Aurochs, genetics, indigenous people and colonists: apropos of the neolithization of Europe

Las analíticas genéticas realizadas sobre los uros (Bos primigenius) del yacimiento de Mendandia (Treviño), han ofrecido un resultado sorprendente: uno de los individuos pertenece al haplotypo T3, generalmente asociado a animales domésticos (Bos taurus). La datación de la muestra (7265 ± 70 BP; Ua 34366) es acorde con las otras conocidas de su nivel, el III-superior, incidiendo en la antigüedad de su Neolítico. El dato es la excusa para reflexionar sobre el proceso neolitizador y adentrarnos en el debate sobre el papel que pudiera corresponder a los indígenas y a los colonos. Para ello se valora la información más actual sobre genética de las poblaciones del principio del Holoceno, las medias promediadas de la extensión por Europa del nuevo modo de vida, así como otros indicios de neolitización prematura. Un compendio de razones que nos lleva a pensar que estamos frente a un fenómeno cultural muy complejo

Aurochs, genetics, indigenous people and colonists: apropos of the neolithization of Europe

El presente trabajo se ha preparado en el seno de los intereses de los proyectos de investigación: HAR2011-26364 “Las Comunidades humanas de la alta Cuenca del Ebro en la Transición Pleistoceno-Holoceno” del Ministerio de Ciencia e Innovación y CGL2009-12703-C03-03 “Geología, geocronología y paleobiología de los Yacimientos de la Sierra de Atapuerca” del Ministerio de Educación y Ciencia. Así mismo se encuadra en el trabajo del Grupo de Investigación en Prehistoria de la Universidad del País Vasco (UPV/EHU) IT-288-07/ UFI 11-09.[ES] Las analíticas genéticas realizadas sobre los uros (Bos primigenius) del yacimiento de Mendandia (Treviño), han ofrecido un resultado sorprendente: uno de los individuos pertenece al haplotypo T3, generalmente asociado a animales domésticos (Bos taurus). La datación de la muestra (7265 ± 70 BP; Ua 34366) es acorde con las otras conocidas de su nivel, el III-superior, incidiendo en la antigüedad de su Neolítico. El dato es la excusa para reflexionar sobre el proceso neolitizador y adentrarnos en el debate sobre el papel que pudiera corresponder a los indígenas y a los colonos. Para ello se valora la información más actual sobre genética de las poblaciones del principio del Holoceno, las medias promediadas de la extensión por Europa del nuevo modo de vida, así como otros indicios de neolitización prematura. Un compendio de razones que nos lleva a pensar que estamos frente a un fenómeno cultural muy complejo.[EN] The mt-DNA analysis of auroch (Bos primigenius) bones from the site of Mendandia (Treviño), has produced a surprising result: one of the specimens has been identified with the genetic haplotype T3, the most common in European domestic cattle and generally considered unique (and indicative) of domestic livestock (Bos taurus). The direct radiocarbon dating of the sample (7265 ± 70 BP; Ua 34366) is consistent with the older Neolithic age of the level that yielded the sample (Level III-superior). This result is an opportunity to think about the process of Neolitization and enter into the debate about the role that may correspond to the indigenous people and immigrants. We evaluate the latest information on population genetics from the beginning of the Holocene as well as the average extension throughout Europe of early Neolithic settlements and lifestyle. The discussion leads us to believe that we are facing a very complex cultural phenomenon

A simulation of the Neolithic transition in Western Eurasia

Farming and herding were introduced to Europe from the Near East and Anatolia; there are, however, considerable arguments about the mechanisms of this transition. Were it people who moved and outplaced the indigenous hunter- gatherer groups or admixed with them? Or was it just material and information that moved-the Neolithic Package-consisting of domesticated plants and animals and the knowledge of its use? The latter process is commonly referred to as cultural diffusion and the former as demic diffusion. Despite continuous and partly combined efforts by archaeologists, anthropologists, linguists, paleontologists and geneticists a final resolution of the debate has not yet been reached. In the present contribution we interpret results from the Global Land Use and technological Evolution Simulator (GLUES), a mathematical model for regional sociocultural development embedded in the western Eurasian geoenvironmental context during the Holocene. We demonstrate that the model is able to realistically hindcast the expansion speed and the inhomogeneous space-time evolution of the transition to agropastoralism in Europe. GLUES, in contrast to models that do not resolve endogenous sociocultural dynamics, also describes and explains how and why the Neolithic advanced in stages. In the model analysis, we uncouple the mechanisms of migration and information exchange. We find that (1) an indigenous form of agropastoralism could well have arisen in certain Mediterranean landscapes, but not in Northern and Central Europe, where it depended on imported technology and material, (2) both demic diffusion by migration or cultural diffusion by trade may explain the western European transition equally well, (3) [...]Comment: Accepted Author Manuscript version accepted for publication in Journal of Archaeological Science. A definitive version will be subsequently published in the Journal of Archaological Scienc

Interrogation of modern and ancient genomes reveals the complex domestic history of cattle

The analysis of mitochondrial and nuclear DNA sequence polymorphisms from modern cattle populations has had a profound impact on our understanding of the events surrounding the domestication of cattle. From these studies, it has been possible to distinguish between pre- and post-domestic genetic differentiation, supporting previous assertions from archaeological studies and, in some cases, revealing novel aspects of the demographic history of cattle. Analyses of genetic material retrieved from the remains of extinct ancestral wild cattle have also added valuable layers of information pertaining to cattle domestic origins; however, information from these investigations have, in general, been limited to small, variable portions of the mitochondrial genome owing to technical challenges associated with the retrieval and amplification of ancient DNA. In recent years, however, new high-throughput, massively parallel genomics technology platforms, such as single-nucleotide polymorphism (SNP) genotyping arrays and next-generation sequencing (NGS), have provided a new impetus to the studies of genetic variation in extant and ancient cattle. Arrays of SNP have facilitated high-resolution genetic surveys of global cattle populations and detection of ancient and recent genomic selective sweeps. Next-generation sequencing analyses of modern and ancient cattle hold great promise for identifying and cataloging of pre- and post-domestication patterns of genomic variation and correlating this with natural and artificial selection processes

Staying out in the cold: glacial refugia and mitochondrial DNA phylogeography in ancient European brown bears

Models for the development of species distribution in Europe typically invoke restriction in three temperate Mediterranean refugia during glaciations, from where recolonization of central and northern Europe occurred. The brown bear, Ursus arctos, is one of the taxa from which this model is derived. Sequence data generated from brown bear fossils show a complex phylogeographical history for western European populations. Long-term isolation in separate refugia is not required to explain our data when considering the palaeontological distribution of brown bears. We propose continuous gene flow across southern Europe, from which brown bear populations expanded after the last glaciation

Archaeological sites as Distributed Long-term Observing Networks of the Past (DONOP)

The authors would also like to acknowledge the support of the National Science Foundation, specifically the Arctic Social Sciences Program, and RANNIS (The Icelandic Center for Research).Archaeological records provide a unique source of direct data on long-term human-environment interactions and samples of ecosystems affected by differing degrees of human impact. Distributed long-term datasets from archaeological sites provide a significant contribution to establish local, regional, and continental-scale environmental baselines and can be used to understand the implications of human decision-making and its impacts on the environment and the resources it provides for human use. Deeper temporal environmental baselines are essential for resource and environmental managers to restore biodiversity and build resilience in depleted ecosystems. Human actions are likely to have impacts that reorganize ecosystem structures by reducing diversity through processes such as niche construction. This makes data from archaeological sites key assets for the management of contemporary and future climate change scenarios because they combine information about human behavior, environmental baselines, and biological systems. Sites of this kind collectively form Distributed Long-term Observing Networks of the Past (DONOP), allowing human behavior and environmental impacts to be assessed over space and time. Behavioral perspectives are gained from direct evidence of human actions in response to environmental opportunities and change. Baseline perspectives are gained from data on species, landforms, and ecology over timescales that long predate our typically recent datasets that only record systems already disturbed by people. And biological perspectives can provide essential data for modern managers wanting to understand and utilize past diversity (i.e., trophic and/or genetic) as a way of revealing, and potentially correcting, weaknesses in our contemporary wild and domestic animal populations.PostprintPeer reviewe

A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla

<p>Abstract</p> <p>Background</p> <p>The early radiation of the <it>Cetartiodactyla </it>is complex, and unambiguous molecular characters are needed to clarify the positions of hippotamuses, camels and pigs relative to the remaining taxa (<it>Cetacea </it>and <it>Ruminantia</it>). There is also a need for informative genealogic markers for Y-chromosome population genetics as well as a sexing method applicable to all species from this group. We therefore studied the sequence variation of a partial sequence of the evolutionary conserved amelogenin gene to assess its potential use in each of these fields.</p> <p>Results and discussion</p> <p>We report a large interstitial insertion in the Y amelogenin locus in most of the <it>Cetartiodactyla </it>lineages (cetaceans and ruminants). This sex-linked size polymorphism is the result of a 460–465 bp inserted element in intron 4 of the amelogenin gene of Ruminants and Cetaceans. Therefore, this polymorphism can easily be used in a sexing assay for these species.</p> <p>When taking into account this shared character in addition to nucleotide sequence, gene genealogy follows sex-chromosome divergence in <it>Cetartiodactyla </it>whereas it is more congruent with zoological history when ignoring these characters. This could be related to a loss of homology between chromosomal copies given the old age of the insertion.</p> <p>The 1 kbp <it>Amel-Y </it>amplified fragment is also characterized by high nucleotide diversity (64 polymorphic sites spanning over 1 kbp in seven haplotypes) which is greater than for other Y-chromosome sequence markers studied so far but less than the mitochondrial control region.</p> <p>Conclusion</p> <p>The gender-dependent polymorphism we have identified is relevant not only for phylogenic inference within the <it>Cetartiodactyla </it>but also for Y-chromosome based population genetics and gender determination in cetaceans and ruminants. One single protocol can therefore be used for studies in population and evolutionary genetics, reproductive biotechnologies, and forensic science.</p

Evolutionary process of Bos taurus cattle in favourable versus unfavourable environments and its implications for genetic selection

The evolutionary processes that have enabled Bos taurus cattle to establish around the globe are at the core to the future success of livestock production. Our study focuses on the history of cattle domestication including the last 60 years of B. taurus breeding programmes in both favourable and unfavourable environments and its consequences on evolution and fitness of cattle. We discuss the emergence of ‘production diseases’ in temperate production systems and consider the evolutionary genetics of tropical adaptation in cattle and conclude that the Senepol, N'Dama, Adaptaur and Criollo breeds, among others with similar evolutionary trajectories, would possess genes capable of improving the productivity of cattle in challenging environments. Using our own experimental evidence from northern Australia, we review the evolution of the Adaptaur cattle breed which has become resistant to cattle tick. We emphasize that the knowledge of interactions between genotype, environment and management in the livestock systems will be required to generate genotypes for efficient livestock production that are both economically and environmentally sustainable. Livestock producers in the 21st century will have less reliance on infrastructure and veterinary products to alleviate environmental stress and more on the animal's ability to achieve fitness in a given production environment

Molecular genetic identification of skeletal remains from the Second World War Konfin I mass grave in Slovenia

This paper describes molecular genetic identification of one third of the skeletal remains of 88 victims of postwar (June 1945) killings found in the Konfin I mass grave in Slovenia. Living relatives were traced for 36 victims. We analyzed 84 right femurs and compared their genetic profiles to the genetic material of living relatives. We cleaned the bones, removed surface contamination, and ground the bones into powder. Prior to DNA isolation using Biorobot EZ1 (Qiagen), the powder was decalcified. The nuclear DNA of the samples was quantified using the real-time polymerase chain reaction method. We extracted 0.8 to 100 ng DNA/g of bone powder from 82 bones. Autosomal genetic profiles and Y-chromosome haplotypes were obtained from 98% of the bones, and mitochondrial DNA (mtDNA) haplotypes from 95% of the bones for the HVI region and from 98% of the bones for the HVII region. Genetic profiles of the nuclear and mtDNA were determined for reference persons. For traceability in the event of contamination, we created an elimination database including genetic profiles of the nuclear and mtDNA of all persons that had been in contact with the skeletal remains. When comparing genetic profiles, we matched 28 of the 84 bones analyzed with living relatives (brothers, sisters, sons, daughters, nephews, or cousins). The statistical analyses showed a high confidence of correct identification for all 28 victims in the Konfin I mass grave (posterior probability ranged from 99.9% to more than 99.999999%)