Article

Phylogeographic analysis of the mid-Holocene Mammoth from Qagnax Cave, St. Paul Island, Alaska

Authors:
If you want to read the PDF, try requesting it from the authors.

Abstract

Remains of a woolly mammoth (Mammuthus primigenius) were found in Qagnaxˆ Cave, a lava tube cave on St. Paul Island in the Pribilof Islands, 500 km west of the Alaskan mainland in the Bering Sea. Several dates converge on 5725 14C yr BP, making these the youngest mammoth remains discovered in North America, and among the few Holocene mammoths known. Genetic analysis of the cytochrome b gene and adjacent regions of the mitochondrial genome demonstrates that the Qagnaxˆ mammoth is highly derived, possessing several unique polymorphisms not found in other mammoths. However, while this is consistent with a recent insular isolation scenario, phylogenetic analysis suggests that the specimen represents a population whose isolation from other mammoths occurred at or well before the terminal Pleistocene submergence of the Bering Land Bridge. It is possible that it represents a member of a “land bridge subclade” of woolly mammoths that remained distinct from mainland Alaskan populations, but was not restricted to highland areas until the land bridge was submerged. Additional eastern Beringian, and particularly insular, mammoth DNA sequences are required to explore this possibility.

No full-text available

Request Full-text Paper PDF

To read the full-text of this research,
you can request a copy directly from the authors.

... Both as typical members of the "Coelodonta-Mammuthus Fauna" in late Pleistocene, the woolly rhinoceros and the woolly mammoth have received unequal attentions at the molecular level. The phylogenetic position of the woolly mammoth has been fully resolved by multiple sampling locations (Yang et al., 1996;Noro et al., 1998;Lister et al., 2001;Debruyne et al., 2003;Krause et al., 2006;Rogaev et al., 2006;Yang et al., 2006;Gilbert et al., 2008;Miller et al., 2008;Enk et al., 2009), whereas DNA studies on Coelodonta antiquitatis were focused only on very limited sampling sites in Europe and northern Asia (Orlando et al., 2003;Binladen et al., 2006;Willerslev et al., 2009;Lorenzen et al., 2011). Among the interested issues of the woolly rhinoceros, the close phylogenetic relationship between this species and the modern Sumatran rhinoceros was accepted by previous ancient DNA studies (Orlando et al., 2003;Willerslev et al., 2009). ...
Article
Full-text available
Ancient DNA data have supported a sister relationship between woolly rhinoceros and extant Sumatran rhinoceros. This relationship has been used to explore the divergent times for the woolly rhinoceros from their relatives. Complete and partial ancient DNA sequences of the mitochondrial cytochrome b (cyt b) gene were retrieved from bones of the late Pleistocene Coelodonta antiquitatis excavated from northern and northeastern China. The newly obtained sequences together with the European and northern Asian Coelodonta antiquitatis sequences from GenBank were used to estimate the evolutionary divergence time. Phylogenetic analyses showed the exchange of genetic information between the Chinese individuals and Coelodonta antiquitatis of north Asia, which also indicated a more recent evolutionary timescale (3.8–4.7 Ma) than previous molecular estimations (17.5–22.8 or 21–26 Ma) for woolly rhinoceros based on the fossil calibration of outgroups. This new timescale was more consistent with the fossil record of the earliest known genus Coelodonta.
... Both as typical members of the "Coelodonta-Mammuthus Fauna" in late Pleistocene, the woolly rhinoceros and the woolly mammoth have received unequal attentions at the molecular level. The phylogenetic position of the woolly mammoth has been fully resolved by multiple sampling locations (Yang et al., 1996;Noro et al., 1998;Lister et al., 2001;Debruyne et al., 2003;Krause et al., 2006;Rogaev et al., 2006;Yang et al., 2006;Gilbert et al., 2008;Miller et al., 2008;Enk et al., 2009), whereas DNA studies on Coelodonta antiquitatis were focused only on very limited sampling sites in Europe and northern Asia (Orlando et al., 2003;Binladen et al., 2006;Willerslev et al., 2009;Lorenzen et al., 2011). Among the interested issues of the woolly rhinoceros, the close phylogenetic relationship between this species and the modern Sumatran rhinoceros was accepted by previous ancient DNA studies (Orlando et al., 2003;Willerslev et al., 2009). ...
Article
Full-text available
Ancient DNA data have supported a sister relationship between woolly rhinoceros and extant Sumatran rhinoceros. This relationship has been used to explore the divergent times for the woolly rhinoceros from their relatives. Complete and partial ancient DNA sequences of the mitochondrial cytochrome b (cyt b) gene were retrieved from bones of the late Pleistocene Coelodonta antiquitatis excavated from northern and northeastern China. The newly obtained sequences together with the European and northern Asian Coelodonta antiquitatis sequences from GenBank were used to estimate the evolutionary divergence time. Phylogenetic analyses showed the exchange of genetic information between the Chinese individuals and Coelodonta antiquitatis of north Asia, which also indicated a more recent evolutionary timescale (3.8–4.7 Ma) than previous molecular estimations (17.5–22.8 or 21–26 Ma) for woolly rhinoceros based on the fossil calibration of outgroups. This new timescale was more consistent with the fossil record of the earliest known genus Coelodonta.
... Our ancient mtDNA sequences were aligned with homologous woolly mammoth sequences available on GenBank [6,10–13,22–25] (see the electronic supplementary material, table S2 for accession numbers) in Geneious v. 5.0.1 [26]. We used Partition Finder [27] to select the best-fit partitioning scheme and DNA substitution model (see electronic supplementary material, table S3). ...
Article
Full-text available
Ancient DNA analyses have provided enhanced resolution of population histories in many Pleistocene taxa. However, most studies are spatially restricted, making inference of species-level biogeographic histories difficult. Here, we analyse mitochondrial DNA (mtDNA) variation in the woolly mammoth from across its Holarctic range to reconstruct its history over the last 200 thousand years (kyr). We identify a previously undocumented major mtDNA lineage in Europe, which was replaced by another major mtDNA lineage 32-34 kyr before present (BP). Coalescent simulations provide support for demographic expansions at approximately 121 kyr BP, suggesting that the previous interglacial was an important driver for demography and intraspecific genetic divergence. Furthermore, our results suggest an expansion into Eurasia from America around 66 kyr BP, coinciding with the first exposure of the Bering Land Bridge during the Late Pleistocene. Bayesian inference indicates Late Pleistocene demographic stability until 20-15 kyr BP, when a severe population size decline occurred.
... Thus, the giant deer (Megaloceros giganteus ) should perhaps be removed from the list of Pleistocene extinctions as it has been shown that they survived in the Urals up to 7,700 years B.P. [22]. Likewise, the mammoth survived on Wrangel Island until about 4,000 years B.P. [20] and on St. Paul Island in the Northern Pacific until 6,000 years B.P. [21,69]. Thus, Wrangel Island did not represent a unique situation, and more Holocene refugia for the mammoth, and possibly other taxa, may await discovery. ...
... Given the above data, the QagnaxˆCaveQagnaxˆQagnaxˆCave mammoth and polar bear remains contribute important new data for understanding Holocene paleoclimatic and paleoenvironmental change in Beringia , as well as the question of Quaternary megafaunal extinctions . In addition, studies of well-preserved mtDNA from the mammoth remains (Enk et al., 2008; Yesner et al., 2008) is allowing assessment of the evolutionary biogeography of the Pribilof mammoths (Noro et al., 1998; Krause et al.. 2006; Rogaev et al., 2006; Barnes et al., 2007). Similar studies are planned for the polar bear remains, to contribute insights into ursid taxonomy and evolution (see Zhang and Ryder 1994; Heaton et al., 1996; Talbot and Shields, 1996). ...
Article
Qagnaxˆ Cave, a lava tube cave on St. Paul Island in the Pribilofs, has recently produced a mid-Holocene vertebrate faunal assemblage including woolly mammoth, polar bear, caribou, and Arctic fox. Several dates on the mammoth remains converge on 5700 14C yr BP. These dates, ~ 2300 yr younger than mammoth dates previously published from the Pribilof Islands, make these the youngest remains of proboscideans, and of non-extinct Quaternary megafauna, recovered from North America. Persistence of mammoths on the Pribilofs is most parsimoniously explained by the isolation of the Pribilofs and the lack of human presence in pre-Russian contact times, but an additional factor may have been the local existence of high-quality forage in the form of grasses enriched by nutrients derived from local Holocene tephras. This interpretation is reinforced by stable carbon and nitrogen isotope values obtained from the mammoth remains. The endpoint of mammoth survival in the Pribilofs is unknown, but maybe coterminous with the arrival of polar bears whose remains in the cave date to the Neoglacial cold period of ~ 4500 to 3500 14C yr BP. The polar bear record corroborates a widespread cooling of the Bering Sea region at that time.
... Continental populations of both species went extinct during the Pleistocene-Holocene transition some 10,000 years ago. Recent paleontological reconsiderations678 and mitochondrial DNA (mtDNA) phylogeographic studies of predominantly Beringian mammoths910111213 reveal a complex evolutionary history (Figure 1a ). Their populations harbored diverse genetic lineages, two of which, haplogroups A and C, were endemic to Eurasia and North America, respectively. ...
Article
Full-text available
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. 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. 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.
... Thus, the giant deer (Megaloceros giganteus ) should perhaps be removed from the list of Pleistocene extinctions as it has been shown that they survived in the Urals up to 7,700 years B.P. [22]. Likewise, the mammoth survived on Wrangel Island until about 4,000 years B.P. [20] and on St. Paul Island in the Northern Pacific until 6,000 years B.P. [21,69]. Thus, Wrangel Island did not represent a unique situation, and more Holocene refugia for the mammoth, and possibly other taxa, may await discovery. ...
Article
Apart from the current human-induced climate change, the Holocene is notable for its stable climate. In contrast, the preceding age, the Pleistocene, was a time of intensive climatic fluctuations, with temperature changes of up to 15 degrees C occurring within a few decades. These climatic changes have substantially influenced both animal and plant populations. Until recently, the prevailing opinion about the effect of these climatic fluctuations on species in Europe was that populations survived glacial maxima in southern refugia and that populations died out outside these refugia. However, some of the latest studies of modern population genetics, the fossil record and especially ancient DNA reveal a more complex picture. There is now strong evidence for additional local northern refugia for a large number of species, including both plants and animals. Furthermore, population genetic analyses using ancient DNA have shown that genetic diversity and its geographical structure changed more often and in more unpredictable ways during the Pleistocene than had been inferred. Taken together, the Pleistocene is now seen as an extremely dynamic era, with rapid and large climatic fluctuations and correspondingly variable ecology. These changes were accompanied by similarly fast and sometimes dramatic changes in population size and extensive gene flow mediated by population movements. Thus, the Pleistocene is an excellent model case for the effects of rapid climate change, as we experience at the moment, on the ecology of plants and animals.
Book
Full-text available
Britain's lynx are missing, and they have been for more than a thousand years. Why have they gone? And might they come back? A mere 15,000 years ago, Britain was a very different place – home to lions, lynx, bears, wolves, bison and many more megafauna. But as the climate changed and human populations expanded, changing habitats and wiping out wildlife, most of the British megafauna disappeared. Will we ever be able to bring these mammals back? And if it's possible, should we? In The Missing Lynx, palaeontologist Ross Barnett uses case studies, new fossil discoveries, biomolecular evidence and more to paint a picture of these lost species, and to explore the significance of their disappearance in ecological terms. He also discusses how the Britons these animals shared their lives with might have viewed them, and questions why some survived while others vanished. Barnett also looks in detail at the realistic potential of reintroductions, rewilding and even of resurrection, both in Britain and overseas, from the innovative Oostvaardersplassen nature reserve to the revolutionary Pleistocene Park in Siberia, which has already seen progress in the revival of 'mammoth steppe' grassland. With the world going through a 'sixth extinction' caused by widespread habitat destruction, climate change and an ever-growing human population, this timely book explores the spaces that extinction has left unfilled, in Britain and elsewhere. By understanding why some of our most charismatic animals are gone, we can look to a brighter future, perhaps with some of these missing beasts returned to the land on which they once lived and died.
Article
Full-text available
Over a span of 50 years, native Californian Donald Lee Johnson made a number of memorable contributions to our understanding of the California Channel Islands. Among these are (1) recognizing that carbonate dunes, often cemented into eolianite and derived from offshore shelf sediments during lowered sea level, are markers of glacial periods on the Channel Islands; (2) identifying beach rock on the Channel Islands as the northernmost occurrence of this feature on the Pacific Coast of North America; (3) recognizing of the role of human activities in historic landscape modification; (4) identifying both the biogenic and pedogenic origins of caliche “ghost forests” and laminar calcrete forms on the Channel Islands; (5) providing the first soil maps of several of the islands, showing diverse pathways of pedogenesis; (6) pointing out the importance of fire in Quaternary landscape history on the Channel Islands, based on detailed stratigraphic studies; and (7), perhaps his greatest contribution, clarifying the origin of Pleistocene pygmy mammoths on the Channel Islands, due not to imagined ancient land bridges, but rather the superb swimming abilities of proboscideans combined with lowered sea level, favorable paleowinds, and an attractive paleovegetation on the Channel Islands. Don was a classic natural historian in the great tradition of Charles Darwin and George Gaylord Simpson, his role models. Don’s work will remain important and useful for many years and is an inspiration to those researching the California Channel Islands today.
Article
Partial DNA sequences of cytochrome b gene (mtDNA) were successfully retrieved from I-ate Pleistocene fossil bone of Mammuthus primigenius collected from the Xiguitu County (Yakeshi), Inner Mongolia Autonomous Region and from Zhaodong, Harbin of Heilongjiang Province in northern China. Two ancient DNA fragments (109 bp and 124 bp) were authenticated by reproducible experiments in two different laboratories and by phylogenctic analysis with other Elephantidae taxa. Phylogenetic analysis using these sequences and published data in either separate or combined datasets indicate unstable relationship among the woolly mammoth and the two living elephants, Elephas and Loxodonta. In addition to the short sequences used to attempt the long independent evolution of Elephantidae terminal taxa, we suggest that a high intra-specific diversity existed in Mammuthus primigenius crossing both spatial and temporal ranges, resulting in a complex and divergent genetic background for DNA sequences so far recovered. The high genetic diversity in the extinct woolly mammoth can explain the apparent instability of Elephantidae taxa on the molecular phylogenctic trees and can reconcile the apparent paradox regarding the unresolved Elephantidae trichotomy.
Article
Full-text available
During the Last Cold Stage, woolly mammoths ranged very widely across Northern Eurasia into North America, but then disappeared as part of the global phenomenon of Late Quaternary megafaunal extinction. The timing and causes of this highly significant event have generated conflicting opinions and much debate. However, the overriding need is for more data, and recent years have seen the accumulation of significant new finds and radiocarbon dating evidence. In particular, research is currently focussing on the geographical pattern of extirpation leading to final extinction, rather than seeking a single ‘last appearance datum’. This Viewpoint article was commissioned by the Editor-in-Chief and is published following the paper by Lõugas et al. (Dating the extinction of European mammoths: new evidence from Estonia. Quat. Sci. Rev. 21 (2002) 1347) to place their finding in a wider context. We give a brief review of the youngest directly dated mammoth remains from different regions of Eurasia, based both on published sources and on our own current research. This includes a very important new record from Cherepovets, North Russian Plain, which together with the new date from Puurmani, Estonia indicates the persistence of mammoth in this region close to the Pleistocene–Holocene boundary. These and other records suggest that the previous picture of mammoths widespread before 12,000 ka BP (uncalibrated radiocarbon years ago), then restricted to limited areas of northern Siberia, although correct in outline, has important exceptions which modify our understanding of mammoth extinction.Despite the many available radiocarbon dates for Eurasian mammoth relative to other extinct megafauna, it is apparent that much more work is needed. Only then can we adequately tackle the important question of the cause or causes of extinction, whether by climatic/environmental change or ‘overkill’ by human hunters.
Article
Full-text available
The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. Availability: MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html. Contact: johnh{at}brahms.biology.rochester.edu
Article
Full-text available
Here we report DNA sequences from mitochondrial cytochrome b gene segments (1,005 base pairs per species) for the extinct woolly mammoth (Mammuthus primigenius) and Steller's sea cow (Hydrodamalis gigas) and the extant Asian elephant (Elephas maximus), the Western Indian manatee (Trichechus manatus), and the hyrax (Procavia capensis). These molecular data have allowed us to construct the phylogeny for the Tethytheria. Our molecular data resolve the trichotomy between the two species of living elephants and the mammoth and confirm that the mammoth was more closely related to the Asian elephant than to the African elephant. Our data also suggest that the sea cow-dugong divergence was likely as ancient as the dugong-manatee split, and it appears to have been much earlier (22 million years ago) than had been previously estimated (4-8 million years ago) by immunological comparison.
Article
Full-text available
We report the retrieval and characterization of multi- and single-copy nuclear DNA sequences from Alaskan and Siberian mammoths (Mammuthus primigenius). In addition, a nuclear copy of a mitochondrial gene was recovered. Furthermore, a 13,000-year-old ground sloth and a 33,000-year-old cave bear yielded multicopy nuclear DNA sequences. Thus, multicopy and single-copy genes can be analyzed from Pleistocene faunal remains. The results also show that under some circumstances, nucleotide sequence differences between alleles found within one individual can be distinguished from DNA sequence variation caused by postmortem DNA damage. The nuclear sequences retrieved from the mammoths suggest that mammoths were more similar to Asian elephants than to African elephants.
Article
Full-text available
Endogenous retrovirus-like elements characterizable by a leucine tRNA primer (ERV-Ls) are reiterated genomic sequences known to be widespread in mammals, including humans. They may have arisen from an ancestral foamy virus-like element by successful germ line infection followed by copy number expansion. However, among mammals, only primates and rodents have thus far exhibited high copy number amplification and sequence diversification. Conventionally, empirical studies of proviral amplification and diversification have been limited to extant species, but taxa having good Quaternary fossil records could potentially be investigated using the techniques of "ancient" DNA research. To examine evolutionary parameters of ERV-Ls across both time and taxa, we characterized this proviral class in the extinct woolly mammoth (Mammuthus primigenius) and living elephants, as well as extant members of the larger clade to which they belong (Uranotheria, a group containing proboscideans, sirenians, hyraxes, and their extinct relatives). Ungulates and carnivores previously analyzed demonstrated low copy numbers of ERV-L sequences, and thus it was expected that uranotheres should as well. Here, we show that all uranothere taxa exhibit unexpectedly numerous and diverse ERV-L sequence complements, indicating active expansion within this group of lineages. Selection is the most parsimonious explanation for observed differences in ERV-L distribution and frequency, with relative success being reflected in the persistence of certain elements over a variety of sampled time depths (as can be observed by comparing sequences from fossil and extant elephantid samples).
Article
Full-text available
In studying the genomes of extinct species, two principal limitations are typically the small quantities of endogenous ancient DNA and its degraded condition, even though products of up to 1,600 base pairs (bp) have been amplified in rare cases. Using small overlapping polymerase chain reaction products, longer stretches of sequences or even whole mitochondrial genomes can be reconstructed, but this approach is limited by the number of amplifications that can be performed from rare samples. Thus, even from well-studied Pleistocene species such as mammoths, ground sloths and cave bears, no DNA sequences of more than about 1,000 bp have been reconstructed. Here we report the complete mitochondrial genome sequence of the Pleistocene woolly mammoth Mammuthus primigenius. We used about 200 mg of bone and a new approach that allows the simultaneous retrieval of multiple sequences from small amounts of degraded DNA. Our phylogenetic analyses show that the mammoth was more closely related to the Asian than to the African elephant. However, the divergence of mammoth, African and Asian elephants occurred over a short time, corresponding to only about 7% of the total length of the phylogenetic tree for the three evolutionary lineages.
Article
Full-text available
Phylogenetic relationships between the extinct woolly mammoth (Mammuthus primigenius), and the Asian (Elephas maximus) and African savanna (Loxodonta africana) elephants remain unresolved. Here, we report the sequence of the complete mitochondrial genome (16,842 base pairs) of a woolly mammoth extracted from permafrost-preserved remains from the Pleistocene epoch--the oldest mitochondrial genome sequence determined to date. We demonstrate that well-preserved mitochondrial genome fragments, as long as approximately 1,600-1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests that M. primigenius and E. maximus are sister species that diverged soon after their common ancestor split from the L. africana lineage. Low nucleotide diversity found between independently determined mitochondrial genomic sequences of woolly mammoths separated geographically and in time suggests that north-eastern Siberia was occupied by a relatively homogeneous population of M. primigenius throughout the late Pleistocene.
Article
Full-text available
In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fortunately, intermediate models employing relaxed molecular clocks have been described. These models open the gate to a new field of "relaxed phylogenetics." Here we introduce a new approach to performing relaxed phylogenetic analysis. We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times. Our approach also provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies. We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data. In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme. Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments. From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution.
Article
Full-text available
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.
Article
Full-text available
It has recently been observed by Ho et al. (Ho SYW, Phillips MJ, Cooper A, Drummond AJ. 2005. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol. 22(7):1561–1568) that apparent rates of molecular evolution increase when measured over short timespans. I investigate whether the data are explainable purely by deleterious mutations. I derive an empirical approximation for the persistence of these mutations in a randomly mating population and, hence, derive lower limits on effective population sizes. These limits are high and get higher if additional reasonable assumptions are made. This casts doubt on whether deleterious mutations are able to explain the apparent rate acceleration.
Article
Full-text available
Author Summary We determined the complete mitochondrial genome of the mastodon (Mammut americanum), a recently extinct relative of the living elephants that diverged about 26 million years ago. We obtained the sequence from a tooth dated to 50,000–130,000 years ago, increasing the specimen age for which such palaeogenomic analyses have been done by almost a complete glacial cycle. Using this sequence, together with mitochondrial genome sequences from two African elephants, two Asian elephants, and two woolly mammoths (all of which have been previously sequenced), we show that mammoths are more closely related to Asian than to African elephants. Moreover, we used a calibration point lying outside the Elephantidae radiation (elephants and mammoths), which enabled us to estimate accurately the time of divergence of African elephants from Asian elephants and mammoths (about 7.6 million years ago) and the time of divergence between mammoths and Asian elephants (about 6.7 million years ago). These dates are strikingly similar to the divergence time for humans, chimpanzees, and gorillas, and raise the possibility that the speciation of mammoth and elephants and of humans and African great apes had a common cause. Despite the similarity in divergence times, the substitution rate within primates is more than twice as high as in proboscideans.
Article
Full-text available
Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up to 48-fold coverage. The observed levels of damage-derived sequencing errors were lower than those observed in previously published frozen bone samples, even though one of the specimens was >50,000 14C years old and another had been stored for 200 years at room temperature. The method therefore sets the stage for molecular-genetic analysis of museum collections.
Article
Full-text available
We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth (Mammuthus primigenius), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material. Three of the sequences present the first complete mtDNA genomes of mammoth clade II. Analysis of these and 13 recently published mtDNA genomes demonstrates the existence of two apparently sympatric mtDNA clades that exhibit high interclade divergence. The analytical power afforded by the analysis of the complete mtDNA genomes reveals a surprisingly ancient coalescence age of the two clades, ≈1–2 million years, depending on the calibration technique. Furthermore, statistical analysis of the temporal distribution of the ¹⁴C ages of these and previously identified members of the two mammoth clades suggests that clade II went extinct before clade I. Modeling of protein structures failed to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep. • mtDNA genome • phylogeny • ancient DNA • next-generation sequencing
Article
Shortly after Russian fur hunters found the uninhabited Pribilof Islands of St. Paul and St. George in the late 1780s, they began forcing Aleut men from the Aleutian Islands and Alaska Peninsula to travel there seasonally to provide labor for the profitable commercial harvest of northern fur seals. Recent archaeological surveys of the earliest Aleut and Russian work camps that were established on the islands show them to be unusual in many respects when compared to contemporary sites in the Aleutian Islands region. These include the absence of precontact site components, their relatively narrow period of occupation, their occupancy by an exclusively or nearly exclusively male population, and their potential as multiethnic settlements to reveal differences between the lives of Russian overseers and Aleut laborers.
Article
Examines the ecology and behaviour of modern elephants to create models for reconstructing the lives and deaths of extinct mammoths and mastodonts. The sources for these models are long-term studies of elephants Loxodonta africana in Zimbabwe, which are described with respect to the implications of anatomical, behavioural and ecological similarities between past and present proboscideans. The first section deals with the classification of fossil and living forms; the physical appearance of mammoths, mastodonts and modern elephants; and a model for understanding mammoths and mastodonts from the social structure and habitat use by modern elephants. The second section has two chapters on actualistic studies of mass deaths and mass kills, and the final section looks at the meaning of sites from the world fossil record, and at the extinctions in North America at the end of the Pleistocene. A lengthy appendix details methods for age determination, and is followed by an extensive reference list and index. -J.W.Cooper
Article
Museum specimens of polar bear from the Pribilof Islands include the skull of an individual shot on St. Paul, and fragmentary remains of uncertain geologic age from a lava cave in Bogoslof Hill, St. Paul, once thought to represent a distinct species. Mammoth remains have been discovered from time to time beginning in 1836, and are here regarded as in part valid evidence that the mam- moth actually lived in the area. The literature pertaining to these species on the Pribilof Islands is reviewed. RÉSUMÉ. L'ours polaire et le mammouth dans les Pribilof. (Au musée Smithso- nian) Les spécimens d'ours polaire des îles de Pribilof comprennent le crâne d'un individu abattu sur l'île Saint-Paul, et des restes fragmentaires, d'âge géologique incertain, provenant d'une caverne dans les laves du mont Bogoslof, sur Saint-Paul, et qu'on a déjà cru représenter une espèce distincte. On a découvert de temps à autre, depuis 1836, des restes de mammouth, et l'auteur les considère comme une preuve partielle valide que le mammouth a vraiment vécu dans la région. On passe en revue les réfhences pertinentes à ces deux espèces pour les Pribilof.
Article
Allen McCartney's career of northern field research began in 1962 in the Aleut region of Alaska, an area to which he has returned many times over the next four decades. During that time, he worked throughout the region, from the Alaska Peninsula to the far western Aleutians, to the isolated Pribilof Islands, and at sites spanning the entire range of human occupation. The depth and breadth of his experience and interests have yielded important insights concerning the Aleut area, specifically, and the circumpolar region, generally. His efforts have also influenced the research goals and careers of many other northern scholars and have assisted in some unforeseen and unacknowledged ways in matters of Aleut land ownership and cultural heritage.
Article
Qagnaxˆ Cave, a lava tube cave on St. Paul Island in the Pribilofs, has recently produced a mid-Holocene vertebrate faunal assemblage including woolly mammoth, polar bear, caribou, and Arctic fox. Several dates on the mammoth remains converge on 5700 14C yr BP. These dates, ~ 2300 yr younger than mammoth dates previously published from the Pribilof Islands, make these the youngest remains of proboscideans, and of non-extinct Quaternary megafauna, recovered from North America. Persistence of mammoths on the Pribilofs is most parsimoniously explained by the isolation of the Pribilofs and the lack of human presence in pre-Russian contact times, but an additional factor may have been the local existence of high-quality forage in the form of grasses enriched by nutrients derived from local Holocene tephras. This interpretation is reinforced by stable carbon and nitrogen isotope values obtained from the mammoth remains. The endpoint of mammoth survival in the Pribilofs is unknown, but maybe coterminous with the arrival of polar bears whose remains in the cave date to the Neoglacial cold period of ~ 4500 to 3500 14C yr BP. The polar bear record corroborates a widespread cooling of the Bering Sea region at that time.
Article
A review of the literature providing radiocarbon-dated localities for mammoths provides a range of temporal and geographic distribution for the genus in North America. The review includes Alaska, Canada, the United States, and Mexico, whereas other studies have concentrated only on the United States. Maps of 5000 year intervals illustrate the range of mammoths in the continent, through time. The post-glacial interval has the highest frequency of dated localities, in part due to the interest in the potential for human association. This interval also records the greatest geographic distribution of the genus in North America.
Article
Submitted to: Dept. of Biology. Vol. 2: Plates. Thesis (Ph. D.)--Harvard University, 1971.
Article
Although the iconic mammoth of the Late Pleistocene, the woolly mammoth (Mammuthus primigenius), has traditionally been regarded as the end point of a single anagenetically evolving lineage, recent paleontological and molecular studies have shown that successive allopatric speciation events must have occurred within Pleistocene Mammuthus in Asia, with subsequent expansion and hybridization between nominal taxa [1, 2]. However, the role of North American mammoth populations in these events has not been adequately explored from an ancient-DNA standpoint. To undertake this task, we analyzed mtDNA from a large data set consisting of mammoth samples from across Holarctica (n = 160) and representing most of radiocarbon time. Our evidence shows that, during the terminal Pleistocene, haplotypes originating in and characteristic of New World populations replaced or succeeded those endemic to Asia and western Beringia. Also, during the Last Glacial Maximum, mammoth populations do not appear to have suffered an overall decline in diversity, despite differing responses on either side of the Bering land bridge. In summary, the "Out-of-America" hypothesis holds that the dispersal of North American woolly mammoths into other parts of Holarctica created major phylogeographic structuring within Mammuthus primigenius populations, shaping the last phase of their evolutionary history before their demise.
Article
DNA was extracted from the extinct American mastodon, the extinct woolly mammoth, and the modern Asian and African elephants to test the traditional morphologically based phylogeny within Elephantidae. Phylogenetic analyses of the aligned sequences of the mitochondrial gene cytochrome b support a monophyletic Asian elephant-woolly mammoth clade when the American mastodon is used as an outgroup. Previous molecular studies were unable to resolve the relationships of the woolly mammoth, Asian elephant, and African elephant because the sequences appear to have evolved at heterogeneous rates and inappropriate outgroups were used for analysis. The results demonstrate the usefulness of fossil molecular data from appropriate sister taxa for resolving phylogenies of highly derived or early radiating lineages.
Article
Complete sequences of cytochrome b (1,137 bases) and 12S ribosomal RNA (961 bases) genes in mitochondrial DNA were successfully determined from the woolly mammoth (Mammuthus primigenius), African elephant (Loxodonta africana), and Asian elephant (Elephas maximus). From these sequence data, phylogenetic relationships among three genera were examined. Molecular phylogenetic trees reconstructed by the neighbor-joining and the maximum parsimony methods provided an identical topology both for cytochrome b and 12S rRNA genes. These results support the "Mammuthus-Loxodonta" clade, which is contrary to some previous morphological reports that Mammuthus is more closely related to Elephas than to Loxodonta.
Article
The spectrum of postmortem damage in mitochondrial DNA was analyzed in a large data set of cloned sequences from ancient human specimens. The most common forms of damage observed are two complementary groups of transitions, termed "type 1" (adenine-->guanine/thymine-->cytosine) and "type 2" (cytosine-->thymine/guanine-->adenine). Single-primer extension PCR and enzymatic digestion with uracil-N-glycosylase confirm that each of these groups of transitions result from a single event, the deamination of adenine to hypoxanthine, and cytosine to uracil, respectively. The predominant form of transition-manifested damage varies by sample, though a marked bias toward type 2 is observed with increasing amounts of damage. The two transition types can be used to identify the original strand, light (L) or heavy (H), on which the initial damage event occurred, and this can increase the number of detected jumping-PCR artifacts by up to 80%. No bias toward H-strand-specific damage events is noted within the hypervariable 1 region of human mitochondria, suggesting the rapid postmortem degradation of the secondary displacement (D-loop) H strand. The data also indicate that, as damage increases within a sample, fewer H strands retain the ability to act as templates for enzymatic amplification. Last, a significant correlation between archaeological site and sample-specific level of DNA damage was detected.
Article
The distribution of postmortem damage in mitochondrial DNA retrieved from 37 ancient human DNA samples was analyzed by cloning and was compared with a selection of published animal data. A relative rate of damage (rho(v)) was calculated for nucleotide positions within the human hypervariable region 1 (HVR1) and cytochrome oxidase subunit III genes. A comparison of damaged sites within and between the regions reveals that damage hotspots exist and that, in the HVR1, these correlate with sites known to have high in vivo mutation rates. Conversely, HVR1 subregions with known structural function, such as MT5, have lower in vivo mutation rates and lower postmortem-damage rates. The postmortem data also identify a possible functional subregion of the HVR1, termed "low-diversity 1," through the lack of sequence damage. The amount of postmortem damage observed in mitochondrial coding regions was significantly lower than in the HVR1, and, although hotspots were noted, these did not correlate with codon position. Finally, a simple method for the identification of incorrect archaeological haplogroup designations is introduced, on the basis of the observed spectrum of postmortem damage.
Article
The phylogenetic relationships between recent Elephantidae (Proboscidea, Mammalia), that is to say extant elephants (Asian and African) and extinct woolly mammoth, have remained unclear to date. The prevailing morphological scheme (mammoth grouped with Asian elephant) is either supported or questioned by the molecular results. Recently, the monophyly of woolly mammoths on mitochondrial grounds has been demonstrated (Thomas, et al., 2000), but it conflicts with previous studies (Barriel et al., 1999; Derenko et al., 1997). Here, we report the partial sequencing of two mitochondrial genes: 128 bp of 12S rDNA and 561 bp of cytochrome b for the Lyakhov mammoth, a 49,000-year-old Siberian individual. We use the most comprehensive sample of mammoth (11 sequences) to determine whether the sequences achieved by former studies were congruent or not. The monophyly of a major subset of mammoths sequences (including ours) is recovered. Such a result is assumed to be a good criterion for ascertaining the origin of ancient DNA. Our sequence is incongruent with that of Yang et al. (1996), though obtained for the same individual. As far as the latter sequence is concerned, a contamination by non-identified exogenous DNA is suspected. The robustness and reliability of the sister group relation between Mammuthus primigenius and Loxodonta africana are examined: down-weighting saturated substitutions has no impact on the topology; analyzing data partitions proves that the support of this clade can be assigned to the most conservative phylogenetic signal; insufficient taxonomic and/or characters sampling contributed to former discordant conclusions. We therefore assume the monophyly of "real mammoth sequences" and the (Mammuthus, Loxodonta) clade.
Article
Island colonization and subsequent dwarfing of Pleistocene proboscideans is one of the more dramatic evolutionary and ecological occurrences, especially in situations where island populations survived end-Pleistocene extinctions whereas those on the nearby mainland did not. For example, Holocene mammoths have been dated from Wrangel Island in northern Russia. In most of these cases, few details are available about the dynamics of how island colonization and extinction occurred. As part of a large radiocarbon dating project of Alaskan mammoth fossils, I addressed this question by including mammoth specimens from Bering Sea islands known to have formed during the end-Pleistocene sea transgression. One date of 7,908 +/- 100 yr bp (radiocarbon years before present) established the presence of Holocene mammoths on St Paul Island, a first Holocene island record for the Americas. Four lines of evidence--265 accelerator mass spectrometer (AMS) radiocarbon dates from Alaskan mainland mammoths, 13 new dates from Alaskan island mammoths, recent reconstructions of bathymetric plots and sea transgression rates from the Bering Sea--made it possible to reconstruct how mammoths became stranded in the Pribilofs and why this apparently did not happen on other Alaskan Bering Sea islands.
Article
The molecular clock has proved to be extremely valuable in placing timescales on evolutionary events that would otherwise be difficult to date. However, debate has arisen about the considerable disparities between molecular and palaeontological or archaeological dates, and about the remarkably high mutation rates inferred in pedigree studies. We argue that these debates can be largely resolved by reference to the "time dependency of molecular rates", a recent hypothesis positing that short-term mutation rates and long-term substitution rates are related by a monotonic decline from the former to the latter. Accordingly, the extrapolation of rates across different timescales will result in invalid date estimates. We examine the impact of this hypothesis with respect to various fields, including human evolution, animal domestication and conservation genetics. We conclude that many studies involving recent divergence events will need to be reconsidered.
Article
The interval since circa 50 Ka has been a period of significant species extinctions among the large mammal fauna. However, the relative roles of an increasing human presence and a synchronous series of complex environmental changes in these extinctions have yet to be fully resolved. Recent analyses of fossil material from Beringia have clarified our understanding of the spatiotemporal pattern of Late Pleistocene extinctions, identifying periods of population turnover well before the last glacial maximum (LGM: circa 21 Ka) or subsequent human expansion. To examine the role of pre-LGM population changes in shaping the genetic structure of an extinct species, we analyzed the mitochondrial DNA of woolly mammoths in western Beringia and across its range. We identify genetic signatures of a range expansion of mammoths, from eastern to western Beringia, after the last interglacial (circa 125 Ka), and then an extended period during which demographic inference indicates no population-size increase. The most marked change in diversity at this time is the loss of one of two major mitochondrial lineages.
Article
An official journal of the Genetics Society, Heredity publishes high-quality articles describing original research and theoretical insights in all areas of genetics. Research papers are complimented by News & Commentary articles and reviews, keeping researchers and students abreast of hot topics in the field.
A mid-Holocene mammoth tusk from St. Paul Island
  • Grover
Grover, M.A., Tedor, R., 2006. A mid-Holocene mammoth tusk from St. Paul Island. Alaska Anthrop. Ass. Prog. Abstr. (Poster).
A Biological Survey of the Pribilof Islands, Alaska, Part I: Birds and Mammals
  • E A Preble
Preble, E.A., 1923. In: Preble, E.A., McAtee, W.L. (Eds.), A Biological Survey of the Pribilof Islands, Alaska, Part I: Birds and Mammals. N Am Fauna, vol. 46, pp. 102–120.
Postglacial Flooding of the Bering Land Bridge: a Geospatial Animation v.1. Institute for Arctic and Alpine Research
  • William F Manley
Manley, William F., 2002. Postglacial Flooding of the Bering Land Bridge: a Geospatial Animation v.1. Institute for Arctic and Alpine Research, University of Colorado, Boulder. (http://instaar.colorado.edu/QGISL/bering_land_bridge).
The Proboscidea: Evolution and Palaoecology of Elephants and their Relatives
  • A M Lister
Lister, A.M., 1996. In: Shoshani, J., Tassy, P. (Eds.), The Proboscidea: Evolution and Palaoecology of Elephants and their Relatives. Oxford University Press, Oxford, pp. 203–213.
A Pribilof Island Cave: Late Quaternary Mammal Bone Assemblages from St. Paul Island, Bering Sea700-year-old Mammoth Remains from the Pribilof Islands
  • K J Crossen
  • R W Graham
  • D W Veltre
  • D R Yesner
Crossen, K.J., Graham, R.W., Veltre, D.W., Yesner, D.R., 2003. A Pribilof Island Cave: Late Quaternary Mammal Bone Assemblages from St. Paul Island, Bering Sea, Alaska. Geol. Soc. Am. Abstr. with Prog., vol. 35, p. 424. Crossen, K.J., Veltre, D.W., Yesner, D.R., Graham, R.W., 2005. 5,700-year-old Mammoth Remains from the Pribilof Islands, Alaska: Last Outpost of North American Megafauna. Geol. Soc. Am. Abstr. with Prog., vol. 37, p. 463.
Late Pleistocene/Holocene mammal bone assemblages from a cave on St. Paul Island: implications for paleoclimatic change and human occupation of the Bering Sea region Patterns of faunal extinction and paleoclimatic change from mid -Holocene mammoth and polar bear remains, Pribilof Islands
  • D W Veltre
  • D R Yesner
  • K J Crossen
  • R W Graham
  • D W Veltre
  • D R Yesner
  • K J Crossen
  • R W Graham
  • J B Coltrain
Veltre, D.W., Yesner, D.R., Crossen, K.J., Graham, R.W., 2004. Late Pleistocene/Holocene mammal bone assemblages from a cave on St. Paul Island: implications for paleoclimatic change and human occupation of the Bering Sea region. Alaska Anthropol. Assoc. Prog. Abstr. 27, 13. Veltre, D.W., Yesner, D.R., Crossen, K.J., Graham, R.W., Coltrain, J.B., 2008. Patterns of faunal extinction and paleoclimatic change from mid -Holocene mammoth and polar bear remains, Pribilof Islands, Alaska. Quat. Res. 70, 40–50.
The World of Elephants: Short Papers and Abstracts of the 2nd International Congress
  • D R Yesner
  • D W Veltre
  • K J Crossen
  • R W Graham
Yesner, D.R., Veltre, D.W., Crossen, K.J., Graham, R.W., 2005b. In: Agenbroad, L.R., Symington, S. (Eds.), The World of Elephants: Short Papers and Abstracts of the 2nd International Congress. Mammoth Site Scientific Papers, vol. 4, pp. 200–204.
The latest woolly mammoths (Mammuthus primigenius Blumenbach) in Europe and Asia: a review of the current evidence
  • Stuart
Geology of the Pribilof Islands
  • Stanley-Brown
Mid - Holocene mammoth remains from Qagnax' Cave, Pribilof Islands, Alaska: implications for megafaunal extinction and peopling of the Americas
  • Yesner
Late Pleistocene/Holocene mammal bone assemblages from a cave on St. Paul Island: implications for paleoclimatic change and human occupation of the Bering Sea region
  • Veltre