Ecophysiology, species distributions and the future of the ectotherm biodiversity

We focus on understanding the physiological consequences of climate change in amphibians and reptiles, extending models of extinction risk and linking them to molecular outcomes. Evidence already shows that climate change has driven extinctions in species inhabiting tropical regions and high elevations. To address this challenge, we model scenarios of demographic collapse in ectotherms, where restricted activity time reduces energy acquisition below the thresholds necessary for survivorship, maintenance, and reproduction. Our work integrates bioinformatics approaches, including the development of R-based tools for modeling and analyzing field and experimental data. We aim to build comprehensive data repositories that capture temperature and precipitation dynamics, which we then combine with amphibian and reptile phylogenies to test whether certain clades are phylogenetically predisposed to extinction as a result of climate change and their evolved life-history strategies.

Biogeography of the Neotropics

We are interested in the ecological and biogeographical factors that shape the rates and patterns of biodiversity distribution in the Neotropics. Our research has highlighted the importance of highlands, such as the Andes, as key sources of ancestral diversity for Amazonia and other regions such as the Choco. Current advances in GIS-based methods have greatly enhanced our ability to reconstruct these diversity patterns with increased precision. Our objectives include: (i) reconstruction of past, present, and future biodiversity in the Neotropics; (ii) quantification of climatic, phylogenetic, and anthropogenic influences using network models; and (iii) application of multivariate comparative methods to identify patterns of species radiations and inform conservation priorities across this region.

Comparative transcriptomics and systems biology of reptiles and amphibians

.

Genomic techniques allow the acquisition of vast amounts of genetic data that are essential for understanding biological diversity. Together with collaborators from Argentina, Ecuador, Colombia, Brazil, and the United States, we investigate exemplar adaptations in lizards and poison frogs. In reptiles, our research focuses on toxin resistance, oxygen metabolism, and other physiological adaptations. In amphibians, we study adaptations associated with aposematism as the co-occurrence of conspicuous coloration and acquired chemical defense. Our projects explore the evolutionary consequences of alkaloid sequestration, including ion channel evolution, assembly of the aposematic syndrome, autoresistance mechanisms, and toxin sequestration, as revealed through frog transcriptomes and other molecular methods. This ongoing collaboration integrates comparative genomics and evolutionary biology to advance our understanding of adaptation and biodiversity shaped by toxins that are sequestered and stored for defense and signaling.

Biocomplexity: Integration among physiological, environmental, behavioral, genetic, and phylogenetic variables

.

.

We are interested in the evolution of complex traits, with a focus on highly integrated phenotypes. First, we study the emergence of aposematism as a network of predator-deterrence adaptations. Our work has revealed a highly correlated set of traits that form aposematic complex phenotypes, including: (i) alkaloid accumulation; (ii) diet specialization on alkaloid-rich prey; and (iii) elevated metabolic rates. Second, we investigate the emergence of mate attraction from acoustic signals as a network of physiological, behavioral, and morphological adaptations, exploring phenotypic networks that organize acoustic signals into sub-networks of spectral, temporal, and structural components. Third, we examine how biotic and abiotic environmental variables have shaped the diversity of complex traits and species. Finally, we aim to identify the overarching genomic–phenotypic–biogeographic network structure exemplified by amphibians with emphasis in poison frogs, integrating evolutionary, ecological, and genomic perspectives.

Complex phenotypes assemblage and persistence in large clades

.

We are interested in how organismal traits are organized into modular units that assemble across increasing levels of organization to produce emergent properties. We view complex phenotypes as networks that can be represented as hierarchical arrangements of nodes (individual traits) connected by edges (interactions). Our current research focuses on estimating network structure from matrices of correlations or covariances among traits, while accounting for phylogenetic signal. To achieve this, we adapt and extend network construction methodologies commonly used in econometrics and social statistics. By implementing these approaches, we are investigating aposematism, biogeography, and the influence of climate and evolutionary history on amphibians and reptiles.

Life history predictors of the rates of molecular evolution in ectotherms

.

We are interested in how life-history traits influence the rates of molecular evolution. Traits such as body size, generation time, production of reactive oxygen species (ROS), and resting metabolic rate (RMR) are known to predict variation in the pace of molecular evolution. However, phylogenetic correlation analyses have not supported a relationship between RMR and molecular evolution in ectotherms. To address this, we are testing alternative measures of metabolism, such as active metabolic rate (AMR), and their association with molecular evolutionary rates. Using multivariate and phylogenetic comparative approaches, we developed a mechanistic hypothesis linking AMR to molecular evolution in poison frogs: faster rates of molecular evolution may arise from increased ROS production in germline cells during periodic bouts of hypoxia and hyperoxia associated with aerobic activity. Moving forward, we aim to test whether this hypothesis extends broadly across complete genomes and transcriptomes in both ectotherms and endotherms.

Multivariate methods in phenotypic network structures

.

Modeling phenotypic networks is essential for understanding the emergence of biological complexity across the Tree of Life. To address this, we have adapted multivariate methods such as Structural Equation Modeling (SEM), partial correlation networks to estimate trait relationship structures such as aposematism and environmental impacts on hemoglobin evolution. Our work has shown that SEM is a powerful approach for testing network structure by estimating multiple models of causal and correlational relationships among traits. Importantly, SEM enables the comparison of alternative network structures that vary in the degree of trait integration. Our ongoing research using SEM focuses on several themes: the reliability of multilevel network models; the incorporation of mixed models for discrete and continuous variables; the use of autocorrelation and longitudinal analyses across phylogenetic structure; the estimation of network structure under different models of trait evolution; and the integration of multi-gene phylogenies to study multi-trait networks.

Describing herp biodiversity and natural history

.

The Neotropics harbor more than half of all living terrestrial organisms and represent one of the most threatened regions due to human development. Despite this richness, many groups of amphibians and reptiles remain poorly studied in terms of their natural history, phylogenies, chemical defenses, behavior, etc. For example, our focal group of reptiles, the Corytophanidae, are well known for their dimorphic head crests and bipedal locomotion, yet these traits have not been examined using geometric morphometric approaches. Similarly, poison frogs represent one of the most species-rich and charismatic clades in the region. The pace of new species descriptions in this group has closely followed the availability of large-scale phylogenies, with more than 330 species currently recognized. However, most studies of phenotypic diversity and natural history have focused narrowly on a few aposematic dendrobatids while most non-aposematic taxa are neglected and many are now considered extinct. We are actively contributing to the description and characterization of new taxa and their phylogenetic relationships, and to date we have described more than ten new species of dendrobatids.