Katharina C. Wollenberg Valero

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

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...

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...

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...

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...

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 ,...

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...

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...

Table S1. Results of principal component analyses for the bioclimatic variables of the Greater Antilles (in Varimaxraw rotated coordinate system) by factor loadings (marked loadings are > 0.7). Table S2. Results of principal component analyses for the bioclimatic variables of the Greater Antilles (in Varimaxraw rotated coordinate system) by Eigenva...

Presence of the Slider turtle in its native range (green dots) and invasive range where it is known to reproduce (red dots), countries from which reproducing populations are known but no specific localities are available (hatched) and potential distribution derived from BIOCLIM SDM (colored): (A) using 19 ‘bioclimate’ variables, approach ‘comprehen...

The evolutionary processes that produce adaptive radiations are enigmatic. They can only be studied after the fact, once a radiation has occurred and been recognized, rather than while the processes are ongoing. One way to connect pattern to process is to study the processes driving divergence today among populations of species that belong to an ad...

With more than 250 species, the Mantellidae is the most species-rich family of frogs in Madagascar. These frogs are highly diversified in morphology, ecology and natural history. Based on a molecular phylogeny of 248 mantellids, we here examine the distribution of three characters reflecting the diversity of eye colouration and two characters of he...

The processes affecting species diversification may also exert an influence on patterns of genetic variability within species. We evaluated the contributions of five variables potentially influencing clade diversification (body size, reproductive mode, range size, microhabitat and skin texture) on mtDNA divergence and polymorphism among populations...

We revise the systematics of a group of little brown leaf litter frogs from Madagascar that are notoriously difficult to di-agnose, the Gephyromantis decaryi complex. Using an integrative combination of molecular data, bioacoustics, and mor-phology, we reveal four divergent evolutionary lineages which all are monophyletic in the mitochondrial gene...

We describe a new species of small diurnal frog of the genus Gephyromantis from Mahasoa, a fragment of mid-altitude rainforest in the northern central east of Madagascar, located to the north east of Lake Alaotra. Analysis of DNA sequences of the mitochondrial 16S rRNA and cytochrome b genes and of the nuclear Rag 1 gene indicate that Gephyromantis...

Amphibians like water, but do they also notice volatile compounds in the air? Yes, they do. Macrolides, such as phoracantholide J (see picture; upper right structure) or the newly discovered natural product gephyromantolide A (left structure), are used for communication by mantelline frogs from Madagascar.

Amphibien mogen Wasser, aber bemerken sie auch fluchtige Verbindungen in der Luft? Ja, das tun sie. Makrolide wie das Phoracantholid J (oben rechts) oder der neue Naturstoff Gephyromantolid A (unten links) werden von den Mantellidae-Froschen aus Madagaskar fur ihre Kommunikation verwendet.

Volatile pheromones in frogs have been detected for the first time in the family Mantellidae from Madagascar. Previously only water-soluble pheromones had been found in amphibians. In their Communication (DOI: 10.1002/anie.201106592), S. Schulz and co-workers show that the femoral ducts of the male frogs contain macrolides and secondary alcohols. T...

The genus Gephyromantis is a clade within the Malagasy-Comoroan family Mantellidae composed of rainforest frogs that live and breed to varying degrees independently from water. Based on DNA sequences of five mitochondrial and five nuclear genes we inferred the phylogeny of these frogs with full taxon coverage at the species level. Our preferred con...