BL7069: BSc course in Evolutionary Biology (15 ECTS), 1 lecture

GG2010: BSc course in Geological Sciences (15 ECTS), co-lead, 3 lectures, 1 field excusion

BL7052: MSc course in Palaeogenetics (15 ECTS), 6 lectures

GG7023: MSc course in Palaeontology (7.5 ECTS), 2 lectures

A selection from Stockholm University publication database

• Wild and domesticated animal abundance is associated with greater late-Holocene alpine plant diversity

  2025. Sandra Garcés-Pastor (et al.). Nature Communications 16

  Article

  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 decadal to centennial timescales, but sedimentary ancient DNA (sedaDNA) does. Here we record 603 plant taxa, as well as 5 wild, and 6 domesticated mammals from 14 lake sediment records over the last 14,000 years in the European Alps. Sheep were the first domesticated animals detected (at 5.8 ka), with cattle appearing at the early Bronze Age (4.2 ka) and goats arriving later (3.5 ka). While sheep had an impact similar to wild ungulates, cattle have been associated with increased plant diversity over the last 2 ka by promoting the diversity of forbs and graminoids. Modelling of the sedaDNA data revealed a significantly larger effect of cattle and wild ungulates than temperature on plant diversity. Our findings highlight the significant alteration of alpine vegetation and the entire ecosystem in the Alps by wild and domesticated herbivores. This study has immediate implications for the maintenance and management of high plant species diversity in the face of ongoing anthropogenic changes in the land use of montane regions.

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• The progressive evolution of cold-adapted species

  2025. John R. Stewart (et al.). Trends in Ecology & Evolution

  Article

  The evolution of cold-adapted terrestrial species underwent two main phases. First, the genera of cold-adapted taxa appeared during the Late Pliocene to Early Pleistocene. The modern day and Late Pleistocene cold-adapted species then arose during and after the Middle Pleistocene Transition. These species evolved through one or more of the following processes: out of the temperate zone, evolving in situ, or through montane preadaptation. Palaeogenetic studies are greatly contributing to our understanding of the timings and modes of evolution of cold-adapted species as well as when their specialised traits evolved. The evolution of polar plant and beetle species is claimed to show greater stasis than that of vertebrates, but could instead reflect morphological conservatism that can be tested with palaeogenetics.

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• A Million Years of Mammoth Mitogenome Evolution

  2025. J. Camilo Chacón-Duque (et al.). Molecular biology and evolution 42 (4)

  Article

  The genomic study of specimens dating to the Early and Middle Pleistocene (EP and MP), a period spanning from 2.6 million years ago (Ma) to 126 thousand years ago (ka), has the potential to elucidate the evolutionary processes that shaped present-day biodiversity. Obtaining genomic data from this period is challenging, but mitochondrial DNA, given its higher abundance compared to nuclear DNA, could play an important role to understand evolutionary processes at this time scale. In this study, we report 34 new mitogenomes, including two EP and nine MP mammoth (Mammuthus spp.) specimens from Siberia and North America and analyze them jointly with >200 publicly available mitogenomes to reconstruct a transect of mammoth mitogenome diversity throughout the last million years. We find that our EP mitogenomes fall outside the diversity of all Late Pleistocene (LP) mammoths, while those derived from MP mammoths are basal to LP mammoth Clades 2 and 3, supporting an ancient Siberian origin of these lineages. In contrast, the geographical origin of Clade 1 remains unresolved. With these new deep-Time mitogenomes, we observe diversification events across all clades that appear consistent with previously hypothesized MP and LP demographic changes. Furthermore, we improve upon an existing methodology for molecular clock dating of specimens >50 ka, demonstrating that specimens need to be individually dated to avoid biases in their age estimates. Both the molecular and analytical improvements presented here highlight the importance of deep-Time genomic data to discover long-lost genetic diversity, enabling better assessments of evolutionary histories.

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• A High-Throughput Ancient DNA Extraction Method for Large-Scale Sample Screening

  2025. Alexandre Gilardet (et al.). Molecular Ecology Resources

  Article

  Large-scale DNA screening of palaeontological and archaeological collections remains a limiting and costly factor for ancient DNA studies. Several DNA extraction protocols are routinely used in ancient DNA laboratories and have even been automated on robotic platforms. Robots offer a solution for high-throughput screening but the costs, as well as necessity for trained technicians and engineers, can be prohibitive for some laboratories. Here, we present a high-throughput alternative to robot-based ancient DNA extraction using a 96-column plate. When compared to routine single MinElute columns, we retrieved highly similar endogenous DNA contents, an important metric in ancient DNA screening. Mitogenomes with a coverage depth greater than 0.1× could be generated and allowed for taxonomic assignment. However, average fragment lengths, DNA damage and library complexities significantly differed between methods but these differences became nonsignificant after modification of our library purification protocol. Our high-throughput extraction method allows generation of 96 extracts within approximately 4 hours of laboratory work while bringing the cost down by ~39% compared to using single columns. Additionally, we formally demonstrate that the addition of Tween-20 during the elution step results in higher complexity libraries, thereby enabling higher genome coverage for the same sequencing effort.

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• SedaDNA shows that transhumance of domestic herbivores has enhanced plant diversity over the Holocene in the Eastern European Alps

  2025. Scarlett Zetter (et al.). The Holocene

  Article

  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 (ka BP) around Großer Winterleitensee (Zirbitzkogel, Austria). Variable intensities of human activities since the Middle Bronze Age (~3.5 ka BP) facilitated the persistence of biodiverse Alpine meadow communities and lowered timberlines below their natural limit. Since the end of the Bronze Age (~2.8 ka BP), human activities, particularly pasturing, and increasing temperatures, emerged as significant drivers of plant community dynamics. The introduction of sheep (Ovis aries) did not reduce wild mammal presence, including red deer (Cervus elaphus), hare (Lepus), European mole (Talpa europaea), bank vole (Myodes glareolus), and short-tailed field vole (Microtus agrestis). During the High & Late Mediaeval Period, (~1150–450 BP), cattle (Bos taurus) and horses (Equus caballus) became the dominant domesticates, while all wild mammals except the short-tailed field vole and Eurasian water shrew (Neomys fodiens) declined or even disappeared. These changes are also accompanied by a significant transformation of plant community structure. The ability to determine both plant responses and animal drivers from the same palaeolimnological sequence vastly improves our ability to partition causes of vegetation change over the Holocene. Here, we reveal that plant biodiversity is maintained or increased by moderate cattle grazing. Therefore, non-intensive domesticated stock grazing is essential for maintaining diverse Alpine meadows.

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• Temporal dynamics of woolly mammoth genome erosion prior to extinction

  2024. Marianne Dehasque (et al.). Cell 187 (14), p3531-3540.e13

  Article

  A number of species have recently recovered from near-extinction. Although these species have avoided the immediate extinction threat, their long-term viability remains precarious due to the potential genetic consequences of population declines, which are poorly understood on a timescale beyond a few generations. Woolly mammoths (Mammuthus primigenius) became isolated on Wrangel Island around 10,000 years ago and persisted for over 200 generations before becoming extinct around 4,000 years ago. To study the evolutionary processes leading up to the mammoths’ extinction, we analyzed 21 Siberian woolly mammoth genomes. Our results show that the population recovered quickly from a severe bottleneck and remained demographically stable during the ensuing six millennia. We find that mildly deleterious mutations gradually accumulated, whereas highly deleterious mutations were purged, suggesting ongoing inbreeding depression that lasted for hundreds of generations. The time-lag between demographic and genetic recovery has wide-ranging implications for conservation management of recently bottlenecked populations.

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• Unravelling reference bias in ancient DNA datasets

  2024. Stephanie Dolenz (et al.). Bioinformatics 40 (7)

  Article

  Motivation: The alignment of sequencing reads is a critical step in the characterization of ancient genomes. However, reference bias and spurious mappings pose a significant challenge, particularly as cutting-edge wet lab methods generate datasets that push the boundaries of alignment tools. Reference bias occurs when reference alleles are favoured over alternative alleles during mapping, whereas spurious mappings stem from either contamination or when endogenous reads fail to align to their correct position. Previous work has shown that these phenomena are correlated with read length but a more thorough investigation of reference bias and spurious mappings for ancient DNA has been lacking. Here, we use a range of empirical and simulated palaeogenomic datasets to investigate the impacts of mapping tools, quality thresholds, and reference genome on mismatch rates across read lengths. Results: For these analyses, we introduce AMBER, a new bioinformatics tool for assessing the quality of ancient DNA mapping directly from BAM-files and informing on reference bias, read length cut-offs and reference selection. AMBER rapidly and simultaneously computes the sequence read mapping bias in the form of the mismatch rates per read length, cytosine deamination profiles at both CpG and non-CpG sites, fragment length distributions, and genomic breadth and depth of coverage. Using AMBER, we find that mapping algorithms and quality threshold choices dictate reference bias and rates of spurious alignment at different read lengths in a predictable manner, suggesting that optimized mapping parameters for each read length will be a key step in alleviating reference bias and spurious mappings.

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• Holocene summer temperature reconstruction from plant sedaDNA and chironomids from the northern boreal forest

  2024. Roseanna J. Mayfield (et al.). Quaternary Science Reviews 345

  Article

  Climate-induced ecotonal shifts are expected to occur in the (sub)arctic and boreal zones in the coming decades. Understanding how these ecosystems have previously responded to climate change can provide greater insight into how ecosystems may develop under existing and future pressures. Here we present a Holocene record from Lake Horntjernet, a lake on the northern edge of the boreal forest in Northern Norway. We show vegetation development and landscape dynamics typical for Northern Fennoscandia during the Holocene. A plant sedaDNA record indicates rapid vegetation development following deglaciation with early arrival of Betula trees/shrubs. Pine forest was established by c. 8500 cal yr BP, and subsequent mid- to late Holocene vegetation assemblages are relatively stable. The aquatic ecosystem community is indicative of climatic change during the early Holocene, while strong coupling with changes in the catchment vegetation affects the water quality during the mid- and late Holocene. The chironomid record indicates lake water acidification following the establishment of pine forest and heathland. Different approaches for temperature reconstruction are calculated and the results are compared to better understand ecosystem-climate relationships and ecosystem resilience to climate change. Chironomid-inferred temperatures indicate early Holocene warming and late Holocene cooling, comparable to independent regional temperature trends. However, lake acidification impedes reliable reconstruction of chironomid-inferred temperatures in the mid-Holocene, a trend recognised in other boreal chironomid records. The application of sedaDNA plant-inferred summer temperature reconstruction is inhibited by the persistence of cold and warm tolerant species within the boreal pine forest. However, a trait-based approach reconstructed temperature trends that aligned with independent regional data. Thus, here we demonstrate the value of combined molecular and fossil-based proxies for elucidating the complex response of a boreal catchment to climate change.

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• Steppe-tundra composition and deglacial floristic turnover in interior Alaska revealed by sedimentary ancient DNA (sedaDNA)

  2024. Charlotte L. Clarke (et al.). Quaternary Science Reviews 334

  Article

  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 shows in unprecedented detail the composition of late-Pleistocene “steppe-tundra” vegetation of ice-free Alaska, part of an intriguing late-Quaternary “no-analogue” biome, and it covers the subsequent changes that led to the development of modern spruce-dominated boreal forest. The site (Chisholm Lake) lies close to key archaeological sites, and the record throws new light on the landscape and resources available to early humans. Initially, vegetation was dominated by forbs found in modern tundra and/or subarctic steppe vegetation (e.g., Potentilla, Draba, Eritrichium, Anemone patens), and graminoids (e.g., Bromus pumpellianus, Festuca, Calamagrostis, Puccinellia), with Salix the only prominent woody taxon. Predominantly xeric, warm-to-cold habitats are indicated, and we explain the mixed ecological preferences of the fossil assemblages as a topo-mosaic strongly affected by insolation load. At ca. 14,500 cal yr BP (calendar years before C.E. 1950), about the same time as well documented human arrivals and coincident with an increase in effective moisture, Betula expanded. Graminoids became less abundant, but many open-ground forb taxa persisted. This woody-herbaceous mosaic is compatible with the observed persistence of Pleistocene megafaunal species (animals weighing ≥44 kg)—important resources for early humans. The greatest taxonomic turnover, marking a transition to regional woodland and a further moisture increase, began ca. 11,000 cal yr BP when Populus expanded, along with new shrub taxa (e.g., Shepherdia, Eleagnus, Rubus, Viburnum). Picea then expanded ca. 9500 cal yr BP, along with shrub and forb taxa typical of evergreen boreal woodland (e.g., Spiraea, Cornus, Linnaea). We found no evidence for Picea in the late Pleistocene, however. Most taxa present today were established by ca. 5000 cal yr BP after almost complete taxonomic turnover since the start of the record (though Larix appeared only at ca. 1500 cal yr BP). Prominent fluctuations in aquatic communities ca. 14,000–9,500 cal yr BP are probably related to lake-level fluctuations prior to the lake reaching its high, near-modern depth ca. 8,000 cal yr BP.

  Read more about Steppe-tundra composition and deglacial floristic turnover in interior Alaska revealed by sedimentary ancient DNA (sedaDNA)

• Uncovering Holocene climate fluctuations and ancient conifer populations: Insights from a high-resolution multi-proxy record from Northern Finland

  2024. J. Sakari Salonen (et al.). Global and Planetary Change 237

  Article

  A series of abrupt climate events linked to circum-North Atlantic meltwater forcing have been recognised in Holocene paleoclimate data. To address the paucity of proxy records able to characterise robustly the regional impacts of these events, we retrieved a sub-centennial resolution, well-dated core sequence from Lake Kuutsja<spacing diaeresis>rvi, northeast Finland. By analysing a range of paleo-environmental proxies (pollen, plant sedimentary ancient DNA, plant macrofossils, conifer stomata, and non-pollen palynomorphs), and supported with proxy-based paleotemperature and moisture reconstructions, we unravel a well-defined sequence of vegetation and climate dynamics over the early-to-middle Holocene. The birch-dominated pioneer vegetation stage was intersected by two transient tree-cover decrease events at 10.4 and 10.1 thousand years ago (ka), likely representing a two-pronged signal of the 10.3 ka climate event. Our data also show a clear signal of the 8.2 ka climate event, previously not well recorded in the European Arctic, with a collapse of the pine-birch forest and replacement by juniper developing in tight synchrony with Greenland isotopic proxies over 8.4-8.0 ka. Supported by climate modelling, severe winter cooling rather than summer might have been driving vegetation disruptions in the early Holocene. The Kuutsja<spacing diaeresis>rvi data indicate an early arrival of Norway spruce (Picea abies) by 9.2 ka (pollen, DNA, and stoma finds), as well as the first evidence for Holocene presence of larch (Larix) in Finland, with pollen finds dating to 9.6-5.9 ka.

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• The potential of lacustrine sedimentary ancient DNA for revealing human postglacial recolonization patterns in northern Sweden – a review

  2024. Ernst Johnson (et al.). Boreas 53 (3), 347-359

  Article

  The postglacial recolonization of Fennoscandian flora and fauna was initiated when the land became accessible as the last ice sheet retreated. In northern Sweden, plants are represented in pollen and macrofossil records, but there is no genetic evidence from the first plants, animals or humans in the region, mainly owing to an absence of osteological finds. The questions of who the first postglacial peoples, or pioneers, were and where they came from therefore remain unanswered. Previous palaeogenomic analyses from remains from adjacent regions have suggested that two main routes into Sweden could have been taken by the pioneers, one from the SW through modern-day Denmark and Norway, and one from the east via Finland. However, no direct genetic evidence from the pioneers of northern Sweden exists. Modern technology has provided the ancient DNA field with an updated toolbox that could allow for novel approaches for revealing the origin and genetic profiles of the first Scandinavians, of which sedimentary ancient DNA (sedaDNA) is well placed. Lake sediments are now a routine source of sedaDNA that have been used to record environmental changes and detect species that lived in the surrounding lake catchment. This review will provide context and background, a summary of the ground-breaking studies within the field of lacustrine sedaDNA, and relevant methodology to address the scientific questions at hand. We conclude that the field is mature enough to provide insight into the origins and arrival times of the first postglacial humans that migrated into northern Sweden.

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• Genomics of adaptive evolution in the woolly mammoth

  2023. David Díez-del-Molino (et al.). Current Biology 33 (9), 1753-1764

  Article

  Ancient genomes provide a tool to investigate the genetic basis of adaptations in extinct organisms. However, the identification of species-specific fixed genetic variants requires the analysis of genomes from multiple individuals. Moreover, the long-term scale of adaptive evolution coupled with the short-term nature of tradi-tional time series data has made it difficult to assess when different adaptations evolved. Here, we analyze 23 woolly mammoth genomes, including one of the oldest known specimens at 700,000 years old, to identify fixed derived non-synonymous mutations unique to the species and to obtain estimates of when these mutations evolved. We find that at the time of its origin, the woolly mammoth had already acquired a broad spectrum of positively selected genes, including ones associated with hair and skin development, fat storage and metabolism, and immune system function. Our results also suggest that these phenotypes continued to evolve during the last 700,000 years, but through positive selection on different sets of genes. Finally, we also identify additional genes that underwent comparatively recent positive selection, including multiple genes related to skeletal morphology and body size, as well as one gene that may have contributed to the small ear size in Late Quaternary woolly mammoths.

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• Deep-time paleogenomics and the limits of DNA survival

  2023. Love Dalén (et al.). Science 382 (6666), 48-53

  Article

  Although most ancient DNA studies have focused on the last 50,000 years, paleogenomic approaches can now reach into the early Pleistocene, an epoch of repeated environmental changes that shaped present-day biodiversity. Emerging deep-time genomic transects, including from DNA preserved in sediments, will enable inference of adaptive evolution, discovery of unrecognized species, and exploration of how glaciations, volcanism, and paleomagnetic reversals shaped demography and community composition. In this Review, we explore the state-of-the-art in paleogenomics and discuss key challenges, including technical limitations, evolutionary divergence and associated biases, and the need for more precise dating of remains and sediments. We conclude that with improvements in laboratory and computational methods, the emerging field of deep-time paleogenomics will expand the range of questions addressable using ancient DNA.

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• Strengthening global-change science by integrating aeDNA with paleoecoinformatics

  2023. John W. Williams (et al.). Trends in Ecology & Evolution 38 (10), 946-960

  Article

  Ancient environmental DNA (aeDNA) data are close to enabling insights into past global-scale biodiversity dynamics at unprecedented taxonomic extent and resolution. However, achieving this potential requires solutions that bridge bioinformatics and paleoecoinformatics. Essential needs include support for dynamic taxonomic inferences, dynamic age inferences, and precise stratigraphic depth. Moreover, aeDNA data are complex and heterogeneous, generated by dispersed researcher networks, with methods advancing rapidly. Hence, expert community governance and curation are essential to building high-value data resources. Immediate recommendations include uploading metabarcoding-based taxonomic inventories into paleoecoinformatic resources, building linkages among open bioinformatic and paleoecoinformatic data resources, harmonizing aeDNA processing workflows, and expanding community data governance. These advances will enable transformative insights into global-scale biodiversity dynamics during large environmental and anthropogenic changes.

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

  2023. Alois Reveret (et al.). Freshwater Biology

  Article

  Environmental DNA is increasingly being used to reconstruct past and present biodiversity including from freshwater ecosystems. Macrophytes are especially good environmental indicators, thus their environmental DNA palaeorecord might shed light on past postglacial environments. 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.

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• Sedimentary Ancient DNA Reveals Local Vegetation Changes Driven by Glacial Activity and Climate

  2023. Lucas D. Elliott (et al.). Quaternary 6 (1)

  Article

  Disentangling the effects of glaciers and climate on vegetation is complicated by the confounding role that climate plays in both systems. We reconstructed changes in vegetation occurring over the Holocene at Jøkelvatnet, a lake located directly downstream from the Langfjordjøkel glacier in northern Norway. We used a sedimentary ancient DNA (sedaDNA) metabarcoding dataset of 38 samples from a lake sediment core spanning 10,400 years using primers targeting the P6 loop of the trnL (UAA) intron. A total of 193 plant taxa were identified revealing a pattern of continually increasing richness over the time period. Vegetation surveys conducted around Jøkelvatnet show a high concordance with the taxa identified through sedaDNA metabarcoding. We identified four distinct vegetation assemblage zones with transitions at ca. 9.7, 8.4 and 4.3 ka with the first and last mirroring climatic shifts recorded by the Langfjordjøkel glacier. Soil disturbance trait values of the vegetation increased with glacial activity, suggesting that the glacier had a direct impact on plants growing in the catchment. Temperature optimum and moisture trait values correlated with both glacial activity and reconstructed climatic variables showing direct and indirect effects of climate change on the vegetation. In contrast to other catchments without an active glacier, the vegetation at Jøkelvatnet has displayed an increased sensitivity to climate change throughout the Middle and Late Holocene. Beyond the direct impact of climate change on arctic and alpine vegetation, our results suggest the ongoing disappearance of glaciers will have an additional effect on plant communities.

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