Dongya Y. Yang

Ancient mitochondrial DNA analysis reveals complexity of indigenous North American turkey domestication.

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.

Early storage and sedentism on the Pacific northwest coast : Ancient DNA analysis of salmon remains from Namu, British Columbia

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.

Identification of ancient remains through genomic sequencing.

Studies of ancient DNA have been hindered by the preciousness of remains, the small quantities of undamaged DNA accessible, and the limitations associated with conventional PCR amplification. In these studies, we developed and applied a genomewide adapter-mediated emulsion PCR amplification protocol for ancient mammalian samples estimated to be between 45,000 and 69,000 yr old. Using 454 Life Sciences (Roche) and Illumina sequencing (formerly Solexa sequencing) technologies, we examined over 100 megabases of DNA from amplified extracts, revealing unbiased sequence coverage with substantial amounts of nonredundant nuclear sequences from the sample sources and negligible levels of human contamination. We consistently recorded over 500-fold increases, such that nanogram quantities of starting material could be amplified to microgram quantities. Application of our protocol to a 50,000-yr-old uncharacterized bone sample that was unsuccessful in mitochondrial PCR provided sufficient nuclear sequences for comparison with extant mammals and subsequent phylogenetic classification of the remains. The combined use of emulsion PCR amplification and high-throughput sequencing allows for the generation of large quantities of DNA sequence data from ancient remains. Using such techniques, even small amounts of ancient remains with low levels of endogenous DNA preservation may yield substantial quantities of nuclear DNA, enabling novel applications of ancient DNA genomics to the investigation of extinct phyla.

Historical Ecology and Biogeography of North Pacific Pinnipeds: Isotopes and Ancient DNA from Three Archaeological Assemblages

ABSTRACT 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 on the Oregon Coast. These three sites occur along an 850 km stretch of coastline between 45° to 55° N. and 123° to 134° W., far southeast of the primary breeding area for northern fur seals today, located on the Pribilof Islands at 57° N. 170° W. We use ancient DNA (aDNA) and carbon (δ13C) and nitrogen (δ15N) isotopes to investigate whether northern fur seal remains from these archaeological sites originated with migratory Pribilof Islands populations. For sites located in Oregon and points north, the isotope values are not distinct from those of the Pribilof fur seals. Although aDNA was recovered from three pinniped species (northern fur seal, Steller sea lion, and Guadalupe fur seal), the paucity of published genetic data from modern northern fur seals prevents us from distinguishing the archaeological specimens from modern Pribilof seals.

Earliest Mexican Turkeys (Meleagris gallopavo) in the Maya Region: Implications for Pre-Hispanic Animal Trade and the Timing of Turkey Domestication

Late Preclassic (300 BC–AD 100) turkey remains identified at the archaeological site of El Mirador (Petén, Guatemala) represent the earliest evidence of the Mexican turkey (Meleagris gallopavo) in the ancient Maya world. Archaeological, zooarchaeological, and ancient DNA evidence combine to confirm the identification and context. The natural pre-Hispanic range of the Mexican turkey does not extend south of central Mexico, making the species non-local to the Maya area where another species, the ocellated turkey (Meleagris ocellata), is indigenous. Prior to this discovery, the earliest evidence of M. gallopavo in the Maya area dated to approximately one thousand years later. The El Mirador specimens therefore represent previously unrecorded Preclassic exchange of animals from northern Mesoamerica to the Maya cultural region. As the earliest evidence of M. gallopavo found outside its natural geographic range, the El Mirador turkeys also represent the earliest indirect evidence for Mesoamerican turkey rearing or domestication. The presence of male, female and sub-adult turkeys, and reduced flight morphology further suggests that the El Mirador turkeys were raised in captivity. This supports an argument for the origins of turkey husbandry or at least captive rearing in the Preclassic.

High Potential for Using DNA from Ancient Herring Bones to Inform Modern Fisheries Management and Conservation

Pacific herring (Clupea pallasi) are an abundant and important component of the coastal ecosystems for the west coast of North America. Current Canadian federal herring management assumes five regional herring populations in British Columbia with a high degree of exchange between units, and few distinct local populations within them. Indigenous traditional knowledge and historic sources, however, suggest that locally adapted, distinct regional herring populations may have been more prevalent in the past. Within the last century, the combined effects of commercial fishing and other anthropogenic factors have resulted in severe declines of herring populations, with contemporary populations potentially reflecting only the remnants of a previously more abundant and genetically diverse metapopulation. Through the analysis of 85 archaeological herring bones, this study attempted to reconstruct the genetic diversity and population structure of ancient herring populations using three different marker systems (mitochondrial DNA (mtDNA), microsatellites and SNPs). A high success rate (91%) of DNA recovery was obtained from the extremely small herring bone samples (often <10 mg). The ancient herring mtDNA revealed high haplotype diversity comparable to modern populations, although population discrimination was not possible due to the limited power of the mtDNA marker. Ancient microsatellite diversity was also similar to modern samples, but the data quality was compromised by large allele drop-out and stuttering. In contrast, SNPs were found to have low error rates with no evidence for deviations from Hardy-Weinberg equilibrium, and simulations indicated high power to detect genetic differentiation if loci under selection are used. This study demonstrates that SNPs may be the most effective and feasible approach to survey genetic population structure in ancient remains, and further efforts should be made to screen for high differentiation markers.This study provides the much needed foundation for wider scale studies on temporal genetic variation in herring, with important implications for herring fisheries management, Aboriginal title rights and herring conservation.

Integrated DNA and fingerprint analyses in the identification of 60-year-old mummified human remains discovered in an Alaskan glacier.

Abstract:  This report describes the identification of a merchant mariner who perished in 1948 when Northwest Airlines Flight 4422, a DC‐4 carrying 24 seamen and six crew members crashed into Mount Sanford, Alaska. Fifty‐one years later, a human forearm and hand were found close by the wreckage of the plane, prompting identification efforts using DNA and fingerprints. There were significant challenges to both the fingerprint and DNA analyses. The hand was badly desiccated, making fingerprint friction‐ridge detail almost invisible and the remains had been embalmed upon discovery, making DNA amplification difficult. We present the results of an interdisciplinary approach that successfully addressed these challenges and ultimately led to the identification of the remains. These efforts relied on efficient fingerprint rejuvenation and imaging techniques that improved print resolution, as well as new DNA extraction techniques optimized for aggressively embalmed remains.

Early human use of anadromous salmon in North America at 11,500 y ago.

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. Salmon represented a critical resource for prehistoric foragers along the North Pacific Rim, and continue to be economically and culturally important; however, the origins of salmon exploitation remain unresolved. Here we report 11,500-y-old salmon associated with a cooking hearth and human burials from the Upward Sun River Site, near the modern extreme edge of salmon habitat in central Alaska. This represents the earliest known human use of salmon in North America. Ancient DNA analyses establish the species as Oncorhynchus keta (chum salmon), and stable isotope analyses indicate anadromy, suggesting that salmon runs were established by at least the terminal Pleistocene. The early use of this resource has important implications for Paleoindian land use, economy, and expansions into northwest North America.

Personal identification of cold case remains through combined contribution from anthropological, mtDNA, and bomb-pulse dating analyses.

In 1968, a childs 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.

Opportunistic Whale Hunting on the Southern Northwest Coast: Ancient DNA, Artifact, and Ethnographic Evidence

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 points 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.