Centre for Molecular Biodiversity Research (ZMB)

2020

[112]

CaBOL - Caucasus Barcode of Life [112]

A Georgian-Armenian-German initiative to build research infrastructures and to explore and barcode the biodiversity of the Caucasus

Project lead:

Funding:

Federal Ministry of Education and Research

[113]

GBOL III: Dark Taxa [113]

The BMBF-funded GBOL, the German Barcode of Life initiative, has been run successfully over the last eight years. It delivered an operative DNA barcode reference library for German animals, fungi and plants. However, a significant proportion of insect taxa has so far been excluded from GBOL and merely all biodiversity research, because no or only very insufficient expertise and information are available that allow to get a grip on them. They are called “Dark Taxa”.

Project lead:

Dr. Ralph S. Peters [114]

Funding:

Federal Ministry of Education and Research

2019

[115]

FOGS - Forensic Genetics for Species Protection [115]

The FOGS project develops DNA-based tools to combat illegal trade in protected animal species.

Project lead:

Funding:

Federal Ministry of Education and Research

[116]

Bombus terrestris genome [116]

Using long read sequencing of DNA and RNA we will improve the genome sequence assembly and annotation of the bufftailed bumblebee Bombus terrestris.

Project lead:

Dr. Eckart Stolle [38]

Funding:

European Union

[117]

Defense systems of Chromodorididae [117]

Chromodorididae is a sea slug group known for the most colorful members. The aposematic coloration is usually discussed in the light of their toxicity. While feeding on sponges, they take up the toxic compounds and store them in special structures along the notum margin. They are used as defense against predators, like fish or crabs. We investigate the evolution and efficiency of these so-called mantle dermal formations within Chromodorididae

Project lead:

Funding:

Federal Ministry of Education and Research, German Academic Exchange Service

[118]

DINA – Diversity of Insects in Nature Protected Areas [118]

In collaboration with the German NABU the ZFMK has been an active partner to initiate a large joint project to understand drivers of insect decline, the DINA project (2019-2022). The goal of the project is to assess and monitor the insect fauna in 21 selected Nature-protected areas using a Malaise trap transect approach. A particular goal of this project is to demonstrate the power of metabarcoding for the rapid and efficient assessment of the insect fauna relying on the GBOL database. Additionally to the insect fauna, landscape parameters including anthropogenic influence will be recorded.

Project lead:

Dr. Livia Schäffler [119]

Funding:

Federal Ministry of Education and Research

[120]

Joint Danube Survey [120]

JDS monitors key water quality elements (including biodiversity) for the length of the Danube River and its major tributaries.

Project lead:

[121]

APPETITE [121]

APPETITE is a new automated process-pipeline for molecular phylogenetic purposes with nearly endless analytical possibilities. APPETITE

Project lead:

[122]

DNA barcoding of benthic invertebrates from Lake Sevan (Armenia) [122]

Building a reference database of DNA barcodes for the Lake Sevan drainage basin

Project lead:

Funding:

German Academic Exchange Service

[123]

End biodiversity loss through improved tracking of threatened invertebrates [123]

In today’s biodiversity crisis, there is an urgent need to monitor terrestrial and aquatic species in their natural habitats, especially those that may be endangered, invasive or elusive. Traditional species observation methods, based on acoustic or observational surveys are inefficient, costly and time consuming. On the other hand, DNA is continuously deposited in the environment from natural processes and this environmental DNA (eDNA) allows us to detect species and reconstruct their communities with a high level of sensitivity.

Project lead:

Dr. Sarah Bourlat [31]

[124]

Integrative Analysis of the influence of pesticides and land use on biodiversity in Germany (INPEDIV) [124]

The interdisciplinary joint project INPEDIV is funded for 3 years by the Leibniz Competition (March 2019 – February 2022). The aim of this study is to investigate consequences of organic and conventional farming for biodiversity in protected areas. By use of traditional methods and new technologies, we will examine agricultural land use effects on a broad range of plant and animal taxa across trophic levels at study sites in the Rhineland and in Brandenburg.

Project lead:

Dr. Livia Schäffler [119]

Funding:

Leibniz Association

[125]

Evolution of Ninetinae [125]

This project focuses on the spider subfamily Ninetinae, tiny cryptic ground-dwellers that are largely restricted to arid habitats. They seem to be ‘basal’ within Pholcidae and thus crucial for reconstructing the evolutionary history of the family.

Project lead:

Dr. Bernhard A. Huber [126]

Funding:

Deutsche Forschungsgemeinschaft

[127]

SYNTHESYS+ NA3.1 [127]

SYNTHESYS+ subproject NA3.1 collects existing standards and practices in the biodiversity and environmental biobanking community and identifies gaps.

Project lead:

Funding:

European Union

2018

[128]

Establishing a standardized and universally applicable set of nuclear-encoded markers for genome-wide multi-locus species delimitation of metazoans [128]

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).

Project lead:

Dr. Dirk Ahrens [129]

Funding:

Deutsche Forschungsgemeinschaft

[130]

Biodiversity of Phyllidiidae in Indonesia [130]

Phyllidiidae is one of the most common sea slug groups in tropical marine habitats. Because of their colors and wide distribution, they are well known to divers. They are also of interest for pharmaceutical research because of their toxic compounds, which they extract from their sponge food. However, little is known about their relationships and especially cryptic speciation within the genera and species. We investigate the biodiversity of these sea slugs in North Sulawesi (Indonesia) and try to clarify the pyhlogenetic relationships within some genera.

Project lead:

[131]

Sherlock [131]

Sherlock is an automated process pipeline for statistical evaluation of patristic tree-distance variation given partitioned or non-partitioned molecular sequence data.

Project lead:

[132]

Apollo population genomics [132]

Parnassius apollo (Papilionidae) is an iconic butterfly species with a wide distribution from Spain to China. The distribution is, however, very spotwise, and e.g. in Germany only a few populations remain. It is the only non-tropical butterfly protected under the CITES The goal of this project is to use whole genome sequencing to investigate the genetic diversity of Parnassius apollo across space and time. To do this we will use both fresh and museum specimens collected across the range of the species, and during the last 120 years.

Project lead:

Dr. Marianne Espeland [108]

Funding:

Zoological Research Museum Alexander Koenig

[133]

ISBER Best Practices: Recommendations for Repositories [133]

Guidance for the collection, handling, storage, and distribution of biological and environmental samples

Project lead:

[134]

Cell banking at the ZFMK Biobank [134]

ZFMK Biobank archives viable cell material for research and ex-situ conservation.

Project lead:

[135]

Plant-pollinator networks in agro-ecosystems [135]

Pollination is crucial for maintaining angiosperm biodiversity and represents one of the most important ecosystem services. With the increasing threats of massive insect decline, studying pollination and associated networks has become more important than ever. In this study, we target the plant-pollinator networks of two important crops (caraway and apple) using a combination of traditional methods with DNA barcoding and metabarcoding.

Project lead:

Prof. Dr. J. Wolfgang Wägele [136]

Funding:

Federal Ministry of Education and Research, Zoological Research Museum Alexander Koenig

2017

[137]

GGBC: Assessment, Monitoring and Management of Caucasian Biodiversity [137]

A Georgian-German initiative to explore and barcode the biodiversity of the Caucasus area

Project lead:

Funding:

Federal Ministry of Education and Research

[138]

AG RICEFISH [138]

The focus of the proposed research group is to study the link between genotype and phenotype of evolutionary adaptive traits, a vital question of evolutionary biology in the postgenomic era. The group will study the morphological and genomic basis of a unique reproduction strategy in Sulawesi ricefishes (Actinopterygii: Adrianichthyidae) called “pelvic brooding”. In pelvic brooding species, females carry the eggs in an abdominal concavity until they hatch, which is assumed to be an adaptation to a predominantly pelagic lifestyle.

Project lead:

Dr. Julia Schwarzer [57]

Funding:

Leibniz Association

[139]

Sequencing museum material [139]

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.

Project lead:

Dr. Marianne Espeland [108]

Funding:

Zoological Research Museum Alexander Koenig

[140]

Evolution of Dexiarchia [140]

The sea slugs of the subgroup Dexiarchia comprise at least 2,000 different species and many more undescribed members. Until today there exists no phylogenetic analysis of Dexiarchia that comprises all major families and corroborates the relationships within this group, which is the aim of our project.

Project lead:

Funding:

Deutsche Forschungsgemeinschaft

[141]

Optimizing and standardizing the preservation of animal tissue for molecular biodiversity research [141]

Towards establishing a clearer, comparative perspective on some of the most commonly used preservation/fixation fluids in zoological biobanking.

Project lead:

2016

[142]

The collections - a cosmos [142]

Maria Gräfin von Linden became the first woman to be made a titular Professor in Germany in 1910

Project lead:

Dr. Katharina Schmidt-Loske [143]

Funding:

Federal Ministry of Education and Research

[144]

3D AMP [144]

This plugin works with ImageJ and Fiji. You can use most kinds of (hyper)stacks with one or more channels in the commonimage formats.

Project lead:

Jörg Adrian [145]

[146]

Biodiversity of Heterobranc... [146]

Biodiversity of marine heterobranchs of South Iranian shore lines and the Persian Gulf

Project lead:

Funding:

Alexander-Koenig-Society e.V.

2015

[147]

Sound library of the Western Rock Nuthatch [147]

In this project, we are creating high-quality sound libraries to facilitate the subsequent development of an automated sound recognizer for the Western Rock Nuthatch Sitta neumayer.

Project lead:

Dr. Till Töpfer [148]

Funding:

Alexander-Koenig-Society e.V.

[149]

Opisthobranch Biodiversity in Indonesia [149]

The Indonesian coastline is characterized by an extremely high biodiversity. This project focusses on a specific bio-system, i.e. Opisthobranchia, their prey organisms, and the associated microorganisms. Based on our knowledge on systematics and ecology of these organisms, the final goal is to identify new drug leads for antibiotics development in a cooperation with colleagues from the Pharmaceutical Biology of the university of Bonn. Sea slugs, forced by the absence of a protective shell, developed highly specialized defense strategies to protect their sensitive epidermis against micro and small organisms, as well as larger predators like fish and crabs. Especially chemical substances fulfill this protective role.

Project lead:

Funding:

Federal Ministry of Education and Research

2014

[150]

Countering Systematic Bias in Phylogenetics [150]

PhyQuart, a new algorithm combining Hennigian logic and Maximum Likelihood estimation, represents a completely new strategy for the evaluation of molecular data based on a site pattern classification for quartets of aligned sequences.

Project lead:

Funding:

Zoological Research Museum Alexander Koenig, European Union

[151]

Incorporation of chloroplasts in Sacoglossa [151]

Some sea slugs incorporate chloroplasts from their algal food in their own body and perform photosynthesis with these „cleptoplastids“. They survive weeks to months without any further food uptake.

Project lead:

Funding:

Deutsche Forschungsgemeinschaft

[152]

Bumbuna Phase II Project [152]

Baseline Study and Ecological Monitoring before and after the inundation of the Bumbuna Hydroelectric Project Reservoir.

Project lead:

Dr. Jan Decher [153]

Funding:

Combined Ecology, BTO Services Ltd., UK

[154]

Island speciation within the… [154]

Landsnails of the genus Theba show an endemic radiation on the Canary Islands and the adjacent West African Continent.

Project lead:

[155]

Immunobiology of the marine… [155]

Investigation of the innate immune system of the heterobranch genus Aplysia.

Project lead:

Funding:

Zoological Research Museum Alexander Koenig

[156]

Evolution of defense strategies in sea slugs [156]

Sea slugs have lost their protective shell and evolved alternative defense strategies against predators (toxins, acids, needles, etc). We investigate these strategies

Project lead:

Funding:

Deutsche Forschungsgemeinschaft

[157]

Evolution of Photosynthesis in Sacoglossa [157]

The loss of the shell in sea slugs enabled the evolution of photosynthetic capability within some groups, but also enforced the evolution of alternative defense strategies. We investigate the origin and efficiency of these various strategies.

Project lead:

Funding:

Deutsche Forschungsgemeinschaft, Zoological Research Museum Alexander Koenig, Alexander-Koenig-Society e.V.

[158]

ESBB & ISBER Enviro-Bio Working Group [158]

The Enviro-Bio Working Group is a collaboration of biodiversity biobanks within ISBER and ESBB, the international and European biobanking societies.

Project lead:

2013

[159]

GFBio [159]

Environmental and biological research is becoming central to major societal challenges related to the Earth’s ecosystems and climate dynamics. To handle the scale and complexity of the scientificquestions being addressed, there is a strong need to integrate knowledge because biological data are currently scattered and difficult to share.

Project lead:

Dr. Peter Grobe [160]

Funding:

Deutsche Forschungsgemeinschaft

[161]

Gene repertoire Characterization [161]

Comparative genomics is in its infancy. Genome sequencing just now generates the data to compare not only model organisms and vertebrates but to actually assess biodiversity. Explaining biodiversity relies on an understanding of underlying mechanisms of genome evolution, which in turn is based on a thorough knowledge of genomic characters and the driving forces shaping them.

Project lead:

Funding:

Deutsche Forschungsgemeinschaft

[162]

FASconCAT-G: extensive alignment preparations [162]

FASconCAT-G offers a wide range of possibilities to edit and concatenate multiple nucleotide, amino acid, and structure sequence alignment files for phylogenetic and population genetic purposes. The main options include sequence renaming, file format conversion, sequence translation, consensus generation of predefined sequence blocks, and RY coding as well as site exclusions in nucleotide sequences and the generation of partitioned files for MrBayes and RAxML analyses.

Project lead:

Funding:

Zoological Research Museum Alexander Koenig

[163]

AliGROOVE – visualization of heterogeneous sequence divergence [163]

AliGROOVE determines and visualizes the content of potentially randomized sequence similarities and alignment ambiguities in multiple sequence alignments.The AliGROOVE algorithm is an adaptation of the recently published ALISCORE masking algorithm (Misof & Misof, 2009, Kück et al., 2010). AliGROOVE summarizes site scores of profiles of sequence similarity normalized over the whole alignment length from each pairwise comparison and translates the obtained scoring distances between sequences into a similarity Matrix

Project lead:

Funding:

Zoological Research Museum Alexander Koenig

[164]

BaCoCa – assessment of sequence biases [164]

BaCoCa is designed to perform multiple statistical analyses on multiple nucleotide and amino-acid sequence alignments. The results of the BaCoCa analyses can be used for a detailed and statistical comprehensive data evaluation. Furthermore, the results can help to identify phylogenetic sequence biases which can lead to incorrect tree reconstructions.The program can handle hundreds of user specified gene and taxon partitions of a single sequence input file in one process run. BaCoCa is a command-line driven program written in Perl and works on WindowsPCs, Macs and Linux running systems.

Project lead:

Funding:

Zoological Research Museum Alexander Koenig

2012

[165]

Selection of Optimal Subsets… [165]

In phylogenomics character matrices with extensive missing data are frequently used. These missing data have potentially detrimental effects on the accuracy and robustness of tree inference. Therefore, many investigators select taxa and genes with high data coverage.

Project lead:

[166]

Identification of sources of error in molecular phylogenetic analyses [166]

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.

Project lead:

Funding:

Zoological Research Museum Alexander Koenig

[167]

Phylogenetic position of… [167]

Project lead:

Dr. Torsten Struck [91]

Funding:

Deutsche Forschungsgemeinschaft

[168]

Leaf beetles - Chrysomelidae [168]

Transcriptome analysis of leaf beetles.

Project lead:

Funding:

University of Hamburg

[169]

Frozen Ark Project [169]

Network for ex-situ conservation of molecular biodiversity

Project lead:

[170]

Global Genome Biodiversity Network (GGBN) [170]

Establishing standards for the preservation of molecular samples and molecular biodiversity.

Project lead:

[171]

1KITE: The evolution of the insects [171]

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…

Project lead:

2011

[172]

GBOL- German Barcode of Life [172]

"German Barcode of Life" ( GBOL ) is a project sponsored by the BMBF and includes the creation of inventories for the gentic characterization of the animals, fungi and plants of germany, using DNA-Barcodes.

Project lead:

Prof. Dr. J. Wolfgang Wägele [136]

Funding:

Federal Ministry of Education and Research

[173]

Molecular Weevil Identification [173]

DNA barcoding the European weevil fauna and building molecular and morphological weevil collections

Project lead:

[174]

Sacoglossa-Evolution of their… [174]

Project lead:

Funding:

Deutsche Forschungsgemeinschaft

[175]

AnnEvol - Evolution and… [175]

Project lead:

Dr. Torsten Struck [91]

Funding:

Deutsche Forschungsgemeinschaft

[176]

Trachysphaera Dwarf Pill Millipedes in the UK [176]

Less than 30 years ago, an isolated population of thwe dwarf pill millipede genus Trachysphaera was discovered on the English Isle of Wight, which were tentatively identified as T. lobata (Ribaut, 1954), albeit male specimens were lacking (Joes & Keay 1986 ). T. lobata is a species known mainly from SE France (Kime & Enghoff 2011), and is difficult to distinguish from four other little known Trachysphaera species occurring at the Spanish-French border, which are above all the very similar T. pyrenaica (Ribaut, 1907), as well as the little known T. rousseti (Demange, 1959), T.

Project lead:

Dr. Thomas Wesener [177]

[178]

FREDIE - Freshwater Diversity… [178]

Freshwater Diversity Identification for Europe: Barcoding all European freshwater fishes, freshwater molluscs and mayflies.

Project lead:

PD Dr. Fabian Herder [179]

Funding:

Leibniz Association

[180]

Fluoreszenzmicroscopical and… [180]

Project lead:

Funding:

Alexander Koenig Stiftung, Alexander-Koenig-Society e.V.

[181]

Automated masking of AFLP markers [181]

AMARE is designed to optimize the signal-to-noise ratio in AFLP data sets (single or multiple primer combinations). It identifies potentially erroneous AFLP genotyping errors as the number of non-reproducible scored markers between replicated AFLP profiles of single individuals. As a measure of overall data quality, it simultaneously estimates general replicate error rates.

Project lead:

Funding:

Zoological Research Museum Alexander Koenig

2010

[182]

The evolution of… [182]

We try to reconstruct a robust backbone tree of holometabolous insects based on extensive transcriptome/genome data. With our transcriptome data we cover all orders within these group of insects and optimize the procedures of tree inference based on these data. Additionally, Rolf Beutel's group is providing extensive 3D morphological data of head, thorax and abdominal structures. Together we are working on the most extensive morphological and molecular data addressing the above mentioned phylogenetic questions. Within this project we have also started to specifically address the "Strepsiptera…

Project lead:

Funding:

Deutsche Forschungsgemeinschaft

[183]

FASconCAT - convenient handling of data matrices [183]

FASconCAT is a user-friendly software that concatenates rapidly different kinds of sequence data into one supermatrix file.

Project lead:

Funding:

Zoological Research Museum Alexander Koenig

2009

[184]

The Atelocerata - a vanishing… [184]

Project lead:

Funding:

Deutsche Forschungsgemeinschaft

[185]

The legacy of the Southern Ocean [185]

Project lead:

Dr. Christoph Mayer [36]

Funding:

Deutsche Forschungsgemeinschaft

[186]

ALISCORE - Masking of Multiple Sequence Alignments [186]

Random similarity of sequences or sequence sections can impede phylogenetic analyses or the identification of gene homologies.

Project lead:

Funding:

Zoological Research Museum Alexander Koenig

[187]

MITOS [187]

A metazoan mitochondrial genome annotation server.

Project lead:

Funding:

Deutsche Forschungsgemeinschaft, German Academic Exchange Service, University of Strasbourg, ANR MITOMOT, Alexander von Humboldt-Foundation

2008

[188]

Sacoglossa [188]

Project lead:

Funding:

Deutsche Forschungsgemeinschaft

2007

[189]

Secondary Metabolites of… [189]

Project lead:

Funding:

Deutsche Forschungsgemeinschaft

[190]

DNA Bank Network [190]

Project lead:

Funding:

Deutsche Forschungsgemeinschaft

[191]

Diversification in space and… [191]

Project lead:

Funding:

Deutsche Forschungsgemeinschaft

[192]

Integrative taxonomy in cryptic weevils [192]

Integrative taxonomy and DNA barcoding in western Palearctic weevils of the subfamily Cryptorhynchinae

Project lead: