Research and publications

• Publications
  74 publications

  Evolutionary history and genomic vulnerability of the extinct giant deer Megaloceros giganteus
  Mikkel-Holger S. Sinding, Marco Gargano, Zihe Li, Emiliano Trucchi, Patrick Arnold, Kevin G. Daly, Valeria Mattiangeli, Sergei Kliver, David Duchene, Daniel Wegmann, Andreas Fueglistaler, Federica Alberti, Greg Gedman, Kathleen Morrill, Kathleen Morrill Pirovich, Brandi Cantarel, Iva Kovacic, Joseph Nesme, Lisen Li, Nicola Heckeberg, Nicola S. Heckeberg, Nigel T. Monaghan, Wilfried Rosendahl, Doris Doeppes, Victoria E. Mullin, Patricia Pecnerova, Patrícia Pečnerová, Rupinder Kaur, Christian Caroe, Christian Carøe, Sarah ST Mak, Sarah S. T. Mak, Love Dalen, Love Dalén, Wen Wang, Eline Lorenzen, Eline D Lorenzen, Beth Shapiro, Daniel G Bradley, Michael Hofreiter, M Thomas.P. Gilbert, M. Thomas P. Gilbert, Michael Vincent Westbury, Michael V. Westbury, (2026) | Preprint

  Gene–environment interactions govern early regeneration in fir and beech: evidence from participatory provenance trials across Europe
  Katalin Csillery, Katalin Csilléry, Justine Charlet de Sauvage, Madleina Caduff, Johannes Alt, Marjorie Bison, Mert Celik, Nicole Ponta, Daniel Wegmann, (2026) | Preprint

  Ancient alleles drive contemporary climate adaptation in an alpine plant
  Science (2025) | Journal article

  Local increases in admixture with hunter-gatherers followed the initial expansion of Neolithic farmers across continental Europe
  Science Advances (2025) | Journal article

  Historic Genomes Uncover Demographic Shifts and Kinship Structures in Post-Roman Central Europe
  Blöcher, Jens and Vallini, Leonardo and Velte, Maren and Eckel, Raphael and Guyon, Léa and Winkelbach, Laura and Thomas, Mark G. and Gharehbaghi, Nadia and Mitchell, Cassandra T. and Schümann, Jonas and Köhler, Sophie and Seyr, Elsa and Krichel, Katharina and Rau, Sophie and Hirsch, Jana and Duras, Jana and Klement, Kristin and Wilkenhöner, Miriam and Vetterdietz, Lisa and Gentilin, Francesca and Müller, Melany and Mücke, Anna-Lena and Zedda, Nicoletta and Tawfik, Youssef and Saal, Eveline and McGlynn, George and Bramanti, Barbara and Orschiedt, Jörg and Molitor, Regina and Fliß, Barbara and Spazier, Ines and Shankland, David and Vetterling, Claus and Karpf, Kurt and Planert, Vera and Hölzl, Stefan and Codreanu-Windauer, Silvia and Quast, Dieter and Mikic, Ilija and Päffgen, Bernd and Brami, Maxime and Richter, Thomas and Chaix, Raphaëlle and Brather-Walter, Susanne and Steffens, Peter and Marquart, Markus and Becker, Thomas and Haberstroh, Jochen and Meier, Mischa and Schmidt-Hofner, Sebastian and Brather, Sebastian and Harbeck, Michaela and Patzold, Steffen and Wegmann, Daniel and Burger, Joachim, (2025) | Preprint

  Testing for changes in population trends from low-cost ecological count data
  Liam Singer, Madleina Caduff, Thierry Aebischer, Primael Tabiti, Aimee Freiberg, Jens Ingensand, Christoph Leuenberger, Daniel Wegmann, Primaël Tabiti, Aimée Freiberg, (2025) | Preprint

  Inference of Locus-Specific Population Mixtures from Linked Genome-Wide Allele Frequencies
  Molecular Biology and Evolution (2024) | Journal article

  Local increases in admixture with hunter-gatherers followed the initial expansion of Neolithic farmers across continental Europe
  Alexandros Tsoupas, Carlos S. Reyna-Blanco, Claudio Sebastian Quilodrán, Jens Blöcher, Maxime Brami, Daniel Wegmann, Joachim Burger, Mathias Currat, Claudio S. Quilodrán, (2024) | Preprint

  Accurate Bayesian inference of sex chromosome karyotypes and sex‐linked scaffolds from low‐depth sequencing data
  Molecular Ecology Resources (2024) | Journal article

  A general framework to quantify and compare ecological impacts under temporal dynamics
  Ecology Letters (2023) | Journal article

  Climate-induced range shifts drive adaptive response via spatio-temporal sieving of alleles
  Nature Communications (2023) | Journal article

  Human evolution: When admixture met selection
  Current Biology (2023) | Journal article

  The spatial distribution and temporal trends of livestock damages caused by wolves in Europe
  Biological Conservation (2023) | Journal article

  A general framework to quantify and compare ecological impacts under temporal dynamics
  Lara Volery, Margarida Vaz, Daniel Wegmann, Sven Bacher, (2022) | Preprint

  Identifying, reducing, and communicating uncertainty in community science: a focus on alien species
  Biological Invasions (2022) | Journal article

  Between fishing and farming: palaeogenomic analyses reveal cross-cultural interactions triggered by the arrival of the Neolithic in the Danube Gorges
  Hofmanová, Z. and Reyna-Blanco, C.S. and de Becdelièvre, C. and Schulz, I. and Blöcher, J. and Jovanovi?, J. and Winkelbach, L. and Figarska, S.M. and Schulz, A. and Por?i?, M. and Kv?tina, P. and Tsoupas, A. and Currat, M. and Buzhilova, A. and Gerritsen, F. and Karul, N. and McGlynn, G. and Orschiedt, J. and Özbal, R. and Peters, J. and Ridush, B. and Terberger, T. and Teschler-Nicola, M. and Zari?a, G. and Zeeb-Lanz, A. and Stefanovi?, S. and Burger, J. and Wegmann, D. , bioRxiv (2022) | Other

  Ancient mitochondrial diversity reveals population homogeneity in Neolithic Greece and identifies population dynamics along the Danubian expansion axis
  Scientific Reports (2022) | Journal article

  The genomic origins of the world's first farmers
  Cell (2022) | Journal article

  Identifying loci under selection via explicit demographic models
  Molecular Ecology Resources (2021) | Journal article

  A sparse observation model to quantify species distributions and their overlap in space and time
  Ecography (2021) | Journal article

  Runes from Lány (Czech Republic) - The oldest inscription among Slavs. A new standard for multidisciplinary analysis of runic bones
  Journal of Archaeological Science (2021) | Journal article

  Trophic niche shifts and phenotypic trait evolution are largely decoupled in Australasian parrots
  BMC Ecology and Evolution (2021) | Journal article

  Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins
  Science Advances (2021) | Journal article

  Ancient genomes provide insights into family structure and the heredity of social status in the early Bronze Age of southeastern Europe
  Scientific Reports (2021) | Journal article

  Detecting Selection from Linked Sites Using an F-Model
  Genetics (2020) | Journal article

  Estimating and accounting for genotyping errors in RAD‐seq experiments
  Molecular Ecology Resources (2020) | Journal article

  Inference of natural selection from ancient DNA
  Evolution Letters (2020) | Journal article

  Apex predators decline after an influx of pastoralists in former Central African Republic hunting zones
  Biological Conservation (2020) | Journal article

  Low Prevalence of Lactase Persistence in Bronze Age Europe Indicates Ongoing Strong Selection over the Last 3,000 Years
  Current Biology (2020) | Journal article

  Evolutionary transcriptomics reveals the origins of olives and the genomic changes associated with their domestication
  The Plant Journal (2019) | Journal article

  Admixture mapping in interspecific Populus hybrids identifies classes of genomic architectures for phytochemical, morphological and growth traits
  New Phytologist (2019) | Journal article

  Statistical Modeling and Inference in Genetics , in Handbook of Statistical Genomics
  (2019), ISBN: 9781119429142 | Book chapter

  A Guide to General-Purpose ABC Software , in Handbook of Approximate Bayesian Computation
  (2018), ISBN: 9781315117195 | Book chapter

  Ancient human parallel lineages within North America contributed to a coastal expansion
  Science (2018) | Journal article

  Population genomic analysis of elongated skulls reveals extensive female-biased immigration in Early Medieval Bavaria
  Proceedings of the National Academy of Sciences (2018) | Journal article

  A guide to general-purpose approximate bayesian computation software
  Kousathanas, A. and Duchen, P. and Wegmann, D. , arXiv (2018) | Other

  Inference of Evolutionary Jumps in Large Phylogenies using Lévy Processes
  Systematic Biology (2017) | Journal article

  First quantitative survey delineates the distribution of chimpanzees in the Eastern Central African Republic
  Biological Conservation (2017) | Journal article

  The Discovery of Wild Date Palms in Oman Reveals a Complex Domestication History Involving Centers in the Middle East and Africa
  Current Biology (2017) | Journal article

  ATLAS: Analysis Tools for Low-depth and Ancient Samples
  Vivian Link, Athanasios Kousathanas, Krishna Veeramah, Christian Sell, Amelie Scheu, Daniel Wegmann, (2017) | Preprint

  Normalisation against Circadian and Age-Related Disturbances Enables Robust Detection of Gene Expression Changes in Liver of Aged Mice
  PLOS ONE (2017) | Journal article

  Inferring Heterozygosity from Ancient and Low Coverage Genomes
  Genetics (2017) | Journal article

  Sino-Himalayan mountains act as cradles of diversity and immigration centres in the diversification of parrotbills (Paradoxornithidae)
  Journal of Biogeography (2016) | Journal article

  Early Neolithic genomes from the eastern Fertile Crescent
  Science (2016) | Journal article

  Early farmers from across Europe directly descended from Neolithic Aegeans
  Proceedings of the National Academy of Sciences (2016) | Journal article

  Selection against recombinant hybrids maintains reproductive isolation in hybridizing Populus species despite F1 fertility and recurrent gene flow
  Molecular Ecology (2016) | Journal article

  Likelihood-Free Inference in High-Dimensional Models
  Genetics (2016) | Journal article

  An Approximate Markov Model for the Wright–Fisher Diffusion and Its Application to Time Series Data
  Genetics (2016) | Journal article

  Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025
  Frontiers in Genetics (2015) | Journal article

  Influenza Virus Drug Resistance: A Time-Sampled Population Genetics Perspective
  Plos Genetics (2014) | Journal article

  Drosophila suzukii: The Genetic Footprint of a Recent, Worldwide Invasion
  Molecular Biology and Evolution (2014) | Journal article

  Demographic history of a recent invasion of house mice on the isolated Island of Gough
  Molecular Ecology (2014) | Journal article

  Analysis of rare variant population structure in Europeans explains differential stratification of gene-based tests
  European Journal of Human Genetics (2014) | Journal article

  Recipient of the 2013 Molecular Ecology Prize: Laurent Excoffier
  Molecular Ecology (2014) | Journal article

  Postglacial expansion and not human influence best explains the population structure in the endangered kea (Nestor notabilis)
  Molecular Ecology (2014) | Journal article

  The influence of genomic context on mutation patterns in the human genome inferred from rare variants
  Genome Research (2013) | Journal article

  Inferring the Geographic Mode of Speciation by Contrasting Autosomal and Sex-Linked Genetic Diversity
  Molecular Biology and Evolution (2013) | Journal article

  Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis
  Nature Genetics (2012) | Journal article

  An Early Divergence of KhoeSan Ancestors from Those of Other Modern Humans Is Supported by an ABC-Based Analysis of Autosomal Resequencing Data
  Molecular Biology and Evolution (2012) | Journal article

  An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People
  Science (2012) | Journal article

  Fitting models of continuous trait evolution to incompletely sampled comparative data using Approximate Bayesian Computation
  Evolution (2012) | Journal article

  Deep sequencing of the LRRK2 gene in 14,002 individuals reveals evidence of purifying selection and independent origin of the p.Arg1628Pro mutation in Europe
  Human Mutation (2012) | Journal article

  Recombination rates in admixed individuals identified by ancestry-based inference
  Nature Genetics (2011) | Journal article

  Historical sampling reveals dramatic demographic changes in western gorilla populations
  Bmc Evolutionary Biology (2011) | Journal article

  Genetic variation in the Sorbs of eastern Germany in the context of broader European genetic diversity
  European Journal of Human Genetics (2011) | Journal article

  Distinguishing between population bottleneck and population subdivision by a Bayesian model choice procedure
  Molecular Ecology (2010) | Journal article

  Bayesian Inference of the Demographic History of Chimpanzees
  Molecular Biology and Evolution (2010) | Journal article

  Bayesian Computation and Model Selection Without Likelihoods
  Genetics (2010) | Journal article

  ABCtoolbox: a versatile toolkit for approximate Bayesian computations
  Bmc Bioinformatics (2010) | Journal article

  A Statistical Evaluation of Models for the Initial Settlement of the American Continent Emphasizes the Importance of Gene Flow with Asia
  Molecular Biology and Evolution (2010) | Journal article

  Large Allele Frequency Differences between Human Continental Groups are more Likely to have Occurred by Drift During range Expansions than by Selection
  Annals of Human Genetics (2009) | Journal article

  Efficient Approximate Bayesian Computation Coupled With Markov Chain Monte Carlo Without Likelihood
  Genetics (2009) | Journal article

  Width of Gene Expression Profile Drives Alternative Splicing
  Plos One (2008) | Journal article

  Molecular diversity after a range expansion in heterogeneous environments
  Genetics (2006) | Journal article