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Statistical Phylogenomics and Machine Learning

Our task

Statistical phylogenetics deals with systematic and statistical errors in phylogeny.

When reconstructing phylogenetic trees (family trees), a number of modelling assumptions are made about the course of actual evolution. If these assumptions are not correct, the reconstruction of the phylogenetic tree is uncertain. An important task is to recognise and prove effects that lead to the reconstruction of false phylogenetic trees.

Contact person

Dr. Christoph Mayer

  • Head of Section
  • Chairman of Staff Council
  • Data Protection Vice-Commissioner

Phone: +49 228 9122 403
E-Mail: c.mayer@leibniz-lib.de

Projects

Publications

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    2025

  • 2025/1

    Schöneberg, Y., Audisio, T.L., Ben Hamadou, A., Forman, M., Král, J., Kořínková, T., Líznarová, E., Mayer, C., Prokopcová, L., Krehenwinkel, H., Prost, S., Kennedy, S.

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    Three Novel Spider Genomes Unveil Spidroin Diversification and Hox Cluster Architecture: Ryuthela nishihirai (Liphistiidae), Uloborus plumipes (Uloboridae) and Cheiracanthium punctorium (Cheiracanthiidae)

    Molecular Ecology resources, 1, 25

  • 2024

  • 2024/12

    Dietz, L., Kukowka, S., Eberle, J., Mayer, C., Niehuis, O., Podsiadlowski, L., Ahrens, D.

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    Museomics reveal origins of East African Pleophylla forest chafers and Miocene forest connectivity

    Molecular Phylogenetics and Evolution, 201

  • 2024/11

    Kulikov, N., Derakhshandeh, F., Mayer, C.

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    Machine learning can be as good as maximum likelihood when reconstructing phylogenetic trees and determining the best evolutionary model on four taxon alignments

    Molecular Phylogenetics and Evolution, 200

  • 2024/8

    Bartsch, S.B., Vogel, J., Ankermann, A., Mayer, C., Peters, R.S.

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    Protocol for the preparation of Wings and Wing Interference Pattern Imaging from ethanol preserved specimens

  • 2024/8

    Vogel, J., Forshage, M., Bartsch, S.B., Ankermann, A., Mayer, C., Falkenhausen, P.v., Rduch, V., Müller, B., Braun, C., Krammer, H., Peters, R.S.

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    Integrative characterisation of the Northwestern European species of Anacharis Dalman, 1823 (Hymenoptera, Cynipoidea, Figitidae) with the description of three new species

    Journal of Hymenoptera Research, 97

  • 2024/8

    Fuhrmann, N., Brasseur, M.V., Bakowski, C.E., Podsiadlowski, L., Prost, S., Krehenwinkel, H., Mayer, C.

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    Chromosome-Level Genome Assembly of the Viviparous Eelpout Zoarces viviparus

    Genome biology and evolution, 8, 16

  • 2024/8

    B. Bartsch, S., Vogel, J., Ankermann, A., Mayer, C.

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    Protocol for the preparation of Wings and Wing Interference Pattern Imaging from ethanol preserved specimens v1

  • 2024/7

    Frandsen, P.B., Holzenthal, R.W., Espeland, M., Breinholt, J., Thomas Thorpe, J.A., Simon, S., Kawahara, A.Y., Plotkin, D., Hotaling, S., Li, Y., Nelson, C.R., Niehuis, O., Mayer, C., Podsiadlowski, L., Donath, A., Misof, B., Moriarty Lemmon, E., Lemmon, A., Morse, J.C., Liu, S., Pauls, S.U., Zhou, X.

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    Phylogenomics recovers multiple origins of portable case making in caddisflies (Insecta: Trichoptera), nature’s underwater architects

    Proceedings - Royal Society. Biological sciences/Proceedings - Royal Society. Biological Sciences, 2026, 291

  • 2024/4

    Dietz, L., Eberle, J., Mayer, C., Kukowka, S., Bohacz, C., Baur, H., Espeland, M., Huber, B., Hutter, C., Mengual, X., Peters, R., Vences, M., Wesener, T., Willmott, K., Misof, B., Niehuis, O., Ahrens, D.

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    Standardized nuclear markers improve and homogenize species delimitation in Metazoa (vol 14, pg 543, 2023)

    Methods in Ecology and Evolution, 4, 15

  • 2023

  • 2023/12

    Dietz, L., Mayer, C., Stolle, E., Eberle, J., Misof, B., Podsiadłowski, L., Niehuis, O., Ahrens, D.

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    Metazoa‐level USCOs as markers in species delimitation and classification

    Molecular Ecology resources, 3, 24

  • 2023/10

    Brasseur, M.V., Leese, F., Schäfer, R.B., Schreiner, V.C., Mayer, C.

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    Transcriptomic sequencing data illuminate insecticide-induced physiological stress mechanisms in aquatic non-target invertebrates

    335

  • 2023/9

    Brasseur, M.V., Buchner, D., Mack, L., Schreiner, V.C., Schäfer, R.B., Leese, F., Mayer, C.

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    Multiple stressor effects of insecticide exposure and increased fine sediment deposition on the gene expression profiles of two freshwater invertebrate species

    1, 35

  • 2023/6

    Dietz, L., Seidel, M., Eberle, J., Misof, B., Pacheco, T.L., Podsiadłowski, L., Ranasinghe, S., Gunter, N.L., Niehuis, O., Mayer, C., Ahrens, D.

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    A transcriptome‐based phylogeny of Scarabaeoidea confirms the sister group relationship of dung beetles and phytophagous pleurostict scarabs (Coleoptera)

    Systematic entomology, 4, 48

  • 2023/4

    Efficient extraction of mitochondrial genes from next‐generation sequencing libraries

    Methods in Ecology and Evolution, 4, 14

  • 2023/2

    Dietz, L., Eberle, J., Mayer, C., Kukowka, S., Bohacz, C., Baur, H., Espeland, M., Huber, B.A., Hutter, C.R., Mengual, X., Peters, R.S., Vences, M., Wesener‍, T., Willmott, K.R., Misof, B., Niehuis, O., Ahrens, D.

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    Standardized nuclear markers improve and homogenize species delimitation in Metazoa

    Methods in Ecology and Evolution, 2, 14

  • 2022

  • 2022/12

    Brasseur, M.V., Beermann, A.J., Elbrecht, V., Grabner, D., Peinert-Voss, B., Salis, R.K., Weiss, M., Mayer, C., Leese, F.

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    Impacts of multiple anthropogenic stressors on the transcriptional response of Gammarus fossarum in a mesocosm field experiment

    1, 23

  • 2022/10

    Mengual, X., Mayer, C., Burt, T.O., Moran, K.M., Dietz, L., Nottebrock, G., Pauli, T., Young, A.D., Brasseur, M.V., Kukowka, S., Kelso, S., Etzbauer, C., Bot, S., Hauser, M., Jordaens, K., Miranda, G.F.G., Ståhls, G., van Steenis, W., Peters, R.S., Skevington, J.H.

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    Systematics and evolution of predatory flower flies (Diptera: Syrphidae) based on exon‐capture sequencing

    2, 48

  • 2022/6

    Joshi, M., Espeland, M., Dincă, V., Vila, R., Tahami, M.S., Dietz, L., Mayer, C., Martin, S., Dapporto, L., Mutanen, M.

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    Delimiting continuity: Comparison of target enrichment and double digest restriction‐site associated DNA sequencing for delineating admixing parapatric Melitaea butterflies

    Systematic entomology, 4, 47

  • 2022/4

    Flury, J.M., Hilgers, L., Herder, F., Spanke, T., Misof, B., Wowor, D., Boneka, F.B., Wantania, L.L., Mokodongan, D.F., Mayer, C., Nolte, A.W., Schwarzer, J.

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    The genetic basis of a novel reproductive strategy in Sulawesi ricefishes: How modularity and a low number of loci shape pelvic brooding

    Evolution, 5, 76

  • 2021

  • 2021/11

    Kohli, M.K., Letsch, H., Greve, C., Béthoux, O., Deregnaucourt, I., Liu, S., Zhou, X., Donath, A., Mayer, C., Podsiadłowski, L., Gunkel, S., Machida, R., Niehuis, O., Rust, J., Wappler, T., Xin, Y., Misof, B., Ware, J.L.

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    Evolutionary history and divergence times of Odonata (dragonflies and damselflies) revealed through transcriptomics

    iScience, 11, 24

  • 2021/10

    Vasilikopoulos, A., Balke, M., Kukowka, S., Pflug, J.M., Martin, S., Meusemann, K., Hendrich, L., Mayer, C., Maddison, D.R., Niehuis, O., Beutel, R.G., Misof, B.

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    Phylogenomic analyses clarify the pattern of evolution of Adephaga (Coleoptera) and highlight phylogenetic artefacts due to model misspecification and excessive data trimming

    Systematic entomology, 4, 46

  • 2021/9

    Stringer, D.N., Bertozzi, T., Meusemann, K., Delean, S., Guzik, M.T., Tierney, S.M., Mayer, C., Cooper, S.J., Javidkar, M., Zwick, A., Austin, A.D.

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    Development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (Philosciidae: Haloniscus)

    PloS one, 9, 16

  • 2021/7

    Letsch, H., Simon, S., Frandsen, P.B., Liu, S., Machida, R., Mayer, C., Misof, B., Niehuis, O., Zhou, X., Wipfler‍, B.

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    Combining molecular datasets with strongly heterogeneous taxon coverage enlightens the peculiar biogeographic history of stoneflies (Insecta: Plecoptera)

    Systematic entomology, 4, 46

  • 2021/3

    Mayer, C., Dietz, L., Call, E., Kukowka, S., Martin, S., Espeland, M.

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    Adding leaves to the Lepidoptera tree: capturing hundreds of nuclear genes from old museum specimens

    Systematic entomology, 3, 46

  • 2021/3

    Call, E., Mayer, C., Twort, V., Dietz, L., Wahlberg, N., Espeland, M.

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    Museomics: Phylogenomics of the Moth Family Epicopeiidae (Lepidoptera) Using Target Enrichment

    Insect systematics and diversity, 2, 5

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