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Alsos, I. G.

Publications and source records attributed to Alsos, I. G..

13 recordsLinked to original sources

The Muskox Way: Humans, plants and animals in northeast Greenland through the Holocene

The Muskox Way hypothesis suggests that the first humans entering northeast Greenland from Arctic Canada followed and hunted muskox. Yet whether muskox arrived before people remains debated, as only two bones predate the Independence culture (4500-3900 cal BP). More broadly, the arrival of plants and animals, and how the three periods of human settlement related to ecosystem changes, remain poorly understood. We analysed sedimentary ancient DNA from lakes in Wandel Dal (Late Sommersoe and Midsommersoe) and Zackenberg, identifying 121 native plants and nine animal taxa. In Wandel Dal, the plant assemblage indicates a warmer climate than today about 8200-3900 years ago, followed by an abrupt change in flora and sedimentation rate at 3900 cal BP, especially at Midsommersoe. Muskox DNA is present continuously at Midsommersoe from 7400 cal BP, about three millennia before humans arrived. The Zackenberg record dates to 12,200 cal BP, with arctic forbs, grasses, ferns and crowberry in the earliest layers, willow from 8200 cal BP and birch from 7200 cal BP, but muskox only in the last 2500 years, the latter period coinciding with Greenlandic Dorset culture. The arrival of the Thule culture in 1400 CE coincides with a slight increase in plant richness at Wandel Dal and an increase in mammal detections. Reindeer occurred only in samples older than 6000 years, consistent with their absence from archaeological bone records. Overall, humans arrived long after the first megafauna and appear to have had limited impact on their populations, although cultural periods coincided with environmental changes.

ecology↗

Dynamic sedimentary ancient DNA models of Fennoscandic Holocene plant communities reveal the role of temperature and competition

Ecosystems are constantly responding to shifting environmental conditions, and the observed structure of ecological communities at any given discrete observation timepoint is part of a larger dynamic response. However, we lack long-term time series of ecosystem responses allowing understanding of the processes driving community dynamics. Sedimentary ancient DNA (sed aDNA) offers novel opportunities to link empirical data with ecological processes, providing near continuous records of plant and animal community changes over millennia. Here, we analyzed metabarcoding data from 10 lakes from Northern Fennoscandia characterizing plant and mammal communities at temporal resolution of 100 years over several millenia. We used sed aDNA data to test how biotic processes, including temperature-dependent plant growth, competition, shading, and herbivory, may have driven the dynamics of Fennoscandic Holocene plant communities since the Last Glacial Maximum. We compared the explanatory power of ordinary differential equation-based models simulating community changes and including these processes. The fit of the models improved with the consideration of temperature dependent densification and biotic interactions, most notably shading. When considering individual taxa, the importance of shading and herbivory was greatest for the dwarf shrubs, while tree and shrub taxa were more often best predicted by models without competition. Our study demonstrates how using sed aDNA time series together with process-based inverse modelling can uncover the mechanisms of species response to climate change, offering potential for more realistic predictions.

ecology↗

Capture probe, metabarcoding, or shotgun sequencing: which best reflects local vegetation?

O_LIMetabarcoding is the most widely applied method for studying plant communities using environmental DNA, with shotgun sequencing and capture probes being alternative methods. Any methods ability to detect and correctly identify plant taxa may vary with DNA preservation, DNA reference library and the size of the local flora, making it difficult to compare results from different environments. C_LIO_LIHere we compare these methods using lake surface-sediments from Northern Fennoscandia with the PhyloNorway genome skim reference library (1500 taxa) that includes almost all species of the regional flora. We also undertook vegetation surveys from around the lakes to estimate the true positive detection rate, identify false positive detections, and provide optimal filtering cut-off thresholds for the three methods. C_LIO_LIOptimal filter cutoffs were one PCR replicate and 3 reads for metabarcoding, and 3.2x10e-6 and 5.6x10e-6 of queried reads, respectively, for the shotgun and capture probe data. Applying these thresholds, the rate of false positives was too high for reliable identification at species level based on shotgun (49%) and capture probes (62%), whereas it was low for metabarcoding (5-12%). All methods were reliable at genus and family levels after applying the optimal filtering thresholds (<4% false positives). Our results show that metabarcoding on average detects 2.1 times as many true positive taxa as shotgun sequencing, and 6.4 times as many taxa as capture probes. Proportions of filtered metabarcoding and shotgun reads were significantly related to abundance categories from vegetation surveys, but this was not the case for capture probe data. C_LIO_LIWe expect the false positive rate of shotgun sequencing to decrease with increasing genome completeness in the reference libraries, and be advantageous for highly degraded DNA with fragments too short for metabarcoding. At present, metabarcoding provides the highest detectability and taxonomic resolution for correct identification of vascular plants. C_LI

ecology↗

Maximizing vegetation representation of the catchment in sedimentary DNA with targeted cores in small lakes

Sedimentary DNA is becoming an invaluable tool for biodiversity assessments across spatial and temporal scales. Accurate interpretation, however, requires a clear understanding of its origin and taphonomy, from transport to preservation processes within lake systems. Insights into these processes are crucial for developing efficient sampling methods for precise ecological monitoring. Our analysis of 42 adjacent surface sediment sample replicates shows that deeper, central samples, with reduced influence from aquatic taxa, exhibit greater taxonomic richness compared to near-shore samples. By comparing these results to systematic vegetation surveys, we demonstrate that central cores are optimal as they capture the main taxonomic richness in the catchment, while marginal samples near inflows are essential for detecting rarer, spatially restricted taxa. This study highlights the potential of central-core sampling to effectively capture vegetation profiles in small, bathymetrically simple lakes, while enhancing the understanding of DNA transport mechanisms in catchments with similar topographic or hydrological characteristics.

ecology↗

Harmonising digitised herbarium data to enhance biodiversity knowledge: creating an updated checklist for the flora of Greenland.

International efforts to digitise herbarium specimens provide the building blocks for a global digital herbarium. However, taxonomic changes and errors can result in inconsistencies when amalgamating specimen metadata, that compromise the assignment of occurrence records to correct taxa, and the subsequent interpretation of patterns in biodiversity. We present a novel workflow to mass-curate digital specimens. By employing existing digital taxonomic backbones, we aggregate specimen names by their accepted name and flag remaining cases for manual review. We then validate names using site-specific floras, balancing automation with taxonomic expert-based curation. Applying our workflow to the vascular plants of Greenland, we harmonised 175,266 digitised herbarium specimens and observations from 92 data providers from the Global Biodiversity Information Facility (GBIF). The harmonised metacollection for the Greenland flora contains 780 plant species. Our workflow increases the number of species known from Greenland compared to other currently available species checklists and increases the mean number of occurrences per species by 42.6. Our workflow illustrates the integration required in order to create a global, universally accessible digital herbarium, and shows how previous obstacles to database curation can be overcome through a combination of automation and expert curation. From the specific perspective of the Greenland flora, our approach arrives at a new checklist of taxa, a new curated metacollection of occurrence data, and revised estimates of plant richness. The list of taxa and their prevalence allow a new basis for biodiversity assessment and conservation planning. Societal Impact StatementDigitising plant collections has allowed for data to be aggregated across multiple collections, forming a single harmonised resource of unprecedented scale. This resource is only accurate once the database names are assigned to one accepted name per species. We established a semi-automated workflow for processing plant name data, leveraging taxonomic backbones and employing taxonomic expertise at key stages. Applying our workflow to the flora of Greenland, we developed a curated checklist of 780 species, capturing greater species richness than previously published, while also curating 175,266 plant records. Our findings redefine our knowledge of Greenlandic plant diversity, while harmonising a vast digital collection for further research.

ecology↗

Early Neolithic forest farming at Seven Springs, Martlesham, Suffolk from sedaDNA and pollen

The importance of small wetlands and springs to Mesolithic cultures is well established. However, few studies have focused on their significance and use by Early Neolithic agro-pastoralists. Here we present a multiproxy palaeoenvironmental analysis, including authenticated sedimentary ancient DNA (sedaDNA), at Seven Springs, Martlesham, UK, indicating that the springs provided an attractive location for pastoral and ritual activity around a palaeochannel surrounded by dense woodland. We demonstrate that sedaDNA can be preserved well within stratigraphically complex wetland sediment sequences, allowing archaeologically valuable insights into crucial periods of change in the prehistoric, where other forms of environmental evidence can be scarce.

ecology↗

Environmental DNA of aquatic macrophytes: the potential for reconstructing past and present vegetation and environments

Environmental DNA is increasingly being used to reconstruct past and present biodiversity including from freshwater ecosystems. Here, we first review and compare studies that use metagenomics, targeted capture, and various barcoding and metabarcoding markers, in order to explore how each of these methods can be used to capture aquatic vegetation diversity and change. We then investigate the extent to which such a record can be leveraged for reconstructing local environmental conditions, using a case study based on macrophyte ecological niches. We find that, with state-of-the-art DNA barcode reference libraries, using metabarcoding to target the P6 loop region of the chloroplast trnL (UAA) intron is optimal to maximise taxonomic resolution and the diversity of past macrophyte communities. Shotgun sequencing also retrieves a high proportion of aquatic macrophyte diversity, but has the lowest taxonomic resolution, and targeted capture needs to be more widely applied before comparisons can be made. From our case study, we infer past aquatic habitats from sedimentary ancient DNA records of macrophyte taxa. We reconstructed Holocene thermal range, continentality, water pH, trophic status, and light conditions in northern Fennoscandia. We show an overall stability since 9,000 years ago, even though individual lakes display different trends and variation in local climatic and physico-chemical conditions. Combined with the availability of near-exhaustive barcode and traits databases, metabarcoding data can support wider ecological reconstructions that are not limited to aquatic plant taxonomic inventories but can also be used to infer past changes in water conditions and their environmental drivers. Sedimentary DNA is also a powerful tool to measure present diversity, as well as to reconstruct past lacustrine and fluvial communities of aquatic macrophytes.

ecology↗

Towards the extended barcode concept: Generating DNA reference data through genome skimming of danish plants

BackgroundRecently, there has been a push towards the extended barcode concept of utilising chloroplast genomes (cpGenome) and nuclear ribosomal DNA (nrDNA) sequences for molecular identification of plants instead of the standard barcode regions. These extended barcodes has a wide range of applications, including biodiversity monitoring and assessment, primer design, and evolutionary studies. However, these extended barcodes are not well represented in global reference databases. To fill this gap, we generated cpGenomes and nrDNA reference data from genome skims of 184 plant species collected in Denmark. We further explored the application of our generated reference data for molecular identifications of plants in an environmental DNA metagenomics study. ResultsWe assembled partial cpGenomes for 82.1% of sequenced species and full or partial nrDNA sequences for 83.7% of species. We added all assemblies to GenBank, of which chloroplast reference data from 101 species and nuclear reference data from 6 species were not previously represented. On average, we recovered 45 genes per species. The rate of recovery of standard barcodes was higher for nuclear barcodes (>89%) than chloroplast barcodes (< 60%). Extracted DNA yield did not affect assembly outcome, whereas high GC content did so negatively. For the in silico simulation of metagenomic reads, taxonomic assignments using the reference data generated had better species resolution (94.9%) as compared to GenBank (18.1%) without any identification errors. ConclusionsGenome skimming generates reference data of both standard barcodes and other loci, contributing to the global DNA reference database for plants.

genomics↗

Molecular dietary analyses of western capercaillies (Tetrao urogallus) reveal a diverse diet

Conservation strategies centred 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). Traditional microhistological analysis of crop contents or faeces and/or direct observations are time-consuming and at low taxonomic resolution. Thus, limited knowledge on diet is hampering conservation efforts. Here we use non-invasive environmental DNA (eDNA) metabarcoding on DNA extracted from faeces to present the first large-scale molecular dietary analysis of capercaillies. Faecal samples were collected from seven populations located in Norway (Finnmark, Troms, Trondelag, Innlandet) and France (Vosges, Jura, Pyrenees) (n=172). We detected 122 plant taxa belonging to 46 plant families of which 37.7% of the detected taxa could be identified at species level. The average dietary richness of each sample was 7 {+/-} 5 SD taxa. The most frequently occurring plant groups with the highest relative read abundance (RRA) were trees and dwarf shrubs, in particular, Pinus and Vaccinium myrtillus, respectively. There was a difference in dietary composition (RRA) between samples collected from the different locations (adonis F5,86= 11.01, p <0.05) and seasons (adonis F2,03= 0.64, p <0.05). Dietary composition also differed between sexes at each location (adonis F1,47 = 2.77, p <0.05), although not significant for all data combined. In total, 35 taxa (36.84% of taxa recorded) were new capercaillie food items compared to existing knowledge. The non-invasive molecular dietary analysis applied in this study provides new ecological understanding of capercaillies diet which can have real conservation implications. The broad variety of diet items indicates that vegetation does not limit food intake. This plasticity in diet suggests that other factors including disturbed mating grounds and not diet could be the main threat to their survival.

ecology↗

Ancient sedimentary DNA shows rapid post-glacial colonisation of Iceland followed by relatively stable vegetation until Landnam

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 infer patterns of colonisation and Holocene vegetation development. Our cores from lakes Torfdalsvatn and Nykurvatn span the last c. 12,000 cal. yr BP and c. 8600 cal. yr BP, respectively. With near-centennial resolution, we identified a total of 191 plant taxa, with 152 taxa identified in the sedimentary record of Torfdalsvatn and 172 plant taxa in the sedimentary record of Nykurvatn. The terrestrial vegetation at Torfdalsvatn was first dominated by bryophytes, arctic herbs such as Saxifraga spp. and grasses. Around 10,100 cal. yr BP, a massive immigration of new taxa was observed, and shrubs and dwarf shrubs became common whereas aquatic macrophytes became dominant. At Nykurvatn, all dominant taxa occurred already in the earliest samples; shrubs and dwarf shrubs were more abundant at this site than at Torfdalsvatn. There was an overall steep increase both in the local and regional species pool until 8000 cal. yr BP, by which time [3/4] of all taxa identified had arrived. In the period 4500-1000 cal. yr BP, a few new taxa of bryophytes, graminoids and forbs are identified. The last millennium, after human settlement of the island (Landnam), is characterised by a sudden disappearance of Juniperus communis, but also reappearance of some high arctic forbs and dwarf shrubs. Notable immigration during the Holocene coincides with periods of dense sea-ice cover, and we hypothesise that this may have acted as a dispersal vector. Thus, although ongoing climate change might provide a suitable habitat in Iceland for a large range of species only found in the neighbouring regions today, the reduction of sea ice may in fact limit the natural colonisation of new plant species.

ecology↗

Holocene plant diversity revealed by ancient DNA from 10 lakes in northern Fennoscandia

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 steeply during the rapidly warming Early Holocene. In contrast to findings from most pollen studies, we show that richness continued to increase through the Middle to Late Holocene even though temperature decreased, with the regional species pool only stabilizing during the last two millennia. Furthermore, overall increase in richness was greater in catchments with higher soil nutrient availability. We suggest that richness will rapidly increase with ongoing warming, especially at localities with high nutrient availability and even in the absence of increased human activity in the region, although delays of millennia may be expected.

ecology↗

Environmental palaeogenomic reconstruction of an Ice Age algal population

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. We shotgun sequenced two lake sediment samples dated to the Last Glacial Maximum and identified N. limnetica as the dominant taxon. We then reconstructed full chloroplast and mitochondrial genomes to explore within-lake population genomic variation. This revealed at least two major haplogroups for each organellar genome, which could be assigned to known varieties of N. limnetica. The approach presented here demonstrates the utility of lake sedimentary ancient DNA (sedaDNA) for population genomic analysis, thereby opening the door to environmental palaeogenomics, which will unlock the full potential of sedaDNA.

genomics↗

Metabarcoding lake sediments: taphonomy and representation of contemporary vegetation in environmental DNA (eDNA) records

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 growing within 2 m from the lake shore, 17-49% (mean 31%) of the identifiable taxa recorded were detected with eDNA. Of the 217 eDNA records, 73% and 12% matched taxa recorded in vegetation surveys within 2 m and up to about 50 m away from the lakeshore, respectively, whereas 16% were not recorded in the vegetation surveys of the same lake. The latter include taxa likely overlooked in the vegetation surveys or growing outside the survey area. The percentages detected were 61, 47, 25, and 15 for dominant, common, scattered, and rare taxa, respectively. Similar numbers for aquatic plants were 88, 88, 33 and 62%, respectively. Detection rate and taxonomic resolution varied among plant families and functional groups with good detection of e.g. Ericaceae, Roseaceae, deciduous trees, ferns, club mosses and aquatics. The representation of terrestrial taxa in eDNA depends on both their distance from the sampling site and their abundance and is sufficient for recording vegetation types. For aquatic vegetation, eDNA may be comparable with, or even superior to, in-lake vegetation surveys and therefore be used as an tool for biomonitoring. For reconstruction of terrestrial vegetation, technical improvements and more intensive sampling is needed to detect a higher proportion of rare taxa although DNA of some taxa may never reach the lake sediments due to taphonomical constrains. Nevertheless, eDNA performs similar to conventional methods of pollen and macrofossil analyses and may therefore be an important tool for reconstruction of past vegetation.

ecology↗