Sedimentary ancient DNA from Lake Skartjorna, Svalbard: assessing the resilience of arctic flora to Holocene climate change

Reconstructing past vegetation and species diversity from arctic lake sediments can be challenging because of low pollen and plant macrofossil concentrations. Information may be enhanced by metabarcoding of sedimentary ancient DNA (sedaDNA). We developed a Holocene record from Lake Skartjørna, Svalbard, using sedaDNA, plant macrofossils and sediment properties, and compared it with published records. All but two genera of vascular plants identified as macrofossils in this or a previous study were identified with sedaDNA. Six additional vascular taxa were found, plus two algal and 12 bryophyte taxa, by sedaDNA analysis, which also detected more species per sample than macrofossil analysis. A shift from Salix polaris-dominated vegetation, with Koenigia islandica, Ranunculaceae and the relatively thermophilic species Arabis alpina and Betula, to Dryas octopetala-dominated vegetation ~6600–5500 cal. BP suggests a transition from moist conditions 1–2°C warmer than today to colder/drier conditions. This coincides with a decrease in runoff, inferred from core lithology, and an independent record of declining lacustrine productivity. This mid-Holocene change in terrestrial vegetation is broadly coincident with changes in records from marine sediments off the west coast of Svalbard. Over the Holocene sedaDNA records little floristic change, and it clearly shows species persisted near the lake during time intervals when they are not detected as macrofossils. The flora has shown resilience in the presence of a changing climate, and, if future warming is limited to 2°C or less, we might expect only minor floristic changes in this region. However, the Holocene record provides no analogues for greater warming

A 24,000-year ancient DNA and pollen record from the Polar Urals reveals temporal dynamics of arctic and boreal plant communities

A 24,000-year record of plant community dynamics, based on pollen and ancient DNA from the sediments (sedaDNA) of Lake Bolshoye Shchuchye in the Polar Ural Mountains, provides detailed information on the flora of the Last Glacial Maximum (LGM) and also changes in plant community composition and dominance. It greatly improves on incomplete records from short and fragmented stratigraphic sequences found in exposed sedimentary sections in the western Russian Arctic. In total, 162 plant taxa were detected by sedaDNA and 115 by pollen analysis. Several shifts in dominance between and within plant functional groups occurred over the studied period, but most taxa appear to have survived in situ. A diverse arctic-alpine herb flora characterised the interval ca. 24,000–17,000 cal years BP and persisted into the Holocene. Around 17,000 cal years BP, sedges (e.g. Carex) and bryophytes (e.g. Bryum, Aulacomnium) increased. The establishment of shrub-tundra communities of Dryas and Vaccinium sp., with potentially some Betula pubescens trees (influx ∼290 grains cm2 year−1), followed at ca. 15,000 cal years BP. Forest taxa such as Picea and ferns (e.g. Dryopteris fragrans, Gymnocarpium dryopteris) established near the lake from ca. 10,000 cal years BP, followed by the establishment of Larix trees from ca. 9000 cal years BP. Picea began to decline from ca. 7000 cal years BP. A complete withdrawal of forest tree taxa occurred by ca. 4000 cal years BP, presumably due to decreasing growing-season temperatures, allowing the expansion of dwarf-shrub tundra and a diverse herb community similar to the present-day vegetation mosaic. Contrary to some earlier comparative studies, sedaDNA and pollen from Lake Bolshoye Shchuchye showed high similarity in the timing of compositional changes and the occurrence of key plant taxa. The sedaDNA record revealed several features that the pollen stratigraphy and earlier palaeorecords in the region failed to detect; a sustained, long-term increase in floristic richness since the LGM until the early Holocene, turnover in grass and forb genera over the Pleistocene-Holocene transition, persistence of a diverse arctic-alpine flora over the late Quaternary, and a variable bryophyte flora through time. As pollen records are often limited by taxonomic resolution, differential productivity and dispersal, sedaDNA can provide improved estimates of floristic richness and is better able to distinguish between different plant assemblages. However, pollen remains superior at providing quantitative estimates of plant abundance changes and detecting several diverse groups (e.g. Poaceae, Cyperaceae, Asteraceae) which may be underreported in the sedaDNA. Joint use of the two proxies provided unprecedented floristic detail of past plant communities and helped to distinguish between long-distance transport of pollen and local presence, particularly for woody plant taxa

The precursors of chocolate aroma.

The subject of this research was an experimental study of the development of chocolate aroma during the commercial processing of cocoa beans. The components of unroasted aroma cocoa beans have been fractionated, and the various groups of substances obtained tested for the development of aroma when roasted. The results obtained provide further evidence of the involvement of simple amino acids, reducing sugars and flavonoids in the formation of the primary aroma of chocolate products, and a mechanism for the formation and mixing of these substances during cocoa fermentation is described. Model mixtures of these compounds have been examined in order to assess the extent of the contribution of individual compounds to the production of the aroma. The reaction of these model mixtures have also been examined under the conditions obtaining during commercial bean roasting, and combined gas chromstography-mase spectrometry has been used to compare their volatile reaction products with these present in roasted cocoa beans. The results of these studies indicate the importance of the natural environment of the precursors in the control of the extent of subsequent reactions, and the consequences of the 'dry state' reaction conditions in this respect. Various types of compound formed in these reactions are described and their possible importance in the recognition of chocolate aroma is discussed. The experimental results are discussed in terms of literature surveys of the current state of knowledge of both chocolate aroma development, and the aroma potential of amino acid-reducing sugar reactions

High-Throughput Sequencing of Six Bamboo Chloroplast Genomes: Phylogenetic Implications for Temperate Woody Bamboos (Poaceae: Bambusoideae)

BACKGROUND: Bambusoideae is the only subfamily that contains woody members in the grass family, Poaceae. In phylogenetic analyses, Bambusoideae, Pooideae and Ehrhartoideae formed the BEP clade, yet the internal relationships of this clade are controversial. The distinctive life history (infrequent flowering and predominance of asexual reproduction) of woody bamboos makes them an interesting but taxonomically difficult group. Phylogenetic analyses based on large DNA fragments could only provide a moderate resolution of woody bamboo relationships, although a robust phylogenetic tree is needed to elucidate their evolutionary history. Phylogenomics is an alternative choice for resolving difficult phylogenies. METHODOLOGY/PRINCIPAL FINDINGS: Here we present the complete nucleotide sequences of six woody bamboo chloroplast (cp) genomes using Illumina sequencing. These genomes are similar to those of other grasses and rather conservative in evolution. We constructed a phylogeny of Poaceae from 24 complete cp genomes including 21 grass species. Within the BEP clade, we found strong support for a sister relationship between Bambusoideae and Pooideae. In a substantial improvement over prior studies, all six nodes within Bambusoideae were supported with ≥0.95 posterior probability from Bayesian inference and 5/6 nodes resolved with 100% bootstrap support in maximum parsimony and maximum likelihood analyses. We found that repeats in the cp genome could provide phylogenetic information, while caution is needed when using indels in phylogenetic analyses based on few selected genes. We also identified relatively rapidly evolving cp genome regions that have the potential to be used for further phylogenetic study in Bambusoideae. CONCLUSIONS/SIGNIFICANCE: The cp genome of Bambusoideae evolved slowly, and phylogenomics based on whole cp genome could be used to resolve major relationships within the subfamily. The difficulty in resolving the diversification among three clades of temperate woody bamboos, even with complete cp genome sequences, suggests that these lineages may have diverged very rapidly

Deciduous Trees and the Application of Universal DNA Barcodes: A Case Study on the Circumpolar Fraxinus

The utility of DNA barcoding for identifying representative specimens of the circumpolar tree genus Fraxinus (56 species) was investigated. We examined the genetic variability of several loci suggested in chloroplast DNA barcode protocols such as matK, rpoB, rpoC1 and trnH-psbA in a large worldwide sample of Fraxinus species. The chloroplast intergenic spacer rpl32-trnL was further assessed in search for a potentially variable and useful locus. The results of the study suggest that the proposed cpDNA loci, alone or in combination, cannot fully discriminate among species because of the generally low rates of substitution in the chloroplast genome of Fraxinus. The intergenic spacer trnH-psbA was the best performing locus, but genetic distance-based discrimination was moderately successful and only resulted in the separation of the samples at the subgenus level. Use of the BLAST approach was better than the neighbor-joining tree reconstruction method with pairwise Kimura's two-parameter rates of substitution, but allowed for the correct identification of only less than half of the species sampled. Such rates are substantially lower than the success rate required for a standardised barcoding approach. Consequently, the current cpDNA barcodes are inadequate to fully discriminate Fraxinus species. Given that a low rate of substitution is common among the plastid genomes of trees, the use of the plant cpDNA “universal” barcode may not be suitable for the safe identification of tree species below a generic or sectional level. Supplementary barcoding loci of the nuclear genome and alternative solutions are proposed and discussed

A phylogeny of the European gentians inferred from chloroplast trnL (UAA) intron sequences

Times Cited: 75International audiencePhylogenetic relationships between the European species of the genus Gentiana L. (Gentianaceae) were inferred from chloroplast trnL (UAA) intron sequence data. The phylogeny obtained is largely in accordance with the classification of species into sections Gentiana, Megalanthe and Calathianae. Few synapomorphies support the branching of the main lineages and thus could suggest a rapid radiation following the colonization of Europe. Within section Gentiana, our results are highly congruent with the previous distinction of G. montserratii Vivant from G. lutea L. Section Megalanthe is divided into two well separated lineages, both of which comprise calcicole and calcifuge species. The 'star phylogeny' obtained in section Calathianae suggests that most of the taxa speciated almost simultaneously. Relative-rate tests between two lineages suggested that section Chondrophyllae displays higher mutation rates than the rest of the genus Gentiana and that cpDNA can violate assumptions of rate constancy at lower taxonomic level. (C) 1996 The Linnean Society of London

The Use Of Chloroplast Dna To Resolve Plant Phylogenies - Noncoding Versus Rbcl Sequences

Times Cited: 174International audienceDirect sequencing of polymerase chain reaction products is now an expanding area of plant systematics and evolution. Within angiosperms the rbcL gene has been widely sequenced and used for inferring plant phylogenies at higher taxonomic levels. Unfortunately rbcL does not usually contain enough information to resolve relationships between closely related genera, such as Hordeum, Triticum, and Aegilops. One solution to this problem could be to analyze noncoding regions of chloroplast DNA, which are supposed to evolve more rapidly than coding regions. Here we present pairwise comparisons among dicots and monocots for rbcL and two noncoding sequences of cpDNA (the trnL (UAA) intron and the intergenic spacer between the trnL (UAA) 3' exon and the trnF (GAA) gene). It appears that these regions evolve faster (more than three times faster, on average) than rbcL, as previously reported, and that the trnL intron evolves at a rate that is the same as that of the intergenic spacer. By the analysis of these regions, the genera Hordeum, Triticum, and Aegilops clearly could be distinguished. A phylogeny using trnL (UAA) intron sequences is also inferred far some species of the genus Gentiana L., clearly illustrating the phylogenetic utility of these zones at the generic level. The advantages and the disadvantages of the use of these regions to resolve plant phylogenies are discussed, as well as the desirability of a preliminary study before every large-scale analysis

Chloroplast Dna Polymorphism At The Intrageneric Level And Plant Phylogenies

Times Cited: 32International audienceAnalysis of chloroplast DNA (cpDNA) sequences is a tool which is being used more and more frequently in plant systematics and evolution. The recent development of polymerase chain reaction (PCR) has enabled sequencing the rbcL gene for a great number of species and to infer phylogemies at higher taxonomic levels. However this gene reaches its lower limits of resolution in resolving relationships among closely related genera. The analysis of non-coding regions, which display higher mutation rates than coding regions, extends the resolution of the molecule. Here we report a high variability in divergence rates for two non-coding regions of the chloroplast genome. Thirty-six species belonging to 10 different genera were sampled and indicated divergence rates that varied 5-8 fold. In order to explain this heterogeneity, three non-exclusive hypotheses involving sampling bias, age of common ancestor and variants of the molecular clock, are proposed and discussed. The potential utility of these two non-coding regions in resolving phylogenetic relationships differs among genera

Comportement hydrique du frêne (Fraxinus excelsior L) dans une formation montagnarde mésoxérophile

L'article décrit les variations diurnes et saisonnières du potentiel hydrique foliaire, de la conductance stomatique et de la transpiration des feuilles d'un frêne dans une station montagnarde mésoxérophile située dans la zone intermédiaire des Alpes nord-occidentales. Le potentiel hydrique de base est très proche du potentiel hydrique du sol à 30 cm de profondeur et en corrélation étroite avec lui. En cas de sécheresse estivale sévère, le potentiel de base peut s'abaisser à -4,8 MPa et le potentiel minimum à -5,5 MPa sans dommage pour les feuilles. En conditions favorables à l'alimentation en eau, la conductance stomatique maximale atteint 200 mmol[H2O] m-2s-1, valeur bien inférieure à celle des frênes des forêts alluviales de plaine. La conductance maximale ne se maintient que brièvement car une fermeture stomatique partielle a lieu au plus tard à midi (heure solaire) et éventuellement dès 7 h. En outre, la conductance maximale diminue quand le sol s'assèche. En conséquence, le frêne de montagne consomme moins d'eau que le frêne de forêt alluviale. Cependant, sa survie au cours des périodes de sécheresse est attribuée à la stratégie de tolérance plus qu'à celle d'évitement.Water relations of ash (Fraxinus excelsior L) in a mesoxerophilic mountain stand. This paper reports on the diurnal and seasonal variations in water potential, stomatal conductance, and transpiration of the leaves of an ash tree in a mesoxerophilic mountain stand situated in the intermediate zone of the north-western Alps. The pre-dawn water potential is close to the soil water potential at 30 cm depth and is closely correlated with the latter. In the case of pronounced summer drought the pre-dawn water potential and minimum water potential of leaves may fall as low as -4.8 MPa and -5.5 MPa, respectively. Under good water supply conditions the maximum stomatal conductance may reach 200 mmol (H2O) m-2.s-1, a value much lower than that of ash leaves in alluvial forests. The maximum stomatal conductance holds for only a short time, as stomata partially close at noon (solar time) at the latest, and in some cases as early as 7 am. Moreover, the maximum stomatal conductance decreases as the soil dries up. Accordingly ash water uptake is less in mountain stands than in alluvial forests. The survival of ash during drought is, however, attributed to tolerance strategy rather than to avoidance strategy