Katharina C. Wollenberg Valero

University College Dublin | UCD · School of Biology and Environmental Science

Understanding the genomic basis of adaptation to different abiotic environments is important in the context of climate change and resulting short‐term environmental fluctuations. Using functional and comparative genomics approaches, we here investigated whether signatures of genomic adaptation to a set of environmental parameters are concentrated i...

Heat alters biology from molecular to ecological levels, but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here, we provide a comprehensive picture of the molecular signatures of this process, by integrating multiomic and phenotypic data. In individual...

Climate change increases the frequency and duration of heat events. Negative effects of heat stress may be exacerbated through the action of social metabolites between aquatic animals. Whilst early life stages are vulnerable to stress-induced damage, they deploy cellular mechanisms to protect cells against mutagens such as ultraviolet rays (UV). Li...

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomics resources is more urge...

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgen...

Amphibians are the most threatened major group of vertebrates worldwide and yet they are lagging behind other taxa in genomic resources that could aid in their conservation management. Here, we provide a status update on genomics technologies, how they have been used in amphibian research, and an outlook on how these approaches could inform future...

Amphibians are the most threatened group of vertebrates and are in dire need of conservation intervention to ensure their continued survival. They exhibit unique features including a high diversity of reproductive strategies, permeable and specialized skin capable of producing toxins and antimicrobial compounds, multiple genetic mechanisms of sex d...

The importance of infaunal bioturbators for the functioning of marine ecosystems cannot be overstated. Inhabitants of estuarine and coastal habitats are expected to show resilience to fluctuations in seawater temperature and pH, which adds complexity to our understanding of the effects of global change drivers. Further, stress responses may be prop...

As the most threatened vertebrate class on earth, amphibians are at the forefront of the biodiversity crisis, with the recognition of global amphibian declines and extinctions dating back several decades now. The current Amphibian Conservation Action Plan is adopting two strategies to address the goal of the amelioration of the amphibian crisis: th...

Protein-protein interaction (PPI) network topology can contribute to explain fundamental properties of genes, from expression levels to evolutionary constraints. Genes central to a network are more likely to be both conserved and highly expressed, whereas genes that are able to evolve in response to selective pressures but expressed at lower levels...

Better understanding how organisms respond to their abiotic environment, especially at the biochemical level, is critical in predicting population trajectories under climate change. In this study, we measured constitutive stress biomarkers and protein post-translational modifications associated with oxidative stress in Gallotia galloti, an insular...

The endocrine disruptive chemical DEHP is a plasticiser often found in marine waters. Here, we assessed the effect of this additive on the number and size of eggs spawned by female mussels during a synchronised spawning event. After achieving the ripeness of the gonads, mussels of both sexes were exposed to two environmentally relevant concentratio...

Large-scale comparative genomics studies offer valuable resources for understanding both functional and evolutionary rate constraints. It is suggested that constraint aligns with the topology of genomic networks, increasing towards the center, with intermediate nodes combining relaxed constraint with higher contributions to the phenotype due to ple...

Arginine methylation is a post-translational modification that consists of the transfer of one or two methyl (CH3) groups to arginine residues in proteins. Several types of arginine methylation occur, namely monomethylation, symmetric dimethylation and asymmetric dimethylation, which are catalysed by different protein arginine methyltransferases (P...

Amphibians are the most threatened group of vertebrates and are in dire need of conservation intervention to ensure their continued survival. They have many unique features including a high diversity of reproductive strategies, permeable and specialized skin capable of producing toxins and antimicrobial compounds, multiple genetic mechanisms of sex...

The Malagasy genus Gephyromantis contains 51 species of primarily terrestrial or scansorial frogs. Although many species are morphologically weakly divergent from each other, the combination of molecular and bioacoustic evi¬dence has led to a continuous flow of species discoveries in the last years. Previous works have notably shown the existence o...

Plastic pollution and changes in oceanic pH are both pressing environmental issues. Little emphasis, however, has been placed on the influence of sex and gametogenesis stage when investigating the effects of such stressors. Here, we examined histology and molecular biomarkers of blue mussels Mytilus edulis exposed for 7 days to a pH 7.7 scenario (−...

Although first biogeographic analyses of Madagascar's amphibian fauna were provided by Blommers-Schlösser and Blanc (1993), these could only provide first hints at possible patterns due to incomplete taxonomic and distributional knowledge at the time. Since this pioneering work, the combination of increased field exploration, integrative taxonomy,...

Heat alters biology from molecular to ecological levels, but may also have unknown indirect effects. This includes the novel concept that animals exposed to abiotic stress can induce stress in naive receivers. Here, we provide a comprehensive picture of the molecular signatures of this process, by integrating multi-omic and phenotypic data. In indi...

Biological organisms can adapt to unstable conditions. This adaptability results from a combination of heterogeneity and plasticity within a population, which means perturbations are unlikely to have the same effect on all population members, allowing time for adaptations to evolve. In this work we show that this behaviour can be duplicated by intr...

Studies on pH stress in marine animals typically focus on direct or species-specific aspects. We here test the hypothesis that a drop to pH = 7.6 indirectly affects the intra- and interspecific interactions of benthic invertebrates by means of chemical communication. We recorded fitness-relevant behaviours of small hermit crabs Diogenes pugilator ,...

Aquatic organisms must cope with both rising and rapidly changing temperatures. These thermal changes can affect numerous traits, from molecular to ecological scales. Biotic stressors are already known to induce the release of chemical cues which trigger behavioural responses in other individuals. In this study, we infer whether fluctuating tempera...

Biological organisms can adapt to unstable conditions. This adaptability results from a combination of heterogeneity and plasticity within a population, which means perturbations are unlikely to have the same effect on all population members, allowing time for adaptations to evolve. In this work we show that this behaviour can be duplicated by intr...

Little is known about the combined effect of environmental factors and contaminants on commercially important marine species, and whether this effect differs by sex. In this study, blue mussels were exposed for seven days to both single and combined stressors (i.e., +3 °C elevated temperature and two environmentally relevant concentrations of the p...

Studies on pH stress in marine animals typically focus on direct or species-specific aspects. We here test the hypothesis that a drop to pH = 7.6 indirectly affects the intra- and interspecific interactions of benthic invertebrates by means of chemical communication. We recorded fitness-relevant behaviours of small hermit crabs Diogenes pugilator,...

Aquatic organisms must cope with both rising and rapidly changing temperatures. These environmental changes can affect numerous traits, from molecular to ecological scales. Biotic stressors can induce the release of chemical cues which trigger behavioural responses in other individuals. In this study, we infer whether abiotic stressors, such as flu...

Beverley, a sleepy town in East Yorkshire, is overrun by strange cats, and there’s not a single plant anywhere in sight (well except for the rows and rows of Broccoli grown deep under the Commons in the Broccoli Mines). This is the future that siblings Ben and Stephanie get thrown into on their last day of year 3 before the summer holidays. Instead...

Background: Functional constraint through genomic architecture is suggested to be an important dimension of genome evolution, but quantitative evidence for this idea is rare. In this contribution, existing evidence and discussions on genomic architecture as constraint for convergent evolution, rapid adaptation, and genic adaptation are summarized...

Increasing atmospheric CO2 levels are largely absorbed by the ocean, decreasing surface water pH. In combination with increasing ocean temperatures, these changes have been identified as a major sustainability threat to future marine life. Interactions between marine organisms are known to depend on biomolecules, although the influence of oceanic p...

In the anuran family Dendrobatidae, aposematic species obtain their toxic or unpalatable alkaloids from dietary sources, a process known as sequestering. To understand how toxicity evolved in this family, it is paramount to elucidate the pathways of alkaloid processing (absorption, metabolism, and sequestering). Here, we used an exploratory skin ge...

Climatic conditions changing over time and space shape the evolution of organisms at multiple levels, including temperate lizards in the family Lacertidae. Here we reconstruct a dated phylogenetic tree of 262 lacertid species based on a supermatrix relying on novel phylogenomic datasets and fossil calibrations. Diversification of lacertids was acco...

In this contribution, the aspects of reptile and amphibian speciation that emerged from research performed over the past decade are reviewed. First, this study assesses how patterns and processes of speciation depend on knowing the taxonomy of the group in question, and discuss how integrative taxonomy has contributed to speciation research in thes...

Understanding the genomic basis of adaptation to different abiotic environments is important for understanding organismal responses to current short-term environmental fluctuations. Using functional and comparative genomics approaches, we here investigated whether genomic adaptation to a set of environmental parameters is contingent across vertebra...

Increasing atmospheric levels of carbon dioxide are largely absorbed by the world's oceans, decreasing surface water pH. In combination with increasing ocean temperatures, these changes have been identified as a major sustainability threat to future marine life. Interactions between marine organisms are known to depend on biomolecules, but the infl...

Speciation processes have long been inferred from phylogenetic, phylogeographic, and biogeographic pattern-driven perspectives. Now much current speciation research is attempting to more directly describe the underlying processes and mechanisms of divergence leading to speciation. Ideally, researchers should integrate both process-and pattern-based...

Speciation processes have long been inferred from phylogenetic, phylogeographic, and biogeographic pattern-driven perspectives. Now much current speciation research is attempting to more directly describe the underlying processes and mechanisms of divergence leading to speciation. Ideally, researchers should integrate both process- and pattern-base...

It is likely that there are constraints on how evolution can progress, and well-known evolutionary phenomena such as convergent evolution, rapid adaptation, and genic evolution would be difficult to explain under the absence of any such evolutionary constraint. One dimension of constraint results from a finite number of environmental conditions, an...

Caribbean Anolis lizards exhibit a complex suite of ecological, morphological, and behavioral traits that allow their specialization to particular microhabitats. These microhabitat specialists, called ecomorphs, have independently evolved on the four islands of the Greater Antilles, and diversification among anole ecomorphs has been the focus of ma...

Ebola virus disease outbreaks in animals (including humans and great apes) start with sporadic host switches from unknown reservoir species. The factors leading to such spillover events are little explored. Filoviridae viruses have a wide range of natural hosts and are unstable once outside hosts. Spillover events, which involve the physical transf...

Our work is providing gestational-stage signatures of placental expression of gene families. The project harnesses the large and professionally collected datasets on placenta transcriptomes in health and in disease. The tools being developed follow the principles of human-information interaction therefore allowing for deep, connected and coherent k...

Integrated knowledge on phenotype, physiology, and genomic adaptations is required to understand the effects of climate on evolution. The functional genomic basis of organismal adaptation to changes in the abiotic environment, its phenotypic consequences, and its possible convergence across vertebrates are still understudied. In this study, we use...

Ebola virus disease outbreaks in mammals (including humans and great apes) start with sporadic host switches from unknown reservoir species. The factors leading to such spillover events are not clearly understood. Filoviridae have a wide range of natural hosts and are unstable once outside hosts. Spillover events, which involve the physical transfe...

Anuran amphibians undergo major morphological transitions during development, but the contribution of their markedly different life-history phases to macroevolution has rarely been analysed. Here we generate testable predictions for coupling versus uncoupling of phenotypic evolution of tadpole and adult life-history phases, and for the underlying e...

Nexus file of morphological characters of tadpoles of mantellid frogs. Characters as in Supplementary Table 5.

Supplementary Figures, Supplementary Tables, Supplementary Methods and Supplementary Refernces

Perl script used to extract list of Gene Ontologies associated with morphology from Mantidactylus betsileanus annotated transcripts, based on list defined on morphology-associated GO terms list in Xenopus laevis.

Nexus file of morphological characters of adult mantellid frogs. Characters as in Supplementary Table 4.

Undergraduate #73 Discipline: Biological Sciences Subcategory: Education Research Question: The central research question of the project is ‘What are the knowledge components that learners exhibit when performing learning transactions on biology topics? Knowledge components describe a mental structure or process that learners use, along with or com...

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009;...

This plot is not part of the published stance but derives from it. The plot shows the number of authors by geographic region (courtesy of Dr. Diego Astua).

Assemblages that are exposed to recurring temporal environmental changes can show changes in their ecological properties. These can be expressed by differences in diversity and assembly rules. Both can be identified using two measures of diversity: functional (FD) and phylogenetic diversity (PD). Frog communities are understudied in this regard, es...

The Quantitative Expertise in the Undergraduate Biology Curriculum (QEUBiC) framework provides an adoptable curriculum framework for infusing key topics in data challenges to biology coursework. Topics in the dimensions of data challenges described by the National Consortium for Data Science as data flow; data analytics and data curation are being...

Several national reports have identified that success in mathematics courses in the first two years of college correlates with retention and graduation in science, technology, engineering and mathematics (STEM) disciplines. Furthermore, collaboration with mathematics faculty is recommended as a strategy to improve mathematics success for college st...

Glioblastoma is the most common brain tumor in adults in which recurrence has been attributed to the presence of cancer stem cells in a hypoxic microenvironment. On the basis of tumor formation in vivo and growth type in vitro, two published microarray gene expression profiling studies grouped nine glioblastoma stem-like (GS) cell lines into one of...

Supplementary File 1 This file contains additional information on data sets used in the study.

The endemic Malagasy frog radiations are an ideal model system to study patterns and processes of speciation in amphibians. Large-scale diversity patterns of these frogs, together with other endemic animal radiations, led to the postulation of new and the application of known hypotheses of species diversification causing diversity patterns in this...

Vertebrate ectotherms such as reptiles provide ideal organisms for the study of adaptation to environmental thermal change. Comparative genomic and exomic studies can recover markers that diverge between warm and cold adapted lineages, but the genes that are functionally related to thermal adaptation may be difficult to identify. We here used a bio...

We provide a DNA barcoding survey of Malagasy amphibians, including 251 of the 292 nominal species known to date, by complementing previous data with 280 newly determined barcoding sequence fragments of the mitochondrial cytochrome oxidase subunit I (COI) gene. Amplification success for the newly determined sequences was highest (94%) with one set...

Communities are thought to be assembled by two types of filters: by the environment relating to the fundamental niche and by biotic interactions relating to the realized niche. Both filters include parameters related to functional traits and their variation along environmental gradients. Here, we infer the general importance of environmental filte...