’ extinction.

The time around 4000 BP marks a key stage from the Late Neolithic to the Early Bronze Age in China. During the time, sheep and cattle husbandry saw rapid development under the Qijia Culture in the Gansu-Qinghai region and also became more common in the Central Plains and Inner Mongolia. In this study, we performed ancient DNA analysis on sheep and cattle remains from four archaeological sites (Changning, Shimao, Taosi and Dashanqian) in northern China, and we obtained mtDNA D-loop fragments (overlapping 271 bp for sheep and overlapping 294 bp for cattle) from 22 of 26 sheep and 44 of 52 cattle remains. The mtDNA haplogroup data reveal that all the sheep DNA samples belong to sub-haplogroups A or B, and all the cattle DNA samples belong to haplogroup T3 or T4. The identification of these common haplogroups again confirms that the ancestors of these early sheep and cattle must have been introduced from outside China, likely from the Near East. The more detailed comparison of haplogroups also indicates potential intensified trade and cultural exchanges between different regions. Furthermore, this study also provides new ancient DNA data for better understanding the origins and spread of sheep and cattle in ancient China.

Ancient DNA analysis of 24 archaeological bovid remains recovered from large Neolithic (6300 BP to 5000 calBP) pit and ditch features at Houtaomuga, Northeast China, identified 23 of these samples as aurochs (Bos primigenius). These DNA-based identifications contrast with the morphological analysis of the remains, which identified them as Bison exiguous. The abundance of auroch remains at this site contradicts the general assumption that this species was not present in large numbers in Neolithic China. It also suggests archaeologists need to revise the notion that wild aurochs played an insignificant role in the lifeways of Neolithic peoples in China. Furthermore, phylogenetic analyses of a 294 bp fragment of the mitochondrial DNA (mtDNA) D-loop indicate the identified aurochs belong to a unique haplogroup (Haplogroup C) that is indigenous to East Asia and made no direct contribution to modern domesticated cattle Bos taurus. Moreover, temporal changes in haplotype frequencies were observed among the identified aurochs, suggesting population fluctuations potentially caused by human hunting activities occurred among Chinese aurochs during the Neolithic. This study also identified one sample (HT31) radiocarbon dated to ca. 5500–5300 calBP as Bos taurus, making it one of the earliest known taurine cattle specimens in China. HT31's location in Northeast China and early date points to the existence of another entrance for domesticated cattle into China, the Northeast China Route via the Mongolian Steppe.

This study uses ancient DNA analysis to identify the species of salmonids from a number of pre-contact Coast Salish settlements in Burrard Inlet, Canada dating from about 390 BCE to CE 1600. Our results indicate that chum salmon (Oncorhynchus keta) dominates all Burrard Inlet zooarchaeological assemblages through time, followed distantly by pink salmon (Oncorhynchus gorbuscha), sockeye (Oncorhynchus nerka), coho (Oncorhynchus kisutch), and Chinook (Oncorhynchus tshawytscha), indicative of very stable local fisheries. These results indicate that the four well-sampled sites appear to have been occupied during the fall and winter and perhaps during the spring.

This study uses multiple scientific methods to analyse a case of trepanation from a cemetery located at the westernmost point along the ancient Silk Road in China dating back to the Early Iron Age. The skull of interest belonged to a middle-aged male; the opening is located on the left posterior side of the skull in the occipital bone. Computer tomography (CT) and microscopic observation show that the incision was unhealed, indicating an immediate death either during or after the operation. The procedure of trepanation might have been used to treat a depressed fracture from inflicted trauma on the individual’s right parietal bone, suggesting the presence of surgical trepanation in early Western China.

Accurate sex identification of archaeological turkey remains is important for deciphering hunting and husbandry practices in pre-contact North America, particularly in the Southwest United States and Mesoamerica where domestic turkeys were raised. Although the sexual dimorphism of turkeys means that relatively complete elements can be distinguished using osteometric approaches, sexing fragmentary or juvenile remains is challenging. Here, we propose a simple and highly-sensitive co-amplification approach which targets highly-repetitive DNA (hrDNA) sequences on the turkey W chromosome. This technique simultaneously co-amplifies both hrDNA and mitochondrial DNA (mtDNA) fragments: the amplification of the W chromosome identifies the heterogametic sex (females), while the mtDNA fragment acts as an internal positive control to monitor for false negative results. To demonstrate the sensitivity and accuracy of this technique, we applied it to 20 modern turkeys and 117 archaeological turkey bones from 25 sites (ca. AD700–1700), including 32 samples from Sand Canyon Pueblo (AD1250–1300). We amplified ancient DNA from 86% of the ancient remains, demonstrating the sensitivity of the technique for targeting nuclear DNA. The correspondence between morphological size and the genetic sex identification for 100% of the complete skeletal elements demonstrates the accuracy and robusticity of this approach. Although within the larger regional assemblage, more males than females were identified (61% vs 39%), the site-specific analysis at Sand Canyon Pueblo suggests that adult male and female turkeys were present in a relatively even ratio.

Prior to the introduction of wheat and barley from Central Asia during the Neolithic period, northern Chinese agricultural groups subsisted heavily on millet. Despite being the focus of many decades of intensive interest and research, the exact route(s), date(s), and mechanisms of the spread and adoption of wheat and barley into the existing well-established millet-based diet in northern China are still debated. As the majority of the important introduced crops are C3plants, while the indigenous millet is C4, archaeologists can effectively identify the consumption of any introduced crops using stable carbon isotope analysis. Here we examine published stable isotope and dental caries data of human skeletal remains from 77 archaeological sites across northern and northwestern China. These sites date between 9000 to 1750 BP, encompassing the period from the beginning of agriculture to wheat’s emergence as a staple crop in northern China. The aim of this study is to evaluate the implications of the spread and adoption of these crops in ancient China. Detailed analysis of human bone collagenδ13C values reveals an almost concurrent shift from a C4-based to a mixed C3/ C4– based subsistence economy across all regions at around 4500–4000 BP. This coincided with a global climatic event, Holocene Event 3 at 4200 BP, suggesting that the sudden change in subsistence economy across northern and northwestern China was likely related to climate change. Moreover, the substantially increased prevalence of dental caries from pre–to post–4000 BP indicates an increase in the consumption of cariogenic cereals during the later period. The results from this study have significant implications for understanding how the adoption of a staple crop can be indicative of large-scale environmental and socio-political changes in a region.

Phenotypic variation is critical for the long-term persistence of species and populations. Anthropogenic activities have caused substantial shifts and reductions in phenotypic variation across diverse taxa, but the underlying mechanism(s) (i.e., phenotypic plasticity and/or genetic evolution) and long-term consequences (e.g., ability to recover phenotypic variation) are unclear. Here we investigate the widespread and dramatic changes in adult migration characteristics of wild Chinook salmon caused by dam construction and other anthropogenic activities. Strikingly, we find an extremely robust association between migration phenotype (i.e., spring-run or fall-run) and a single locus, and that the rapid phenotypic shift observed after a recent dam construction is explained by dramatic allele frequency change at this locus. Furthermore, modeling demonstrates that continued selection against the spring-run phenotype could rapidly lead to complete loss of the spring-run allele, and an empirical analysis of populations that have already lost the spring-run phenotype reveals they are not acting as sustainable reservoirs of the allele. Finally, ancient DNA analysis suggests the spring-run allele was abundant in historical habitat that will soon become accessible through a large-scale restoration (i.e., dam removal) project, but our findings suggest that widespread declines and extirpation of the spring-run phenotype and allele will challenge reestablishment of the spring-run phenotype in this and future restoration projects. These results reveal the mechanisms and consequences of human-induced phenotypic change and highlight the need to conserve and restore critical adaptive variation before the potential for recovery is lost.

Domestic taurine cattle ( Bos taurus ) were introduced to China from Central Asia between 3600 and 2000 cal BCE. Most of the earliest domestic cattle remains in China come from sacrificial or ritual contexts, especially in the form of oracle bones used in divination rituals. These oracle bones became closely tied to royal authority and are the source of the earliest written inscriptions in ancient China. In this article, we use ancient DNA to identify uninscribed bovine oracle bones from the Longshan period archaeological sites of Taosi and Zhoujiazhuang (late third millennium BCE). We found that in addition to making oracle bones out of domestic cattle scapulae, people also used aurochs (wild cattle: Bos primigenius ) scapulae for oracle bone divination. Wild water buffalo ( Bubalus mephistopheles ) were also exploited at Zhoujiazhuang, but we did not identify water buffalo oracle bones in our analysis. We propose some morphological criteria that may be useful for distinguishing between these animals, but conclude that it is not always possible to identify bovine scapulae based on morphology alone. Our results indicate that wild and domestic bovines were sometimes present at the same sites and their bones were used in similar ways to make oracle bones. This raises the possibility that these species interbred and that people in ancient China may have experimented with managing indigenous Chinese wild bovines.

Long-term use of herring by Alaska Natives is not well-documented over space or through time, yet this information can illuminate pre-industrial patterns of herring abundance and distribution. Such information is important to understand the sustained relationships Alaska Native fishers and egg collectors have had with herring. Understanding the genetics of pre-industrial herring may also inform management of the fish and fisheries to insure their survival into the future. In this paper, we attempt a contextualized account of the long-term history of Alaska Native herring fisheries, bringing together archaeological, ethnographic, and ethnohistorical data. We tie these together as background for presenting the preliminary results of the NSF-funded project, The Archaeology of Herring: Reconstructing the Past to Redeem the Future (No. 1203868). We have now tested 84 herring bone samples from 17 archaeological sites in Alaska expanding beyond Speller et al. (2012), having tripled the earlier archaeological dataset. The oldest herring bones identified archaeologically in Alaska are dated to more than 10,000 cal BP. Early Holocene and Middle Holocene sites have also yielded herring bones, although most of the record dates to the last 2400 years. Preservation of genetic information is effectively complete for the last 2400 years, but achievable back to the terminal Pleistocene (68% success rate for samples between 10,500 and 2400 cal BP). This gives considerable confidence to the potential to expand the analyses and develop a richer pattern of biological variability. The resulting data show genetic continuity between archaeological and modern herring populations. The main technical challenge for the future is to extract adequate amounts of nuclear DNA from the ancient samples for identifying more informative DNA markers that can be used to more effectively reveal any population diversity and/or population size changes over time when compared to modern herring.

The importance of the study of archaeological sites outside the Yangtze and Yellow River Valleys has been increasingly recognized as these peoples also played important roles in the formation of Chinese civilization. In Northeast China the boundary between sedentary agriculturists and nomadic pastoralists has fluctuated over the vast Dongbei Plain (Northeast Plain) providing opportunities to explore relationships between stress exposure, subsistence, and cultural complexity. The human remains for the present study were recovered from the upper level of the Houtaomuga site (2250–2050 BP) on the Dongbei plain, Northeast China, and categorized as Hanshu II cultural period. Inhabitants are believed to have practiced mixed hunting–gathering–fishing with limited millet cultivation. This study explores the dental expression of stress episodes in this period. Our results show overall 72.73% of the individuals examined (40/55) exhibited linear enamel hypoplasia (LEH). Additional data from labial/buccal casts from 105 teeth of 30 individuals from the upper level of the site reveal the duration of growth disruption, counted as numbers of perikymata in the occlusal wall of each hypoplastic defect, ranged from 2 to 14. Stress episodes, calculated as ranging from 17 to 28 days at the low end to 98 to 154 days for the longer duration events, are consistent with values reported from sites in other parts of the world. Examination of anterior permanent teeth for LEH also indicates that infants and children of Houtaomuga experienced extremely high levels of stress, sufficient to affect the developing teeth of almost all the inhabitants. In future examination of enamel hypoplasia of the pastoralists from the Neolithic levels of the site can provide time depth for this study of population stress, and facilitate our understanding of the changes in lifeways and adaptive strategies across subsistence transitions and climate change in Northeast China.

This comparative study aims to examine dental lesions of three skeletal populations from Late Bronze Age North China to examine relationships between subsistence patterns and oral health in the past. The skeletal remains represent a unique series of ancient human populations who adopted different subsistence practices: Chenjiagou (ca. 3000–2200 BP) from Henan, Central China, representing an intensified agricultural practice; Houtaomuga (ca. 2250–2050 BP) from Jilin, Northeast China, representing hunting-gathering-fishing with limited mixed agriculture, Jinggouzi (ca. 2530–2440 BP) from Inner Mongolia of China, representing pastoral economy. The prevalences of dental caries, antemortem tooth loss, abscesses, and pulp chamber exposure were investigated in this study to examine potential connections between oral health and subsistance strategies. This study reveals that 1) overall, the worst oral health status was observed in the agriculturalists (Chenjiagou) when comparing with those of the mixed hunter-fisher-gatherers (Houtaomuga) and pastoralists (Jinggouzi); 2) dental pathological lesions (uncommon in subadults) were found to increase significantly with age in all three studied populations; 3) females were found to develop more severe dental lesions than males in all three sites, especially for the molars. This study demonstrates that high carbohydra dietary intake can significantly worsen oral health, which is consistent with observations from many other parts of the world. More studies are needed to investigate the causes of sex differences in severity of dental lesions between agriculturalists and non-agriculturalists.

Whales have long been an important part of Pacific Northwest Coast human subsistence and lifeways. Native peoples on the Oregon Coast were not known to hunt whales, but a humpback whale phalange with an embedded bone harpoon at the Par-Tee site (35CLT20) and ethnographic accounts raised the possibility of opportunistic whale hunting. We analyzed a suite of whale remains from Par-Tee and performed ancient DNA-based species identifications on 30 specimens. The assemblage includes gray whales (Eschrichtius robustus, 60.7% of the assemblage), humpbacks (Megaptera novaeangliae, 32.1%), minkes (Balaenoptera acutorostrata, 3.6%), and orcas (Orcinus orca, 3.6%). While the species composition is similar to those found in archaeological deposits from systematic whaling areas in Washington and Vancouver Island, bone modification patterns and element representation reveal important differences. Our analysis demonstrates that whales were likely a supplementary part of human subsistence at Par-Tee and, while op...

Prior to European settlement, Indigenous peoples sustainably harvested Atlantic salmon (Salmo salar) and lake trout (Salvelinus namaycush) from Lake Ontario for centuries. Previous studies have suggested Indigenous peoples were able to maintain the productivity of Atlantic salmon and lake trout fisheries in the Great Lakes region through the use of resource management strategies. Since males tend to be the surplus sex among salmonids, one way in which Indigenous peoples could have managed Atlantic salmon and lake trout stocks was through the preferential harvesting of males. Here, we sought to investigate whether Indigenous peoples traditionally used sex-selective fishing to manage Lake Ontario Atlantic salmon and lake trout stocks. To address this question, we modified a DNA-based sex identification method developed for ancient Pacific salmonid (Oncorhynchus spp.) remains to make it applicable to archaeological Atlantic salmonid (Salmo spp.) and char (Salvelinus spp.) remains. This method assigns sex identities to samples through two PCR assays that co-amplify a fragment of the Y-specific salmonid master sex-determining gene (sexually dimorphic on the Y-chromosome gene) and an internal positive control, consisting of a fragment of the mitochondrial D-loop or nuclear clock1b gene. We applied this method to 61 Atlantic salmon and lake trout remains from the Antrex site (AjGv-38), a Middle Ontario Iroquoian (ca. CE 1250 to 1300) village located in the Lake Ontario watershed. Using this method, we successfully assigned sex identities to 51 of these remains (83.61% success rate), highlighting our method’s sensitivity and efficacy. Statistical analyses indicate neither the aggregate sex ratio nor the sex ratios obtained for the individual species were male-biased. This suggests Antrex’s Middle Ontario Iroquoian inhabitants probably did not practice male-selective fishing for Atlantic salmon or lake trout.

Osteoarthritis, one of the most common pathological conditions observed in human skeletal remains, is traditionally thought to only affect the structures within the joint capsule. We examined the osteoarthritic distal femora of an individual from Ancient North China, ca. 475-221 BCE. The standard signs of osteoarthritis, marginal lipping and extensive eburnation, were observed in the patellofemoral compartment of the knee joint. In addition however were bilateral pressure-caused fossae on the extra-articular anterior surfaces of the distal femora 10 mm proximal to the large osteophytes at the apex of the patellar surfaces. Anatomy and possible pathogenesis of knee arthritis are explored in order to come to a tentative aetiology of the extra-articular lesions. These lesions are suggested to be a new criterion for identifying severe knee arthritis. The osteological phenomenon is then placed into archaeological context of the Warring States period of ancient China.

Pacific salmonid (Oncorhynchusspp.) remains are routinely recovered from archaeological sites in northwestern North America but typically lack sexually dimorphic features, precluding the sex identification of these remains through morphological approaches. Consequently, little is known about the deep history of the sex-selective salmonid fishing strategies practiced by some of the region’s Indigenous peoples. Here, we present a DNA-based method for the sex identification of archaeological Pacific salmonid remains that integrates two PCR assays that each co-amplify fragments of thesexually dimorphic on the Y chromosome(sdY) gene and an internal positive control (Clock1aor D-loop). The first assay co-amplifies a 95 bp fragment ofsdYand a 108 bp fragment of the autosomalClock1agene, whereas the second assay co-amplifies the samesdYfragment and a 249 bp fragment of the mitochondrial D-loop region. This method’s reliability, sensitivity, and efficiency, were evaluated by applying it to 72 modern Pacific salmonids from five species and 75 archaeological remains from six Pacific salmonids. The sex identities assigned to each of the modern samples were concordant with their known phenotypic sex, highlighting the method’s reliability. Applications of the method to dilutions of modern DNA samples indicate it can correctly identify the sex of samples with as little as ~39 pg of total genomic DNA. The successful sex identification of 70 of the 75 (93%) archaeological samples further demonstrates the method’s sensitivity. The method’s reliance on two co-amplifications that preferentially amplifysdYhelps validate the sex identities assigned to samples and reduce erroneous identifications caused by allelic dropout and contamination. Furthermore, by sequencing the D-loop fragment used as a positive control, species-level and sex identifications can be simultaneously assigned to samples. Overall, our results indicate the DNA-based method reported in this study is a sensitive and reliable sex identification method for ancient salmonid remains.

Description of archaeological sites and contexts, and detailed methods for radiocarbon dating, isotopic analysis and ancient DNA analysis.

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.

This study reports ancient DNA (aDNA) and stable isotope analyses of eight dog skeletal elements from the Cathlapotle site on the Lower Columbia River of the western United States. The aDNA analysis confirmed the elements as dogs (Canis lupus familiaris). Two haplotypes were found, both of which group within dog Clade A, and have patchy distributions to the north in British Columbia and as far south as Teotihuacan (Mexico). The isotopic analysis showed that the dogs' dietary protein was derived almost exclusively from marine sources. Lower Columbia River ethnohistoric accounts and Cathlapotle zooarchaeological records indicate that while marine fish were dietary keystones, the local diet was more diverse, and included terrestrial organisms and freshwater fishes. This apparent discrepancy raises the possibility the dogs were selectively fed. Thus their diet may not be a close proxy for human diet in this context.

This research investigates the prevalence of human osteoarthritis at Yinxu, the last capital of the Late Shang dynasty (ca. 1250-1046 B.C.), to gain insights about lifeways of early urban populations in ancient China. A total of 167 skeletal remains from two sites (Xiaomintun and Xin'anzhuang) were analyzed to examine osteoarthritis at eight appendicular joints and through three spinal osseous indicators. High osteoarthritis frequencies were found in the remains with males showing significantly higher osteoarthritis on the upper body (compared to that of the females). This distinctive pattern becomes more obvious for males from Xiaomintun. Furthermore, Xiaomintun people showed significantly higher osteoarthritis in both sexes than those from Xin'anzhuang. Higher upper body osteoarthritis is speculated to be caused by repetitive lifting and carrying heavy-weight objects, disproportionately adding more stress and thus more osseous changes to the upper than the lower body. Such lifting-carrying could be derived from intensified physical activities in general and specialized occupations in particular. Higher osteoarthritis in males may reveal a gendered division of labour, with higher osteoarthritis in Xiaomintun strongly indicating an occupational difference between the two sites. The latter speculation can be supported by the recovery of substantially more bronze-casting artifacts in Xiaomintun. It is also intriguing that relatively higher osteoarthritis was noticed in Xiaomintun females, which seems to suggest that those women might have also participated in bronze-casting activities as a "family business." Such a family-involved occupation, if it existed, may have contributed to establishment of occupation-oriented neighborhoods as proposed by many Shang archaeologists.

In 1968, a child's cranium was recovered from the banks of a northern Canadian river and held in a trust until the "cold case" was reopened in 2005. The cranium underwent reanalysis at the Centre for Forensic Research, Simon Fraser University, using recently developed anthropological analysis, "bomb-pulse" radiocarbon analysis, and forensic DNA techniques. Craniometrics, skeletal ossification, and dental formation indicated an age-at-death of 4.4 ± 1 year. Radiocarbon analysis of enamel from two teeth indicated a year of birth between 1958 and 1962. Forensic DNA analysis indicated the child was a male, and the obtained mitochondrial profile matched a living maternal relative to the presumed missing child. These multidisciplinary analyses resulted in a legal identification 41 years after the discovery of the remains, highlighting the enormous potential of combining radiocarbon analysis with anthropological and mtDNA analyses in producing confident personal identifications for forensic cold cases dating to within the last 60 years.

We use ancient DNA analysis to identify Pacific salmon vertebrae to species in order to provide an important line of evidence that helps to establish the timing of seasonal residence at a Pacific Northwest Coast village site. Ancient DNA results from House 2 at Dionisio Point allow a characterization of the salmon fishery. Ten of eleven randomly selected smaller-sized salmon vertebrae were positively identified as sockeye salmon ( Oncorhynchus nerka ) while only a single pink salmon ( Oncorhynchus gorbuscha ) was identified. Of the 322 whole salmon vertebrae identified from House 2 occupation deposits during zooarchaeological analysis, 58 percent measure less than 8.0 mm and 70 percent are less than 8.5 mm in maximum transverse diameter. Together with documented aspects of the material record from Dionisio Point, most notably the vertebrate fauna from House 2, the indication that sockeye was the primary focus of the Dionisio Point salmon fishery suggests the site was inhabited during the spring and summer. This approach to the identification of season-specific site occupation has the potential for application over much of the Northeast Pacific.

We reiterate the basis for our interpretation of the Namu site as a winter-village settlement from at least 7000 B.P., and note that Monks and Orchard do not provide an alternative interpretation of the available data. They also mistakenly suggest an assertion on our part that all Northwest Coast villages were dependent on a salmon-based storage economy by 1000 B.P. We never argued for this point. Finally, Monks and Orchard offer a lengthy defense of methods for seasonality estimation, which we support. We used those same methods, and continue to support their refinement and application toward understanding the nature of seasonal activity at Namu.

The debates over the origin of modern humans have long been centered on two competing theories: the “Out-of-Africa” (single-place origin) theory and the “Multi-regional Evolution” theory. China is an extremely important region where many ancient human fossils were collected along with numerous associated faunal remains and artefacts. These cultural remains, unearthed from different areas in the country and covering a long time span, will help clarify the controversy. The study of cultural materials in China is expected to shed important light on biological evolutionary patterns and social and technical developments of those early humans as well as their environmental conditions. Based on the analysis of Chinese fossils and associated materials, in conjunction with some genetic studies, this paper aims at evaluating each of the two theories in order to stimulate more discussions. Our study suggests that the evolutionary model of “Continuity with Hybridization“ is most relevant in reflecting the current understanding of human evolutionary history in China. Furthermore, we propose that the concept of regional diversity of evolutionary models should be seriously considered to illustrate different evolutionary modes applied to different parts of the world.

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.

Domestic horses played a pivotal role in ancient China, but their exact origin remains controversial. To investigate the origin of Chinese domestic horses, we analyzed mitochondrial DNA (mtDNA) from 35 horse remains, aged between 4000 and 2000 years, excavated from nine archaeological sites in northern China. The Chinese ancient horses exhibited high matrilineal diversity, falling into all the seven haplogroups (A–G) observed in modern horses. These results suggest that several maternal lines were introduced into the gene pool of Chinese horses in the past. Haplogroups A and F were more prevalent in ancient horses than the other haplogroups. Interestingly, only haplogroups A and F were present in the samples older than 4000 years, while the more recent horses (between 2000 and 3000 years BP) fell into all seven haplogroups. Comparison with DNA data of present-day horses suggests that haplogroup F is like to be an ancient haplogroup of East Asian origin. These analyses also suggest that the origin of Chinese domestic horses is complex, and external mtDNA input occurred after initial domestication. Our results indicate that the Chinese ancient horses are more related to the modern Mongolian horses. Lastly, our results cannot support the previous hypothesis that early Chinese domestic horses were derived from the Przewalski horse.

Recent zooarchaeological studies on water buffalo ( Bubalus sp.) remains from China and south Asia question the traditional view that water buffalo were first domesticated in Neolithic China over 7000 years ago. The results from several recent population genetic studies of modern domesticated buffalo ( Bubalus bubalis ) are not consistent with each other, placing the original center of buffalo's domestication in south Asia, southeast Asia, or China. This paper reports a study using an ancient DNA approach to analyze water buffalo remains from Neolithic sites in north China to investigate their affinities with modern domesticated water buffalo, and to shed light on the origin of modern domesticated water buffalo in China. A 169 bp fragment of D-loop mitochondrial DNA was successfully amplified and verified for 13 of 24 bone samples obtained from seven archaeological sites along the Wei River valley in Shaanxi Province, China. The bone samples which yielded positive DNA can be dated to 8000–3600 cal. BP. The phylogenetic analysis of the obtained DNA sequences along with modern water buffalo sequences indicated that the ancient water buffalos were not the direct ancestor of modern domesticated water buffalo. However, the phylogenetic analysis, along with BLAST searches of these ancient DNA sequences, did demonstrate their relatedness to water buffalo more so than to any other bovid species, confirming the existence of indigenous wild (but now extinct) water buffalo species ( B. mephistopheles ) in ancient China. The DNA analysis of these ancient remains failed to establish direct links between modern domesticated water buffalo ( B. bubalis ) and indigenous water buffalo ( B. mephistopheles ) from ancient China. If further DNA studies of more ancient remains from other regions of China confirm the observation of solely indigenous water buffalo species in ancient China, it would suggest modern water buffalo might not have been first domesticated in China.

The search for the origins of syphilis has a long history in the medical and anthropological literatures. If we know more about the emergence of the pathogen that causes the disease in humans we will understand its evolution through time and space as well as shed light on its current state in living populations. Ancient DNA techniques used to isolate Treponema pallidum subsp. pallidum DNA from archaeological human specimens provide direct evidence of its existence in the past. However to date, only Kolman et al. (1999) have been successful in this endeavour, while other attempts have failed (e.g., Barnes and Thomas, 2006; Bouwman and Brown, 2005). Why has there been little success? This paper serves to compliment and add relevant information to Bouwman and Brown’s and Barnes and Thomas’ discussion concerning our inability to apply ancient DNA techniques to study venereal syphilis in past human populations. Our approach utilized 15 different human specimens from different geographies and different temporal periods: eight samples come from medically diagnosed individuals archived during the American Civil War period; six originate from the United Kingdom and predate 1492 with four of these samples having been previously analyzed by Bouwman and Brown and one sample comes from historic Canada. Human mitochondrial and amelogenin DNA, as well as several genes from the Treponema organism were analyzed revealing the relatively good preservation of human multi-copy and single copy DNA but not treponemal DNA. This study also incorporates a unique molecular experiment using rabbits infected with venereal syphilis to help illustrate that treponemal DNA disseminates to bone early during the first stages of infection but is not present in later stages of the disease using the techniques presented in this study. 2007 Elsevier Ltd. All rights reserved.

espanolResumen: Dos maneras de utilizacion de las ballenas se han documentado en la costa Noroeste de Norteamerica. Estas son, la caceria sistematica y la utilizacion de ballenas encontradas muertas en la playa. Etnograficamente, la caza sistematica fue practicada unicamente por grupos Indigenas del sur-oeste de la Isla de Vancouver y la Peninsula Olimpica del estado de Washington. Esta caceria se realizaba con tecnologia especialmente disenada para dicha actividad. Se sabe que otros grupos etnicos de la costa noreste de Norte America no cazaban, sino que utilizaban los restos de ballenas encontradas sin vida en la playa. Una punta de hueso alojada en parte de la estructura osea digital de una ballena, encontrada en Par-Tee, en la costa norte de Oregon, representa la evidencia arqueologica de la caceria de ballenas en este lugar. Esta caceria posiblemente ocurrio hace 1,300 a 1,600 anos. Muestras de ADN antiguo extraido de la estructura osea digital de la ballena sugiere que se trata de una ballena jorobada (Megaptera novaeangliae). El ADN proveniente de la punta de hueso encontrada revela que esta fue hecha de hueso de ciervo (Cervus elaphus). En este trabajo de investigacion, presentamos informacion etnohistorica de la costa noroeste de Norteamerica describiendo la caceria de ballenas ?oportunista?, la cual incluye diversas tecnologias. Segun nuestro estudio, muchos grupos de la costa Noroeste de Norteamerica seguramente de vez en cuando cazaban ballenas en el pasado, y dicha caceria se realizo mediante la utilizacion de tecnologia no-especializada EnglishAbstract: Two modes of whale use have been documented on the Northwest Coast of North America, namely systematic whale hunting and whale scavenging. Ethnographically, systematic hunting was practiced only by Native groups of southwestern Vancouver Island and the northern Olympic Peninsula of Washington State. This hunting was undertaken with technology specifically designed for the task. Other groups on the Northwest Coast reportedly did not hunt whales but did utilize beached animals. Here we present archaeological evidence of whaling from the northern Oregon coast site of Par-Tee in the form of a bone point lodged in a whale phalange. This hunting likely occurred 1,300 to 1,600 years ago. Ancient DNA extracted from the phalange proves it to be a humpback whale (Megaptera novaeangliae). DNA recovered from the bone point indicates that it is made from elk (Cervus elaphus) bone, and the point?s DNA sequence is identical to that from unmodified elk bone from Par-Tee, suggesting the whale was locally hunted. We present ethnohistoric data from the southern Northwest Coast describing opportunistic whale hunting with a variety of technologies. We argue that many groups along the west coast of North America likely occasionally hunted whales in the past and that this hunting occurred using nonspecialized technologies.

Zooarchaeology has the potential to make significant contributions to knowledge of pinniped biogeography of import to both archaeologists and environmental scientists. We analyzed northern fur seal remains found in three archaeological sites located along the outer coast of the Northeast Pacific Ocean: Cape Addington Rockshelter in southeast Alaska, Ts’ishaa on the west coast of Vancouver Island, and the Netarts Sandspit site

We propose a simple and effective approach to simultaneously co-amplify both cytochrome b and D-loop fragments to evaluate DNA preservation and to monitor possible contaminations in the analysis of degraded animal DNA samples. We have applied this approach to over 200 ancient salmon samples and 25 ancient whale DNA samples, clearly demonstrating its multiple benefits for analysis of degraded DNA samples, and the ease in which co-amplification can be optimized for different taxa. This simple, cost-efficient and genomic DNA-saving approach can be used routinely in the analysis of minute and degraded DNA samples in wildlife forensics, food inspection, conservation biology and ancient faunal remains.

Ancient DNA identification of salmon remains from the site of Namu on the central coast of British Columbia shows use of a variety of species and an emphasis on pink salmon over the course of the past 7,000 years. These results support arguments that Namu was a permanent village settlement dependent on a salmon storage economy throughout this time. This pattern of subsistence and settlement predates by several millennia the first substantial evidence for population expansion or social differentiation in the region. Periodic salmon shortages in the period after 2000 cal B.C., which are associated with local and regional disruptions in settlement and increased reliance on more marginal resources, appear to be the result of failures in the pink salmon fishery.

This study applied ancient DNA techniques to achieve accurate species identifications for the archaeological salmon remains recovered from the prehistoric pithouse village of Keatley Creek in British Columbia, Canada. Previous archaeological studies indicate that economic stratification within the community might have resulted in differential access to some preferred salmon species, such as sockeye and chinook. Unambiguous ancient DNA species identification now makes it possible to more accurately address the issue of early salmon resource utilization in the region. This study analyzed 60 salmon remains from two specialized structures and two residential structures in order to identify any species differences among bony salmon remains found within the structure. Although high success rates (over 90%) were obtained for ancient DNA tests, only three species (chinook, sockeye and coho salmon) were identified from the remains. Pink salmon was not identified among the tested sample, despite the fact that it was originally assumed to be a staple species for the site's native inhabitants. The absence of pink salmon in our sample significantly altered the picture of early salmon fishing activities in the region. As a result, the effects of economic stratification on differential access to the remaining so-called preferred species of sockeye and chinook within the four structures studied were not as dramatic as previously thought, although differences among the structures could still be observed.

Ancient DNA analysis was carried out on 20 archaeological rabbit remains from an early Pueblo II period site in Colorado (circa 1000 A.D.) to explore the possibility of obtaining accurate rabbit genus and species identifications. The presence of abundant rabbit remains at archaeological sites in the American Southwest indicates the importance of rabbit species in the subsistence economy and ritual activities of early aboriginal populations. The study of these remains is hindered by the difficulty of accurate identification due to the fragmentary nature of the bones and the lack of genus- and species-specific morphological features. A short cytochrome b gene fragment was amplified and sequenced to produce a genetic profile for each bone sample. At the genus level, the DNA identifications were consistent with those based on the analysis of mandible morphology for the majority of specimens. When compared to species-specific reference DNA sequences, Lepus americanus and Lepus californicus samples were easily identified. Identification of an unexpected L. americanus (snowshoe hare) from the remains provided new information concerning hunting ranges or exchange between groups in the region. Sylvilagus nuttallii and Sylvilagus audubonii, however, could not be confidently differentiated at this point due to the difficulty in obtaining accurate species-specific reference sequences. The inability to obtain such reference sequences can be a serious problem for DNA species identification of non-domestic animals that lack population-level genetic data and have few sequences available in GenBank. The lack of the DNA data increases the possibility that inappropriate reference sequences could be applied, resulting in false species identification even when authentic DNA is retrieved and amplified from ancient remains. 2004 Elsevier Ltd. All rights reserved.

Contamination is of utmost concern when working with ancient DNA as it easily leads to false positive results. The best way to prevent or minimize contamination is to start precautionary measures as early as possible, ideally commencing with sample collection and preparation by field archaeologists. This paper discusses the nature of contamination in ancient DNA studies and offers some practical guidelines as to how archaeologists in the field can “clean-collect” samples for ancient DNA analysis. Methods for preparing contaminated samples from museum collections for ancient DNA analysis are also discussed.