Three questions animate our research. How does biodiversity change in time and space? What biological processes fuel biodiversity? What are the social factors of environmental degradation?
Doctoral candidate William Thomas is a candidate no more after successfully defending his dissertation! Congratulations to Dr. Thomas!
Doctoral candidate Nicolette Sipperly presented at Botany Conference 2023. Nicolette showed results from her phenotypic comparisons across populations of Draba albertina, and connections between art and science. Congratulations to Nicolette!
Doctoral candidates Alexis Brown and William Thomas presented at Evolution 2023. While Lexi presented “Evidence for novel molecular mechanisms for resisting sensorineural hearing loss in echolocating bats,” Bill presented “Comparative transcriptomics reveal life history tradeoffs associated with the evolution of a seasonal size plasticity in shrews.” Congratulations to both!
Liliana M. Dávalos is Professor of Conservation Biology at Stony Brook University’s Department of Ecology and Evolution. Centered on biodiversity, her research applies a range of molecular and quantitative tools ranging from molecular evolution to spatial statistics.
PhD in Ecology, Evolution,and Environmental Biology, 2004
Columbia University (New York, New York)
Certificate in Environmental Policy Studies, 2001
Columbia University (New York, New York)
BSc in Biology (emphasis on Genetics), 1997
Universidad del Valle (Cali, Colombia)
To model the impacts of narco-trafficking and land grabbing in the Amazon.Watch video
2022 Celebration of Teaching Awards.Watch video
This annual lecture, like the Environmental Studies Program, takes an interdisciplinary approach to the natural environment and human interaction with it.Watch video
For outstanding teaching and true caring for students.
Symposia bring together outstanding young scientists to discuss exciting advances and opportunities in a broad range of disciplines.See profile
Land grabbing is known to hasten deforestation in the Amazon, and narcotrafficking is thought to promote land grabbing. Yet, region-wide analyses of impact impacts from both narcotrafficking and land grabbing are lacking. By compiling georeferenced databases of land grabbing and narcotrafficking indicators such as cocaine seizures, I will estimate the deforestation impacts of these factors. Models will also estimate how trafficking responds to suppression by including counter- trafficking activities as predictors, and thus anticipate forest impacts from drug policy shifts. Thus, this project connects local forest outcomes to national policies, and transnational threats to human communities. Narcotrafficking is an understudied factor in environmental degradation and human rightsviolations across the Amazon. But despite its transnational scope, and links to forest loss and extractivism, it remains understudied. By analyzing narcotrafficking as a driver of deforestation via land grabbing and thereby generating predictive models, my project will contribute to strengthening human and environmental security.
We propose to explore Azolla as a solution to present-day scalable carbon capture by linking it with the Nitro-Oxidation Process (NOP) for sequestration. While the NOP has been found to be effective at producing nanocelluloses for application ranging from soil amendments to water filters, its potential for stabilizing carbon has yet to be evaluated. Because the NOP separates carbon in cellulose from effluents that contain remaining elements, this process can enable efficient phosphorus (and other nutrient element) recycling. This dual potential for carbon storage and nutrient recovery, however, remains to be tested. Demonstrating maximal carbon capture rates, and the suitability of the NOP to both stabilize Azolla biomass and reuse nutrients will make this project competitive with a diverse suite of potential funders.
In nature, encounters between humans and wildlife correlate with greater viral burdens in wildlife and therefore with higher risk of new viral pathogens spilling over into human populations. Yet, the factors contributing to this risk remain poorly understood, especially among highly mobile, but tightly packed populations of animals, such as cave-dwelling bats. Using the Egyptian fruitbat as a study system, this project seeks to understand how factors such as access to food, overall animal health, and responses to immune challenges influence each other in the wild to control the degree of viral infection in populations experiencing variable exposure to humans. The project will use highly integrative approaches to illuminate the fundamental biology of disease risk and to enhance the capacity to predict risks of viral spillover from bats to other wildlife or to humans. The project will also have broader impact on education and training by implementing an innovative active-learning experience, called “From the Bat Cave – Integrative Disease Research for Undergraduates”, in which postdoctoral researchers will learn to apply integrative research and mentoring methods to involve cohorts of undergraduate students in research and peer-peer mentoring through GBatNet, a NSF-funded international network of bat research groups.
We will establish a unique multi-disciplinary approach that combines computational genomics, structural biology and biochemistry, and ecology and genomics, to characterize APOBEC enzymes and their evolution across several bat species that harbour viruses with zoonotic potential. Using wet-lab experimental results, we will build deep learning-based models to predict mutability in viruses of bat origin and use these to predict the potential variation of bat viruses in humans following a hypothetical zoonotic transmission. This will be the first functional study of a key facet of the bat immune system which plays a pivotal role in virus evolution and transmissibility to humans.
Why are bats so likely to carry coronaviruses, yet seem little affected by them? Many studies have focused on their immune system, but there is much to learn about the cells viruses attack upon entry.
All aspects of society have been upended by COVID-19. While most research has understandably focused on clinical applications, how the ancestors of SARS-CoV2 survive and circulate in nature is vital to both prevent future epidemics and help health professionals develop therapeutic treatments.
In support of RA Kristjan Mets. While scientific reaction to the COVID-19 pandemic has been swift, the risk of SARS-CoV-2 spilling back into native North American wildlife and feral domestic animals remains underexplored. Experimental infections of a variety of hosts, serological analyses of the cats in Wuhan, and cases of COVID-19 among tigers and lions in the Bronx Zoo, all have shown transmission back to wildlife and feral cats is highly probable. Tools are urgently needed to determine which of these animal populations are at greatest risk of establishing a native reservoir, and where the overlap with human populations is greatest. We propose to model the risk of spillover to animal populations and conversely the risk of future secondary spillover by combining models of molecular interaction between the virus and potential hosts, with multi- species Susceptible-Infectious-Recovered (SIR) models. Complementing decades of experience in vertebrate genomics (Dávalos) with expertise in epidemiology (Meliker), and spatial dynamics of wildlife disease (Mets), ours is the ideal team to quickly generate and test the necessary models to avert this risk.
To answer the question of how the shrew shrinks and then regrows its brain, we will establish this unusual species as a new model, by studying the biological, molecular, biochemical and genetic processes behind this reversible size change.
We assembled a group of socio-environmental scientists to analyze and model the natural and human factors that determine the extinction and resilience of insular vertebrate fauna and leverage this understanding into metrics for use in conservation assessments.
We propose to develop a cross-scale research program that focuses on the relationships between phylogenetic diversity, genetic diversity and functional diversity of a biologically and economically important taxonomic group; bats.
This project focuses on pairs of closely related bat species that sharply differ in their longevity. Detailed genome comparisons between closely related species with different life spans will test different theories of aging.
This training program responds to the challenges of new careers at the interface between science and decision making with an interdisciplinary set of new courses and a suite of activities united by the theme of “Scientific Training and Research to Inform DEcisions” (STRIDE).
The project focuses on a relatively unexplored yet crucial aspect of plant-animal mutualisms; volatile chemical communication between plants and vertebrate frugivores.
This project focuses on a diverse group of tropical bats in which various species evolved acute, specialized hearing, supersensitive eyes, the ability to smell subtle plant chemicals, or highly developed vomeronasal systems (thought to contribute to mating and social hierarchy).
The goal of this project was to discover the mechanisms underlying the survival of remnant populations in the WNS-affected area.
Noctilionoid bats comprise more than 200 species that span the entire ecological diversity of land mammals. They range from tiny insectivores and nectarivores to large carnivores, and even vampire bats. This is an unparalleled system for understanding how, when, and where bats evolved new diets, changed roosting habits and developed different kinds of echolocation. Together with the N. B. Simmons Lab, we are generating species-level phylogenies using molecular and morphological data, and including fossils of >20 extinct species. These phylogenies provide frameworks for investigating patterns and processes of ecological adaptation, speciation, and extinction across a hyperdiverse group of mammals.
The project will generate hypotheses about the evolutionary relationships of 5 different groups of bats, each containing at least one exclusively Antillean species. These evolutionary relationships will then be used to establish the timing and pattern of separation among bat species in the Antilles and their South and Central American relatives, and will also be compared with similar hypotheses about other terrestrial organisms. Drs. Nancy Simmons, Rob DeSalle, and Liliana Davalos will use standard methods for obtaining and analyzing morphological and molecular data from the study groups. Patterns of evolutionary relationships resulting from these data will be compared applying at least 5 different approaches.
High viral tolerance coupled with an extraordinary regulation of the immune response makes bats a great model to study host-pathogen evolution. Although many immune-related gene gains and losses have been previously reported in bats, important gene families such as antimicrobial peptides (AMPs) remain understudied. We built an exhaustive bioinformatic pipeline targeting the major gene families of defensins and cathelicidins to explore AMP diversity and analyze their evolution and distribution across six bat families. A combination of manual and automated procedures identified 29 AMP families across queried species, with α-, β-defensins, and cathelicidins representing around 10% of AMP diversity. Gene duplications were inferred in both α-defensins, which were absent in five species, and three β-defensin gene subfamilies, but cathelicidins did not show significant shifts in gene family size and were absent in Anoura caudifer and the pteropodids. Based on lineage-specific gains and losses, we propose diet and diet-related microbiome evolution may determine the evolution of α- and β-defensins gene families and subfamilies. These results highlight the importance of building species-specific libraries for genome annotation in non-model organisms and shed light on possible drivers responsible for the rapid evolution of AMPs. By focusing on these understudied defenses, we provide a robust framework for explaining bat responses to pathogens.
Evolvability is an emergent hallmark of cancer that depends on intra-tumor heterogeneity and, ultimately, genetic variation. Mutations generated by APOBEC3 cytidine deaminases can contribute to genetic variation and the consequences of APOBEC activation differ depending on the stage of cancer, with the most significant impact observed during the early stages. However, how APOBEC activity shapes evolutionary patterns of genes in the host genome and differential impacts on cancer-associated and non-cancer genes remain unclear. Analyzing over 40,000 human protein-coding transcripts, we identified distinct distribution patterns of APOBEC3A/B TC motifs between cancer-related genes and controls, suggesting unique associations with cancer. Studying a bat species with many more APOBEC3 genes, we found diverse motif patterns in orthologs of cancer genes compared to controls, similar to humans and suggesting APOBEC evolution to reduce impacts on the genome rather than the converse. Simulations confirmed that APOBEC-induced heterogeneity enhances cancer evolution, shaping clonal dynamics through bimodal introduction of mutations in certain classes of genes. Our results suggest that a major consequence of the bimodal distribution of APOBEC affects greater cancer heterogeneity.
APOBEC3, an enzyme subfamily that plays a role in virus restriction by generating mutations at particular DNA motifs or mutational ‘hotspots’, can drive viral mutagenesis with host-specific preferential hotspot mutations contributing to pathogen variation. While previous analysis of viral genomes from the 2022 Mpox (formerly Monkeypox) disease outbreak has shown a high frequency of C>T mutations at TC motifs, suggesting recent mutations are human APOBEC3-mediated, how emerging monkeypox virus (MPXV) strains will evolve as a consequence of APOBEC3-mediated mutations remains unknown. By measuring hotspot under-representation, depletion at synonymous sites, and a combination of the two, we analyzed APOBEC3-driven evolution in human poxvirus genomes, finding varying hotspot under-representation patterns. While the native poxvirus molluscum contagiosum exhibits a signature consistent with extensive coevolution with human APOBEC3, including depletion of TC hotspots, variola virus shows an intermediate effect consistent with ongoing evolution at the time of eradication. MPXV, likely the result of recent zoonosis, showed many genes with more TC hotspots than expected by chance (over-representation) and fewer GC hotspots than expected (under-representation). These results suggest the MPXV genome: (1) may have evolved in a host with a particular APOBEC GC hotspot preference, (2) has inverted terminal repeat (ITR) regions—which may be exposed to APOBEC3 for longer during viral replication—and longer genes likely to evolve faster, and therefore (3) has a heightened potential for future human APOBEC3-meditated evolution as the virus spreads in the human population. Our predictions of MPXV mutational potential can both help guide future vaccine development and identification of putative drug targets and add urgency to the task of containing human Mpox disease transmission and uncovering the ecology of the virus in its reservoir host.