Welcome to the Lab

Studying the evolution of traits, species and their conservation

Photo by Jan Pauel

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

    Aaron Goldberg

    Graduated (MA) Spring 2011.

    Alessondra Bruno

    Kings Park High School, 2014.

    Alex Lengers

    Graduated (MA) Spring 2017.

    Alexis Brown

    PhD Student.

    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 STRIDE Fellow.

    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 Dimensions/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.

    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

    .js-id-current

    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 Very Extended Phenotype: connecting genetics and evolution to ecological function

    Does not admit new students. 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; bees. Switched to bats, summer of 2019.

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

    Does not admit 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 new training program responds to this challenge 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

    Within‐clade allometric relationships represent standard laws of scaling between energy and size, and their outliers provide new avenues for physiological and ecological research. According to the metabolic level boundaries hypothesis, metabolic rates as a function of mass are expected to scale closer to 0.67 when driven by surface‐related processes (e.g., heat or water flux), while volume‐related processes (e.g., activity) generate slopes closer to one. In birds, daily energy expenditure (DEE) scales with body mass (M) in the relationship log (DEE) = 2.35 + 0.68 * log (M), consistent with surface‐level processes driving the relationship. However, taxon‐specific patterns differ from the scaling slope of all birds. Hummingbirds have the highest mass‐specific metabolic rates among all vertebrates. Previous studies on a few hummingbird species, without accounting for the phylogeny, estimated that the DEE‐body mass relationship for hummingbirds was log (DEE) = 1.72 + 1.21 * log (M). Contrary to theoretical expectations, this slope greater than 1 indicates that larger hummingbirds are less metabolically efficient than smaller hummingbirds. We collected DEE and mass data for 12 hummingbird species, which, combined with published data, represented 17 hummingbird species in eight of nine hummingbird clades over a six‐fold size range of body size (2.7 ‐ 17.5 g). After accounting for phylogenetic relatedness, we found daily energy expenditure scales with body mass as log (DEE) = 2.04 + 0.95 * log (M). This slope of 0.95 is lower than previously estimated for hummingbirds, but much higher than the slope for all birds (0.68). The high slopes of torpor, hovering and flight potentially explain the high interspecific DEE slope for hummingbirds compared to other endotherms.

    Gene duplication is a key source of evolutionary innovation, and multigene families evolve in a birth-death process, continuously duplicating and pseudogenizing through time. To empirically test hypotheses about adaptive expansion and contraction of multigene families across species, models infer gene gain and loss in light of speciation events and these inferred gene family expansions may lead to interpretations of adaptations in particular lineages. While the relative abundance of a gene subfamily in the subgenome may reflect its functional importance, tests based on this expectation can be confounded by the complex relationship between the birth-death process of gene subfamily evolution and the species phylogeny. Using simulations, we confirmed tree heterogeneity as a confounding factor in inferring multi-gene adaptation, causing spurious associations between shifts in birth-death rate and lineages with higher branching rates. We then used the olfactory receptor (OR) repertoire, the largest gene family in the mammalian genome, of different bat species with divergent diets to test whether expansions in olfactory receptors are associated with shifts to frugivorous diets. After accounting for tree heterogeneity, we robustly inferred that certain OR subfamilies exhibited expansions associated with dietary shifts to frugivory. Taken together, these results suggest ecological correlates of individual OR gene subfamilies can be identified, setting the stage for detailed inquiry into within-subfamily functional differences.

    Bats account for ~20% of all extant mammal species and are considered exceptional given their extraordinary adaptations, including biosonar, true flight, extreme longevity, and unparalleled immune systems. To understand these adaptations, we generated reference-quality genomes of six species representing the key divergent lineages. We assembled these genomes with a novel pipeline incorporating state-of-the-art long-read and long-range sequencing and assembly techniques. The genomes were annotated using a maximal evidence approach, de novo predictions, protein/mRNA alignments, Iso-seq long read and RNA-seq short read transcripts, and gene projections from our new TOGA pipeline, retrieving virtually all (>99%) mammalian BUSCO genes. Phylogenetic analyses of 12,931 protein coding-genes and 10,857 conserved non-coding elements identified across 48 mammalian genomes helped to resolve bats’ closest extant relatives within Laurasiatheria, supporting a basal position for bats within Scrotifera. Genome-wide screens along the bat ancestral branch revealed (a) selection on hearing-involved genes (e.g LRP2, SERPINB6, TJP2), which suggest that laryngeal echolocation is a shared ancestral trait of bats; (b) selection (e.g INAVA, CXCL13, NPSR1) and loss of immunity related proteins (e.g. LRRC70, IL36G), including pro-inflammatory NF-kB signalling; and © expansion of the APOBEC family, associated with restricting viral infection, transposon activity and interferon signalling. We also identified unique integrated viruses, indicating that bats have a history of tolerating viral pathogens, lethal to other mammal species. Non-coding RNA analyses identified variant and novel microRNAs, revealing regulatory relationships that may contribute to phenotypic diversity in bats. Together, our reference-quality genomes, high-quality annotations, genome-wide screens and in-vitro tests revealed previously unknown genomic adaptations in bats that may explain their extraordinary traits.

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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
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