Markus Pfenninger

Markus Pfenninger
Senckenberg Biodiversität und Klima - Forschungszentrum | BiK-F · Adaptation and Climate

Prof. Dr.

About

282
Publications
51,090
Reads
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6,293
Citations
Citations since 2016
145 Research Items
3622 Citations
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20162017201820192020202120220100200300400500600
20162017201820192020202120220100200300400500600
Introduction
The focus of my research is the genomic basis of niche evolution, speciation/hybridisation and local adaptation with closely related species pairs and intraspecific variation in land and freshwater snails, non-biting midges, ants, cats, extremophile molly fishes and everything else that's not up the tree (trees, by the way, as well) at count three. We take an integrative approach: field studies, ecological and evolutionary experiments, comparative genomic approaches and experimental evolution. The ultimate vision thereby is to relate ecological differences functionally to their genomic basis. In addition, translational projects on mosquito pest management and mutational impact of anthropogenic substances are pursued.
Additional affiliations
October 2010 - present
Senckenberg Biodiversität und Klima - Forschungszentrum
Position
  • Head of Department
January 2010 - present
Senckenberg Forschungsinstitut

Publications

Publications (282)
Article
Full-text available
Background The extent and impact of evolutionary change occurring in natural populations in response to rapid anthropogenic impact is still poorly understood on the genome-wide level. Here, we explore the genetic structure, demographic history, population differentiation, and domestic introgression based on whole genome data of the endangered Europ...
Article
Full-text available
Natural populations experience continuous and often transient changes of environmental conditions. These in turn may result in fluctuating selection pressures leading to variable demographic and evolutionary population responses. Rapid adaptation as short‐term response to a sudden environmental change has in several cases been attributed to polygen...
Article
Driven by globalization, urbanization and climate change, the distribution range of invasive vector species has expanded to previously colder ecoregions. To reduce health‐threatening impacts on humans, insect vectors are extensively studied. Population genomics can reveal the genomic basis of adaptation and help to identify emerging trends of vecto...
Article
Full-text available
Natural populations are constantly exposed to fluctuating environmental changes that negatively affect their fitness in unpredictable ways. While theoretical models show the possibility of counteracting these environmental changes through rapid evolutionary adaptations, there have been few empirical studies demonstrating such adaptive tracking in n...
Book
The 30 Years' War seems very far in the past nowadays. Yet it had a decisive impact on Germany, from language to collective psychology. The Battle of Höchst in 1622 was decisive for the further course of the war. Based on extensive research in original sources, the events surrounding the battle are reconstructed in detail. The richly illustrated bo...
Preprint
Full-text available
Background Driven by globalization, urbanization and climate change, the distribution range of invasive vector species has expanded to previously colder ecoregions. To reduce health-threatening impacts on humans, insect vectors are extensively studied. Population genomics can reveal the genomic basis of adaptation and help to identify emerging tren...
Article
Hybridisation between domestic and wild taxa can pose severe threats to wildlife conservation, and human induced hybridisation, often linked to species' introductions and habitat degradation, may promote reproductive opportunities between species for which natural interbreeding would be highly unlikely. Using a biome specific approach, we examine t...
Article
Full-text available
Mutations are the ultimate source of heritable variation and therefore the fuel for evolution, but direct estimates of mutation rates exist only for few species. We estimated the spontaneous single nucleotide mutation rate among clonal generations in the waterflea Daphnia galeata with a short-term mutation accumulation approach. Individuals from ei...
Article
Human‐induced degradation of biodiversity is arguably the greatest problem facing humanity. Climate change, changes in land and sea use and other factors are synergistically eroding biodiversity at an unprecedented rate and scale (Díaz et al. 2019). This article is protected by copyright. All rights reserved.
Article
Susceptibility to hazardous materials and contamination is largely determined by genetic make-up and evolutionary history of affected organisms. Yet evolutionary adaptation and microevolutionary processes triggered by contaminants are rarely considered in ecotoxicology. Using an evolve and resequencing approach, we investigated genome-wide response...
Preprint
Full-text available
Natural populations experience continuous and often transient changes of environmental conditions. These in turn may result in fluctuating selection pressures leading to variable demographic and evolutionary population responses. Rapid adaptation as short-term response to a sudden environmental change has in several cases been attributed to polygen...
Article
Full-text available
The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here, we present a chromosome-level assembly of the more...
Article
Most organisms respond and can adapt to photoperiodic changes. This affects measurable end points like developmental time, survival and fertility. For ectotherms like Chironomus riparius, temperature is the most studied environmental cue regulating their life cycle, whereas photoperiodic influence is neglected. However, the developmental speed betw...
Article
Full-text available
Freshwater mussels cannot spread through oceanic barriers and represent a suitable model to test the continental drift patterns. Here, we reconstruct the diversification of Oriental freshwater mussels (Unionidae) and revise their taxonomy. We show that the Indian Subcontinent harbors a rather taxonomically poor fauna, containing 25 freshwater musse...
Article
Evolutionary adaptation and phenotypic plasticity are important processes on how organisms respond to pollutant exposure. We dissected here the contribution of both processes to increased tolerance in Chironomus riparius to cadmium (Cd) exposure in a multi-generation experiment and inferred the underlying genomic basis. We simulated environmentally...
Article
Full-text available
Hybridization and introgression are recognized as an important source of variation that influence adaptive processes; both phenomena are frequent in the genus Daphnia, a keystone zooplankton taxon in freshwater ecosystems that comprises several species complexes. To investigate genome-wide consequences of introgression between species, we provide h...
Article
Full-text available
Accurate estimates of genome sizes are important parameters for both theoretical and practical biodiversity genomics. We present here a fast, easy‐to‐implement and accurate method to estimate genome size from the number of bases sequenced and the mean sequencing depth. To estimate the latter, we take advantage of the fact that an accurate estimatio...
Preprint
Full-text available
Evolutionary processes and acquired tolerance to toxicants are important factors governing how animals respond to chemical exposure. Evidence for increased tolerance to cadmium (Cd), a widely distributed toxic metal in aquatic environments, in Chironomus riparius is conflicting and still questioned if it happens through phenotypic plasticity or gen...
Article
Mutation is the source of genetic variation and the fundament of evolution. Temperature has long been suggested to have a direct impact on realized spontaneous mutation rates. If mutation rates vary in response to environmental conditions, such as the variation of the ambient temperature through space and time, they should no longer be described as...
Article
Full-text available
Species living in sympatry and sharing a similar niche often express parallel phenotypes as a response to similar selection pressures. The degree of parallelism within underlying genomic levels is often unexplored, but can give insight into the mechanisms of natural selection and adaptation. Here, we use multi‐dimensional genomic associations to as...
Article
Full-text available
In the course of global climate change, central Europe is experiencing more frequent and prolonged periods of drought. The drought years 2018 and 2019 affected European beeches ( Fagus sylvatica L.) differently: even in the same stand, drought damaged trees neighboured healthy trees, suggesting that the genotype rather than the environment was resp...
Article
Full-text available
Among all molluscs, land snails are a scientifically and economically interesting group comprising edible species, alien species and agricultural pests. Yet, despite their high diversity, the number of genome drafts publicly available is still scarce. Here, we present the draft genome assembly of the land snail Candidula unifasciata, a widely distr...
Article
Full-text available
Despite the global biodiversity of terrestrial gastropods and their ecological and economic importance, the genomic basis of ecological adaptation and speciation in land snail taxa is still largely unknown. Here, we combined whole-genome re-sequencing with population genomics to evaluate the historical demography and the speciation process of two c...
Preprint
Full-text available
Precise estimates of genome sizes are important parameters for both theoretical and practical biodiversity genomics. We present here a fast, easy-to-implement and precise method to estimate genome size from the number of bases sequenced and the mean sequence coverage. To estimate the latter, we take advantage on the fact that a precise estimation o...
Preprint
Full-text available
Background The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Results Here we present a chromosome-level as...
Preprint
Full-text available
Motivation The question of determining whether a Single-Nucleotide Polymorphism (SNP) or a variant in general leads to a change in the amino acid sequence of a protein coding gene is often a laborious and time-consuming challenge. Here, we introduce the tbg file format for storing genomic data and tbg-tools, a user-friendly toolbox for the faster a...
Preprint
Full-text available
Hybridization and introgression are recognized as an important source of variation that influence adaptive processes; both phenomena are frequent in the genus Daphnia, a keystone zooplankton taxon in freshwater ecosystems that comprises several species complexes. To investigate genome-wide consequences of introgression between species, we provide h...
Preprint
Full-text available
Among all molluscs, land snails are an economically and scientifically interesting group comprising edible species, alien species and agricultural pests. Yet, despite its high diversity, the number of whole genomes publicly available is still scarce. Here, we present the draft genome assembly of the land snail Candidula unifasciata , a widely distr...
Article
Full-text available
Background Next Generation Sequencing (NGS) is the fundament of various studies, providing insights into questions from biology and medicine. Nevertheless, integrating data from different experimental backgrounds can introduce strong biases. In order to methodically investigate the magnitude of systematic errors in single nucleotide variant calls,...
Article
A new geomitrid, Candidula conglomeratica sp. nov., discovered in Genoa (Liguria) and Alessandria (Piedmont) provinces (Italy), is described. Whilst its anatomical morphology is similar to that of Candidula unifasciata, its shell is distinct from all other species of Candidula. Genetic data confirm the separation of C. conglomeratica sp. nov. from...
Preprint
Full-text available
In the course of global climate change, central Europe is experiencing more frequent and prolonged periods of drought. The drought years 2018 and 2019 affected European beeches ( Fagus sylvatica L.) differently: even in the same stand, drought damaged trees neighboured healthy trees, suggesting that the genotype rather than the environment was resp...
Article
Existing mutagenicity tests for metazoans lack the direct observation of enhanced germline mutation rates after exposure to anthropogenic substances, therefore being inefficient. Cadmium (Cd) is a metal described as a mutagen in mammalian cells and listed as a group 1 carcinogenic and mutagenic substance. But Cd mutagenesis mechanism is not yet cle...
Article
Full-text available
Divergence is mostly viewed as a progressive process often initiated by selection targeting individual loci, ultimately resulting in ever increasing genomic isolation due to linkage. However, recent studies show that this process may stall at intermediate stable equilibrium states without achieving complete genomic isolation. We tested the extent o...
Preprint
Full-text available
Mutation is the source of genetic variation and the fundament of evolution. At the interphase of ecology and evolution, temperature has long been suggested to have a direct impact on realised spontaneous mutation rates. The question is whether mutation rates can be a species-specific constant under variable environmental conditions, such as variati...
Article
Full-text available
Mosquito-borne diseases are a continuous challenge to public health. To prevent transmission, Integrated Vector Management (IVM) applies preventive, control, and communicational strategies that should be feasible, environmentally benign, and sustainable. IVM shows higher efficiency when being supported by local communities. Accordingly, we applied...
Preprint
Existing mutagenicity tests for metazoans lack the direct observation of enhanced germline mutation rates after exposure to anthropogenic substances, therefore being inefficient. Cadmium (Cd) is a metal described as a mutagen in mammalian cells and listed as a group 1 carcinogenic and mutagenic substance. But Cd mutagenesis mechanism is not yet cle...
Preprint
Full-text available
Mutations are the ultimate source of heritable variation and therefore the fuel for evolution, but direct 16 estimates exist only for few species. We estimated the spontaneous nucleotide mutation rate among 17 clonal generations in the waterflea Daphnia galeata with a short term mutation accumulation 18 approach. Individuals from eighteen mutation...
Article
Cadmium (Cd) is a non-essential highly toxic metal and its presence in the environment has been a concern over the years. On the present study we adopt the spiked water exposure scenario to study early Cd contamination across five generations of the model organism Chironomus riparius. Animals were, at the beginning of each generation, submitted to...
Preprint
Full-text available
Background Next Generation Sequencing (NGS) is the fundament of various studies providing insights into questions from biology and medicine. Nevertheless, integrating data from different experimental backgrounds can introduce strong biases. In order to methodically investigate the magnitude of systematic errors, we performed a cross-sectional obser...
Preprint
Full-text available
Background Next Generation Sequencing (NGS) is the fundament of various studies, providing insights into questions from biology and medicine. Nevertheless, integrating data from different experimental backgrounds can introduce strong biases. In order to methodically investigate the magnitude of systematic errors in single nucleotide variant calls,...
Preprint
Full-text available
Background Next Generation Sequencing (NGS) is the fundament of various studies, providing insights into questions from biology and medicine. Nevertheless, integrating data from different experimental backgrounds can introduce strong biases. In order to methodically investigate the magnitude of systematic errors in single nucleotide variant calls,...
Article
Full-text available
The advent of new and affordable high-throughput sequencing techniques allows for the investigation of the genetic basis of environmental adaptation throughout the plant and animal kingdom. The framework of genotype-environment associations (GEA) provides a powerful link by correlating the geographic distribution of genotype patterns of individuals...
Preprint
Full-text available
Natural populations are constantly exposed to fluctuating environmental changes that negatively affect their fitness in unpredictable ways. While theoretical models show the possibility of counteracting these environmental changes through rapid evolutionary adaptations, there have been few empirical studies demonstrating such adaptive tracking in n...
Article
Full-text available
Hybridisation between wild taxa and their domestic congeners is a significant conservation issue. Domestic species frequently outnumber their wild relatives in population size and distribution and may therefore genetically swamp the native species. The European wildcat (Felis silvestris) has been shown to hybridise with domestic cats (Felis catus)....
Article
Full-text available
Chironomus riparius is of great importance as a study species in various fields like ecotoxicology, molecular genetics, developmental biology and ecology. However, only a fragmented draft genome exists to date, hindering the recent rush of population genomic studies in this species. Making use of 50 NGS datasets, we present a hybrid genome assembly...
Article
Full-text available
Anoles are a group of lizards that offer a wide range of opportunities to study different biological topics. In this work, we examined some aspects of the morphology from 139 individuals of green anoles collected in urban parks of Santo Domingo and the Distrito Nacional. We investigated evidence of hybridization between the two Hispaniola endemic s...
Article
Full-text available
Global climate change (GCC) increasingly threatens biodiversity through the loss of species, and the transformation of entire ecosystems. Many species are challenged by the pace of GCC because they might not be able to respond fast enough to changing biotic and abiotic conditions. Species can respond either by shifting their range, or by persisting...
Article
Full-text available
Arion vulgaris Moquin-Tandon, 1855 is regarded as one of the 100 most invasive species in Europe. The native distribution range of this species is uncertain, but for many years, the Iberian Peninsula has been considered as the area of origin. However, recent studies indicate that A. vulgaris probably originated from France. We have investigated the...
Article
Evolve and Resquence (E&R) studies are a useful tool to study genomic processes during rapid adaptation, e.g. in the framework of adaptive responses to global climate change. We applied different thermal regimes to a natural Chironomus riparius (Diptera) population in an E&R framework to infer its evolutionary potential for rapid thermal adaptation...
Article
Active species reintroduction is an important conservation tool when aiming for the restoration of biological communities and ecosystems. The effective monitoring of reintroduction success is a crucial factor in this process. Here, we used a combination of environmental DNA (eDNA) techniques and species distribution models (SDMs) to evaluate the su...
Article
Full-text available
The success of social insects is largely intertwined with their highly advanced chemical communication system that facilitates recognition and discrimination of species and nest-mates, recruitment, and division of labour. Hydrocarbons, which cover the cuticle of insects, not only serve as waterproofing agents but also constitute a major component o...
Preprint
Background: Chironomus riparius is of great importance as a study species in various fields like ecotoxicology, molecular genetics, developmental biology and ecology. However, only a fragmented draft genome exists to date, hindering the recent rush of population genomic studies in this species. Findings: Making use of 50 NGS datasets, we present a...
Article
Full-text available
Background The invasive temperate mosquito Aedes japonicus japonicus is a potential vector for various infectious diseases and therefore a target of vector control measures. Even though established in Germany, it is unclear whether the species has already reached its full distribution potential. The possible range of the species, its annual populat...
Article
Chironomus riparius is a well‐established model organism in various fields such as ecotoxicology and ecology, and therefore, environmental preferences, ecological interactions and metabolic traits are well‐studied. With the recent publication of a high‐quality draft genome, as well as different population genetic parameters such as mutation and rec...
Article
Full-text available
Effects of seasonal or daily temperature variation on fitness and physiology of ectothermic organisms and their ways to cope with such variations have been widely studied. However, the way multivoltines organisms cope with temperature variations from one generation to the next is still not well understood. The aim of this study was to investigate w...
Article
Full-text available
The ability of organisms to respond to predation threat by exhibiting induced defenses is well documented, but studies on the potential mechanistic basis for such responses are scarce. Here, we examine the transcriptomic response to predator kairomones of two functionally distinct developmental stages in embryos of the aquatic snail Radix balthica:...