Antibiotic resistance is ancient.
D’Costa Vanessa, Christine E. King, Lindsay Kalan, Mariya Morar, Wilson W.L. Sung, Carsten Schwarz, Duane Froese, Grant Zazula, Fabrice Calmels, Régis Debruyne, Brian G. Golding, Hendrik N. Poinar, Gerard D. Wright.
Nature 2011, 477(7365):457-461.
DOI: 10.1038/nature10388

Abstract

The discovery of antibiotics more than 70 years ago initiated a period of drug innovation and implementation in human and animal health and agriculture. These discoveries were tempered in all cases by the emergence of resistant microbes. This history has been interpreted to mean that antibiotic resistance in pathogenic bacteria is a modern phenomenon; this view is reinforced by the fact that collections of microbes that predate the antibiotic era are highly susceptible to antibiotics. Here we report targeted metagenomic analyses of rigorously authenticated ancient DNA from 30,000-year-old Beringian permafrost sediments and the identification of a highly diverse collection of genes encoding resistance to β-lactam, tetracycline and glycopeptide antibiotics. Structure and function studies on the complete vancomycin resistance element VanA confirmed its similarity to modern variants. These results show conclusively that antibiotic resistance is a natural phenomenon that predates the modern selective pressure of clinical antibiotic use.

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Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths.
Enk Jacob, Alison Devault, Régis Debruyne, Christine E King, Todd Treangen, Dennis O’Rourke, Steven L Salzberg, Daniel Fisher, Ross MacPhee and Hendrik Poinar.
Genome Biology 2011, 12(5):R51.
DOI:10.1186/gb-2011-12-5-r51

Abstract

Background

Late Pleistocene North America hosted at least two divergent and ecologically distinct species of mammoth: the periglacial woolly mammoth (Mammuthus primigenius) and the subglacial Columbian mammoth (Mammuthus columbi). To date, mammoth genetic research has been entirely restricted to woolly mammoths, rendering their genetic evolution difficult to contextualize within broader Pleistocene paleoecology and biogeography. Here, we take an interspecific approach to clarifying mammoth phylogeny by targeting Columbian mammoth remains for mitogenomic sequencing.

Results

We sequenced the first complete mitochondrial genome of a classic Columbian mammoth, as well as the first complete mitochondrial genome of a North American woolly mammoth. Somewhat contrary to conventional paleontological models, which posit that the two species were highly divergent, the M. columbi mitogenome we obtained falls securely within a subclade of endemic North American M. primigenius.

Conclusions

Though limited, our data suggest that the two species interbred at some point in their evolutionary histories. One potential explanation is that woolly mammoth haplotypes entered Columbian mammoth populations via introgression at subglacial ecotones, a scenario with compelling parallels in extant elephants and consistent with certain regional paleontological observations. This highlights the need for multi-genomic data to sufficiently characterize mammoth evolutionary history. Our results demonstrate that the use of next-generation sequencing technologies holds promise in obtaining such data, even from non-cave, non-permafrost Pleistocene depositional contexts.

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Anatomy and phylogenetic value of the mandibular and coronoid canals and their associated foramina in proboscideans (Mammalia).
Ferretti, Marco & Régis Debruyne.
Zoological Journal of the Linnean Society 2011, 161(2):391-413.
DOI: 10.1111/j.1096-3642.2010.00637.x

Abstract

Characters associated with the mandibular canal are differently distributed among proboscidean lineages and provide useful information on the systematics and relationships of proboscideans. The aim of the paper is to describe the pattern of the mandibular canal and its associated foramina in proboscideans in order to fully appreciate the extent of interspecific variation of these structures within the group and to discuss its systematic and phylogenetic value. Outgroup comparison indicates that the condition presented by the basal proboscidean Phosphatherium is morphotypic for proboscideans. Primitive proboscidean characters are: the low position of the mandibular foramen, and its crescent-shaped outline, the occurrence of a coronoid foramen (canal), the occurrence of two lateral mental foramina, the posterior one at the level of (or slightly behind) the posterior margin of the symphysis, the anterior one in a more distal position, the absence of a medial mental foramen (MMF), the mandibular canal set just below the tooth row. The occurrence of a single lateral mental foramen might represent a shared derived character ofDaouitherium, Numidotherium, and Barytherium. A unique derived feature of the Elephantinae mandible is the occurrence of a medial mental foramen, on the medial side of the incisive part of the mandible. MMF has never been observed in other proboscideans excluding elephantines. The very high frequency of MMF observed in Mammuthus meridionalis-M. trogontherii-M. primigenius (>93 per cent of the studied specimens) could be considered a synapomorphy of this group.

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Regional differences in bone collagen δ13C and δ15N of Pleistocene mammoths: Implications for paleoecology of the mammoth steppe.
Szpak Paul, Darren R. Gröcke, Régis Debruyne, Ross D.E. MacPhee, R.D. Guthrie, Grant D. Zazula, W.P. Patterson, & Hendrik N. Poinar.
Palaeogeography Palaeoclimatology Palaeoecology 2010, 286(1-2):88-96.
doi: 10.1016/j.palaeo.2009.12.009

Abstract

In this study, we present bone collagen d13C and d15N values from a large set of Pleistocene woolly mammoths (Mammuthus primigenius) from Siberia, Alaska and Yukon. Overall, results for mammoth specimens from eastern Beringia (Alaska and Yukon) significantly differ, for both d13C and d15N values, from those from western Beringia. In agreement with palynological, entomological, and physiographic data from the same regions, these isotopic differences strongly imply that the ‘mammoth steppe,’ the extensive ice-free region spanning northern Eurasia and northwestern North America, was ecologically variable along its east-west axis to a significant degree. Prior to the Last Glacial Maximum (LGM), the high-latitude portions of Siberia and the Russian Far East appear to have been colder and more arid than central Alaska and Yukon, which were ecologically more diverse. However, during the LGM itself, isotopic signatures of mammoths from eastern Beringia strongly support the argument that this region experienced an extremely cold and arid climate as well. In terms of overall temporal trend, Beringia thus went from a condition prior to the LGM of greater ecological variability in the east to one of uniformly cold and dry conditions during the LGM.

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A Quantitative Approach to Detect and Overcome PCR Inhibition in Ancient DNA Extracts.
King, Christine E.,  Régis Debruyne, Melanie Kuch, Carsten Schwarz, & Hendrik N. Poinar.
Biotechniques 2009, 47(5):351-356.
DOI: 10.2144/000113244

Abstract

Inhibition is problematic in many applications of PCR, particularly those involving degraded or low amounts of template DNA, when simply diluting the extract is undesirable. Two basic approaches to monitoring inhibition in such samples using real-time or quantitative PCR (qPCR) have been proposed. The first method analyzes the quantification cycle (Cq) deviation of a spiked internal positive control. The second method considers variations in reaction efficiency based on the slopes of individual amplification plots. In combining these methods, we observed increased Cq values together with reduced amplification efficiencies in some samples, as expected; however, deviations from this pattern in other samples support the use of both measurements. Repeat inhibition testing enables optimization of PCR facilitator combinations and sample dilution such that DNA yields and/or quantitative accuracy can be maximized in subsequent PCR runs. Although some trends were apparent within sample types, differences in inhibition levels, optimal reactions conditions, and expected recovery of DNA under these conditions suggest that all samples be routinely tested with this approach.

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Download the supplementary table 1 (XLS format): listing of agreements to MIQE qPCR guidelines [21ko]
Download the supplementary table 2 (XLS format): results of inhibition tests [38ko]

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This article has been cited 7 times since 2009. Access its citation report

The “time-dependency of molecular rates of evolution revisited”: how well-calibrated paleontological evidence can clear the mess in the Bayesian debate generated by poorly calibrated uninformative molecular data.
Debruyne, R. & H.N. Poinar.
Journal of Vertebrate Paleontology 2009, 29(Supplement to 3):86A.

Published Abstract

One of the predictions of the neutral theory of molecular evolution is that the long-term rate of substitution between two lineages can only be inferior to their instantaneous rate of mutation, due to the fixation of transient polymorphisms through time. Accordingly, some recent work supports that a drastic acceleration in the molecular rates as divergence time approaches zero is a general and predictable feature. It has become since then a hotly debated topic in both systematics and evolutionary biology. Although, observations of such ‘accelerations’ in the molecular rates within recent evolutionary time have been documented, some recent models describe a phenomenon an order of magnitude beyond them. Indeed, it allows a variation within a wide range of rates (beyond 20 fold) during an extended period of time (up to two million years). Although intuitively appealing and explaining well the original data, this model supports a serious and prolonged impact of deleterious mutations and would thus require large adjustments in the current evolutionary paradigm of genomes.
Recently, both the model of the time-dependency and the significance of the rate acceleration phenomenon have been put in question. In this communication, our primary objective is to re-address the nature of the causal factor(s) of the rate acceleration described by previous models, as well as their biological meaning. Based on previously published material, we suggest that the emphasis placed upon the divergence time in the current explanation of this phenomenon has hidden other relevant factors such as the information content of the datasets. In order to compare the performance of the strict “time-dependency” model with a more inclusive “signal-dependency” hypothesis, we examine both the impact of sequence length and the relative advantages & disadvantages of alternative calibration methods over the estimates of the rates. We illustrate the theoretical benefits of well-documented paleontological evidence on the inference of the rates through a case-study of modern and extinct Elephantoids. We thus conclude that the hypothesis for a signal-dependent artifact appears to model the data more accurately and explains some inconsistencies between published reports on evolutionary rates and paleontological data.

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Comment on “DNA from Pre-Clovis Human Coprolites in Oregon, North America”.
Poinar Hendrik N., Stuart Fiedel, Kirsti Bos, Chrsitine E. King, Alison M. Devault, Melanie Kuch, & Régis Debruyne.
Science 2009, 325(5937):148.
DOI: 10.1126/science.1168182

Abstract

Gilbert et al. (Reports, 9 May 2008, p. 786) analyzed DNA from radiocarbon-dated paleofecal remains from Paisley Cave, Oregon, which ostensibly demonstrate a human presence in North America predating the well-established Clovis complex. We question the authenticity of their DNA results and argue that in the absence of intact stratigraphy and diagnostic artifacts, and in view of carbon isotope anomalies, the radiocarbon dates of the oldest specimens are unreliable.

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Further reading

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Read also the comment by Goldberg et al. on “DNA from Pre-Clovis Human Coprolites in Oregon, North America”. And make your own conclusions.

Time-Dependency of Molecular Rates in Ancient DNA Datasets, a Sampling Artifact?
Debruyne Régis & Hendrik N. Poinar.
Syst Biol 2009, 58(3):348-359.
DOI: 10.1093/sysbio/syp028

POINTS OF VIEW (extract)

It is common knowledge that the instantaneous rate of mutation (RoM) in DNA sequences exceeds the long-term rate of substitution (RoS) when measured in interspecific phylogenetic analyses. The neutral theory of molecular evolution describes this temporary excess diversity as transient polymorphisms either removed from the population through the actions of purifying selection or fixed by random genetic drift over a few generations (Kimura 1983). Observations of these “accelerations” in the molecular rates within recent evolutionary time have been documented (Parsons et al. 1997; Lambert et al. 2002); however, they did not resolve the magnitude and duration of this phenomenon. Howell et al. (2003) have addressed these issues through pedigree analyses of human mitochondrial (mt) hypervariable region (HVR) sequences and have suggested a 5- to 10-fold acceleration compared with the long-term RoS. In addition, Burridge et al. (2008) have shown that the calibration of the mt clock for galaxiid fishes using geological divergence dates with cytochrome b and control region sequences supports a transition period during which the RoM would decrease toward the RoS extending up to ~200 kyr (Burridge et al. 2008). However, the general applicability of these specific results remains untested…

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This article has been cited 14 times since 2009. Access its citation report

What controls for the new era of high-throuput sequencing in ancient DNA?

Debruyne Régis.

CAPA/ACAP Newsletter 2009(1):14.

Abstract

The advent of polymerase chain reaction at the end of the 1980s provoked a first revolution in ancient DNA studies, with the numerous successes and as many pitfalls known from the past decade, generally caused by false positive identification of non-authentic DNA. The specialists of ancient DNA have responded to those pitfalls by the creation of a wide set of proper controls which have been diversely appreciated and followed with time. With the opening of a new era of high-throuput sequencing, the field of ancient DNA now stands at the dawn of a second revolution. However, once again, the development of these new technologies is accompanied by its own limitations, the critical analysis of which has already led to controversial conclusions. Here we select a few of those controversial outcomes and praise for the establishment of a new set of controls, adapted to the safe study of ancient DNA using high-throuput sequencing technologies.

New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains.
Schwarz Carsten, Régis Debruyne, Melanie Kuch, Elizabth McNally, Henry Schwarcz, Andrew Aubrey, Jeffrey Bada, Hendrik N. Poinar.
Nucleic Acids Research 2009, 37(10): 3215–3229.
DOI:10.1093/nar/gkp159

Abstract

Despite being plagued by heavily degraded DNA in palaeontological remains, most studies addressing the state of DNA degradation have been limited to types of damage which do not pose a hindrance to Taq polymerase during PCR. Application of serial qPCR to the two fractions obtained during extraction (demineralization and protein digest) from six permafrost mammoth bones and one partially degraded modern elephant bone has enabled further insight into the changes which endogenous DNA is subjected to during diagenesis. We show here that both fractions exhibit individual qualities in terms of the prevailing type of DNA (i.e. mitochondrial versus nuclear DNA) as well as the extent of damage, and in addition observed a highly variable ratio of mitochondrial to nuclear DNA among the six mammoth samples. While there is evidence suggesting that mitochondrial DNA is better preserved than nuclear DNA in ancient permafrost samples, we find the initial DNA concentration in the bone tissue to be as relevant for the total accessible mitochondrial DNA as the extent of DNA degradation post-mortem. We also evaluate the general applicability of indirect measures of preservation such as amino-acid racemization, bone crystallinity index and thermal age to these exceptionally well-preserved samples.

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This article has been cited 16 times since 2009. Access its citation report.