Lake Store Finnsjøen – a key for understanding Lateglacial/early Holocene vegetation and ice sheet dynamics in the central Scandes Mountains

The Lateglacial (LG) deglaciation and vegetation development in the Scandes Mountains has been debated for a century. Here we present new evidence from microfossils, radiocarbon dated plant macrofossils and sedimentary ancient DNA from laminated sediments in Lake Store Finnsjøen (1260 m a.s.l.) at Dovre, Central Norway. Combined with previous results from three other Dovre lakes, this allows for new interpretations of events during and immediately after the LG deglaciation. The Finnsjøen sediments present the first uninterrupted record of local vegetation development in the Scandes Mountains from the late Younger Dryas (YD), ca 12,000 cal years BP, to the early Holocene around 9700 cal years BP. The local vegetation in late YD/early Holocene was extremely sparse with pioneer herbs (e.g. Artemisia norvegica, Beckwithia, Campanula cf. uniflora, Koenigia, Oxyria, Papaver, Saxifraga spp.) and dwarf-shrubs (Betula nana, Salix including Salix polaris). From 11,300 cal years BP, local vegetation rapidly closed with dominant Dryas, Saxifraga spp., and Silene acaulis. From ca 10,700 cal years BP, open birch-forests with juniper, Empetrum nigrum and other dwarf-shrubs developed. Pine forests established within the area from 10,300 cal years BP. We identified the cold Preboreal Oscillation (PBO), not earlier described from pollen data in South Norway, around 11,400 cal years BP by a regional pollen signal. Distinct local vegetation changes were not detected until the post-PBO warming around 11,300 cal years BP. Apparently, the earlier warming at the YD/Holocene transition at 11,650 cal years BP was too weak and short-lived for vegetation closure at high altitudes at Dovre. For the first time, we demonstrate a regional glacier readvance and local ice cap formations during the YD in the Scandes Mountains. In two of the deep lakes with small catchments, YD glaciation blocked sedimentation without removing old sediments and caused a hiatus separating sediments of the ice-free LG interstadial (LGI) from those of the ice-free Holocene period. Both regional glaciers and local ice caps caused hiati. Ice-free pre-YD conditions at Dovre followed by a YD readvance point to a scenario that is intermediate between the maximum ice model postulating a thick glacier during the entire LG, and the minimum ice model postulating thin and multi-domed early LG ice

ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases

<p>Abstract</p> <p>Background</p> <p>During the last 15 years the internal transcribed spacer (ITS) of nuclear DNA has been used as a target for analyzing fungal diversity in environmental samples, and has recently been selected as the standard marker for fungal DNA barcoding. In this study we explored the potential amplification biases that various commonly utilized ITS primers might introduce during amplification of different parts of the ITS region in samples containing mixed templates ('environmental barcoding'). We performed <it>in silico </it>PCR analyses with commonly used primer combinations using various ITS datasets obtained from public databases as templates.</p> <p>Results</p> <p>Some of the ITS primers, such as ITS1-F, were hampered with a high proportion of mismatches relative to the target sequences, and most of them appeared to introduce taxonomic biases during PCR. Some primers, e.g. ITS1-F, ITS1 and ITS5, were biased towards amplification of basidiomycetes, whereas others, e.g. ITS2, ITS3 and ITS4, were biased towards ascomycetes. The assumed basidiomycete-specific primer ITS4-B only amplified a minor proportion of basidiomycete ITS sequences, even under relaxed PCR conditions. Due to systematic length differences in the ITS2 region as well as the entire ITS, we found that ascomycetes will more easily amplify than basidiomycetes using these regions as targets. This bias can be avoided by using primers amplifying ITS1 only, but this would imply preferential amplification of 'non-dikarya' fungi.</p> <p>Conclusions</p> <p>We conclude that ITS primers have to be selected carefully, especially when used for high-throughput sequencing of environmental samples. We suggest that different primer combinations or different parts of the ITS region should be analyzed in parallel, or that alternative ITS primers should be searched for.</p

Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding

DNA barcoding should provide rapid, accurate and automatable species identifications by using a standardized DNA region as a tag. Based on sequences available in GenBank and sequences produced for this study, we evaluated the resolution power of the whole chloroplast trnL (UAA) intron (254–767 bp) and of a shorter fragment of this intron (the P6 loop, 10–143 bp) amplified with highly conserved primers. The main limitation of the whole trnL intron for DNA barcoding remains its relatively low resolution (67.3% of the species from GenBank unambiguously identified). The resolution of the P6 loop is lower (19.5% identified) but remains higher than those of existing alternative systems. The resolution is much higher in specific contexts such as species originating from a single ecosystem, or commonly eaten plants. Despite the relatively low resolution, the whole trnL intron and its P6 loop have many advantages: the primers are highly conserved, and the amplification system is very robust. The P6 loop can even be amplified when using highly degraded DNA from processed food or from permafrost samples, and has the potential to be extensively used in food industry, in forensic science, in diet analyses based on feces and in ancient DNA studies

What can cold-induced transcriptomes of Arctic Brassicaceae tell us about the evolution of cold tolerance?

publishedVersio

History and evolution of the afroalpine fora: in the footsteps of Olov Hedberg

The monumental work of Olov Hedberg provided deep insights into the spectacular and fragmented tropical alpine flora of the African sky islands. Here we review recent molecular and niche modelling studies and re-examine Hedberg’s hypotheses and conclusions. Colonisation started when mountain uplift established the harsh diurnal climate with nightly frosts, accelerated throughout the last 5 Myr (Plio-Pleistocene), and resulted in a flora rich in local endemics. Recruitment was dominated by long-distance dispersals (LDDs) from seasonally cold, remote areas, mainly in Eurasia. Colonisation was only rarely followed by substantial diversification. Instead, most of the larger genera and even species colonised the afroalpine habitat multiple times independently. Conspicuous parallel evolution occurred among mountains, e.g., of gigantism in Lobelia and Dendrosenecio and dwarf shrubs in Alchemilla. Although the alpine habitat was ~ 8 times larger and the treeline was ~ 1000 m lower than today during the Last Glacial Maximum, genetic data suggest that the flora was shaped by strong intermountain isolation interrupted by rare LDDs rather than ecological connectivity. The new evidence points to a much younger and more dynamic island scenario than envisioned by Hedberg: the afroalpine flora is unsaturated and fragile, it was repeatedly disrupted by the Pleistocene climate oscillations, and it harbours taxonomic and genetic diversity that is unique but severely depauperated by frequent bottlenecks and cycles of colonisation, extinction, and recolonisation. The level of intrapopulation genetic variation is alarmingly low, and many afroalpine species may be vulnerable to extinction because of climate warming and increasing human impact.publishedVersio

Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures

Background In order to understand the role of herbivores in trophic webs, it is essential to know what they feed on. Diet analysis is, however, a challenge in many small herbivores with a secretive life style. In this paper, we compare novel (high-throughput pyrosequencing) DNA barcoding technology for plant mixture with traditional microhistological method. We analysed stomach contents of two ecologically important subarctic vole species, Microtus oeconomus and Myodes rufocanus, with the two methods. DNA barcoding was conducted using the P6-loop of the chloroplast trnL (UAA) intron. Results Although the identified plant taxa in the diets matched relatively well between the two methods, DNA barcoding gave by far taxonomically more detailed results. Quantitative comparison of results was difficult, mainly due to low taxonomic resolution of the microhistological method, which also in part explained discrepancies between the methods. Other discrepancies were likely due to biases mostly in the microhistological analysis. Conclusion We conclude that DNA barcoding opens up for new possibilities in the study of plant-herbivore interactions, giving a detailed and relatively unbiased picture of food utilization of herbivores

Vicariance, dispersal, and hybridization in a naturally fragmented system: the afro-alpine endemics Carex monostachya and C. runssoroensis (Cyperaceae)

Published version available at https://doi.org/10.1007/s00035-015-0162-2. The naturally fragmented habitat on the tallest African mountains provides a good model system to study vicariance, dispersal, and hybridization. Many mountains are separated by lowland that likely was unsuitable for high-alpine plants even during cold climatic periods. We explore the relative importance of these processes using two endemic sister species: the widespread Ethiopian/eastern East African Carex monostachya and the mainly western East African C. runssoroensis. These bog-forming sedges co-occur in some mountains and are hypothesized to hybridize. The two species were distinctly differentiated for genome-wide Amplified Fragment Length Polymorphisms (AFLPs), also in one mountain where they co-occur. However, the plants from another mountain showed strong signals of admixture. The results suggest initial divergence into one western and one northern/eastern lineage, followed by long-distance dispersal resulting in secondary contact zones. Also within species genetic diversity was clearly structured with distinct genetic groups on some, but not all mountains. Differentiation levels varied considerably and did not always correspond to the extent of lowland habitat between mountains. The narrow Rift Valley in the otherwise nearly contiguous highlands in Ethiopia appears to present a much stronger barrier to dispersal than the extensive lowlands separating Ethiopia from East Africa. This may be a general pattern since it has been documented also for other afro-alpine specie

I Olov Hedbergs fotspor: Plantenes evolusjon i det afrikanske høyfjellet

Floraen i det tropiske afrikanske høyfjellet er spektakulær og rik på endemiske (stedegne) arter, og ikke minst er forekomstene av plantearter ekstremt fragmentert på grunn av lange avstander mellom de enkelte fjellene (fig. 1). Denne særegne floraen ble dyptpløyende analysert av Olov Hedberg i hans monumentale verk fra 1957 (Hedberg 1957) og i påfølgende arbeider (f.eks. Hedberg 1961, Hedberg 1969). Studier basert på molekylære data og nisjemodellering har senere gitt sterk støtte til flere av hans hypoteser, men også ledet til ny og overraskende innsikt. Plantenes innvandring til det afrikanske høyfjellet startet allerede da fjellhevingen skapte det spesielle tropisk-alpine døgnklimaet med frost hver natt og høye dagtemperaturer året rundt. Antallet arter økte deretter betydelig gjennom de siste 5 millioner år (plio-pleistocen) og faktisk helt fram til vår tid. En stor del av floraen oppstod etter langdistansespredning fra fjerne, kalde områder, hovedsakelig i Eurasia. Plantenes innvandring ble bare i noen få tilfeller fulgt av betydelig diversifisering (f.eks. hos marikåpe Alchemilla) – tvert imot har slekter som er artsrike i det afrikanske høyfjellet, ofte vist seg å ha spredt seg uavhengig dit gjentatte ganger (f.eks. starr Carex), noe til og med enkeltarter som vår egen fjellskrinneblom Arabis alpina har gjort. De nye studiene tyder på at den afrikanske høyfjellsfloraen har utvikletseg under et mye yngre og mer dynamisk øy-scenario enn det Hedberg så for seg: Den framstår som umettet og sårbar for framtidige klima- og arealendringer på grunn av katastrofale forstyrrelser under klimasvingningene gjennom de siste par millioner år. Den rommer artsmangfold og genetisk diversitet som er unikt, men sterkt svekket av genetiske «flaskehalser» og sykluser av innvandring, utdøing og gjeninnvandring. Det er usedvanlig lite genetisk variasjon i dagens populasjoner, noe som kan bety at mange arter står i fare for å dø ut på grunn av klimaoppvarming og økende menneskelig påvirkning

Genetic consequences of climate change for northern plants

Climate change will lead to loss of range for many species, and thus to loss of genetic diversity crucial for their long-term persistence. We analysed range-wide genetic diversity (amplified fragment length polymorphisms) in 9581 samples from 1200 populations of 27 northern plant species, to assess genetic consequences of range reduction and potential association with species traits. We used species distribution modelling (SDM, eight techniques, two global circulation models and two emission scenarios) to predict loss of range and genetic diversity by 2080. Loss of genetic diversity varied considerably among species, and this variation could be explained by dispersal adaptation (up to 57%) and by genetic differentiation among populations (FST; up to 61%). Herbs lacking adaptations for long-distance dispersal were estimated to lose genetic diversity at higher rate than dwarf shrubs adapted to long-distance dispersal. The expected range reduction in these 27 northern species was larger than reported for temperate plants, and all were predicted to lose genetic diversity according to at least one scenario. SDM combined with FST estimates and/or with species trait information thus allows the prediction of species' vulnerability to climate change, aiding rational prioritization of conservation efforts

Sources of variation in small rodent trophic niche: New insights from DNA metabarcoding and stable isotope analysis

Intraspecific competition for food is expected to increase the trophic niche width of consumers, defined here as their diet diversity, but this process has been little studied in herbivores. Population densities of small rodents fluctuate greatly, providing a good study model to evaluate effects of competition on trophic niche. We studied resource use in five arctic small rodent populations of four species combining DNA metabarcoding of stomach contents and stable isotope analysis (SIA). Our results suggest that for small rodents, the most pronounced effect of competition on trophic niche is due to increased use of secondary habitats and to habitat-specific diets, rather than an expansion of trophic niche in primary habitat. DNA metabarcoding and SIA provided complementary information about the composition and temporal variation of herbivore diets. Combing these two approaches requires caution, as the underlying processes causing observed patterns may differ between methodologies due to different spatiotemporal scales. The final version of this research has been published in Isotopes in Environmental and Health Studies. © 2014 Taylor & Franci