Conservation Genetics


Research priorities

Our research focuses on

  • the development of new methods for genetic wildlife monitoring
  • the application of molecular genetic procedures for wildlife monitoring and the determination of population genetic patterns of threatened species
  • the impact of genetic factors on the survival capability of natural populations, as well as the impact of anthropogenic environmental changes on the genetic structure.

Regarding the development of methods, we focus on the change from the conventional microsatellites to modern SNP marker systems, the establishment and optimisation of species identification based on environmental samples (eDNA), and the development of genotype databases. Genetic marker systems are applied for the detection of rare and elusive species, the reconstruction of dispersal pathways and gene flow patterns, as well as for the determination of introgression rates in mammals, insects, and other groups. Experimental populations of Chironomus riparius are our main model organisms for analysing genetic threats (e.g. inbreeding, genetic impoverishment). The analyses are conducted in close cooperation with BiK-F and external partners.

Our projects are financed with funds for fundamental research (DFG, LOEWE, SAW funding scheme of the Leibniz Association, Portuguese Science Foundation), as well as through cooperation with authorities (e.g. BMU, BfN, HMUELV, SMUL, MUGV, LfU) and conservation organisations (including BUND, BN, ZGF, WWF, RSPB).

On this page, you get an exemplary overview of some of our research priorities. If you are interested in cooperation regarding the genetic analysis of wildlife, click here, write us an email to or call us on +49 6051-619543138.

In the following you will find our most important projects.

Development of SNP-based marker systems for wildlife

Inferring genetic patterns of ongoing recolonization of Central Europe by elusive, large carnivores using novel SNP marker systems for noninvasive samples

The currently observed recolonisation of Central and Western Europe by previously near-extinct carnivores is an important topic for science and society. A detailed, cross-border knowledge about migration routes population growth and gene flow patterns are important for comprehensive wildlife monitoring, and are also the foundation for the scientific analysis of this natural experiment about the coexistence between large carnivores and humans in densely populated areas.

The project
The aim of the SAW project is the establishment of a competence network for the development of novel genetic markers systems for studying endangered European carnivores. To meet this aim we first analyse variable nucleotide positions (single nucleotide polymorphisms; SNPs) in the genome of five large carnivores (brown bear, Eurasian otter, wolf, lynx, wildcat) by next generation sequencing or large scale SNP chips. These markers are tested for their variability across European populations by data base queries. In parallel, we investigate different SNP genotyping technologies for their applicability for non-invasively collected sample material. The final marker systems will be tested on multiple populations of each species and compared with the results of other methods. By means of genotyping of samples from Central and Eastern Europe we will study general genetic diversity, gene flow and the impact of landscape genetic factors, in order to identify the genetic patterns of Europe’s recolonisation. All data will be stored in a genetic data base to facilitate future projects and search queries with regard to the origin of samples of unknown status, and thereby deciphering large-scale gene flow.

Project partners
Marker development and population genetic analyses are carried out cooperatively by the three primary project partners Senckenberg (Dr. Carsten Nowak, Dr. Robert Kraus), Leibniz Institute for Zoo and Wildlife Research (Dr. Jörns Fickel, Dr. Daniel Förster), and TU Munich (Prof. Dr. Ralph Kühn, Dipl.-Biol. Helmut Bayerl). The combination of the aforementioned factors – joint expertise, development of standardised marker systems and installation of a genetic data base – allows the inference of dispersal patterns, isolation factors, and distribution shifts across multiple studies on scales that surpass single, regional studies.

Genetic monitoring of the wildcat

Since 2006 mitochondrial DNA sequencing of hair samples was used to delineate wildcat from domestic cat in the Senckenberg Conservation Genetics Lab. Early 2009 we added microsatellite analysis in order to allow for individual assignment, hybrid detection and fine-scale analysis of population divergence, reproductive isolation and the identification of landscape barriers. So far we have analysed several thousands of hair samples collected from valerian-treated lure sticks in Germany, Luxemburg, Austria and further regions. These data have reshaped the known distribution range of wildcats in central Europe and have led to the discovery of wildcat presence in numerous regions, such as the Kellerwald-Edersee National Park and UNESCO world heritage site, the Rhön mountains, the Steiermark region in Austria or in Saxony.  Moreover, we estimate population size of regional populations and have estimated the effects of major landscape elements, such as the Rhine river valley or the Autobahn A3 in Germany (Hartmann et al., 2013). Our analyses are done in close cooperation with the BUND (Friends of the Earth Germany). 

Kathrin and Annika conduct the wildcat research in the frame of their PhD projects, and Susanne, Dino, and Mascha conduct lab analyses, sample logistics, and help in methodological improvements.
The wildcat
The European wildcat serves as flagship species for the conservation of unfragmented, near-natural broad-leave forests. Historic persection  as well as habitat loss and fragmentation has led to a severe population decline. Since the second half of the 20th century, the wildcat is expanding in Germany. Data on wildcat presence was, however, only sparely distributed, due to the elusiveness of this species and the difficulty to discriminate it from its domestic form –  wildcats show well-distinct black tail-rings, 4-5 black stripes on their neck, and a blurred stripe pattern at the flanks, which is best visible around the shoulders (Krüger et al. 2009). Road kills are analysed by morphometric determination of skull and gut size.

Krüger, M., Hertwig ST, Jetschke G, Fischer MS (2009) Evaluation of anatomical characters and the question of hybridization with domestic cats in the wildcat population of Thuringia, Germany. Journal of Zoological Systematics and Evolutionary Research 47: 268-282.

Lure stick method
The lure stick method (Simon and Hupe, 2007; Steyer et al., 2013) allows for simple and effective wildcat detection and monitoring. Since its routine implementation in wildcat monitoring activities in Germany it has rapidly expanded the knowledge on wildcat distribution across the country. The method is straightforward: A simple wooden stick (60 cm) is roughened with a steel brush and sharpened on one side. Drive the stick into the ground, so that it stands solid and treat it with valerian extract (from the pharmacy) as scent lure. Cats will be attracted, rub, and leave hairs that can be sampled every few days up to a week.  Check this clip for Kathrin’s charming YouTube instructions. Enjoy! 

DNA analysis of hair samples
Hairs contain low amounts of DNA, mostly in the hair follicle. This DNA has to be preserved and treated with caution until it arrives in the laboratory where we will take care of it. Please consider the following golden rules:

  • Keep hairs dry, humidity leads to rapid DNA degradation, please use our envelopes with silica gel.
  • Sample several hairs with follicles from the lure stick. The more hairs we have the higher is the chance of successful analysis.
  • Do not freeze or cool the hairs in the fridge. Place them at constant room temperature or slightly below, keep samples dark, send them to us asap.
  • Keep samples in a closed bag, to avoid contamination with cat hairs.
  • Transfer hairs with forceps, do not use tape. 

Analysis of mitochondrial DNA haplotypes
Mitochondrial sequence analysis is widely used for species discrimination and identification. DNA-barcoding, for instance, relies on a small stretch of mitochondrial DNA (mtDMA). MtDNA is more frequent in the cell than nuclear (chromosomal) DNA and is therefore easier to extract from hair samples compared to nuclear DNA. MtDNA analysis is often successful with only a single hair, it allows for a reasonable distinction between wild- and domestic cats, but it will not account for the effects of hybridisation nor is it 100% safe. It only reveals the maternal ancestral lineage of a sample, as mtDNA is inherited via the mother’s egg only. A hybrid between a domestic male cat and a wildcat female will show a mitochondrial wildcat haplotype. Moreover, wildcats and domestic cats share some common haplotypes. Thus, we use mtDNA mostly as a fast prescreening to identify potential wildcat samples that can be used for microsatellite analysis.

A genetic fingerprint for cats: microsatellites

A nuclear microsatellite analysis is feasible if a hair sample contains several hairs with bulbs. For this we run 14 variable microsatellite markers and a sex marker with three PCR replicates per hair sample. Fragment lengths of the replicates are compared to exclude genotyping errors and generate a consensus genotype. The resulting genotype information is used to assign individuals, calculate relatedness and assess population structure. Our reference dataset of >500 morphologically checked wild- and domestic cats of various origins ensures safe discrimination of both forms and the identification of hybrids.

In the framework of the following projects, we cooperate with several project partners:

  • Wildcat monitoring in Germany and adjacent regions (several project partners)
  • Wildcat Leap (BUND Friends of the Earth Germany)
  • Monitoring of the wildcat in the Kellerwald-Edersee National Park (Kellerwald-Edersee National Park, Institut für Tierökologie und Naturbildung)
  • Analysis of the population structure and barrier effects on the wildcat in the Rheingau-Taunus Area (Hessen Forst FENA)
  • Regional population structure and reconstruction of  the recolonisation of wildcat habitats in the Rhön (RhönNatur e.V., Rhön Biosphere Reserve)

Options for scientific cooperation
We conduct genetic analyses of hair samples in order to identify and individualise wildcats.

Since the1st of July 2015 the sample form (Excel) cannot be used any more. Please use our online tool:

Important Notes

Please read the information sheets above thoroughly and particularly note the following:

Use of data: We reserve the use of the data that we obtained from your samples for ourselves in the form of presentations and publications. Exceptions from this rule must be discussed in advance of sample processing. The wolf monitoring data remain in the possession of the federal states of Germany.
Online tool: You must use our online tool to place an order.
Options for scientific cooperation

In the framework of scientific cooperation, the Conservation Genetics Section provides the following services regarding the identification and analysis of mammal species:

  • DNA extraction
  • Analysis of mitochondrial DNA
  • Analysis using Microsatellites

National Reference Centre for lynx and wolf

Wolves and lynx regain their former habitats in Germany. In doing so, they are faced with people who have had no practice in dealing with large carnivores for generations. Since the wolves have started to return to the Lausitz, it has become obvious that we need efficient wildlife management in order to facilitate a peaceful coexistence of humans and wildlife. Detailed information about temporal trends in the distribution and abundance of a species are an essential basis for implementing conservation measures. In this project, we develop and establish modern molecular genetic methods for the monitoring of wolves and lynx. The genetic monitoring is based on the use of non-invasively collected sample material, such as scats or hairs. Through highly sensitive genetic procedures such as microsatellite analyses, information about species determination, sex, and population assignment can be obtained. By analysing the genetic structure, we can measure dispersal, migration, genetic fitness, and pack structures. As large carnivores are very elusive and therefore usually cannot be observed, the evidence of species presence achieved through molecular genetic methods is a great asset for the research and conservation of these fascinating animals.

Information regarding the national genetic wolf monitoring at Senckenberg (in German)

The Reference Centre
As a result of an intense, multistage selection process, the German Federal Agency for Nature Conservation (BfN) has selected the Senckenberg Research Institute as the national reference centre. Subsequently, the Ländergemeinschaft Naturschutz (LANA) decided on its conference in Saarbrücken in 2009 to take that advice and use the Senckenberg Research Institute as the “National Reference Centre for Genetic Monitoring of Lynx and Wolves”.

The development and establishment of molecular markers for the genetic wildlife monitoring and identification of carnivore species based on saliva and kills are important parts of our work. Verena, Dino, Susanne, Mascha, Martina, and Carsten are working on this project. Further information about this can be obtained from our poster  “Who killed my sheep?”. 


  • Genetic monitoring of wolves in Germany (federal authorities, Wildbiologisches Büro LUPUS)
  • Genetic monitoring of lynx in Germany (federal authorities, National Park Harz)
  • Analysis of wolf samples from Western Poland (The Association for Nature WOLF) 

Genetic monitoring of the common hamster

During earlier studies at the University of Gießen Tobias established a new method for the non-invasive genetic assessment of Common hamsters (Reiners et al. 2011) and he conducted the first pilot study on genetic hamster monitoring in the region of Hesse/ Germany.

Since early 2012 he has extended the genetic hamster monitoring further, with the ultimate goal to establish the method as a rapid and effective tool for sound hamster monitoring and status assessment.

 Noninvasive hairtrap used for genetic hamster monitoring 
We do currently collect DNA samples and genotype data from hamsters across its Western European range in order to establish a reference centre for Common Hamster genetics at Senckenberg. Until now we have collected a database consisting of >1000 individual hamster genotypes (microsatellites).

Our project partners are: Dr. Ulrich WeinholdInstitut für Faunistik & LUBWJulien Eidenschenk, ONCFS – Elsass Maurice La Haye & Gerard Müskens – Radboug Universität Nimwegen & Alterra Wageningen 

Distribution in Germany and Europe
The Common hamster (Cricetus cricetus L., 1758) is a critically endangered species throughout Western Europe and listed on Annex IV in the European Habitat Directive.  Population decline has been particularly dramatic in its most western distribution edge in The Netherlands, Belgium and France. New data show that currently a similar decline is ongoing in several parts of Central and Eastern Europe

Common Hamster
The Common hamster is the only species within the genus Cricetus. A characteristic is the invert colouring of his fur. Adults may reach a body size of 200-300 mm and weight 200-650 g. Females may reproduce up to three times per season, with clutch sizes of 2-8 youngs. Juveniles reach maturity with a few weeks only and females may reproduce already within the first season.


  • Genetic evaluation of the Dutch captive breeding programmes (Alterra Wageningen & Radboug University Nijmegen)
  • Genetic study on wild and captive-bred common hamsters in Alsace (ONCFS – Office National de la Chasse et de la Faune Sauvage)
  • Genetic monitoring of common hamsters in the Rhein-Neckar County (IFF – Institut für Faunistik, LUBW – Landesanstalt für Umwelt, Messungen und Naturschutz Baden-Württemberg)

Genetic monitoring of the beaver

Since 2010 we have been analysing the genetic structure of beavers in Central Europe. The project was initiated by the local environmental agency of Hesse, aiming for information about the origin of new, isolated beaver occurrences in the region and the unknown subspecies status of these new populations. Since then we have started to collect beaver samples from across various populations in Germany and adjacent regions, aiming to unravel the consequences of multiple, unconcerted reintroduction events in this region. The main task is to answer if a) Central Europe hosts potentially invasive North American beavers (C. canadensis), b) different introduced beaver lineages (“subspecies”) interbreed and form new populations, c) intermixed populations show high genetic diversity compared to the bottlenecked relict populations.

fact sheet for non-invasive genetic beaver sampling (in German)

The beaver and its impact on biodiversity
Beavers are the largest rodents in the northern hemisphere; no species except for humans have a comparably high impact on landscape structure. Their dambuilding and tree cutting activities convert the homogenised, impoverished German landscapes along rivers and creeks into biodiversity hotspots. With these activities beavers help to restore river systems and aid in reversing the human-caused homogenisation of our nature. Unfortunately, we hardly give beavers any space for doing so, as most running waters lack significant floodplain areas and landuse often ends directly at the waterside.

History of Beavers in Germany
The Eurasian beaver (Castor fiber) was brought to extinction across Germany, except for a small relict population along the Elbe river in the federal state Sachsen-Anhalt. Due to strict protection and several successful reintroductions the number of Elbe beavers (Castor fiber albicus) has been constantly increasing since the mid-20th century. However, besides Elbe beavers other beaver lineages were as well used for reintroductions. Bavarian beavers, for instance, are of various origins, such as the Rhone region, Scandinavia and the Voronezh breeding station in Russia.
Results of our genetic beaver studies
The analysis of >250 beavers across Germany and adjacent regions showed that

  • American beavers are restricted to a small area in the border zone of Rheinland-Pfalz, Luxembourg and Belgium.
    different beaver lineages successfully merge in many regions, leading to the disappearance of the classically recognised beaver “subspecies”.
    genetic diversity increases sharply in admixed populations, whereas single relict lineages, such as the Elbe beaver, comprise very low genetic variation.
  • Along with new findings of Horn et al., 2014 (Molecular Ecology), our findings suggest that admixture between different relict population should be generally accepted or even favoured, as single beaver lineages such as the Elbe beaver comprise low levels of genetic variation and form anthropogenic relicts rather that real subspecies.

We provide genetic analysis services for hair and tissue samples in order to individualise beavers and to determine their origin. Clickhere for futher information.

Genetic population structure of the brown bear

The brown bear (Ursus arctos) was once distributed across Eurasia. While the species still occurs over large parts of Russia, European bears persisted only in several scattered populations in remote mountain regions. Within the mountainous Balkan region (e.g. Greece, Serbia, Republic of Macedonia, Bulgaria, Romania), for instance, bears still occur in viable populations. Unfortunately, bear populations are not considered entirely safe. Rapid land use change, deforestation, and growing traffic infrastructure impact bears in previously safe habitats. However, sound wildlife monitoring that may quantify the effects of environmental change on these bear populations will be hard to implement, as proper bear census data as well as reliable data on the delineation of management units are lacking in many regions.

Genetic analysis provides information on population densities and geneflow patterns
In cooperation with several local project partners (e.g. A. Dutsov, Balkani Wildlife Society, Bulgaria; C. Domokos, MILVUS, Romania; A. Karamanlidis, ARCTUROS, Greece) we help to assess the genetic structure of bears in the region. In Bulgaria, for instance, we have genotyped more than 300 samples (scat, hairs, tissue) of bears from all major mountain slopes (Stara Planina, Rhodopen, Pirin, Rila). The analysis resulted in a first census estimation based on solid scientific data. Through the comparison of genotypes obtained from different regions we identify migration corridors, potential barriers to dispersal, and test the validity of the official distinction of bear populations in the region (Dinaric-Pindos, Eastern Balkan, Carpathian) (click here). This knowledge will hopefully help to refine effective bear management and conservation strategies. Project members are Christiane, Carsten, Tobias and Violeta. The activities were financially supported by the Frankfurt Zoological Society and the LIFE programme until 2013. Currently we continue the project on self-funding.

Further information
In our literature list you will find our latest publications from this project (Bidon et al., 2013; Frosch et al., 2011; Frosch et al., 2014; Nowak et al., 2014).

eDNA-based monitoring of aquatic invertebrates (only in German)

Entwicklung von hochsensitiven eDNA-basierten Nachweismethoden für aquatische Arten: Pilotprojekt Krebspest

Was ist eDNA?
Environmental DNA (eDNA) ist DNA, die aus Umweltproben wie beispielsweise Wasser- oder Bodenproben extrahiert werden kann. Sie besteht aus einer komplexen Mischung genomischer DNA von verschiedenen, in den jeweiligen Lebensräumen vorkommenden Organismen. Ein Teil der isolierten eDNA stammt dabei aus lebenden Zellen (intrazelluläre DNA), ein anderer Teil der DNA kommt als freies Molekül im untersuchten Milieu vor (extrazelluläre DNA), welches durch natürliche Prozesse wie beispielsweise einer Abstoßung toten Gewebes (z. B. Schuppen) eines Organismus freigesetzt wurde. Diese DNA kann durch Filterung oder direkte Entnahme von Wasserproben extrahiert werden und über PCR-basierte Methoden auf das Vorhandensein artspezifischer Sequenzmuster abgesucht werden. Im Pilotprojekt testen wir die Eignung von eDNA-basierten Nachweismethoden am Lachs (Salmo salar) und dem Krebspesterreger (Aphanomyces astaci).

Detektion der Krebspest in Hessen mittels Wasserproben
Nordamerikanische Flusskrebsarten wie beispielsweise der Signalkrebs Pacifastacus leniusculus können den für die einheimischen Flußkrebsarten gefährlichen Krebspesterreger Aphanomyces astaci übertragen, wodurch deren Restbestände bundesweit gefährdet sind. In einem gerade begonnenen Kooperationsprojekt unter Beteiligung des Senckenberg Fachgebiets Naturschutzgenetik (Projektbeteiligte: Claudia Wittwer, Dr. Carsten Nowak), der Senckenberg Sektion Fluss- und Auenökologie (Dr. Stefan Stoll) sowie dem Biodiversität und Klima Forschungszentrum (BiK-F) (Prof. Marco Thines) wird an einer eDNA- basierten Standardmethode zum Freilandnachweis der Krebspest gearbeitet, die die herkömmliche Methode der gewebebasierten Krebspestdetektion ablösen soll. Diese Methode kann dann in Zukunft im Rahmen eines nichtinvasiven Gewässermonitorings auch auf Neozoen sowie auf gefährdete und seltene Arten übertragen werden. Grundlage für die Etablierung und Weiterentwicklung ist die enge Kooperation mit Dr. Trude Vrålstad vom Norwegian Veterinarian Institute in Oslo, die den Grundstock für die eDNA-basierte Krebspestdetektion gelegt hat. Auftraggeber des Pilotprojektes sind die Hessischen Regierungspräsidien Darmstadt, Gießen und Kassel.