The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.

invertebrate herbivory on dwarf birch (Betula glandulosa-nana 1 complex) increases with temperature and precipitation across the tundra biome ' Polar biology, vol. 40, no. 11, pp. 2265-2278. DOI: 10.1007%2Fs00300-017-2139 Digital Object Identifier (DOI): 10.1007%2Fs00300-017-2139-7 Link: Link to publication record in Edinburgh Research Explorer Document Version: Peer reviewed version Published In: Polar biology General rightsCopyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policyThe University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact openaccess@ed.ac.uk providing details, and we will remove access to the work immediately and investigate your claim. Chronic, low intensity herbivory by invertebrates, termed background herbivory, has been understudied in tundra, 78 yet its impacts are likely to increase in a warmer Arctic. The magnitude of these changes is however hard to 79 predict as we know little about the drivers of current levels of invertebrate herbivory in tundra. We assessed the 80 intensity of invertebrate herbivory on a common tundra plant, the dwarf birch (Betula glandulosa-nana complex), 81 and investigated its relationship to latitude and climate across the tundra biome. Leaf damage by defoliating, 82 mining and gall-forming invertebrates was measured in samples collected from 192 sites at 56 locations. Our 83 results indicate that invertebrate herbivory is nearly ubiquitous across the tundra biome but occurs at low 84 intensity. On average, invertebrates damaged 11.2% of the leaves and removed 1.4% of total leaf area. The 85 damage was mainly caused by external leaf feeders, and most damaged leaves were only slightly affected (12% 86 leaf area lost). Foliar damage was consistently positively correlated with mid-summer (July) temperature and, to a 87 lesser extent, precipitation in the year of data collection, irrespective of latitude. Our models predict that, on 88 average, foliar losses to invertebrates on dwarf birch are likely to increase by 6-7% over the current levels with a 1 89 °C increase in summer temperatures. Our results show that invertebrate herbivory on dwarf birch is small in 90 magnitude but given its prevalence and dependence on climatic variables, background invertebrate herbivory 91 should be included in predictions of climate change impacts on tundra ecosystems. 92 3

Abstract. Organic matter deposited in ancient, ice-rich permafrost sediments is vulnerable to climate change and may contribute to the future release of greenhouse gases; it is thus important to get a better characterization of the plant organic matter within such sediments. From a Late Quaternary permafrost sediment core from the Buor Khaya Peninsula, we analysed plant-derived sedimentary ancient DNA (sedaDNA) to identify the taxonomic composition of plant organic matter, and undertook palynological analysis to assess the environmental conditions during deposition. Using sedaDNA, we identified 154 taxa and from pollen and non-pollen palynomorphs we identified 83 taxa. In the deposits dated between 54 and 51 kyr BP, sedaDNA records a diverse low-centred polygon plant community including recurring aquatic pond vegetation while from the pollen record we infer terrestrial open-land vegetation with relatively dry environmental conditions at a regional scale. A fluctuating dominance of either terrestrial or swamp and aquatic taxa in both proxies allowed the local hydrological development of the polygon to be traced. In deposits dated between 11.4 and 9.7 kyr BP (13.4–11.1 cal kyr BP), sedaDNA shows a taxonomic turnover to moist shrub tundra and a lower taxonomic richness compared to the older samples. Pollen also records a shrub tundra community, mostly seen as changes in relative proportions of the most dominant taxa, while a decrease in taxonomic richness was less pronounced compared to sedaDNA. Our results show the advantages of using sedaDNA in combination with palynological analyses when macrofossils are rarely preserved. The high resolution of the sedaDNA record provides a detailed picture of the taxonomic composition of plant-derived organic matter throughout the core, and palynological analyses prove valuable by allowing for inferences of regional environmental conditions.

We conducted a systematic literature review of the current state of research on the social perceptions of invasive species, aiming to provide guidance towards transdisciplinary research and participatory decision making. In order to detect patterns regarding publication trends and factors determining social perceptions of invasive species, we applied qualitative content as well as quantitative data analysis. By applying content analysis, we identified five main categories of influence on the perception of invasive species: ecological conditions, social conditions, values and beliefs, impacts, and benefits. The disciplinary focus of the research was predominantly interdisciplinary, followed by a social sciences approach. Our review revealed a disproportionate use of quantitative methods in research on social perceptions of invasive species, yet quantitative methods were less likely to identify benefits as factors determining the perception of invasive species. However, without the understanding of perceived benefits, researchers and managers lack the socio-cultural context these species are embedded in. Our review also revealed the geographical, methodological and taxonomic bias of research on perceptions of invasive species. The majority of studies focused on the local public, whereas fewer than half of the studies focused on decision-makers. Furthermore, our results showed differences in the social perceptions of invasive species among different stakeholder groups. Consensus over the definition and terminology of invasive species was lacking whereas differences in terminology were clearly value-laden. In order to foster sustainable management of invasive species, research on social perceptions should focus on a transdisciplinary and transparent discourse about the inherent values of invasion science.

Ecosystem boundaries, such as the Arctic-Boreal treeline, are strongly coupled with climate and were spatially highly dynamic during past glacial-interglacial cycles. Only a few studies cover vegetation changes since the last interglacial, as most of the former landscapes are inundated and difficult to access. Using pollen analysis and sedimentary ancient DNA (sedaDNA) metabarcoding, we reveal vegetation changes on Bol’shoy Lyakhovsky Island since the last interglacial from permafrost sediments. Last interglacial samples depict high levels of floral diversity with the presence of trees (Larix, Picea, Populus) and shrubs (Alnus, Betula, Ribes, Cornus, Saliceae) on the currently treeless island. After the Last Glacial Maximum, Larix re-colonised the island but disappeared along with most shrub taxa. This was probably caused by Holocene sea-level rise, which led to increased oceanic conditions on the island. Additionally, we applied two newly developed larch-specific chloroplast markers to evaluate their potential for tracking past population dynamics from environmental samples. The novel markers were successfully re-sequenced and exhibited two variants of each marker in last interglacial samples. SedaDNA can track vegetation changes as well as genetic changes across geographic space through time and can improve our understanding of past processes that shape modern patterns.

Increasing drought periods as a result of global climate change pose a threat to many tree species by possibly outpacing their adaptive capabilities. Revealing the genetic basis of drought stress response is therefore implemental for future conservation strategies and risk assessment. Access to informative genomic regions is however challenging, especially for conifers, partially due to their large genomes, which puts constraints on the feasibility of whole genome scans. Candidate genes offer a valuable tool to reduce the complexity of the analysis and the amount of sequencing work and costs. For this study we combined an improved drought stress phenotyping of needles via a novel terahertz water monitoring technique with Massive Analysis of cDNA Ends to identify candidate genes for drought stress response in European silver fir (Abies alba Mill.). A pooled cDNA library was constructed from the cotyledons of six drought stressed and six well-watered silver fir seedlings, respectively. Differential expression analyses of these libraries revealed 296 candidate genes for drought stress response in silver fir (247 up- and 49 down-regulated) of which a subset was validated by RT-qPCR of the twelve individual cotyledons. A majority of these genes code for currently uncharacterized proteins and hint on new genomic resources to be explored in conifers. Furthermore, we could show that some traditional reference genes from model plant species (GAPDH and eIF4A2) are not suitable for differential analysis and we propose a new reference gene, TPC1, for drought stress expression profiling in needles of conifer seedlings.

ABSTRACT:The interactions between different metazooplankters (cladocerans, rotifers, copepods), protozoans (ciliates, nanoflagellates) and bacteria (mixed lakewater culture) were examined in laboratory microcosm experiments. Growth of bacteria was stimulated in batch cultures by the addition of glucose. During 24 h experiments most of the bacterial production was consumed by nanoflagellates which achieved high growth rates. Moderate biomasses of copepods, rotifers or small cladocerans (Bosmina longirostris, Ceriodaphnia reticulata) had no or only weak effects on protozoan development. In contrast, Daphnia (D. galeata. D. magna) in higher densities consumed protozoans and bacteria simultaneously. Bacterial abundance was strongly reduced in all treatments but bacteria were either mainly consumed by protozoans (nanoflagellates) or by metazoans (Daphnia). This resulted in striking differences in the bacterial morphology of the remaining bacteria after 24 h. A shift in bacterial size structure towards the appearance of large aggregates and long filaments correlated to predation by protozoans. These protozoan-resistant morphotypes dominated ungrazed bacterial biomass after 24 h. When bacteria grew wlthout predation or when Daphnja suppressed protozoan growth, the onglnal bacterial size structure largely remained, and freely dispersed rods and cocci predominated. These model experiments illustrate the different impacts of metazoan and protozoan grazers which could both control bacterial production but produced a very different bacterial biomass distribution.

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