An R package for statistical provenance analysis

© 2016 Elsevier B.V. This paper introduces provenance, a software package within the statistical programming environment R, which aims to facilitate the visualisation and interpretation of large amounts of sedimentary provenance data, including mineralogical, petrographic, chemical and isotopic provenance proxies, or any combination of these. provenance comprises functions to: (a) calculate the sample size required to achieve a given detection limit; (b) plot distributional data such as detrital zircon U-Pb age spectra as Cumulative Age Distributions (CADs) or adaptive Kernel Density Estimates (KDEs); (c) plot compositional data as pie charts or ternary diagrams; (d) correct the effects of hydraulic sorting on sandstone petrography and heavy mineral composition; (e) assess the settling equivalence of detrital minerals and grain-size dependence of sediment composition; (f) quantify the dissimilarity between distributional data using the Kolmogorov-Smirnov and Sircombe-Hazelton distances, or between compositional data using the Aitchison and Bray-Curtis distances; (e) interpret multi-sample datasets by means of (classical and nonmetric) Multidimensional Scaling (MDS) and Principal Component Analysis (PCA); and (f) simplify the interpretation of multi-method datasets by means of Generalised Procrustes Analysis (GPA) and 3-way MDS. All these tools can be accessed through an intuitive query-based user interface, which does not require knowledge of the R programming language. provenance is free software released under the GPL-2 licence and will be further expanded based on user feedback

Effects on Plant Growth and Reproduction of a Peach R2R3-MYB Transcription Factor Overexpressed in Tobacco

In plants, anthocyanin production is controlled by MYB and bHLH transcription factors. In peach, among the members of these families, MYB10.1 and bHLH3 have been shown to be the most important genes for production of these pigments during fruit ripening. Anthocyanins are valuable molecules, and the overexpression of regulatory genes in annual fast-growing plants has been explored for their biotechnological production. The overexpression of peach MYB10.1 in tobacco plants induced anthocyanin pigmentation, which was particularly strong in the reproductive parts. Pigment production was the result of an up-regulation of the expression level of key genes of the flavonoid biosynthetic pathway, such as NtCHS, NtCHI, NtF3H, NtDFR, NtANS, and NtUFGT, as well as of the proanthocyanidin biosynthetic pathway such as NtLAR. Nevertheless, phenotypic alterations in transgenic tobacco lines were not only limited to anthocyanin production. Lines showing a strong phenotype (type I) exhibited irregular leaf shape and size and reduced plant height. Moreover, flowers had reduced length of anther\u2019s filament, nondehiscent anthers, reduced pistil length, aborted nectary glands, and impaired capsule development, but the reproductive parts including androecium, gynoecium, and petals were more pigmented that in wild type. Surprisingly, overexpression of peach MYB10.1 led to suppression of NtMYB305, which is required for floral development and, of one of its target genes, NECTARIN1 (NtNCE1), involved in the nectary gland formation. MYB10.1 overexpression up-regulated JA biosynthetic (NtAOS) and signaling (NtJAZd) genes, as well as 1-aminocyclopropane-1-carboxylate oxidase (NtACO) in flowers. The alteration of these hormonal pathways might be among the causes of the observed floral abnormalities with defects in both male and female gametophyte development. In particular, approximately only 30% of pollen grains of type I lines were viable, while during megaspore formation, there was a block during FG1 (St3-II). This block seemed to be associated to an excessive accumulation of callose. It can be concluded that the overexpression of peach MYB10.1 in tobacco not only regulates flavonoid biosynthesis (anthocyanin and proanthocyanidin) in the reproductive parts but also plays a role in other processes such as vegetative and reproductive development

Provenance and recycling of Sahara Desert sand

We here present the first comprehensive provenance study of the Sahara Desert using a combination of multiple provenance proxies and state-of-the-art statistical analysis. Our dataset comprises 44 aeolian-dune samples, collected across the region from 12°N (Nigeria) to 34°N (Tunisia) and from 33°E (Egypt) to 16°W (Mauritania) and characterized by bulk-petrography, heavy-mineral, and detrital-zircon Usingle bondPb geochronology analyses. A set of statistical tools including Multidimensional Scaling, Correspondence Analysis, Individual Difference Scaling, and General Procrustes Analysis was applied to discriminate among sample groups with the purpose to reveal meaningful compositional patterns and infer sediment transport pathways on a geological scale. The overall homogenity across sand samples, however, precluded a detailed narrative. Saharan dune fields are, with a few local exceptions, composed of pure quartzose sand with very poor heavy-mineral suites dominated by durable zircon, tourmaline, and rutile. Some feldspars, amphibole, epidote, garnet, or staurolite occur closer to basement exposures, and carbonate grains, clinopyroxene and olivine near a basaltic field in Libya. Relatively varied compositions also characterize sand along the Nile Valley and the southern front of the Anti-Atlas fold belt in Morocco. Otherwise, from the Sahel to the Mediterranean Sea and from the Nile River to the Atlantic Ocean, sand consists nearly exclusively of quartz and durable minerals. These have been concentrated through multiple cycles of erosion, deposition, and diagenesis of Phanerozoic siliciclastic rocks during the long period of relative tectonic quiescence that followed the Neoproterozoic Pan-African orogeny, the last episode of major crustal growth in the region. The principal ultimate source of recycled sand is held to be represented by the thick blanket of quartz-rich sandstones that were deposited in the Cambro-Ordovician from the newly formed Arabian-Nubian Shield in the east to Mauritania in the west. Durability of zircon grains and their likelihood to be recycled from older sedimentary rocks argues against the assumption, too often implicitly taken for granted in provenance studies based on detrital-zircon ages, that their age distribution reflects transport pathways existing at the time of deposition rather than inheritance from multiple and remote landscapes of the past

Provenance of Kalahari Sand: Paleoweathering and recycling in a linked fluvial-aeolian system

We here review what is known about the dunefields and fluvial systems of the Kalahari Basin in terms of geological setting and Quaternary dynamics and set out what has been hypothesized about the provenance of Kalahari sand so far. Previous work has tackled this problem by applying a limited number of techniques (mostly sediment textures and heavy minerals) to parts of the large dryland. The generally highly quartzose mineralogy of aeolian dunes and their compositional variability have been only broadly evaluated and several sedimentological issues have thus remained controversial, including the relative role played by fluvial processes versus aeolian reworking of older sediments and weathering controls. This reveals a need for a systematic provenance study that considers the entire basin. For this reason, here we combine original petrographic, heavy-mineral, and detrital-zircon geochronology data with previously published clay-mineral, geochemical, and geochronological information to present the first comprehensive provenance study of the vast Kalahari sand sea. Our multi-proxy dataset comprises 100 samples, collected across the Kalahari Basin from 11°S (NW Zambia) to 28°S (NW South Africa) and from 15°E (Angola) to 28°30′W (Zimbabwe). Kalahari aeolian-dune sand mostly consists of monocrystalline quartz associated with durable heavy minerals and thus drastically differs from coastal dunefields of Namibia and Angola, which are notably richer in feldspar, lithic grains, and chemically labile clinopyroxene. The western Kalahari dunefield of southeastern Namibia is distinguished by its quartz-rich feldspatho-quartzose sand, indicating partly first-cycle provenance from the Damara Belt and Mesoproterozoic terranes. Within the basin, supply from Proterozoic outcrops is documented locally. Composition varies notably at the western and eastern edges of the sand sea, reflecting partly first-cycle fluvial supply from crystalline basements of Cambrian to Archean age in central Namibia and western Zimbabwe. Basaltic detritus from Jurassic Karoo lavas is dominant in aeolian dunes near Victoria Falls. Bulk-sediment petrography and geochemistry of northern and central Kalahari pure quartzose sand, together with heavy-mineral and clay-mineral assemblages, indicate extensive recycling via aeolian and ephemeral-fluvial processes in arid climate of sediment strongly weathered during previous humid climatic stages in subequatorial Africa. Distilled homogenized composition of aeolian-dune sand thus reverberates the echo of paleo-weathering passed on to the present landscape through multiple episodes of fluvial and aeolian recycling. Intracratonic sag basins such as the Kalahari contain vast amounts of quartz-rich polycyclic sand that may be tapped by rivers eroding backwards during rejuvenation stages associated with rift propagation. Such an event may considerably increase the sediment flux to the ocean, fostering the progradation of river-fed continental-embankments, as documented by augmented accumulation rates coupled with upward increasing mineralogical durability in the post-Tortonian subsurface succession of the Zambezi Delta. The Central Kalahari is not a true desert. It has none of the naked, shifting sand dunes that typify the Sahara and other great deserts of the world. In some years the rains may exceed twenty — once even forty — inches, awakening a magic green paradise.” Mark Owens, Cry of the Kalahari

Zircon as a provenance tracer: Coupling Raman spectroscopy and Usingle bondPb geochronology in source-to-sink studies

Usingle bondPb zircon geochronology is one of the most widely used techniques in sedimentary provenance analysis. Unfortunately, the ability of this method to identify sediment sources is often degraded by sediment recycling and mixing of detritus from different source rocks sharing similar age signatures. These processes create non-unique zircon Usingle bondPb age signatures and thereby obscure the provenance signal. We here address this problem by combining detrital zircon Usingle bondPb geochronology with Raman spectroscopy. The position and width of the Raman signal in zircon scales with its degree of metamictization, which in turn is sensitive to temperature. Thus, combined U-Pb + Raman datasets encode information about the crystallization history of detrital zircons as well as their thermal history. Using three borehole samples from Mozambique as part of a source-to-sink study of interest for hydrocarbon exploration, we show that zircon populations with similar Usingle bondPb age distributions can exhibit different Raman signatures. The joint U-Pb + Raman analysis allowed us to identify three different annealing trends, which were linked to specific thermal events. Thus we were able to differentiate a dominant Pan-African Usingle bondPb age peak into several sub-populations and highlight the major effect of Karoo tectono-magmatic events. In our case study, we used Raman also as a means to systematically identify all zircon grains in heavy-mineral mounts, resulting in considerable time savings. Raman spectroscopy is a non-destructive and cost-effective method that is easily integrated in the zircon Usingle bondPb dating workflow to augment the resolution power of detrital zircon Usingle bondPb geochronology

The Segmented Zambezi Sedimentary System from Source to Sink: 1. Sand Petrology and Heavy Minerals

The Zambezi River rises at the center of southern Africa, flows across the low-relief Kalahari Plateau, meets Karoo basalt, plunges into Victoria Falls, follows along Karoo rifts, and pierces through Precambrian basement to eventually deliver its load onto the Mozambican passive margin. Reflecting its polyphase evolution, the river is subdivided into segments with different geological and geomorphological character, a subdivision finally fixed by man’s construction of large reservoirs and faithfully testified by sharp changes in sediment composition. Pure quartzose sand recycled from Kalahari desert dunes in the uppermost tract is next progressively enriched in basaltic rock fragments and clinopyroxene. Sediment load is renewed first downstream of Lake Kariba and next downstream of Lake Cahora Bassa, documenting a stepwise decrease in quartz and durable heavy minerals. Composition becomes quartzo-feldspathic in the lower tract, where most sediment is supplied by high-grade basements rejuvenated by the southward propagation of the East African rift. Feldspar abundance in Lower Zambezi sand has no equivalent among big rivers on Earth and far exceeds that in sediments of the northern delta, shelf, and slope, revealing that provenance signals from the upper reaches have ceased to be transmitted across the routing system after closure of the big dams. This high-resolution petrologic study of Zambezi sand allows us to critically reconsider several dogmas, such as the supposed increase of mineralogical “maturity” during long-distance fluvial transport, and forges a key to unlock the rich information stored in sedimentary archives, with the ultimate goal to accurately reconstruct the evolution of this mighty river flowing across changing African landscapes since the late Mesozoic

The Euphrates-Tigris-Karun river system: Provenance, recycling and dispersal of quartz-poor foreland-basin sediments in arid climate

We present a detailed sediment-provenance study on the modern Euphrates-Tigris-Karun fluvial system and Mesopotamian foreland basin, one of the cradles of humanity. Our rich petrographic and heavy-mineral dataset, integrated by sand geochemistry and U–Pb age spectra of detrital zircons, highlights the several peculiarities of this large source-to-sink sediment-routing system and widens the spectrum of compositions generally assumed as paradigmatic for orogenic settings. Comparison of classical static versus upgraded dynamic petrologic models enhances the power of provenance analysis, and allows us to derive a more refined conceptual model of reference and to verify the limitations of the approach. Sand derived from the Anatolia-Zagros orogen contains abundant lithic grains eroded from carbonates, cherts, mudrocks, arc volcanics, obducted ophiolites and ophiolitic mélanges representing the exposed shallow structural level of the orogen, with relative scarcity of quartz, K-feldspar and mica. This quartz-poor petrographic signature, characterizing the undissected composite tectonic domain of the entire Anatolia-Iranian plateau, is markedly distinct from that of sand shed by more elevated and faster-eroding collision orogens such as the Himalaya. Arid climate in the region allows preservation of chemically unstable grains including carbonate rock fragments and locally even gypsum, and reduces transport capacity of fluvial systems, which dump most of their load in Mesopotamian marshlands upstream of the Arabian/Persian Gulf allochemical carbonate factory. Quartz-poor sediment from the Anatolia-Zagros orogen mixes with quartz-rich recycled sands from Arabia along the western side of the foreland basin, and is traced all along the Gulf shores as far as the Rub' al-Khali sand sea up to 4000 km from Euphrates headwaters

Dynamic uplift, recycling, and climate control on the petrology of passive-margin sand (Angola)

The subequatorial Angolan continental margin offers excellent conditions to test textbook theories on the composition of passive-margin sediments generated in different climatic and tectonic regimes. We use here comprehensive petrographic, heavy-mineral, geochemical and zircon-geochronology datasets on modern fluvial, beach, shelfal, and deep-marine sands and muds collected from hyperarid northern Namibia to hyperhumid Congo to investigate and assess: a) how faithfully sand mineralogy reflects the lithological and time structures of source rocks in a tectonically active rifted margin; b) in what climatic and geomorphological conditions the mark of chemical weathering becomes strong and next overwhelming; and, c) to what extent the effect of weathering can be isolated from quartz dilution by recycling of older siliciclastic strata and other physical controls including hydraulic sorting and mechanical wear. A new refined classification of feldspatho-quartzose and quartzose sands and sandstones is proposed.First-cycle quartzo-feldspathic to feldspar-rich feldspatho-quartzose sand eroded from mid-crustal granitoid gneisses of the Angola Block exposed in the dynamically uplifted Bié-Huila dome is deposited in arid southern Angola, whereas quartz-rich feldspatho-quartzose to quartzose sand characterizes the lower-relief, less deeply dissected, and more intensely weathered rifted margin of humid northern Angola. Pure quartzose, largely recycled sand is generated in the vast, low-lying hyperhumid continental interiors drained by the Congo River. The progressive relative increase of durable minerals toward the Equator results from three distinct processes acting in accord: active tectonic uplift in the arid south, and progressively stronger weathering coupled with more extensive recycling in the humid north. The quartz/feldspar ratio increases and the plagioclase/feldspar ratio decreases rapidly in first-cycle sand generated farther inland in the Catumbela catchment, reflecting stronger weathering in wet interior highlands. Discriminating weathering from recycling control is difficult in northern Angola. Although textural features including deep etch pits even on relatively resistant minerals such as quartz and microcline or rounded outline and abraded overgrowths provide valuable independent information, recycling remains as a most elusive problem in provenance analysis of terrigenous sediments