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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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    2026

  • 2026/02

    Postma, A., Klynsmith, L., Duong, T.A., Allison, J.D., Smidt, W., Waterhouse, R.M., Lesny, P., Oeyen, J.P., Petersen, M., Martin, S., Liu, S., Zhou, X., Ziesmann, T., Donath, A., Mayer, C., Misof, B., Niehuis, O., Peters, R.S., Podsiadlowski, L., Coetzee, M.P.A., Joubert, F., Slippers, B.

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    Genome and transcriptome‐based identification and expression profiling of chemosensory gene families across developmental stages and tissues in Sirex noctilio (Hymenoptera: Siricidae)

    Insect Molecular Biology

  • 2025

  • 2025/10

    Dietz, L., Eberle, J., Kukowka, S., Podsiadlowski, L., Bazzato, E., Stange, M., Warnock, R.C.M., Niehuis, O., Mayer, C., Ahrens, D.

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    Cryptic Species Can Be Phylogenetically Old Despite Strong Sex-Biased Dispersal

    Systematic Biology

  • 2025/07

    Brasseur, M., Bakowski, C., Mayer, C., Podsiadlowski, L.

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    Heat stress responsive genes are not affected by ocean warming: long-term environmental monitoring and acute thermal stress experiments identify non-overlapping sets of differentially expressed genes in a marine fish

  • 2025/03

    Arsic, P., Mayer, C.

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    Ali-U-Net: A Convolutional Transformer Neural Net for Multiple Sequence Alignment of DNA Sequences. A proof of concept

  • 2025/01

    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

  • 2024/08

    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

  • 2024/08

    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

  • 2024/08

    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

  • 2024/08

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

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

  • 2024/04

    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

  • 2023/01

    Brasseur, M.V., Astrin, J.J., Geiger, M.F., Mayer, C.

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    Author response for "MitoGeneExtractor: Efficient extraction of mitochondrial genes from next‐generation sequencing libraries"

  • 2020

  • 2020/11

    Meusemann, K., Trautwein, M., Friedrich, F., Beutel, R.G., Wiegmann, B.M., Donath, A., Podsiadlowski, L., Petersen, M., Niehuis, O., Mayer, C., Bayless, K.M., Shin, S., Liu, S., Hlinka, O., Minh, B.Q., Kozlov, A., Morel, B., Peters, R.S., Bartel, D., Grove, S., Zhou, X., Misof, B., Yeates, D.K.

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    Are fleas highly modified Mecoptera? Phylogenomic resolution of Antliophora (Insecta: Holometabola)

  • 2020/10

    Vasilikopoulos, A., Misof, B., Meusemann, K., Lieberz, D., Flouri, T., Beutel, R.G., Niehuis, O., Wappler, T., Rust, J., Peters, R.S., Donath, A., Podsiadlowski, L., Mayer, C., Bartel, D., Böhm, A., Liu, S., Kapli, P., Greve, C., Jepson, J.E., Liu, X., Zhou, X., Aspöck, H., Aspöck, U.

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    Correction to: An integrative phylogenomic approach to elucidate the evolutionary history and divergence times of Neuropterida (Insecta: Holometabola)

    BMC evolutionary biology, 1, 20

  • 2020/07

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

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    How old are dragonflies and damselflies? Odonata (Insecta) transcriptomics resolve familial relationships

  • 2019

  • 2019/10

    Vizán-Rico, H.I., Mayer, C., Petersen, M., McKenna, D.D., Zhou, X., Gómez-Zurita, J.

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    Patterns and Constraints in the Evolution of Sperm Individualization Genes in Insects, with an Emphasis on Beetles

    Genes, 10, 10

  • 2017

  • 2017/01

    Gunkel, S., Rust, J., Wappler, T., Mayer, C., Niehuis, O., Misof, B.

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    A posteriori evaluation of molecular divergence dates using empirical estimates of time-heterogeneous fossilization rates

    bioRxiv

  • 2015

  • 2015/07

    Kjer, K.M., Ware, J.L., Rust, J., Wappler, T., Lanfear, R., Jermiin, L.S., Zhou, X., Aspöck, H., Aspöck, U., Beutel, R.G., Blanke, A., Donath, A., Flouri, T., Frandsen, P.B., Kapli, P., Kawahara, A.Y., Letsch, H., Mayer, C., McKenna, D.D., Meusemann, K., Niehuis, O., Peters, R.S., Wiegmann, B.M., Yeates, D.K., von Reumont, B.M., Stamatakis, A., Misof, B.

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    Response to Comment on “Phylogenomics resolves the timing and pattern of insect evolution”

    Science, 6247, 349

  • 2011

  • 2011/08

    Kurtenbach, S., Mayer, C., Pelz, T., Hatt, H., Leese, F., Neuhaus, E.M.

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    Molecular evolution of a chordate specific family of G protein-coupled receptors

    BMC evolutionary biology, 1, 11

  • 2011/03

    Dietz, L., Mayer, C., Arango, C.P., Leese, F.

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    The mitochondrial genome of Colossendeis megalonyx supports a basal position of Colossendeidae within the Pycnogonida

    Molecular Phylogenetics and Evolution, 3, 58

  • 2010

  • 2010/06

    Spanier, K.I., Leese, F., Mayer, C., Colbourne, J.K., Gilbert, D., Pfrender, M.E., Tollrian, R.

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    Predator-induced defences in Daphnia pulex: Selection and evaluation of internal reference genes for gene expression studies with real-time PCR

    BMC molecular biology, 1, 11

  • 2010/04

    Mayer, C., Leese, F., Tollrian, R.

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    Genome-wide analysis of tandem repeats in Daphnia pulex-a comparative approach

    BMC genomics, 1, 11

  • 2010/03

    Krabbe, K., Leese, F., Mayer, C., Tollrian, R., Held, C.

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    Cryptic mitochondrial lineages in the widespread pycnogonid Colossendeis megalonyx Hoek, 1881 from Antarctic and Subantarctic waters

    Polar biology, 3, 33

  • 2009

  • 2009/01

    Kraemer, L., Beszteri, B., Gäbler-Schwarz, S., Held, C., Leese, F., Mayer, C., Pöhlmann, K., Frickenhaus, S.

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    STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design

    BMC bioinformatics, 1, 10

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