Species determination based on genetic evidence is an indispensable tool in archaeology, forensics, ecology, and food authentication. Most available analytical approaches involve compromises with ...regard to the number of detectable species, high cost due to low throughput, or a labor-intensive manual process. Here, we introduce "Species by Proteome INvestigation" (SPIN), a shotgun proteomics workflow for analyzing archaeological bone capable of querying over 150 mammalian species by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Rapid peptide chromatography and data-independent acquisition (DIA) with throughput of 200 samples per day reduce expensive MS time, whereas streamlined sample preparation and automated data interpretation save labor costs. We confirm the successful classification of known reference bones, including domestic species and great apes, beyond the taxonomic resolution of the conventional peptide mass fingerprinting (PMF)-based Zooarchaeology by Mass Spectrometry (ZooMS) method. In a blinded study of degraded Iron-Age material from Scandinavia, SPIN produces reproducible results between replicates, which are consistent with morphological analysis. Finally, we demonstrate the high throughput capabilities of the method in a high-degradation context by analyzing more than two hundred Middle and Upper Palaeolithic bones from Southern European sites with late Neanderthal occupation. While this initial study is focused on modern and archaeological mammalian bone, SPIN will be open and expandable to other biological tissues and taxa.
Animals are an integral part of deposition practices during the Danish Iron Age, and they probably represent the most common form of deposit within southern Scandinavia. Recently Gotfredsen published ...a volume on animals within Danish Iron Age grave contexts, but similarly comprehensive studies of animals from other contexts have not been attempted. Thus, classic sites such as Valmose, Bukkerup Langmose, and Sorte Muld still stand as the type sites for Danish Iron Age animal deposits. This article will demonstrate that there are good reasons for exploring deposits in more detail and investigate the significant variation in the treatment and quantities of sacrificial animal deposits. Furthermore, the current study has revealed a deposition pattern where a primary animal is often in the company of one or more secondary animals, the latter typically represented by a few bones. Salpetermosen Syd (MNS50010), south of Hillerød in North Zealand, Denmark is the main case study, but comparisons are made to several sites across Denmark where a similar deposition pattern has been observed.
Significance
Goats were among the first domestic animals and today are an important livestock species; archaeozoological evidence from the Zagros Mountains of western Iran indicates that goats were ...managed by the late ninth/early eighth millennium. We assess goat assemblages from Ganj Dareh and Tepe Abdul Hosein, two Aceramic Neolithic Zagros sites, using complementary archaeozoological and archaeogenomic approaches. Nuclear and mitochondrial genomes indicate that these goats were genetically diverse and ancestral to later domestic goats and already distinct from wild goats. Demographic profiles from bone remains, differential diversity patterns of uniparental markers, and presence of long runs of homozygosity reveal the practicing and consequences of management, thus expanding our understanding of the beginnings of animal husbandry.
The Aceramic Neolithic (∼9600 to 7000 cal BC) period in the Zagros Mountains, western Iran, provides some of the earliest archaeological evidence of goat (
Capra hircus
) management and husbandry by circa 8200 cal BC, with detectable morphological change appearing ∼1,000 y later. To examine the genomic imprint of initial management and its implications for the goat domestication process, we analyzed 14 novel nuclear genomes (mean coverage 1.13X) and 32 mitochondrial (mtDNA) genomes (mean coverage 143X) from two such sites, Ganj Dareh and Tepe Abdul Hosein. These genomes show two distinct clusters: those with domestic affinity and a minority group with stronger wild affinity, indicating that managed goats were genetically distinct from wild goats at this early horizon. This genetic duality, the presence of long runs of homozygosity, shared ancestry with later Neolithic populations, a sex bias in archaeozoological remains, and demographic profiles from across all layers of Ganj Dareh support management of genetically domestic goat by circa 8200 cal BC, and represent the oldest to-this-date reported livestock genomes. In these sites a combination of high autosomal and mtDNA diversity, contrasting limited Y chromosomal lineage diversity, an absence of reported selection signatures for pigmentation, and the wild morphology of bone remains illustrates domestication as an extended process lacking a strong initial bottleneck, beginning with spatial control, demographic manipulation via biased male culling, captive breeding, and subsequently phenotypic and genomic selection.
The analysis of the DNA entrapped in ancient shells of molluscs has the potential to shed light on the evolution and ecology of this very diverse phylum. Ancient genomics could help reconstruct the ...responses of molluscs to past climate change, pollution, and human subsistence practices at unprecedented temporal resolutions. Applications are however still in their infancy, partly due to our limited knowledge of DNA preservation in calcium carbonate shells and the need for optimized methods for responsible genomic data generation. To improve ancient shell genomic analyses, we applied high-throughput DNA sequencing to 27 Mytilus mussel shells dated to ~111-6500 years Before Present, and investigated the impact, on DNA recovery, of shell imaging, DNA extraction protocols and shell sub-sampling strategies. First, we detected no quantitative or qualitative deleterious effect of micro-computed tomography for recording shell 3D morphological information prior to sub-sampling. Then, we showed that double-digestion and bleach treatment of shell powder prior to silica-based DNA extraction improves shell DNA recovery, also suggesting that DNA is protected in preservation niches within ancient shells. Finally, all layers that compose Mytilus shells, i.e., the nacreous (aragonite) and prismatic (calcite) carbonate layers, with or without the outer organic layer (periostracum) proved to be valuable DNA reservoirs, with aragonite appearing as the best substrate for genomic analyses. Our work contributes to the understanding of long-term molecular preservation in biominerals and we anticipate that resulting recommendations will be helpful for future efficient and responsible genomic analyses of ancient mollusc shells.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Animals are an integral part of deposition practices during the Danish Iron Age, and they probably represent the most common form of deposit within southern Scandinavia. Recently Gotfredsen published ...a volume on animals within Danish Iron Age grave contexts, but similarly comprehensive studies of animals from other contexts have not been attempted. Thus, classic sites such as Valmose, Bukkerup Langmose, and Sorte Muld still stand as the type sites for Danish Iron Age animal deposits. This article will demonstrate that there are good reasons for exploring deposits in more detail and investigate the significant variation in the treatment and quantities of sacrificial animal deposits. Furthermore, the current study has revealed a deposition pattern where a primary animal is often in the company of one or more secondary animals, the latter typically represented by a few bones. Salpetermosen Syd (MNS50010), south of Hillerød in North Zealand, Denmark is the main case study, but comparisons are made to several sites across Denmark where a similar deposition pattern has been observed.
Archaeological evidence for penned animals is increasingly used to indicate managed livestock. Advances in techniques allowing the identification of dung and urine-derived components in sediments ...have enabled the expansion of this line of enquiry. Corralling animals into settlements protected them from predators at night and provided more control over their breeding. Deposits associated with livestock management at Neolithic settlements across Southwest Asia sometimes contain bones of perinatal animals. Reviewing the literature, it is evident that these faunal remains are not systematically reported or preserved in all burial environments. However, their distribution may reflect different patterns of livestock integration into human settlements. The presence of perinatal remains at sites where early livestock herding took place has important implications. Not only are they compelling evidence for herd management, particularly if there is also evidence for penning deposits, but also death of livestock during the perinatal phase of life informs us about the health of animals in early herds. This in turn, provides information about the skills needed by early pastoralists as they developed animal management strategies and the possible effect of transmissible diseases as animals were kept together in closer proximity.
Middle Nubian Horizon faunal material has rarely been the main focus of study, both in relation to the daily consumption of animals as well as the symbolic and ritualised use of fauna in a burial ...context. Owing to the excavation history of the area, the data available in the archaeological literature is often based on other sources than actual excavated faunal material. This article presents an interpretation based on an analysis of five Pan-grave cemeteries excavated by the Scandinavian Joint Expedition to Sudanese Nubia (SJE) in 1961–64, focusing on the large SJE 47 cemetery. The results reveal a consistent tradition of faunal deposit practices and the existence of two distinct types of deposits varying in both context and content. The most characteristic evidence is the large number of cut and painted skulls of goat (Capra hircus), sheep (Ovis aries) and cattle (Bos taurus), deposited in circular ditches around the graves. Through the use of ethnographic analogies and an in-depth analysis of these Pan-grave faunal remains the aim is to position this evidence in a wider context of ritual practices and cultural consumption.
Abstract Species determination based on genetic evidence is an indispensable tool in archaeology, forensics, ecology, and food authentication. Most available analytical approaches involve compromises ...with regard to the number of detectable species, high cost due to low throughput, or a labor-intensive manual process. Here, we introduce “Species by Proteome INvestigation” (SPIN), a shotgun proteomics workflow for analyzing archaeological bone capable of querying over 150 mammalian species by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Rapid peptide chromatography and data-independent acquisition (DIA) with throughput of 200 samples per day reduce expensive MS time, whereas streamlined sample preparation and automated data interpretation save labor costs. We confirm the successful classification of known reference bones, including domestic species and great apes, beyond the taxonomic resolution of the conventional peptide mass fingerprinting (PMF)-based Zooarchaeology by Mass Spectrometry (ZooMS) method. In a blinded study of degraded Iron-Age material from Scandinavia, SPIN produces reproducible results between replicates, which are consistent with morphological analysis. Finally, we demonstrate the high throughput capabilities of the method in a high-degradation context by analyzing more than two hundred Middle and Upper Palaeolithic bones from Southern European sites with late Neanderthal occupation. While this initial study is focused on modern and archaeological mammalian bone, SPIN will be open and expandable to other biological tissues and taxa.
Major migration events in Holocene Eurasia have been characterized genetically at broad regional scales
. However, insights into the population dynamics in the contact zones are hampered by a lack of ...ancient genomic data sampled at high spatiotemporal resolution
. Here, to address this, we analysed shotgun-sequenced genomes from 100 skeletons spanning 7,300 years of the Mesolithic period, Neolithic period and Early Bronze Age in Denmark and integrated these with proxies for diet (
C and
N content), mobility (
Sr/
Sr ratio) and vegetation cover (pollen). We observe that Danish Mesolithic individuals of the Maglemose, Kongemose and Ertebølle cultures form a distinct genetic cluster related to other Western European hunter-gatherers. Despite shifts in material culture they displayed genetic homogeneity from around 10,500 to 5,900 calibrated years before present, when Neolithic farmers with Anatolian-derived ancestry arrived. Although the Neolithic transition was delayed by more than a millennium relative to Central Europe, it was very abrupt and resulted in a population turnover with limited genetic contribution from local hunter-gatherers. The succeeding Neolithic population, associated with the Funnel Beaker culture, persisted for only about 1,000 years before immigrants with eastern Steppe-derived ancestry arrived. This second and equally rapid population replacement gave rise to the Single Grave culture with an ancestry profile more similar to present-day Danes. In our multiproxy dataset, these major demographic events are manifested as parallel shifts in genotype, phenotype, diet and land use.
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