Ancient DNA reveals late survival of mammoth and horse in interior Alaska

Causes of late Quaternary extinctions of large mammals (" megafauna") continue to be debated, especially for continental losses, because spatial and temporal patterns of extinction are poorly known. Accurate latest appearance dates (LADs) for such taxa are critical for interpreting the process of extinction. The extinction of woolly mammoth and horse in northwestern North America is currently placed at 15,000-13,000 calendar years before present (yr BP), based on LADs from dating surveys of macrofossils (bones and teeth). Advantages of using macrofossils to estimate when a species became extinct are offset, however, by the improbability of finding and dating the remains of the last-surviving members of populations that were restricted in numbers or con-fined to refugia. Here we report an alternative approach to detect 'ghost ranges' of dwindling populations, based on recovery of ancient DNA from perennially frozen and securely dated sediments (sedaDNA). In such contexts, sedaDNA can reveal the molecular presence of species that appear absent in the macrofossil record. We show that woolly mammoth and horse persisted in interior Alaska until at least 10,500 yr BP, several thousands of years later than indicated from macrofossil surveys. These results contradict claims that Holocene survival of mammoths in Beringia was restricted to ecologically isolated high-latitude islands. More importantly, our finding that mammoth and horse overlapped with humans for several millennia in the region where people initially entered the Americas challenges theories that megafaunal extinction occurred within centuries of human arrival or were due to an extraterrestrial impact in the late Pleistocene.

Phylogenetic and phylogeographic analysis of the genus Orestias (Teleostei: Cyprinodontidae) in the southern Chilean Altiplano: The relevance of ancient and recent divergence processes in speciation

This study presents phylogenetic molecular data of the Chilean species of Orestias to propose an allopatric divergence hypothesis and phylogeographic evidence that suggests the relevance of abiotic factors in promoting population divergence in this complex. The results reveal that diversification is still ongoing, e.g. in the Ascotán salt pan, where populations of Orestias ascotanensis restricted to individual freshwater springs exhibit strong genetic differentiation, reflecting putative independent evolutionary units. Diversification of Orestias in the southern Altiplano may be linked to historical vicariant events and contemporary variation in water level; these processes may have affected the populations from the Plio-Pleistocene until the present.

The Death Cults of prehistoric Malta:Mysteries of the Ancient Ones

reprinted

Care and Management of Ancient Stone Monuments During Environmental Change

Ancient stone monuments (ASMs), such as standing stones and rock art panels, are powerful and iconic expressions of Britain’s rich prehistoric past that have major economic and tourism value. However, ASMs are under pressure due to increasing anthropogenic exposure and changing climatic conditions, which accelerate their rates of disrepair. Although scientific data exists on the integrity of stone monuments, most applies to “built” systems; therefore, additional work specific to ASMs in the countryside is needed to develop better-informed safeguarding strategies. Here, we use Neolithic and Bronze Age rock art panels across Northern England as a case study for delineating ASM management actions required to enhance monument preservation. The state of the rock art is described first, including factors that led to current conditions. Rock art management approaches then are described within the context of future environments, which models suggest to be more dynamic and locally variable. Finally, a Condition Assessment and Risk Evaluation (CARE) scheme is proposed to help prioritise interventions; an example of which is provided based on stone deterioration at Petra in Jordon. We conclude that more focused scientific and behavioural data, specific to deterioration mechanisms, are required for an ASM CARE scheme to be successful.

Estimating policy positions from political texts

The analysis of policy-based party;;competition will not make serious progress beyond the constraints of (a) the unitary actor assumption and (b) a static approach to analyzing party competition between elections until a method is available for deriving; reliable and valid time-series estimates of the policy positions of large numbers of political actors. Retrospective estimation of these positions;In past party systems will require a method for estimating policy positions from political texts.

Previous hand-coding content analysis schemes deal with policy emphasis rather than policy positions. We propose a new hand-coding scheme for policy positions, together with a new English language computer,coding scheme that is compatible with this. We apply both schemes; to party manifestos from Britain and Ireland in 1992 and 1997 and cross validate the resulting estimates with :those derived from quite independent expert surveys and with previous,manifesto analyses.

There is a high degree of cross validation between coding methods. including computer coding. This implies that it is indeed possible to use computer-coded content analysis to derive reliable and valid estimates of policy positions from political texts. This will allow vast Volumes of text to be coded, including texts generated by individuals and other internal party actors, allowing the empirical elaboration of dynamic rather than static models of party competition that move beyond the unitary actor assumption.

Phylogeny and ancient DNA of Sus provides insights into neolithic expansion in Island Southeast Asia and Oceania

Human settlement of Oceania marked the culmination of a global colonization process that began when humans first left Africa at least 90,000 years ago. The precise origins and dispersal routes of the Austronesian peoples and the associated Lapita culture remain contentious, and numerous disparate models of dispersal (based primarily on linguistic, genetic, and archeological data) have been proposed. Here, through the use of mtDNA from 781 modern and ancient Sus specimens, we provide evidence for an early human-mediated translocation of the Sulawesi warty pig (Sus celebensis) to Flores and Timor and two later separate human-mediated dispersals of domestic pig (Sus scrofa) through Island Southeast Asia into Oceania. Of the later dispersal routes, one is unequivocally associated with the Neolithic (Lapita) and later Polynesian migrations and links modern and archeological Javan, Sumatran, Wallacean, and Oceanic pigs with mainland Southeast Asian S. scrofa. Archeological and genetic evidence shows these pigs were certainly introduced to islands east of the Wallace Line, including New Guinea, and that so-called "wild" pigs within this region are most likely feral descendants of domestic pigs introduced by early agriculturalists. The other later pig dispersal links mainland East Asian pigs to western Micronesia, Taiwan, and the Philippines. These results provide important data with which to test current models for human dispersal in the region. © 2007 by The National Academy of Sciences of the USA.

Genome analysis of a simultaneously predatory and prey-independent, novel Bdellovibrio bacteriovorus from the River Tiber, supports in silico predictions of both ancient and recent lateral gene transfer from diverse bacteria

BACKGROUND: Evolution equipped Bdellovibrio bacteriovorus predatory bacteria to invade other bacteria, digesting and replicating, sealed within them thus preventing nutrient-sharing with organisms in the surrounding environment. Bdellovibrio were previously described as "obligate predators" because only by mutations, often in gene bd0108, are 1 in ~1x10(7) of predatory lab strains of Bdellovibrio converted to prey-independent growth. A previous genomic analysis of B. bacteriovorus strain HD100 suggested that predatory consumption of prey DNA by lytic enzymes made Bdellovibrio less likely than other bacteria to acquire DNA by lateral gene transfer (LGT). However the Doolittle and Pan groups predicted, in silico, both ancient and recent lateral gene transfer into the B. bacteriovorus HD100 genome.

RESULTS: To test these predictions, we isolated a predatory bacterium from the River Tiber- a good potential source of LGT as it is rich in diverse bacteria and organic pollutants- by enrichment culturing with E. coli prey cells. The isolate was identified as B. bacteriovorus and named as strain Tiberius. Unusually, this Tiberius strain showed simultaneous prey-independent growth on organic nutrients and predatory growth on live prey. Despite the prey-independent growth, the homolog of bd0108 did not have typical prey-independent-type mutations. The dual growth mode may reflect the high carbon content of the river, and gives B. bacteriovorus Tiberius extended non-predatory contact with the other bacteria present. The HD100 and Tiberius genomes were extensively syntenic despite their different cultured-terrestrial/freshly-isolated aquatic histories; but there were significant differences in gene content indicative of genomic flux and LGT. Gene content comparisons support previously published in silico predictions for LGT in strain HD100 with substantial conservation of genes predicted to have ancient LGT origins but little conservation of AT-rich genes predicted to be recently acquired.

CONCLUSIONS: The natural niche and dual predatory, and prey-independent growth of the B. bacteriovorus Tiberius strain afforded it extensive non-predatory contact with other marine and freshwater bacteria from which LGT is evident in its genome. Thus despite their arsenal of DNA-lytic enzymes; Bdellovibrio are not always predatory in natural niches and their genomes are shaped by acquiring whole genes from other bacteria.

EU Cross-Border Cooperation and Conflict Transformation in the Basque and Irish Border Regions

Comparative research on violent conflict in the Basque Country and Ireland has yielded a sizable body of published academic work. Less well explored is the relationship between conflict transformation and cross-border cooperation in that specific comparative context. This paper provides a comparative examination of Third (not for profit) sector cross-border cooperation as conflict transformation in the Basque (France/Spain) and Irish (UK/Ireland) border regions. To what extent does cross-border cooperation contribute to peacebuilding in the two last violent ethnonationalist conflicts in Western Europe? The comparison is based on the premise that the EU played a different role in both cases. In the Irish case, the EU contributed to the institutionalization of a peace process that included cross-border cooperation between third sector organizations among the policy instruments contributing to conflict transformation. In the Basque case, the unilateral renunciation of violence by ETA (Euskadi eta Askatasuna) in 2010 did not generate the consistent involvement of the EU in a comparable institutional peace process. However, some third sector organizations used EU instruments for cross-border economic, social and cultural cooperation between France and Spain in order to reinforce their cross-border networks, which indirectly impacted on conflict transformation. The effectiveness of this cross-border cooperation for conflict transformation is assessed comparatively. To what extent does this increase in cross-border cooperation “from below” connect to wider institutional and social processes of conflict transformation in Ireland and the Basque Country? Crucially, does the strengthening of cross-border relations on shared issues mollify or sharpen existing identity cleavages? Also considered is the sustainability of such cooperation in these regions in light of the less favourable post-2004 EU funding environment, and the post-2008 economic and political turmoil affecting the relevant EU member states, especially Ireland and Spain.

Polybius’ ‘previous landslide’: Proof that Hannibal’s invasion route crossed the col de la traversette

Both Polybius and Livy described a landslide/landslip that blocked the Punic Army’s exfiltration from a high col on the water divide in the Western Alps. The landslide, more aptly termed rockfall, has been a source of contention amongst classicists for centuries despite the fact that only two cols—Clapier and Traversette—exhibit rockfall debris on the lee side of the Alps. While the Clapier rockfall is too small and too young to have provided blockage, the Traversette debris is nearly as Polybius described it when he retraced the invasion route some 60 years after the event. His ‘two-tier’ description of the deposit, a doublet of younger and older rock rubble, including measurements of width and volume are close to modern measurements and prove that he knew, in advance, the route Hannibal had followed. It would take a practiced eye to correctly identify the stratigraphic complexity inherent in the Traversette Rockfall. Here we present weathering ratios, soil stratigraphic, mineral, chemical and microbiological evidence in support of Polybius’ observations as a considerable background database for future geoarchaeological exploration.