Temporal genetic change in the last remaining population of woolly mammoth

During the Late Pleistocene, the woolly mammoth (Mammuthus primigenius) experienced a series of local extinctions generally attributed to human predation or environmental change. Some small and isolated populations did however survive far into the Holocene. Here, we investigated the genetic consequences of the isolation of the last remaining mammoth population on Wrangel Island. We analysed 741 bp of the mitochondrial DNA and found a loss of genetic variation in relation to the isolation event, probably caused by a demographic bottleneck or a founder event. However, in spite of ca 5000 years of isolation, we did not detect any further loss of genetic variation. Together with the relatively high number of mitochondrial haplotypes on Wrangel Island near the final disappearance, this suggests a sudden extinction of a rather stable population.     

Climate change, humans, and the extinction of the woolly mammoth

Woolly mammoths inhabited Eurasia and North America from late Middle Pleistocene (300 ky BP [300,000 years before present]), surviving through different climatic cycles until they vanished in the Holocene (3.6 ky BP). The debate about why the Late Quaternary extinctions occurred has centred upon environmental and human-induced effects, or a combination of both. However, testing these two hypotheses—climatic and anthropogenic—has been hampered by the difficulty of generating quantitative estimates of the relationship between the contraction of the mammoth's geographical range and each of the two hypotheses. We combined climate envelope models and a population model with explicit treatment of woolly mammoth–human interactions to measure the extent to which a combination of climate changes and increased human pressures might have led to the extinction of the species in Eurasia. Climate conditions for woolly mammoths were measured across different time periods: 126 ky BP, 42 ky BP, 30 ky BP, 21 ky BP, and 6 ky BP. We show that suitable climate conditions for the mammoth reduced drastically between the Late Pleistocene and the Holocene, and 90% of its geographical range disappeared between 42 ky BP and 6 ky BP, with the remaining suitable areas in the mid-Holocene being mainly restricted to Arctic Siberia, which is where the latest records of woolly mammoths in continental Asia have been found. Results of the population models also show that the collapse of the climatic niche of the mammoth caused a significant drop in their population size, making woolly mammoths more vulnerable to the increasing hunting pressure from human populations. The coincidence of the disappearance of climatically suitable areas for woolly mammoths and the increase in anthropogenic impacts in the Holocene, the coup de grâce, likely set the place and time for the extinction of the woolly mammoth.     

Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths

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.     

Complete Mitochondrial Genome and Phylogeny of Pleistocene Mammoth Mammuthus primigenius

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 ~1,600–1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests thatM. primigenius andE. maximus are sister species that diverged soon after their common ancestor split from theL. 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 ofM. primigenius throughout the late Pleistocene.     

Complete Mitochondrial Genome and Phylogeny of Pleistocene MammothMammuthus primigenius

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 ~1,600–1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests thatM. primigenius andE. maximus are sister species that diverged soon after their common ancestor split from theL. 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 ofM. primigenius throughout the late Pleistocene.     

Complete Mitochondrial Genome and Phylogeny of Pleistocene MammothMammuthus primigenius

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 ~1,600–1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests thatM. primigenius andE. maximus are sister species that diverged soon after their common ancestor split from theL. 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 ofM. primigenius throughout the late Pleistocene.     

A case for resurrecting lost species—review essay of Beth Shapiro’s, “How to Clone a Mammoth: The Science of De-extinction”

The title of Beth Shapiro’s ‘How to Clone a Mammoth’ contains an implicature: it suggests that it is indeed possible to clone a mammoth, to bring extinct species back from the dead. But in fact Shapiro both denies this is possible, and denies there would be good reason to do it even if it were possible. The de-extinct ‘mammoths’ she speaks of are merely ecological proxies for mammoths—elephants re-engineered for cold-tolerance by the addition to their genomes of a few mammoth genes. Shapiro’s denial that genuine species de-extinction is possible is based on her assumption that resurrected organisms would need to be perfectly indistinguishable from the creatures that died out. In this article I use the example of an extinct New Zealand wattlebird, the huia, to argue—contra Shapiro—that there are compelling reasons to resurrect certain species if it can be done. I then argue—again, contra Shapiro—that synthetically created organisms needn’t be perfectly indistinguishable from their genetic forebears in order for species de-extinction to be successful.     

Revision of Late Pleistocene and Holocene Galliformes Fauna from the Crimean Mountains

The Late Pleistocene and Holocene Galliformes faunas from the Crimean Mountains included seven species of birds belonging to the families Phasianidae and Tetraonidae: Phasianus colchicus, Alectoris chukar, Perdix perdix, Coturnix coturnix, Lyrurus tetrix, Lagopus mutus, and Lagopus lagopus. The habitation of Gallus representatives in the Crimea in the Late Pleistocene has not been confirmed. Representatives of the family Phasianidae were present in the Crimean fauna at least for most of the Late Pleistocene. All of them survived until the Late Holocene. Pheasants became extinct around the eighteenth century, and the rock partridge seems to have disappeared only in the first half of the twentieth century. The species were restored in the Crimea in the second half of the twentieth century. Gray partridges were common resident birds of the Crimean Mountains throughout the Late Pleistocene and Holocene. Quail was not a numerous breeding species of the Crimean Mountains at the same time, but mass migration of this species through the Crimea appeared only at the end of the Late Pleistocene and evolved over the Holocene warming. Species of Tetraonidae appeared in the fauna of the Crimea long before the beginning of the cold-phase maximum of the last glaciations but no later than 28000 years ago and became extinct in the Early Holocene warming but no later than 9000 years ago.     

Mammals in Last 30 to 7 ka Interval (Late Pleistocene-Early Holocene) in Southern Uruguay (Santa Lucía River Basin): Last Occurrences,Climate, and Biogeography

Fossiliferous Quaternary sedimentary beds in the Santa Lucía Basin (southern Uruguay) are potentially useful for the study of the last occurrences of extinct taxa, as well as the environmental and climatic patterns in the late Pleistocene to the early Holocene. They have provided a chronological framework (AMS ¹⁴C and Optically Stimulated Luminescence dates), a mammalian diversity and interpretations of last occurrence, the climatic-environmental setting, and some associated biogeographic processes. The ages produced encompass the last 30 to 7 ka interval (latest Pleistocene-early Holocene). The mammalian assemblage (36 genera, 24 species) includes typical South American late Pleistocene mammals, extinct species of extant genera, and some extant species that still exist elsewhere on the continent. The preservation pattern includes articulated and semi-articulated skeletons of large and small mammals. The presence in the southern Uruguayan Pampean area of some mammals currently inhabiting Patagonia, northwest and central Argentina (Dolichotis, Galea, Microcavia, Chaetophractus, Lagostomus, and Vicugna) is explained by the predominance of open areas and cold climates associated with the Last Glacial Maximum. The mammalian record depicts local extinctions or shifting ranges occurring in latest Pleistocene or early Holocene. The sedimentary chronological framework and taphonomic features suggest the persistence into the early Holocene of Eutatus seguini, Morenelaphus brachyceros, Equus neogeus, Hemiauchenia sp., Lama sp., and Vicugna sp. Glyptodon and Glossotherium seem to persist at least to the latest Pleistocene. This pattern can substantiate the hypothesis that some megafauna and large mammals persisted for some millennia alongside people with extinction occurring before, during, and after human colonization.     

Process-explicit models reveal pathway to extinction for woolly mammoth using pattern-oriented validation

Pathways to extinction start long before the death of the last individual. However, causes of early stage population declines and the susceptibility of small residual populations to extirpation are typically studied in isolation. Using validated process-explicit models, we disentangle the ecological mechanisms and threats that were integral in the initial decline and later extinction of the woolly mammoth. We show that reconciling ancient DNA data on woolly mammoth population decline with fossil evidence of location and timing of extinction requires process-explicit models with specific demographic and niche constraints, and a constrained synergy of climatic change and human impacts. Validated models needed humans to hasten climate-driven population declines by many millennia, and to allow woolly mammoths to persist in mainland Arctic refugia until the mid-Holocene. Our results show that the role of humans in the extinction dynamics of woolly mammoth began well before the Holocene, exerting lasting effects on the spatial pattern and timing of its range-wide extinction.     

Successful genotyping of microsatellites in the woolly mammoth

Genetic analyses using ancient DNA from Pleistocene and early Holocene fossils have largely relied on mitochondrial DNA (mtDNA) sequences. Among woolly mammoths, Mammuthus primigenius, mtDNA analyses have identified 2 distinct clades (I and II) that diverged 1-2 Ma. Here, we establish that microsatellite markers can be effective on Pleistocene samples, successfully genotyping woolly mammoth specimens at 2 loci. Although significant differentiation at the 2 microsatellite loci was not detected between 16 clade I and 4 clade II woolly mammoths, our results demonstrate that the nuclear population structure of Pleistocene species can be examined using fast-evolving nuclear microsatellite markers.     

The relative role of relatives in conspecific brood parasitism

Conspecific brood parasites lay their eggs in the nests of other females in the same population, leading to a fascinating array of possible ‘games’ among parasites and their hosts ( Davies 2000 ; Lyon & Eadie 2008 ). Almost 30 years ago, Andersson & Eriksson (1982) first suggested that perhaps this form of parasitism was not what it seemed—indeed, perhaps it was not parasitism at all! Andersson & Eriksson (1982) observed that conspecific brood parasitism (CBP) was disproportionally common in waterfowl (Anatidae), a group of birds for which natal philopatry is female‐biased rather than the more usual avian pattern of male‐biased natal philopatry. Accordingly, Andersson (1984) reasoned (and demonstrated in an elegantly simple model) that relatedness among females might facilitate the evolution of CBP—prodding us to reconsider it as a kin‐selected and possibly cooperative breeding system rather than a parasitic interaction. The idea was much cited but rarely tested empirically until recently—a number of new studies, empowered with a battery of molecular techniques, have now put Andersson’s hypothesis to the test ( Table 1 ). The results are tantalizing, but also somewhat conflicting. Several studies, focusing on waterfowl, have found clear evidence that hosts and parasites are often related ( Andersson & Åhlund 2000 ; Roy Nielsen et al. 2006 ; Andersson & Waldeck 2007 ; Waldeck et al. 2008 ; Jaatinen et al. 2009 ; Tiedemann et al. 2011 ). However, this is not always the case ( Semel & Sherman 2001 ; Anderholm et al. 2009 ; and see Pöysa 2004 ). In a new study reported in this issue of Molecular Ecology, Jaatinen et al. (2011a) provide yet another twist to this story that might explain not only why such variable results have been obtained, but also suggests that the games between parasites and their hosts—and the role of kinship in these games—may be even more complex than Andersson (1984) imagined. Indeed, the role of kinship in CBP may be very much one of relative degree!

Table 1. A summary of recent studies that have tested for evidence of relatedness between hosts and parasites in avian conspecific brood parasites

SHORT COMMUNICATION: A phantom extinction? New insights into extinction dynamics of the Don‐hare Lepus tanaiticus

The Pleistocene to Holocene transition was accompanied by a worldwide extinction event affecting numerous mammalian species. Several species such as the woolly mammoth and the giant deer survived this extinction wave, only to go extinct a few thousand years later during the Holocene. Another example for such a Holocene extinction is the Don‐hare, Lepus tanaiticus, which inhabited the Russian plains during the late glacial. After being slowly replaced by the extant mountain hare (Lepus timidus), it eventually went extinct during the middle Holocene. Here, we report the phylogenetic relationship of L. tanaiticus and L. timidus based on a 339‐basepair (bp) fragment of the mitochondrial D‐loop. Phylogenetic tree‐ and network reconstructions do not support L. tanaiticus and L. timidus being different species. Rather, we suggest that the two taxa represent different morphotypes of a single species and the extinction of ‘L. tanaiticus’ represents the disappearance of a local morphotype rather than the extinction of a species.     

North Atlantic marine communities through time

How and why ecological communities change their species membership over time and space is a central issue in ecology and evolution. Phylogeographic approaches based on animal mitochondrial DNA sequences have been important for revealing historical patterns of individual species and can provide qualitative comparisons among species. Exciting new methods, particularly implementing approximate Bayesian computation (ABC – Beaumont et al. 2002 ), now allow model‐based quantitative comparisons among species and permit the probabilistic exploration of alternative community‐level hypotheses (see review by Hickerson et al. 2010 ). In this issue of Molecular Ecology, Ilves et al. (2010) use an ABC approach to bring fresh insights into the well‐studied question of how North Atlantic coastal species contracted and expanded their ranges in response to late Pleistocene/Holocene climate fluctuations.     

Meet the new mammoth,same as the old? Resurrecting the <Emphasis Type="Italic">Mammuthus primigenius</Emphasis>

Media reporters often announce that we are on the verge of bringing back the woolly mammoth, even while there is growing consensus among scientists that resurrecting the mammoth is unlikely. In fact, current “de-extinction” efforts are not designed to bring back a mammoth, but rather adaptations of the mammoth using close relatives. For example, Harvard scientists are working on creating an Asian elephant with the thick coat of a mammoth by merging mammoth and elephant DNA. But how should such creatures be classified? Are they elephants, mammoths, or both? Answering these questions requires getting clear about the concept of reproduction. What I hope to show is that with an appropriate notion of reproduction—one for which I will argue—resurrecting a member of Mammuthus primigenius is a genuine possibility.     

Heritability not missing—genetic basis of sexual weaponry uncovered

The chase to uncover the genetic underpinnings of quantitative traits of ecological and evolutionary importance has been on for a good while. However, the potential power of genome‐wide association studies (GWAS) as an approach to identify genes of interest in wild animal populations has remained untapped. Setting technical and economic explanations aside, the sobering lack of success in human GWAS might have fed this restraint. Namely, while GWAS have successfully identified genetic variants associated with hundreds of complex traits (e.g. Ku et al. 2010 ), these variants have generally captured only a low percentage of variance in traits known to be highly heritable—an observation came to be known as the ‘missing heritability’ ( Maher 2008 ; Aulchenko et al. 2009 ). Hence, if the vastly resourced human studies have been unsuccessful (but see: Yang et al. 2010 ), why should we expect that less resourced studies of wild animal populations would be able do better? In this issue of Molecular Ecology, Johnston et al. (2011) prove this line of thinking wrong. In an impressive and what may well be the most advanced gene mapping study ever performed in a wild population, they identify a single locus (RXFP2) responsible for explaining horn phenotype in feral domestic sheep from St Kilda ( Fig. 1 ). This same locus is also shown to account for up to 76% of additive genetic variance in horn size in male sheep: this contrasts sharply with most human GWAS where mapped loci explain only a modest proportion of genetic variation in a given trait.

Figure 1 Open in figure viewer PowerPoint The Soay sheep of the St Kilda archipelago are a primitive feral breed of domestic sheep. Pictured are a male with vestigial horns (=‘scurred’; left) and two normal‐horned males (centre and right). Photograph courtesy of Peter Korsten.     

Evolution,diversity and interactions with past human populations of recently extinct Pholidoscelis lizards (Squamata: Teiidae) from the Guadeloupe Islands (French West-Indies)

This paper aims to demonstrate how subfossil bone remains from Pleistocene and Holocene deposits can help to reconstruct the history of recently extinct taxa through the example of Pholidoscelis lizards from the Guadeloupe Islands in the French West Indies. To achieve this, we conducted a new anatomical and zooarchaeological study of fossil Pholidoscelis remains collected from 23 archaeological and paleontological deposits on the Guadeloupe Islands from which this genus is nowadays absent. Our results shed light on the past existence of large Pholidoscelis lizards on all the Guadeloupe islands but also on the difficulties of confident specific identification for these remains. Nevertheless, we suggest a possible past occurrence of the now extinct Pholidoscelis major on nearly all of the Guadeloupe islands. In addition, we identified a new Pholidoscelis species, Pholidoscelis turukaeraensis sp. nov., on Marie-Galante Island, where no Pholidoscelis lizards were previously reported. This new species underwent an increase in size after the end of the Pleistocene period, possibly due to reduced predation pressure. We also highlight the consumption of Pholidoscelis lizards by pre-Columbian Amerindians and the huge impact of European colonization, which led to the extinction of all these lizards in less than 300 years.http://zoobank.org/urn:lsid:zoobank.org:pub:15C39436-A083-483F-B35E-78807B606904     

A new species of the genus <Emphasis Type="Italic">Bibio</Emphasis> (Diptera,Bibionidae) from the tundra of the Asian part of Russia

A new species, Bibio tschernovi Kriv., from the Taimyr Peninsula, the Chukchi Autonomous Area, and Wrangel Island is described. It is closely related to the Palaearctic B. pomonae (Fabr.) and to two North American species, B. bryanti Johnson, 1929 and B. holtii McAtee, 1921, in the wing structure. New data on the distribution of B. nigriventris Haliday, 1833 and B. pomonae (Fabricius, 1775) are presented. A key to the species of the pomonae group, based on males, is presented.     

Genotyping of Capreolus pygargus fossil DNA from Denisova cave reveals phylogenetic relationships between ancient and modern populations

Background

The extant roe deer (Capreolus Gray, 1821) includes two species: the European roe deer (C. capreolus) and the Siberian roe deer (C. pygargus) that are distinguished by morphological and karyotypical differences. The Siberian roe deer occupies a vast area of Asia and is considerably less studied than the European roe deer. Modern systematics of the Siberian roe deer remain controversial with 4 morphological subspecies. Roe deer fossilized bones are quite abundant in Denisova cave (Altai Mountains, South Siberia), where dozens of both extant and extinct mammalian species from modern Holocene to Middle Pleistocene have been retrieved.

Methodology/Principal Findings

We analyzed a 629 bp fragment of the mitochondrial control region from ancient bones of 10 Holocene and four Pleistocene Siberian roe deer from Denisova cave as well as 37 modern specimen belonging to populations from Altai, Tian Shan (Kyrgyzstan), Yakutia, Novosibirsk region and the Russian Far East. Genealogical reconstructions indicated that most Holocene haplotypes were probably ancestral for modern roe deer populations of Western Siberia and Tian Shan. One of the Pleistocene haplotypes was possibly ancestral for modern Yakutian populations, and two extinct Pleistocene haplotypes were close to modern roe deer from Tian Shan and Yakutia. Most modern geographical populations (except for West Siberian Plains) are heterogeneous and there is some tentative evidence for structure. However, we did not find any distinct phylogenetic signal characterizing particular subspecies in either modern or ancient samples.

Conclusion/Significance

Analysis of mitochondrial DNA from both ancient and modern samples of Siberian roe deer shed new light on understanding the evolutionary history of roe deer. Our data indicate that during the last 50,000 years multiple replacements of populations of the Siberian roe deer took place in the Altai Mountains correlating with climatic changes. The Siberian roe deer represent a complex and heterogeneous species with high migration rates and without evident subspecies structure. Low genetic diversity of the West Siberian Plain population indicates a recent bottleneck or founder effect.