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, 286:88-96.
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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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 Linnaean Society 2010, sous presse.

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 of Daouitherium, 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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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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Télécharger la Table supplémentaire 1 (XLS):  liste d’agrément aux consignes MIQE de qPCR [21ko]>
Télécharger la Table supplémentaire 2 (XLS): résultats des test d’inhibition [38ko]>

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Depuis 2003, nous avons accumulé des centaines (que dis-je: des milliers) d’observations sur des mandibules de proboscidiens fossiles et actuels afin de tester nos hypothèses quant au statut diagnostique de certaines formes de ces caractères chez les mammouths.

Après avoir rapidement abordé le sujet dans ma thèse, et réalisé un poster avec Marco pour le IMC9 de Sapporo en 2005, nous allons enfin publier une version détaillée de cette analyse dans le Zoological Journal of the Linnaean Society, où notre article intitulé “Anatomy and phylogenetic value of the mandibular and coronoid canals and their associated foramina in proboscideans (Mammalia)” vient d’être accepté.

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.
Régis Debruyne & Hendrik 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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Revolutions and crises in Ancient DNA: at the dawn of large-scale paleogenomics, what have we learnt from our previous mistakes?
Régis Debruyne

In Program and Abstracts of  The International Meeting of the French Network of Paleogenetics “Ancient DNA :  from mitochondrial to nuclear DNA, from the evolution of populations to the selection of characters”, IJM, Paris:14

Published Abstract

The implementation of molecular cloning and the advent of polymerase chain reaction have provoked what can be seen as two successive revolutions in ancient DNA studies. Despite numerous successes during those first two decades, the field has long been plagued by unsupported results, generally caused by false positive identification of non-authentic DNA. Some specialists of ancient DNA have responded to those pitfalls by the creation of a wide set of proper controls which have been diversely appreciated, causing a schism between the groups whether following those guidelines or not.
With the opening in 2005 of a new era of large-scale paleogenomics using high-throuput sequencing, the field of ancient DNA has been standing at the dawn of a third revolution. Once again, the development of its underlying 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.

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Les participants au congrès 25 ans de paléogénétique de l'IJM

]]> http://regis.cubedeglace.com/news/853/feed/ 0 http://regis.cubedeglace.com/news/861/ http://regis.cubedeglace.com/news/861/#comments Fri, 10 Jul 2009 08:20:17 +0000 Régis http://regis.cubedeglace.com/?p=861 Au terme d’un imbroglio politico-éditorial dont seuls les journaux comme Science semblent avoir le secret, nous venons enfin de publier un nouveau commentaire technique à l’égard des travaux de T. Gilbert et associés. Cette fois, nous nous sommes attachés à démontrer la vacuité des soi-disants “preuves” d’une présence humaine pré-Clovis en Amérique du Nord à partir des éléments retrouvés dans la grotte de Paisley en Oregon.

En marge de la publication conjointe de notre équipe avec Stuart Fiedel, des collègues de Philadelphie ont également publié un autre commentaire technique à l’égard du même article original, où ils démontrent que les “coprolites” prétendûment humains sont bien plus probablement des restes d’excréments d’herbivores…

Conformes a leur habitude, les auteurs originaux persistent à nier l’évidence de ces nouveaux arguments, s’attachant à leurs resultats comme un anatife à son vieux pneu. C’est un choix.

Je vous laisse juges.

De mon côté, j’en ai profité pour mettre à jour la page wikipedia relative à ce gisement afin de tenir compte des ces derniers resultats.