Search

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.

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 haplo-type 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. Key words: Peace River, Late Pleistocene, paleoenvironment, Tse'K'wa, Charlie Lake Cave. De l'ADN ancien a ete extrait d'os de spermophiles de 12 500 a 10 500 ans d'age provenant de Tse'K'wa, un site archeologique de la region de la riviere de la Paix, dans le nord-est de la Colombie-Britannique (Canada). L'analyse d'ADN mitochondrial issu de sept individus demontre qu'il s'agit dans tous les cas d'Urocitellus richardsonii (spermophiles de Richardson), une espece aujourd'hui absente de la region. Des analyses phylogenetiques et de sequences indiquent que ces specimens ont tous en commun un haplotype de la region de controle mitochondriale qui n'avait pas encore ete documente et qui est le plus etroitement relie a des haplotypes observes dans des specimens modernes provenant de la Saskatchewan et du Montana. A la fin du Pleistocene, ces spermophiles ont elargi leur aire de repartition vers le nord et l'ouest pour former des communautes dans des regions de vegetation ouverte creees dans la foulee de la fonte de glaciers et la vidange de lacs glaciaires. Ils ont par la suite disparu de la region de la riviere de la Paix quand des forets ont remplace les communautes de plantes pionnieres. [Traduit par la Redaction] Mots-cles: riviere de la Paix, Pleistocene tardif, paleoenvironnement, Tse'K'wa, grotte du lac Charlie., Introduction Numerous species of ground squirrels live in a wide range of habitats in North America and the Old World (Yensen and Sherman 2003) and are potentially useful indicators of [...]

The short‐tailed albatross (Phoebastria albatrus) is a threatened seabird whose present‐day range encompasses much of the North Pacific. Within this species, there are two genetic clades (Clades 1 and 2) that have distinctive morphologies and foraging ecologies. Due to a global population collapse in the late 19th and early 20th centuries, the frequency of these clades among the short‐tailed albatross population that historically foraged off British Columbia, Canada, is unclear. To document the species' historical genetic structure in British Columbia, we applied ancient DNA (aDNA) analysis to 51 archaeological short‐tailed albatross specimens from the Yuquot site (Borden site number: DjSp‐1) that span the past four millennia. We obtained a 141 bp cytochrome b sequence from 43 of the 51 (84.3%) analyzed specimens. Analyses of these sequences indicate 40 of the specimens belong to Clade 1, while 2 belong to Clade 2. We also identified a single specimen with a novel cytochrome b haplotype. Our results indicate that during the past four millennia most of the short‐tailed albatrosses foraging near Yuquot belonged to Clade 1, while individuals from other lineages made more limited use of the area. Comparisons with the results of previous aDNA analyses of archaeological albatrosses from Japanese sites suggest the distribution of Clades 1 and 2 differed. While both albatross clades foraged extensively in the Northwest Pacific, Clade 1 albatrosses appear to have foraged along the west coast of Vancouver Island to a greater extent. Due to their differing distributions, these clades may be exposed to different threats. [ABSTRACT FROM AUTHOR]

We describe a simple method for extracting polymerase chain reaction-amplifiable DNA from ancient bones without the use of organic solvents. Bone powders are digested with proteinase K, and the DNA is purified directly using silica-based spin columns (QIAquick[TM], QIAGEN). The efficiency of this protocol is demonstrated using human bone samples ranging in age from 15 to 5,000 years old. KEY WORDS DNA extraction; Ancient bone; PCR inhibitors; Silica-based spin columns

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. [ABSTRACT FROM AUTHOR]

Marine mammals often exhibit significant sexual segregation in their diet and habitat use but these differences have not been studied systematically in historic or ancient populations due to the difficulties associated with determining the sex of skeletal elements based on gross morphology. Using a combined ancient DNA and stable isotope approach, we document a sexual difference in the foraging ecology of late 19th century beluga whales (Delphinapterus leucas) from the Canadian High Arctic. Using two PCR assays that coamplify fragments of the Y‐linked SRY and X‐linked ZFX genes, we assigned reproducible sex identities to 35 beluga specimens. This provided a basis for investigating sex‐specific differences in foraging ecology using stable carbon and nitrogen isotope analyses of bone collagen. These isotopic data demonstrate that although both males and females primarily consumed Arctic cod, males utilized a wider range of prey than females, feeding on high trophic level benthic prey (sculpins) to a greater extent. Because bone collagen integrates prey isotopic compositions over the course of several years these sex‐based differences in beluga bone collagen isotopic compositions reflect long‐term and sustained sexual differences in foraging. [ABSTRACT FROM AUTHOR]

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 C3 plants, 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 collagen δ13C 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. [ABSTRACT FROM AUTHOR]

Highlights • Report the first non-clinical documentation of extra-articular pressure resorption in skeletal remains with severe knee osteoarthritis. • Suggest that abnormally high pressure on the distal femur by inflamed suprapatellar bursa causes bone resorption and fossa formation. • Propose that extra-articular regions in close proximity to joints require the same close examination as the joint surfaces. • Suggest this lesion is potentially a new criterion for assessing severity of arthritis in human skeletal remains. • The extra-articular fossae are sequellae of arthritis of knee. Abstract 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. [ABSTRACT FROM AUTHOR]

Pacific salmonid (Oncorhynchus spp.) 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 the sexually dimorphic on the Y chromosome (sdY) gene and an internal positive control (Clock1a or D-loop). The first assay co-amplifies a 95 bp fragment of sdY and a 108 bp fragment of the autosomal Clock1a gene, whereas the second assay co-amplifies the same sdY fragment 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 amplify sdY helps 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. [ABSTRACT FROM AUTHOR]

Rockfish (Sebastes spp.) are a common marine fish in nearshore and continental shelf environments in the North Pacific Ocean. They are frequently identified in coastal archaeological sites in western North America; however, the morphological similarity of rockfish species limits conventional zooarchaeological identifications to the genus level. This study applies ancient DNA analysis to 96 archaeological rockfish specimens from four sites on separate islands in an archipelago on western Vancouver Island, British Columbia, Canada. Two of the archaeological sites are located within a marine protected area specifically designed to facilitate the recovery of inshore rockfish populations; two sites are located outside this boundary and remain subject to considerable fishing pressure. Using mitochondrial 16S and control region DNA sequences, we identify at least twelve different rockfish species utilized during the past 2,500 years. Identification of rockfish at closely spaced and contemporaneously occupied sites confirms that a variety of Sebastes species were consistently exploited at each site, with more exposed areas having a higher number of species present. Identification results indicate that four of the twelve species did not occur within the conservation area boundary and, instead, were found in sites where commercial and recreational fishing continues to be permitted. This study demonstrates that ancient DNA identifications of archaeological assemblages can complement and expand perspective on modern day fisheries conservation and management in this National Park Reserve and First Nations ancestral territory. [ABSTRACT FROM AUTHOR]

Horses were a dominant component of North American Pleistocene land mammal communities and their remains are well represented in the fossil record. Despite the abundant material available for study, there is still considerable disagreement over the number of species of Equus that inhabited the different regions of the continent and on their taxonomic nomenclature. In this study, we investigated cheek tooth morphology and ancient mtDNA of late Pleistocene Equus specimens from the Western Interior of North America, with the objective of clarifying the species that lived in this region prior to the end-Pleistocene extinction. Based on the morphological and molecular data analyzed, a caballine (Equus ferus) and a non-caballine (E. conversidens) species were identified from different localities across most of the Western Interior. A second non-caballine species (E. cedralensis) was recognized from southern localities based exclusively on the morphological analyses of the cheek teeth. Notably the separation into caballine and non-caballine species was observed in the Bayesian phylogenetic analysis of ancient mtDNA as well as in the geometric morphometric analyses of the upper and lower premolars. Teeth morphologically identified as E. conversidens that yielded ancient mtDNA fall within the New World stilt-legged clade recognized in previous studies and this is the name we apply to this group. Geographic variation in morphology in the caballine species is indicated by statistically different occlusal enamel patterns in the specimens from Bluefish Caves, Yukon Territory, relative to the specimens from the other geographic regions. Whether this represents ecomorphological variation and/or a certain degree of geographic and genetic isolation of these Arctic populations requires further study. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 opportunistic whale hunting likely occurred, it may have been secondary to scavenging and utilization of beached and/or drift whales. [ABSTRACT FROM AUTHOR]

Through the analysis of human skeletal remains and mortuary practice in Yinxu, this study investigates the impact of early urbanization on the commoners during the Late Shang dynasty (ca. 1250–1046 B.C.). A total of 347 individuals examined in this study represent non-elites who were recovered from two different burial contexts (formally buried in lineage cemeteries and randomly scattered in refuse pits). Frequencies of enamel hypoplasia (childhood stress), cribra orbitalia (childhood stress and frailty) and osteoperiostitis (adult stress) were examined to assess systemic stress exposure. Our results reveal that there was no significant difference in the frequency of enamel hypoplasia between two burial groups and between sexes, suggesting these urban commoners experienced similar stresses during childhood, but significantly elevated levels of cribra orbitalia and osteoperiostitis were observed in the refuse pit female cohort. Theoretically, urbanization would have resulted in increased population density in the urban centre, declining sanitary conditions, and increased risk of resource shortage. Biologically, children would be more vulnerable to such physiological disturbance; as a result, high percentages of enamel hypoplasia (80.9% overall) and cribra orbitalia (30.3% overall) are observed in Yin commoners. Adults continued to suffer from stress, resulting in high frequencies of osteoperiostitis (40.0% total adults); in particular, in the refuse pit females who may also reflect a compound impact of gender inequality. Our data show that the non-elite urban population in the capital city of Late Shang Dynasty had experienced extensive stress exposure due to early urbanization with further social stratification only worsening the situation, and eventually contributing to collapse of the Shang Dynasty. [ABSTRACT FROM AUTHOR]

AbstractThis study characterizes how Native Americans living on the Oregon coast used whales and small cetaceans prior to European contact. We present an original analysis of a large subsample (NISP = 1177) of archaeological cetacean remains from the Palmrose (35CLT47) site, and new identifications from the previously analyzed Par-Tee (35CLT20; NISP = 31) and Tahkenitch Landing (35DO130; NISP = 33) sites. Using zooarchaeological and biomolecular analyses we report species presence and modification patterns to characterize use. Gray (Eschrichtius robustus) and humpback whale (Megaptera novaeangliae) were the most commonly identified whale species and likely preferred source of food, oil, bone for tool manufacture, and possibly sinew. Dolphins and porpoises, especially harbor porpoise (Phocoena phocoena), were a source of food and possibly bone for tool manufacture. While site inhabitants may have engaged in opportunistic hunting, the presence of species such as blue (Balaenoptera musculus) and Cuvier’s beaked whale (Ziphius cavirostris) suggests collection of beached animals was also an important acquisition strategy. Our study demonstrates the value of: (1) biomolecular analyses for improved species identifications and understanding of species richness; and (2) thorough zooarchaeological analyses to fully understand dietary and cultural contributions of cetaceans to pre-contact lifeways on the Oregon coast. [ABSTRACT FROM AUTHOR]

The Columbian Exchange resulted in a widespread movement of humans, plants and animals between the Old and New Worlds. The late 15th to early 16th century transfer of cattle from the Iberian Peninsula and Canary Islands to the Caribbean laid the foundation for the development of American creole cattle (Bos taurus) breeds. Genetic analyses of modern cattle from the Americas reveal a mixed ancestry of European, African and Indian origins. Recent debate in the genetic literature centers on the ‘African’ haplogroup T1 and its subhaplogroups, alternatively tying their origins to the initial Spanish herds, and/or from subsequent movements of taurine cattle through the African slave trade. We examine this problem through ancient DNA analysis of early 16th century cattle bone from Sevilla la Nueva, the first Spanish colony in Jamaica. In spite of poor DNA preservation, both T3 and T1 haplogroups were identified in the cattle remains, confirming the presence of T1 in the earliest Spanish herds. The absence, however, of “African-derived American” haplotypes (AA/T1c1a1) in the Sevilla la Nueva sample, leaves open the origins of this sub-haplogroup in contemporary Caribbean cattle. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 mt DNA analyses in producing confident personal identifications for forensic cold cases dating to within the last 60 years. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Studies the amplification of human mitochondrial DNA. Polymerase chain reaction (PCR) amplification; Positive amplifications of negative controls; Sequence of PCR products; Levels of contamination; Sensitivity of PCR amplification.

Presents a method used in the extraction of polymerase chain reaction-amplifiable deoxyribonucleic acid (DNA) from ancient bones. Advent of polymerase chain reaction; Analysis of the extraction protocol; Success of extraction protocols; Results of tests conducted.

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. [ABSTRACT FROM AUTHOR]