ALBERT

Description: Leprosy was endemic in Europe until the Middle Ages. Using DNA array capture, we have obtained genome sequences of Mycobacterium leprae from skeletons of five medieval leprosy cases from the United Kingdom, Sweden, and Denmark. In one case, the DNA was so well preserved that full de novo assembly of the ancient bacterial genome could be achieved through shotgun sequencing alone. The ancient M. leprae sequences were compared with those of 11 modern strains, representing diverse genotypes and geographic origins. The comparisons revealed remarkable genomic conservation during the past 1000 years, a European origin for leprosy in the Americas, and the presence of an M. leprae genotype in medieval Europe now commonly associated with the Middle East. The exceptional preservation of M. leprae biomarkers, both DNA and mycolic acids, in ancient skeletons has major implications for palaeomicrobiology and human pathogen evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schuenemann, Verena J -- Singh, Pushpendra -- Mendum, Thomas A -- Krause-Kyora, Ben -- Jager, Gunter -- Bos, Kirsten I -- Herbig, Alexander -- Economou, Christos -- Benjak, Andrej -- Busso, Philippe -- Nebel, Almut -- Boldsen, Jesper L -- Kjellstrom, Anna -- Wu, Huihai -- Stewart, Graham R -- Taylor, G Michael -- Bauer, Peter -- Lee, Oona Y-C -- Wu, Houdini H T -- Minnikin, David E -- Besra, Gurdyal S -- Tucker, Katie -- Roffey, Simon -- Sow, Samba O -- Cole, Stewart T -- Nieselt, Kay -- Krause, Johannes -- New York, N.Y. -- Science. 2013 Jul 12;341(6142):179-83. doi: 10.1126/science.1238286. Epub 2013 Jun 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Archaeological Sciences, University of Tubingen, 72070 Tubingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23765279" target="_blank"〉PubMed〈/a〉

Description: Modern strains of Mycobacterium tuberculosis from the Americas are closely related to those from Europe, supporting the assumption that human tuberculosis was introduced post-contact. This notion, however, is incompatible with archaeological evidence of pre-contact tuberculosis in the New World. Comparative genomics of modern isolates suggests that M. tuberculosis attained its worldwide distribution following human dispersals out of Africa during the Pleistocene epoch, although this has yet to be confirmed with ancient calibration points. Here we present three 1,000-year-old mycobacterial genomes from Peruvian human skeletons, revealing that a member of the M. tuberculosis complex caused human disease before contact. The ancient strains are distinct from known human-adapted forms and are most closely related to those adapted to seals and sea lions. Two independent dating approaches suggest a most recent common ancestor for the M. tuberculosis complex less than 6,000 years ago, which supports a Holocene dispersal of the disease. Our results implicate sea mammals as having played a role in transmitting the disease to humans across the ocean.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4550673/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4550673/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bos, Kirsten I -- Harkins, Kelly M -- Herbig, Alexander -- Coscolla, Mireia -- Weber, Nico -- Comas, Inaki -- Forrest, Stephen A -- Bryant, Josephine M -- Harris, Simon R -- Schuenemann, Verena J -- Campbell, Tessa J -- Majander, Kerttu -- Wilbur, Alicia K -- Guichon, Ricardo A -- Wolfe Steadman, Dawnie L -- Cook, Della Collins -- Niemann, Stefan -- Behr, Marcel A -- Zumarraga, Martin -- Bastida, Ricardo -- Huson, Daniel -- Nieselt, Kay -- Young, Douglas -- Parkhill, Julian -- Buikstra, Jane E -- Gagneux, Sebastien -- Stone, Anne C -- Krause, Johannes -- 098051/Wellcome Trust/United Kingdom -- AI090928/AI/NIAID NIH HHS/ -- MC_U117581288/Medical Research Council/United Kingdom -- R01 AI090928/AI/NIAID NIH HHS/ -- Medical Research Council/United Kingdom -- England -- Nature. 2014 Oct 23;514(7523):494-7. doi: 10.1038/nature13591. Epub 2014 Aug 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Archaeological Sciences, University of Tubingen, Ruemelinstrasse 23, 72070 Tubingen, Germany [2]. ; 1] School of Human Evolution and Social Change, Arizona State University, PO Box 872402, Tempe, Arizona 85287-2402, USA [2]. ; 1] Department of Archaeological Sciences, University of Tubingen, Ruemelinstrasse 23, 72070 Tubingen, Germany [2] Center for Bioinformatics, University of Tubingen, Sand 14, 72076 Tubingen, Germany [3]. ; 1] Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland [2] University of Basel, Petersplatz 1, CH-4003 Basel, Switzerland [3]. ; Center for Bioinformatics, University of Tubingen, Sand 14, 72076 Tubingen, Germany. ; 1] Genomics and Health Unit, FISABIO-Public Health, Avenida Cataluna 21, 46020 Valencia, Spain [2] CIBER (Centros de Investigacion Biomedica en Red) in Epidemiology and Public Health, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellon 11, Planta 0, 28029 Madrid, Spain. ; Department of Archaeological Sciences, University of Tubingen, Ruemelinstrasse 23, 72070 Tubingen, Germany. ; Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. ; Department of Archaeology, University of Cape Town, Private Bag X1, Rondebosch, 7701, South Africa. ; School of Human Evolution and Social Change, Arizona State University, PO Box 872402, Tempe, Arizona 85287-2402, USA. ; CONICET, Laboratorio de Ecologia Evolutiva Humana (FACSO, UNCPBA), Departamento de Biologia (FCEyN, UNMDP), Calle 508 No. 881 (7631), Quequen, Argentina. ; Department of Anthropology, University of Tennessee, 250 South Stadium Hall, Knoxville, Tennessee 37996, USA. ; Department of Anthropology, Indiana University, 701 East Kirkwood Avenue, Bloomington, Indiana 47405-7100, USA. ; 1] Molecular Mycobacteriology, Forschungszentrum Borstel, Parkallee 1, 23845 Borstel, Germany [2] German Center for Infection Research, Forschungszentrum Borstel, Parkallee 1, 23845 Borstel, Germany. ; McGill International TB Centre, McGill University, 1650 Cedar Avenue, Montreal H3G 1A4, Canada. ; Biotechnology Institute, CICVyA-INTA Castelar, Dr. Nicolas Repetto y De Los Reseros S/N, (B1686IGC) Hurlingham, Buenos Aires, Argentina. ; Instituto de Investigaciones Marinas y Costeras (CONICET-UNMdP), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, San Luis 1722, Mar del Plata 7600, Argentina. ; 1] Department of Medicine, Imperial College, London W2 1PG, UK [2] Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK. ; 1] Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland [2] University of Basel, Petersplatz 1, CH-4003 Basel, Switzerland. ; 1] Department of Archaeological Sciences, University of Tubingen, Ruemelinstrasse 23, 72070 Tubingen, Germany [2] Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tubingen, Tubingen 72070, Germany [3] Max Planck Institute for Science and History, Khalaische Strasse 10, 07745 Jena, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25141181" target="_blank"〉PubMed〈/a〉

Description: Technological advances in DNA recovery and sequencing have drastically expanded the scope of genetic analyses of ancient specimens to the extent that full genomic investigations are now feasible and are quickly becoming standard. This trend has important implications for infectious disease research because genomic data from ancient microbes may help to elucidate mechanisms of pathogen evolution and adaptation for emerging and re-emerging infections. Here we report a reconstructed ancient genome of Yersinia pestis at 30-fold average coverage from Black Death victims securely dated to episodes of pestilence-associated mortality in London, England, 1348-1350. Genetic architecture and phylogenetic analysis indicate that the ancient organism is ancestral to most extant strains and sits very close to the ancestral node of all Y. pestis commonly associated with human infection. Temporal estimates suggest that the Black Death of 1347-1351 was the main historical event responsible for the introduction and widespread dissemination of the ancestor to all currently circulating Y. pestis strains pathogenic to humans, and further indicates that contemporary Y. pestis epidemics have their origins in the medieval era. Comparisons against modern genomes reveal no unique derived positions in the medieval organism, indicating that the perceived increased virulence of the disease during the Black Death may not have been due to bacterial phenotype. These findings support the notion that factors other than microbial genetics, such as environment, vector dynamics and host susceptibility, should be at the forefront of epidemiological discussions regarding emerging Y. pestis infections.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3690193/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3690193/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bos, Kirsten I -- Schuenemann, Verena J -- Golding, G Brian -- Burbano, Hernan A -- Waglechner, Nicholas -- Coombes, Brian K -- McPhee, Joseph B -- DeWitte, Sharon N -- Meyer, Matthias -- Schmedes, Sarah -- Wood, James -- Earn, David J D -- Herring, D Ann -- Bauer, Peter -- Poinar, Hendrik N -- Krause, Johannes -- R24 HD044943/HD/NICHD NIH HHS/ -- Canadian Institutes of Health Research/Canada -- England -- Nature. 2011 Oct 12;478(7370):506-10. doi: 10.1038/nature10549.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21993626" target="_blank"〉PubMed〈/a〉

Description: The geographic and temporal origins of the domestic dog remain controversial, as genetic data suggest a domestication process in East Asia beginning 15,000 years ago, whereas the oldest doglike fossils are found in Europe and Siberia and date to 〉30,000 years ago. We analyzed the mitochondrial genomes of 18 prehistoric canids from Eurasia and the New World, along with a comprehensive panel of modern dogs and wolves. The mitochondrial genomes of all modern dogs are phylogenetically most closely related to either ancient or modern canids of Europe. Molecular dating suggests an onset of domestication there 18,800 to 32,100 years ago. These findings imply that domestic dogs are the culmination of a process that initiated with European hunter-gatherers and the canids with whom they interacted.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thalmann, O -- Shapiro, B -- Cui, P -- Schuenemann, V J -- Sawyer, S K -- Greenfield, D L -- Germonpre, M B -- Sablin, M V -- Lopez-Giraldez, F -- Domingo-Roura, X -- Napierala, H -- Uerpmann, H-P -- Loponte, D M -- Acosta, A A -- Giemsch, L -- Schmitz, R W -- Worthington, B -- Buikstra, J E -- Druzhkova, A -- Graphodatsky, A S -- Ovodov, N D -- Wahlberg, N -- Freedman, A H -- Schweizer, R M -- Koepfli, K-P -- Leonard, J A -- Meyer, M -- Krause, J -- Paabo, S -- Green, R E -- Wayne, R K -- New York, N.Y. -- Science. 2013 Nov 15;342(6160):871-4. doi: 10.1126/science.1243650.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Section of Genetics and Physiology, University of Turku, Itainen Pitkakatu 4, 20014 Turku, Finland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24233726" target="_blank"〉PubMed〈/a〉

Description: Mycobacterium lepromatosis is an uncultured human pathogen associated with diffuse lepromatous leprosy and a reactional state known as Lucio's phenomenon. By using deep sequencing with and without DNA enrichment, we obtained the near-complete genome sequence of M. lepromatosis present in a skin biopsy from a Mexican patient, and compared it...

Description: Herbaria archive a record of changes of worldwide plant biodiversity harbouring millions of specimens that contain DNA suitable for genome sequencing. To profit from this resource, it is fundamental to understand in detail the process of DNA degradation in herbarium specimens. We investigated patterns of DNA fragmentation and nucleotide misincorporation by analysing 86 herbarium samples spanning the last 300 years using Illumina shotgun sequencing. We found an exponential decay relationship between DNA fragmentation and time, and estimated a per nucleotide fragmentation rate of 1.66 x 10 –4 per year, which is six times faster than the rate estimated for ancient bones. Additionally, we found that strand breaks occur specially before purines, and that depurination-driven DNA breakage occurs constantly through time and can to a great extent explain decreasing fragment length over time. Similar to what has been found analysing ancient DNA from bones, we found a strong correlation between the deamination-driven accumulation of cytosine to thymine substitutions and time, which reinforces the importance of substitution patterns to authenticate the ancient/historical nature of DNA fragments. Accurate estimations of DNA degradation through time will allow informed decisions about laboratory and computational procedures to take advantage of the vast collection of worldwide herbarium specimens.

Description: Although investigations of medieval plague victims have identified Yersinia pestis as the putative etiologic agent of the pandemic, methodological limitations have prevented large-scale genomic investigations to evaluate changes in the pathogen's virulence over time. We screened over 100 skeletal remains from Black Death victims of the East Smithfield mass burial site (1348–1350, London, England). Recent methods of DNA enrichment coupled with high-throughput DNA sequencing subsequently permitted reconstruction of ten full human mitochondrial genomes (16 kb each) and the full pPCP1 (9.6 kb) virulence-associated plasmid at high coverage. Comparisons of molecular damage profiles between endogenous human and Y. pestis DNA confirmed its authenticity as an ancient pathogen, thus representing the longest contiguous genomic sequence for an ancient pathogen to date. Comparison of our reconstructed plasmid against modern Y. pestis shows identity with several isolates matching the Medievalis biovar; however, our chromosomal sequences indicate the victims were infected with a Y. pestis variant that has not been previously reported. Our data reveal that the Black Death in medieval Europe was caused by a variant of Y. pestis that may no longer exist, and genetic data carried on its pPCP1 plasmid were not responsible for the purported epidemiological differences between ancient and modern forms of Y. pestis infections.

Description: From historical and archeological records, it is posited that the European medieval household was a combination of close relatives and recruits. However, this kinship structure has not yet been directly tested at a genomic level on medieval burials. The early 7th century CE burial at Niederstotzingen, discovered in 1962, is the most complete and richest example of Alemannic funerary practice in Germany. Excavations found 13 individuals who were buried with an array of inscribed bridle gear, jewelry, armor, and swords. These artifacts support the view that the individuals had contact with France, northern Italy, and Byzantium. This study analyzed genome-wide sequences recovered from the remains, in tandem with analysis of the archeological context, to reconstruct kinship and the extent of outside contact. Eleven individuals had sufficient DNA preservation to genetically sex them as male and identify nine unique mitochondrial haplotypes and two distinct Y chromosome lineages. Genome-wide analyses were performed on eight individuals to estimate genetic affiliation to modern west Eurasians and genetic kinship at the burial. Five individuals were direct relatives. Three other individuals were not detectably related; two of these showed genomic affinity to southern Europeans. The genetic makeup of the individuals shares no observable pattern with their orientation in the burial or the cultural association of their grave goods, with the five related individuals buried with grave goods associated with three diverse cultural origins. These findings support the idea that not only were kinship and fellowship held in equal regard: Diverse cultural appropriation was practiced among closely related individuals as well.

Description: By 4000 years ago, people had introduced maize to the southwestern United States; full agriculture was established quickly in the lowland deserts but delayed in the temperate highlands for 2000 years. We test if the earliest upland maize was adapted for early flowering, a characteristic of modern temperate maize. We sequenced fifteen 1900-year-old maize cobs from Turkey Pen Shelter in the temperate Southwest. Indirectly validated genomic models predicted that Turkey Pen maize was marginally adapted with respect to flowering, as well as short, tillering, and segregating for yellow kernel color. Temperate adaptation drove modern population differentiation and was selected in situ from ancient standing variation. Validated prediction of polygenic traits improves our understanding of ancient phenotypes and the dynamics of environmental adaptation.