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  • 1.
    Ahmed, Engy
    et al.
    Stockholm Univ, Dept Geol Sci, SE-10691 Stockholm, Sweden.;Stockholm Univ, Bolin Ctr Climate Res, SE-10691 Stockholm, Sweden.;Sci Life Lab, Tomtebodavagen 23A, SE-17165 Solna, Sweden..
    Parducci, Laura
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Unneberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Ågren, Rasmus
    Chalmers Univ Technol, Dept Chem & Biol Engn, Sci Life Lab, SE-41296 Gothenburg, Sweden..
    Schenk, Frederik
    Stockholm Univ, Dept Geol Sci, SE-10691 Stockholm, Sweden.;Stockholm Univ, Bolin Ctr Climate Res, SE-10691 Stockholm, Sweden..
    Rattray, Jayne E.
    Stockholm Univ, Dept Geol Sci, SE-10691 Stockholm, Sweden.;Stockholm Univ, Bolin Ctr Climate Res, SE-10691 Stockholm, Sweden.;Univ Calgary, Biol Sci, 2500 Univ Dr NW, Calgary, AB, Canada..
    Han, Lu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics. Jilin Univ, Coll Life Sci, Ancient DNA Lab, Changchun, Jilin, Peoples R China..
    Muschitiello, Francesco
    Stockholm Univ, Dept Geol Sci, SE-10691 Stockholm, Sweden.;Stockholm Univ, Bolin Ctr Climate Res, SE-10691 Stockholm, Sweden.;Columbia Univ, Lamont Doherty Earth Observ, 61 Route 9NW, Palisades, NY USA..
    Pedersen, Mikkel W.
    Univ Cambridge, Dept Zool, Downing St, Cambridge CB2 3EJ, England..
    Smittenberg, Rienk H.
    Stockholm Univ, Dept Geol Sci, SE-10691 Stockholm, Sweden.;Stockholm Univ, Bolin Ctr Climate Res, SE-10691 Stockholm, Sweden..
    Yamoah, Kweku Afrifa
    Stockholm Univ, Dept Geol Sci, SE-10691 Stockholm, Sweden.;Stockholm Univ, Bolin Ctr Climate Res, SE-10691 Stockholm, Sweden..
    Slotte, Tanja
    Stockholm Univ, Dept Ecol Environm & Plant Sci, SE-10691 Stockholm, Sweden.;Sci Life Lab, Tomtebodavagen 23A, SE-17165 Solna, Sweden..
    Wohlfarth, Barbara
    Stockholm Univ, Dept Geol Sci, SE-10691 Stockholm, Sweden.;Stockholm Univ, Bolin Ctr Climate Res, SE-10691 Stockholm, Sweden..
    Archaeal community changes in Lateglacial lake sediments: Evidence from ancient DNA2018In: Quaternary Science Reviews, ISSN 0277-3791, E-ISSN 1873-457X, Vol. 181, p. 19-29Article in journal (Refereed)
    Abstract [en]

    The Lateglacial/early Holocene sediments from the ancient lake at Hasseldala Port, southern Sweden provide an important archive for the environmental and climatic shifts at the end of the last ice age and the transition into the present Interglacial. The existing multi-proxy data set highlights the complex interplay of physical and ecological changes in response to climatic shifts and lake status changes. Yet, it remains unclear how microorganisms, such as Archaea, which do not leave microscopic features in the sedimentary record, were affected by these climatic shifts. Here we present the metagenomic data set of Hasseldala Port with a special focus on the abundance and biodiversity of Archaea. This allows reconstructing for the first time the temporal succession of major Archaea groups between 13.9 and 10.8 ka BP by using ancient environmental DNA metagenomics and fossil archaeal cell membrane lipids. We then evaluate to which extent these findings reflect physical changes of the lake system, due to changes in lake-water summer temperature and seasonal lake-ice cover. We show that variations in archaeal composition and diversity were related to a variety of factors (e.g., changes in lake water temperature, duration of lake ice cover, rapid sediment infilling), which influenced bottom water conditions and the sediment-water interface. Methanogenic Archaea dominated during the Allerod and Younger Dryas pollen zones, when the ancient lake was likely stratified and anoxic for large parts of the year. The increase in archaeal diversity at the Younger Dryas/Holocene transition is explained by sediment infilling and formation of a mire/peatbog. (C) 2017 Elsevier Ltd. All rights reserved.

  • 2.
    Bergfeldt, Nora
    et al.
    Stockholm Univ, Ctr Palaeogenet, Stockholm, Sweden.;Stockholm Univ, Dept Zool, Stockholm, Sweden.;Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden..
    Kirdök, Emrah
    Mersin Univ, Inst Sci, Dept Biotechnol, Mersin, Turkiye..
    Oskolkov, Nikolay
    Lund Univ, Dept Biol, Sci Life Lab, Natl Bioinformat Infrastructure Sweden, Lund, Sweden..
    Mirabello, Claudio
    Linköping Univ, Dept Phys Chem & Biol, Sci Life Lab, Linköping, Sweden..
    Unneberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Fraser, Magdalena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Sanchez-Quinto, Federico
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Jorgensen, Roger
    Univ Tromso, Arctic Univ Norway, Tromso Univ Museum, Tromso, Norway..
    Skar, Birgitte
    NTNU Univ Museum, Dept Archaeol & Cultural Hist, Trondheim, Norway..
    Liden, Kerstin
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden..
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Storå, Jan
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden..
    Götherström, Anders
    Stockholm Univ, Ctr Palaeogenet, Stockholm, Sweden.;Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden..
    Identification of microbial pathogens in Neolithic Scandinavian humans2024In: Scientific Reports, E-ISSN 2045-2322, Vol. 14, no 1, article id 5630Article in journal (Refereed)
    Abstract [en]

    With the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. Salmonella enterica, a bacterium that may have been the cause of death for the infected individuals, was found in two Neolithic samples from Battle Axe culture contexts. Several species of the bacterial genus Yersinia were found in Neolithic individuals from Funnel Beaker culture contexts as well as from later Neolithic context. Transmission of e.g. Y. enterocolitica may have been facilitated by the denser populations in agricultural contexts.

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  • 3.
    Bysani, Madhusudhan
    et al.
    Lund Univ, Scania Univ Hosp, Diabet Ctr, Dept Clin Sci,Epigenet & Diabet Unit, Malmo, Sweden.
    Agren, Rasmus
    Chalmers Univ Technol, Sci Life Lab, Natl Bioinformat Infrastruct Sweden, Dept Biol & Biol Engn, Gothenburg, Sweden.
    Davegardh, Cajsa
    Lund Univ, Scania Univ Hosp, Diabet Ctr, Dept Clin Sci,Epigenet & Diabet Unit, Malmo, Sweden.
    Volkov, Petr
    Lund Univ, Scania Univ Hosp, Diabet Ctr, Dept Clin Sci,Epigenet & Diabet Unit, Malmo, Sweden.
    Ronn, Tina
    Lund Univ, Scania Univ Hosp, Diabet Ctr, Dept Clin Sci,Epigenet & Diabet Unit, Malmo, Sweden.
    Unneberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bacos, Karl
    Lund Univ, Scania Univ Hosp, Diabet Ctr, Dept Clin Sci,Epigenet & Diabet Unit, Malmo, Sweden.
    Ling, Charlotte
    Lund Univ, Scania Univ Hosp, Diabet Ctr, Dept Clin Sci,Epigenet & Diabet Unit, Malmo, Sweden.
    ATAC-seq reveals alterations in open chromatin in pancreatic islets from subjects with type 2 diabetes2019In: Scientific Reports, E-ISSN 2045-2322, Vol. 9, article id 7785Article in journal (Refereed)
    Abstract [en]

    Impaired insulin secretion from pancreatic islets is a hallmark of type 2 diabetes (T2D). Altered chromatin structure may contribute to the disease. We therefore studied the impact of T2D on open chromatin in human pancreatic islets. We used assay for transposase-accessible chromatin using sequencing (ATAC-seq) to profile open chromatin in islets from T2D and non-diabetic donors. We identified 57,105 and 53,284 ATAC-seq peaks representing open chromatin regions in islets of nondiabetic and diabetic donors, respectively. The majority of ATAC-seq peaks mapped near transcription start sites. Additionally, peaks were enriched in enhancer regions and in regions where islet-specific transcription factors (TFs), e.g. FOXA2, MAFB, NKX2.2, NKX6.1 and PDX1, bind. Islet ATAC-seq peaks overlap with 13 SNPs associated with T2D (e.g. rs7903146, rs2237897, rs757209, rs11708067 and rs878521 near TCF7L2, KCNQ1, HNF1B, ADCY5 and GCK, respectively) and with additional 67 SNPs in LD with known T2D SNPs (e.g. SNPs annotated to GIPR, KCNJ11, GLIS3, IGF2BP2, FTO and PPARG). There was enrichment of open chromatin regions near highly expressed genes in human islets. Moreover, 1,078 open chromatin peaks, annotated to 898 genes, differed in prevalence between diabetic and non-diabetic islet donors. Some of these peaks are annotated to candidate genes for T2D and islet dysfunction (e.g. HHEX, HMGA2, GLIS3, MTNR1B and PARK2) and some overlap with SNPs associated with T2D (e.g. rs3821943 near WFS1 and rs508419 near ANK1). Enhancer regions and motifs specific to key TFs including BACH2, FOXO1, FOXA2, NEUROD1, MAFA and PDX1 were enriched in differential islet ATAC-seq peaks of T2D versus non-diabetic donors. Our study provides new understanding into how T2D alters the chromatin landscape, and thereby accessibility for TFs and gene expression, in human pancreatic islets.

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  • 4.
    Lauterbur, M. Elise
    et al.
    Univ Arizona, Dept Ecol & Evolutionary Biol, Tucson, AZ 85721 USA.
    Cavassim, Maria Izabel A.
    Univ Calif Los Angeles, Dept Ecol & Evolutionary Biol, Los Angeles, CA USA.
    Gladstein, Ariella L.
    Embark Vet Inc, Boston, MA USA.
    Gower, Graham
    Univ Copenhagen, Globe Inst, Sect Mol Ecol & Evolut, Copenhagen, Denmark.
    Pope, Nathaniel S.
    Univ Oregon, Inst Ecol & Evolut, Eugene, OR USA.
    Tsambos, Georgia
    Univ Melbourne, Sch Math & Stat, Melbourne, Australia.
    Adrion, Jeffrey
    Ancestry DNA, San Francisco, CA USA.
    Belsare, Saurabh
    Univ Oregon, Inst Ecol & Evolut, Eugene, OR USA.
    Biddanda, Arjun
    54Gene Inc, Washington, DC USA.
    Caudill, Victoria
    Univ Oregon, Inst Ecol & Evolut, Eugene, OR USA.
    Cury, Jean
    Univ Paris Saclay, CNRS, INRIA, Lab Interdisciplinaire Sci Numer, Orsay, France.
    Echevarria, Ignacio
    Univ Glasgow, Sch Life Sci, Glasgow, Scotland.
    Haller, Benjamin C.
    Cornell Univ, Dept Computat Biol, Ithaca, NY USA.
    Hasan, Ahmed R.
    Univ Toronto, Dept Cell & Syst Biol, Toronto, ON, Canada.;Univ Toronto Mississauga, Dept Biol, Mississauga, ON, Canada.
    Huang, Xin
    Univ Vienna, Dept Evolutionary Anthropol, Vienna, Austria.;Univ Vienna, Human Evolut & Archaeol Sci HEAS, Vienna, Austria.
    Iasi, Leonardo Nicola Martin
    Max Planck Inst Evolutionary Anthropol, Dept Evolutionary Genet, Leipzig, Germany.
    Noskova, Ekaterina
    ITMO Univ, Comp Technol Lab, St Petersburg, Russia.
    Obsteter, Jana
    Agr Inst Slovenia, Dept Anim Sci, Ljubljana, Slovenia.
    Pavinato, Vitor Antonio Correa
    Ohio State Univ, Entomol Dept, Wooster, OH USA.
    Pearson, Alice
    Univ Cambridge, Dept Genet, Cambridge, England.;Univ Cambridge, Dept Zool, Cambridge, England.
    Peede, David
    Brown Univ, Dept Ecol Evolut & Organismal Biol, Providence, RI USA.;Brown Univ, Ctr Computat Mol Biol, Providence, RI USA.
    Perez, Manolo F.
    Univ Fed Sao Carlos, Dept Genet & Evolut, Sao Carlos, Brazil.
    Rodrigues, Murillo F.
    Univ Oregon, Inst Ecol & Evolut, Eugene, OR USA.
    Smith, Chris C. R.
    Univ Oregon, Inst Ecol & Evolut, Eugene, OR USA.
    Spence, Jeffrey P.
    Stanford Univ, Dept Genet, Sch Med, Stanford, CA USA.
    Teterina, Anastasia
    Univ Oregon, Inst Ecol & Evolut, Eugene, OR USA.
    Tittes, Silas
    Univ Oregon, Inst Ecol & Evolut, Eugene, OR USA.
    Unneberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Vazquez, Juan Manuel
    Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA USA.
    Waples, Ryan K.
    Univ Washington, Dept Biostat, Seattle, WA USA.
    Wohns, Anthony Wilder
    Broad Inst MIT & Harvard, Cambridge, MA USA.
    Wong, Yan
    Univ Oxford, Big Data Inst, Li Ka Shing Ctr Hlth Informat & Discovery, Oxford, England.
    Baumdicker, Franz
    Eberhard Karls Univ Tubingen, Cluster Excellence Controlling Microbes Fight Infe, Tubingen, Germany.
    Cartwright, Reed A.
    Arizona State Univ, Sch Life Sci, Tempe, AZ USA.;Arizona State Univ, Biodesign Inst, Tempe, AZ USA.
    Gorjanc, Gregor
    Univ Edinburgh, Roslin Inst, Edinburgh, Scotland.;Univ Edinburgh, Royal Dick Sch Vet Studies, Edinburgh, Scotland.
    Gutenkunst, Ryan N.
    Univ Arizona, Dept Mol & Cellular Biol, Tucson, AZ USA.
    Kelleher, Jerome
    Univ Oxford, Big Data Inst, Li Ka Shing Ctr Hlth Informat & Discovery, Oxford, England.
    Kern, Andrew D.
    Univ Oregon, Inst Ecol & Evolut, Eugene, OR USA.
    Ragsdale, Aaron P.
    Univ Wisconsin Madison, Dept Integrat Biol, Madison, WI USA.
    Ralph, Peter L.
    Univ Oregon, Inst Ecol & Evolut, Eugene, OR USA.;Univ Oregon, Dept Math, Eugene, OR USA.
    Schrider, Daniel R.
    Univ North Carolina Chapel Hill, Dept Genet, Chapel Hill, NC USA.
    Gronau, Ilan
    Reichman Univ, Efi Arazi Sch Comp Sci, Herzliyya, Israel.
    Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations2023In: eLIFE, E-ISSN 2050-084X, Vol. 12, article id RP84874Article in journal (Refereed)
    Abstract [en]

    Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic datasets remains a major obstacle. Today, more realistic simulations are possible thanks to large increases in the quantity and quality of available genetic data, and the sophistication of inference and simulation software. However, implementing these simulations still requires substantial time and specialized knowledge. These challenges are especially pronounced for simulating genomes for species that are not well-studied, since it is not always clear what information is required to produce simulations with a level of realism sufficient to confidently answer a given question. The community-developed framework stdpopsim seeks to lower this barrier by facilitating the simulation of complex population genetic models using up-to-date information. The initial version of stdpopsim focused on establishing this framework using six well-characterized model species (Adrion et al., 2020). Here, we report on major improvements made in the new release of stdpopsim (version 0.2), which includes a significant expansion of the species catalog and substantial additions to simulation capabilities. Features added to improve the realism of the simulated genomes include non-crossover recombination and provision of species-specific genomic annotations. Through community-driven efforts, we expanded the number of species in the catalog more than threefold and broadened coverage across the tree of life. During the process of expanding the catalog, we have identified common sticking points and developed the best practices for setting up genome-scale simulations. We describe the input data required for generating a realistic simulation, suggest good practices for obtaining the relevant information from the literature, and discuss common pitfalls and major considerations. These improvements to stdpopsim aim to further promote the use of realistic whole-genome population genetic simulations, especially in non-model organisms, making them available, transparent, and accessible to everyone.

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  • 5.
    Nguyen, Diem
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Peona, Valentina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Unneberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Suh, Alexander
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Jern, Patric
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Transposon- and Genome Dynamics in the Fungal Genus Neurospora: Insights from Nearly Gapless Genome Assemblies2022In: Fungal Genetics Reports, Vol. 66, no 1Article in journal (Refereed)
    Abstract [en]

    A large portion of nuclear DNA is composed of transposable element (TE) sequences, whose transposition is controlled by diverse host defense strategies in order to maintain genomic integrity. One such strategy is the fungal-specific Repeat-Induced Point mutation (RIP) that hyper-mutates repetitive DNA sequences. While RIP is found across Fungi, it has been shown to vary in efficiency. The filamentous ascomycete Neurospora crassa has been a pioneer in the study of RIP, but data on TEs and RIP from other species in the genus is limited. In this study, we investigated 18 nearly gapless genome assemblies of ten Neurospora species, which diverged from a common ancestor about 7 MYA, to determine and compare genome-wide TE distribution and their associated RIP patterns. Four of these assemblies, generated by PacBio technology, represent new genomic datasets. We showed that the TE contents (8.7-18.9%) covary with genome sizes that range between 37.8-43.9 Mb. Degraded copies of Long Terminal Repeat (LTR) retrotransposons were abundant among the identified TEs, and these are distributed across the genome at varying frequencies. In all investigated Neurospora genomes, TE sequences had signs of numerous C-to-T substitutions, suggesting that RIP occurred in all species, and accordingly, RIP signatures correlated with TE-dense regions in all genomes. In conclusion, essentially gapless genome assemblies allowed us to identify TEs in Neurospora genomes, and reveal that TEs contribute to genome size variation in this group. Our study suggests that TEs and RIP are highly correlated in each examined Neurospora species, and hence, the pattern of interaction is conserved over the investigated evolutionary timescale. Finally, with our results, we verify that RIP signatures can be used to facilitate the identification of TE-rich regions in the genome. The comprehensive genomic dataset of Neurospora is a rich resource for further in- depth analyses of fungal genomes by the community. 

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  • 6.
    Parducci, Laura
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Alsos, Inger Greve
    Univ Tromso, Arctic Univ Norway, Tromso Museum, Tromso, Norway.
    Unneberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Pedersen, Mikkel W.
    Univ Cambridge, Dept Zool, Cambridge, England.
    Han, Lu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics. Jilin Univ, Ancient DNA Lab, Coll Life Sci, Changchun, Jilin, Peoples R China.
    Lammers, Youri
    Univ Tromso, Arctic Univ Norway, Tromso Museum, Tromso, Norway.
    Salonen, J. Sakari
    Univ Helsinki, Dept Geosci & Geog, Helsinki, Finland.
    Valiranta, Minna M.
    Univ Helsinki, Ecosyst & Environm Res Programme, ECRU, Helsinki, Finland.
    Slotte, Tanja
    Stockholm Univ, Dept Ecol Environm & Plant Sci, Stockholm, Sweden;Sci Life Lab, Solna, Sweden.
    Wohlfarth, Barbara
    Stockholm Univ, Dept Geol Sci, Stockholm, Sweden;Stockholm Univ, Bolin Ctr Climate Res, Stockholm, Sweden.
    Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden2019In: Frontiers in Ecology and Evolution, E-ISSN 2296-701X, Vol. 7, article id 189Article in journal (Refereed)
    Abstract [en]

    The lake sediments of Hasseldala Port in south-east Sweden provide an archive of local and regional environmental conditions similar to 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 sediments dating to the Allerod (14.1-12.7 ka BP), Younger Dryas (12.7-11.7 ka BP), and Preboreal (<11.7 ka BP). Number of reads and taxa were not associated with sample age or organic content. This suggests that, beyond the initial rapid degradation, DNA is still present. The proportion of recovered plant DNA was low, but allowed identifying an important number of plant taxa, thus adding valid information on the composition of the local vegetation. Importantly, DNA provides a stronger signal of plant community changes than plant micro- and plant macrofossil analyses alone, since a larger number of new taxa were recorded in Younger Dryas samples. A comparison between the three proxies highlights differences and similarities and supports earlier findings that plants growing close to or within a lake are recorded by DNA. Plant macrofossil remains moreover show that tree birch was present close to the ancient lake since the Allerod; together with the DNA results, this indicates that boreal to subarctic climatic conditions also prevailed during the cold Younger Dryas interval. Increasing DNA reference libraries and enrichment strategies prior to sequencing are necessary to improve the potential and accuracy of plant identification using the shotgun metagenomic approach.

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  • 7.
    Pochon, Zoe
    et al.
    Ctr Palaeogenet, Stockholm, Sweden.;Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden..
    Bergfeldt, Nora
    Ctr Palaeogenet, Stockholm, Sweden.;Stockholm Univ, Dept Zool, Stockholm, Sweden.;Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden..
    Kirdok, Emrah
    Mersin Univ, Fac Sci, Dept Biotechnol, Mersin, Turkey..
    Vicente, Mario
    Ctr Palaeogenet, Stockholm, Sweden.;Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden..
    Naidoo, Thijessen
    Uppsala University, Science for Life Laboratory, SciLifeLab. Ctr Palaeogenet, Stockholm, Sweden.;Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden.;Sci Life Lab, Ancient DNA Unit, Stockholm, Sweden..
    van der Valk, Tom
    Ctr Palaeogenet, Stockholm, Sweden.;Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden..
    Altinisik, N. Ezgi
    Hacettepe Univ, Dept Anthropol, Human G Lab, TR-06800 Beytepe, Ankara, Turkey..
    Krzewinska, Maja
    Ctr Palaeogenet, Stockholm, Sweden.;Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden..
    Dalen, Love
    Ctr Palaeogenet, Stockholm, Sweden.;Stockholm Univ, Dept Zool, Stockholm, Sweden..
    Gotherstrom, Anders
    Mirabello, Claudio
    Linköping Univ, Dept Phys Chem & Biol, Sci Life Lab, Natl Bioinformat Infrastruct Sweden, Linköping, Sweden..
    Unneberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Oskolkov, Nikolay
    Lund Univ, Dept Biol, Sci Life Lab, Natl Bioinformat Infrastruct Sweden, Lund, Sweden..
    aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow2023In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 24, no 1, article id 242Article in journal (Refereed)
    Abstract [en]

    Analysis of microbial data from archaeological samples is a growing field with great potential for understanding ancient environments, lifestyles, and diseases. However, high error rates have been a challenge in ancient metagenomics, and the availability of computational frameworks that meet the demands of the field is limited. Here, we propose aMeta, an accurate metagenomic profiling workflow for ancient DNA designed to minimize the amount of false discoveries and computer memory requirements. Using simulated data, we benchmark aMeta against a current state-of-the-art workflow and demonstrate its superiority in microbial detection and authentication, as well as substantially lower usage of computer memory.

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  • 8.
    Yazdi, Homa Papoli
    et al.
    Lund Univ, Dept Biol, Lund, Sweden..
    Olito, Colin
    Lund Univ, Dept Biol, Lund, Sweden..
    Kawakami, Takeshi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Embark Vet Inc, Boston, MA USA..
    Unneberg, Per
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Schou, Mads F.
    Lund Univ, Dept Biol, Lund, Sweden..
    Cloete, Schalk W. P.
    Western Cape Dept Agr, Directorate Anim Sci, Elsenburg, South Africa.;Stellenbosch Univ, Dept Anim Sci, Matieland, South Africa..
    Hansson, Bengt
    Lund Univ, Dept Biol, Lund, Sweden..
    Cornwallis, Charlie K.
    Lund Univ, Dept Biol, Lund, Sweden..
    The evolutionary maintenance of ancient recombining sex chromosomes in the ostrich2023In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 19, no 6, article id e1010801Article in journal (Refereed)
    Abstract [en]

    Sex chromosomes have evolved repeatedly across the tree of life and often exhibit extreme size dimorphism due to genetic degeneration of the sex-limited chromosome (e.g. the W chromosome of some birds and Y chromosome of mammals). However, in some lineages, ancient sex-limited chromosomes have escaped degeneration. Here, we study the evolutionary maintenance of sex chromosomes in the ostrich (Struthio camelus), where the W remains 65% the size of the Z chromosome, despite being more than 100 million years old. Using genome-wide resequencing data, we show that the population scaled recombination rate of the pseudoautosomal region (PAR) is higher than similar sized autosomes and is correlated with pedigree-based recombination rate in the heterogametic females, but not homogametic males. Genetic variation within the sex-linked region (SLR) (& pi; = 0.001) was significantly lower than in the PAR, consistent with recombination cessation. Conversely, genetic variation across the PAR (& pi; = 0.0016) was similar to that of autosomes and dependent on local recombination rates, GC content and to a lesser extent, gene density. In particular, the region close to the SLR was as genetically diverse as autosomes, likely due to high recombination rates around the PAR boundary restricting genetic linkage with the SLR to only similar to 50Kb. The potential for alleles with antagonistic fitness effects in males and females to drive chromosome degeneration is therefore limited. While some regions of the PAR had divergent male-female allele frequencies, suggestive of sexually antagonistic alleles, coalescent simulations showed this was broadly consistent with neutral genetic processes. Our results indicate that the degeneration of the large and ancient sex chromosomes of the ostrich may have been slowed by high recombination in the female PAR, reducing the scope for the accumulation of sexually antagonistic variation to generate selection for recombination cessation.

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