Welcome to the Lab

Studying the evolution of traits, species and their conservation

Photo by Angelique Corthals

Experience

Professor
Stony Brook University
May 2008 - Present · New York
Responsibilities include:
  • Project leadership
  • Course design, instruction & assessment
  • Service

  • Lecturer
    Open University
    January 2007 - May 2008 · Milton Keynes

    Taught evolution and researched molecular ecology

    Honors & Awards

    Human Frontier Science Program Award
    Human Frontier Science Program
    July 2019 - June 2022

    To investigate evolution and mechanisms of seasonal reversible size changes in a mammal.

    See notice

    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.

    See profile

    Lab Members

    .js-id-Researchers

    Julie Micko

    UG student.

    Jessica Semel

    UG student.

    Aaron Goldberg

    Graduated (MA) Spring 2011.

    Alessondra Bruno

    Kings Park High School, 2014.

    Alex Lengers

    Graduated (MA) Spring 2017.

    Alexis Brown

    PhD Student and RAPID RA.

    Anna McPherran

    PhD Student and STRIDE Fellow.

    Anne Szeto

    Graduated (BSc) Spring 2011.

    Dimensions REU, 2015.

    Bonnie Lei

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

    Brandon Baird

    Brandon graduated (BSc) Spring 2011. Joined the CUNY Graduate Program in 2013.

    Cameron Morales

    Sanford H. Calhoun High School, 2014.

    Clara Tucker

    UG student.

    Courtney Cheng

    Smithtown High School East, 2014.

    DJ Pantino

    Graduated (BSc) Spring 2013.

    Danny Rojas

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

    Edward Li

    Stuyvesant High School, 2013.

    Elise Lauterbur

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

    Elodia Caballero

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

    Emily Leung

    Graduated (BSc) Spring 2015.

    Fanny Cornejo

    IDPAS PhD candidate.

    Gabrielle Donnelly

    Smithtown High School East, 2013.

    Genna Tudda

    Graduated (MA) Spring 2013.

    Gregory Poterewicz

    US-FWS REU, 2013-2015.

    Hannah Rosenthal

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

    Johana Peña

    Brentwood High School, 2012.

    US-FWS REU, 2016.

    Jonah Rothleder

    Jonah graduated (BSc) Spring 2013.

    Kaitlyn Malewicz

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

    Katie Martin

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

    Kendra Cornejo

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

    Kenneth He

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

    Kristjan Mets

    PhD Candidate and OVPR RA.

    Laura Barger

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

    Laurel Yohe

    Graduated (PhD) Spring 2018, Dimensions postdoctoral researcher 2018-2019. Currently a NSF postdoctoral researcher at Yale University.

    Margarita Bartasunaite

    Dimensions REU, 2015.

    Marianne S. Moore

    IRACDA Postdoctoral Fellow 2013-2015. Currently faculty at Arizona State University.

    Marisa Lim

    Graduated (PhD) Fall 2018. Currently a postdoctoral researcher at the Wildlife Conservation Society.

    Mark Hall

    Completed his volunteer project in 2012.

    Melissa Zheng

    Graduated (BSc) Spring 2012.

    Nancy Wei

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

    Nicolette Sipperly

    PhD Candidate (Hollister lab).

    Omar M. Warsi

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

    Paul Donat

    PhD Candidate (Hollister lab) and Rules of Life RA.

    Peter J. Connell

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

    Ramatu Abubakar

    Dimensions REU, 2015.

    Romain Dahan

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

    Samantha DeRosa

    Smithtown High School West, 2014.

    Samantha DelSerra

    Graduated (MA) Winter 2014.

    Samuel Gochman

    Half Hollow Hills High School West, 2013.

    Dimensions REU, 2015.

    Undergraduate researcher, 2018-2019.

    Trinity Chen

    UG student.

    William R. Thomas

    PhD Student and HFSP RA.

    Xiaoyu Zhang

    Graduated (MA) Fall 2013.

    Yasin Perez

    Brentwood High School, 2013-2014.

    Yesha Shah

    Graduated (BSc) Spring 2013.

    Zachary Rowe

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

    Projects

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    Bat goblet cells as immuno-hotspots for infection of coronavirus

    Data available to new students. 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

    Data available to new students. 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

    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

    New students welcome! 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 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.

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

    Data available for new students. 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.

    Genomics of exceptions to scaling of longevity to body size

    Data available to new students. 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

    This training program responds to the challenges of new careers at teh 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

    Data available to new students. 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

    Data available to new students. 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

    Does not admit new students. 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

    Does not admit new students. 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.

    Recent Publications

    With over two-hundred species distributed across most of mainland Mexico, Central and South America, and islands in the Caribbean Sea, the Phyllostomidae bat family (American leaf-nosed bats) is one of the world’s most diverse mammalian families in terms of its trophic, or feeding, diversity. From an insectivorous ancestry, extant species have evolved into several dietary classes, including blood-feeding, vertebrate carnivory, and the consumption of nectar, pollen, and fruit, in a period of about 30 million years.

    Bats possess extraordinary adaptations, including flight, echolocation, extreme longevity and unique immunity. High-quality genomes are crucial for understanding the molecular basis and evolution of these traits. Here we incorporated long-read sequencing and state-of-the-art scaffolding protocols1 to generate, to our knowledge, the first reference-quality genomes of six bat species (Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pipistrellus kuhlii and Molossus molossus). We integrated gene projections from our ‘Tool to infer Orthologs from Genome Alignments’ (TOGA) software with de novo and homology gene predictions as well as short- and long-read transcriptomics to generate highly complete gene annotations. To resolve the phylogenetic position of bats within Laurasiatheria, we applied several phylogenetic methods to comprehensive sets of orthologous protein-coding and noncoding regions of the genome, and identified a basal origin for bats within Scrotifera. Our genome-wide screens revealed positive selection on hearing-related genes in the ancestral branch of bats, which is indicative of laryngeal echolocation being an ancestral trait in this clade. We found selection and loss of immunity-related genes (including pro-inflammatory NF-κB regulators) and expansions of anti-viral APOBEC3 genes, which highlights molecular mechanisms that may contribute to the exceptional immunity of bats. Genomic integrations of diverse viruses provide a genomic record of historical tolerance to viral infection in bats. Finally, we found and experimentally validated bat-specific variation in microRNAs, which may regulate bat-specific gene-expression programs. Our reference-quality bat genomes provide the resources required to uncover and validate the genomic basis of adaptations of bats, and stimulate new avenues of research that are directly relevant to human health and disease1.

    Although cases of independent adaptation to the same dietary niche have been documented in mammalian ecology, the molecular correlates of such shifts are seldom known. Here, we used genomewide analyses of molecular evolution to examine two lineages of bats that, from an insectivorous ancestor, have both independently evolved obligate frugivory: the Old World family Pteropodidae and the neotropical subfamily Stenodermatinae. New genome assemblies from two neotropical fruit bats (Artibeus jamaicensis and Sturnira hondurensis ) provide a framework for comparisons with Old World fruit bats. Comparative genomics of 10 bat species encompassing dietary diversity across the phylogeny revealed convergent molecular signatures of frugivory in both multigene family evolution and single‐copy genes. Evidence for convergent molecular adaptations associated with frugivorous diets includes the composition of three subfamilies of olfactory receptor genes, losses of three bitter taste receptor genes, losses of two digestive enzyme genes and convergent amino acid substitutions in several metabolic genes. By identifying suites of adaptations associated with the convergent evolution of frugivory, our analyses both reveal the extent of molecular mechanisms under selection in dietary shifts and will facilitate future studies of molecular ecology in mammals.

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    Contact

    • 631 632 1554
    • 630 Life Sciences Building, Stony Brook University, New York, 11794, USA
    • Wednesday 12:30 to 14:30
      or by appointment
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    Frequent Topics

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