Population genetics, biogeographical, evolutionary and systematics research are all based on analyses of the genetic material DNA and its products. In the Molecular Genetics Laboratories, DNA is isolated, purified and amplified for examination. The working copies of DNA, the information carrier RNA, can also be isolated and used for synthesis of complementary DNA (cDNA). DNA and RNA are prepared for the applied methods of genome and transcriptome analyses.
To produce the necessary quantities of material, DNA segments are amplified in a process called polymerase chain reaction (PCR). In the laboratories, the three areas pre-PCR, PCR, and post-PCR are spatially separated to prevent contamination of samples with unwanted DNA. DNA from very old material can be isolated and processed in the so-called Ancient-DNA Laboratory, which is specifically designed to prevent contamination of the material under study with “foreign” DNA.
The analytical methods include Sanger sequencing and investigations of microsatellites. The Molecular Genetics Facilities are closely interlinked with the Integrated Zoological Research Laboratory.
Methodology (Selection):
- DNA isolation (manual and automated)
- RNA extraction/mRNA enrichment
- cDNA synthesis
- PCR
- Library Preparation for NGS Sequencing
- Fragment analysis (microsatellites)
- Spectrophotometry and fluorescence measurements
Equipment (selection):
Qiagen Biosprint 96
Based on magnetic particle technology and used for automated isolation of genomic DNA
Agilent Bioanalyzer
For chip-based high-resolution fragment analysis of DNA, RNA and proteins. Used for quality control of next-generation sequencing libraries as well as RNA and DNA extractions
NanoDrop (UV-Vis spectrophotometer)
Used to determine the concentration of nucleic acids in a micro volume range using UV-Vis spectrophotometry
Qubit 2.0 (Fluorometer)
Benchtop fluorometer for quantifying low concentrations of DNA/RNA
LI-COR (DNA Analyzer)
Used for DNA sequencing and microsatellite analysis
ABI 3130xl (Genetic Analyzer)
16-capillary sequencer for Sanger sequencing, microsatellite, and fragment analysis
Biomek 4000 (pipetting robot)
Liquid handler for automated pipetting
Applications:
Genomic and transcriptome analyses
Advanced methods allow for sequencing of large parts of genomes beyond individual genes. For instance, by combining expression and phylostratigraphic analyses, it was possible to identify the first radula-forming tissue transcriptome in the viviparous freshwater snail Tylomelania sarasinorum. The radula (rasping tongue) is the central food intake organ and a peculiarity of molluscs. The gene expression of radula tissue is very specific, but more similar to the mantle than to the foot. The results also show that the genetic basis of both radula and shell formation was formed by novel orchestration of existing genes as well as continuous evolution of new genes. A significantly increased proportion of radula-specific genes has emerged since the stem molluscs evolved, suggesting that novel genes for radula development were particularly important.
Publication:
Leon Hilgers, Stefanie Hartmann, Michael Hofreiter, Thomas von Rintelen, Novel Genes, Ancient Genes, and Gene Co-Option Contributed to the Genetic Basis of the Radula, a Molluscan Innovation, Molecular Biology and Evolution, Volume 35, Issue 7, July 2018, Pages 1638–1652, https://doi.org/10.1093/molbev/msy052
On the basis of comparative transcriptome analyses of two frog species (Pelophylax lessonae and Silurana tropicalis) LTR retroelements were shown to function as parts of complex genetic networks and, contrary to earlier assumptions, are not ’junk DNA‘ or ’harmful genomic parasites’.
Publication:
Grau, J., Poustka, A., Meixner, M., Plötner, J. (2014): LTR retroelements are intrinsic components of transcriptional networks in frogs. BMC Genomics 201415:626
https://doi.org/10.1186/1471-2164-15-626
Studies on bats
Molecular genetic studies on bats (Chiroptera) are a focus of our work. The genetic structure of a bat species complex (Myotis nattereri sensu lato) common in the western Palearctic was analysed using mitochondrial and nuclear DNA. The results allow for assessing the systematics and protection status of genetically distinct lineages.
Publication:
Çoraman, E, Dietz, C, Hempel, E, et al. Reticulate evolutionary history of a Western Palaearctic Bat Complex explained by multiple mtDNA introgressions in secondary contacts. J Biogeogr. 2019; 46: 343– 354.
https://doi.org/10.1111/jbi.13509
In another project, mother-offspring groups were identified based on microsatellites in nursery colonies of the noctule bat (Nyctalus noctula). Their social behaviour was analysed using novel tracking sensors. The results showed that mothers guide their young to new quarters and thus secure social cohesion. This form of maternal care has not been observed in bats before.
Publication:
Ripperger, S., Günther, L., Wieser, H., Duda, N., Hierold, M., Cassens, B., Kapitza, R., Koelpin, A. & Mayer, F. 2019 Proximity sensors on common noctule bats reveal evidence that mothers guide juveniles to roosts but not food. Biol. Lett. 15, 20180884. (doi:10.1098/rsbl.2018.0884).
https://doi.org/10.1098/rsbl.2018.0884
Project:
BATS (German)
Hybridisation and polyploidisation in European water frogs
Water frogs (Pelophylax esculentus complex) are a suitable model to study speciation processes including hybridization and polyploidisation. Based on molecular data (microsatellites, mtDNA) the edible frog (Pelophylax esculentus), a hybrid form originally derived from crossings between the pool frog (P. lessonae) and the marsh frog (P. ridibundus), was shown to have developed several times independently. Compared to edible frogs from Central and Eastern Europe, the genetic variability of the hybrid form is lowest in North-Western Europe. The loss of genetic variability because of post-glacial migration processes is discussed as the cause of this gradient of variability.
Publication:
Hoffmann, A. , Plötner, J. , Pruvost, N. B., Christiansen, D. G., Röthlisberger, S. , Choleva, L. , Mikulíček, P. , Cogălniceanu, D. , Sas‐Kovács, I. , Shabanov, D. , Morozov‐Leonov, S. and Reyer, H. (2015), Genetic diversity and distribution patterns of diploid and polyploid hybrid water frog populations (Pelophylax esculentus complex) across Europe. Mol Ecol, 24: 4371-4391. https://doi.org/10.1111/mec.13325
Analysis of ancient DNA
Bone detectives in the museum
The analysis of ancient DNA from collection material is a common task at the Molecular Genetics Laboratories. In addition to the analysis of the genetic material of extinct species, molecular data can also contribute to the identification and classification of collection material. For instance, during the bomb attacks of the Second World War, a holotype skeleton of the Sei whale (Balaenoptera borealis) was scattered. Through extensive research and investigations, including examinations of DNA from bone material, skeletal parts, including the skull, have been identified as parts of the holotype.
Publication:
Haberland, C., Hampe, O., Autenrieth, M., et al. (2018). Balaenoptera borealis Lesson, 1828: rediscovery of a holotype. Mammalia, 0(0), pp.
https://doi.org/10.1515/mammalia-2017-0149
From wild boar to domestic pig
Over the past 100 years, pig breeding has focused on high meat yields. In a joint project, researchers from the Martin-Luther-Universität Halle-Wittenberg, the Leibniz Institute for Farm Animal Biology in Dummersdorf, and the Museum für Naturkunde investigate the genomic changes induced by human-controlled selection, studying the two breeds German Large White and German Landrace in comparison to wild boars, the ancestral species of domestic pigs. DNA samples from old bones of these breeds from the scientific collections of the Museum für Haustierkunde “Julius Kühn” and the Museum für Naturkunde Berlin are analysed.
Identification and description of species
DNA analysis is increasingly used in species descriptions and systematics revisions. Recently, an international team of researchers, including scientists from the Museum für Naturkunde, discovered a snake species in North-Western Liberia and South-Eastern Guinea that was named Atractaspis branchi in honour of the late South African reptile researcher Professor William Roy Branch. In addition to morphological features, mitochondrial DNA data were part of the species description.
Publication:
Rödel M, Kucharzewski C, Mahlow K, Chirio L, Pauwels OSG, Carlino P, Sambolah G, Glos J (2019) A new stiletto snake (Lamprophiidae, Atractaspidinae, Atractaspis) from Liberia and Guinea, West Africa. Zoosystematics and Evolution 95(1): 107-123.
https://doi.org/10.3897/zse.95.31488