968 results on '"ORLANDO, LUDOVIC"'
Search Results
352. Mammoth and Elephant Phylogenetic Relationships: Mammut Americanum, the Missing Outgroup
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Orlando, Ludovic, primary, Hänni, Catherine, additional, and Douady, Christophe J., additional
- Published
- 2007
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353. Ancient and modern environmental DNA.
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Winther Pedersen, Mikkel, Overballe-Petersen, Søren, Ermini, Luca, Der Sarkissian, Clio, Haile, James, Hellstrom, Micaela, Spens, Johan, Thomsen, Philip Francis, Bohmann, Kristine, Cappellini, Enrico, Bærholm Schnell, Ida, Wales, Nathan A., Carøe, Christian, Campos, Paula F., Schmidt, Astrid M. Z., P. Gilbert, M. Thomas, Hansen, Anders J., Orlando, Ludovic, and Willerslev, Eske
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FOSSIL DNA ,FOSSIL biomolecules ,MOLECULAR paleontology ,BIODIVERSITY - Abstract
DNA obtained from environmental samples such as sediments, ice or water (environmental DNA, eDNA), represents an important source of information on past and present biodiversity. It has revealed an ancient forest in Greenland, extended by several thousand years the survival dates for mainland woolly mammoth in Alaska, and pushed back the dates for spruce survival in Scandinavian ice-free refugia during the last glaciation. More recently, eDNA was used to uncover the past 50 000 years of vegetation history in the Arctic, revealing massive vegetation turnover at the Pleistocene/Holocene transition, with implications for the extinction of megafauna. Furthermore, eDNA can reflect the biodiversity of extant flora and fauna, both qualitatively and quantitatively, allowing detection of rare species. As such, trace studies of plant and vertebrate DNAin the environment have revolutionized our knowledge of biogeography. However, the approach remains marred by biases related toDNAbehaviour in environmental settings, incomplete reference databases and false positive results due to contamination.We provide a review of the field. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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354. Does the 43 bp sequence from an 800 000 year old Cretan dwarf elephantid really rewrite the textbook on mammoths?
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Orlando, Ludovic, primary, Pagés, Marie, additional, Calvignac, Sébastien, additional, Hughes, Sandrine, additional, and Hänni, Catherine, additional
- Published
- 2006
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355. Geographic distribution of an extinct equid ( Equus hydruntinus : Mammalia, Equidae) revealed by morphological and genetical analyses of fossils
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ORLANDO, LUDOVIC, primary, MASHKOUR, MARJAN, additional, BURKE, ARIANE, additional, DOUADY, CHRISTOPHE J., additional, EISENMANN, VÉRA, additional, and HÄNNI, CATHERINE, additional
- Published
- 2006
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356. Revisiting Neandertal diversity with a 100,000 year old mtDNA sequence
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Orlando, Ludovic, primary, Darlu, Pierre, additional, Toussaint, Michel, additional, Bonjean, Dominique, additional, Otte, Marcel, additional, and Hänni, Catherine, additional
- Published
- 2006
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357. Twelve Years of Neandertal Genetic Discoveries: State-of-the-Art and Future Challenges.
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Orlando, Ludovic and Hänni, Catherine
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- 2011
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358. Ancient DNA analysis reveals woolly rhino evolutionary relationships
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Orlando, Ludovic, primary, Leonard, Jennifer A., additional, Thenot, Aurélie, additional, Laudet, Vincent, additional, Guerin, Claude, additional, and Hänni, Catherine, additional
- Published
- 2003
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359. Napoleon Bonaparte and the fate of an Amazonian rat: new data on the taxonomy of Mesomys hispidus (Rodentia: Echimyidae)
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Orlando, Ludovic, primary, Mauffrey, Jean-François, additional, Cuisin, Jacques, additional, Patton, James L, additional, Hänni, Catherine, additional, and Catzeflis, François, additional
- Published
- 2003
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360. Ancient DNA and the Population Genetics of Cave Bears (Ursus spelaeus) Through Space and Time
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Orlando, Ludovic, primary, Bonjean, Dominique, additional, Bocherens, Herve, additional, Thenot, Aurelie, additional, Argant, Alain, additional, Otte, Marcel, additional, and Hänni, Catherine, additional
- Published
- 2002
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361. Ancient DNA analysis reveals divergence of the cave bear, Ursus spelaeus , and brown bear, Ursus arctos , lineages
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Loreille, Odile, primary, Orlando, Ludovic, additional, Patou-Mathis, Marylène, additional, Philippe, Michel, additional, Taberlet, Pierre, additional, and Hänni, Catherine, additional
- Published
- 2001
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362. LA DOMESTICATION DU CHEVAL VUE PAR L'ADN ANCIEN/CE QUE RÉVÈLE LE SÉQUENÇAGE DE L'ADN SUR LA DOMESTICATION DU CHEVAL.
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ORLANDO, Ludovic Antoine Alexandre and LANGLOIS, Bertrand
- Abstract
Copyright of Ethnozootechnie is the property of Societe d Ethnozootechnie 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.)
- Published
- 2016
363. Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation that underlies Dun camouflage color in horses
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Imsland, Freyja, McGowan, Kelly, Rubin, Carl-Johan, Henegar, Corneliu, Sundström, Elisabeth, Berglund, Jonas, Schwochow, Doreen, Gustafson, Ulla, Imsland, Páll, Lindblad-Toh, Kerstin, Lindgren, Gabriella, Mikko, Sofia, Millon, Lee, Wade, Claire, Schubert, Mikkel, Orlando, Ludovic, Penedo, Maria Cecilia T, Barsh, Gregory S, and Andersson, Leif
- Abstract
Dun is a wild-type coat color in horses characterized by pigment dilution with a striking pattern of dark areas termed primitive markings. Here we show that pigment dilution in Dun horses is due to radially asymmetric deposition of pigment in the growing hair caused by localized expression of the T-box 3 (TBX3) transcription factor in hair follicles, which in turn determines the distribution of hair follicle melanocytes. Most domestic horses are non-dun, a more intensely pigmented phenotype caused by regulatory mutations impairing TBX3 expression in the hair follicle, resulting in a more circumferential distribution of melanocytes and pigment granules in individual hairs. We identified two different alleles (non-dun1 and non-dun2) causing non-dun color. non-dun2 is a recently derived allele, whereas the Dun and non-dun1 alleles are found in ancient horse DNA, demonstrating that this polymorphism predates horse domestication. These findings uncover a new developmental role for T-box genes and new aspects of hair follicle biology and pigmentation.
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- 2016
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364. gargammel: a sequence simulator for ancient DNA.
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Renaud, Gabriel, Hanghøj, Kristian, Willerslev, Eske, and Orlando, Ludovic
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NUCLEOTIDE sequence ,BIOLOGICAL extinction ,FRAGMENTATION reactions ,DNA damage ,GENOMES - Abstract
Summary: Ancient DNA has emerged as a remarkable tool to infer the history of extinct species and past populations. However, many of its characteristics, such as extensive fragmentation, damage and contamination, can influence downstream analyses. To help investigators measure how these could impact their analyses in silico, we have developed gargammel, a package that simulates ancient DNA fragments given a set of known reference genomes. Our package simulates the entire molecular process from post-mortem DNA fragmentation and DNA damage to experimental sequencing errors, and reproduces most common bias observed in ancient DNA datasets. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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365. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans.
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Raghavan, Maanasa, Skoglund, Pontus, Graf, Kelly E., Metspalu, Mait, Albrechtsen, Anders, Moltke, Ida, Rasmussen, Simon, Stafford Jr, Thomas W., Orlando, Ludovic, Metspalu, Ene, Karmin, Monika, Tambets, Kristiina, Rootsi, Siiri, Mägi, Reedik, Campos, Paula F., Balanovska, Elena, Balanovsky, Oleg, Khusnutdinova, Elza, Litvinov, Sergey, and Osipova, Ludmila P.
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GENOMES ,PALEOLITHIC Period ,NATIVE Americans ,EAST Asians ,GENEALOGY ,Y chromosome - Abstract
The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians, there is no consensus with regard to which specific Old World populations they are closest to. Here we sequence the draft genome of an approximately 24,000-year-old individual (MA-1), from Mal'ta in south-central Siberia, to an average depth of 1×. To our knowledge this is the oldest anatomically modern human genome reported to date. The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic and Mesolithic European hunter-gatherers, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages. Similarly, we find autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native Americans, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought. Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World. Gene flow from the MA-1 lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians. Sequencing of another south-central Siberian, Afontova Gora-2 dating to approximately 17,000 years ago, revealed similar autosomal genetic signatures as MA-1, suggesting that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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366. Monitoring endangered freshwater biodiversity using environmental DNA.
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THOMSEN, PHILIP FRANCIS, KIELGAST, JOS, IVERSEN, LARS L., WIUF, CARSTEN, RASMUSSEN, MORTEN, GILBERT, M. THOMAS P, ORLANDO, LUDOVIC, and WILLERSLEV, ESKE
- Subjects
FRESHWATER biodiversity ,ENDANGERED species ,DNA ,WILDLIFE conservation ,FRESHWATER organisms - Abstract
Freshwater ecosystems are among the most endangered habitats on Earth, with thousands of animal species known to be threatened or already extinct. Reliable monitoring of threatened organisms is crucial for data-driven conservation actions but remains a challenge owing to nonstandardized methods that depend on practical and taxonomic expertise, which is rapidly declining. Here, we show that a diversity of rare and threatened freshwater animals-representing amphibians, fish, mammals, insects and crustaceans-can be detected and quantified based on DNA obtained directly from small water samples of lakes, ponds and streams. We successfully validate our findings in a controlled mesocosm experiment and show that DNA becomes undetectable within 2 weeks after removal of animals, indicating that DNA traces are near contemporary with presence of the species. We further demonstrate that entire faunas of amphibians and fish can be detected by high-throughput sequencing of DNA extracted from pond water. Our findings underpin the ubiquitous nature of DNA traces in the environment and establish environmental DNA as a tool for monitoring rare and threatened species across a wide range of taxonomic groups. [ABSTRACT FROM AUTHOR]
- Published
- 2012
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367. Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records and sedimentary ancient DNA Meta-barcoding.
- Author
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JØRGENSEN, TINA, KJÆR, KURT H., HAILE, JAMES, RASMUSSEN, MORTEN, BOESSENKOOL, SANNE, ANDERSEN, KENNETH, COISSAC, ERIC, TABERLET, PIERRE, BROCHMANN, CHRISTIAN, ORLANDO, LUDOVIC, GILBERT, M. THOMAS P., and WILLERSLEV, ESKE
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CHEMICAL composition of plants ,PLANT DNA ,BAR codes ,SHIELDS (Geology) ,SEDIMENTS ,ICE sheets - Abstract
Nunataks are isolated bedrocks protruding through ice sheets. They vary in age, but represent island environments in 'oceans' of ice through which organism dispersals and replacements can be studied over time. The J.A.D. Jensen's Nunataks at the southern Greenland ice sheet are the most isolated nunataks on the northern hemisphere - some 30 km from the nearest biological source. They constitute around 2 km
2 of ice-free land that was established in the early Holocene. We have investigated the changes in plant composition at these nunataks using both the results of surveys of the flora over the last 130 years and through reconstruction of the vegetation from the end of the Holocene Thermal Maximum (5528 ± 75 cal year BP) using meta-barcoding of plant DNA recovered from the nunatak sediments ( sedaDNA). Our results show that several of the plant species detected with sedaDNA are described from earlier vegetation surveys on the nunataks (in 1878, 1967 and 2009). In 1967, a much higher biodiversity was detected than from any other of the studied periods. While this may be related to differences in sampling efforts for the oldest period, it is not the case when comparing the 1967 and 2009 levels where the botanical survey was exhaustive. As no animals and humans are found on the nunataks, this change in diversity over a period of just 42 years must relate to environmental changes probably being climate-driven. This suggests that even the flora of fairly small and isolated ice-free areas reacts quickly to a changing climate. [ABSTRACT FROM AUTHOR]- Published
- 2012
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368. Meta-barcoding of 'dirt' DNA from soil reflects vertebrate biodiversity.
- Author
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ANDERSEN, KENNETH, BIRD, KAREN LISE, RASMUSSEN, MORTEN, HAILE, JAMES, BREUNING-MADSEN, HENRIK, KJÆR, KURT H., ORLANDO, LUDOVIC, GILBERT, M. THOMAS P., and WILLERSLEV, ESKE
- Subjects
MITOCHONDRIAL DNA ,FOSSIL vertebrates ,FOSSIL DNA ,FOSSIL elephants ,HAPLOTYPES ,BIODIVERSITY - Abstract
DNA molecules originating from animals and plants can be retrieved directly from sediments and have been used for reconstructing both contemporary and past ecosystems. However, the extent to which such 'dirt' DNA reflects taxonomic richness and structural diversity remains contentious. Here, we couple second generation high-throughput sequencing with 16S mitochondrial DNA (mtDNA) meta-barcoding, to explore the accuracy and sensitivity of 'dirt' DNA as an indicator of vertebrate diversity, from soil sampled at safari parks, zoological gardens and farms with known species compositions. PCR amplification was successful in the full pH range of the investigated soils (6.2 ± 0.2 to 8.3 ± 0.2), but inhibition was detected in extracts from soil of high organic content. DNA movement (leaching) through strata was evident in some sporadic cases and is influenced by soil texture and structure. We find that DNA from the soil surface reflects overall taxonomic richness and relative biomass of individual species. However, one species that was recently introduced was not detected. Furthermore, animal behaviour was shown to influence DNA deposition rates. The approach potentially provides a quick methodological alternative to classical ecological surveys of biodiversity, and most reliable results are obtained with spatial sample replicates, while relative amounts of soil processed per site is of less importance. [ABSTRACT FROM AUTHOR]
- Published
- 2012
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369. A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational stability.
- Author
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JØRGENSEN, TINA, HAILE, JAMES, MÖLLER, PER, ANDREEV, ANDREI, BOESSENKOOL, SANNE, RASMUSSEN, MORTEN, KIENAST, FRANK, COISSAC, ERIC, TABERLET, PIERRE, BROCHMANN, CHRISTIAN, BIGELOW, NANCY H., ANDERSEN, KENNETH, ORLANDO, LUDOVIC, GILBERT, M. THOMAS P., and WILLERSLEV, ESKE
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SEDIMENTARY basins ,PALYNOLOGY ,PERMAFROST ecosystems ,FOSSIL DNA ,COMPARATIVE studies - Abstract
Although ancient DNA from sediments ( sedaDNA) has been used to investigate past ecosystems, the approach has never been directly compared with the traditional methods of pollen and macrofossil analysis. We conducted a comparative survey of 18 ancient permafrost samples spanning the Late Pleistocene (46-12.5 thousand years ago), from the Taymyr Peninsula in northern Siberia. The results show that pollen, macrofossils and sedaDNA are complementary rather than overlapping and, in combination, reveal more detailed information on plant palaeocommunities than can be achieved by each individual approach. SedaDNA and macrofossils share greater overlap in plant identifications than with pollen, suggesting that sedaDNA is local in origin. These two proxies also permit identification to lower taxonomic levels than pollen, enabling investigation into temporal changes in species composition and the determination of indicator species to describe environmental changes. Combining data from all three proxies reveals an area continually dominated by a mosaic vegetation of tundra-steppe, pioneer and wet-indicator plants. Such vegetational stability is unexpected, given the severe climate changes taking place in the Northern Hemisphere during this time, with changes in average annual temperatures of >22 °C. This may explain the abundance of ice-age mammals such as horse and bison in Taymyr Peninsula during the Pleistocene and why it acted as a refugium for the last mainland woolly mammoth. Our finding reveals the benefits of combining sedaDNA, pollen and macrofossil for palaeovegetational reconstruction and adds to the increasing evidence suggesting large areas of the Northern Hemisphere remained ecologically stable during the Late Pleistocene. [ABSTRACT FROM AUTHOR]
- Published
- 2012
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370. Proteomic Analysis of a Pleistocene Mammoth Femur Reveals More than One Hundred Ancient Bone Proteins.
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Cappellini, Enrico, Jensen, Lars J., Szklarczyk, Damian, Ginolhac, Aurélien, da Fonseca, Rute A. R., Stafford, Thomas W., Holen, Steven R., Collins, Matthew J., Orlando, Ludovic, Willerslev, Eske, Gilbert, M. Thomas P., and Olsen, Jesper V.
- Published
- 2012
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371. Genetics and population analysis Accurate continuous geographic assignment from low- to high-density SNP data.
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Guillot, Gilles, Jónsson, Hákon, Hinge, Antoine, Manchih, Nabil, and Orlando, Ludovic
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SINGLE nucleotide polymorphisms ,GENOTYPES ,EPIDEMIOLOGY ,WILDLIFE management ,POACHING ,NESTED clade analysis ,LAPLACE distribution - Abstract
Motivation: Large-scale genotype datasets can help track the dispersal patterns of epidemiological outbreaks and predict the geographic origins of individuals. Such genetically-based geographic assignments also show a range of possible applications in forensics for profiling both victims and criminals, and in wildlife management, where poaching hotspot areas can be located. They, however, require fast and accurate statistical methods to handle the growing amount of genetic information made available from genotype arrays and next-generation sequencing technologies. Results: We introduce a novel statistical method for geopositioning individuals of unknown origin from genotypes. Our method is based on a geostatistical model trained with a dataset of georeferenced genotypes. Statistical inference under this model can be implemented within the theoretical framework of Integrated Nested Laplace Approximation, which represents one of the major recent breakthroughs in statistics, as it does not require Monte Carlo simulations. We compare the performance of our method and an alternative method for geospatial inference, SPA in a simulation framework. We highlight the accuracy and limits of continuous spatial assignment methods at various scales by analyzing genotype datasets from a diversity of species, including Florida Scrubjay birds Aphelocoma coerulescens, Arabidopsis thaliana and humans, representing 41-197,146 SNPs. Our method appears to be best suited for the analysis of medium-sized datasets (a few tens of thousands of loci), such as reduced-representation sequencing data that become increasingly available in ecology. Availability and implementation: http://www2.imm.dtu.dk∼gigu/Spasiba/. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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372. Author Correction: Late Quaternary dynamics of Arctic biota from ancient environmental genomics
- Author
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Wang, Yucheng, Pedersen, Mikkel Winther, Alsos, Inger Greve, De Sanctis, Bianca, Racimo, Fernando, Prohaska, Ana, Coissac, Eric, Owens, Hannah Lois, Merkel, Marie Kristine Føreid, Fernandez-Guerra, Antonio, Rouillard, Alexandra, Lammers, Youri, Alberti, Adriana, Denoeud, France, Money, Daniel, Ruter, Anthony H., McColl, Hugh, Larsen, Nicolaj Krog, Cherezova, Anna A., Edwards, Mary E., Fedorov, Grigory B., Haile, James, Orlando, Ludovic, Vinner, Lasse, Korneliussen, Thorfinn Sand, Beilman, David W., Bjørk, Anders A., Cao, Jialu, Dockter, Christoph, Esdale, Julie, Gusarova, Galina, Kjeldsen, Kristian K., Mangerud, Jan, Rasic, Jeffrey T., Skadhauge, Birgitte, Svendsen, John Inge, Tikhonov, Alexei, Wincker, Patrick, Xing, Yingchun, Zhang, Yubin, Froese, Duane G., Rahbek, Carsten, Bravo, David Nogues, Holden, Philip B., Edwards, Neil R., Durbin, Richard, Meltzer, David J., Kjær, Kurt H., Möller, Per, and Willerslev, Eske
- Published
- 2022
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373. Sex in the city: Uncovering sex-specific management of equine resources from prehistoric times to the Modern Period in France
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Clavel, Benoît, Lepetz, Sébastien, Chauvey, Lorelei, Schiavinato, Stéphanie, Tonasso-Calvière, Laure, Liu, Xuexue, Fages, Antoine, Khan, Naveed, Seguin-Orlando, Andaine, Der Sarkissian, Clio, Clavel, Pierre, Estrada, Oscar, Alioğlu, Duha, Gaunitz, Charleen, Aury, Jean-Marc, Barme, Maude, Bodu, Pierre, Olive, Monique, Bignon-Lau, Olivier, Castel, Jean-Christophe, Boudadi-Maligne, Myriam, Boulbes, Nicolas, Bourgois, Alice, Decanter, Franck, Foucras, Sylvain, Frère, Stéphane, Gardeisen, Armelle, Jouanin, Gaëtan, Méla, Charlotte, Morand, Nicolas, Nieto Espinet, Ariadna, Perdereau, Aude, Putelat, Olivier, Rivière, Julie, Robin, Opale, Salin, Marilyne, Valenzuela-Lamas, Silvia, Vallet, Christian, Yvinec, Jean-Hervé, Wincker, Patrick, and Orlando, Ludovic
- Abstract
•Magdalenian horse hunt not focused on isolated bachelors.•Iron Age and gallo-Roman sacrificial rituals have been preferentially oriented to male horses.•During Antiquity, the Middle Ages and the Modern Period, cities are largely dominated by horse males.•In rural contexts, females and subadults of both sexes were maintained to sustain production demands.
- Published
- 2022
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374. Unravelling reference bias in ancient DNA datasets.
- Author
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Dolenz, Stephanie, van der Valk, Tom, Jin, Chenyu, Oppenheimer, Jonas, Sharif, Muhammad Bilal, Orlando, Ludovic, Shapiro, Beth, Dalén, Love, and Heintzman, Peter D
- Subjects
- *
FOSSIL DNA , *SEQUENCE alignment , *DEAMINATION , *CYTOSINE , *ALLELES - Abstract
Motivation The alignment of sequencing reads is a critical step in the characterization of ancient genomes. However, reference bias and spurious mappings pose a significant challenge, particularly as cutting-edge wet lab methods generate datasets that push the boundaries of alignment tools. Reference bias occurs when reference alleles are favoured over alternative alleles during mapping, whereas spurious mappings stem from either contamination or when endogenous reads fail to align to their correct position. Previous work has shown that these phenomena are correlated with read length but a more thorough investigation of reference bias and spurious mappings for ancient DNA has been lacking. Here, we use a range of empirical and simulated palaeogenomic datasets to investigate the impacts of mapping tools, quality thresholds, and reference genome on mismatch rates across read lengths. Results For these analyses, we introduce AMBER, a new bioinformatics tool for assessing the quality of ancient DNA mapping directly from BAM-files and informing on reference bias, read length cut-offs and reference selection. AMBER rapidly and simultaneously computes the sequence read mapping bias in the form of the mismatch rates per read length, cytosine deamination profiles at both CpG and non-CpG sites, fragment length distributions, and genomic breadth and depth of coverage. Using AMBER, we find that mapping algorithms and quality threshold choices dictate reference bias and rates of spurious alignment at different read lengths in a predictable manner, suggesting that optimized mapping parameters for each read length will be a key step in alleviating reference bias and spurious mappings. Availability and implementation AMBER is available for noncommercial use on GitHub (https://github.com/tvandervalk/AMBER.git). Scripts used to generate and analyse simulated datasets are available on Github (https://github.com/sdolenz/refbias_scripts). [ABSTRACT FROM AUTHOR]
- Published
- 2024
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375. Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae.
- Author
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Klumplerova, Marie, Splichalova, Petra, Oppelt, Jan, Futas, Jan, Kohutova, Aneta, Musilova, Petra, Kubickova, Svatava, Vodicka, Roman, Orlando, Ludovic, and Horin, Petr
- Subjects
MAJOR histocompatibility complex ,EQUIDAE ,ANTIGEN presenting cells ,BINDING sites ,INDIVIDUAL differences ,CELL membranes - Abstract
Background: The mammalian Major Histocompatibility Complex (MHC) is a genetic region containing highly polymorphic genes with immunological functions. MHC class I and class II genes encode antigen-presenting molecules expressed on the cell surface. The MHC class II sub-region contains genes expressed in antigen presenting cells. The antigen binding site is encoded by the second exon of genes encoding antigen presenting molecules. The exon 2 sequences of these MHC genes have evolved under the selective pressure of pathogens. Interspecific differences can be observed in the class II sub-region. The family Equidae includes a variety of domesticated, and free-ranging species inhabiting a range of habitats exposed to different pathogens and represents a model for studying this important part of the immunogenome. While equine MHC class II DRA and DQA loci have received attention, the genetic diversity and effects of selection on DRB and DQB loci have been largely overlooked. This study aimed to provide the first in-depth analysis of the MHC class II DRB and DQB loci in the Equidae family. Results: Three DRB and two DQB genes were identified in the genomes of all equids. The genes DRB2, DRB3 and DQB3 showed high sequence conservation, while polymorphisms were more frequent at DRB1 and DQB1 across all species analyzed. DQB2 was not found in the genome of the Asiatic asses Equus hemionus kulan and E. h. onager. The bioinformatic analysis of non-zero-coverage-bases of DRB and DQB genes in 14 equine individual genomes revealed differences among individual genes. Evidence for recombination was found for DRB1, DRB2, DQB1 and DQB2 genes. Trans-species allele sharing was identified in all genes except DRB1. Site-specific selection analysis predicted genes evolving under positive selection both at DRB and DQB loci. No selected amino acid sites were identified in DQB3. Conclusions: The organization of the MHC class II sub-region of equids is similar across all species of the family. Genomic sequences, along with phylogenetic trees suggesting effects of selection as well as trans-species polymorphism support the contention that pathogen-driven positive selection has shaped the MHC class II DRB/DQB sub-regions in the Equidae. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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376. Author Correction: Spotted phenotypes in horses lost attractiveness in the Middle Ages.
- Author
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Wutke, Saskia, Benecke, Norbert, Sandoval-Castellanos, Edson, Döhle, Hans-Jürgen, Friederich, Susanne, Gonzalez, Javier, Hallsson, Jón Hallsteinn, Hofreiter, Michael, Lõugas, Lembi, Magnell, Ola, Morales-Muniz, Arturo, Orlando, Ludovic, Pálsdóttir, Albína Hulda, Reissmann, Monika, Ruttkay, Matej, Trinks, Alexandra, and Ludwig, Arne
- Subjects
PHENOTYPES ,MIDDLE Ages - Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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- View/download PDF
377. Ancient Genomes Reveal Unexpected Horse Domestication and Management Dynamics.
- Author
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Orlando, Ludovic
- Subjects
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WILD horses , *HORSE breeds , *GENOMES , *TWENTIETH century - Abstract
The horse was essential to past human societies but became a recreational animal during the twentieth century as the world became increasingly mechanized. As the author reviews here, recent studies of ancient genomes have revisited the understanding of horse domestication, from the very early stages to the most modern developments. They have uncovered several extinct lineages roaming the far ends of Eurasia some 4000 years ago. They have shown that the domestic horse has been significantly reshaped during the last millennium and experienced a sharp decline in genetic diversity within the last two centuries. At a time when no truly wild horses exist any longer, this calls for enhanced conservation in all endangered populations. These include the Przewalski's horse native to Mongolia, and the many local breeds side‐lined by the modern agenda, but yet representing the living heritage of over five millennia of horse breeding. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
378. An endothelial regulatory module links blood pressure regulation with elite athletic performance.
- Author
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Fegraeus, Kim, Rosengren, Maria K., Naboulsi, Rakan, Orlando, Ludovic, Åbrink, Magnus, Jouni, Ahmad, Velie, Brandon D., Raine, Amanda, Egner, Beate, Mattsson, C Mikael, Lång, Karin, Zhigulev, Artemy, Björck, Hanna M., Franco-Cereceda, Anders, Eriksson, Per, Andersson, Göran, Sahlén, Pelin, Meadows, Jennifer R. S., and Lindgren, Gabriella
- Subjects
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REGULATION of blood pressure , *HORSE breeding , *ATHLETIC ability , *MOLECULAR genetics , *HAPLOTYPES , *BLOOD pressure measurement , *BLOOD pressure - Abstract
The control of transcription is crucial for homeostasis in mammals. A previous selective sweep analysis of horse racing performance revealed a 19.6 kb candidate regulatory region 50 kb downstream of the Endothelin3 (EDN3) gene. Here, the region was narrowed to a 5.5 kb span of 14 SNVs, with elite and sub-elite haplotypes analyzed for association to racing performance, blood pressure and plasma levels of EDN3 in Coldblooded trotters and Standardbreds. Comparative analysis of human HiCap data identified the span as an enhancer cluster active in endothelial cells, interacting with genes relevant to blood pressure regulation. Coldblooded trotters with the sub-elite haplotype had significantly higher blood pressure compared to horses with the elite performing haplotype during exercise. Alleles within the elite haplotype were part of the standing variation in pre-domestication horses, and have risen in frequency during the era of breed development and selection. These results advance our understanding of the molecular genetics of athletic performance and vascular traits in both horses and humans. Author summary: A previous study discovered that a genomic region close to the Endothelin3 gene was associated with harness racing performance. Here, careful phenotypic documentation of athletic performance and blood pressure measurements in horses, followed by state-of-the-art genomics, allowed us to identify a 5.5 kb regulatory region located approximately 50 kb 3' of the EDN3 gene. A comparative analysis of the region using human HiCap data supported a regulatory role as, in endothelial cells, interaction was observed between the region and multiple genes relevant to blood pressure regulation and athletic performance. Long range cis-regulatory modules are critical for cooperatively controlling multiple genes located within transcriptionally active domains. We measured blood pressure in Coldblooded trotters during exercise and demonstrated that horses with two copies of the elite-performing haplotype had lower blood pressure during exercise and better racing performance results, compared to horses with two copies of the sub-elite performing haplotype. In addition, horses with the elite-performing haplotype also had higher levels of Endothelin3 in plasma. The results reported here are important for understanding the biological mechanisms behind blood pressure regulation in relation to racing performance in both horses and humans. [ABSTRACT FROM AUTHOR]
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- 2024
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379. Author Correction: Population genomics of the Viking world
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Margaryan, Ashot, Lawson, Daniel J., Sikora, Martin, Racimo, Fernando, Rasmussen, Simon, Moltke, Ida, Cassidy, Lara M., Jørsboe, Emil, Ingason, Andrés, Pedersen, Mikkel W., Korneliussen, Thorfinn, Wilhelmson, Helene, Buś, Magdalena M., de Barros Damgaard, Peter, Martiniano, Rui, Renaud, Gabriel, Bhérer, Claude, Moreno-Mayar, J. Víctor, Fotakis, Anna K., Allen, Marie, Allmäe, Raili, Molak, Martyna, Cappellini, Enrico, Scorrano, Gabriele, McColl, Hugh, Buzhilova, Alexandra, Fox, Allison, Albrechtsen, Anders, Schütz, Berit, Skar, Birgitte, Arcini, Caroline, Falys, Ceri, Jonson, Charlotte Hedenstierna, Błaszczyk, Dariusz, Pezhemsky, Denis, Turner-Walker, Gordon, Gestsdóttir, Hildur, Lundstrøm, Inge, Gustin, Ingrid, Mainland, Ingrid, Potekhina, Inna, Muntoni, Italo M., Cheng, Jade, Stenderup, Jesper, Ma, Jilong, Gibson, Julie, Peets, Jüri, Gustafsson, Jörgen, Iversen, Katrine H., Simpson, Linzi, Strand, Lisa, Loe, Louise, Sikora, Maeve, Florek, Marek, Vretemark, Maria, Redknap, Mark, Bajka, Monika, Pushkina, Tamara, Søvsø, Morten, Grigoreva, Natalia, Christensen, Tom, Kastholm, Ole, Uldum, Otto, Favia, Pasquale, Holck, Per, Sten, Sabine, Arge, Símun V., Ellingvåg, Sturla, Moiseyev, Vayacheslav, Bogdanowicz, Wiesław, Magnusson, Yvonne, Orlando, Ludovic, Pentz, Peter, Jessen, Mads Dengsø, Pedersen, Anne, Collard, Mark, Bradley, Daniel G., Jørkov, Marie Louise, Arneborg, Jette, Lynnerup, Niels, Price, Neil, Gilbert, M. Thomas P., Allentoft, Morten E., Bill, Jan, Sindbæk, Søren M., Hedeager, Lotte, Kristiansen, Kristian, Nielsen, Rasmus, Werge, Thomas, and Willerslev, Eske
- Abstract
A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03328-2.
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- 2021
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380. Historical management of equine resources in France from the Iron Age to the Modern Period
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Lepetz, Sébastien, Clavel, Benoît, Alioğlu, Duha, Chauvey, Lorelei, Schiavinato, Stéphanie, Tonasso-Calvière, Laure, Liub, Xuexue, Fages, Antoine, Khan, Naveed, Seguin-Orlando, Andaine, Der Sarkissian, Clio, Clavel, Pierre, Estrada, Oscar, Gaunitz, Charleen, Aury, Jean-Marc, Barme, Maude, Boulbes, Nicolas, Bourgois, Alice, Decanter, Franck, Foucras, Sylvain, Frère, Stéphane, Gardeisen, Armelle, Jouanin, Gaëtan, Méla, Charlotte, Morand, Nicolas, Nieto Espinet, Ariadna, Perdereau, Aude, Putelat, Olivier, Rivière, Julie, Robinf, Opale, Salin, Marilyne, Valenzuela-Lamas, Silvia, Vallet, Christian, Yvinec, Jean-Hervé, Wincker, Patrick, and Orlando, Ludovic
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•The Horse is the only equid species identified in the Iron Age archaeological record from France.•Mules represent an abundant fraction of the equine bone assemblages from France during the Roman Period, while donkeys were almost absent.•Donkeys of exceptional size were present in France during the Late Antiquity.•Following the collapse of the Roman Empire, donkeys replaced mules and became an important element of economic activities.
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- 2021
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381. Does the 43bp sequence from an 800000 year old Cretan dwarf elephantid really rewrite the textbook on mammoths?
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Orlando, Ludovic, Pagés, Marie, Calvignac, Sébastien, Hughes, Sandrine, and Hänni, Catherine
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Pigmy elephants inhabited the islands from the Mediterranean region during the Pleistocene period but became extinct in the course of the Holocene. Despite striking distinctive anatomical characteristics related to insularity, some similarities with the lineage of extant Asian elephants have suggested that pigmy elephants could be most probably seen as members of the genus Elephas. Poulakakis et al.(2006) have recently challenged this view by recovering a short mtDNA sequence from an 800 000 year old fossil of the Cretan pigmy elephant (Elephas creticus). According to the authors of this study, a deep taxonomic revision of Cretan dwarf elephants would be needed, as the sequence exhibits clear affinities with woolly mammoth haplotypes. However, we point here many aspects that seriously weaken the strength of the ancient DNA evidence reported.
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- 2007
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382. Horse males became over-represented in archaeological assemblages during the Bronze Age
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Fages, Antoine, Seguin-Orlando, Andaine, Germonpré, Mietje, and Orlando, Ludovic
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•We generated low-coverage DNA data for 19 new Upper Paleolithic horses from Belgium.•We determined the molecular sex of 249 horse remains spanning the last 40,000 years.•Osseous assemblages showed balanced male:female sex ratios until 3900 years cal. BP.•Osseous assemblages post-3900 years cal. BP became strongly biased towards males.
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- 2020
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383. Author Correction: Improved reference genome for the domestic horse increases assembly contiguity and composition.
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Kalbfleisch, Theodore S., Rice, Edward S., DePriest, Michael S., Walenz, Brian P., Hestand, Matthew S., Vermeesch, Joris R., O'Connell, Brendan L., Fiddes, Ian T., Vershinina, Alisa O., Saremi, Nedda F., Petersen, Jessica L., Finno, Carrie J., Bellone, Rebecca R., McCue, Molly E., Brooks, Samantha A., Bailey, Ernest, Orlando, Ludovic, Green, Richard E., Miller, Donald C., and Antczak, Douglas F.
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GENOMES ,HORSES - Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper. [ABSTRACT FROM AUTHOR]
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- 2019
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384. Improved reference genome for the domestic horse increases assembly contiguity and composition.
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Kalbfleisch, Theodore S., Rice, Edward S., DePriest, Michael S., Walenz, Brian P., Hestand, Matthew S., Vermeesch, Joris R., O′Connell, Brendan L., Fiddes, Ian T., Vershinina, Alisa O., Saremi, Nedda F., Petersen, Jessica L., Finno, Carrie J., Bellone, Rebecca R., McCue, Molly E., Brooks, Samantha A., Bailey, Ernest, Orlando, Ludovic, Green, Richard E., Miller, Donald C., and Antczak, Douglas F.
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NUCLEOTIDE sequencing ,GENOMES ,HORSES ,CHROMOSOMES ,COMPUTATIONAL biology - Abstract
Recent advances in genomic sequencing technology and computational assembly methods have allowed scientists to improve reference genome assemblies in terms of contiguity and composition. EquCab2, a reference genome for the domestic horse, was released in 2007. Although of equal or better quality compared to other first-generation Sanger assemblies, it had many of the shortcomings common to them. In 2014, the equine genomics research community began a project to improve the reference sequence for the horse, building upon the solid foundation of EquCab2 and incorporating new short-read data, long-read data, and proximity ligation data. Here, we present EquCab3. The count of non-N bases in the incorporated chromosomes is improved from 2.33 Gb in EquCab2 to 2.41 Gb in EquCab3. Contiguity has also been improved nearly 40-fold with a contig N50 of 4.5 Mb and scaffold contiguity enhanced to where all but one of the 32 chromosomes is comprised of a single scaffold. Theodore Kalbfleisch et al. present an improved genome assembly for the domestic horse by combining short- and long-read data, as well as proximity ligation data. They improve contiguity of the assembly by 40-fold, with a 10-fold reduction in gaps. [ABSTRACT FROM AUTHOR]
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- 2018
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385. The prehistoric peopling of Southeast Asia
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McColl, Hugh, Racimo, Fernando, Vinner, Lasse, Demeter, Fabrice, Gakuhari, Takashi, Moreno-Mayar, J Víctor, Van Driem, George, Gram Wilken, Uffe, Seguin-Orlando, Andaine, De La Fuente Castro, Constanza, Wasef, Sally, Shoocongdej, Rasmi, Souksavatdy, Viengkeo, Sayavongkhamdy, Thongsa, Saidin, Mohd Mokhtar, Allentoft, Morten E, Sato, Takehiro, Malaspinas, Anna-Sapfo, Aghakhanian, Farhang A, Korneliussen, Thorfinn, Prohaska, Ana, Margaryan, Ashot, De Barros Damgaard, Peter, Kaewsutthi, Supannee, Lertrit, Patcharee, Nguyen, Thi Mai Huong, Hung, Hsiao-Chun, Minh Tran, Thi, Nghia Truong, Huu, Nguyen, Giang Hai, Shahidan, Shaiful, Wiradnyana, Ketut, Matsumae, Hiromi, Shigehara, Nobuo, Yoneda, Minoru, Ishida, Hajime, Masuyama, Tadayuki, Yamada, Yasuhiro, Tajima, Atsushi, Shibata, Hiroki, Toyoda, Atsushi, Hanihara, Tsunehiko, Nakagome, Shigeki, Deviese, Thibaut, Bacon, Anne-Marie, Duringer, Philippe, Ponche, Jean-Luc, Shackelford, Laura, Patole-Edoumba, Elise, Nguyen, Anh Tuan, Bellina-Pryce, Bérénice, Galipaud, Jean-Christophe, Kinaston, Rebecca, Buckley, Hallie, Pottier, Christophe, Rasmussen, Simon, Higham, Tom, Foley, Robert A, Lahr, Marta Mirazón, Orlando, Ludovic, Sikora, Martin, Phipps, Maude E, Oota, Hiroki, Higham, Charles, Lambert, David M, and Willerslev, Eske
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2. Zero hunger ,Asian People ,Genome, Human ,Human Migration ,Population ,Genetic Variation ,Humans ,14. Life underwater ,Sequence Analysis, DNA ,DNA, Ancient ,Asia, Southeastern ,History, Ancient - Abstract
The human occupation history of Southeast Asia (SEA) remains heavily debated. Current evidence suggests that SEA was occupied by Hòabìnhian hunter-gatherers until ~4000 years ago, when farming economies developed and expanded, restricting foraging groups to remote habitats. Some argue that agricultural development was indigenous; others favor the "two-layer" hypothesis that posits a southward expansion of farmers giving rise to present-day Southeast Asian genetic diversity. By sequencing 26 ancient human genomes (25 from SEA, 1 Japanese Jōmon), we show that neither interpretation fits the complexity of Southeast Asian history: Both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting island SEA and Vietnam. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.
386. Late Quaternary dynamics of Arctic biota from ancient environmental genomics
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Wang, Yucheng, Pedersen, Mikkel Winther, Alsos, Inger Greve, De Sanctis, Bianca, Racimo, Fernando, Prohaska, Ana, Coissac, Eric, Owens, Hannah Lois, Merkel, Marie Kristine F��reid, Fernandez-Guerra, Antonio, Rouillard, Alexandra, Lammers, Youri, Alberti, Adriana, Denoeud, France, Money, Daniel, Ruter, Anthony H, McColl, Hugh, Larsen, Nicolaj Krog, Cherezova, Anna A, Edwards, Mary E, Fedorov, Grigory B, Haile, James, Orlando, Ludovic, Vinner, Lasse, Korneliussen, Thorfinn Sand, Beilman, David W, Bj��rk, Anders A, Cao, Jialu, Dockter, Christoph, Esdale, Julie, Gusarova, Galina, Kjeldsen, Kristian K, Mangerud, Jan, Rasic, Jeffrey T, Skadhauge, Birgitte, Svendsen, John Inge, Tikhonov, Alexei, Wincker, Patrick, Xing, Yingchun, Zhang, Yubin, Froese, Duane G, Rahbek, Carsten, Nogues, David Bravo, Holden, Philip B, Edwards, Neil R, Durbin, Richard, Meltzer, David J, Kj��r, Kurt H, M��ller, Per, and Willerslev, Eske
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631/208/212/2142 ,13. Climate action ,631/208/514/2254 ,704/158/2165 ,38/23 ,article ,45/22 ,14. Life underwater ,15. Life on land ,631/158/2463 ,631/158/2462 - Abstract
During the last glacial-interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1-8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe-tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe-tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 �� 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 �� 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics.
387. Convergent genomic signatures of domestication in sheep and goats
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Alberto, Florian J., Boyer, Frédéric, Orozco-terWengel, Pablo, Streeter, Ian, Servin, Bertrand, de Villemereuil, Pierre, Benjelloun, Badr, Librado, Pablo, Biscarini, Filippo, Colli, Licia, Barbato, Mario, Zamani, Wahid, Alberti, Adriana, Engelen, Stefan, Stella, Alessandra, Joost, Stéphane, Ajmone-Marsan, Paolo, Negrini, Riccardo, Orlando, Ludovic, Rezaei, Hamid Reza, Naderi, Saeid, Clarke, Laura, Flicek, Paul, Wincker, Patrick, Coissac, Eric, Kijas, James, Tosser-Klopp, Gwenola, Chikhi, Abdelkader, Bruford, Michael W., Taberlet, Pierre, Pompanon, François, and Nextgen Consortium
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Asiatic mouflon ,domestication ,sheep ,goats ,Bezoar ibex ,whole genome sequence data ,signatures of domestication - Abstract
The evolutionary basis of domestication has been a longstanding question and its genetic architecture is becoming more tractable as more domestic species become genome-enabled. Before becoming established worldwide, sheep and goats were domesticated in the fertile crescent 10,500 years before present (YBP) where their wild relatives remain. Here we sequence the genomes of wild Asiatic mouflon and Bezoar ibex in the sheep and goat domestication center and compare their genomes with that of domestics from local, traditional, and improved breeds. Among the genomic regions carrying selective sweeps differentiating domestic breeds from wild populations, which are associated among others to genes involved in nervous system, immunity and productivity traits, 20 are common to Capra and Ovis. The patterns of selection vary between species, suggesting that while common targets of selection related to domestication and improvement exist, different solutions have arisen to achieve similar phenotypic end-points within these closely related livestock species.
388. Late Quaternary horses in Eurasia in the face of climate and vegetation change
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Leonardi, Michela, Boschin, Francesco, Giampoudakis, Konstantinos, Beyer, Robert M, Krapp, Mario, Bendrey, Robin, Sommer, Robert, Boscato, Paolo, Manica, Andrea, Nogues-Bravo, David, and Orlando, Ludovic
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Europe ,Asia ,Archaeology ,Databases, Factual ,13. Climate action ,Climate Change ,Animals ,Horses ,15. Life on land ,Adaptation, Physiological ,Ecosystem - Abstract
Wild horses thrived across Eurasia until the Last Glacial Maximum to collapse after the beginning of the Holocene. The interplay of climate change, species adaptability to different environments, and human domestication in horse history is still lacking coherent continental-scale analysis integrating different lines of evidence. We assembled temporal and geographical information on 3070 horse occurrences across Eurasia, frequency data for 1120 archeological layers in Europe, and matched them to paleoclimatic and paleoenvironmental simulations for the Late Quaternary. Climate controlled the distribution of horses, and they inhabited regions in Europe and Asia with different climates and ecosystem productivity, suggesting plasticity to populate different environments. Their decline in Europe during the Holocene appears associated with an increasing loss and fragmentation of open habitats. Europe was the most likely source for the spread of horses toward more temperate regions, and we propose both Iberia and central Asia as potential centers of domestication., M.L. was supported by a Marie-Curie Individual Fellowship (MSCA-IF-657852). This work was supported by the Danish National Research Foundation (grant no. DNRF94); Initiative d’Excellence Chaires d’attractivité, Université de Toulouse (OURASI); and the Villum Fonden miGENEPI research project. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 681605). K.G. and D.N.-B. thank Sapere Aude EliteForsk, DFF (Det Frie Forskningsråd), and the Danish National Research Foundation (DNRF96). A.M., M.K., and R.M.B. were supported by the European Research Council Consolidator grant 647787-LocalAdaptation.
389. The prehistoric peopling of Southeast Asia
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McColl, Hugh, Racimo, Fernando, Vinner, Lasse, Demeter, Fabrice, Gakuhari, Takashi, Moreno-Mayar, J. Víctor, Van Driem, George, Wilken, Uffe Gram, Seguin-Orlando, Andaine, De La Fuente Castro, Constanza, Wasef, Sally, Shoocongdej, Rasmi, Souksavatdy, Viengkeo, Sayavongkhamdy, Thongsa, Saidin, Mohd Mokhtar, Allentoft, Morten E., Sato, Takehiro, Malaspinas, Anna-Sapfo, Aghakhanian, Farhang A., Korneliussen, Thorfinn, Prohaska, Ana, Margaryan, Ashot, De Barros Damgaard, Peter, Kaewsutthi, Supannee, Lertrit, Patcharee, Nguyen, Thi Mai Huong, Hung, Hsiao-Chun, Tran, Thi Minh, Truong, Huu Nghia, Nguyen, Giang Hai, Shahidan, Shaiful, Wiradnyana, Ketut, Matsumae, Hiromi, Shigehara, Nobuo, Yoneda, Minoru, Ishida, Hajime, Masuyama, Tadayuki, Yamada, Yasuhiro, Tajima, Atsushi, Shibata, Hiroki, Toyoda, Atsushi, Hanihara, Tsunehiko, Nakagome, Shigeki, Deviese, Thibaut, Bacon, Anne-Marie, Duringer, Philippe, Ponche, Jean-Luc, Shackelford, Laura, Patole-Edoumba, Elise, Nguyen, Anh Tuan, Bellina-Pryce, Bérénice, Galipaud, Jean-Christophe, Kinaston, Rebecca, Buckley, Halie, Pottier, Christophe, Rasmussen, Simon, Higham, Tom, Foley, Robert A., Lahr, Marta Mirazón, Orlando, Ludovic, Sikora, Martin, Phipps, Maude E., Oota, Hiroki, Higham, Charles, Lambert, David M., and Willerslev, Eske
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2. Zero hunger ,570 Life sciences ,biology ,410 Linguistics ,14. Life underwater
390. Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago
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Rasmussen, Simon, Allentoft, Morten Erik, Nielsen, Kasper, Orlando, Ludovic, Sikora, Martin, Sjögren, Karl-Göran, Pedersen, Anders Gorm, Schubert, Mikkel, Van Dam, Alex, Kapel, Christian Moliin Outzen, Nielsen, Henrik Bjørn, Brunak, Søren, Avetisyan, Pavel, Epimakhov, Andrey, Khalyapin, Mikhail Viktorovich, Gnuni, Artak, Kriiska, Aivar, Lasak, Irena, Metspalu, Mait, Moiseyev, Vyacheslav, Gromov, Andrei, Pokutta, Dalia, Saag, Lehti, Varul, Liivi, Yepiskoposyan, Levon, Sicheritz-Pontén, Thomas, Foley, Robert A, Lahr, Marta Mirazón, Nielsen, Rasmus, Kristiansen, Kristian, and Willerslev, Eske
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DNA, Bacterial ,Europe ,Plague ,Asia ,Yersinia pestis ,Animals ,Humans ,Siphonaptera ,Tooth ,History, Ancient ,History, Medieval ,3. Good health - Abstract
The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it originated remains contentious. Here, we report the oldest direct evidence of Yersinia pestis identified by ancient DNA in human teeth from Asia and Europe dating from 2,800 to 5,000 years ago. By sequencing the genomes, we find that these ancient plague strains are basal to all known Yersinia pestis. We find the origins of the Yersinia pestis lineage to be at least two times older than previous estimates. We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague. Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics.
391. Ancient hepatitis B viruses from the Bronze Age to the Medieval period
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Mühlemann, Barbara, Jones, Terry C, Damgaard, Peter De Barros, Allentoft, Morten E, Shevnina, Irina, Logvin, Andrey, Usmanova, Emma, Panyushkina, Irina P, Boldgiv, Bazartseren, Bazartseren, Tsevel, Tashbaeva, Kadicha, Merz, Victor, Lau, Nina, Smrčka, Václav, Voyakin, Dmitry, Kitov, Egor, Epimakhov, Andrey, Pokutta, Dalia, Vicze, Magdolna, Price, T Douglas, Moiseyev, Vyacheslav, Hansen, Anders J, Orlando, Ludovic, Rasmussen, Simon, Sikora, Martin, Vinner, Lasse, Osterhaus, Albert DME, Smith, Derek J, Glebe, Dieter, Fouchier, Ron AM, Drosten, Christian, Sjögren, Karl-Göran, Kristiansen, Kristian, and Willerslev, Eske
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Recombination, Genetic ,Hepatitis B virus ,Asia ,Genotype ,Human Migration ,virus diseases ,Hominidae ,Hepatitis B ,History, Medieval ,3. Good health ,Europe ,Evolution, Molecular ,Africa ,Animals ,Humans ,History, Ancient ,Phylogeny - Abstract
Hepatitis B virus (HBV) is a major cause of human hepatitis. There is considerable uncertainty about the timescale of its evolution and its association with humans. Here we present 12 full or partial ancient HBV genomes that are between approximately 0.8 and 4.5 thousand years old. The ancient sequences group either within or in a sister relationship with extant human or other ape HBV clades. Generally, the genome properties follow those of modern HBV. The root of the HBV tree is projected to between 8.6 and 20.9 thousand years ago, and we estimate a substitution rate of 8.04 × 10-6-1.51 × 10-5 nucleotide substitutions per site per year. In several cases, the geographical locations of the ancient genotypes do not match present-day distributions. Genotypes that today are typical of Africa and Asia, and a subgenotype from India, are shown to have an early Eurasian presence. The geographical and temporal patterns that we observe in ancient and modern HBV genotypes are compatible with well-documented human migrations during the Bronze and Iron Ages1,2. We provide evidence for the creation of HBV genotype A via recombination, and for a long-term association of modern HBV genotypes with humans, including the discovery of a human genotype that is now extinct. These data expose a complexity of HBV evolution that is not evident when considering modern sequences alone.
392. Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers
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Sikora, Martin, Seguin-Orlando, Andaine, Martins Conde E Sousa, Vitor, Albrechtsen, Anders, Korneliussen, Thorfinn, Ko, Amy, Rasmussen, Simon, Dupanloup, Isabelle, Nigst, Philip R., Bosch, Marjolein D., Renaud, Gabriel, Allentoft, Morten E., Margaryan, Ashot, Vasilyev, Sergey V., Veselovskaya, Elizaveta V., Borutskaya, Svetlana B., Deviese, Thibaut, Comeskey, Dan, Higham, Tom, Manica, Andrea, Foley, Robert, Meltzer, David J., Nielsen, Rasmus, Excoffier, Laurent, Mirazon Lahr, Marta, Orlando, Ludovic, and Willerslev, Eske
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570 Life sciences ,biology ,10. No inequality - Abstract
Present-day hunter-gatherers (HGs) live in multilevel social groups essential to sustain a population structure characterized by limited levels of within-band relatedness and inbreeding.When these wider social networks evolved among HGs is unknown. To investigate whether the contemporary HG strategy was already present in the Upper Paleolithic, we used complete genome sequences from Sunghir, a site dated to ~34,000 years before the present, containing multiple anatomically modern human individuals.We show that individuals at Sunghir derive from a population of small effective size, with limited kinship and levels of inbreeding similar to HG populations. Our findings suggest that Upper Paleolithic social organization was similar to that of living HGs, with limited relatedness within residential groups embedded in a larger mating network.
393. Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds
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Schubert, Mikkel, Orlando, Ludovic, Schaefer, Robert J, Lindgren, Gabriella, Brem, Gottfried, Jagannathan, Vidhya, Polani, Sagi, Mickelson, James R, Fries, Ruedi, MacLeod, James N, Rieder, Stefan, Tetens, Jens, Lopes, Maria Susana, Wade, Claire M, Thaller, Georg, Distl, Ottmar, Leeb, Tosso, Bailey, Ernest, Bar-Gal, Gila Kahila, Barrey, Eric, Gerber, Vinzenz, McCue, Molly E, Kalbfleisch, Ted, McCoy, Annette, Metzger, Julia, Mach, Núria, Penedo, Cecilia, Bannasch, Danika L, Brooks, Samantha A, Haase, Bianca, Verini-Supplizi, Andrea, Da Câmara Machado, Artur, Tammen, Imke, Finno, Carrie J, and Wallner, Barbara
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2. Zero hunger ,630 Agriculture ,570 Life sciences ,biology ,590 Animals (Zoology) ,610 Medicine & health - Abstract
BACKGROUND To date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array. RESULTS Using whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, and genotypes from lower-density, legacy SNP arrays, a subset of ~5 million high-quality, high-density array candidate SNPs were selected based on breed representation and uniform spacing across the genome. Considering probe design recommendations from a commercial vendor (Affymetrix, now Thermo Fisher Scientific) a set of ~2 million SNPs were selected for a next-generation high-density SNP chip (MNEc2M). Genotype data were generated using the MNEc2M array from a cohort of 332 horses from 20 breeds and a lower-density array, consisting of ~670 thousand SNPs (MNEc670k), was designed for genotype imputation. CONCLUSIONS Here, we document the steps taken to design both the MNEc2M and MNEc670k arrays, report genomic and technical properties of these genotyping platforms, and demonstrate the imputation capabilities of these tools for the domestic horse.
394. The first horse herders and the impact of early Bronze Age steppe expansions into Asia
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De Barros Damgaard, Peter, Martiniano, Rui, Kamm, Jack, Moreno-Mayar, J Víctor, Kroonen, Guus, Peyrot, Michaël, Barjamovic, Gojko, Rasmussen, Simon, Zacho, Claus, Baimukhanov, Nurbol, Zaibert, Victor, Merz, Victor, Biddanda, Arjun, Merz, Ilja, Loman, Valeriy, Evdokimov, Valeriy, Usmanova, Emma, Hemphill, Brian, Seguin-Orlando, Andaine, Yediay, Fulya Eylem, Ullah, Inam, Sjögren, Karl-Göran, Iversen, Katrine Højholt, Choin, Jeremy, De La Fuente, Constanza, Ilardo, Melissa, Schroeder, Hannes, Moiseyev, Vyacheslav, Gromov, Andrey, Polyakov, Andrei, Omura, Sachihiro, Senyurt, Süleyman Yücel, Ahmad, Habib, McKenzie, Catriona, Margaryan, Ashot, Hameed, Abdul, Samad, Abdul, Gul, Nazish, Khokhar, Muhammad Hassan, Goriunova, OI, Bazaliiskii, Vladimir I, Novembre, John, Weber, Andrzej W, Orlando, Ludovic, Allentoft, Morten E, Nielsen, Rasmus, Kristiansen, Kristian, Sikora, Martin, Outram, Alan K, Durbin, Richard, and Willerslev, Eske
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2. Zero hunger ,Asia ,Chromosomes, Human, Y ,Whole Genome Sequencing ,Genome, Human ,Human Migration ,Genetic Drift ,DNA, Mitochondrial ,Grassland ,Domestication ,Europe ,Asian People ,Animals ,Humans ,Horses ,DNA, Ancient ,History, Ancient ,Language - Abstract
The Yamnaya expansions from the western steppe into Europe and Asia during the Early Bronze Age (~3000 BCE) are believed to have brought with them Indo-European languages and possibly horse husbandry. We analyzed 74 ancient whole-genome sequences from across Inner Asia and Anatolia and show that the Botai people associated with the earliest horse husbandry derived from a hunter-gatherer population deeply diverged from the Yamnaya. Our results also suggest distinct migrations bringing West Eurasian ancestry into South Asia before and after, but not at the time of, Yamnaya culture. We find no evidence of steppe ancestry in Bronze Age Anatolia from when Indo-European languages are attested there. Thus, in contrast to Europe, Early Bronze Age Yamnaya-related migrations had limited direct genetic impact in Asia.
395. Isotopic biographies reveal horse rearing and trading networks in medieval London.
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Pryor, Alexander J. E., Ameen, Carly, Liddiard, Robert, Baker, Gary, Kanne, Katherine S., Milton, J. Andy, Standish, Christopher D., Hambach, Bastian, Orlando, Ludovic, Chauvey, Lorelei, Schiavinato, Stephanie, Calvière-Tonasso, Laure, Tressières, Gaetan, Wagner, Stefanie, Southon, John, Shapiro, Beth, Pipe, Alan, Creighton, Oliver H., and Outram, Alan K.
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HORSES , *FOSSIL DNA , *BIRTHPLACES , *ISOTOPIC analysis , *CARBON isotopes , *HORSE breeds - Abstract
This paper reports a high-resolution isotopic study of medieval horse mobility, revealing their origins and in-life mobility both regionally and internationally. The animals were found in an unusual horse cemetery site found within the City of Westminster, London, England. Enamel strontium, oxygen, and carbon isotope analysis of 15 individuals provides information about likely place of birth, diet, and mobility during the first approximately 5 years of life. Results show that at least seven horses originated outside of Britain in relatively cold climates, potentially in Scandinavia or the Western Alps. Ancient DNA sexing data indicate no consistent sex-specific mobility patterning, although three of the five females came from exceptionally highly radiogenic regions. Another female with low mobility is suggested to be a sedentary broodmare. Our results provide direct and unprecedented evidence for a variety of horse movement and trading practices in the Middle Ages and highlight the importance of international trade in securing high-quality horses for medieval London elites. [ABSTRACT FROM AUTHOR]
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- 2024
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396. Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood.
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Wagner, Stefanie, Seguin‐Orlando, Andaine, Leplé, Jean‐Charles, Leroy, Thibault, Lalanne, Céline, Labadie, Karine, Aury, Jean‐Marc, Poirier, Sandy, Wincker, Patrick, Plomion, Christophe, Kremer, Antoine, and Orlando, Ludovic
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CULTIVARS , *WHITE oak , *WOOD , *LITTLE Ice Age , *GENOMES , *ENGLISH oak , *HARDWOODS - Abstract
Whole genome characterizations of crop plants based on ancient DNA have provided unique keys for a better understanding of the evolutionary origins of modern cultivars, the pace and mode of selection underlying their adaptation to new environments and the production of phenotypes of interest. Although forests are among the most biologically rich ecosystems on earth and represent a fundamental resource for human societies, no ancient genome sequences have been generated for trees. This contrasts with the generation of multiple ancient reference genomes for important crops. Here, we sequenced the first ancient tree genomes using two white oak wood remains from Germany dating to the Last Little Ice Age (15th century CE, 7.3× and 4.0×) and one from France dating to the Bronze Age (1700 BCE, 3.4×). We assessed the underlying species and identified one medieval remains as a hybrid between two common oak species (Quercus robur and Q. petraea) and the other two remains as Q. robur. We found that diversity at the global genome level had not changed over time. However, exploratory analyses suggested that a reduction of diversity took place at different time periods. Finally, we determined the timing of leaf unfolding for ancient trees for the first time. The study extends the application of ancient wood beyond the classical proxies of dendroclimatology, dendrochronology, dendroarchaeology and dendroecology, thereby enhancing resolution of inferences on the responses of forest ecosystems to past environmental changes, epidemics and silvicultural practices. see also the Perspective by Andrew L. Hipp and Desanka Lazic [ABSTRACT FROM AUTHOR]
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- 2024
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397. Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes.
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Janečka, Jan E., Davis, Brian W., Ghosh, Sharmila, Paria, Nandina, Das, Pranab J., Orlando, Ludovic, Schubert, Mikkel, Nielsen, Martin K., Stout, Tom A. E., Brashear, Wesley, Li, Gang, Johnson, Charles D., Metz, Richard P., Zadjali, Al Muatasim Al, Love, Charles C., Varner, Dickson D., Bellott, Daniel W., Murphy, William J., Chowdhary, Bhanu P., and Raudsepp, Terje
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Dynamic evolutionary processes and complex structure make the Y chromosome among the most diverse and least understood regions in mammalian genomes. Here, we present an annotated assembly of the male specific region of the horse Y chromosome (eMSY), representing the first comprehensive Y assembly in odd-toed ungulates. The eMSY comprises single-copy, equine specific multi-copy, PAR transposed, and novel ampliconic sequence classes. The eMSY gene density approaches that of autosomes with the highest number of retained X-Y gametologs recorded in eutherians, in addition to novel Y-born and transposed genes. Horse, donkey and mule testis RNAseq reveals several candidate genes for stallion fertility. A novel testis-expressed XY ampliconic sequence class, ETSTY7, is shared with the parasite Parascaris genome, providing evidence for eukaryotic horizontal transfer and inter-chromosomal mobility. Our study highlights the dynamic nature of the Y and provides a reference sequence for improved understanding of equine male development and fertility. The rapidly evolving Y chromosome accumulates male-benefit genes but is often poorly characterized in many mammals. Here, the authors assemble the male specific region of the horse Y chromosome and investigate its evolution and function. [ABSTRACT FROM AUTHOR]
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- 2018
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398. Author Correction: 137 ancient human genomes from across the Eurasian steppes
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de Barros Damgaard, Peter, Marchi, Nina, Rasmussen, Simon, Peyrot, Michael, Renaud, Gabriel, Korneliussen, Thorfinn, Moreno-Mayar, J. Victor, Pedersen, Mikkel Winther, Goldberg, Amy, Usmanova, Emma, Baimukhanov, Nurbol, Loman, Valeriy, Hedeager, Lotte, Pedersen, Anders Gorm, Nielsen, Kasper, Afanasiev, Gennady, Akmatov, Kunbolot, Aldashev, Almaz, Alpaslan, Ashyk, Baimbetov, Gabit, Bazaliiskii, Vladimir I., Beisenov, Arman, Boldbaatar, Bazartseren, Boldgiv, Bazartseren, Dorzhu, Choduraa, Ellingvag, Sturla, Erdenebaatar, Diimaajav, Dajani, Rana, Dmitriev, Evgeniy, Evdokimov, Valeriy, Frei, Karin M., Gromov, Andrey, Goryachev, Alexander, Hakonarson, Hakon, Hegay, Tatyana, Khachatryan, Zaruhi, Khaskhanov, Ruslan, Kitov, Egor, Kolbina, Alina, Kubatbek, Tabaldiev, Kukushkin, Alexey, Kukushkin, Igor, Lau, Nina, Margaryan, Ashot, Merkyte, Inga, Mertz, Ilya V., Mertz, Viktor K., Mijiddorj, Enkhbayar, Moiyesev, Vyacheslav, Mukhtarova, Gulmira, Nurmukhanbetov, Bekmukhanbet, Orozbekova, Z., Panyushkina, Irina, Pieta, Karol, Smrcka, Vaclav, Shevnina, Irina, Logvin, Andrey, Sjogren, Karl-Goran, Štolcova, Tereza, Taravella, Angela M., Tashbaeva, Kadicha, Tkachev, Alexander, Tulegenov, Turaly, Voyakin, Dmitriy, Yepiskoposyan, Levon, Undrakhbold, Sainbileg, Varfolomeev, Victor, Weber, Andrzej, Wilson Sayres, Melissa A., Kradin, Nikolay, Allentoft, Morten E., Orlando, Ludovic, Nielsen, Rasmus, Sikora, Martin, Heyer, Evelyne, Kristiansen, Kristian, and Willerslev, Eske
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with In this Article, Angela M. Taravella and Melissa A. Wilson Sayres have been added to the author list (associated with: School of Life Sciences, Center for Evolution and Medicine, The Biodesign Institute, Arizona State University, Tempe, AZ, USA). The author list and Author Information section have been corrected online.
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- 2018
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399. Author Correction: Ancient hepatitis B viruses from the Bronze Age to the Medieval period
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Muhlemann, Barbara, Jones, Terry C., de Barros Damgaard, Peter, Allentoft, Morten E., Shevnina, Irina, Logvin, Andrey, Usmanova, Emma, Panyushkina, Irina P., Boldgiv, Bazartseren, Bazartseren, Tsevel, Tashbaeva, Kadicha, Merz, Victor, Lau, Nina, Smrcka, Vaclav, Voyakin, Dmitry, Kitov, Egor, Epimakhov, Andrey, Pokutta, Dalia, Vicze, Magdolna, Price, T. Douglas, Moiseyev, Vyacheslav, Hansen, Anders J., Orlando, Ludovic, Rasmussen, Simon, Sikora, Martin, Vinner, Lasse, Osterhaus, Albert D. M. E., Smith, Derek J., Glebe, Dieter, Fouchier, Ron A. M., Drosten, Christian, Sjogren, Karl-Goran, Kristiansen, Kristian, and Willerslev, Eske
- Abstract
In Fig. 2 of this Letter, the ‘E’ and ‘G’ clade labels were inadvertently reversed, and in Table 2 the genotype of DA27 was ‘D1’ instead of ‘D5’. These have been corrected online.
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- 2018
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400. Spotted phenotypes in horses lost attractiveness in the Middle Ages.
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Wutke, Saskia, Benecke, Norbert, Sandoval-Castellanos, Edson, Döhle, Hans-Jürgen, Friederich, Susanne, Gonzalez, Javier, Hallsson, Jón Hallsteinn, Hofreiter, Michael, Lõugas, Lembi, Magnell, Ola, Morales-Muniz, Arturo, Orlando, Ludovic, Pálsdóttir, Albína Hulda, Reissmann, Monika, Ruttkay, Matej, Trinks, Alexandra, and Ludwig, Arne
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Horses have been valued for their diversity of coat colour since prehistoric times; this is especially the case since their domestication in the Caspian steppe in ~3,500 BC. Although we can assume that human preferences were not constant, we have only anecdotal information about how domestic horses were influenced by humans. Our results from genotype analyses show a significant increase in spotted coats in early domestic horses (Copper Age to Iron Age). In contrast, medieval horses carried significantly fewer alleles for these phenotypes, whereas solid phenotypes (i.e., chestnut) became dominant. This shift may have been supported because of (i) pleiotropic disadvantages, (ii) a reduced need to separate domestic horses from their wild counterparts, (iii) a lower religious prestige, or (iv) novel developments in weaponry. These scenarios may have acted alone or in combination. However, the dominance of chestnut is a remarkable feature of the medieval horse population. [ABSTRACT FROM AUTHOR]
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- 2016
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