Appendix A. Gene identity within the cultivated species, and between the cultivated species and different wild species in tomato

High salinity is a severe constraint on tomato growth and productivity in many regions and situations. To obtain an ideal gene donor for improving the salt tolerance of tomato cultivars, the potential of tolerance response to salinity were evaluated for 14 tomato accessions including wild and cultivated species. By investigation of seed germination and seedling survival, a common cultivar, Solanum lycopersicum 'moneymaker', is evidenced significantly salt-tolerant among them and correspondingly, a wild accession, Solanum cheesmanniae 'LA0317', is most vulnerable to salinity. The performance of Moneymaker and LA0317 upon salinity was then compared in detail for their growth inhibition and some physiological changes. Complete dominance of Moneymaker and its high gene identity in tomato species lead us to use it in microarray experiment and apply it as gene donor for salt tolerance. The results indicated some mechanism differences between Moneymaker and LA0317 in salt response, proposed the potentially high salt tolerance of cultivated tomato and implied that Moneymaker is a valuable gene donor in this field, potentially minimizing the growth inhibition and yield reduction in transgenic plants.

The late Pliocene pollen record of ODP Site 108-658 off Cape Blanc, Atlantic Ocean

A 200 m long marine pollen record from ODP Site 658 (21°N, 19°W) reveals cyclic fluctuations in vegetation and continental climate in northwestern Africa from 3.7 to 1.7 Ma. These cycles parallel oxygen isotope stages. Prior to 3.5 Ma, the distribution of tropical forests and mangrove swamps reached Cape Blanc, 5°N of the present distribution. Between 3.5 and 2.6 Ma, forests occurred at this latitude during irregular intervals and nearly disappeared afterwards. Likewise, a Saharan paleoriver flowed continuously until isotope Stage 134 (3.35 Ma). When river discharge ceased, wind transport of pollen grains prevailed over fluvial transport. Pollen indicators of trade winds gradually increased between 3.3 and 2.5 Ma. A strong aridification of the climate of northwestern Africa occurred during isotope Stage 130 (3.26 Ma). Afterwards, humid conditions reestablised followed by another aridification around 2.7 Ma. Repetitive latitudinal shifts of vegetation zones ranging from wooded savanna to desert flora dominated for the first time between between 2.6 and 2.4 Ma as a response to the glacial stages 104, 100 and 98. Although climatic conditions, recorded in the Pliocene, were not as dry as those of the middle and Late Pleistocene, latitudinal vegetation shifts near the end of the Pliocene resembled those of the interglacial-glacial cycles of the Brunhes chron.

Results of a sediment profile and water analyses from Lake Hancza in northeastern Poland

We investigated the sedimentary record of Lake Hancza (northeastern Poland) using a multi-proxy approach, focusing on early to mid-Holocene climatic and environmental changes. AMS 14C dating of terrestrial macrofossils and sedimentation rate estimates from occasional varve thickness measurements were used to establish a chronology. The onset of the Holocene at c. 11600 cal. a BP is marked by the decline of Lateglacial shrub vegetation and a shift from clastic-detrital deposition to an autochthonous sedimentation dominated by biochemical calcite precipitation. Between 10000 and 9000 cal. a BP, a further environmental and climatic improvement is indicated by the spread of deciduous forests, an increase in lake organic matter and a 1.7% rise in the oxygen isotope ratios of both endogenic calcite and ostracod valves. Rising d18O values were probably caused by a combination of hydrological and climatic factors. The persistence of relatively cold and dry climate conditions in northeastern Poland during the first one and a half millennia of the Holocene could be related to a regional eastern European atmospheric circulation pattern. Prevailing anticyclonic circulation linked to a high-pressure cell above the retreating Scandinavian Ice Sheet might have blocked the influence of warm and moist Westerlies and attenuated the early Holocene climatic amelioration in the Lake Hancza region until the final decay of the ice sheet.

Palynology on lake sediments from the Pyrenees

A multi-proxy palaeoecological investigation including pollen, plant macrofossil, radiocarbon and sedimentological analyses, was performed on a small mountain lake in the Eastern Pyrenees. This has allowed the reconstruction of: (1) the vegetation history of the area based on five pollen diagrams and eight AMS14C dates and (2) the past lake-level changes, based on plant macrofossil, lithological and pollen analysis of two stratigraphical transects correlated by pollen analysis. The palaeolake may have appeared before the Younger Dryas; the lake-level was low and the vegetation dominated by cold steppic grasslands. The lake-level rose to its highest level during the Holocene in the Middle Atlantic (at ca. 5060±45 b.p.). Postglacial forests (Quercetum mixtum and Abieto-Fagetum) developed progressively in the lower part of the valley, while dense Pinus uncinata forests rapidly invaded the surroundings of the mire and remained the dominant local vegetation until present. The observed lowering of the lake levels during the Late Atlantic and the Subboreal (from 5060 ± B.P. to 3590±40 b.p.) was related to the overgrowth of the mire. The first obvious indications of anthropogenic disturbances of the vegetation are recorded at the Atlantic/Subboreal boundary as a reduction in the forest component, which has accelerated during the last two millennia.

Pollen record and age determinations of a profile at Cape Mamontov Klyk, Siberia

Non-glaciated Arctic lowlands in north-east Siberia were subjected to extensive landscape and environmental changes during the Late Quaternary. Coastal cliffs along the Arctic shelf seas expose terrestrial archives containing numerous palaeoenvironmental indicators (e.g., pollen, plant macro-fossils and mammal fossils) preserved in the permafrost. The presented sedimentological (grain size, magnetic susceptibility and biogeochemical parameters), cryolithological, geochronological (radiocarbon, accelerator mass spectrometry and infrared-stimulated luminescence), heavy mineral and palaeoecological records from Cape Mamontov Klyk record the environmental dynamics of an Arctic shelf lowland east of the Taymyr Peninsula, and thus, near the eastern edge of the Eurasian ice sheet, over the last 60 Ky. This region is also considered to be the westernmost part of Beringia, the non-glaciated landmass that lay between the Eurasian and the Laurentian ice caps during the Late Pleistocene. Several units and subunits of sand deposits, peat-sand alternations, ice-rich palaeocryosol sequences (Ice Complex) and peaty fillings of thermokarst depressions and valleys were presented. The recorded proxy data sets reflect cold stadial climate conditions between 60 and 50 Kya, moderate inderstadial conditions between 50 and 25 Kya and cold stadial conditions from 25 to 15 Kya. The Late Pleistocene to Holocene transition, including the Allerød warm period, the early to middle Holocene thermal optimum and the late Holocene cooling, are also recorded. Three phases of landscape dynamic (fluvial/alluvial, irregular slope run-off and thermokarst) were presented in a schematic model, and were subsequently correlated with the supraregional environmental history between the Early Weichselian and the Holocene.

A 20 m spatial resolution seamless multisource Digital Elevation/Depth Model for Lizard Island, northern Great Barrier Reef

Hydrographers have traditionally referred to the nearshore area as the "white ribbon" area due to the challenges associated with the collection of elevation data in this highly dynamic transitional zone between terrestrial and marine environments. Accordingly, available information in this zone is typically characterised by a range of datasets from disparate sources. In this paper we propose a framework to 'fill' the white ribbon area of a coral reef system by integrating multiple elevation and bathymetric datasets acquired by a suite of remote-sensing technologies into a seamless digital elevation model (DEM). A range of datasets are integrated, including field-collected GPS elevation points, terrestrial and bathymetric LiDAR, single and multibeam bathymetry, nautical chart depths and empirically derived bathymetry estimations from optical remote sensing imagery. The proposed framework ranks data reliability internally, thereby avoiding the requirements to quantify absolute error and results in a high resolution, seamless product. Nested within this approach is an effective spatially explicit technique for improving the accuracy of bathymetry estimates derived empirically from optical satellite imagery through modelling the spatial structure of residuals. The approach was applied to data collected on and around Lizard Island in northern Australia. Collectively, the framework holds promise for filling the white ribbon zone in coastal areas characterised by similar data availability scenarios. The seamless DEM is referenced to the horizontal coordinate system MGA Zone 55 - GDA 1994, mean sea level (MSL) vertical datum and has a spatial resolution of 20 m.

Palynological and stratigraphic record from Löddigsee in Mecklenburg-Vorpommern, Germany

A Late Pleistocene and Holocene sediment core from the nowadays terrestrialised portion of the Löddigsee in Southern Mecklenburg, Germany was palynologically investigated. The lake is situated in the rarely investigated Young moraine area at the transition from the Weichselian to the Saalian glaciation. The high-resolution pollen diagram contributes to the establishment of the north-eastern German Late Pleistocene pollen stratigraphy. The vegetation distribution pattern after the end of the Weichselian is in good agreement with other studies from North-eastern Germany, but also has its own characteristics. The Holocene vegetation development reveals features from the north-eastern and north-western German lowlands. A special focus was laid on the environmental history of the two settlements on an island within the lake (Late Neolithic and Younger Slavic period), which were preserved under moist conditions. Both settlements were constructed during a period of low lake level. Although there is evidence of agriculture in the area during the respective periods, the two island settlements seem to have served other purposes.

Microphytobenthos composition in Heron Reef, Australia, by High Performance Liquid Chromatography (HPLC) (July 2012)

We quantified pigment biomarkers by high performance liquid chromatography (HPLC) to obtain a broad taxonomic classification of microphytobenthos (MPB) (i.e. identification of dominant taxa). Three replicate sediment cores were collected at 0, 50 and 100 m along transects 5-9 in Heron Reef lagoon (n=15) (Fig. 1). Transects 1-4 could not be processed because the means to have the samples analysed by HPLC were not available at the time of field data collection. Cores were stored frozen and scrapes taken from the top of each one and placed in cryovials immersed in dry ice. Samples were sent to the laboratory (CSIRO Marine and Atmospheric Research, Hobart, Australia) where pigments were extracted with 100% acetone during fifteen hours at 4°C after vortex mixing (30 seconds) and sonication (15 minutes). Samples were then centrifuged and filtered prior to the analysis of pigment composition with a Waters - Alliance HPLC system equipped with a photo-diode array detector. Pigments were separated using a Zorbax Eclipse XDB-C8 stainless steel 150 mm x 4.6 mm ID column with 3.5 µm particle size (Agilent Technologies) and a binary gradient system with an elevated column temperature following a modified version of the Van Heukelem and Thomas (2001) method. The separated pigments were detected at 436 nm and identified against standard spectra using Waters Empower software. Standards for HPLC system calibration were obtained from Sigma (USA) and DHI (Denmark).

Radiocarbon ages and pollen record of a sediment core from Lake Lyadhej-To

An 1180-cm long core recovered from Lake Lyadhej-To (68°15'N, 65°45'E, 150 m a.s.l.) at the NW rim of the Polar Urals Mountains reflects the Holocene environmental history from ca. 11,000 cal. yr BP. Pollen assemblages from the diamicton (ca. 11,000-10,700 cal. yr BP) are dominated by Pre-Quaternary spores and redeposited Pinaceae pollen, pointing to a high terrestrial input. Turbid and nutrient-poor conditions existed in the lake ca. 10,700-10,550 cal. yr BP. The chironomid-inferred reconstructions suggest that mean July temperature increased rapidly from 10.0 to 11.8 °C during this period. Sparse, treeless vegetation dominated on the disturbed and denuded soils in the catchment area. A distinct dominance of planktonic diatoms ca. 10,500-8800 cal. yr BP points to the lowest lake-ice coverage, the longest growing season and the highest bioproductivity during the lake history. Birch forest with some shrub alder grew around the lake reflecting the warmest climate conditions during the Holocene. Mean July temperature was likely 11-13 °C and annual precipitation-400-500 mm. The period ca. 8800-5500 cal. yr BP is characterized by a gradual deterioration of environmental conditions in the lake and lake catchment. The pollen- and chironomid-inferred temperatures reflect a warm period (ca. 6500-6000 cal. BP) with a mean July temperature at least 1-2 °C higher than today. Birch forests disappeared from the lake vicinity after 6000 cal. yr BP. The vegetation in the Lyadhej-To region became similar to the modern one. Shrub (Betula nana, Salix) and herb tundra have dominated the lake catchment since ca. 5500 cal. yr BP. All proxies suggest rather harsh environmental conditions. Diatom assemblages reflect relatively short growing seasons and a longer persistence of lake-ice ca. 5500-2500 cal. yr BP. Pollen-based climate reconstructions suggest significant cooling between ca. 5500 and 3500 cal. yr BP with a mean July temperature 8-10 °C and annual precipitation-300-400 mm. The bioproductivity in the lake remained low after 2500 cal. yr BP, but biogeochemical proxies reflect a higher terrestrial influx. Changes in the diatom content may indicate warmer water temperatures and a reduced ice cover on the lake. However, chironomid-based reconstructions reflect a period with minimal temperatures during the lake history.

Pollen record and age determination of profile CS98-10 at Cape Shpindler, Yugorski Peninsula, northwest Russia

New pollen and radiocarbon data from an 8.6-m coastal section, Cape Shpindler (69°43' N; 62°48' E), Yugorski Peninsula, document the latest Pleistocene and Holocene environmental history of this low Arctic region. Twelve AMS 14C dates indicate that the deposits accumulated since about 13,000 until 2000 radiocarbon years BP. A thermokarst lake formed ca. 13,000-12,800 years BP, when scarce arctic tundra vegetation dominated the area. By 12,500 years BP, a shallow lake existed at the site, and Arctic tundra with Poaceae, Cyperaceae, Salix, Saxifraga, and Artemisia dominated nearby vegetation. Climate was colder than today. Betula nana became dominant during the Early Preboreal period about 9500 years BP, responding to a warm event, which was one of the warmest during the Holocene. Decline in B. nana and Salix after 9500 years BP reflects a brief event of Preboreal cooling. A subsequent increase in Betula and Alnus fruticosa pollen percentages reflects amelioration of environmental conditions at the end of Preboreal period (ca. 9300 years BP). A decline in arboreal taxa later, with a dramatic increase in herb taxa, reflects a short cold event at about 9200 years BP. The pollen data reflect a northward movement of tree birch, peaking at the middle Boreal period, around 8500 years BP. Open Betula forest existed on the Kara Sea coast of the Yugorski Peninsula during the Atlantic period (8000-4500 years BP), indicating that climate was significantly warmer than today. Deteriorating climate around the Atlantic-Subboreal boundary (ca. 4500 years BP) is recorded by a decline in Betula percentages. Sedimentation slowed at the site, and processes of denudation and/or soil formation started at the beginning of the Subatlantic period, when vegetation cover on Yugorski Peninsula shifted to near-modern assemblages.

Pollen record from Eifel maar

A new interglacial pollen sequence from the Döttinger dry maar in the Eifel region of the Rheinish Schield is presented. Palynology is used to correlated to several classical north German Holsteinian sites. The lake sediments reveal the complete interglacial and also 60 m of laminated sediments from the glacial preceding the Holsteinian. The interglacial section indicates limnic conditions in its lower part and telmatic conditions in its upper part with an intermediate episode of peat formation. Ash layers document internsive volcansim during the interglacial in the Eifel region. Some of the north German Holsteinian sites reval spikes of high abundance of Pinus, Beutal and Poaceae and/or setbacks of more demanding taxa during the interglacial, often interpreted as cold events. The Döttingen profile shows similar pattern, but with little response from the thermophilous pollen taxa. In the Döttingen sequence these vegetation 'anomalies' are preceded, or accompanied by phases of active volcanism. The role/interaction of climate and/or volcanism as a likely cause for these vegetation 'anomalies' ist still to be quantified.

Dissolution of a spatially variable DNAPL (dense non aqueous phase liquid) source

Dissolution of non-aqueous phase liquids (NAPLs) or gases into groundwater is a key process, both for contamination problems originating from organic liquid sources, and for dissolution trapping in geological storage of CO2. Dissolution in natural systems typically will involve both high and low NAPL saturations and a wide range of pore water flow velocities within the same source zone for dissolution to groundwater. To correctly predict dissolution in such complex systems and as the NAPL saturations change over time, models must be capable of predicting dissolution under a range of saturations and flow conditions. To provide data to test and validate such models, an experiment was conducted in a two-dimensional sand tank, where the dissolution of a spatially variable, 5x5 cm**2 DNAPL tetrachloroethene source was carefully measured using x-ray attenuation techniques at a resolution of 0.2x0.2 cm**2. By continuously measuring the NAPL saturations, the temporal evolution of DNAPL mass loss by dissolution to groundwater could be measured at each pixel. Next, a general dissolution and solute transport code was written and several published rate-limited (RL) dissolution models and a local equilibrium (LE) approach were tested against the experimental data. It was found that none of the models could adequately predict the observed dissolution pattern, particularly in the zones of higher NAPL saturation. Combining these models with a model for NAPL pool dissolution produced qualitatively better agreement with experimental data, but the total matching error was not significantly improved. A sensitivity study of commonly used fitting parameters further showed that several combinations of these parameters could produce equally good fits to the experimental observations. The results indicate that common empirical model formulations for RL dissolution may be inadequate in complex, variable saturation NAPL source zones, and that further model developments and testing is desirable.