Dávalos Lab

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?

Dávalos Lab
Nicolette Sipperly presents at Botany 2023
Nicolette Sipperly presents at Botany 2023

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 present at Evolution 2023
Doctoral candidates present at Evolution 2023

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

Liliana M. Dávalos

Professor of Conservation Biology

Stony Brook University

Principal Investigator

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.

Interests
  • Molecular Evolution
  • Phylogenetics
  • Environmental Science
Education
  • 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)

Experience

Professor
Stony Brook University
May 2008 - Present · New York
  • Instructor and research lab leader
  • External fundraising for research: >$6.2M, >$3.1M as principal investigator
  • Internal team management: >10-person team of scientists ranging from undergraduate to postdoctoral researchers
  • Generating, coordinating, and leading collaborations: successfully delivering global multi-team projects

  • Awards Director
    Society for Systematic Biologists
    Apr 2020 - Jun 2023
  • Judging panel convener and organizer for three annual awards
  • Allocated $150K in research awards based on scientific merit primarily to graduate students
  • Generated instructions and rubrics to improve chance from applicants from diverse backgrounds
  • Coordinated and conducted surveys in support for diversity, inclusion, and equity goals

  • Consultant
    United Nations Office on Drug and Crime
    2021 - 2022
  • Study designer and data analyst
  • Analyzed literature on main deforestation drivers in the Amazon
  • Designed, interpreted, and visualized Bayesian geostatistical models
  • Coordinated and wrote the report

  • Honors & Awards

    Inaugural cohort of Fulbright Amazonia
    Fulbright Amazonia 2022-2024
    June 2023 - December 2023

    To model the impacts of narco-trafficking and land grabbing in the Amazon.

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    Florida International University Biology Department
    2023 Glaser Visiting Professorship
    13-17 March 2023

    Center for Excellence in Learning and Teaching
    2022 Award for Excellence in Assessment
    5 May 2022

    2022 Celebration of Teaching Awards.

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    Middlebury College Environmental Studies Program
    Margolin Environmental Affairs Lecture
    22 April 2021

    This annual lecture, like the Environmental Studies Program, takes an interdisciplinary approach to the natural environment and human interaction with it.

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    Teaching Excellence Award
    Stony Brook University College of Arts and Sciences
    April 2016

    For outstanding teaching and true caring for students.


    Kavli Frontiers of Science Israeli-American Symposium
    Kavli Frontiers of Science
    June 2013

    Symposia bring together outstanding young scientists to discuss exciting advances and opportunities in a broad range of disciplines.

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    Meet the Lab

    Principal Investigator

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    Liliana M. Dávalos

    Professor of Conservation Biology

    Administration

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    Das Tuhi, Sayonthoni

    Lab Manager.

    Researchers

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    Rayfield, Kristen

    NSF Integrative Biology Postdoctoral Fellow.

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    Thomas, William R.

    Presidential Innovation and Excellence Fund Postdoctoral Fellow.

    Graduate Students

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    Brown, Alexis

    PhD Candidate and GFC RA.

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    Donat, Paul

    PhD Candidate.

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    Johnson, Kaylee

    PhD Student.

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    Michielsen, Nathan

    MSc Candidate.

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    Sipperly, Nicolette

    PhD Candidate and Hurst Della Pietra Donation RA.

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    Wood, Georgiana

    Ma student.

    Alumni

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    Abubakar, Ramatu

    Dimensions REU, 2015.

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    Afzal, Sanah

    Dimensions REU, 2015.

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    Baird, Brandon

    Brandon graduated (BSc) Spring 2011.

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    Barger, Laura

    Ward Melville High School, 2010. Graduated Spring 2011 and entered the University of Pennsylvania Fall 2011.

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    Bartasunaite, Margarita

    Dimensions REU, 2015.

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    Bedoya, Maria Alejandra

    Maria Alejandra graduated (BSc) Spring 2023. Currently at Cenicaña

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    Bruno, Alessondra

    Kings Park High School, 2014.

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    Caballero, Elodia

    Brentwood High School, 2012. Graduated Spring 2013 and entered Columbia University Fall 2013.

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    Chen, Trinity

    Graduated (BSc) Winter 2023.

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    Cheng, Courtney

    Smithtown High School East, 2014.

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    Connell, Peter J.

    Oceanside High School, 2010. Graduated Spring 2011 and entered SUNY Environmental Science and Forestry Fall 2011.

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    Cornejo, Fanny

    Former IDPAS PhD candidate.

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    Cornejo, Kendra

    Brentwood High School, 2010. Graduated Spring 2011 and entered Brown University Fall 2011.

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    Dahan, Romain

    Graduated (MA) Spring 2014. Joined a PhD at Arizona State University in 2014.

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    DelSerra, Samantha

    Graduated (MA) Winter 2014.

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    DeRosa, Samantha

    Smithtown High School West, 2014.

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    Donnelly, Gabrielle

    Smithtown High School East, 2013.

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    Gochman, Samuel

    Half Hollow Hills High School West, 2013.

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    Goldberg, Aaron

    Graduated (MA) Spring 2011.

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    Hall, Mark

    Completed his volunteer project in 2012.

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    He, Kenneth

    King’s Park High School, 2015. Graduated Spring 2016.

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    Heder, Sarah

    Undergraduate researcher, 2018-2019.

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    Islam, Amena

    Graduated (BSc) Spring 2021.

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    Lama, Tanya

    NSF Rules of Life and IRACDA Postdoctoral Fellow. Currently faculty at Smith College.

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    Lauterbur, M. Elise

    Graduated (PhD) Spring 2019. Currently a postdoctoral researcher at the University of Arizona.

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    Lei, Bonnie

    Walnut High School, 2010. Graduated Spring 2011, Harvard University 2015, currently at Microsoft.

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    Lengers, Alex

    Graduated (MA) Spring 2017.

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    Leung, Emily

    Graduated (BSc) Spring 2015.

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    Li, Edward

    Stuyvesant High School, 2013.

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    Lim, Marisa

    Graduated (PhD) Fall 2018. Currently a researcher at 10X Genomics.

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    Loop, Isabelle

    Graduated (BSc) Spring 2021.

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    Malewicz, Kaitlyn

    Undergraduate researcher, 2018-2019. Joined a PhD at Virginia Tech University.

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    Martin, Katie

    Graduated (MA) Spring 2017. Joined a PhD at the University of Central Florida.

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    McPherran, Anna

    Graduated (Ma) Spring 2022.

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    Medina, Mirena

    Graduated (BSc) Spring 2022.

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    Mets, Kristjan

    Graduated (PhD) Spring 2022.

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    Micko, Julie

    Graduated (BSc) Spring 2021.

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    Moore, Marianne S.

    IRACDA Postdoctoral Fellow 2013-2015. Currently faculty at the University of the Virgin Islands.

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    Morales, Cameron

    Sanford H. Calhoun High School, 2014.

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    Navillo, John

    US-FWS REU, 2016.

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    Pantino, DJ

    Graduated (BSc) Spring 2013.

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    Patil, Bhavana

    Dimensions REU, 2015.

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    Peña, Johana

    Brentwood High School, 2012.

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    Perez, Yasin

    Brentwood High School, 2013-2014.

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    Poterewicz, Gregory

    US-FWS REU, 2013-2015.

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    Rojas, Danny

    FCT-Portugal Postdoctoral Fellow 2013-2017. Currently faculty at Universidad Javeriana, Cali, Colombia.

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    Rosenthal, Hannah

    Smithtown High School West, 2015. Graduated Spring 2017 and entered Cornell University Fall 2017.

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    Rothleder, Jonah

    Graduated (BSc) Spring 2013.

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    Rowe, Zachary

    Smithtown High School East, 2012. Graduated Spring 2013, entered Stony Brook University Fall 2013.

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    Semel, Jessica

    Graduated (BSc) Spring 2021.

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    Shah, Yesha

    Graduated (BSc) Spring 2013.

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    Szeto, Anne

    Graduated (BSc) Spring 2011.

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    Talavera, Hannah

    Graduated (BSc) Spring 2023.

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    Tucker, Clara

    Graduated (Ma) Spring 2022.

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    Tudda, Genna

    Graduated (MA) Spring 2013.

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    Vaccaro, Sarah

    Graduated (BSc) Spring 2022.

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    Warsi, Omar M.

    Graduated (PhD) Fall 2014. Currently a researcher at Uppsala University.

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    Wei, Nancy

    Herricks High School, 2012. Graduated Spring 2013, entered Northwestern University (biological sciences) Fall 2013.

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    Yohe, Laurel R.

    Graduated (PhD) Spring 2017, Dimensions postdoctoral researcher 2017-2018. Currently faculty at University of North Carolina, Charlotte.

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    Zhang, Xiaoyu

    Graduated (MA) Fall 2013.

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    Zheng, Melissa

    Graduated (BSc) Spring 2012.

    .js-id-current
    Estimating the Impact of Narcotrafficking on Amazon Forest Conversion and LandGrabbing

    Estimating the Impact of Narcotrafficking on Amazon Forest Conversion and LandGrabbing

    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.

    A Path to Climate Stability: Unleashing the Power of Azolla for Carbon Sequestration

    A Path to Climate Stability: Unleashing the Power of Azolla for Carbon Sequestration

    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.

    Integrated mechanisms of environment-host-virome interactions

    Integrated mechanisms of environment-host-virome interactions

    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.

    Biochemical and genomic characterization of APOBEC-virus coevolution in bats

    Biochemical and genomic characterization of APOBEC-virus coevolution in bats

    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.

    Global Union of Bat Diversity Networks (GBatNet)

    Global Union of Bat Diversity Networks (GBatNet)

    Bats play critical roles in ecosystems globally. However, key aspects of bat biology, from the causes and consequences of population declines to their ability to transmit viruses to people, remain poorly understood. This AccelNet project establishes the Global Union of Bat Diversity Networks (GBatNet) to fill key knowledge gaps and create an international structure to accelerate discoveries across disciplines and borders. The network of networks fosters new avenues for global research exchange through coordination of joint research, education, and outreach. GBatNet links 14 regional and global networks with a shared vision to address pressing questions in bat biology of direct relevance to ecosystem and human health.

    Bat goblet cells as immuno-hotspots for infection of coronavirus

    Bat goblet cells as immuno-hotspots for infection of coronavirus

    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.

    Immunological adaptations in bats to moderate the effect of coronavirus infection

    Immunological adaptations in bats to moderate the effect of coronavirus infection

    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.

    Inter-Species Modeling for Spillback/Spillover Avoidance

    Inter-Species Modeling for Spillback/Spillover Avoidance

    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.

    Regrowing the brain; evolution and mechanisms of seasonal reversible size changes in a mammal

    Regrowing the brain; evolution and mechanisms of seasonal reversible size changes in a mammal

    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.

    The death and life of biodiversity: modeling extinction and resilience on islands

    The death and life of biodiversity: modeling extinction and resilience on islands

    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.

    The Very Extended Phenotype: connecting genetics and evolution to ecological function

    The Very Extended Phenotype: connecting genetics and evolution to ecological function

    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.

    Genomics of exceptions to scaling of longevity to body size

    Genomics of exceptions to scaling of longevity to body size

    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.

    Interdisciplinary Graduate Training to Understand and Inform Decision Processes Using Advanced Spatial Data Analysis and Visualization

    Interdisciplinary Graduate Training to Understand and Inform Decision Processes Using Advanced Spatial Data Analysis and Visualization

    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).

    Chance or necessity? Adaptive vs. non adaptive evolution in plant-frugivore interactions

    Chance or necessity? Adaptive vs. non adaptive evolution in plant-frugivore interactions

    The project focuses on a relatively unexplored yet crucial aspect of plant-animal mutualisms; volatile chemical communication between plants and vertebrate frugivores.

    Discovering genomic and developmental mechanisms that underlie sensory innovations critical to adaptive diversification

    Discovering genomic and developmental mechanisms that underlie sensory innovations critical to adaptive diversification

    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).

    Uncovering skin immune proteins as predictors of resistance against WNS

    Uncovering skin immune proteins as predictors of resistance against WNS

    The goal of this project was to discover the mechanisms underlying the survival of remnant populations in the WNS-affected area.

    Diversification in Noctilionoid Bats

    Diversification in Noctilionoid Bats

    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.

    Historical Biogeography of the Antilles

    Historical Biogeography of the Antilles

    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.

    The evolution of antimicrobial peptides in Chiroptera
    The evolution of antimicrobial peptides in Chiroptera

    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.

    Evolutionary potential of the monkeypox genome arising from interactions with human APOBEC3 enzymes
    Evolutionary potential of the monkeypox genome arising from interactions with human APOBEC3 enzymes

    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.