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152. Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis.

Author

Gilbert, M Thomas P, Binladen, Jonas, Miller, Webb, Wiuf, Carsten, Willerslev, Eske, Poinar, Hendrik, Carlson, John E, Leebens-Mack, James H, Schuster, Stephan C, Gilbert, M Thomas P, Binladen, Jonas, Miller, Webb, Wiuf, Carsten, Willerslev, Eske, Poinar, Hendrik, Carlson, John E, Leebens-Mack, James H, and Schuster, Stephan C

Abstract

Udgivelsesdato: January 2007, Although ancient DNA (aDNA) miscoding lesions have been studied since the earliest days of the field, their nature remains a source of debate. A variety of conflicting hypotheses exist about which miscoding lesions constitute true aDNA damage as opposed to PCR polymerase amplification error. Furthermore, considerable disagreement and speculation exists on which specific damage events underlie observed miscoding lesions. The root of the problem is that it has previously been difficult to assemble sufficient data to test the hypotheses, and near-impossible to accurately determine the specific strand of origin of observed damage events. With the advent of emulsion-based clonal amplification (emPCR) and the sequencing-by-synthesis technology this has changed. In this paper we demonstrate how data produced on the Roche GS20 genome sequencer can determine miscoding lesion strands of origin, and subsequently be interpreted to enable characterization of the aDNA damage behind the observed phenotypes. Through comparative analyses on 390,965 bp of modern chloroplast and 131,474 bp of ancient woolly mammoth GS20 sequence data we conclusively demonstrate that in this sample at least, a permafrost preserved specimen, Type 2 (cytosine-->thymine/guanine-->adenine) miscoding lesions represent the overwhelming majority of damage-derived miscoding lesions. Additionally, we show that an as yet unidentified guanine-->adenine analogue modification, not the conventionally argued cytosine-->uracil deamination, underpins a significant proportion of Type 2 damage. How widespread these implications are for aDNA will become apparent as future studies analyse data recovered from a wider range of substrates.

Published
2007

153. Shotgun Mitogenomics Provides a Reference Phylogenetic Framework and Timescale for Living Xenarthrans.

Author

Gibb, Gillian C., Condamine, Fabien L., Kuch, Melanie, Enk, Jacob, Moraes-Barros, Nadia, Superina, Mariella, Poinar, Hendrik N., and Delsuc, Frédéric

Abstract

Xenarthra (armadillos, sloths, and anteaters) constitutes one of the four major clades of placental mammals. Despite their phylogenetic distinctiveness in mammals, a reference phylogeny is still lacking for the 31 described species. Here we used Illumina shotgun sequencing to assemble 33 new complete mitochondrial genomes, establishing Xenarthra as the first major placental clade to be fully sequenced at the species level for mitogenomes. The resulting data set allowed the reconstruction of a robust phylogenetic framework and timescale that are consistent with previous studies conducted at the genus level using nuclear genes. Incorporating the full species diversity of extant xenarthrans points to a number of inconsistencies in xenarthran systematics and species definition. We propose to split armadillos into two distinct families Dasypodidae (dasypodines) and Chlamyphoridae (euphractines, chlamyphorines, and tolypeutines) to better reflect their ancient divergence, estimated around 42 Ma. Species delimitation within long-nosed armadillos (genus Dasypus) appeared more complex than anticipated, with the discovery of a divergent lineage in French Guiana. Diversification analyses showed Xenarthra to be an ancient clade with a constant diversification rate through time with a species turnover driven by high but constant extinction. We also detected a significant negative correlation between speciation rate and past temperature fluctuations with an increase in speciation rate corresponding to the general cooling observed during the last 15 My. Biogeographic reconstructions identified the tropical rainforest biome of Amazonia and the Guiana Shield as the cradle of xenarthran evolutionary history with subsequent dispersions into more open and dry habitats. [ABSTRACT FROM AUTHOR]

Published
2016
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154. Out of America: Ancient DNA Evidence for a New World Origin of Late Quaternary Woolly Mammoths

Author

Debruyne, Regis, Chu, Genevieve, King, Christine E., Bos, Kirsti, Kuch, Melanie, Schwarz, Carsten, Szpak, Paul, Gröcke, Darren R., Matheus, Paul, Zazula, Grant, Guthrie, Dale, Froese, Duane, Buigues, Bernard, de Marliave, Christian, Flemming, Clare, Poinar, Debi, Fisher, Daniel, Southon, John, Tikhonov, Alexei N., MacPhee, Ross D.E., and Poinar, Hendrik N.

Published
2008
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157. Erratum: A draft genome of Yersinia pestis from victims of the Black Death

Author

Bos, Kirsten I., primary, Schuenemann, Verena J., additional, Golding, G. Brian, additional, Burbano, Hernán A., additional, Waglechner, Nicholas, additional, Coombes, Brian K., additional, McPhee, Joseph B., additional, N.DeWitte, Sharon, additional, Meyer, Matthias, additional, Schmedes, Sarah, additional, Wood, James, additional, Earn, David J. D., additional, Herring, D. Ann, additional, Bauer, Peter, additional, Poinar, Hendrik N., additional, and Krause, Johannes, additional

Published
2011
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158. Antibiotic resistance is ancient

Author

D’Costa, Vanessa M., primary, King, Christine E., additional, Kalan, Lindsay, additional, Morar, Mariya, additional, Sung, Wilson W. L., additional, Schwarz, Carsten, additional, Froese, Duane, additional, Zazula, Grant, additional, Calmels, Fabrice, additional, Debruyne, Regis, additional, Golding, G. Brian, additional, Poinar, Hendrik N., additional, and Wright, Gerard D., additional

Published
2011
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165. Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA

Author

Poinar, Hendrik N., primary, Schwarz, Carsten, additional, Qi, Ji, additional, Shapiro, Beth, additional, MacPhee, Ross D. E., additional, Buigues, Bernard, additional, Tikhonov, Alexei, additional, Huson, Daniel H., additional, Tomsho, Lynn P., additional, Auch, Alexander, additional, Rampp, Markus, additional, Miller, Webb, additional, and Schuster, Stephan C., additional

Published
2006
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166. Osteocalcin protein sequences of Neanderthals and modern primates

Author

Nielsen-Marsh, Christina M., primary, Richards, Michael P., additional, Hauschka, Peter V., additional, Thomas-Oates, Jane E., additional, Trinkaus, Erik, additional, Pettitt, Paul B., additional, Karavanić, Ivor, additional, Poinar, Hendrik, additional, and Collins, Matthew J., additional

Published
2005
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171. Molecular caving

Author

Hofreiter, Michael, primary, Mead, Jim I., additional, Martin, Paul, additional, and Poinar, Hendrik N., additional

Published
2003
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176. Ancient DNA

Author

Hofreiter, Michael, primary, Serre, David, additional, Poinar, Hendrik N., additional, Kuch, Melanie, additional, and Pääbo, Svante, additional

Published
2001
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180. Neandertal Genetics

Author

Cooper, Alan, primary, Poinar, Hendrik N., additional, Pääbo, Svante, additional, Radovc̆ić, J., additional, Debénath, A., additional, Caparros, Miguel, additional, Barroso-Ruiz, Cecilio, additional, Bertranpetit, Jaume, additional, Nielsen-Marsh, Christina, additional, Hedges, Robert E. M., additional, and Sykes, Bryan, additional

Published
1997
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186. Mylodon darwinii DNA sequences from ancient fecal hair shafts.

Author

Clack, Andrew A., MacPhee, Ross D.E., and Poinar, Hendrik N.

Subjects
NUCLEOTIDE sequence, FOSSIL DNA, GERMPLASM conservation, GROUND sloths, COPROLITES, PHYLOGEOGRAPHY
Abstract

Summary: Preserved hair has been increasingly used as an ancient DNA source in high throughput sequencing endeavors, and it may actually offer several advantages compared to more traditional ancient DNA substrates like bone. However, cold environments have yielded the most informative ancient hair specimens, while its preservation, and thus utility, in temperate regions is not well documented. Coprolites could represent a previously underutilized preservation substrate for hairs, which, if present therein, represent macroscopic packages of specific cells that are relatively simple to separate, clean and process. In this pilot study, we report amplicons 147–152 base pairs in length (w/primers) from hair shafts preserved in a south Chilean coprolite attributed to Darwin''s extinct ground sloth, Mylodon darwinii. Our results suggest that hairs preserved in coprolites from temperate cave environments can serve as an effective source of ancient DNA. This bodes well for potential molecular-based population and phylogeographic studies on sloths, several species of which have been understudied despite leaving numerous coprolites in caves across of the Americas. [ABSTRACT FROM AUTHOR]

Published
2012
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187. Time Dependency of Molecular Rates in Ancient DNA Data Sets, A Sampling Artifact?

Author

DEBRUYNE, REGIS and POINAR, HENDRIK N.

Subjects
*NUCLEOTIDE sequence, *PHYLOGENY, *DNA, *GENES, *BIOLOGY, *BAYESIAN analysis
Abstract

The article discusses the time dependency of molecular rates in DNA sequences when measured in interspecific phylogenetic analyses. It references a study by S. Y. Ho et al which proposed a time-dependency model in which the rate reflects a direct response of the divergence time between the terminals. It addresses the nature of the causal factors of the rate acceleration described by Ho et al and their biological meaning. It also summarizes the results of the Bayesian analyses for the posterior distribution of the rate of change (ROC).

Published
2009
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189. Herald waves of cholera in nineteenth century London

Author

Tien, Joseph H., Poinar, Hendrik N., Fisman, David N., and Earn, David J. D.

Abstract

Deaths from cholera in London, UK, were recorded weekly from 1824 to 1901. Three features of the time series stand out: (i) cholera deaths were strongly seasonal, with peak mortality almost always in the summer, (ii) the only non-summer outbreaks occurred in the spring of 1832, the autumn of 1848 and the winter of 1853, and (iii) extraordinarily severe summer outbreaks occurred in 1832, 1849, 1854 and 1866 (the four ‘great’ cholera years). The non-summer outbreaks of 1832, 1848 and 1853 appear to have been herald waves of newly invading cholera strains. In addition, a simple mathematical model confirms that a non-summer introduction of a new cholera strain can result in an initial herald wave, followed by a severe outbreak the following summer. Through the analysis of the genomes of nineteenth-century specimens, it may be possible to identify the strains that caused these herald waves and the well-known cholera epidemics that followed.

Published
2011
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190. Ask a DNA Expert.

Author

POINAR, HENDRIK and TESAR, ALEX

Subjects
ANIMAL cloning, DE-extinction
Abstract

An interview with Hendrik Poinar, director of the McMaster Ancient DNA Centre, about cloning an animal, possibility of extracting deoxyribonucleic acid (DNA) from ancient species, and possibility of de-extinction is presented.

Published
2021

191. Probe design for simultaneous, targeted capture of diverse metagenomic targets

Author

Dickson, Zachery W., Hackenberger, Dirk, Kuch, Melanie, Marzok, Art, Banerjee, Arinjay, Rossi, Laura, Klowak, Jennifer Ann, Fox-Robichaud, Alison, Mossmann, Karen, Miller, Matthew S., Surette, Michael G., Golding, Geoffrey Brian, and Poinar, Hendrik

Abstract

The compounding challenges of low signal, high background, and uncertain targets plague many metagenomic sequencing efforts. One solution has been DNA capture, wherein probes are designed to hybridize with target sequences, enriching them in relation to their background. However, balancing probe depth with breadth of capture is challenging for diverse targets. To find this balance, we have developed the HUBDesign pipeline, which makes use of sequence homology to design probes at multiple taxonomic levels. This creates an efficient probe set capable of simultaneously and specifically capturing known and related sequences. We validated HUBDesign by generating probe sets targeting the breadth of coronavirus diversity, as well as a suite of bacterial pathogens often underlying sepsis. In separate experiments demonstrating significant, simultaneous enrichment, we captured SARS-CoV-2 and HCoV-NL63 in a human RNA background and seven bacterial strains in human blood. HUBDesign (https://github.com/zacherydickson/HUBDesign) has broad applicability wherever there are multiple organisms of interest.

Published
2021
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193. American mastodon mitochondrial genomes suggest multiple dispersal events in response to Pleistocene climate oscillations.

Author

Karpinski, Emil, Hackenberger, Dirk, Zazula, Grant, Widga, Chris, Duggan, Ana T., Golding, G. Brian, Kuch, Melanie, Klunk, Jennifer, Jass, Christopher N., Groves, Pam, Druckenmiller, Patrick, Schubert, Blaine W., Arroyo-Cabrales, Joaquin, Simpson, William F., Hoganson, John W., Fisher, Daniel C., Ho, Simon Y. W., MacPhee, Ross D. E., and Poinar, Hendrik N.

Subjects
PHYLOGEOGRAPHY, EFFECT of human beings on climate change, GENOMES, OSCILLATIONS, ICE sheets, POPULATION dynamics
Abstract

Pleistocene glacial-interglacial cycles are correlated with dramatic temperature oscillations. Examining how species responded to these natural fluctuations can provide valuable insights into the impacts of present-day anthropogenic climate change. Here we present a phylogeographic study of the extinct American mastodon (Mammut americanum), based on 35 complete mitochondrial genomes. These data reveal the presence of multiple lineages within this species, including two distinct clades from eastern Beringia. Our molecular date estimates suggest that these clades arose at different times, supporting a pattern of repeated northern expansion and local extirpation in response to glacial cycling. Consistent with this hypothesis, we also note lower levels of genetic diversity among northern mastodons than in endemic clades south of the continental ice sheets. The results of our study highlight the complex relationships between population dispersals and climate change, and can provide testable hypotheses for extant species expected to experience substantial biogeographic impacts from rising temperatures. Pleistocene population dynamics can inform the consequences of current climate change. This phylogeography of 35 complete American mastodon mitochondrial genomes suggests distinct lineages in this species repeatedly expanded northwards and then went locally extinct in response to glacial cycles. [ABSTRACT FROM AUTHOR]

Published
2020
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195. The origins and genomic diversity of American Civil War Era smallpox vaccine strains

Author

Duggan, Ana T., Klunk, Jennifer, Porter, Ashleigh F., Dhody, Anna N., Hicks, Robert, Smith, Geoffrey L., Humphreys, Margaret, McCollum, Andrea M., Davidson, Whitni B., Wilkins, Kimberly, Li, Yu, Burke, Amanda, Polasky, Hanna, Flanders, Lowell, Poinar, Debi, Raphenya, Amogelang R., Lau, Tammy T. Y., Alcock, Brian, McArthur, Andrew G., Golding, G. Brian, Holmes, Edward C., and Poinar, Hendrik N.

Abstract

Vaccination has transformed public health, most notably including the eradication of smallpox. Despite its profound historical importance, little is known of the origins and diversity of the viruses used in smallpox vaccination. Prior to the twentieth century, the method, source and origin of smallpox vaccinations remained unstandardised and opaque. We reconstruct and analyse viral vaccine genomes associated with smallpox vaccination from historical artefacts. Significantly, we recover viral molecules through non-destructive sampling of historical materials lacking signs of biological residues. We use the authenticated ancient genomes to reveal the evolutionary relationships of smallpox vaccination viruses within the poxviruses as a whole.

Published
2020
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196. Additional file 6 of The origins and genomic diversity of American Civil War Era smallpox vaccine strains

Author

Duggan, Ana T., Klunk, Jennifer, Porter, Ashleigh F., Dhody, Anna N., Hicks, Robert, Smith, Geoffrey L., Humphreys, Margaret, McCollum, Andrea M., Whitni B. Davidson, Wilkins, Kimberly, Li, Yu, Burke, Amanda, Polasky, Hanna, Flanders, Lowell, Poinar, Debi, Amogelang R. Raphenya, Lau, Tammy T. Y., Alcock, Brian, McArthur, Andrew G., G. Brian Golding, Holmes, Edward C., and Poinar, Hendrik N.

Subjects
3. Good health
Abstract

Additional file 6: Figure S2. Maximum likelihood trees for Mutter vaccine strains called in reference to alternative VACV genomes.

197. Additional file 13 of The origins and genomic diversity of American Civil War Era smallpox vaccine strains

Author

Duggan, Ana T., Klunk, Jennifer, Porter, Ashleigh F., Dhody, Anna N., Hicks, Robert, Smith, Geoffrey L., Humphreys, Margaret, McCollum, Andrea M., Whitni B. Davidson, Wilkins, Kimberly, Li, Yu, Burke, Amanda, Polasky, Hanna, Flanders, Lowell, Poinar, Debi, Amogelang R. Raphenya, Lau, Tammy T. Y., Alcock, Brian, McArthur, Andrew G., G. Brian Golding, Holmes, Edward C., and Poinar, Hendrik N.

Subjects
3. Good health
Abstract

Additional file 13: Figure S7. Comparison of terminal damage patterns of VK01.

198. Additional file 8 of The origins and genomic diversity of American Civil War Era smallpox vaccine strains

Author

Duggan, Ana T., Klunk, Jennifer, Porter, Ashleigh F., Dhody, Anna N., Hicks, Robert, Smith, Geoffrey L., Humphreys, Margaret, McCollum, Andrea M., Whitni B. Davidson, Wilkins, Kimberly, Li, Yu, Burke, Amanda, Polasky, Hanna, Flanders, Lowell, Poinar, Debi, Amogelang R. Raphenya, Lau, Tammy T. Y., Alcock, Brian, McArthur, Andrew G., G. Brian Golding, Holmes, Edward C., and Poinar, Hendrik N.

Subjects
3. Good health
Abstract

Additional file 8: Figure S4. Regression analyses of root-to-tip genetic distance on the ML phylogeny against either year of collection or year of sequencing.

199. Additional file 7 of The origins and genomic diversity of American Civil War Era smallpox vaccine strains

Author

Duggan, Ana T., Klunk, Jennifer, Porter, Ashleigh F., Dhody, Anna N., Hicks, Robert, Smith, Geoffrey L., Humphreys, Margaret, McCollum, Andrea M., Whitni B. Davidson, Wilkins, Kimberly, Li, Yu, Burke, Amanda, Polasky, Hanna, Flanders, Lowell, Poinar, Debi, Amogelang R. Raphenya, Lau, Tammy T. Y., Alcock, Brian, McArthur, Andrew G., G. Brian Golding, Holmes, Edward C., and Poinar, Hendrik N.

Subjects
3. Good health
Abstract

Additional file 7: Figure S3. GrapeTree analysis of 79 OPXV.

200. The origins and genomic diversity of American Civil War Era smallpox vaccine strains

Author

Duggan, Ana T, Klunk, Jennifer, Porter, Ashleigh F, Dhody, Anna N, Hicks, Robert, Smith, Geoffrey L, Humphreys, Margaret, McCollum, Andrea M, Davidson, Whitni B, Wilkins, Kimberly, Li, Yu, Burke, Amanda, Polasky, Hanna, Flanders, Lowell, Poinar, Debi, Raphenya, Amogelang R, Lau, Tammy TY, Alcock, Brian, McArthur, Andrew G, Golding, G Brian, Holmes, Edward C, and Poinar, Hendrik N

Subjects
Ancient DNA, viruses, Vaccination, virus diseases, Genetic Variation, Vaccinia virus, History, 19th Century, Genome, Viral, 16. Peace & justice, complex mixtures, 3. Good health, American Civil War, Humans, Metagenome, Smallpox Vaccine, Smallpox
Abstract

Vaccination has transformed public health, most notably including the eradication of smallpox. Despite its profound historical importance, little is known of the origins and diversity of the viruses used in smallpox vaccination. Prior to the twentieth century, the method, source and origin of smallpox vaccinations remained unstandardised and opaque. We reconstruct and analyse viral vaccine genomes associated with smallpox vaccination from historical artefacts. Significantly, we recover viral molecules through non-destructive sampling of historical materials lacking signs of biological residues. We use the authenticated ancient genomes to reveal the evolutionary relationships of smallpox vaccination viruses within the poxviruses as a whole.

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