Post-genomics approaches towards monitoring changes within the microbial ecology of the gut

The human gut microbiota, comprising many hundreds of different microbial species, has closely co-evolved with its human host over the millennia. Diet has been a major driver of this co-evolution, in particular dietary non-digestible carbohydrates. This dietary fraction reaches the colon and becomes available for microbial fermentation, and it is in the colon that the great diversity of gut microorganisms resides. For the vast majority of our evolutionary history humans followed hunter-gatherer life-styles and consumed diets with many times more non-digestible carbohydrates, fiber and whole plant polyphenol rich foods than typical Western style diets today.

The ecology of crusading: investigating the environmental impact of holy war and colonisation at the frontiers of medieval Europe

The Crusades in the Near East, eastern Baltic and Iberian Peninsula (in the context of the Reconquest/reconquista) were accompanied by processes of colonisation, characterising the expansion of medieval Europe and resulting in the creation of frontier societies at the fringes of Christendom. Colonisation was closely associated with — indeed, depended on — the exploitation of local environments, but this dimension is largely missing from studies of the crusading frontiers. This paper, the product of a European Science Foundation Exploratory Workshop on 'The Ecology of Crusading' in 2009, surveys the potential for investigating the environmental impact of the crusading movement in all three frontier regions. It considers a diverse range of archaeological, palaeoenvironmental and written sources, with the aim of situating the societies created by the Crusades within the context of medieval colonisation and human ecological niche construction. It demonstrates that an abundant range of data exists for developing this largely neglected and disparately studied aspect of medieval frontier societies into a significant research programme.

The earth, the sky and the water's edge: changing beliefs in the earlier prehistory of Northern Europe

There have been two kinds of study of ancient beliefs in the earlier prehistory of Scandinavia. One considers the impact of ideas which originated further to the south and east. It considers a cosmology based on the movements of the sun. A second tradition develops out of the ethnography of the circumpolar region and combines archaeological evidence with the beliefs of hunter-gatherers. It postulates the existence of a three-tier cosmology in which people could communicate between different worlds. This paper argues that certain elements that are thought to epitomize the ‘Southern’ system might have been suggested by existing ideas within Scandinavia itself. Both sets of beliefs came to influence one another, but they became increasingly distinct towards the end of the Bronze Age. This paper reconsiders the rock carvings, metalwork and mortuary cairns of that period and the Iron Age in relation to the process of religious change.

The greening of Arabia: multiple opportunities for human occupation of the Arabian peninsula during the Late Pleistocene inferred from an ensemble of climate model simulations

Climate models are potentially useful tools for addressing human dispersals and demographic change. The Arabian Peninsula is becoming increasingly significant in the story of human dispersals out of Africa during the Late Pleistocene. Although characterised largely by arid environments today, emerging climate records indicate that the peninsula was wetter many times in the past, suggesting that the region may have been inhabited considerably more than hitherto thought. Explaining the origins and spatial distribution of increased rainfall is challenging because palaeoenvironmental research in the region is in an early developmental stage. We address environmental oscillations by assembling and analysing an ensemble of five global climate models (CCSM3, COSMOS, HadCM3, KCM, and NorESM). We focus on precipitation, as the variable is key for the development of lakes, rivers and savannas. The climate models generated here were compared with published palaeoenvironmental data such as palaeolakes, speleothems and alluvial fan records as a means of validation. All five models showed, to varying degrees, that the Arabia Peninsula was significantly wetter than today during the Last Interglacial (130 ka and 126/125 ka timeslices), and that the main source of increased rainfall was from the North African summer monsoon rather than the Indian Ocean monsoon or from Mediterranean climate patterns. Where available, 104 ka (MIS 5c), 56 ka (early MIS 3) and 21 ka (LGM) timeslices showed rainfall was present but not as extensive as during the Last Interglacial. The results favour the hypothesis that humans potentially moved out of Africa and into Arabia on multiple occasions during pluvial phases of the Late Pleistocene.

Pleistovultur nevesi gen. et sp nov (Aves: Vulturidae) and the diversity of condors and vultures in the South American Pleistocene

Pleistovultur nevesi, a new genus and species of a large Vulturidae is described from the Upper Pleistocene or beginning of the Holocene, based on a complete and well preserved right tibiotarsus from the Cuvieri cave deposits, one of the hundreds of caves of the Lagoa Santa region in Minas Gerais state, Brazil. Also described here is a distal half of a left tibiotarsus from Gruta dos Brejoes, a cave in Morro do Chapeu, Bahia state, Brazil, which probably belongs to another not-yet-known genus and species of the Vulturidae. The described material, added to prior literature, is proof of the appreciable diversity of the Vulturidae during the Pleistocene in South America.

POSTMARITAL RESIDENCE PRACTICE IN SOUTHERN BRAZILIAN COASTAL GROUPS: CONTINUITY AND CHANGE

The coastal plains of the States of Parana and Santa Catarina, in Southern Brazil, were first settled around 6000 B.P. by shellmound builders, a successful fisher-hunter-gatherer population that inhabited the coastal lowlands practically unchanged for almost five thousand years. Shellmounds were typically occupied as residential sites as well as cemeteries, and are usually associated with rich alimentary zones. Around 1200 B.P., the first evidence of ceramics brought from the interior is found in coastal areas, and together with ceramics there is a progressive abandonment of shellmound construction in favor of flat cold shallow sites. Here we consider if these changes were reflected in the postmarital residence practice of coastal groups, i.e., if the arrival or intensification of contact with groups from the interior resulted in changes in this aspect of social structure among the coastal groups. To test the postmarital residence practice we analyzed within-group variability ratios between males and females, following previous studies on the topic. and between-group, correlations between Mahalanobis distances and geographic distances. The results suggest that in the pre-ceramic series a matrilocal, postmarital residential system predominated, while in the ceramic period there was a shift toward patrilocality. This favors the hypothesis that the changes experienced by coastal groups after 1200 B.P. affected not only their economy and material culture, but important aspects of their sociopolitical organization as well.

A river runs through it - ancient DNA data on the neolithic populations of the Great Hungarian Plain

This thesis was part of a multidisciplinary research project funded by the German Research Foundation (“Bevölkerungsgeschichte des Karpatenbeckens in der Jungsteinzeit und ihr Einfluss auf die Besiedlung Mitteleuropas”, grant no. Al 287/10-1) aimed at elucidating the population history of the Carpathian Basin during the Neolithic. The Carpathian Basin was an important waypoint on the spread of the Neolithic from southeastern to central Europe. On the Great Hungarian Plain (Alföld), the first farming communities appeared around 6000 cal BC. They belonged to the Körös culture, which derived from the Starčevo-Körös-Criş complex in the northern Balkans. Around 5600 cal BC the Alföld-Linearbandkeramik (ALBK), so called due to its stylistic similarities with the Transdanubian and central European LBK, emerged in the northwestern Alföld. Following a short “classical phase”, the ALBK split into several regional subgroups during its later stages, but did not expand beyond the Great Hungarian Plain. Marking the beginning of the late Neolithic period, the Tisza culture first appeared in the southern Alföld around 5000 cal BC and subsequently spread into the central and northern Alföld. Together with the Herpály and Csőszhalom groups it was an integral part of the late Neolithic cultural landscape of the Alföld. Up until now, the Neolithic cultural succession on the Alföld has been almost exclusively studied from an archaeological point of view, while very little is known about the population genetic processes during this time period. The aim of this thesis was to perform ancient DNA (aDNA) analyses on human samples from the Alföld Neolithic and analyse the resulting mitochondrial population data to address the following questions: is there population continuity between the Central European Mesolithic hunter-gatherer metapopulation and the first farming communities on the Alföld? Is there genetic continuity from the early to the late Neolithic? Are there genetic as well as cultural differences between the regional groups of the ALBK? Additionally, the relationships between the Alföld and the neighbouring Transdanubian Neolithic as well as other European early farming communities were evaluated to gain insights into the genetic affinities of the Alföld Neolithic in a larger geographic context. 320 individuals were analysed for this study; reproducible mitochondrial haplogroup information (HVS-I and/or SNP data) could be obtained from 242 Neolithic individuals. According to the analyses, population continuity between hunter-gatherers and the Neolithic cultures of the Alföld can be excluded at any stage of the Neolithic. In contrast, there is strong evidence for population continuity from the early to the late Neolithic. All cultural groups on the Alföld were heavily shaped by the genetic substrate introduced into the Carpathian Basin during the early Neolithic by the Körös and Starčevo cultures. Accordingly, genetic differentiation between regional groups of the ALBK is not very pronounced. The Alföld cultures are furthermore genetically highly similar to the Transdanubian Neolithic cultures, probably due to common ancestry. In the wider European context, the Alföld Neolithic cultures also highly similar to the central European LBK, while they differ markedly from contemporaneous populations of the Iberian Peninsula and the Ukraine. Thus, the Körös culture, the ALBK and the Tisza culture can be regarded as part of a “genetic continuum” that links the Neolithic Carpathian Basin to central Europe and likely has its roots in the Starčevo -Körös-Criş complex of the northern Balkans.

Archaeology in Switzerland between lakes and mountains.

Switzerland has an extraordinarily rich archaeological heritage from the Neolithic and the Bronze Age, dating back nearly 7000 years. Since the mid-19th century, the first pile dwellings were discovered in the lakes of the Central Plateau. Since 2011 these sites are part of the UNESCO world heritage „Prehistoric pile-dwellings around the Alps“. Not only lakes, but also Swiss mountains preserve extraordinary archaeological remains: from an alpine pass in the Bernese Alps prehistoric objects are melting out from the ice. Perfect preservation conditions and modern archaeological methods allow exploring the development of early agrarian societies in this part of the world. We can reconstruct their settlements and follow their exchange with other communities. Archaeology under water and in alpine environments allows fascinating insights into the beginnings of our history.

Pliocene and Pleistocene abundance of siliceous microfossil assemblages in ODP Leg 127 sites

A close examination of the siliceous microfossil assemblages from the sediments of ODP Leg 127, Japan Sea Sites 794, 795, and 797, reveals that upper Pliocene and Pleistocene assemblages have been subjected to more dissolution than have lower Pliocene assemblages. This conclusion is based on semiquantitative observations of samples processed for diatoms and radiolarians. Although preservation of opaline microfossils in some upper Pliocene and Pleistocene samples is better than others, in general, the poorly preserved state of these assemblages supports the notion that opal dissolution, in response to lowered productivity, is responsible for the paucity of siliceous microfossils in upper Pliocene and Pleistocene sediments. The lithological transition from diatomaceous oozes to silts and clays corresponds to a change between dominantly well preserved to more poorly preserved siliceous assemblages, and is termed the late Pliocene Japan Sea opal dissolution transition zone (ODTZ). The base of the ODTZ is defined as the uppermost occurrence of high abundances of moderately to well preserved valves of the diatom Coscinodiscus marginatus. The dissolution transition zone is characterized by partially dissolved refractory assemblages of radiolarians, the presence of C. marginatus girdles, C. marginatus fragments, siliceous sponge spicules, and a general decrease in weakly silicified, less solution resistant diatoms upward in the section. The top of the dissolution transition zone marks the level where whole C. marginatus valves and C. marginatus fragments are no longer present in significant numbers. Dissolution of the late Pliocene and Pleistocene opaline assemblages is attributed mainly to changes in paleoceanographic circulation patterns and decreased nutrient (dissolved silicon) contents of the water column, and possibly dissolution at the sediment/water interface, rather than to post-depositional dissolution or diagenesis. We suggest that the transition from silica-rich to silica-poor conditions in the Japan Sea was due to fluctuations of deep-water exchange with the Pacific through the Tsugaru Strait between 2.9 and 2.3 Ma.

Miocene to Pleistocene planktonic foraminifer biostratigraphy of ODP Leg 135 sites

Diverse and well-preserved planktonic foraminifers were recovered from six sites (834-839) drilled in the Lau Basin. Planktonic faunas from the Tongan Platform sites varied from those of the Lau Basin sites by being less well preserved (Site 840) to being very poorly preserved and very sparse (Site 841); at Site 841 most samples were barren. All sites penetrated a volcaniclastic sequence in which thick ash beds were encountered; foraminifer populations within the ash beds were often very small, making it difficult to obtain biostratigraphic data. No hiatuses were encountered in the upper Miocene to Pleistocene sections of the Lau Basin, but a possible break occurs at Site 840 on the Tongan Platform. Site 834 penetrated through a Quaternary-Pliocene sequence overlying basaltic basement, and topmost Miocene (Zone N17B) sediments interbedded within the volcanic sequence. Site 835 penetrated into the lower Pliocene (Zones N19 to N19-20). Site 836 penetrated the shortest section, with Zone N22 {Globorotalia (Truncorotalia) crassaformis hessi Subzone) directly overlying basalts. Site 837 penetrated into the basal part of Zone N22 (Globigerinoides quadrilobatus fistulosus Subzone) overlying basalt. Site 838 failed to encounter basalts, with the oldest sediment being from Zone N22 (Globigerinoides quadrilobatus fistulosus Subzone). Site 839, within the same basin as Site 838, located Zone N22 (Globigerinoides quadrilobatus fistulosus Subzone) sediments directly overlying igneous basement. Site 840 penetrated into the upper Miocene Zone N17A without encountering any major unconformity. Site 841, studied mainly from core-catcher samples, penetrated a Quaternary to questionable upper Miocene sequence that was in fault contact with middle Miocene (Zones N8 to N9) sediments. For the Lau Basin sites, reworking was encountered only in Sites 834 and 835. Site 834 was drilled adjacent to the Lau Ridge, on which are developed numerous reef al and shallow-water environments, where erosional conditions could have been expected during sea-level lowstands. Site 835 was drilled in a narrow basin that has been remote from these erosional influences; slumping and erosion of material from the adjacent basin slopes appears to have been the source of the reworking. For the Tongan Platform sites, reworking was observed only in the lower part of the upper Miocene section at Site 841, where late Eocene larger foraminifers are present in conglomerates and grits. The presence of Globorotalia (Globorotalia) multicamerata and small specimens of Sphaeroidinellopsis spp. in the Pleistocene of Site 840 may indicate reworking, but this is not clear. Unit I, which marks a reduction in volcanic activity in the Lau Basin, ranges in age from the lower part of Zone N22 (Globigerinoides quadrilobatus fistulosus Subzone) at Sites 834 and 835, to within Zone N22 (Globorotalia crassaformis hessi Subzone) at Sites 836 to 838, and within the upper part of Zone N22 (Bolliella praeadamsi Subzone) at Site 839. Units II and III are generally represented by thick to very thick ash beds, which generally contain low-diversity and often poorly preserved assemblages. Igneous sources seem to have remained important contributors of sediment up to the present day.

Pleistocene chronology of sediments from the Lomonosov Ridge

Despite its importance in the global climate system, age-calibrated marine geologic records reflecting the evolution of glacial cycles through the Pleistocene are largely absent from the central Arctic Ocean. This is especially true for sediments older than 200 ka. Three sites cored during the Integrated Ocean Drilling Program's Expedition 302, the Arctic Coring Expedition (ACEX), provide a 27 m continuous sedimentary section from the Lomonosov Ridge in the central Arctic Ocean. Two key biostratigraphic datums and constraints from the magnetic inclination data are used to anchor the chronology of these sediments back to the base of the Cobb Mountain subchron (1215 ka). Beyond 1215 ka, two best fitting geomagnetic models are used to investigate the nature of cyclostratigraphic change. Within this chronology we show that bulk and mineral magnetic properties of the sediments vary on predicted Milankovitch frequencies. These cyclic variations record "glacial" and "interglacial" modes of sediment deposition on the Lomonosov Ridge as evident in studies of ice-rafted debris and stable isotopic and faunal assemblages for the last two glacial cycles and were used to tune the age model. Potential errors, which largely arise from uncertainties in the nature of downhole paleomagnetic variability, and the choice of a tuning target are handled by defining an error envelope that is based on the best fitting cyclostratigraphic and geomagnetic solutions.

Simulated agricultural subsistence, timing of transition, and percentage of immigrant farmers

Farming and herding were introduced to Europe from the Near East and Anatolia; there are, however, considerable arguments about the mechanisms of this transition. Were it the people who moved and either outplaced, or admixed with, the indigenous hunter-gatherer groups? Or was it material and information that moved---the Neolithic Package---consisting of domesticated plants and animals and the knowledge of their use? The latter process is commonly referred to as cultural diffusion and the former as demic diffusion. Despite continuous and partly combined efforts by archaeologists, anthropologists, linguists, palaeontologists and geneticists, a final resolution of the debate has not yet been reached. In the present contribution we interpret results from the Global Land Use and technological Evolution Simulator (GLUES). GLUES is a mathematical model for regional sociocultural development, embedded in the geoenvironmental context, during the Holocene. We demonstrate that the model is able to realistically hindcast the expansion speed and the inhomogeneous space-time evolution of the transition to agropastoralism in western Eurasia. In contrast to models that do not resolve endogenous sociocultural dynamics, our model describes and explains how and why the Neolithic advanced in stages. We uncouple the mechanisms of migration and information exchange and also of migration and the spread of agropastoralism. We find that: (1) An indigenous form of agropastoralism could well have arisen in certain Mediterranean landscapes, but not in Northern and Central Europe, where it depended on imported technology and material. (2) Both demic diffusion by migration and cultural diffusion by trade may explain the western European transition equally well. (3) Migrating farmers apparently contribute less than local adopters to the establishment of agropastoralism. Our study thus underlines the importance of adoption of introduced technologies and economies by resident foragers.

Geochemistry and Hg isotopic composition of mid-Pleistocene sapropel of ODP Hole 161-974C

The concentrations of mercury (Hg) and other trace metals (Ni, Cu, Zn, Mo, Ba, Re, U) and the Hg isotopic composition were examined across a dramatic redox and productivity transition in a mid-Pleistocene Mediterranean Sea sapropel sequence. Characteristic trace metal enrichment in organic-rich layers was observed, with organic-rich sapropel layers ranging in Hg concentration from 314 to 488 ng/g (avg = 385), with an average enrichment in Hg by a factor of 5.9 compared to organic-poor background sediments, which range from 39 to 94 ng/g Hg (avg = 66). Comparison of seawater concentrations and sapropel accumulations of trace metals suggests that organic matter quantitatively delivers Hg to the seafloor. Near complete scavenging of Hg from the water column renders the sapropel Hg isotopic composition representative of mid-Pleistocene Mediterranean seawater. Sapropels have an average d202Hg value of -0.91 per mil ± 0.15 per mil (n = 5, 1 SD) and D199Hg value of 0.11 per mil ± 0.03 per mil (n = 5, 1 SD). Background sediments have an average d202Hg of -0.76 per mil ± 0.16 per mil (n = 5, 1 SD) and D199Hg of 0.05 per mil ± 0.01 per mil (n = 5, 1 SD), which is indistinguishable from the sapropel values. We suggest that the sapropel isotopic composition is most representative of the mid-Pleistocene Tyrrhenian Sea.

Stable isotopic record of late Pliocene and Pleistocene foraminifera of ODP Site 114-704

We studied the stable isotopic and carbonate stratigraphy of ODP Hole 704A to reconstruct the paleoceanographic evolution of the eastern subantarctic sector of the South Atlantic Ocean. Site 704 is well positioned with respect to latitude (46°52.8'S, 7°25.3'E) and bathymetry (2532 m) to monitor past migrations in the position of Polar Front Zone (PFZ) and changes in deep-water circulation during the late Pliocene-Pleistocene. Several important changes occurred in proxy paleoceanographic indicators across the Gauss/Matuyama boundary at 2.47 Ma: (1) accumulation rates of biogenic sedimentary components increased by an order of magnitude (Froelich et al., this volume); (2) planktonic d1 8O values increased by an average of 0.5 per mil; (3) the amplitude of the benthic d18O signal increased; (4) the accumulation rate of ice-rafted detritus increased several fold (Warnke and Allen, this volume); and (5) carbon isotopic ratios of benthic foraminifers decreased by 0.5 per mil, as did the d13C of the fine-fraction carbonate by 1.5 per mil (Mead et al., 1991, doi:10.2973/odp.proc.sr.114.152.1991), but no change occurred in planktonic foraminiferal d13C values. Most of these changes are consistent with more frequent expansions and contractions of the PFZ over Site 704 after 2.47 Ma, bringing cold, nutrient-rich waters to 47°S that stimulated both carbonate and siliceous productivity. The synchronous increase in d18O values and ice-rafted detritus accumulation in Hole 704A indicates that the 2.4 Ma paleoceanographic event included ice volume growth on both Antarctica and Northern Hemisphere continents. The decrease in benthic d13C values indicates that the ventilation rate of Southern Ocean deep water decreased and the nutrient content increased during glacial events after 2.5 Ma. At the Gauss/Matuyama boundary, benthic d13C values of the Southern Ocean shifted toward those of the Pacific end member, indicating a decrease in the relative mixing ratio of Northern Component Water and Circumpolar Deep Water. During the early Matuyama (~2.3 to 1.7 Ma), the PFZ generally occupied a southerly position with respect to Site 704 and carbonate productivity prevailed. Exceptions to these general conditions occurred during strong glacial events of the early Matuyama (e.g., isotopic stages 82, 78, 74, and 70), when the PFZ migrated to the north and opal sedimentation predominated at Site 704. At 1.7 Ma, the PFZ migrated toward the equator and occupied a more northerly position for a prolonged interval between ~1.7 and 1.5 Ma. Beginning at ~1.5-1.4 Ma, surface and bottom water parameters (d18O, d13C, %CaCO3, and %opal) in the subantarctic South Atlantic became highly correlated such that glacial events (d18O maxima) corresponded to d13C and carbonate minima and opal maxima. This pattern is typical of the correlation found during the latest Pleistocene in the Southern Ocean (Charles and Fairbanks, in press). This event coincided with increased suppression of Northern Component Water during glacial events after 1.5 Ma (Raymo et al., 1990, doi:10.1016/0012-821X(90)90051-X), which may have influenced the climatology of the Southern Hemisphere by altering the flux of heat and salt to the Southern Ocean).