ALBERT

Description: We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost 400,000 polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of Western and Far Eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, approximately 8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a approximately 24,000-year-old Siberian. By approximately 6,000-5,000 years ago, farmers throughout much of Europe had more hunter-gatherer ancestry than their predecessors, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but also from a population of Near Eastern ancestry. Western and Eastern Europe came into contact approximately 4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced approximately 75% of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least approximately 3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for a steppe origin of at least some of the Indo-European languages of Europe.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haak, Wolfgang -- Lazaridis, Iosif -- Patterson, Nick -- Rohland, Nadin -- Mallick, Swapan -- Llamas, Bastien -- Brandt, Guido -- Nordenfelt, Susanne -- Harney, Eadaoin -- Stewardson, Kristin -- Fu, Qiaomei -- Mittnik, Alissa -- Banffy, Eszter -- Economou, Christos -- Francken, Michael -- Friederich, Susanne -- Pena, Rafael Garrido -- Hallgren, Fredrik -- Khartanovich, Valery -- Khokhlov, Aleksandr -- Kunst, Michael -- Kuznetsov, Pavel -- Meller, Harald -- Mochalov, Oleg -- Moiseyev, Vayacheslav -- Nicklisch, Nicole -- Pichler, Sandra L -- Risch, Roberto -- Rojo Guerra, Manuel A -- Roth, Christina -- Szecsenyi-Nagy, Anna -- Wahl, Joachim -- Meyer, Matthias -- Krause, Johannes -- Brown, Dorcas -- Anthony, David -- Cooper, Alan -- Alt, Kurt Werner -- Reich, David -- GM100233/GM/NIGMS NIH HHS/ -- R01 HG006399/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2015 Jun 11;522(7555):207-11. doi: 10.1038/nature14317. Epub 2015 Mar 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Australian Centre for Ancient DNA, School of Earth and Environmental Sciences &Environment Institute, University of Adelaide, Adelaide, South Australia 5005, Australia. ; 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA. ; Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA. ; 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA [3] Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. ; Institute of Anthropology, Johannes Gutenberg University of Mainz, D-55128 Mainz, Germany. ; 1] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA [3] Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany [4] Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100049, China. ; Institute for Archaeological Sciences, University of Tubingen, D-72070 Tubingen, Germany. ; 1] Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Science, H-1014 Budapest, Hungary [2] Romisch Germanische Kommission (RGK) Frankfurt, D-60325 Frankfurt, Germany. ; Archaeological Research Laboratory, Stockholm University, 114 18 Stockholm, Sweden. ; Departments of Paleoanthropology and Archaeogenetics, Senckenberg Center for Human Evolution and Paleoenvironment, University of Tubingen, D-72070 Tubingen, Germany. ; State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany. ; Departamento de Prehistoria y Arqueologia, Facultad de Filosofia y Letras, Universidad Autonoma de Madrid, E-28049 Madrid, Spain. ; The Cultural Heritage Foundation, Vasteras 722 12, Sweden. ; Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, St Petersburg 199034, Russia. ; Volga State Academy of Social Sciences and Humanities, Samara 443099, Russia. ; Deutsches Archaeologisches Institut, Abteilung Madrid, E-28002 Madrid, Spain. ; 1] Institute of Anthropology, Johannes Gutenberg University of Mainz, D-55128 Mainz, Germany [2] State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany [3] Danube Private University, A-3500 Krems, Austria. ; Institute for Prehistory and Archaeological Science, University of Basel, CH-4003 Basel, Switzerland. ; Departamento de Prehistoria, Universitat Autonoma de Barcelona, E-08193 Barcelona, Spain. ; Departamento de Prehistoria y Arqueolgia, Universidad de Valladolid, E-47002 Valladolid, Spain. ; 1] Institute of Anthropology, Johannes Gutenberg University of Mainz, D-55128 Mainz, Germany [2] Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Science, H-1014 Budapest, Hungary. ; State Office for Cultural Heritage Management Baden-Wurttemberg, Osteology, D-78467 Konstanz, Germany. ; Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany. ; 1] Institute for Archaeological Sciences, University of Tubingen, D-72070 Tubingen, Germany [2] Departments of Paleoanthropology and Archaeogenetics, Senckenberg Center for Human Evolution and Paleoenvironment, University of Tubingen, D-72070 Tubingen, Germany [3] Max Planck Institute for the Science of Human History, D-07745 Jena, Germany. ; Anthropology Department, Hartwick College, Oneonta, New York 13820, USA. ; 1] Institute of Anthropology, Johannes Gutenberg University of Mainz, D-55128 Mainz, Germany [2] State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany [3] Danube Private University, A-3500 Krems, Austria [4] Institute for Prehistory and Archaeological Science, University of Basel, CH-4003 Basel, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25731166" target="_blank"〉PubMed〈/a〉

Description: Ancient DNA makes it possible to observe natural selection directly by analysing samples from populations before, during and after adaptation events. Here we report a genome-wide scan for selection using ancient DNA, capitalizing on the largest ancient DNA data set yet assembled: 230 West Eurasians who lived between 6500 and 300 bc, including 163 with newly reported data. The new samples include, to our knowledge, the first genome-wide ancient DNA from Anatolian Neolithic farmers, whose genetic material we obtained by extracting from petrous bones, and who we show were members of the population that was the source of Europe's first farmers. We also report a transect of the steppe region in Samara between 5600 and 300 bc, which allows us to identify admixture into the steppe from at least two external sources. We detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mathieson, Iain -- Lazaridis, Iosif -- Rohland, Nadin -- Mallick, Swapan -- Patterson, Nick -- Roodenberg, Songul Alpaslan -- Harney, Eadaoin -- Stewardson, Kristin -- Fernandes, Daniel -- Novak, Mario -- Sirak, Kendra -- Gamba, Cristina -- Jones, Eppie R -- Llamas, Bastien -- Dryomov, Stanislav -- Pickrell, Joseph -- Arsuaga, Juan Luis -- de Castro, Jose Maria Bermudez -- Carbonell, Eudald -- Gerritsen, Fokke -- Khokhlov, Aleksandr -- Kuznetsov, Pavel -- Lozano, Marina -- Meller, Harald -- Mochalov, Oleg -- Moiseyev, Vyacheslav -- Guerra, Manuel A Rojo -- Roodenberg, Jacob -- Verges, Josep Maria -- Krause, Johannes -- Cooper, Alan -- Alt, Kurt W -- Brown, Dorcas -- Anthony, David -- Lalueza-Fox, Carles -- Haak, Wolfgang -- Pinhasi, Ron -- Reich, David -- GM100233/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2015 Dec 24;528(7583):499-503. doi: 10.1038/nature16152. Epub 2015 Nov 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. ; Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. ; Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. ; Independent researcher, Santpoort-Noord, The Netherlands. ; School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland. ; Institute for Anthropological Research, Zagreb 10000, Croatia. ; Department of Anthropology, Emory University, Atlanta, Georgia 30322, USA. ; Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland. ; Australian Centre for Ancient DNA, School of Biological Sciences &Environment Institute, University of Adelaide, Adelaide, South Australia 5005, Australia. ; Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia. ; Department of Paleolithic Archaeology, Institute of Archaeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia. ; Centro Mixto UCM-ISCIII de Evolucion y Comportamiento Humanos, 28040 Madrid, Spain. ; Departamento de Paleontologia, Facultad Ciencias Geologicas, Universidad Complutense de Madrid, 28040 Madrid, Spain. ; Centro Nacional de Investigacion sobre Evolucion Humana (CENIEH), 09002 Burgos, Spain. ; IPHES. Institut Catala de Paleoecologia Humana i Evolucio Social, Campus Sescelades-URV, 43007 Tarragona, Spain. ; Area de Prehistoria, Universitat Rovira i Virgili (URV), 43002 Tarragona, Spain. ; Netherlands Institute in Turkey, Istiklal Caddesi, Nur-i Ziya Sokak 5, Beyog lu 34433, Istanbul, Turkey. ; Volga State Academy of Social Sciences and Humanities, Samara 443099, Russia. ; State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany. ; Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, St Petersburg 199034, Russia. ; Department of Prehistory and Archaeology, University of Valladolid, 47002 Valladolid, Spain. ; The Netherlands Institute for the Near East, Leiden RA-2300, the Netherlands. ; Max Planck Institute for the Science of Human History, D-07745 Jena, Germany. ; Institute for Archaeological Sciences, University of Tubingen, D-72070 Tubingen, Germany. ; Danube Private University, A-3500 Krems, Austria. ; Institute for Prehistory and Archaeological Science, University of Basel, CH-4003 Basel, Switzerland. ; Anthropology Department, Hartwick College, Oneonta, New York 13820, USA. ; Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26595274" target="_blank"〉PubMed〈/a〉

Description: The evolution of the ratite birds has been widely attributed to vicariant speciation, driven by the Cretaceous breakup of the supercontinent Gondwana. The early isolation of Africa and Madagascar implies that the ostrich and extinct Madagascan elephant birds (Aepyornithidae) should be the oldest ratite lineages. We sequenced the mitochondrial genomes of two elephant birds and performed phylogenetic analyses, which revealed that these birds are the closest relatives of the New Zealand kiwi and are distant from the basal ratite lineage of ostriches. This unexpected result strongly contradicts continental vicariance and instead supports flighted dispersal in all major ratite lineages. We suggest that convergence toward gigantism and flightlessness was facilitated by early Tertiary expansion into the diurnal herbivory niche after the extinction of the dinosaurs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mitchell, Kieren J -- Llamas, Bastien -- Soubrier, Julien -- Rawlence, Nicolas J -- Worthy, Trevor H -- Wood, Jamie -- Lee, Michael S Y -- Cooper, Alan -- New York, N.Y. -- Science. 2014 May 23;344(6186):898-900. doi: 10.1126/science.1251981.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, North Terrace Campus, South Australia 5005, Australia. ; School of Biological Sciences, Flinders University, South Australia 5001, Australia. ; Landcare Research, Post Office Box 40, Lincoln 7640, New Zealand. ; Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, North Terrace Campus, South Australia 5005, Australia. South Australian Museum, North Terrace, South Australia 5000, Australia. ; Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, North Terrace Campus, South Australia 5005, Australia. alan.cooper@adelaide.edu.au.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24855267" target="_blank"〉PubMed〈/a〉

Description: Understanding the evolution of Australia’s extinct marsupial megafauna has been hindered by a relatively incomplete fossil record and convergent or highly specialized morphology, which confound phylogenetic analyses. Further, the harsh Australian climate and early date of most megafaunal extinctions (39–52 ka) means that the vast majority of fossil remains are unsuitable for ancient DNA analyses. Here, we apply cross-species DNA capture to fossils from relatively high latitude, high altitude caves in Tasmania. Using low-stringency hybridization and high-throughput sequencing, we were able to retrieve mitochondrial sequences from two extinct megafaunal macropodid species. The two specimens, Simosthenurus occidentalis (giant short-faced kangaroo) and Protemnodon anak (giant wallaby), have been radiocarbon dated to 46–50 and 40–45 ka, respectively. This is significantly older than any Australian fossil that has previously yielded DNA sequence information. Processing the raw sequence data from these samples posed a bioinformatic challenge due to the poor preservation of DNA. We explored several approaches in order to maximize the signal-to-noise ratio in retained sequencing reads. Our findings demonstrate the critical importance of adopting stringent processing criteria when distant outgroups are used as references for mapping highly fragmented DNA. Based on the most stringent nucleotide data sets (879 bp for S. occidentalis and 2,383 bp for P. anak ), total-evidence phylogenetic analyses confirm that macropodids consist of three primary lineages: Sthenurines such as Simosthenurus (extinct short-faced kangaroos), the macropodines (all other wallabies and kangaroos), and the enigmatic living banded hare-wallaby Lagostrophus fasciatus (Lagostrophinae). Protemnodon emerges as a close relative of Macropus (large living kangaroos), a position not supported by recent morphological phylogenetic analyses.

Description: Several archaeological studies in the Central Andes have pointed at the temporal coincidence of climatic fluctuations (both long- and short-term) and episodes of cultural transition and changes of socioeconomic structures throughout the pre-Columbian period. Although most scholars explain the connection between environmental and cultural changes by the impact of climatic...

Description: Marsupials exhibit great diversity in ecology and morphology. However, compared with their sister group, the placental mammals, our understanding of many aspects of marsupial evolution remains limited. We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species. This tree allows us to analyze the evolution of habitat preference and geographic distributions of marsupial species through time. We found a pattern of mesic-adapted lineages evolving to use more arid and open habitats, which is broadly consistent with regional climate and environmental change. However, contrary to the general trend, several lineages subsequently appear to have reverted from drier to more mesic habitats. Biogeographic reconstructions suggest that current views on the connectivity between Australia and New Guinea/Wallacea during the Miocene and Pliocene need to be revised. The antiquity of several endemic New Guinean clades strongly suggests a substantially older period of connection stretching back to the Middle Miocene and implies that New Guinea was colonized by multiple clades almost immediately after its principal formation.

Description: The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.

Description: Some recent academic and popular literature implies that the problem of the colonization of the Americas has been largely resolved in favor of one specific model: a Pacific coastal migration, dependent on high marine productivity, from the Bering Strait to South America, thousands of years before Clovis, the earliest widespread cultural manifestation south of the glacial ice. Speculations on maritime adaptations and typological links (stemmed points) across thousands of kilometers have also been advanced. A review of the current genetic, archeological, and paleoecological evidence indicates that ancestral Native American population expansion occurred after 16,000 years ago, consistent with the archeological record, particularly with the earliest securely dated sites after ~15,000 years ago. These data are largely consistent with either an inland (ice-free corridor) or Pacific coastal routes (or both), but neither can be rejected at present. Systematic archeological and paleoecological investigations, informed by geomorphology, are required to test each hypothesis.

Description: Los estudios de selección y caracterización de potenciales estructuras y formaciones geológicas como almacenes de CO₂ son costosos y se encuentran sometidos a un alto riesgo de fracaso, especialmente cuando la estructura considerada es un acuífero salino profundo. Con el fin de minimizar el coste y el riesgo exploratorio, se hace necesaria una etapa previa de selección y posterior caracterización que deberá englobar la identificación de parámetros técnicos y socio-económicos y el estudio de los afloramientos de las formaciones almacén y sello. El estudio de dichos afloramientos permite estimar valores de determinados parámetros petrofísicos, geomecánicos y otras propiedades hidrogeológicas. En este artículo, se presentan resultados de una campaña de caracterización en la cuenca del Duero y la digitalización y análisis de muestras petrográficas de campañas previas realizadas por el Instituto Geológico y Minero de España. Tras la evaluación de los resultados petrofísicos se puede considerar como más favorable la facies Utrillas por presentar mejores valores de porosidad y permeabilidad (al Hg) y una composición mineralógica más estable y madura, siempre en comparación con las areniscas y arcosas rojas del Buntsandstein. Sin embargo, la presencia de mayor proporción de feldespato potásico en la fracción granular de esta última unidad, podría favorecer el atrapamiento mineral e iónico, pero esta consideración se basa en datos cualitativos, que deberán ser contrastados en posteriores trabajos, evaluando también la pérdida de porosidad y permeabilidad, parámetros que se consideran igualmente relevantes en el cálculo del ratio de inyección.