Divergent T-fO2 paths during crystallisation of H2O-rich and H2O-poor magmas as recorded by Ce and U in zircon, with implications for TitaniQ and TitaniZ geothermometry

During solidification of magma chambers as systems closed to chemical exchange with environs, the residual siliceous melt may follow a trend of rising, constant, or decreasing oxidation state, relative to reference buffers such as nickel + nickel oxide (NNO) or fayalite + magnetite + quartz. Titanomagnetite–hemoilmenite thermometry and oxybarometry on quenched volcanic suites yield temperature versus oxygen fugacity arrays of varied positive and negative slopes, the validity of which has been disputed for several years. We resolve the controversy by introducing a new recorder of magmatic redox evolution employing temperature- and redox-sensitive trace-element abundances in zircon. The zircon/melt partition coefficients of cerium and uranium vary oppositely in response to variation of magma redox state, but vary in tandem as temperature varies. Plots of U/Pr versus Ce4+/Ce3+ in zircon provide a robust test for change in oxidation state of the melt during zircon crystallisation from cooling magma, and the plots discriminate thermally induced from redox-induced variation of Ce4+/Ce3+ in zircon. Temperature-dependent lattice strain causes Ce4+/Ce3+ in zircon to increase strongly as zircon crystallises from cooling magma at constant Ce4+/Ce3+ ratio in the melt. We examine 19 zircon populations from igneous complexes in varied tectonic settings. Variation of zircon Ce4+/Ce3+ due to minor variation in melt oxidation state during crystallisation is resolvable in 11 cases but very subordinate to temperature dependence. In many zircon populations described in published literature, there is no resolvable change in redox state of the melt during tenfold variation of Ce4+/Ce3+ in zircons. Varied magmatic redox trends indicated by different slopes on plots of zircon U/Pr versus Ce4+/Ce3+ are corroborated by Fe–Ti-oxide-based T–ƒO2 trends of correspondingly varied slopes. Zircon and Fe–Ti-oxide compositions agree that exceptionally, H2O-rich arc magmas tend to follow a trend of rising oxidation state of the melt during late stages of fluid-saturated magmatic differentiation at upper-crustal pressures. We suggest that H2 and/or SO3 and/or Fe2+ loss from the melt to segregating fluid is largely responsible. Conversely, zircon and Fe–Ti-oxide compositions agree in indicating that H2O-poor magmas tend to follow a T–ƒO2 trend of decreasing oxidation state of the melt during late stages of magmatic differentiation at upper-crustal pressures, because the precipitating mineral assemblage has higher Fe3+/Fe2+ than coexisting rhyolitic melt. We present new evidence showing that the Fe–Ti-oxide oxybarometer calibration by Ghiorso and Evans (Am J Sci 308(9):957–1039, 2008) retrieves experimentally imposed values of ƒO2 in laboratory syntheses of Fe–Ti-oxide pairs to a precision of ± 0.2 log unit, over a large experimental temperature range, without systematic bias up to at least log ƒO2 ≈ NNO + 4.4. Their titanomagnetite–hemoilmenite geothermometer calibration has large systematic errors in application to Ti-poor oxides that precipitate from very oxidised magmas. A key outcome is validation of Fe–Ti-oxide-based values of melt TiO2 activity for use in Ti-in-zircon thermometry and Ti-in-quartz thermobarometry.We thank Paul Agnew and Alan Kobussen of Rio Tinto Exploration for financial support and for authorisation to publish research results. Additional financial support was provided by the ARC Centre of Excellence for Core to Crust Fluid Systems Grant CE110001017. MLF acknowledges the support of the Australian Research Council through the Future Fellowship Grant scheme (FT110100241). MLF also acknowledges support from the Australian Research Council through Linkage Project LP120100668. BDR acknowledges WMC Resources Ltd for financial support of his PhD research. RRL thanks the University of Bristol for a Benjamin Meaker Visiting Professorship which afforded an opportunity to clarify his understanding of this material through discussions with Professors Jon Blundy and Chris Hawkesworth

Tectonic evolution, petrochemistry, geochronology and palaeohydrology of the Tampakan porphyry and high sulphidation epithermal Cu-Au deposit Mindanao, Phillipines

Magmatic-related porphyry copper and high-sulphidation epithermal copper-gold ore deposits in continent-margin and intra-oceanic arcs of the Pacific Rim are spatially clustered in discrete volcanic arc segments. Ore-forming episodes likewise occur within discrete time intervals and are temporally associated with intervals of compression within arcs. Understanding the spatial and temporal controls on fertility of magmas requires detailed multidisciplinary studies of young, ore-productive districts where the tectonic evolution of the arc can be closely integrated with the evolution of crustal stress, with the timing of mineralisation and with evolution of petrological, petrochemical and magmatic physico-chemical properties. The late Miocene to Recent magmatism of the Tampakan ore district of southern Mindanao, Philippines, provides this opportunity. Porphyry copper and high sulphidation epithermal mineralisation within the giant Tampakan Cu-Au deposit (2500 Mt@ 0.48% Cu) are hosted by a polygenetic volcanic complex that was constructed over the past 7 Myr. This interval spans the pre-, syn- and late-collision stages of arc-arc collision in the southern Mindanao segment of the Sangihe arc. Synthesis of tectonic reconstructions and of plate motions from GPS data reveal that crustal compression in southern Mindanao commenced at ~7 Ma and peaked at ~4-3 Ma as subduction waned at the divergent Sangihe and Halmahera subduction systems, and during establishment of the nascent Philippine Trench and Cotabato Trench subduction systems. Porphyry Cu mineralisation at 4.24-4.26 Ma (⁴⁰Ar- ³⁹Ar) and high-sulphidation Cu-Au mineralisation at 3.24-3.28 Ma (⁴⁰Ar- ³⁹ Ar; K/Ar) formed during peak compression. Crustal deformation was manifested by regional folding and thrust faulting. Laser-ablation ICPMS ²³⁸U-²⁰⁶Pb dating of detrital and rock-hosted zircon grains, together with ⁴⁰Ar-³⁹Ar and K/Ar radiometric dating and whole-rock chemistry define five magmatic cycles which extended from the late Miocene to the present. These produced four stratovolcanoes that were built and eroded in successive eruptive and erosional cycles. These semi-continuous magmatic products recorded the covariation of magmatic physico-chemical variables as the arc underwent a transition from normal subduction to cessation of subduction associated with compressive crustal stress during arc-arc collision. The volcanic series evolved from water-poor pyroxene-hornblende-phyric basaltic andesites to hornblende-pyroxene andesites and to waterrich hornblende-biotite dacites. Major and trace element chemical data reveal progressive advance of hornblende saturation, and retreat of plagioclase saturation in the crystallisation sequence of successive magmatic cycles. High Sr/Y ratios are commonly attributed as a chemical feature of adakites, which are ascribed an origin by partial melting of an eclogitic source where refractory garnet retains Y. In contrast, high Sr/Y ratios in the Tampakan district are caused by hydrous, high-pressure crystal fractionation in the lower crust, where suppression of plagioclase crystallisation by high magmatic water activities allows Sr to accumulate during crystal fractionation, and crystallisation of hornblende to form lower-crustal hornblende-augitemagnetite cumulates depletes Y from the residual melt. This element ratio (Sr/Y) is identified as a qualitative indicator of the magmatic water activity, and is a robust guide to the ore-forming potential of a magmatic series. Magmatic temperatures for the series range from 765°C to 909°C and volcanic log /02 varies between NNO+l.53 and NN0+2.50. Sulphur abundances in the melt are low (312 to 57 ppm) and decrease systematically with temperature. Data points for the series plot around the anhydrite-saturation curve in :ΣSmelt-temperature coordinates, consistent with sulphur speciation calculations based on measured oxygen fugacity that indicate SO₃:H₂S abundance proportions between ~200: 1 and ~6,000: 1 in the melt. The magmatic series were saturated with anhydrite during much of their evolution. Magmatic water contents were calculated for the successive magmatic cycles that erupted over the past 7 Myr. Magmatic water contents calculated using the Housh and Luhr (1991) plagioclase-melt Na-Ca exchange geohygrometer reveal water contents that increase from 4.1 % in the late Miocene to up to 8.2 % in the Pleistocene. ²³⁸U-²⁰⁶Pb geochronology on 471 zircon samples from the Tampakan volcanic succession were used to parameterise time series in chemical compositions of volcanic rocks and phenocrysts, and time-series in magmatic temperature, oxygen fugacity and wt.% H₂0 in the pre-eruptive magma over the past 7 Myr. U/Ti, U/Ge and Th/Ti ratios in dated detrital zircon grains resolve multiple million-year-scale magma recharge-and-crystallisation cycles within a long-lived lowercrustal chamber. This deep reservoir resides at 18-22 km depth (~5-6 kbars; Al-in-hornblende geobarometry). The cyclic ramp-up and drop of these element ratios coincides with a 7 Myr-long "sawtooth" cyclic ramp-up in concentrations of volatiles and crystal incompatible trace elements in erupted andesites and dacites. Water contents climbed from 4.1 wt.% to 8.2 wt.% as SiO₂ evolved from 57 to 67 wt.%, because the accumulation of volatiles in residual melt was passed down through multiple cycles of magma-chamber replenishment, magma mixing and crystallisation. The lower-crustal chamber was periodically tapped to form overlying subvolcanic chambers and four overprinting stratovolcanoes within the late Miocene to Recent Tampakan polygenetic volcanic complex. A lower-crustal magma chamber having a long lifespan and slow crystallisation rate relative to the frequency of recharge is required in order to generate the observed petrochemical trends and cyclic climb magmatic water content relative to SiO₂ content of the melts. This longevity is thermally and physically permissible where magma entrapment in the lower crust occurs in compressive stress regimes beneath volcanic arc segments that undergo transient collision, or are under-thrust by buoyant segments of the subducting plate. Calculated buoyancy forces of 1-3 km thick basaltic to andesitic melt columns in the ductile lower crust are comparable to horizontal tectonic stresses in orogenic zones, indicating that melt entrapment can be modulated by an ambient stress regime that inhibits magma ascent by dyke propagation. Numerical thermal models created using the 2-D graphical, user-interactive, heat flow program KWare HEAT predict that lower-crustal sills that are entrapped in the lower crust cool extremely slowly, with residual melt fractions remaining above the wet solidus for several million years, so intermittently erupted magmas exhibit chemical continuity over the ~3-10 Myr period of crustal compression in collisional volcanic arcs. The results from this integrated study of the Tampakan district indicate that the spatial and temporal clustering of magmatic Cu-Au porphyry ores in volcanic arcs is a product of shared regional compressive stress which inhibits magma ascent by sub-vertical dyke propagation and promotes development of sub-horizontal magma chambers in the lower crust, where the trapped magma proceeds to crystallise cumulates until the residual melt evolves to sufficient buoyancy to propagate sub-vertical dykes. Volcanics and epizonal plutons related to porphyry-Cu ore in the Tampakan district display trace-element evidence that the melts segregated from high pressure (lower-crustal) cumulates consisting largely of Al-rich augite and hornblende, but little or no plagioclase. Magma chambers in hot lower crust cool very slowly and live long enough to undergo multiple, million-year-scale cycles of magma replenishment and fractional crystallisation and tapping, over the course of which concentrations of "incompatible components" such as H₂O, Cl and SO₃ are passed on through multiple cycles of chamber replenishment and crystallisation and minor discharge and so accumulate to exceptional concentrations relative to major elements (Si₂, AliO₃, Na₂O etc). Successive batches of increasingly H₂O-rich melt leaving the lower crustal chamber began to exsolve a hydrothermal fluid at successively greater depths. Hydrothermal fluids that exsolve at greater depths are denser and more efficient in scavenging Cu from the melt, because the fluid-melt partition coefficient of Cu is extremely pressure sensitive. This study suggests that the transition to metallogenic fertility of magmas at convergent margins is ultimately modulated by compressional stress that induces deep entrapment, build-up to anomalously high water contents and consequent magmatichydrothermal fluid exsolution at deep mid-crustal depths in ascending magmas, and segregation of Cu-rich brines to apical parts of the ascending magma body. The superposition of both porphyry Cu and high-sulphidation-epithermal Cu-Au mineralisation in the Tampakan deposit, and the partial preservation of the host stratovolcanic edifice, allows investigation of the genetic relationship between these two deposit styles and study of the uppercrustal palaeohydrology of a stratocone-centred, ore-forming magmatic-hydrothermal system. ⁴⁰Ar-³⁹Ar dating reveals that the porphyry Cu mineralisation formed during the early Pliocene (4.24 ± 0.02 Ma, 4.26 ± 0.02 Ma), whereas high-sulphidation-epithermal mineralisation formed during the middle Pliocene (3.23 ± 0.03 Ma, 3.34 ± 0.05 Ma, 3.28 ± 0.06 Ma). The ~1 Myr age difference requires their formation from separate magmatic-hydrothermal systems that were established in the upper crust from different batches of melt. Petrochemical trends indicate that both hydrothermal systems emanated from epizonal magma chambers fed from a shared, longlived lower crustal magma reservoir. Erosion of Cycle 3 andesites during collisional uplift exposed porphyry-Cu-stage quartz stockwork veins at the palaeosurface in less than ~ 350 Kyr after porphyry mineralisation. After unroofing of the porphyry system, construction of the Cycle 4a middle Pliocene volcanic centre commenced at 3.93 Ma. A cryptic unconformity between Cycle 3 and Cycle 4a andesites became the principal surface for a stratigraphic groundwater aquifer that acted as a condensor for high-sulphidation-stage magmatic volatiles. Three aspects of the Tampakan high-sulphidation-epithermal palaeohydrological system are investigated: 1) the physical properties and hydrological transport mechanics of the magmatic supercritical fluids along the "magmatic vapor plume" from the site of accumulation in the carapace beneath the deposit to the meteoric- and magmatic-fluid mixing environment within the deposit; 2) identification of the composition and thermal properties of the fluid end-members and the geometry of mixing paths within the deposit; 3) the geometry and relative mixing ratios of magmatic and meteoric groundwater in various regional alteration zones of the district and the effect of topographic forcing of hybrid hydrothermal fluids along the western flank of the volcanic complex. The Tampakan high-sulphidation epithermal mineralisation formed from a dense vapor-like supercritical fluid with a density of ~ 0 .15 to 0 .25 g/ cc that exsolved from a relatively mafic andesitic melt emplaced at shallow depths of 2.6 km to 4 km. These melts had significantly less magmatic water (~3-4 wt.% H20) than the more evolved andesitic melts associated with precursor porphyry Cu mineralisation (~ 6.0 wt.% H20). The lower water content of highsulphidation- stage melts allowed shallower crustal emplacement and fluid exsolution as a low-density vapor, whereas more water-rich porphyry-stage melts from the preceding cycle exsolved a dense supercritical brine phase (0.3 to 0.45 g/cc) at deeper (~ 6 to 8 km) crustal levels. Pressure and enthalpy constraints calculated for the high-sulphidation-stage magmatic fluid at several points along its flow path provide substantial insights into the magmatic fluid transport process. The magmatic vapor ascended along a nearly isochoric decompression path from the site of exsolution to the site of fluid mixing. The density of the vapor increased from ~0.2 g/cc to ~0.3 g/cc over a vertical ascent distance of ~1.2 km. During transit, the vapor cooled conductively by ~350°C. The nearly isochoric vapor transport mechanism through the lithostatically pressured, ductile rock column requires propagation of fluid-filled, fine-scale, migratory hydrofractures, with intimate contact between the vapor and the ductile wall rocks during vapor ascent. This ensured substantial conductive cooling (~875°C to ~525°C) along the ascent path and that thermal contraction of the vapor balanced the tendency to expand with decompression. Instantaneous isoenthalpic decompression of the magmatic-vapor-charged mobile hydrofractures at the lithostatic-hydrostatic interface (brittle/ductile transition) near the base of the deposit, was associated with "instantaneous" cooling of the supercritical vapor from ~525°C to ~375°C. This pressure-temperature quenching efficiently condensed magmatic vapor to a modestly saline (5 wt.% NaCl equivalent) condensate that concurrently mixed with ambient meteoric water within a palaeo-aquifer at the base of the hydrostatic regime. Cooling of the dense magmatic condensate liquid (~0.62 g/cc) by dilution in the mixing column was associated with hydrolysis of SO₂ to H₂SO₄ , HSO₄ , SO₄ and to H₂S which in turn produced a vertical pH gradient and a vertical textural zonation in alteration facies in the advanced-argillic lithocap. Oxygen-isotope and enthalpy balances indicate that sericite in the deep portions of the deposit and pyrophyllite at higher and peripheral regions precipitated from hybrid magmatic-meteoric waters which comprised ~50% magmatic condensate. The hot, hybrid fluids formed a thermally buoyant plume due to transfer of heat from the high-enthalpy magmatic vapor into the meteoric water regime. The plume ascended and became entrained into a stratabound aquifer system on the west slope of the volcano. A substantial hydraulic head in the aquifer is implied by downstratigraphic- slope deflections in the time-integrated proxy fluid isotherms identified by calibration of PIMA II™ infrared spectral parameters with the chemical composition of potassic white mica. These calibrations reveal chemical trends in the composition of potassic white micas that can be tracked across several alteration environments. A central, and deep-seated, hightemperature zone of nearly stoichiometric muscovite coincides with the locus of the inferred magmatic vapour plume. This zone is transitional to shallower and peripheral regions where there is an increasing replacement of K ions by neutral H₂O molecules in the potassic white mica crystal structure, and decreasing Cu and Au grades. These trends reflect a central, deep-level zone of high fluid temperatures, with cooling paths deflected down-palaeo-slope at shallower levels in the volcanic edifice. Substantial magmatic fluid ascended into the hydrostatic regime along a 5 km by 1.5 km wide NNE-trending fault zone that partly controlled mineralisation. Lateral outflow of the hybrid fluids was controlled by regional dilational faults that transect the volcanic centre. Zoning of hydrothermal mineral compositions and assemblages reveal a superb example of hydrothermal plume-groundwater interaction and downslope dispersion. The plume of heated meteoric water and admixed magmatic condensate in the hydrostatic environment was centred within the Tampakan deposit. The deposit is located where gradients in the hybrid fluid's temperature proportion of magmatic fluid are greatest. Mineralisation was localised in the zone of steep temperature and pressure gradients associated with the interface between a deep lithostatic-pressured plume and a shallow hydrostatic-pressured plume

Historisches Ortslexikon für die Altmark

Das zweibändige Historische Ortslexikon für die Altmark erfasst sämtliche Ortschaften und Wohnplätze der Altmark (in den Grenzen von 1686) mit eigenem Namen, die seit dem hochmittelalterlichen Landesausbau schriftlich überliefert sind. Jeder Artikel enthält neben Ortsnamen, geografischer Lage und Kreiszugehörigkeit Informationen zur ersten schriftlichen Erwähnung, zu Art und Verfassung der Siedlung nebst Gemeindezugehörigkeit, Gemarkungsgröße, Siedlungsform, Gerichtszugehörigkeit sowie insbesondere zu Herrschaftszugehörigkeit, Wirtschafts- und Sozialstruktur, schließlich zu Baudenkmalen und Bevölkerungsziffern. Die Ortsbeschreibungen werden ergänzt durch einen umfangreichen Index, ein Wüstungsregister und eine kartografische Darstellung der Altmark. Somit steht Historikern und ortsgeschichtlich Interessierten ein umfassendes Nachschlagewerk zur Verfügung, das auf der umfassenden Auswertung der gedruckten Literatur, aber vor allem der archivalischen Zeugnisse beruht und das als Grundlage für weiterführende lokalhistorische Arbeiten unverzichtbar bleiben wird

Statistical Methods for Identifying Demographic Structure in DNA Sequence Alignments

All life on Earth, from viruses and bacteria, trees and flowers, to birds and human beings, can be traced back to a single common ancestor. However, the evolutionary history that led to this diversity of life is a complicated story that we do not yet fully understand. Since the discovery of the structure of deoxyribonucleic acid (DNA) in 1953, and the development of DNA sequencing technology, researchers have been using similarities and differences in the genomes of organisms to better understand the relationships between species. However, due to the complexity of the evolutionary history of life, simplifying assumptions must be made to make mathematical models tractable. It must then be of paramount importance for researchers to be able to identify when the simplifying assumptions of a specific model are unreasonable. In this thesis we present two projects, and although they are different in implementation, both attempt to investigate simplifying assumptions in the closely related fields of population genetics and phylogenetics. However, we also present applications of our projects where the results of our work are not used in assessing assumptions for further analyses, but are of standalone interest to researchers. Our first project is concerned with the development of a method for constructing coordinate representations for single-copy DNA, such as mitochondrial DNA (mtDNA) or Y-chromosomal DNA, analogous to the use of PCA for nuclear DNA. We construct a coordinate system such that, given p informative sites in an alignment of n individuals, returns p-dimensional coordinates for each n individuals. We order the dimensions by the proportion of variability each dimension captures in the overall genetic diversity. From these coordinates in \genetic space" researchers may perform a number of down stream analyses. It is possible to optimally visualise high-dimensional sequence data in two or three dimensions. One may use our method to identify closely related individuals, identify sites in the alignment that are closely linked, or to use the same coordinate space to nd sites that are closely linked with groups of individuals. Finally, one may choose to test for significant relationships between the structure of the coordinates in genetic space, and metadata recorded on sequenced individuals, indicating demographic variables that are highly related to the evolutionary history of an alignment. This final application of our method, where one may test for demographic structure in sequence data, is of key importance to the theme of discovering when simplifying assumptions of analyses are not reasonable. Through the comparison of coordinates in gene space, and any demographic variables of interest, researchers may explore whether or not the individuals in the alignment indicate population substructure. For example, one may investigate if there appears to be a phylogeographic structure to the individuals forming distinct subpopulations, and if migration appears to occur between subpopulations. Through empirical data, we show that our method can readily recover tree-like structure, identify strong genetic groupings based on qualitative traits and show that we are able to recover phylogeographic signal given provenanced sampling information. We show that our method can even be used to suggest routes of migration based on mtDNA. Finally we apply our method to modern Aboriginal Australian mtDNA to show strong evidence for discrete geographic populations of Aboriginal Australian peoples that display permanence on the Australian landscape dating back to the original colonisation of Australia 50 thousand years before present (kya). Our second project is concerned with identifying departures from a tree-like evolutionary history at the species level. It is not uncommon for closely related species (Species A and C say) to still be capable of interbreeding, and producing viable \hybrid" offγspring (Species B say). Under these conditions, a phylogenetic tree cannot describe the evolutionary history of the hybrid species, and instead an admixture graph may be a better description. We begin by considering the evolutionary history of three species: a hybrid organism that has undergone some independent evolution (Species B), and two \parent" organisms, Species A and C. Relatively long, contiguous regions of the genome of Species B will have undergone no recombination since the admixture event. These regions will have been contributed by either Species A (and hence will be more closely related to Species A), or Species C. We aim to estimate the proportion of the genome contributed by Species A, and denote this by considering the proportion of informative site patterns that indicate evidence for the two possible ancestries. The mixing proportion is the parameter of interest in our analyses. However, due to the classical problem of the non-identifiability of mixing parameters in multinomial distributions, we describe two Bayesian methods for estimating γ. Our first method places prior distributions on the parameters of the model, and uses Approximate Bayesian Computation (ABC) to estimate the marginal posterior distribution of γ. Our second, closely related method, instead estimates the marginal posterior distribution of via numerical integration. We show via a simulation study that our methods can accurately estimate the true value of γ, and perform well under biologically reasonable scenarios. However, we also find that our methods suffer from a relatively small positive bias for small values of γ, i.e., when one species of the parent species contributes very little to the genome of the hybrid species. We compare the performance of our method to the popular method of the ratio of f4 statistics. We do this by estimating the proportion of Neanderthal ancestry in pre-ice age European human samples and comparing our results to the finding of Fu et al. [18]. We show that our method recovers extremely similar estimates of Neanderthal ancestry with no apparent systematic bias when compared to the results of Fu et al.. Finally we apply our method to the genomes of Late Pleistocene European bison (Bison bonasus) and Steppe Bison (Bison priscus) to understand the evolutionary history of bovid megafauna in Europe over the last seventy thousand years. It was thought that before 10 kya the only bovid present in Europe was the Steppe bison. However, from bone samples found dating from the present day, and back to approximately 70 kya, mtDNA indicated a second bison species was also roaming Europe before 10 kya, more closely related to modern cattle than the Steppe bison. After nuclear DNA was sequenced, we were able to show that this new species of bovid was actually a hybrid offspring of Aurochs (the ancestor of modern cattle) and Steppe bison, an event that occurred approximately 120 kya. We used our method, in concert with the ratio of f4 statistics, to show that the hybrid species contained approximately 10% Aurochs and 90% Steppe bison ancestry.Thesis (Ph.D.) -- University of Adelaide, School of Mathematical Sciences, 201

PyDamage: automated ancient damage identification and estimation for contigs in ancient DNAde novoassembly

DNA de novo assembly can be used to reconstruct longer stretches of DNA (contigs), including genes and even genomes, from short DNA sequencing reads. Applying this technique to metagenomic data derived from archaeological remains, such as paleofeces and dental calculus, we can investigate past microbiome functional diversity that may be absent or underrepresented in the modern microbiome gene catalogue. However, compared to modern samples, ancient samples are often burdened with environmental contamination, resulting in metagenomic datasets that represent mixtures of ancient and modern DNA. The ability to rapidly and reliably establish the authenticity and integrity of ancient samples is essential for ancient DNA studies, and the ability to distinguish between ancient and modern sequences is particularly important for ancient microbiome studies. Characteristic patterns of ancient DNA damage, namely DNA fragmentation and cytosine deamination (observed as C-to-T transitions) are typically used to authenticate ancient samples and sequences, but existing tools for inspecting and filtering aDNA damage either compute it at the read level, which leads to high data loss and lower quality when used in combination with de novo assembly, or require manual inspection, which is impractical for ancient assemblies that typically contain tens to hundreds of thousands of contigs. To address these challenges, we designed PyDamage, a robust, automated approach for aDNA damage estimation and authentication of de novo assembled aDNA. PyDamage uses a likelihood ratio based approach to discriminate between truly ancient contigs and contigs originating from modern contamination. We test PyDamage on both on simulated aDNA data and archaeological paleofeces, and we demonstrate its ability to reliably and automatically identify contigs bearing DNA damage characteristic of aDNA. Coupled with aDNA de novo assembly, Pydamage opens up new doors to explore functional diversity in ancient metagenomic datasets

Historisches Ortslexikon für die Altmark

Das zweibändige Historische Ortslexikon für die Altmark erfasst sämtliche Ortschaften und Wohnplätze der Altmark (in den Grenzen von 1686) mit eigenem Namen, die seit dem hochmittelalterlichen Landesausbau schriftlich überliefert sind. Jeder Artikel enthält neben Ortsnamen, geografischer Lage und Kreiszugehörigkeit Informationen zur ersten schriftlichen Erwähnung, zu Art und Verfassung der Siedlung nebst Gemeindezugehörigkeit, Gemarkungsgröße, Siedlungsform, Gerichtszugehörigkeit sowie insbesondere zu Herrschaftszugehörigkeit, Wirtschafts- und Sozialstruktur, schließlich zu Baudenkmalen und Bevölkerungsziffern. Die Ortsbeschreibungen werden ergänzt durch einen umfangreichen Index, ein Wüstungsregister und eine kartografische Darstellung der Altmark. Somit steht Historikern und ortsgeschichtlich Interessierten ein umfassendes Nachschlagewerk zur Verfügung, das auf der umfassenden Auswertung der gedruckten Literatur, aber vor allem der archivalischen Zeugnisse beruht und das als Grundlage für weiterführende lokalhistorische Arbeiten unverzichtbar bleiben wird

A systematic investigation of human DNA preservation in medieval skeletons

Ancient DNA (aDNA) analyses necessitate the destructive sampling of archaeological material. Currently, the cochlea, part of the osseous inner ear located inside the petrous pyramid, is the most sought after skeletal element for molecular analyses of ancient humans as it has been shown to yield high amounts of endogenous DNA. However, destructive sampling of the petrous pyramid may not always be possible, particularly in cases where preservation of skeletal morphology is of top priority. To investigate alternatives, we present a survey of human aDNA preservation for each of ten skeletal elements in a skeletal collection from Medieval Germany. Through comparison of human DNA content and quality we confirm best performance of the petrous pyramid and identify seven additional sampling locations across four skeletal elements that yield adequate aDNA for most applications in human palaeogenetics. Our study provides a better perspective on DNA preservation across the human skeleton and takes a further step toward the more responsible use of ancient materials in human aDNA studies.Introduction Results Discussion Conclusions Methods - Sample selection, pre‑treatment, and bone powder generation - DNA extraction, library preparation, and sequencing - Evaluation criteria - Contamination estimates - Mapping - Calculations - Mixed effects modellin

A Woman with a Sword? : Weapon Grave at Suontaka Vesitorninmäki, Finland

Publisher Copyright: © 2021 European Association of Archaeologists.In 1968, a weapon grave with brooches was found at Suontaka Vesitorninmäki, Hattula, Finland. Since then, the grave has been interpreted as evidence of powerful women, even female warriors and leaders in early medieval Finland. Others have denied the possibility of a woman buried with a sword and tried to explain it as a double burial. We present the first modern analysis of the grave, including an examination of its context, a soil sample analysis for microremains, and an aDNA analysis. Based on these analyses, we suggest a new interpretation: the Suontaka grave possibly belonged to an individual with sex-chromosomal aneuploidy XXY. The overall context of the grave indicates that it was a respected person whose gender identity may well have been non-binary.Peer reviewe

Differential nuclear and mitochondrial DNA preservation in post-mortem teeth with implications for forensic and ancient DNA studies

Major advances in genetic analysis of skeletal remains have been made over the last decade, primarily due to improvements in post-DNA-extraction techniques. Despite this, a key challenge for DNA analysis of skeletal remains is the limited yield of DNA recovered from these poorly preserved samples. Enhanced DNA recovery by improved sampling and extraction techniques would allow further advancements. However, little is known about the post-mortem kinetics of DNA degradation and whether the rate of degradation varies between nuclear and mitochondrial DNA or across different skeletal tissues. This knowledge, along with information regarding ante-mortem DNA distribution within skeletal elements, would inform sampling protocols facilitating development of improved extraction processes. Here we present a combined genetic and histological examination of DNA content and rates of DNA degradation in the different tooth tissues of 150 human molars over short-medium post-mortem intervals. DNA was extracted from coronal dentine, root dentine, cementum and pulp of 114 teeth via a silica column method and the remaining 36 teeth were examined histologically. Real time quantification assays based on two nuclear DNA fragments (67 bp and 156 bp) and one mitochondrial DNA fragment (77 bp) showed nuclear and mitochondrial DNA degraded exponentially, but at different rates, depending on post-mortem interval and soil temperature. In contrast to previous studies, we identified differential survival of nuclear and mtDNA in different tooth tissues. Furthermore histological examination showed pulp and dentine were rapidly affected by loss of structural integrity, and pulp was completely destroyed in a relatively short time period. Conversely, cementum showed little structural change over the same time period. Finally, we confirm that targeted sampling of cementum from teeth buried for up to 16 months can provide a reliable source of nuclear DNA for STR-based genotyping using standard extraction methods, without the need for specialised equipment or large-volume demineralisation steps.Denice Higgins, Adam B. Rohrlach, John Kaidonis, Grant Townsend, Jeremy J. Austi

Mitogenomes reveal two major influxes of Papuan ancestry across Wallacea following the last glacial maximum and Austronesian contact

The tropical archipelago of Wallacea contains thousands of individual islands interspersed between mainland Asia and Near Oceania, and marks the location of a series of ancient oceanic voyages leading to the peopling of Sahul—i.e., the former continent that joined Australia and New Guinea at a time of lowered sea level—by 50,000 years ago. Despite the apparent deep antiquity of human presence in Wallacea, prior population history research in this region has been hampered by patchy archaeological and genetic records and is largely concentrated upon more recent history that follows the arrival of Austronesian seafarers ~3000–4000 years ago (3–4 ka). To shed light on the deeper history of Wallacea and its connections with New Guinea and Australia, we performed phylogeographic analyses on 656 whole mitogenomes from these three regions, including 186 new samples from eight Wallacean islands and three West Papuan populations. Our results point to a surprisingly dynamic population history in Wallacea, marked by two periods of extensive demographic change concentrated around the Last Glacial Maximum ~15 ka and post-Austronesian contact ~3 ka. These changes appear to have greatly diminished genetic signals informative about the original peopling of Sahul, and have important implications for our current understanding of the population history of the region.1. Introduction 2. Materials and Methods 2.1. Sample Collection and Ethics 2.2. Mitochondrial Sequence Generation 2.3. Combined Wallacea–Sahul Dataset 2.4. Phylogenetic Parameter Estimation 2.5. Using Ancestral Node Dates from Geographically Exclusive Clades to Infer Demographic History 2.6. Migration Model Inference and Testing 2.7. Simulating and Estimating the Timing of Migration Events 3. Results 3.1. Summary of New Mitochondrial Haplogroups from Wallacea and West Papua 3.2. Phylogeographic Analyses 4. Discussion 4.1. Post-LGM Population Expansions and Movements 4.2. Redistribution of Papuan mtDNA Lineages Following Austronesian Contact 4.3. Comparison with Wallacean Archaeological and Linguistic Records 5. Conclusion