Youri Lammers

• UiT The Arctic University of Norway

In the face of human land use and climate dynamics, it is essential to know the key drivers of plant species diversity in montane regions. However, the relative roles of climate and ungulates in alpine ecosystem change is an open question. Neither observational data nor traditional palaeoecological data have the power to resolve this issue over dec...

We present a decade-long research initiative of biodiversity genomics, which aimed at sequencing all vascular plant species occurring in the biodiversity hotspot of the European Alps, along with related lineages occurring in other mountain ranges and the arctic region. We detail the sampling and sequencing strategies, an online database for genome...

The Eastern European Alps boasts highly biodiverse ecosystems and a rich archaeological history. However, there is limited research on the enduring impacts of historical climate change and human activities on plant biodiversity in this region. Using sedimentary ancient DNA, we reconstructed plant and animal dynamics from 8500 years before present (...

When tracing vegetation dynamics over long timescales, obtaining enough floristic information to gain a detailed understanding of past communities and their transitions can be challenging. The first high-resolution sedimentary DNA (sedaDNA) metabarcoding record from lake sediments in Alaska—reported here—covers nearly 15,000 years of change. It sho...

Sedimentary ancient DNA (sedaDNA) has rarely been used to obtain population‐level data due to either a lack of taxonomic resolution for the molecular method used, limitations in the reference material or inefficient methods. Here, we present the potential of multiplexing different PCR primers to retrieve population‐level genetic data from sedaDNA s...

Sedimentary ancient DNA (sedaDNA) is continuing to revolutionise our understanding of past biological and geological processes by retrieving and analysing the ancient DNA preserved in lake, cave, open terrestrial, midden, permafrozen, and marine environments (Crump 2021). The study of sedaDNA began in the late 1990s (Coolen and Overmann 1998) with...

Animals with large energy requirements are forced to optimize their hunting strategy, which may result in differentiation of the diet between sexes and across seasons. Here, we examined spatiotemporal variation in the diet of both sexes of the Pond Bat Myotis dasycneme, a species known to have spatial segregation of sexes when the young are born an...

The unglaciated Alaskan interior saw major climatic changes during deglaciation, undergoing a transition from a cool, dry climate and herb-dominated late-Pleistocene vegetation through a period of increasing, but fluctuating, levels of warmth and moisture to near-modern boreal-forest conditions. Previous isotopic and lake-level studies and climate...

The European Alps are highly rich in species, but their future may be threatened by ongoing changes in human land use and climate. Here, we reconstructed vegetation, temperature, human impact and livestock over the past ~12,000 years from Lake Sulsseewli, based on sedimentary ancient plant and mammal DNA, pollen, spores, chironomids, and microcharc...

Both climate change and anthropogenic disturbance affect vegetation composition, but it is difficult to separate these drivers of vegetation change from one another. A better understanding of past vegetation dynamics is necessary to disentangle the influence of different forcing factors and assess future vegetation change. Here we present the first...

Population size has increasingly been taken as the driver of past human environmental impact worldwide, and particularly in the Arctic. However, sedimentary ancient DNA (sedaDNA), pollen and archaeological data show that over the last 12,000 years, paleoeconomy and culture determined human impacts on the terrestrial ecology of Arctic Norway. The la...

Although sedimentary ancient DNA (sedaDNA) is increasingly used to reconstruct past ecosystem changes, we do not yet know much about its preservation conditions across geological time, resulting in potential biases and uncertainties in data interpretation. In this study, we obtained sedaDNA records from around 15 lakes from the Arctic and sub-Arcti...

During the last glacial–interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1–8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across t...

Conservation strategies centered around species habitat protection rely on species’ dietary information. One species at the focal point of conservation efforts is the herbivorous grouse, the western capercaillie (Tetrao urogallus), which is an indicator species for forest biodiversity conservation. Non-molecular means used to study their diet are t...

The effects of climate change on species richness are debated but can be informed by the past. Here, we generated a sedimentary ancient DNA dataset covering 10 lakes and applied novel methods for data harmonization. We assessed the impact of Holocene climate changes and nutrients on terrestrial plant richness in northern Fennoscandia. We find that...

Metagenomics can generate data on the diet of herbivores, without the need for primer selection and PCR enrichment steps as is necessary in metabarcoding. Metagenomic approaches to diet analysis have remained relatively unexplored, requiring validation of bioinformatic steps. Currently, no metagenomic herbivore diet studies have utilized both chlor...

Understanding patterns of colonisation is important for explaining both the distribution of single species and anticipating how ecosystems may respond to global warming. Insular flora may be especially vulnerable because oceans represent severe dispersal barriers. Here we analyse two lake sediment cores from Iceland for ancient sedimentary DNA to i...

Palaeogenomics has greatly increased our knowledge of past evolutionary and ecological change, but has been restricted to the study of species that preserve either as or within fossils. Here we show the potential of shotgun metagenomics to reveal population genomic information for a taxon that does not preserve in the body fossil record, the algae...

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...

Understanding patterns of colonisation is important for explaining both the distribution of single species and anticipating how ecosystems may respond to global warming. Insular flora may be especially vulnerable because oceans represent severe dispersal barriers. Here we analyse two lake sediment cores from Iceland for ancient sedimentary DNA to i...

The effects of climate change on species richness is debated but can be informed by the past. Here, we assess the impact of Holocene climate changes and nutrients on terrestrial plant richness across multiple sites from northern Fennoscandia using new sedimentary ancient DNA (sedaDNA) data quality control methods. We find that richness increased st...

Andøya on the NW coast of Norway is a key site for understanding the Last Glacial Maximum (LGM) in northern Europe. Controversy has arisen concerning the local conditions, especially about the timing and extent of local glacial cover, maximum July temperatures and whether pine and/or spruce could have grown there. We reviewed all existing data and...

Palaeogenomics has greatly increased our knowledge of past evolutionary and ecological change, but has been restricted to the study of species that preserve as fossils. Here we show the potential of shotgun metagenomics to reveal population genomic information for a taxon that does not preserve in the body fossil record, the algae Nannochloropsis....

Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshl...

The lake sediments of Hässeldala Port in south-east Sweden provide an archive of local and regional environmental conditions ~14.5–9.5 ka BP (thousand years before present) and allow testing DNA sequencing techniques to reconstruct past vegetation changes. We combined shotgun sequencing with plant micro- and macrofossil analyses to investigate sedi...

While there are extensive macro- and microfossil records of a range of plants and animals from the Quaternary, earthworms and their close relatives amongst annelids are not preserved as fossils and therefore the knowledge of their past distributions is limited. This lack of fossils means that clitellate worms (Annelida) are currently underused in p...

We present a Holocene record of floristic diversity and environmental change for the central Varanger Peninsula, Finnmark, based on ancient DNA extracted from the sediments of a small lake (sedaDNA). The record covers the period c. 10 700 to 3300 cal. a BP and is complemented by pollen data. Measures of species richness, sample evenness, and beta-d...

Metabarcoding of lake sediments have been shown to reveal current and past biodiversity, but little is known about the degree to which taxa growing in the vegetation are represented in environmental DNA (eDNA) records. We analysed composition of lake and catchment vegetation and vascular plant eDNA at 11 lakes in northern Norway. Out of 489 records...

Taxa removed during filtering. All DNA reads that have 100% match to the reference libraries and have been removed during the second last step of filtering (see S2 Table). (XLSX)

Comments on true and false positives. (DOCX)

All taxa recorded in the vegetation surveys. (<2 m and/or larger surveys) at 11 lakes in northern Norway. Number refers to the highest abundance recorded among 2–17 vegetation polygons in the larger vegetation surveys (1 = rare, 2 = scattered, 3 = frequent, and 4 = dominant). Thus, 2316 records were combined to give one vegetation record per specie...

Number of sequence reads remaining after each filtering step for 42 samples from modern lake sediment collected in northern Norway, 6 extraction negative controls, 6 PCR negative controls and 2 PCR positive controls. Six individually tagged PCR repeats were run for each sample, giving a total of 336 PCR samples. Numbers of sequences and unique sequ...

Effect of different filtering criteria on the number of true positives. True positive (TP, defined as species also detected in vegetation surveys thus lower than the numbers given in Table 2) and False Positives (FP, defined as species not found in the regional flora; including 15 potential food plants) per lake and in total. The criteria used in t...

Retrieval of positive controls from raw orbitool output file. The file consisted of 12706536 reads of 581 sequences, 98% match). Note that not all taxa used in the positive controls were present in the reference library but they match to closely related taxa. (DOCX)

The probability of detection in eDNA and vegetation. The probability that all taxa in the vegetation were recorded (Vegetation), and that the DNA records represents true and false positives. Mean probability, standard deviation (SD) are given for each lake. (DOCX)

Metabarcoding of lake sediments may reveal current and past biodiversity, but little is known about the degree to which taxa growing in the vegetation are represented in environmental DNA (eDNA) records. We analysed composition of lake and catchment vegetation and vascular plant eDNA at 11 lakes in northern Norway. Out of 489 records of taxa growin...

Chikanda is a traditional dish made with wild-harvested ground orchid tubers belonging to three orchidioid genera, Disa, Satyrium and Habenaria, all of which are CITES appendix II-listed. Identification of collected orchid tubers is very difficult and documentation of constituent species in prepared chikanda has hitherto been impossible. Here ampli...

The integration of invasive species into native food webs represent multifarious dynamics of ecological and evolutionary processes. We document incorporation of Prunus serotina (black cherry) into native insect food webs. We find that P. serotina harbours a herbivore community less dense but more diverse than its native relative, P. padus (bird che...

Calculations of conversion of cyanogenic glycoside contents for dry and fresh weight leaves

Information on insect herbivore damage in historical collection specimens from the National Herbarium, Leiden, for Prunus serotina and Prunus padus

Explanatory variables and response variables for the test of parasitzation of caterpillars on P. serotina and P. padus

Structure analysis and AMOVA on SNP data for Gonioctena quinquepunctata

Full data on NMR analysis of Prunus leaves

Oligonucleotides used for the SNP-analysis of Gonioctena quinquepunctata

Full data on identities and numbers of herbivores collected on each individual Prunus serotina and Prunus padus in National Park Zuid-Kennemerland

SNP Loci that showed indications of genetic differentiation between both host plants in the leaf beetle Gonioctena quinquepunctata

SNP genotype data on Gonioctena quinquepunctata

ANOVA and GLM results for the Gonioctena quinquepunctata host preference tests

The integration of invasive species into native food webs represent multifarious dynamics of ecological and evolutionary processes. We document incorporation of Prunus serotina (black cherry) into native insect food webs. We find that P. serotina harbours a herbivore community less dense but more diverse than its native relative, P. padus (bird che...

The integration of invasive species into native food webs represent multifarious dynamics of ecological and evolutionary processes. We document incorporation of Prunus serotina (black cherry) into native insect food webs. We find that P. serotina harbours a herbivore community less dense but more diverse than its native relative, P. padus (bird che...

Background Understanding the molecular basis of domestication can provide insights into the processes of rapid evolution and crop improvement. Here we demonstrated the processes of carrot domestication and identified genes under selection based on transcriptome analyses. Results The root transcriptomes of widely differing cultivated and wild carro...

Western European coastal sand dunes are highly important for nature conservation. Communities of the creeping willow (Salix repens) represent one of the most characteristic and diverse vegetation types in the dunes. We report here the results of the first kingdom-wide fungal diversity assessment in S. repens coastal dune vegetation. We carried out...

Recent years have seen a surge in projects that produce large volumes of structured, machine-readable biodiversity data. To make these data amenable to processing by generic, open source “data enrichment” workflows, they are increasingly being represented in a variety of standards-compliant interchange formats. Here, we report on an initiative in w...

Pollen, botanical macrofossils, chemical components and ancient DNA were studied in samples from the rumen of a frozen Yakutian bison (Bison priscus) that lived ca. 10,500 cal a BP. The dialkyl glycerol ether lipid archaeol (2,3-di-O-phytanyl-sn-glycerol) was detected and is interpreted to have been derived from methanogenic Archaea in the rumen. T...

The 96 transcriptome-based gene models used for primer development, primers and reference sequences. Table S2. Testing of 96 primer pairs for cross-amplification for the genus Triturus. Table S3. Sampling details. Table S4. Number of reads per individual per marker. Table S5. Filtered SNP report used to construct consensus sequences. Table S6. Alle...

Next-generation sequencing is a fast and cost-effective way to obtain sequence data for non-model organisms for many markers and for many individuals. We describe a protocol through which we obtain orthologous markers for the crested newts (Amphibia: Salamandridae: Triturus), suitable for analysis of interspecific hybridization. We use transcriptom...

Mixtures of internationally traded organic substances can contain parts of species protected by the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). These mixtures often raise the suspicion of border control and customs offices, which can lead to confiscation, for example in the case of Traditional Chinese me...

Hybrid zones are regions where genetically distinct populations meet, mate and produce offspring. In such zones, genetically less compatible gene combinations are usually generated, resulting in reduced fitness, and hybrid zones are often maintained because of continuous removal of unfit genotypes, balanced by gene flow into the zone from the paren...

Invasive individuals from the pest species Jacobaea vulgaris show different allocation patterns in defence and growth compared with native individuals. To examine if these changes are caused by fast evolution, it is necessary to identify native source populations and compare these with invasive populations. For this purpose, we are in need of intra...