Search

For the first time, this paper presents a complex study of the burial of the ancient Russian woman from the classic “Vyatich” mound from the Kremenyie burial site (Moscow region). The mounds and synchronized ground cremation burials are combined at this unique 12th-century burial site. The aim of this research is to examine the historical details of the person from the mound using conventional archaeological, anthropological, and archaeoparasitology methodologies along with modern paleogenetics methods. The burial site is characterized by a general “archaic” rite, manifested in the late preservation of the cremation rite along with the burial. According to anthropological data, an elderly woman, over forty, was buried there. She was identified as a member of the local population by radiogenic strontium isotope (87Sr/86Sr) study. Rich grave content and the fact that the body was buried in the middle of the mound indicate the woman's high social standing in the community. According to archaeoparasitological data, the eating habits of the woman appear to be characterized by the consumption of uncooked or insufficiently thermally prepared freshwater fish. The complete mtDNA sequence reconstruction indicates that it belongs to haplogroup V1a1, one of the Western Eurasian haplogroup V branches. To date, this represents the first case of the V1a1 mitogroup being found in the Russian Plain during ancient times. A representative of the Danish Viking clan from the Oxford burial site of the XI century was the closest of the ancient samples to the mtDNA of the studied woman, which indicates a genetic relationship on the maternal lineage with the medieval Northwestern European population. Single nucleotide substitution A7299G in the mitogenome of the woman clusters her with present-day Russians from the Belgorod and Pskov regions and shows the continuity of the modern Russian population with the Ancient Russians. Thus, the results of our study demonstrate the private details of the individual as common historical features, which include the ceremonial side of burial and belonging to the maternal genetic lineage preserved in the modern gene pool of the Russian population.

The biogeographic and demographic history of the house mouse, Mus musculus domesticus, has been closely linked to human history since pre-Neolithic times – this species first appeared in the Near East and subsequently dispersed westward with humans into regions with local Mus species. However, if this issue is now well known for the eastern Mediterranean, data are still lacking for the western Mediterranean, and especially for north-western Africa. In the present study, we combine morphological, geometric morphometric and genetic analyses to Mus remains from the Moroccan site of Rirha, dating to the Mauretanian period (5th to 1st century BC). Thanks to this multidisciplinary approach, we were able to confirm the first asserted record of the house mouse in a well-established archaeological context in the Maghreb. The morphometric and genetic results are largely congruent, with a single discrepancy observed for one specimen, which may be linked to possible hybridization between M. m. domesticus and M. spretus species. Further analyses are required on material from other North African sites dating to earlier chrono-cultural periods to better document the oldest appearance and the dispersal of the house mouse in the south-western Mediterranean through time. [ABSTRACT FROM AUTHOR]

Archaeologists in the Canary Islands have gathered substantial quantitative data from radiocarbon measurements and aDNA analyses. While undeniably helpful and necessary for apprehending past human activity, their interpretation, based on theories underpinning models developed for island chains, has lagged, leaving a gap in our understanding of processes of occupation and social network systems. The decontextualized nature of the archaeological landscape of the Canaries and a lack of consensus about proper radiocarbon methodologies are some of the factors contributing to heated scholarly debate. Here, for the Canary Islands, the author reviews the current literature on aDNA and discusses settlement theories, the chronological evidence used for occupation models, and how such perspectives align with current thinking on island colonization. [ABSTRACT FROM AUTHOR]

Copyright of Stratum Plus Journal is the property of P.P. Stratum plus and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Tropical freshwater lakes are well known for their high biodiversity, and particularly the East African Great Lakes are renowned for their adaptive radiation of cichlid fishes. While comparative phylogenetic analyses of extant species flocks have revealed patterns and processes of their diversification, little is known about evolutionary trajectories within lineages, the impacts of environmental drivers, or the scope and nature of now‐extinct diversity. Time‐structured palaeodata from geologically young fossil records, such as fossil counts and particularly ancient DNA (aDNA) data, would help fill this large knowledge gap. High ambient temperatures can be detrimental to the preservation of DNA, but refined methodology now allows data generation even from very poorly preserved samples. Here, we show for the first time that fish fossils from tropical lake sediments yield endogenous aDNA. Despite generally low endogenous content and high sample dropout, the application of high‐throughput sequencing and, in some cases, sequence capture allowed taxonomic assignment and phylogenetic placement of 17% of analysed fish fossils to family or tribe level, including remains which are up to 2700 years old or weigh less than 1 mg. The relationship between aDNA degradation and the thermal age of samples is similar to that described for terrestrial samples from cold environments when adjusted for elevated temperature. Success rates and aDNA preservation differed between the investigated lakes Chala, Kivu and Victoria, possibly caused by differences in bottom water oxygenation. Our study demonstrates that the sediment records of tropical lakes can preserve genetic information on rapidly diversifying fish taxa over time scales of millennia. [ABSTRACT FROM AUTHOR]

Rapid global warming is severely impacting Arctic ecosystems and is predicted to transform the abundance, distribution and genetic diversity of Arctic species, though these linkages are poorly understood. We address this gap in knowledge using palaeogenomics to examine how earlier periods of global warming influenced the genetic diversity of Atlantic walrus (Odobenus rosmarus rosmarus), a species closely associated with sea ice and shallow-water habitats. We analysed 82 ancient and historical Atlantic walrus mitochondrial genomes (mitogenomes), including now-extinct populations in Iceland and the Canadian Maritimes, to reconstruct the Atlantic walrus' response to Arctic deglaciation. Our results demonstrate that the phylogeography and genetic diversity of Atlantic walrus populations was initially shaped by the last glacial maximum (LGM), surviving in distinct glacial refugia, and subsequently expanding rapidly in multiple migration waves during the late Pleistocene and early Holocene. The timing of diversification and establishment of distinct populations corresponds closely with the chronology of the glacial retreat, pointing to a strong link between walrus phylogeography and sea ice. Our results indicate that accelerated ice loss in the modern Arctic may trigger further dispersal events, likely increasing the connectivity of northern stocks while isolating more southerly stocks putatively caught in small pockets of suitable habitat. [ABSTRACT FROM AUTHOR]

Copyright of Antropo is the property of Antropo and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The Cypriot pygmy hippopotamus is an extinct Mediterranean species that inhabited the island of Cyprus during the Late Pleistocene. This iconic species last appears at the archaeological site of Akrotiri Aetokremnos, dated to ~12 500 cal. BP. Taxonomically, the Cypriot pygmy hippopotamus has been assigned to Hippopotamus minor , which, based on morphology, is more closely related to the common hippopotamus (Hippopotamus amphibius ; today present only in Sub-Saharan Africa) than to the West African pygmy hippopotamus (Choeropsis liberiensis). Despite adverse conditions for preservation that greatly reduce the likelihood of DNA preservation in subfossil samples from hot environments, we recovered and analysed ancient DNA from petrous bones excavated from Akrotiri Aetokremnos. By whole mitogenome hybridization capture and exhaustive high-throughput sequencing, we were able to investigate the molecular phylogeny and taxonomic status of the Cypriot pygmy hippopotamus. The results of our low-coverage ancient mitogenomic analyses support the close phylogenetic affinity of H. minor to H. amphibius , with their divergence estimated at ~1.36 or 1.58 Mya, depending on the molecular dating method. To our knowledge, this study constitutes the first step towards reconstruction of the molecular phylogeny of Mediterranean Hippopotaminae. [ABSTRACT FROM AUTHOR]

Palaeogenetics is becoming increasingly important in tackling archaeological issues. However, analyses of ancient DNA can be hampered or even prevented by the state of preservation of samples due to poor storage conditions, and because of contamination by modern DNA. The beDNA project for a national archaeological genetic data and sample bank (banque d’échantillons et de Données Nationale Archéogénétique) is developing the means to enable future palaeogenetic analyses by systematically storing human skeletal samples, with the constraints inherent to the preservation of ancient DNA taken into account. This project comprises (1) a systematic protocol for "clean" sampling of human remains to be common to all archaeological operations, (2) a dedicated storage space for samples, suited to aDNA preservation, (3) a database linking sites with the samples stored in the bank, (4) approval of sample analysis requests by authorities, after expert review. The test phase of the project, which began in September 2020 in the Île-de-France region, enabled us to evaluate and adjust both the sampling protocol in the field and the transfer process to the beDNA bank. This note describes the different stages envisaged for each sample, from the archaeological field to the genetics laboratory, as well as the development of the experimental phase and initial feedback from it.

This article brings to the attention of historians the recent discoveries by palaeogeneticists of a pandemic of plague in Europe during the fourth and third millennia BCE that contributed to the decline of the once-thriving Neolithic farming population of Anatolian origin and opened the way to the migration of nomadic herders equipped with bronze weapons who came from the steppes of southern Russia. As the geneticists' sequencing of ancient DNA has revealed, the ancestry of central, northern and western Europeans changed from predominantly Anatolian to largely (or, in some areas, predominantly) the steppe nomads. Besides the change in ancestry, the genetic sequencing of Bronze Age European populations also provides evidence that the arrival of the Yamnaya changed their social structures and gender relations and contributed to the spread of the Indo-European languages. [ABSTRACT FROM AUTHOR]

Leopard complex spotting is inherited by the incompletely dominant locus, LP, which also causes congenital stationary night blindness in homozygous horses. We investigated an associated single nucleotide polymorphism in the TRPM1 gene in 96 archaeological bones from 31 localities from Late Pleistocene (approx. 17 000 YBP) to medieval times. The first genetic evidence of LP spotting in Europe dates back to the Pleistocene. We tested for temporal changes in the LP associated allele frequency and estimated coefficients of selection by means of approximate Bayesian computation analyses. Our results show that at least some of the observed frequency changes are congruent with shifts in artificial selection pressure for the leopard complex spotting phenotype. In early domestic horses from Kirklareli-Kanligecit (Turkey) dating to 2700-2200 BC, a remarkably high number of leopard spotted horses (six of 10 individuals) was detected including one adult homozygote. However, LP seems to have largely disappeared during the late Bronze Age, suggesting selection against this phenotype in early domestic horses. During the Iron Age, LP reappeared, probably by reintroduction into the domestic gene pool from wild animals. This picture of alternating selective regimes might explain how genetic diversity was maintained in domestic animals despite selection for specific traits at different times.

The oldest confirmed remains of domestic dogs in North America are from mid-continent archaeological sites dated approximately 9900 calibrated years before present (cal BP). Although this date suggests that dogs may not have arrived alongside the first Native Americans, the timing and routes for the entrance of New World dogs remain uncertain. Here, we present a complete mitochondrial genome of a dog from southeast Alaska, dated to 10 150 ± 260 cal BP. We compared this high-coverage genome with data from modern dog breeds, historical Arctic dogs and American precontact dogs (PCDs) from before European arrival. Our analyses demonstrate that the ancient dog belongs to the PCD lineage, which diverged from Siberian dogs around 16 700 years ago. This timing roughly coincides with the minimum suggested date for the opening of the North Pacific coastal (NPC) route along the Cordilleran Ice Sheet and genetic evidence for the initial peopling of the Americas. This ancient southeast Alaskan dog occupies an early branching position within the PCD clade, indicating it represents a close relative of the earliest PCDs that were brought alongside people migrating from eastern Beringia southward along the NPC to the rest of the Americas. The stable isotope δ13C value of this early dog indicates a marine diet, different from the younger mid-continent PCDs' terrestrial diet. Although PCDs were largely replaced by modern European dog breeds, our results indicate that their population decline started approximately 2000 years BP, coinciding with the expansion of Inuit peoples, who are associated with traditional sled-dog culture. Our findings suggest that dogs formed part of the initial human habitation of the New World, and provide insights into their replacement by both Arctic and European lineages. [ABSTRACT FROM AUTHOR]

The notion of "emerging infectious diseases" (EID) as a category of global health concerns was created in the 1990s to acknowledge that, although public health interventions, vaccines, and antibiotics since the late 19th century had given wealthier parts of the world control over most infectious diseases, the experience of Ebola and HIV/AIDS showed that new human diseases could still arise. "Emerging diseases" have clear histories, and the task the field of EID set itself has been to make those histories as short as possible—to catch emerging diseases as close to their origin as possible and snuff them out before they can become pandemics. In contrast, many of the known infectious diseases, those that were allegedly "conquered" by the rise of biomedicine in the late 19th and early 20th centuries and which (aside from smallpox) nonetheless still persist today, were assumed to have existed "since time immemorial." Their histories had no specific time‐depth, no documentable origins, and few discernible narrative arcs. The advent of a new field of research, palaeogenetics, has made possible an evolutionary perspective on pathogenic microorganisms, bringing hitherto unimaginable specificity to their documentable histories. Many origin stories, and nearly all globalization stories, fall within periods that historians and archaeologists study intensively. I argue that the diseases that have proved best suited to global expansion since the advent of the Holocene—those that became pandemics, like COVID‐19—are those that have best exploited humans' global networks and behaviors in a given age. This recognition, in turn, gives the fields of both global health and history of medicine a new agenda. [ABSTRACT FROM AUTHOR]

There is a growing body of evidence demonstrating the impacts of human arrival in new "pristine" environments, including terrestrial habitat alterations and species extinctions. However, the effects of marine resource utilization prior to industrialized whaling, sealing, and fishing have largely remained understudied. The expansion of the Norse across the North Atlantic offers a rare opportunity to study the effects of human arrival and early exploitation of marine resources. Today, there is no local population of walruses on Iceland, however, skeletal remains, place names, and written sources suggest that walruses existed, and were hunted by the Norse during the Settlement and Commonwealth periods (870–1262 AD). This study investigates the timing, geographic distribution, and genetic identity of walruses in Iceland by combining historical information, place names, radiocarbon dating, and genomic analyses. The results support a genetically distinct, local population of walruses that went extinct shortly after Norse settlement. The high value of walrus products such as ivory on international markets likely led to intense hunting pressure, which—potentially exacerbated by a warming climate and volcanism—resulted in the extinction of walrus on Iceland. We show that commercial hunting, economic incentives, and trade networks as early as the Viking Age were of sufficient scale and intensity to result in significant, irreversible ecological impacts on the marine environment. This is to one of the earliest examples of local extinction of a marine species following human arrival, during the very beginning of commercial marine exploitation. [ABSTRACT FROM AUTHOR]

Few members of the Pleistocene megafauna have been as extensively studied as cave bears. Multidisciplinary research into cave bears has provided insights into their morphology, ecology, and evolution. Genetic studies have profited from the availability of large numbers of well-preserved remains. As a result, 'ancient DNA (aDNA)' from cave bears has provided significant insights into cave bear ecology, phylogeography and even potential causes of their extinction. Here I review the contributions that genetic research has made to our understanding of cave bear biology and evaluate the potential that new, genomic tools provide to shed further light onto how these iconic representatives of the Pleistocene megafauna lived and died. [ABSTRACT FROM AUTHOR]

Aim: The islands of the south‐western Indian Ocean region are home to many endemic bird species, with their closest relatives occurring in Africa and Madagascar, Eurasia, the Sunda Islands, and the Australasian region. Among owls, the extant endemic scops owls (genus Otus) from Madagascar, Comoros, Seychelles, and Socotra are related to the Southeast Asian species, O. sunia, the Oriental scops owl. Three owl species, presumably Otus derivatives, twice the size of standard scops owls and now extinct, once inhabited the Mascarene Islands, and have been placed in a separate genus, Mascarenotus. Insular apomorphies have made their precise relationships difficult to determine. Here we investigate the phylogenetic position of these enigmatic owls. Location: The Mascarene Islands (Réunion, Mauritius, Rodrigues) in the south‐western Indian Ocean. Methods: Phylogenetic relationships were reconstructed using ancient DNA extracted from subfossil remains. Fragments of cytochrome b gene were amplified and sequenced. The ancient sequences were analysed with modern sequences of 19 ingroup Otus taxa using Bayesian and Maximum Likelihood methods. Results: The Mauritian extinct species M. sauzieri was reconstructed as the sister to both O. pauliani (Grand Comoro) and O. rutilus (Madagascar). The Rodrigues extinct species M. murivorus was the sister, in a star‐like differentiation, to the preceding clade as well as the remaining Comorian species and a clade formed by O. insularis (Seychelles) and O. sunia. Main conclusions: The ancestor of O. sunia simultaneously colonized Rodrigues Island (evolving into Otus murivorus), Madagascar, and part of the Comoros Islands around 3 million years ago. Later, presumably from Madagascar, new lineages colonized Grand Comoro and Mauritius (O. sauzieri). Independently, a more recent O. sunia ancestor colonized the Seychelles Islands and Socotra. These colonizations were probably favoured by Pliocene cyclonic events, stronger and more frequent than today. Several features, including giantism, wing reduction, and a relative decrease in skull and orbit size evolved convergently in the polyphyletic species O. sauzieri and O. murivorus. [ABSTRACT FROM AUTHOR]

SUMMARY: While some species of parasites can be identified to species level from archaeological remains using microscopy (i.e. Enterobius vermicularis, Clonorchis sinensis), others can only be identified to family or genus level as different species produce eggs with similar morphology (i.e. Tænia sp. and Echinococcus sp.). Molecular and immunological approaches offer the possibility to provide more precise determination at the species level. They can also identify taxa when classic parasite markers such as eggs or cysts have been destroyed over time. However, biomolecules can be poorly preserved and modern reference DNA is available only for a limited number of species of parasites, leading to the conclusion that classic microscopic observation should be combined with molecular analyses. Here we present a review of the molecular approaches used over the past two decades to identify human pathogenic helminths (Ascaris sp., Trichuris sp., E. vermicularis, Fasciola sp. etc.) or protists (Giardia sp., Trypanosoma sp., Leishmania sp. etc.). We also discuss the prospects for studying the evolution of parasites with genetics and genomics. [ABSTRACT FROM AUTHOR]

The genetic analysis of calcified remains of past organisms, mainly bones and teeth, enrich largely our knowledge of the evolution of animal and plant species and their domestication, the evolution of human lineages, the peopling of the continents, the admixture between different human lineages, the Neolithic diffusion, the composition of necropolises, etc. In this way, paleogenetic data potentially enrich archaeological data and help archaeologists, archaeobiologists and palaeoanthropologists to interpret archaeological sites. Paleogenetic analyses are performed on ancient DNA molecules, which, if preserved at all, are much degraded and most of the time present at trace amounts. Therefore, their analysis is challenging but the methods are becoming more and more efficient. The produced data are extremely useful for archaeology and biology, and some of them are even surprising.

The field of ancient DNA (aDNA) has recently been in a state of exponential growth, largely driven by the uptake of Next Generation Sequencing (NGS) techniques. Much of this work has focused on the mammalian megafauna and ancient humans, with comparatively less studies looking at micromammal fauna, despite the potential of these species in testing evolutionary, environmental and taxonomic theories. Several factors make micromammal fauna ideally suited for aDNA extraction and sequencing. Micromammal subfossil assemblages often include the large number of individuals appropriate for population level analyses, and, furthermore, the assemblages are frequently found in cave sites where the constant temperature and sheltered environment provide favourable conditions for DNA preservation. This review looks at studies that include the use of aDNA in molecular analysis of micromammal fauna, in order to examine the wide array of questions that can be answered in the study of small mammals using new palaeogenetic techniques. This study highlights the bias in current aDNA studies and assesses the future use of aDNA as a tool for the study of micromammal fauna. [ABSTRACT FROM AUTHOR]

Bird remains that are difficult to identify taxonomically using morphological methods, are common in the palaeontological record. Other types of challenging avian material include artefacts and food items from endangered taxa, as well as remains from aircraft strikes. We here present a DNA-based method that enables taxonomic identification of bird remains, even from material where the DNA is heavily degraded. The method is based on the amplification and sequencing of two short variable parts of the 16S region in the mitochondrial genome. To demonstrate the applicability of this approach, we evaluated the method on a set of Holocene and Late Pleistocene postcranial bird bones from several palaeontological and archaeological sites in Europe with good success. [ABSTRACT FROM AUTHOR]

Global warming is predicted to cause substantial habitat rearrangements, with the most severe effects expected to occur in high-latitude biomes. However, one major uncertainty is whether species will be able to shift their ranges to keep pace with climate-driven environmental changes. Many recent studies on mammals have shown that past range contractions have been associated with local extinctions rather than survival by habitat tracking. Here, we have used an interdisciplinary approach that combines ancient DNA techniques, coalescent simulations and species distribution modelling, to investigate how two common cold-adapted bird species, willow and rock ptarmigan ( Lagopus lagopus and Lagopus muta), respond to long-term climate warming. Contrary to previous findings in mammals, we demonstrate a genetic continuity in Europe over the last 20 millennia. Results from back-casted species distribution models suggest that this continuity may have been facilitated by uninterrupted habitat availability and potentially also the greater dispersal ability of birds. However, our predictions show that in the near future, some isolated regions will have little suitable habitat left, implying a future decrease in local populations at a scale unprecedented since the last glacial maximum. [ABSTRACT FROM AUTHOR]

Written sources show that livestock were traded during the Roman period. However, there is scarce information available to characterise this trade because of its invisibility in the archaeological record. In our paper, we shed light on this issue by applying both osteometric and genetic analyses on cattle remains from the Roman trading post of Empúries (Catalonia) to determine how livestock contributed to Roman trade and, thus, to the economy of the Empire. Analysis of 26 cattle metacarpals from Empúries has allowed us to document the presence of different cattle morphotypes in this city during its Early Roman occupation. The morphological and genetic differences seen in Empúries cattle can be explained through trade of different cattle varieties, more appropriate for milk production and/or traction than the local stock. Once arrived at the port of Empúries, these imported cattle would have then been distributed to surrounding villas. Copyright © 2016 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Recent palaeogenetic studies indicate a highly dynamic history in collared lemmings ( Dicrostonyx spp.), with several demographical changes linked to climatic fluctuations that took place during the last glaciation. At the western range margin of D. torquatus, these changes were characterized by a series of local extinctions and recolonizations. However, it is unclear whether this pattern represents a local phenomenon, possibly driven by ecological edge effects, or a global phenomenon that took place across large geographical scales. To address this, we explored the palaeogenetic history of the collared lemming using a next-generation sequencing approach for pooled mitochondrial DNA amplicons. Sequences were obtained from over 300 fossil remains sampled across Eurasia and two sites in North America. We identified five mitochondrial lineages of D. torquatus that succeeded each other through time across Europe and western Russia, indicating a history of repeated population extinctions and recolonizations, most likely from eastern Russia, during the last 50 000 years. The observation of repeated extinctions across such a vast geographical range indicates large-scale changes in the steppe-tundra environment in western Eurasia during the last glaciation. All Holocene samples, from across the species' entire range, belonged to only one of the five mitochondrial lineages. Thus, extant D. torquatus populations only harbour a small fraction of the total genetic diversity that existed across different stages of the Late Pleistocene. In North American samples, haplotypes belonging to both D. groenlandicus and D. richardsoni were recovered from a Late Pleistocene site in south-western Canada. This suggests that D. groenlandicus had a more southern and D. richardsoni a more northern glacial distribution than previously thought. This study provides significant insights into the population dynamics of a small mammal at a large geographical scale and reveals a rather complex demographical history, which could have had bottom-up effects in the Late Pleistocene steppe-tundra ecosystem. [ABSTRACT FROM AUTHOR]

Anthropogenic environmental changes are considered critical drivers of the genetic structure of populations and communities through, for example, the facilitation of introgressive hybridization between syntopic species. However, the mechanisms by which environmental perturbations trigger changes in the genetic structure of populations and communities, such as the processes that determine the directionality of hybridization and patterns of mitochondrial introgression over many generations, remain largely unexplored. In this study, the changes in genetic structure of hybridizing members of the Daphnia longispina species complex were reconstructed over the last 100 years for three large temperate lakes under strong anthropogenic pressures via palaeogenetic analyses of resting egg banks. Drastic changes in the genetic structure of the Daphnia community, associated with hybridization events between D. longispina and D. galeata and subsequent introgression, were detected in Lakes Geneva and Bourget. In Lake Bourget, these changes were induced by the successful establishment of D. galeata with rising phosphorus levels and reinforced by the sensitivity of D. longispina to fish predation pressure. In Lake Geneva, the pattern of hybridization during eutrophication is more likely a function of the original taxonomic composition of the species complex in this lake. Lakes seem to require at least a meso-oligotrophic status to allow D. galeata populations to establish and accordingly no D. galeata genotypes were found in the egg bank of oligotrophic Lake Annecy. In contrast to the generally assumed pattern of unidirectional hybridization in this species complex, bidirectional hybridization was recorded in Lakes Geneva and Bourget. Our results also demonstrate complex genetic trajectories within this species complex and highlight the irreversibility of changes in the genotypic architecture of populations driven by local human pressures. Finally, we show that extensive hybridization and introgression do not necessarily result in a large and homogenous hybrid swarm. [ABSTRACT FROM AUTHOR]

This palaeogenetic study focused on the analysis of a late prehispanic Argentinean group from the Humahuaca valley, with the main aim of reconstructing its (micro)evolutionary history. The Humahuaca valley, a natural passageway from the eastern plains to the highlands, was the living environment of Andean societies whose cultural but especially biological diversity is still poorly understood. We analyzed the DNA extracted from 39 individuals who populated this upper valley during the Regional Development period (RDP) (between the 11th and 15th centuries CE), to determine their maternal and paternal genetic ancestry. Some mitochondrial and Y-chromosomal haplotypes specific to the Andean region are consistent with an origin in the highlands of Central Andes. On the other hand, a significant genetic affinity with contemporary admixed communities of the Chaco area was detected. Expectedly, recent demographic events, such as the expansion of the Inca Empire or the European colonization, have changed the original mitochondrial gene pool of the ancient Humahuaca Valley community. Finally, we identified a particular geographical organization of the prehispanic populations of Northwestern Argentina. Our results suggest that the communities of the region were divided between two different spheres of interaction, which is consistent with assumptions made by means of craniometric traits. [ABSTRACT FROM AUTHOR]

The Late Pleistocene global extinction of many terrestrial mammal species has been a subject of intensive scientific study for over a century, yet the relative contributions of environmental changes and the global expansion of humans remain unresolved. A defining component of these extinctions is a bias toward large species, with the majority of small-mammal taxa apparently surviving into the present. Here, we investigate the population-level history of a key tundra-specialist small mammal, the collared lemming (Dicrostonyx torquatus), to explore whether events during the Late Pleistocene had a discernible effect beyond the large mammal fauna. Using ancient DNA techniques to sample across three sites in North-West Europe, we observe a dramatic reduction in genetic diversity in this species over the last 50,000 y. We further identify a series of extinction-recolonization events, indicating a previously unrecognized instability in Late Pleistocene small-mammal populations, which we link with climatic fluctuations. Our results reveal climate-associated, repeated regional extinctions in a keystone prey species across the Late Pleistocene, a pattern likely to have had an impact on the wider steppe-tundra community, and one that is concordant with environmental change as a major force in structuring Late Pleistocene biodiversity. [ABSTRACT FROM AUTHOR]

The last glaciation was a dynamic period with strong impact on the demography of many species and populations. In recent years, mitochondrial DNA sequences retrieved from radiocarbon-dated remains have provided novel insights into the history of Late Pleistocene populations. However, genotyping of loci from the nuclear genome may provide enhanced resolution of population-level changes. Here, we use four autosomal microsatellite DNA markers to investigate the demographic history of woolly mammoths ( Mammuthus primigenius) in north-eastern Siberia from before 60 000 years ago up until the species' final disappearance c. 4000 years ago. We identified two genetic groups, implying a marked temporal genetic differentiation between samples with radiocarbon ages older than 12 thousand radiocarbon years before present (ka) and those younger than 9 ka. Simulation-based analysis indicates that this dramatic change in genetic composition, which included a decrease in individual heterozygosity of approximately 30%, was due to a multifold reduction in effective population size. A corresponding reduction in genetic variation was also detected in the mitochondrial DNA, where about 65% of the diversity was lost. We observed no further loss in genetic variation during the Holocene, which suggests a rapid final extinction event. [ABSTRACT FROM AUTHOR]

Abstract: The contribution of palaeogenetic data to the study of various aspects of hominin biology and evolution has been significant, and has the potential to increase substantially with the widespread implementation of next generation sequencing techniques. Here we discuss the present state-of-the-art of ancient human DNA analysis and the characteristics of hominin aDNA that make sequence validation particularly complex. A brief overview of the development of anthropological palaeogenetic analysis is given to illustrate the technical challenges motivating recent technological advancements. [Copyright &y& Elsevier]

Summary: The Equidae have a long evolutionary history that has interested palaeontologists for a long time. Their morphology-based taxonomy, however, is a matter of controversy. Since most equid species are now extinct, the phylogenetic tree based on genetic data can be established only imperfectly via deduction of present day genomes and little is known about the past genetic diversity of these species. Recent studies of ancient DNA preserved in fossil bones have led to a simplification of the phylogenetic tree and the classification system. The situation is still particularly unclear for the wild asses whose geographical distribution in the Pleistocene and the early Holocene stretched from Northern Africa to Eurasia before they became endangered or extinct. Therefore, we performed a phylogeographic study of bone remains of wild asses covering their former geographic range over the past 100,000 years based on the analysis of ancient mitochondrial DNA. Here, we will not show but rather discuss our results calling the morphology-based classification into question and indicating that morphological criteria alone can be an unreliable index in inferring various equid species. Indeed, the diversity of mitochondrial lineages in populations with similar morphology along with genetic signatures shared between morphologically distinct animals reveal a significant morphological plasticity among Equus species. The classification of palaeontological species based on morphological and genetic criteria will be discussed. [ABSTRACT FROM AUTHOR]

In the graveyards of Divaky-Padelky za humny (dating between 9th and 11th centuries AD) and Znojmo-Hradiste (Great Moravian period) an attempt has been made to extract the samples in so called sterile way for the purpose of genetic analysis. In the research period during 2008 the exhumation of grave No. 160 in the graveyard of Divaky was carried out using this sterile method and afterwards the anthropological and genetic analysis of the skeletal remains was completed. The anthropological analysis showed that the skeleton was a female, aged between 24-30 years and this result was confirmed by the genetic analysis using the section of the SRY gene and analyzing the gene for amelogenin. Due to the fact that the method of exhumation at Divaky was both time-consuming and physically demanding and at the same time prevented the thorough documentation of the site, in 2009 a new method was used. Prior to the actual exhumation of the skeleton, one long bone was lifted from the grave using a sterile method and this proved to be a more suitable way because it did not interrupt the flow of the research. During the next research season of 2009 and 2010 this method was applied at both graveyards. The experiences at both Divaky and Znojmo show that this way of on- site preparation and laboratory processing of skeletal remains is more suitable in the lifting of bone tissue for genetic analysis. [ABSTRACT FROM AUTHOR]

Abstract: Tuberculosis is a major cause of death but infected people with effective immunity may remain healthy for years, suggesting long-term co-existence of host and pathogen. Direct detection and characterisation of ancient microbial DNA and lipid biomarkers confirms palaeopathological diagnoses. Archaeological Mycobacterium tuberculosis resembles extant lineages indicating the timescale for evolutionary changes is considerably longer than originally believed. [Copyright &y& Elsevier]

Abstract: In many ways, palaeogenomics began when the first ancient DNA sequence was reported. This first sequence was derived from a stuffed museum specimen of the quagga, an extinct mammal related to the zebra. Unspecified and unselected DNA was extracted from the quagga specimen, cloned into a bacterial library, and then sequenced. It took another 17 years and the development of PCR before two independent groups successfully sequenced the complete mitochondrial genomes from several extinct moa species. Only 4 years later, using the original approach of cloning nonspecific ancient DNA extract and shotgun sequencing, the first ancient nuclear DNA sequences were determined, this time from the extinct cave bear. Since these early successes, palaeogenomics has rapidly expanded, because of both technological development and increasing interest in ancient DNA research. New methods, developed since the cave bear sequence was reported, have produced nuclear DNA on a megabase scale from two extinct species, the mammoth and the Neanderthal, our closest relative. For both species, low-coverage genome-sequencing projects have been proposed. It is likely that these will be successful, given the rapid technical development in sequencing techniques. This review carefully examines both the promise and the current limitations of palaeogenomic analyses for both mitochondrial and nuclear DNA. [Copyright &y& Elsevier]

Abstract: Recently, palaeogenetics encountered enormous success when parts of the nuclear genomes of mammoth and Neanderthal man were analysed. Their bones, however, had been preserved in environments favourable to DNA preservation, i.e., permafrost regions and caves in temperate regions. Few studies have tackled archaeological bones from hot, arid regions, although they bear great significance for the study of evolution of humans and the precursors of modern societies. According to archaeological evidence, a key event in neolithisation, the domestication of cattle, took place around 10,000 years ago in Southwest Asia. Genetic data from prehistoric bovine bones preserved in this region might shed light on this process, but the palaeogenetic approach has been hampered by poor DNA preservation. Here, I discuss various aspects of DNA preservation in fossils and the production of reliable palaeogenetic data and present methodological improvements that have enabled us to shed light on the process of cattle domestication in Southwest Asia and its spread into western Europe. [Copyright &y& Elsevier]

Ancient DNA has received much attention since the mid-1980s, when the first sequence of an extinct animal species was recovered from a museum specimen. Since then, the majority of ancient DNA studies have focused predominantly on animal species, while studies in plant palaeogenetics have been rather limited, with the notable exception of cultivated species found in archaeological sites. Here, we outline the recent developments in the analysis of plant ancient DNA. We emphasize the trend from species identification to population-level investigation and highlight the potential and the difficulties in this field, related to DNA preservation and to risks of contamination. Further efforts towards the analysis of ancient DNA from the abundant store of fossil plant remains should provide new research opportunities in palaeoecology and phylogeography. In particular, intraspecific variation should be considered not only in cultivated plants but also in wild taxa if palaeogenetics is to become a fully emancipated field of plant research.New Phytologist(2005)doi: 10.1111/j.1469-8137.2005.01360.x© New Phytologist(2005) [ABSTRACT FROM AUTHOR]