Dr. Kevin Karbstein

Postdoc FSU Jena, Guest Researcher FMNH Gainesville

Research Interests

Profilbild2

Foto: Kevin Karbstein
  • Phylogenomics
  • Hybridization, Polyploidy, and Asexuality
  • Machine Learning / Deep Learning
  • R-Programming and -Statistics
  • Integrative Taxonomy
  • Speciation and Biodiversity
  • Geometric Morphometrics
  • Traits, Environment, and Genetics
  • Adaptation to (Extreme) Climatic Conditions
  • Red List Mapping of Endangered Plant Species
  • CV

    PostDoc

    • 01/2026 – present:  Guest researcher, Department of Natural History, Laboratory of Molecular Systematics and Evolutionary Genetics (P. Soltis), Florida Museum of Natural History (FMNH), University of Florida, USA.
    • 07/2025 – present:  Research assistant / Habilitation Candidate, Institute of Biodiversity, Ecology and Evolution, Professorship of Integrative Plant Taxonomy (M. Appelhans), Friedrich-Schiller-University of Jena – in collaboration with Senckenberg Institute for Plant Form and Function (SIP), Germany.
    • 07/2025 – 01/2026:  Research assistant, Department of Natural History, Laboratory of Molecular Systematics and Evolutionary Genetics (P. Soltis), Florida Museum of Natural History (FMNH), University of Florida, USA. Supported by DAAD.
    • 10/2022 – 06/2025:  Research assistant, Department of Biogeochemical Integration (Bio.AI, J. Wäldchen), Max Planck Institute for Biogeochemistry, Jena, Germany.
    • 10/2022 – 06/2025: Guest researcher, Data-intensive Systems and Visualization Group (dAI.SY, P. Mäder), Technical University of Ilmenau, Ilmenau, Germany.
    • 10/2021 – 09/2022:  Research assistant, Albrecht-von-Haller-Institute for Plant Science, Department of Systematics, Biodiversity and Evolution of Plants with Herbarium (E. Hörandl), Georg-August-University Göttingen, Germany.

    PhD

    • 12/2017 – 10/2021:  PhD student, Albrecht-von-Haller-Institute for Plant Science, Department of Systematics, Biodiversity and Evolution of Plants with Herbarium (E. Hörandl), Georg-August-University Göttingen, Germany. PhD-thesis (DFG, SPP 1991 TaxonOmics): "The biodiversity of apomictic polyploid plants: the Ranunculus auricomus complex." Final grade: "summa cum laude".

    Completed Studies

    • 10/2014 – 09/2017:  Master of Science in Evolution, Ecology and Systematics, Institute of Systematic Botany with Herbarium Haussknecht and Botanical Garden (K. Prinz, C. Römermann & F. Hellwig), Friedrich-Schiller-University Jena, Germany.
    • 10/2015 – 03/2016: Research Internship at Forest Research Center FFK Gotha, Germany.
    • 03/2014, 05/2015, 07/2015: Field Practical Courses in Canary Islands (Spain), Provence (France), and Alps (Austria).
    • 08/2015 – 09/2015: Spanish and Environmental Education School Academia Pradoventura, Prado del Rey (Spain).
    • 10/2011 – 09/2014:  Bachelor of Science Biology, Institute of Systematic Botany with Herbarium Haussknecht and Botanical Garden (K. Prinz, F. Hellwig), Friedrich-Schiller-University Jena, Germany.
  • Publication List

     Software Packages

    1. Karbstein K. GenomeXtract: A toolkit to easily find, compare, and assemble NCBI genomes. GitHub repository, version 0.1.4, 2025. https://github.com/kevinkarbstein/GenomeXtractExterner Link  https://doi.org/10.5281/zenodo.17783448Externer Link
    2. Kösters L*, Karbstein K*. LazyModeler: An R package for automatic simplification, check, and visualization of regression models. Github repository, version 0.2.2, 2025. https://github.com/LMKoesters/LazyModelerExterner Link 

    Peer-reviewed Articles

    1. Phillips C, Feulner M, Karbstein K, Meyer N, Weigel A, Steinbauer MJ: Apomixis supports niche-edge adaptation in allopolyploid hybrids in Whitebeams. Under review in Annals of Botany.
    2. Kösters L*, Karbstein K*. LazyModeler: An R package for automatic simplification, check, and visualization of regression models. under review in Journal of Open Source Software. https://github.com/openjournals/joss-reviews/issues/7865Externer Link
    3. Westhus W, Zündorf H-J, Karbstein K: Die Thüringische Botanische Gesellschaft e. V.: Thüringens Pflanzenwelt gemeinsam entdecken. Landschaftspflege und Naturschutz in Thüringen, 2025; 61(4); 152-155. https://tlubn.thueringen.de/fileadmin/000_TLUBN/Service/Publikationen/LNT_Sonderhefte/download/LNT_2025_04_SH.pdfExterner Link
    4. Karbstein K, Choudhary N, Xie T, Tomasello S, Wagner ND, Barke BH, Paetzold C, Bradican JP, Preick M, Himmelbach A, Stein N, Papantonis A, Irisarri I, de Vries J, Pucker B, Hörandl E. Assembling genomes of non-model plants: A case study with evolutionary insights from Ranunculus (Ranunculaceae). The Plant Journal, 2025; 123; e70390. https://doi.org/10.1111/tpj.70390Externer Link
    5. Karbstein K, Lemke T, Westhus W, Rzanny M, Hodač L, Bebber A, Fritz A, Wittich HC, Boho D, Mäder P, Wäldchen J. App-based mapping of FFH- and Red List plant species using Flora Incognita. Landschaftspflege und Naturschutz in Thüringen, 2025; 61 (2); 51-58. https://tlubn.thueringen.de/fileadmin/000_TLUBN/Service/Publikationen/LNT/download/LNT_Digitalausgabe_Heft_02_2025.pdfExterner Link
    6. Kösters L, Karbstein K, Hofmann M, Hodač L, Mäder P, Wäldchen J. Data Fusion for Integrative Species Identification using Deep Learning. Systematic Biology, 2025; 00; 1-52. https://doi.org/10.1093/sysbio/syaf026Externer Link.
    7. Tarieiev A, Karbstein K, Gailing O. Phylogenetic and taxonomic insights into Betula: low-coverage whole genome sequencing and plastome analysis with focus on the rare Ukrainian endemic species Betula klokovii Zaverucha. BioRxiv: https://doi.org/10.1101/2025.01.15.632994Externer Link
    8. Hodač L, Karbstein K, Kösters L, Rzanny M, Wittich HC, Boho D, Šubrt D, Mäder P, Wäldchen J. Deep learning to capture leaf shape in plant images: Validation by geometric morphometrics. The Plant Journal, 2024; 120; 1343-1357. https://doi.org/10.1111/tpj.17053Externer Link 
    9. Tomasello S, Manzo E, Karbstein K. Comparative plastome assembly of the yellow ironweed (Verbesina alternifolia) using Nanopore and Illumina reads. Frontiers in Plant Science, 2024; 15; 1-10. https://doi.org/10.3389/fpls.2024.1429494Externer Link
    10. Karbstein K, Kösters L, Hodač L, Hofmann M, Hörandl E, Tomasello S, Wagner ND, Emerson BC, Albach DC, Scheu S, Bradler S, de Vries J, Irisarri I, Li H, Soltis P, Mäder P, Wäldchen J. Species delimitation 4.0: integrative taxonomy meets artificial intelligence. Trends in Ecology and Evolution, 2024; 39; 771-784. https://doi.org/10.1016/j.tree.2023.11.002Externer Link 
    11. Bradican JP, Tomasello S, Boscutti F, Karbstein K, Hörandl E. Phylogenomics of southern European taxa in the Ranunculus auricomus species complex: The apple doesn’t fall far from the tree. Plants, 2023; 12; 3664. https://doi.org/10.3390/plants12213664Externer Link 
    12. Karbstein K, Römermann C, Hellwig F, Prinz K. Population size affected by environmental variability impacts genetics, traits, and plant performance in Trifolium montanum. Ecology and Evolution, 2023; 13; e10376. https://doi.org/10.1002/ece3.10376Externer Link
    13. Hodač L*, Karbstein K*, Tomasello S, Wäldchen, J, Bradican, JP, Hörandl E. Geometric morphometric versus genomic patterns in a large polyploid plant species complex. Biology, 2023; 12; 418. https://doi.org/10.3390/biology12030418Externer Link
    14. Karbstein K, Tomasello S, Hodač L, Wagner N, Marincek P, Barke BH, Pätzold C, Hörandl E. Untying Gordian knots: unraveling reticulate polyploid plant evolution by genomic data using the large Ranunculus auricomus species complex. New Phytologist, 2022; 235; 2081-2098. https://doi.org/10.1111/nph.18284Externer Link; BioRxiv: https://doi.org/10.1101/2021.08.30.458250Externer Link
    15. Karbstein K, Tomasello S, Hodač L, Lorberg E, Daubert M, Hörandl E. Moving beyond assumptions: polyploidy and environmental effects explain a geographic parthenogenesis scenario in European plants. Molecular Ecology, 2021; 30; 2659-2675. https://doi.org/10.1111/mec.15919Externer Link
    16. Karbstein K, Gockel S, Frischbier N, Kahlert K, Konnert, M, Profft I. 'High-altitude spruces' in Central Europe - a summarizing contribution to phenotypic and (epi)genetic differentiation within Picea abies (L.) H.KARST. Allgemeine Forst- und Jagdzeitschrift (AFJZ), 2021; 9/10; 197-211. https://doi.org/10.23765/afjz0002068Externer Link
    17. Strecker T, Jesch A, Bachmann D, Jüds M, Karbstein K, Ravenek J, Roscher, C, Weigelt A, Eisenhauer N, Scheu S. Incorporation of mineral nitrogen into the soil food web as affected by plant community composition. Ecology and Evolution, 2021; 11; 4295-4309. https://doi.org/10.1002/ece3.7325Externer Link 
    18. Karbstein K, Rahmsdorf E, Tomasello S, Hodač L, Hörandl E. Breeding system of diploid sexuals within the Ranunculus auricomus complex and its role in a geographical parthenogenesis scenario. Ecology and Evolution, 2020; 10; 14435-14450. https://doi.org/10.1002/ece3.7073Externer Link
    19. Barke BH, Karbstein K, Daubert M, Hörandl E. The relation of meiotic behaviour to hybridity, polyploidy and apomixis in the Ranunculus auricomus complex (Ranunculaceae). BMC Plant Biology, 2020; 20; 523. https://doi.org/10.1186/s12870-020-02654-3Externer Link
    20. Karbstein K, Tomasello S, Hodač L, Dunkel FG, Daubert M, Hörandl E. Phylogenomics supported by geometric morphometrics reveals delimitation of sexual species within the polyploid apomictic Ranunculus auricomus complex (Ranunculaceae). Taxon, 2020; 69; 1191-1220. https://doi.org/10.1002/tax.12365Externer Link; BioRxiv: https://doi.org/10.1101/2020.01.07.896902Externer Link
    21. Tomasello S, Karbstein K, Hodač L, Pätzold C, Hörandl E. Phylogenomics unravels Quarternary vicariance and allopatric speciation patterns in temperate-montane plant species: a case study on the Ranunculus auricomus species complex. Molecular Ecology, 2020; 29; 2031-2049. https://doi.org/10.1111/mec.15458Externer Link; BioRxiv: https://doi.org/10.1101/2020.01.06.895904Externer Link 
    22. Karbstein K, Prinz K, Hellwig F, Römermann C. Plant intraspecific functional trait variation is related to within-habitat heterogeneity and genetic diversity in Trifolium montanum L. Ecology and Evolution, 2020; 10; 5015-5033. https://doi.org/10.1002/ece3.6255Externer Link 
    23. Karbstein K, Tomasello S, Prinz K. Desert-like badlands and surrounding (semi-)dry grasslands of Central Germany promote small-scale phenotypic and genetic differentiation in Thymus praecox. Ecology and Evolution, 2019; 9; 14066–14084. https://doi.org/10.1002/ece3.5844Externer Link 

    Thesis

    1. Karbstein K. Untying Gordian knots - The evolution and biogeography of the large European apomictic polyploid Ranunculus auricomus plant complex. Dissertation, University of Göttingen, 2021; 1-475. http://hdl.handle.net/21.11130/00-1735-0000-0008-5946-6Externer Link

    *shared first authorships

  • National and International Activities

    Reviews for scientific journals (latest first)

    • Molecular Ecology, Methods in Ecology and Evolution, New Phytologist, Critical Reviews in Plant Science, Taxon, Scientific Reports, Frontiers in Plant Sciences, Plos One, Biology, Botanical Journal of the Linnean Society, Journal of Biogeography, American Journal of Botany, Ecology and Evolution, etc.

    Conferences, Organized Workshops, and Guided Excursions

    International Botanical Trips

    • Central Europe (Semi-dry grasslands and high altitudes)
    • Mediterranean region (Spain & Canary Islands)
    • USA (California & Florida)
  • Awards
    • 06/2025: MDPI Biology 2023 Best Paper Award
    • 03/2023: Bernhardt-Rensch-Award 2023 (young talent award for outstanding achievements in the field of biological systematics)
  • Funding
    • DFG Grant for AI-based Integrative Taxonomy in Thymus
    • DAAD Short-Team PostDoc Grant for University of Florida, Gainesville, USA
    • Seed Money for Post-Doc Grant within DFG SPP 1991 Taxon-Omics for Whole Genome Resequencing in Thymus
    • Travel Grants: Universitätsbund Göttingen e.V. DBG Bonn, DAAD IBC Madrid
  • Memberships

Current Project 1 (FSU, MPI-BGC) - Integrative taxon-omics and machine learning to decipher reticulate plant speciation – a proof-of-concept from Thymus (Lamiaceae) 

Modern integrative taxonomy combines 21st century high-throughput genomics and other complementary data sources (e.g., morphology, ploidy, reproduction, or ecology), and has started to become the new gold standard for species delimitation. It has also raised the awareness that what we call species can be ill-founded entities because of morphology-based, regional species descriptions. This is particularly true for taxonomically complex groups characterized by young origins, hybridization, or polyploidy. Here, the challenges of modern taxonomy become apparent: lack of appropriate analytical tools for intricate evolutionary processes or highly subjective ranking and manual fusion of datasets. 

Now, integrative taxonomy combined with machine learning (ML) enables standardized feature learning and data fusion to reduce subjectivity in species delimitation but also the ability to learn and handle intricate evolutionary processes. 

Here, we will use the economically important plant genus Thymus, which comprises hundreds of di- to polyploid, partly hybridogenous taxa distributed across Eurasia, with unknown evolutionary relationships and species status. We will perform whole-genome resequencing (WGR) based on DNA extracts from herbarium specimens, focusing on widespread diploid progenitors and important polyploid derivatives. Genome-wide SNPs, nuclear genes and plastome sequences, as well as ploidy, morphological, and ecological data will be analyzed using classical model-based approaches to clarify species boundaries. Nevertheless, this is prone to species over-splitting (e.g., DNA) or lumping (e.g., morphology), and is usually integrated on a manual basis. 

We will therefore also analyze Thymus datasets using state-of-the-art, fusion-based ML delimitation approaches based on specific pretraining rounds and learning of reticulate evolutionary relationships. ML results will be compared with classical DNA and integrative species delimitation results to obtain different views on species boundaries in relation to reticulate evolutionary processes and to make final taxonomic treatments. 

The DFG project aims to improve species delimitation by making it more integrative, objective, and suitable for reticulate evolution, while also accelerating the study of plant biodiversity in times of global change. 

ELAN Link: https://gepris.dfg.de/gepris/projekt/564834741?language=enExterner Link 

Contrasting Thymus morphotypes: (left) creeping, purple flowering T. pulegioides (sect. Serpyllum) with slightly dissected upper calyx teeth, and (right) erect, whitish flowering T. mastichina (sect. Mastichina) with hairy, deeply dissected upper calyx teeth (© Alchetron.com).

Foto: Left: Kevin Karbstein, right: Alchetron.com

Current Project 2 (FSU, FMNH) - Collectus: A new multi-omics pipeline in specimen-based phylogenomic and biodiversity research

Despite recent advances in genomics, efficient strategies are lacking to generate multi-omics datasets from a standard laboratory procedure or bioinformatic pipeline. This is especially needed for the 3-4 billion specimens currently housed in the world‘s herbaria and other natural history collections awaiting genomic analysis. Collectomics approaches apply diverse methods to integrate multidimensional, high-throughput specimen-based data, crucial for understanding and documenting biodiversity, especially for phylogenomic analyses and species delimitation in taxonomically complex groups shaped by hybridization, polyploidy, or apomixis. In such groups, the combination of genome-wide variants, nuclear genes, and organellar information is often necessary to disentangle species relationships and uncover cryptic diversity, a pressing need given the current rate of biodiversity loss. We developed a Python-based pipeline using state-of-the-art tools to assemble these data in addition to ploidy estimation. The pipeline maps Illumina reads from whole-genome resequencing (WGR) at relatively low haploid genome coverage (<30×), target enrichment (HybSeq), and genome skimming to available high-quality genomes. We tested the pipeline on datasets from Thymus (thyme), Vaccinium (blueberry), and Zanthoxylum (prickly ash), comparing fresh and herbarium material across different ages and sequencing coverages. In WGR tests of Thymus, we obtained expected ploidal levels (2x, 4x) and recovered up to 1,978,481 SNPs, 758 single-copy nuclear genes, and 151-kbp complete plastomes, even from a plant specimen collected in 1829. Our pipeline enables efficient assembly of genomic data for biodiversity research and provides a practical solution for leveraging natural history collections in the genomic era.

Funding Agencies

  • FSU Logo
  • DFG Logo
  • DAAD Logo
  • MPI-BGC Logo
  • UF Logo2
  • FMNH Logo

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