Late Quaternary loss of genetic diversity in muskox (Ovibos)

BACKGROUND: The modern wildherd of the tundra muskox (Ovibos moschatus) is native only to the New World (northern North America and Greenland), and its genetic diversity is notably low. However, like several other megafaunal mammals, muskoxen enjoyed a holarctic distribution during the late Pleistocene. To investigate whether collapse in range and loss of diversity might be correlated, we collected mitochondrial sequence data (hypervariable region and cytochrome b) from muskox fossil material recovered from localities in northeastern Asia and the Arctic Archipelago of northern North America, dating from late Pleistocene to late Holocene, and compared our results to existing databases for modern muskoxen. RESULTS: Two classes of haplotypes were detected in the fossil material. "Surviving haplotypes" (SHs), closely similar or identical to haplotypes found in modern muskoxen and ranging in age from ~22,000 to ~160 yrbp, were found in all New World samples as well as some samples from northeastern Asia. "Extinct haplotypes" (EHs), dating between ~44,000 and ~18,000 yrbp, were found only in material from the Taimyr Peninsula and New Siberian Islands in northeastern Asia. EHs were not found in the Holocene muskoxen specimens available for this study, nor have they been found in other studies of extant muskox populations. CONCLUSION: We provisionally interpret this evidence as showing that genetic variability was reduced in muskoxen after the Last Glacial Maximum but before the mid-Holocene, or roughly within the interval 18,000-4,000 yrbp. Narrowing this gap further will require the recovery of more fossils and additional genetic information from this interval

Radiocarbon Chronologies and Extinction Dynamics of the Late Quaternary Mammalian Megafauna of the Taimyr Peninsula, Russian Federation

This paper presents 75 new radiocarbon dates based on late Quaternary mammal remains recovered from eastern Taimyr Peninsula and adjacent parts of the northern Siberian lowlands, Russian Federation, including specimens of woolly mammoth (Mammuthus primigenius), steppe bison (Bison priscus), muskox (Ovibos moschatus), moose (Alces alces), reindeer (Rangifer tarandus), horse (Equus caballus) and wolf (Canis lupus). New evidence permits reanalysis of megafaunal extinction dynamics in the Asian high Arctic periphery. Increasingly, radiometric records of individual species show evidence of a gap at or near the Pleistocene/Holocene boundary (PHB). In the past, the PHB gap was regarded as significant only when actually terminal, i.e., when it marked the apparent ‘‘last’’ occurrence of a species (e.g., current ‘‘last’’ occurrence date for woolly mammoth in mainland Eurasia is 9600 yr BP). However, for high Arctic populations of horses and muskoxen the gap marks an interruption rather than extinction, because their radiocarbon records resume, nearly simultaneously, much later in the Holocene. Taphonomic effects, ΔC14 flux, and biased sampling are unlikely explanations for these hiatuses. A possible explanation is that the gap is the signature of an event, of unknown nature, that prompted the nearly simultaneous crash of many megafaunal populations in the high Arctic and possibly elsewhere in Eurasia.

Anatomy, death, and preservation of a woolly mammoth (Mammuthus primigenius) calf, Yamal Peninsula, northwest Siberia

A well-preserved woolly mammoth calf found in northwest Siberia offers unique opportunities to investigate mammoth anatomy, behavior, life history and taphonomy. Analysis of the fluvial setting where the specimen was found suggests it was derived from eroding bluffs during ice-out flooding in June 2006. It then lay exposed on a point-bar surface until recovery the following May. AMS dating of bone collagen and plant tissues from the intestine provide age estimates that average about 41,800 14C yrBP. Anatomical features of interest include a hemispherical mass, apparently composed of brown fat, on the back of the neck. This may have functioned in thermoregulation for the neonate mammoth, born before onset of spring. Abundant subcutaneous fat and milk residues in the alimentary tract demonstrate that this animal was in good nutritional condition before death, making other features of its life history relevant for general studies of mammoth paleobiology. Plant remains from the intestine (mixed with milk residue in a manner consistent with frequent, small meals) show evidence of mastication by adult mammoths, suggesting that this calf ingested fecal material, probably from its mother and presumably to inoculate its intestinal tract with a microbial assemblage derived from a healthy adult. Discrepancies between the season of death we infer (spring) and seasonal indicators from the intestine implicate coprophagy (involving old fecal boli) by the mother. This animal’s trachea and bronchi are completely occluded with fine-grained vivianite (hydrated iron phosphate) such as occurs in some lacustrine settings. Because this vivianite does not penetrate the lung beyond the bronchi, we infer that it must have entered as a viscous mass that occluded the airway, causing asphyxia. Nodular vivianite in the cranial region and interiors of long bones must have originated postmortem, but its distribution may be partly controlled by peripheral vasoconstriction, a physiological response to asphyxia. Nodular vivianite may have formed from iron derived from hemoglobin and phosphate liberated by partial demineralization of bones. Demineralization could have been caused by lactic acid, for which the main evidence is loss of tissues dominated by Type 1 collagen (denatured in lactic acid). We propose that this was consequent on postmortem colonization of the body by lactic acid-producing bacteria. These bacteria and their metabolites may have promoted preservation during the time before the body was incorporated in permafrost and could also have inhibited scavenging and bacterial decomposition following recent exposure of the specimen.

Data from: X-Ray computed tomography of two mammoth calf mummies

Two female woolly mammoth neonates from permafrost in the Siberian Arctic are the most complete mammoth specimens known. Lyuba, found on the Yamal Peninsula, and Khroma, from northernmost Yakutia, died at ages of approximately one and two months, respectively. Both specimens were CT-scanned, yielding detailed information on the stage of development of their dentition and skeleton and insight into conditions associated with death. Both mammoths died after aspirating mud. Khroma's body was frozen soon after death, leaving her tissues in excellent condition, whereas Lyuba's body underwent postmortem changes that resulted in authigenic formation of nodules of the mineral vivianite associated with her cranium and within diaphyses of long bones. CT data provide the only comprehensive approach to mapping vivianite distribution. Three-dimensional modeling and measurement of segmented long bones permits comparison between these individuals and with previously recovered specimens. CT scans of long bones and foot bones show developmental features such as density gradients that reveal ossification centers. The braincase of Khroma was segmented to show the approximate morphology of the brain; its volume is slightly less (∼2,300 cm3) than that of neonate elephants (∼2,500 cm3). Lyuba's premaxillae are more gracile than those of Khroma, possibly a result of temporal and/or geographic variation but probably also reflective of their age difference. Segmentation of CT data and 3-D modeling software were used to produce models of teeth that were too complex for traditional molding and casting techniques

Supplemental Data 1

Animation based on segmented or thresholded features from a full-body CT-scan of Lyuba, a woolly mammoth neonate from the Yamal Peninsula, Siberi

Steller’s sea cow genome suggests this species began going extinct before the arrival of Paleolithic humans

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Dirt, dates and DNA:OSL and radiocarbon chronologies of perenially frozen sediments in Siberia, and their implications for sedimentary ancient DNA studies

The sedimentary ancient DNA (sedaDNA) technique offers a potentially invaluable means of investigating species evolution and extinction dynamics in high-latitude environments. An implicit assumption of the sedaDNA approach is that the extracted DNA is autochthonous with the host deposit and that it has not been physically transported from older source deposits or reworked within the sedimentary profile by postdepositional mixing. In this paper we investigate whether these fundamental conditions are upheld at seven perennially frozen wetland sites across the Taimyr Peninsula and coastal lowlands of north-central Siberia. Optically stimulated luminescence (OSL) and radiocarbon (14C) dating are used to constrain the ages of both the inorganic and organic fractions of perennially frozen deposits from which sedaDNA of extinct and extant species have been recovered. OSL and 14C age/depth profiles, as well as single-grain equivalent dose (De) distribution characteristics, are used to assess the stratigraphic integrity of these sedaDNA sequences by (i) identifying the presence of primary or reworked organic and inorganic material, and (ii) examining the types of depositional and postdepositional processes that have affected specific sedimentary facies. The results of this study demonstrate that even though DNA preservation and stratigraphic integrity are commonly superior in perennially frozen settings, this does not, in itself, guarantee the suitability of the sedaDNA approach. The combined OSL and 14C chronologies reveal that certain perennially frozen sites may be poorly suited for sedaDNA analysis, and that careful site selection is paramount to ensuring the accuracy of any sedaDNA study – particularly for ‘latest appearance date’ estimates of extinct taxa