| 1. |
- Serge, M. A., et al.
(författare)
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Testing the Effect of Relative Pollen Productivity on the REVEALS Model : A Validated Reconstruction of Europe-Wide Holocene Vegetation
- 2023
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Ingår i: Land. - : MDPI. - 2073-445X. ; 12:5
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Tidskriftsartikel (refereegranskat)abstract
- Reliable quantitative vegetation reconstructions for Europe during the Holocene are crucial to improving our understanding of landscape dynamics, making it possible to assess the past effects of environmental variables and land-use change on ecosystems and biodiversity, and mitigating their effects in the future. We present here the most spatially extensive and temporally continuous pollen-based reconstructions of plant cover in Europe (at a spatial resolution of 1 degrees x 1 degrees) over the Holocene (last 11.7 ka BP) using the 'Regional Estimates of VEgetation Abundance from Large Sites' (REVEALS) model. This study has three main aims. First, to present the most accurate and reliable generation of REVEALS reconstructions across Europe so far. This has been achieved by including a larger number of pollen records compared to former analyses, in particular from the Mediterranean area. Second, to discuss methodological issues in the quantification of past land cover by using alternative datasets of relative pollen productivities (RPPs), one of the key input parameters of REVEALS, to test model sensitivity. Finally, to validate our reconstructions with the global forest change dataset. The results suggest that the RPPs.st1 (31 taxa) dataset is best suited to producing regional vegetation cover estimates for Europe. These reconstructions offer a long-term perspective providing unique possibilities to explore spatial-temporal changes in past land cover and biodiversity.
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| 2. |
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| 3. |
- Roberts, N., et al.
(författare)
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Europe's lost forests : a pollen-based synthesis for the last 11,000 years
- 2018
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- 8000 years ago, prior to Neolithic agriculture, Europe was mostly a wooded continent. Since then, its forest cover has been progressively fragmented, so that today it covers less than half of Europe's land area, in many cases having been cleared to make way for fields and pasture-land. Establishing the origin of Europe's current, more open land-cover mosaic requires a long-term perspective, for which pollen analysis offers a key tool. In this study we utilise and compare three numerical approaches to transforming pollen data into past forest cover, drawing on >1000 C-14-dated site records. All reconstructions highlight the different histories of the mixed temperate and the northern boreal forests, with the former declining progressively since similar to 6000 years ago, linked to forest clearance for agriculture in later prehistory (especially in northwest Europe) and early historic times (e.g. in north central Europe). In contrast, extensive human impact on the needle-leaf forests of northern Europe only becomes detectable in the last two millennia and has left a larger area of forest in place. Forest loss has been a dominant feature of Europe's landscape ecology in the second half of the current interglacial, with consequences for carbon cycling, ecosystem functioning and biodiversity.
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| 4. |
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| 5. |
- Johansson, Henrik J., et al.
(författare)
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Breast cancer quantitative proteome and proteogenomic landscape
- 2019
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Ingår i: Nature Communications. - : NATURE PUBLISHING GROUP. - 2041-1723. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- In the preceding decades, molecular characterization has revolutionized breast cancer (BC) research and therapeutic approaches. Presented herein, an unbiased analysis of breast tumor proteomes, inclusive of 9995 proteins quantified across all tumors, for the first time recapitulates BC subtypes. Additionally, poor-prognosis basal-like and luminal B tumors are further subdivided by immune component infiltration, suggesting the current classification is incomplete. Proteome-based networks distinguish functional protein modules for breast tumor groups, with co-expression of EGFR and MET marking ductal carcinoma in situ regions of normal-like tumors and lending to a more accurate classification of this poorly defined subtype. Genes included within prognostic mRNA panels have significantly higher than average mRNA-protein correlations, and gene copy number alterations are dampened at the protein-level; underscoring the value of proteome quantification for prognostication and phenotypic classification. Furthermore, protein products mapping to non-coding genomic regions are identified; highlighting a potential new class of tumor-specific immunotherapeutic targets.
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| 6. |
- Racimo, F., et al.
(författare)
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The spatiotemporal spread of human migrations during the European Holocene
- 2020
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424. ; 117:16, s. 8989-9000
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Tidskriftsartikel (refereegranskat)abstract
- The European continent was subject to two major migrations of peoples during the Holocene: the northwestward movement of Anatolian farmer populations during the Neolithic and the westward movement of Yamnaya steppe peoples during the Bronze Age. These movements changed the genetic composition of the continent's inhabitants. The Holocene was also characterized by major changes in vegetation composition, which altered the environment occupied by the original hunter-gatherer populations. We aim to test to what extent vegetation change through time is associated with changes in population composition as a consequence of these migrations, or with changes in climate. Using ancient DNA in combination with geostatistical techniques, we produce detailed maps of ancient population movements, which allow us to visualize how these migrations unfolded through time and space. We find that the spread of Neolithic farmer ancestry had a two-pronged wavefront, in agreement with similar findings on the cultural spread of farming from radiocarbon-dated archaeological sites. This movement, however, did not have a strong association with changes in the vegetational landscape. In contrast, the Yamnaya migration speed was at least twice as fast and coincided with a reduction in the amount of broad-leaf forest and an increase in the amount of pasture and natural grasslands in the continent. We demonstrate the utility of integrating ancient genomes with archaeometric datasets in a spatiotemporal statistical framework, which we foresee will enable future studies of ancient populations' movements, and their putative effects on local fauna and flora.
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| 7. |
- Woodbridge, Jessie, et al.
(författare)
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Pollen-inferred regional vegetation patterns and demographic change in Southern Anatolia through the Holocene
- 2019
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Ingår i: The Holocene. - : SAGE Publications. - 0959-6836 .- 1477-0911. ; 29:5, s. 728-741
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Tidskriftsartikel (refereegranskat)abstract
- Southern Anatolia is a highly significant area within the Mediterranean, particularly in terms of understanding how agriculture moved into Europe from neighbouring regions. This study uses pollen, palaeoclimate and archaeological evidence to investigate the relationships between demography and vegetation change, and to explore how the development of agriculture varied spatially. Data from 21 fossil pollen records have been transformed into forested, parkland and open vegetation types using cluster analysis. Patterns of change have been explored using non-metric multidimensional scaling (nMDS) and through analysis of indicator groups, such as an Anthropogenic Pollen Index, and Simpson’s Diversity. Settlement data, which indicate population densities, and summed radiocarbon dates for archaeological sites have been used as a proxy for demographic change. The pollen and archaeological records confirm that farming can be detected earlier in Anatolia in comparison with many other parts of the Mediterranean. Dynamics of change in grazing indicators and the OJCV (Olea, Juglans, Castanea and Vitis) index for cultivated trees appear to match cycles of population expansion and decline. Vegetation and land use change is also influenced by other factors, such as climate change. Investigating the early impacts of anthropogenic activities (e.g. woodcutting, animal herding, the use of fire and agriculture) is key to understanding how societies have modified the environment since the mid–late Holocene, despite the capacity of ecological systems to absorb recurrent disturbances. The results of this study suggest that shifting human population dynamics played an important role in shaping land cover in central and southern Anatolia.
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| 8. |
- Zhu, Yafeng, et al.
(författare)
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Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow
- 2018
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Proteogenomics enable the discovery of novel peptides (from unannotated genomic protein-coding loci) and single amino acid variant peptides (derived from single-nucleotide polymorphisms and mutations). Increasing the reliability of these identifications is crucial to ensure their usefulness for genome annotation and potential application as neoantigens in cancer immunotherapy. We here present integrated proteogenomics analysis workflow (IPAW), which combines peptide discovery, curation, and validation. IPAW includes the SpectrumAI tool for automated inspection of MS/MS spectra, eliminating false identifications of single-residue substitution peptides. We employ IPAW to analyze two proteomics data sets acquired from A431 cells and five normal human tissues using extended (pH range, 3-10) high-resolution isoelectric focusing (HiRIEF) pre-fractionation and TMT-based peptide quantitation. The IPAW results provide evidence for the translation of pseudogenes, lncRNAs, short ORFs, alternative ORFs, N-terminal extensions, and intronic sequences. Moreover, our quantitative analysis indicates that protein production from certain pseudogenes and lncRNAs is tissue specific.
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