Dr. Christoph Mayer

Head of Section
Deputy Data Protection Commissioner

Statistical Phylogenetics and Phylogenomics, Staff Council

Tel: +49 228 9122-403

Fax: +49 228 9122-212

Mail: C.Mayer [at] zfmk.de

Tabs

Profile

Field of work

I am a senior scientist at the Leibniz Institute for the Analysis of Biodiversity Change (LIB) in Bonn, (Research Museum Alexander Koenig).

Research interests

Development of methods for the analysis of large data sets.

I am interested in

- genome analyses

- differential gene extression

- machine learning

Further information

Software:

BaitFisher and BaitFilter
A software suite to design hybrid enrichment baits from multiple sequence alignments. Published in 2016 BaitFisher became a widely used software. It is avaiable in github: BaitFisher and BaitFilter on GitHub: https://github.com/cmayer/BaitFisher-package

Phobos
A microsatellite, minisatellite and satellite search tool by Christoph Mayer
http://www.ruhr-uni-bochum.de/spezzoo/cm/cm_phobos.htm
Phobos has been integrated into the following molecular biology analysis tools, which in particular offer a convenient interfaces for designing flanking primers of microsatellites.
Commercial users always need to obtain a user license directly from the author of Phobos, Christoph Mayer.

PolyMoSim
A program to simulate molecular evolution, such that every branch of a tree can be assigned a different evolutinary model by Christoph Mayer

SAMS
Splits Analysis Methods, Christoph Mayer, Sandra Meid, Wolfgang Waegele.

STAMP
Microsatellite marker design extension for the Staden package.

DeepNNPhylogeny:
https://github.com/cmayer/DeepNNPhylogeny

Reference:

Mayer, C., Sann, M., Donath, A., Meixner, M., Podsiadlowski, L., Peters, R.S., Petersen, M., Meusemann, K., Liere, K., Wägele, J.-W., Misof, B., Bleidorn, C., Ohl, M., Niehuis, O., 2016. BaitFisher: A Software Package for Multispecies Target DNA Enrichment Probe Design. Mol. Biol. Evol. 33, 1875–1886. https://doi.org/10.1093/molbev/msw056

Kraemer, L., Beszteri, B., Gaebler-Schwarz, S., Held, C., Leese, F., Mayer, C., Poehlmann, K. & Frickenhaus, S. (2009)

STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design.
BMC Bioinformatics 10:41.

Phobos plugin for Geneious.
Geneious is a commercial and easy to use DNA and protein sequence analysis tool.
In order to use the tandem repeat detection capabilities of Phobos in Geneious one has to install the command-line version of Phobos (version 3.3.10 or higher) as well as the Phobos plugin.

Sat-stat - Statstical analysis of Phobos output. Sat-stat compuputes tandem repeat characteristics of genomes analysed with Phobos. (Will be made available soon.)

Projects

The section "Statistical Phylogenetics & Phylogenomics" contributes to several Projects at the ZFMK as well as to external projects.

2021

The impact of mutualistic and parasitic life histories on butterfly diversification in an increasingly arid world

Understanding the mechanisms leading to diversification of species across time in a changing world remains a challenge. Africa was largely covered by forests until the middle Oligocene, when geological and climatic changes led to increasing aridification of the landmass. The current, iconic savanna and grassland ecosystems did not become well-established until around 8 million years ago. The effect of this increasing aridification on diversification has not been well-studied in animals, and especially not in insects.

Unit:

Lepidoptera, Statistical Phylogenetics and Phylogenomics, Staff Council, Herpetology, Morphology Laboratory

Project lead:

Dr. Marianne Espeland

Funding:

Deutsche Forschungsgemeinschaft

2020

Utilizing environmental genomics to study multiple agricultural stressor impacts on stream invertebrates and ecosystem functions

Der Verlust an Biodiversität nimmt rasant zu und hat nachteilige Folgen für Ökosystemfunktionen und -dienstleistungen. Hiervon sind in besonderer Weise Fließgewässer betroffen. Zu den wichtigsten Ursachen des Biodiversitätsverlustes in Fließgewässern gehören landwirtschaftliche Stressoren, wie z.B. Pestizide. Pestizide sind allerdings selten alleiniger Stressor, sondern wirken oft zusammen mit anderen Stressoren wie z.B. einem gesteigerten Feinsedimenteintrag aus Ackerflächen. Interaktionen solch multipler Stressoren können zu komplexen nichtlinearen Stressantworten führen.

Unit:

Statistical Phylogenetics and Phylogenomics, Staff Council

Project lead:

Dr. Christoph Mayer

2018

Establishing a standardized and universally applicable set of nuclear-encoded markers for genome-wide multi-locus species delimitation of metazoans

Methods for delimiting species based on multi-gene nucleotide information are well established and provide the means to complement the classical COI barcoding approach, whose limitations are well known. Our research project aims at establishing a standardized set of single-copy nuclear-encoded markers for genome-wide multi-locus species delimitation by exploiting comparative genomic data and applying target DNA enrichment. Candidate markers are so-called Universal Single-Copy Orthologs (USCOs).

Unit:

Coleoptera, Arachnids, Statistical Phylogenetics and Phylogenomics, Staff Council, Directorate, Chair Systematic Zoology, Lepidoptera, Hymenoptera, Molecular Laboratory, Centre for Molecular Biodiversity Research (zmb), Myriapoda, Diptera

Project lead:

Dr. Dirk Ahrens

Funding:

Deutsche Forschungsgemeinschaft

2017

Sequencing museum material

In this project we investigate how we efficiently can use old, dried, museum materil for phylogenomic studies. A hybrid enrichment kit for Lepidoptera is being designed and first test are promising, indicating that hundreds of genes can be successfully seqeunced for over 130 year old material.

Unit:

Lepidoptera, Statistical Phylogenetics and Phylogenomics, Centre for Molecular Biodiversity Research (zmb)

Project lead:

Dr. Marianne Espeland

Funding:

Zoological Research Museum Alexander Koenig

2012

Identification of sources of error in molecular phylogenetic analyses

The aim of our study was to test the robustness and efficiency of maximum likelihood with respect to different long branch effects on multiple-taxon trees.

Unit:

Algorithmic Development, Chair Systematic Zoology, Centre for Biodiversity Monitoring and Conservation Science (zbm), Directorate, Centre for Molecular Biodiversity Research (zmb), Chair Molecular Biodiversity Research, Statistical Phylogenetics and Phylogenomics, Staff Council

Project lead:

Dr. Patrick Kück

Funding:

Zoological Research Museum Alexander Koenig

1KITE: The evolution of the insects

Insects are one of the most species-rich groups of metazoan organisms. They play a pivotal role in most non-marine ecosystems and many insect species are of enormous economical and medical importance. Unraveling the evolution of insects is essential for understanding how life in terrestrial and limnic environments evolved. The 1KITE (1K Insect Transcriptome Evolution) project aims to study the transcriptomes (that is the entirety of expressed genes) of 1,000 insect species encompassing all recognized insect orders. For each species, so-called ESTs (Expressed Sequence Tags) will be produced…

Unit:

Directorate, Chair Systematic Zoology, Directorate Staff, Biodiversity Informatics, Computational Genomics, High-performance Computing, Statistical Phylogenetics and Phylogenomics, Staff Council, Centre for Biodiversity Monitoring and Conservation Science (zbm), Education, Biobank, Hymenoptera, Chair Molecular Biodiversity Research, Centre for Molecular Biodiversity Research (zmb)

Project lead:

Prof. Dr. Bernhard Misof

2009

The legacy of the Southern Ocean

Unit:

Statistical Phylogenetics and Phylogenomics, Staff Council

Project lead:

Dr. Christoph Mayer

Funding:

Deutsche Forschungsgemeinschaft

Publications

Published in

2017

Dowling, D., Pauli, T., Donath, A., Meusemann, K., Podsiadlowski, L., Petersen, M., Peters, R.S., Mayer, C., Liu, S., Zhou, X., Misof, B., Niehuis, O. (2017): Phylogenetic Origin and Diversification of RNAi Pathway Genes in Insects. Genome Biology and Evolution 8(12), 3784-3793. doi:10.1093/gbe/evw281

[more]

Biswas, M.K., Mayer, C., Deng, X., 2017. Repeats in the transcribed regions: comprehensive characterization and comparison of Citrus spp. Front. Agr. Sci. Eng. 4, 421–432. https://doi.org/10.15302/J-FASE-2017160

[more]

Mock, T., Otillar, R.P., Strauss, J., McMullan, M., Paajanen, P., Schmutz, J., Salamov, A., Sanges, R., Toseland, A., Ward, B.J., Allen, A.E., Dupont, C.L., Frickenhaus, S., Maumus, F., Veluchamy, A., Wu, T., Barry, K.W., Falciatore, A., Ferrante, M.I., Fortunato, A.E., Glöckner, G., Gruber, A., Hipkin, R., Janech, M.G., Kroth, P.G., Leese, F., Lindquist, E.A., Lyon, B.R., Martin, J., Mayer, C., Parker, M., Quesneville, H., Raymond, J.A., Uhlig, C., Valas, R.E., Valentin, K.U., Worden, A.Z., Armbrust, E.V., Clark, M.D., Bowler, C., Green, B.R., Moulton, V., van Oosterhout, C., Grigoriev, I.V., 2017. Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. Nature 541, 536–540. doi:10.1038/nature20803

[more]

Peters, R.S., Krogmann, L., Mayer, C., Donath, A., Gunkel, S., Meusemann, K., Kozlov, A., Podsiadlowski, L., Petersen, M., Lanfear, R., Diez, P.A., Heraty, J., Kjer, K.M., Klopfstein, S., Meier, R., Polidori, C., Schmitt, T., Liu, S., Zhou, X., Wappler, T., Rust, J., Misof, B., Niehuis, O. (2017): Evolutionary History of the Hymenoptera. Current Biology. 27, 1013–1018. https://doi.org/10.1016/j.cub.2017.01.027

[more]

2016

Pauli, T., Vedder, L., Dowling, D., Petersen, M., Meusemann, K., Donath, A., Peters, R.S., Podsiadlowski, L., Mayer, C., Liu, S., Zhou, X., Heger, P., Wiehe, T., Hering, L., Mayer, G., Misof, B., Niehuis, O. (2016): Transcriptomic data from panarthropods shed new light on the evolution of insulator binding proteins in insects. BMC Genomics 17, 861. doi:10.1186/s12864-016-3205-1

[more]

de Araújo, C.A.C., Mayer, C., Waniek, P.J., Azambuja, P., Jansen, A.M., 2016. Differentiation of Trypanosoma cruzi I (TcI) and T. cruzi II (TcII) genotypes using genes encoding serine carboxypeptidases. Parasitology Research 1–9.

[more]

Mayer, C., Sann, M., Donath, A., Meixner, M., Podsiadlowski, L., Peters, R.S., Petersen, M., Meusemann, K., Liere, K., Wägele, J.-W., Misof, B., Bleidorn, C., Ohl, M., Niehuis, O. (2016): BaitFisher: A software package for multispecies target DNA enrichment probe design. Molecular Biology and Evolution doi:10.1093/molbev/msw056

[more]

2015

Kjer KM, Ware JL, Rust J, Wappler T, Lanfear R, Jermiin LS, Zhou X, Aspöck H, Aspöck U, Beutel RG, Blanke A, Donath A, Flouri T, Frandsen PB, Kapli P, Kawahara AY, Letsch H, Mayer C, McKenna DD, Meusemann K, Niehuis O, Peters RS, Wiegmann BM, Yeates DK, von Reumont BM, Stamatakis A, Misof B. (2015): INSECT PHYLOGENOMICS. Response to Comment on "Phylogenomics resolves the timing and pattern of insect evolution". – Science 349: 487.

[more]

Lars Dietz, Claudia P. Arango, Jana S. Dömel, Kenneth M. Halanych, Avril M. Harder, Christoph Held, Andrew R. Mahon, Christoph Mayer, Roland R. Melzer, Greg W. Rouse, Andrea Weis, Nerida G. Wilson, Florian Leese (2015): Regional differentiation and extensive hybridization between mitochondrial clades of the Southern Ocean giant sea spider Colossendeis megalonyx. Royal Society Open Science, 2 (7):140424

[more]

Manosh Kumar Biswas, Yuxuan Liu, Chunyu Li, Ou Sheng, Christoph Mayer, Ganjun Yi (2015): Genome-Wide Computational Analysis of Musa Microsatellites: Classification, Cross-Taxon Transferability, Functional Annotation, Association with Transposons & miRNAs, and Genetic Marker Potential, PloS one, 10 (6): e0131312

[more]

Paul B Frandsen, Brett Calcott, Christoph Mayer, Robert Lanfear, Automatic selection of partitioning schemes for phylogenetic analyses using iterative k-means clustering of site rates, (2015) BMC Evolutionary Biology, 15 (1):13

[more]

2014

Bernhard Misof, Shanlin Liu, Karen Meusemann, Ralph S. Peters, Alexander Donath, Christoph Mayer, Paul B. Frandsen, Jessica Ware, Tomáš Flouri, Rolf G. Beutel, Oliver Niehuis, Malte Petersen, Fernando Izquierdo-Carrasco, Torsten Wappler, Jes Rust, Andre J. Aberer, Ulrike Aspöck, Horst Aspöck, Daniela Bartel, Alexander Blanke, Simon Berger, Alexander Böhm, Thomas R. Buckley, Brett Calcott, Junqing Chen, Frank Friedrich, Makiko Fukui, Mari Fujita, Carola Greve, Peter Grobe, Shengchang Gu, Ying Huang, Lars S. Jermiin, Akito Y. Kawahara, Lars Krogmann, Martin Kubiak, Robert Lanfear, Harald Letsch, Yiyuan Li, Zhenyu Li, Jiguang Li, Haorong Lu, Ryuichiro Machida, Yuta Mashimo, Pashalia Kapli, Duane D. McKenna, Guanliang Meng, Yasutaka Nakagaki, José Luis Navarrete-Heredia, Michael Ott, Yanxiang Ou, Günther Pass, Lars Podsiadlowski, Hans Pohl, Björn M. von Reumont, Kai Schütte, Kaoru Sekiya, Shota Shimizu, Adam Slipinski, Alexandros Stamatakis, Wenhui Song, Xu Su, Nikolaus U. Szucsich, Meihua Tan, Xuemei Tan, Min Tang, Jingbo Tang, Gerald Timelthaler, Shigekazu Tomizuka, Michelle Trautwein, Xiaoli Tong, Toshiki Uchifune, Manfred G. Walzl, Brian M. Wiegmann, Jeanne Wilbrandt, Benjamin Wipfler, Thomas K. F. Wong, Qiong Wu, Gengxiong Wu, Yinlong Xie, Shenzhou Yang, Qing Yang, David K. Yeates, Kazunori Yoshizawa, Qing Zhang, Rui Zhang, Wenwei Zhang, Yunhui Zhang, Jing Zhao, Chengran Zhou, Lili Zhou, Tanja Ziesmann, Shijie Zou, Yingrui Li, Xun Xu, Yong Zhang, Huanming Yang, Jian Wang, Jun Wang, Karl M. Kjer, Xin Zhou (2014): Phylogenomics resolves the timing and pattern of insect evolution. - Science 346 ( 6210): 763-767.

[more]

Links:

1KITE - Project @ ZFMK
Abstract
Reprint
Full text

LANFEAR, R., CALCOTT, B., KAINER, D., MAYER, C. AND STAMATAKIS, A. (2014) Selecting optimal partitioning schemes for phylogenomic datasets, BMC evolutionary biology, 14(1), p. 82.

[more]

Links:

Link - PDF

Manosh Kumar Biswas, Qiang Xu, Christoph Mayer, Xiuxin Deng (2014):Genome wide characterization of short tandem repeat markers in sweet orange (Citrus sinensis), 9 (8):e104182

[more]

Peters, R.S.*, Meusemann, K.*, Petersen, M., Mayer, C., Wilbrandt, J., Ziesmann, T., Donath, A., et al. (2014): The evolutionary history of holometabolous insects inferred from transcriptome-based phylogeny and comprehensive morphological data. BMC Evolutionary Biology 14:52 http://www.biomedcentral.com/1471-2148/14/52 * equal contributors

[more]

Links:

Link - PDF

2013

DAMBACH J., RAUPACH M.J., MAYER, C. SCHWARZER, J. and LEESE, F. (2013) Isolation and characterization of nine polymorphic microsatellite markers for the deep-sea shrimp Nematocarcinus lanceopes (Crustacea: Decapoda: Caridea) BMC Research Notes 2013, 6:75

[more]

Meusemann, K., Peters, R.S., Petersen, M., Donath, A., Niehuis, O., Mayer, C., Aspöck, U. et al. (2013): Phylogeny of the holometabolous insect orders – new insights from transcriptomes and morphology. BioSyst.EU 2013 Global systematics! 18-22 February 2013 Abstract volume: 139-140.

[more]

Niehuis, O., Sann, M., Mayer, C., Meusemann, K., Donath, A., Peters, R.S., Bleidorn, C., Ohl, M. (2013): Potential and limits of the 1KITE transcript data for facilitating the application of DNA enrichment protocols in insect phylogenetics. Abstract Volume 6th Dresden Meeting on Insect Phylogeny.

[more]

READ, B.A., KEGEL, J., KLUTE, M.J., KUO, A., LEFEBVRE, S.C., MAUMUS, F., MAYER, C., MILLER, J., MONIER, A., SALAMOV, A., YOUNG, J., AGUILAR, M., CLAVERIE, J.M., FRICKENHAUS, S., GONZALEZ, K., HERMAN, E.K., LIN, Y.C., NAPIER, J., OGATA, H., SARNO, A.F., et al. (2013) Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature 499, 209–213 (11 July 2013)

[more]

Stemmer, K., Burghardt, I., Mayer, C., Reinicke, G., Wägele, H., Tollrian, R., Leese, F. (2013) Morphological and genetic analyses of xeniid soft coral diversity (Octocorallia; Alcyonacea), Organisms Diversity & Evolution 13(2): 135-150.

[more]

Documents:

stemmer_et_al_2013_ode_xeniidae.pdf

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Dr. Christoph Mayer

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Field of work

Research interests

Further information

2021

The impact of mutualistic and parasitic life histories on butterfly diversification in an increasingly arid world

2020

Utilizing environmental genomics to study multiple agricultural stressor impacts on stream invertebrates and ecosystem functions

2018

Establishing a standardized and universally applicable set of nuclear-encoded markers for genome-wide multi-locus species delimitation of metazoans

2017

Sequencing museum material

2012

Identification of sources of error in molecular phylogenetic analyses

1KITE: The evolution of the insects

2009

The legacy of the Southern Ocean

2017

2016

2015

2014

2013

Pages

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Dr. Christoph Mayer

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Field of work

Research interests

Further information

2021

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2018

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2012

2009

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2017

2016

2015

2014

2013

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