Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants

Background Simple Sequence Repeats (SSRs) are widely used in population genetic studies but their classical development is costly and time-consuming. The ever-increasing available DNA datasets generated by high-throughput techniques offer an inexpensive alternative for SSRs discovery. Expressed Sequence Tags (ESTs) have been widely used as SSR source for plants of economic relevance but their application to non-model species is still modest. Methods Here, we explored the use of publicly available ESTs (GenBank at the National Center for Biotechnology Information-NCBI) for SSRs development in non-model plants, focusing on genera listed by the International Union for the Conservation of Nature (IUCN). We also search two model genera with fully annotated genomes for EST-SSRs, Arabidopsis and Oryza, and used them as controls for genome distribution analyses. Overall, we downloaded 16 031 555 sequences for 258 plant genera which were mined for SSRsand their primers with the help of QDD1. Genome distribution analyses in Oryza and Arabidopsis were done by blasting the sequences with SSR against the Oryza sativa and Arabidopsis thaliana reference genomes implemented in the Basal Local Alignment Tool (BLAST) of the NCBI website. Finally, we performed an empirical test to determine the performance of our EST-SSRs in a few individuals from four species of two eudicot genera, Trifolium and Centaurea. Results We explored a total of 14 498 726 EST sequences from the dbEST database (NCBI) in 257 plant genera from the IUCN Red List. We identify a very large number (17 102) of ready-to-test EST-SSRs in most plant genera (193) at no cost. Overall, dinucleotide and trinucleotide repeats were the prevalent types but the abundance of the various types of repeat differed between taxonomic groups. Control genomes revealed that trinucleotide repeats were mostly located in coding regions while dinucleotide repeats were largely associated with untranslated regions. Our results from the empirical test revealed considerable amplification success and transferability between congenerics. Conclusions The present work represents the first large-scale study developing SSRs by utilizing publicly accessible EST databases in threatened plants. Here we provide a very large number of ready-to-test EST-SSR (17 102) for 193 genera. The cross-species transferability suggests that the number of possible target species would be large. Since trinucleotide repeats are abundant and mainly linked to exons they might be useful in evolutionary and conservation studies. Altogether, our study highly supports the use of EST databases as an extremely affordable and fast alternative for SSR developing in threatened plants.

Climate-pollen relationships AD 1901-1996 in two small mires near the forest limit in the northern and central Swiss Alps

Climatic relationships were established in two 210Pb dated pollen sequences from small mires closely surrounded by forest just below actual forest limits (but about 300 m below potential climatic forest limits) in the northern Swiss Alps (suboceanic in climate; mainly with Picea) and the central Swiss Alps (subcontinental; mainly Pinus cembra and Larix) at annual or near-annual resolution from ad 1901 to 1996. Effects of vegetational succession were removed by splitting the time series into early and late periods and by linear detrending. Both pollen concentrations detrended by the depth-age model and modified percentages (in which counts of dominant pollen types are down-weighted) are correlated by simple linear regression with smoothed climatic parameters with one-and two-year timelags, including average monthly and April/September daylight air temperatures and with seasonal and annual precipitation sums. Results from detrended pollen concentrations suggest that peat accumulation is favoured in the northern-Alpine mire either by early snowmelt or by summer precipitation, but in the central-Alpine mire by increased precipitation and cooler summers, suggesting a position of the northern-Alpine mire near the upper altitudinal limit of peat formation, but of the central-Alpine mire near the lower limit. Results from modified pollen percentages indicate that pollen pro duction by plants growing near their upper altitudinal limit is limited by insufficient warmth in summer, and pollen production by plants growing near their lower altitudinal limit is limited by too-high temperatures. Only weakly significant pollen/climate relationships were found for Pinus cembra and Larix, probably because they experience little climatic stress growing 300 m below the potential climatic forest limit.

CopywriteR: DNA copy number detection from off-target sequence data.

Current methods for detection of copy number variants (CNV) and aberrations (CNA) from targeted sequencing data are based on the depth of coverage of captured exons. Accurate CNA determination is complicated by uneven genomic distribution and non-uniform capture efficiency of targeted exons. Here we present CopywriteR, which eludes these problems by exploiting 'off-target' sequence reads. CopywriteR allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. CopywriteR outperforms existing methods and constitutes a widely applicable alternative to available tools.

Treeline Fluctuations Recorded for 12,500 Years by Soil Profiles, Pollen, and Plant Macrofossils in the Central Swiss Alps

Past treelines can rarely be recorded by pollen percentages alone, but pollen concentration, pollen influx, and plant macrofossils (including stomata of conifers) are more reliable indicators. In addition, ancient forest soils above today's treeline may trace the maximum upper expansion of the forest since the last glaciation. Charcoal in such soil profiles may be radiocarbon dated. Our example from the Central Swiss Alps at the Alpe d'Essertse consists of a plant-macrofossil diagram and pollen diagrams of the pond Gouille Rion at 2343 m a.s.l. and a sequence of soil profiles from 1780 m to 2600 m a.s.l. The area around the pond was forested with LariJc decidua and Pinus cembra between 9500 and 3600 BP. After 4700 BP the forest became more open and Juniperus nana and Alnus viridis expanded (together with Picea abies in the subalpine forest). Between 1700 and 900 BP the Juniperus nana and Alnus viridis scrubs declined while meadows and pastures took over, so that the pond Gouille Rion was definitively above timber­ line. The highest Holocene treeline was at 2400 to 2450 m a.s.l. (i.e. 50 to 100 m higher than the uppermost single specimen of Pinus cembra today) between 9000 and 4700 BP, but it is not yet dated in more detail. The highest charcoal of Pinus cembra at 2380 m a.s.l. has a radiocarbon date of 6010 ± 70 BP. Around 6900 BP a strong climatic deterioration caused an opening of timberline forest. First indicators of anthropogenic influence occurred at 4700 BP, when the forest limit started to move down. The lowering of timberline after 4700 BP was probably due to combined effects of human and climatic impact.

Environmental control on the occurrence of high-coercivity magnetic minerals and formation of iron sulfides in a 640 ka sediment sequence from Lake Ohrid (Balkans)

The bulk magnetic mineral record from Lake Ohrid, spanning the past 637 kyr, reflects large-scale shifts in hydrological conditions, and, superimposed, a strong signal of environmental conditions on glacial–interglacial and millennial timescales. A shift in the formation of early diagenetic ferrimagnetic iron sulfides to siderites is observed around 320 ka. This change is probably associated with variable availability of sulfide in the pore water. We propose that sulfate concentrations were significantly higher before  ∼  320 ka, due to either a higher sulfate flux or lower dilution of lake sulfate due to a smaller water volume. Diagenetic iron minerals appear more abundant during glacials, which are generally characterized by higher Fe / Ca ratios in the sediments. While in the lower part of the core the ferrimagnetic sulfide signal overprints the primary detrital magnetic signal, the upper part of the core is dominated by variable proportions of high- to low-coercivity iron oxides. Glacial sediments are characterized by high concentration of high-coercivity magnetic minerals (hematite, goethite), which relate to enhanced erosion of soils that had formed during preceding interglacials. Superimposed on the glacial–interglacial behavior are millennial-scale oscillations in the magnetic mineral composition that parallel variations in summer insolation. Like the processes on glacial–interglacial timescales, low summer insolation and a retreat in vegetation resulted in enhanced erosion of soil material. Our study highlights that rock-magnetic studies, in concert with geochemical and sedimentological investigations, provide a multi-level contribution to environmental reconstructions, since the magnetic properties can mirror both environmental conditions on land and intra-lake processes.

Litter nutrients and retranslocation in a central African rain forest dominated by ectomycorrhizal trees

In the strongly seasonal, but annually very wet, parts of the tropics, low-water availability in the short dry season leads to a semi-deciduous forest, one which is also highly susceptible to nutrient loss from leaching in the long wet season. Patterns in litterfall were compared between forest with low (LEM) and high (HEM) abundances of ectomycorrhizal trees in Korup National Park, Cameroon, over 26 months in 1990–92. Leaf litter was sorted into 26 abundant species which included six ectomycorrhizal species, and of these three were the large grove-forming trees Microberlinia bisulcata, Tetraberlinia bifoliolata and Tetraberlinia moreliana. Larger-tree species shed their leaves with pronounced peaks in the dry season, whereas other species had either weaker dependence, showed several peaks per year, or were wet-season shedders. Although total annual litterfall differed little between forest types, in the HEM forest (dominated by M. bisulcata) the dry-season peak was more pronounced and earlier than that in the LEMforest. Species differed greatly in their mean leaf litterfall nutrient concentrations, with an approx. twofold range for nitrogen and phosphorus, and 2.5–3.5-fold for potassium, magnesium and calcium. In the dry season, LEM and HEM litter showed similar declines in P and N concentration, and increases in K and Mg; some species, especially M. bisculcata, showed strong dry-wet season differences. The concentration of P (but not N) was higher in the leaf litter of ectomycorrhizal than nonectomycorrhizal species. Retranslocation of N and P was lower among the ectomycorrhizal than nonectomycorrhizal species by approx. twofold. It is suggested that, within ectomycorrhizal groves on this soil low in P, a fast decomposition rate with minimal loss of mineralized P is possible due to the relatively high litter P not limiting the cycle at this stage, combined with an efficient recapture of released P by the surface organic layer of ectomycorrhizas and fine roots. This points to a feedback between two essential controlling steps (retranslocation and mineralization) in a tropical rain forest ecosystem dominated by ectomycorrhizal trees.

Human–climate interactions in the central Mediterranean region during the last millennia: The laminated record of Lake Butrint (Albania)

Lake Butrint (39°47 N, 20°1 E) is a ca. 21 m deep, coastal lagoon located in SW Albania where finely-laminated sediments have been continuously deposited during the last millennia. The multi-proxy analysis (sedimentology, high-resolution elemental geochemistry and pollen) of a 12 m long sediment core, supported by seven AMS radiocarbon dates and 137Cs dating, enable a precise reconstruction of the environmental change that occurred in the central Mediterranean region during the last ∼4.5 cal kyrs BP. Sediments consist of triplets of authigenic carbonates, organic matter and clayey laminae. Fluctuations in the thickness and/or presence of these different types of seasonal laminae indicate variations in water salinity, organic productivity and runoff in the lake's catchment, as a result of the complex interplay of tectonics, anthropogenic forcing and climate variability. The progradation of the Pavllo river delta, favoured by variable human activity from the nearby ancient city of Butrint, led to the progressive isolation of this hydrological system from the Ionian Sea. The system evolved from an open bay to a restricted lagoon, which is consistent with archaeological data. An abrupt increase in mass-wasting activity between 1515 and 1450 BC, likely caused by nearby seismic activity, led to the accumulation of 24 homogenites, up to 17 cm thick. They have been deposited during the onset of finely laminated sedimentation, which indicates restricted, anoxic bottom water conditions and higher salinity. Periods of maximum water salinity, biological productivity, and carbonate precipitation coincide with warmer intervals, such as the early Roman Warm Period (RWP) (500 BC–0 AD), the Medieval Climate Anomaly (MCA) (800–1400 AD) and recent times (after 1800 AD). Conversely, lower salinity and more oxic conditions, with higher clastic input were recorded during 1400–500 BC, the Late Roman and the Early Medieval periods (0–800 AD) and during the Little Ice Age (1400–1800 AD). Hydrological fluctuations recorded in Butrint are in phase with most central and western Mediterranean records and correlate with NAO variability. In contrast, opposite hydrological patterns have been recorded in the Eastern Balkans and the Levant during the last millennium, emphasizing a complex spatial variability in the region. Phases of maximum settlement intensity in Butrint (Roman-Late Antique) coincide with warmer and/or stable climate periods (0–800 AD and MCA, respectively), indicating a long-term influence of climatic conditions on human activities. The Late Holocene sedimentary record of Lake Butrint demonstrates the complex interplay of climate variability, tectonics and human impact in the recent evolution of coastal Mediterranean regions.

Influence of catchment quality and altitude on the water and sediment composition of 68 small lakes in Central Europe

68 lakes (63 Swiss, 2 French and 3 Italian) located in an altitudinal range between 334 and 2339m spanning a wide range of land-use have been investigated. The aim of the study was to discuss influences of geographic location, vegetation and land-use in the catchment area on the water and sediment chemistry of small lakes. Detailed quantitative description of land-use, vegetation, and climate in the watershed of all lakes was established. Surface and bottom water samples collected from each lake were analyzed for major ions and nutrients. Correlations were interpreted using linear regression analysis. Chemical parameters of water and sediment reflect the characteristics of the catchment areas. All lakes were alkaline since they were situated on calcareous bedrock. Concentrations of nitrogen and phosphorus strongly increase with increasing agricultural land-use. Na and K, however, are positively correlated with the amount of urbanization within the catchment area. These elements as well as dissolved organic carbon (DOC), Mg, Ca, and alkalinity, increase when the catchment is urbanized or used for agriculture. Total nitrogen and organic carbon in the sediments decrease distinctly if large parts of the catchment consist of bare land. No correlations between sediment composition and maximum water depth or altitude of the lakes were found.¶Striking differences in the water compositions of lakes above and below approximately 700 m of altitude were observed. Concentrations of total nitrogen and nitrate, total phosphorus, DOC, Na, K, Mg, Ca, and alkalinity are distinctly higher in most lakes below 700 m than above, and the pH of the bottom waters of these lakes is generally lower. Estimates of total nitrogen concentrations, even in remote areas, indicate that precipitation is responsible for increased background concentrations. At lower altitudes nitrogen concentrations in lakes is explained by the nitrogen loaded rain from urban areas deposited on the catchment, and with high percentages of agricultural land-use in the watershed.

Stable isotope response to lake eutrophication: Calibration of a high-resolution lacustrine sequence from Baldeggersee, Switzerland

Stable isotope analyses of discrete seasonal layers from a 108-yr annually laminated freeze-core from Baldeg-gersee, a small, eutrophic lake in central Switzerland, provide information on the climatological and environmental factors, including lake eutrophication, that control oxygen and carbon isotopic composition of epilimnic biologically induced calcite precipitate. During the last 100 yr, Baldeggersee has undergone major increases in productivity and eutrophication in response to nutrient loading from agriculture and industrialization in the lake's watershed. Calibration of the isotopic signal in Baldeggersee to historical limnological data quantitatively links evidence of isotopic depletion in the sedimented calcite to trophic state of the lake. δ18O values from the spring/summer “light” sediment layers steadily diverged to more depleted values in response to historical eutrophication: measured δ18O values were up to 21.5‰ more negative than calculated equilibrium δ18O values. Evidence for 13C depletion in the calcite, relative to equilibrium values, is more difficult to ascertain because of an overall dominance of isotopic enrichment in the dissolved inorganic pool as productivity in Baldeggersee increases. A positive association exists between the degree of oxygen-18 depletion and the calcite crystal size. Thus, large amorphous calcite grains can be used as a proxy for recognizing apparent isotopic nonequilibrium in sediment sequences from highly productive lacustrine environments from all geologic time scales. In contrast to the light layers, the oxygen isotopic composition of the calcite in the late summer/fall “dark” sediment layers is unaffected by the apparent isotope nonequilibrium. Oxygen and carbon isotope values from the dark laminae in the Baldeggersee sediment therefore provide environmental and climatological proxies that can be calibrated with known environmental and regional climate data for the last century.

Tectonic evolution of the Proterozoic Itremo Group metasediments in central Madagascar

The major geologic units of the Itremo region in central Madagascar include: (1) upper amphibolite to granulite facies (higher grade) Precambrian rocks, mainly para- and orthogneisses, and migmatites; (2) the newly defined Itremo Nappes, a fold-and-thrust belt containing the Proterozoic Itremo Group sediments, metamorphosed at greenschist to lower amphibolite facies (lower grade) conditions: (3) Middle Neoproterozoic and Late Neoproterozoic-Cambrian intrusives. The stratigraphic succession of the Itremo Group in the eastern part of the Itremo region is, from bottom to top: quartzites, metapelites, metacarbonates and metapelites overlain by metacarbonates. During D1 the Itremo Group sediments were detached from their continental substratum, deformed into a fold-and-thrust nappe (Itremo Nappes), and transported on top of higher grade rocks that are intruded by Middle Neoproterozoic (c. 797–780 Ma) granites and gabbros. A second phase of deformation shortening (D2) affected both the Itremo Sedimentary Nappes and structurally underlying higher-grade rocksunits, and formed large-scale N-S-trending F2 folds. S1 axial plane foliations in Itremo Group sediments are truncated by Late Neoproterozoic-Cambrian granites (c. 570–540 Ma). The age of the formation of the Itremo Nappes is not well constrained: they formed in Neoproterozoic times between 780 and 570 Ma.