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

The Spread of Malaria to Southern Europe in Antiquity: New Approaches to Old Problems

The discoveries in the late nineteenth century that malaria is caused by protozoan parasites, which are transmitted by mosquitoes, quickly led to intense speculation about its history in antiquity. The historiography of malaria has passed through three distinct phases during the last hundred years or so. The first generation of historians to consider the effects of malaria did exaggerate its significance in some respects. The argument by W H S Jones that the Greek doctrine of fevers was based on malaria was generally and rightly accepted. However, it is not surprising that his view that malaria was a major reason for the degeneration of the moral character of the ancient Greeks attracted little sympathy. The eradication of malaria from southern Europe in the 1930s and 1940s contributed to a decline of interest in the subject. Subsequently medical historians and even professional malariologists tended to minimize the historical significance of malaria. The revisionist tendencies of this second phase of research led to attempts to reassess some of the details of the evidence upon which Jones had relied. For example, Leonard Bruce-Chwatt and Julian de Zulueta rejected Jones's belief that Plasmodium falciparum, the most dangerous of the four species of human malaria, was already active in Greece in the fifth century BC. They suggested that it started to spread in southern Europe only during the time of the Roman Empire and attributed all the references to intermittent tertian fevers in Hippocratic texts dating to the fifth and fourth centuries BC to the less virulent P. vivax. Although the literature produced during this second phase of scholarship was in many ways more sophisticated, it still suffered from some of the same weaknesses; in particular, analysis proceeded in a purely qualitative manner, without any consideration of the effects of malaria on historical human populations in quantitative terms. A second weakness was a tendency to make generalizations covering the whole of Mediterranean Europe. Since many types of mosquito are incapable of transmitting malaria to humans, mosquito breeding sites do not occur everywhere, and many mosquitoes do not fly further than a few hundred yards from their breeding sites, malaria can only be really understood by micro-analyses, conducted at a very local level, of geography, hydrology, climate, competition between different species of mosquito for breeding sites, and human activities.</jats:p

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

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

Mitogenomes from Egyptian Cattle Breeds: New Clues on the Origin of Haplogroup Q and the Early Spread of Bos taurus from the Near East

Background Genetic studies support the scenario that Bos taurus domestication occurred in the Near East during the Neolithic transition about 10 thousand years (ky) ago, with the likely exception of a minor secondary event in Italy. However, despite the proven effectiveness of whole mitochondrial genome data in providing valuable information concerning the origin of taurine cattle, until now no population surveys have been carried out at the level of mitogenomes in local breeds from the Near East or surrounding areas. Egypt is in close geographic and cultural proximity to the Near East, in particular the Nile Delta region, and was one of the first neighboring areas to adopt the Neolithic package. Thus, a survey of mitogenome variation of autochthonous taurine breeds from the Nile Delta region might provide new insights on the early spread of cattle rearing outside the Near East. Methodology Using Illumina high-throughput sequencing we characterized the mitogenomes from two cattle breeds, Menofi (N = 17) and Domiaty (N = 14), from the Nile Delta region. Phylogenetic and Bayesian analyses were subsequently performed. Conclusions Phylogenetic analyses of the 31 mitogenomes confirmed the prevalence of haplogroup T1, similar to most African cattle breeds, but showed also high frequencies for haplogroups T2, T3 and Q1, and an extremely high haplotype diversity, while Bayesian skyline plots pointed to a main episode of population growth ~12.5 ky ago. Comparisons of Nile Delta mitogenomes with those from other geographic areas revealed that (i) most Egyptian mtDNAs are probably direct local derivatives from the founder domestic herds which first arrived from the Near East and the extent of gene flow from and towards the Nile Delta region was limited after the initial founding event(s); (ii) haplogroup Q1 was among these founders, thus proving that it underwent domestication in the Near East together with the founders of the T clades

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