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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When so, things can happen like you burn out your brakes in the middle of nowhere’s night, or you get to dissect a frozen mammoth.
That happened. It feels like a dream to remember, a nightlong journey within the withins of a baby mammoth from Siberia. Humans called him Khroma. Like the metal carried away by the river. Like colors too, in a way.

There are clues I was not dreaming fully. Like elephant stones errant in the middle of giant steps. I leave you one to try. Courtesy of universcience.tv

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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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.

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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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.