Biology
Our faculty are interested in a wide range of organisms and research areas. They have received funding from the John Templeton Foundation, the National Institutes of Health, the National Science Foundation, and other prestigious funding agencies and foundations.
Areas of Research include:
- Animal behavior
- Bioinformatics
- Cell biology
- Development
- Ecology
- Evolution
- Genetics
- Marine biology
- Molecular biology
- Molecular evolution/systematics
- Neuroscience
- Physiology
- Population biology
- Signal Transduction
Submissions from 2024
Many-to-many mapping: A simulation study of how the number of traits and tasks affect the evolution of form and function, Philip Bergmann and Isabel Tonelli-Sippel
A genotyping array for the globally invasive vector mosquito, Aedes albopictus, Luciano Veiga Cosme, Margaret Corley, Thomas Johnson, Dave W. Severson, Guiyun Yan, Xiaoming Wang, Nigel Beebe, Andrew Maynard, Mariangela Bonizzoni, Ayda Khorramnejad, Ademir Jesus Martins, José Bento Pereira Lima, and Todd P. Livdahl
The effects of land use change on ant communities in New England, Amelia K.L. Curry, Joseph A. Nelsen, Dale R. Stevens, and Kaitlyn A. Mathis
Transcription factor expression landscape in Drosophila embryonic cell lines, Robert A. Drewell, Daniel Klonaros, and Jacqueline Dresch
The effect of urbanization and temperature on thermal tolerance, foraging performance, and competition in cavity-dwelling ants, Brooke A. Harris, Dale Stevens, and Kaitlyn A. Mathis
Sulfur assimilation using gaseous carbonyl sulfideby the soil fungus Trichoderma harzianum, Ryuka Iizuka, Shohei Hattori, Yusuke Kosaka, Yoshihito Masaki, Yusuke Kawano, Iwao Ohtsu, David Hibbett, Yoko Katayama, and Makoto Yoshida
Are weapon allometries steeper in major or minor males? A meta-analysis, Sydney A. Kochensparger
An exploration of how plant and soil characteristics shape the Hypericum perforatum microbiome in three habitats, Renee H. Petipas, Steven A. Higgins, Chantal Koechli, Spencer J. Davenport, Chandra Jack, Monica A. Geber, and Daniel A. Buckley
The role of ant-mediated biological interactions in agroecosystems, Madison Sankovitz, Monique J. Rivera, Tobias Manjarress, and Kaitlyn A. Mathis
Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus, Jacob L. Steenwyck, Charu Balamurugan, Huzefa A. Raja, Carla Gonçalves, Ningxiao Li, Frank Martin, Judith Berman, Nicholas H. Oberlies, John G. Gibbons, Gustavo H. Goldman, David M. Geiser, Jos Houbraken, David Hibbett, and Antonis Rokas
Herptile gut microbiomes: a natural system to study multi-kingdom interactions between filamentous fungi and bacteria, Lluvia Vargas-Gastélum, Alexander S. Romer, Marjan Ghotbi, Jason W. Dallas, Reed. N. Alexander, Kylie C. Moe, Kerry L. McPhail, George F. Neuhaus, Leila Shadmani, Joseph W. Spatafora, Jason E. Stajich, Javier F. Tabima, and Donald M. Walker
Capitella teleta gets left out: possible evolutionary shift causes loss of left tissues rather than increased neural tissue from dominant-negative BMPR1, Nicole B. Webster and Néva P. Meyer
Population-level immunologic variation in wild threespine stickleback (Gasterosteus aculeatus), Anika M. Wohlleben, Javier F. Tabima, Néva P. Meyer, and Natalie C. Steinel
Submissions from 2023
New tRNA-targeting transposons that hijack phage and vesicles, Emily Dart and Nathan A. Ahlgren
Diverse Marine T4-like Cyanophage Communities Are Primarily Comprised of Low-Abundance Species Including Species with Distinct Seasonal, Persistent, Occasional, or Sporadic Dynamics, Emily Dart, Jed A. Fuhrman, and Nathan A. Ahlgren
Investigating the sequence landscape in the Drosophila initiator core promoter element using an enhanced MARZ algorithm, Jacqueline Dresch, Regan D. Conrad, Daniel Klonaros, and Robert Drewell
The Dictyostelium discoideum genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing, Robert Drewell, Tayla C. Cormier, Jacob L. Steenwyk, James St Denis, Javier F. Tabima, Jacqueline Dresch, and Denis A. Larochelle
Vertical habitat stratification in Aedes triseriatus and Aedes hendersoni (Diptera: Culicidae): complications associated with sloped and flood-prone landscapes, Jamie Fitzgerald and Todd P. Livdahl
Transcriptome profile in Drosophila Kc and S2 embryonic cell lines, Daniel Klonaros, Jacqueline M. Dresch, and Robert A. Drewell
Comparative Genomic Analysis of 31 Phytophthora Genomes Reveals Genome Plasticity and Horizontal Gene Transfer, Brent A. Kronmiller, Nicolas Feau, Danyu Shen, Javier F. Tabima, Shahin S. Ali, Andrew D. Armitage, Felipe Arredondo, Bryan A. Bailey, Stephanie R. Bollmann, Angela Dale, Richard J. Harrison, Kelly Hrywkiw, Takao Kasuga, Rebecca McDougal, Charlotte F. Nellist, Preeti Panda, Sucheta Tripathy, Nari M. Williams, Wenwu Ye, Yuanchao Wang, Richard C. Hamelin, and Niklaus Grünwald
Transcriptomics of Temporal- versus Substrate-Specific Wood Decay in the Brown-Rot Fungus Fibroporia radiculosa, Byoungnam Min, Steven Ahrendt, Anna Lipzen, Cristina E. Toapanta, Robert A. Blanchette, Dan Cullen, and David Hibbett
Unraveling the functional dark matter through global metagenomics, Georgios A. Pavlopoulos, Fotis A. Baltoumas, Sirui Liu, Oguz Selvitopi, Antonio Pedro Camargo, Stephen Nayfach, Ariful Azad, Simon Roux, Lee Call, Natalia N. Ivanova, Min I. Chen, David Paez-Espino, Evangelos Karatzas, and Nathan Ahlgren
Behavioral diversity and biomechanical determinants of the outcome of a fish predator–prey interaction, Milton Q.G.A., III and Philip Bergmann
Phylogenomics reveals the history of host use in mosquitoes, John Soghigan, Charles Sither, Silvia Andrade Justi, Gen Morinaga, Brian K. Cassel, Christopher J. Vitek, Todd P. Livdahl, Siyang Xia, Andrea Gloria-Soria, Jeffrey R. Powell, Thomas Zavortink, Christopher M. Hardy, Nathan D. Burkett-Cadena, Lawrence E. Reeves, Richard C. Wilkerson, Robert R. Dunn, David K. Yeates, Maria Anice Sallum, Brian D. Byrd, Michelle D. Trautwein, Yvonne-Marie Linton, Michael H. Reiskind, and Brian M. Wiegmann
Rapid New Diagnostic LAMP (Loop-Mediated Isothermal Amplification) Assays to Distinguish Among the Four Lineages of Phytophthora ramorum, Kelsey L. Søndreli, Javier F. Tabima Restrepo, and Jared M. LeBoldus
Evolution of chemical-cue-mediated antipredator behavior in threespine stickleback populations experiencing northern pike predation, Dale R. Stevens, Melissa A. Graham, Christina I. Bardjis, Susan A. Foster, John A. Baker, and Kaitlyn A. Mathis
Integrating environmental complexity and the plasticity-first hypothesis to study responses to human-altered habitats, Dale R. Stevens, Matthew Wund, and Kaitlyn B. Mathis
Multiple measures of structural racism as predictors of U.S. county-level COVID-19 cases and deaths, Rosalie A. Torres Stone, Nathan A. Ahlgren, and Philip J. Bergmann
Editorial: MorphoEvoDevo: a multilevel approach to elucidate the evolution of metazoan organ systems, Andreas Wanninger, Pedro Martinez, and Néva P. Meyer
Submissions from 2022
County-level societal predictors of COVID-19 cases and deaths changed through time in the United States: A longitudinal ecological study, Philip J. Bergmann, Nathan A. Ahlgren, and Rosalie A. Torres Stone
Performance and Kinematic Differences Between Terrestrial and Aquatic Running in Anolis Sagrei, Amy Y. Cheu, Samantha A. Reed, Sara D. Mann, and Philip J. Bergmann
Coordinating tiny limbs and long bodies: Geometric mechanics of lizard terrestrial swimming, Baxi Chong, Tianyu Wang, Eva Erickson, Philip J. Bergmann, and Daniel I. Goldman
Genome Sequence of the Estuarine Synechococcus sp. Strain NB0720_010, Campbell A. MacKenzie, Marcia F. Marston, Javier F. Tabima, and Nathan A. Ahlgren
Submissions from 2021
How head shape and substrate particle size affect fossorial locomotion in lizards, Philip J. Bergmann and David S. Berry
Linking ecomechanical models and functional traits to understand phenotypic diversity, Timothy E. Higham, Lara A. Ferry, Lars Schmitz, Duncan J. Irschick, Samuel Starko, Philip S.L. Anderson, Philip J. Bergmann, Heather A. Jamniczky, Leandro R. Monteiro, Dina Navon, Julie Messier, Emily Carrington, Stacy C. Farina, Kara L. Feilich, L. Patricia Hernandez, Michele A. Johnson, Sandy M. Kawano, Chris J. Law, Sarah J. Longo, Christopher H. Martin, Patrick T. Martone, Alejandro Rico-Guevara, Sharlene E. Santana, and Karl J. Niklas
Niche partitioning of low-light adapted Prochlorococcus subecotypes across oceanographic gradients of the North Pacific Subtropical Front, Anne W. Thompson, Kathleen Kouba, and Nathan A. Ahlgren
Submissions from 2020
Genomic mosaicism underlies the adaptation of marine Synechococcus ecotypes to distinct oceanic iron niches, Nathan A. Ahlgren, Bernard Shafer Belisle, and Michael D. Lee
Genome sequences of synechococcus sp. Strain MIT S9220 and cocultured cyanophage SynMITS9220M01, B. Shafer Belisle, Andres A.Avila Paz, Angelina R. Carpenter, Tayla C. Cormier, Adam J. Lewis, Linnea S. Menin, Daniel R. Oliveira, Bukyung Song, Amy Szeto, Elizabeth I. Tchantouridze, Kayleigh A. Watson, Mary T. Yohannes, and Nathan A. Ahlgren
Convergent evolution of elongate forms in craniates and of locomotion in elongate squamate reptiles, Philip J. Bergmann, Sara D.W. Mann, Gen Morinaga, Elyse S. Freitas, and Cameron D. Siler
Locomotion and palaeoclimate explain the re-evolution of quadrupedal body form in Brachymeles lizards, Philip J. Bergmann, Gen Morinaga, Elyse S. Freitas, Duncan J. Irschick, Günter P. Wagner, and Cameron D. Siler
Using 3D-digital photogrammetry to examine scaling of the body axis in burrowing skinks, Leah DeLorenzo, Abby Vander Linden, Philip J. Bergmann, Gunter P. Wagner, Cameron D. Siler, and Duncan J. Irschick
Genetic tool development in marine protists: emerging model organisms for experimental cell biology, Drahomíra Faktorová, R. Ellen R. Nisbet, José A. Fernández Robledo, Elena Casacuberta, Lisa Sudek, Andrew E. Allen, Manuel Ares, Cristina Aresté, Cecilia Balestreri, Adrian C. Barbrook, Patrick Beardslee, Sara Bender, David S. Booth, François Yves Bouget, Chris Bowler, Susana A. Breglia, Colin Brownlee, Gertraud Burger, Heriberto Cerutti, Rachele Cesaroni, Miguel A. Chiurillo, Thomas Clemente, Duncan B. Coles, Jackie L. Collier, Elizabeth C. Cooney, Kathryn Coyne, Roberto Docampo, Christopher L. Dupont, Virginia Edgcomb, Elin Einarsson, Pía A. Elustondo, and Deborah Robertson
Long-term stability and Red Queen-like strain dynamics in marine viruses, J. Cesar Ignacio-Espinoza, Nathan A. Ahlgren, and Jed A. Fuhrman
Evolution of fossorial locomotion in the transition from tetrapod to snake-like in lizards, Gen Morinaga and Philip J. Bergmann
Identifying viruses from metagenomic data using deep learning, Jie Ren, Kai Song, Chao Deng, Nathan A. Ahlgren, Jed A. Fuhrman, Yi Li, Xiaohui Xie, Ryan Poplin, and Fengzhu Sun
Investigating cellular and molecular mechanisms of neurogenesis in Capitella teleta sheds light on the ancestor of Annelida, A. Sur, A. Renfro, P. J. Bergmann, and N. P. Meyer
A network-based integrated framework for predicting virus–prokaryote interactions, Weili Wang, Jie Ren, Kujin Tang, Emily Dart, Julio Cesar Ignacio-Espinoza, Jed A. Fuhrman, Jonathan Braun, Fengzhu Sun, and Nathan A. Ahlgren
Submissions from 2019
Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes, Nathan A. Ahlgren, Clara A. Fuchsman, Gabrielle Rocap, and Jed A. Fuhrman
Multi-year dynamics of fine-scale marine cyanobacterial populations are more strongly explained by phage interactions than abiotic, bottom-up factors, Nathan A. Ahlgren, Jessica N. Perelman, Yi Chun Yeh, and Jed A. Fuhrman
The convergent evolution of snake-like forms by divergent evolutionary pathways in squamate reptiles*, Philip J. Bergmann and Gen Morinaga
Marine Synechococcus isolates representing globally abundant genomic lineages demonstrate a unique evolutionary path of genome reduction without a decrease in GC content, Michael D. Lee, Nathan A. Ahlgren, Joshua D. Kling, Nathan G. Walworth, Gabrielle Rocap, Mak A. Saito, David A. Hutchins, and Eric A. Webb
Angles and waves: intervertebral joint angles and axial kinematics of limbed lizards, limbless lizards, and snakes, Gen Morinaga and Philip J. Bergmann
Optimizing de novo genome assembly from PCR-amplified metagenomes, Simon Roux, Gareth Trubl, Danielle Goudeau, Nandita Nath, Estelle Couradeau, Nathan A. Ahlgren, Yuanchao Zhan, David Marsan, Feng Chen, Jed A. Fuhrman, Trent R. Northen, Matthew B. Sullivan, Virginia I. Rich, Rex R. Malmstrom, and Emiley A. Eloe-Fadrosh
Submissions from 2018
Dynamics of Prochlorococcus Diversity and Photoacclimation During Short-Term Shifts in Water Column Stratification at Station ALOHA, Anne W. Thompson, Ger van den Engh, Nathan A. Ahlgren, Kathleen Kouba, Samantha Ward, Samuel T. Wilson, and David M. Karl
Are there general laws for digit evolution in squamates? The loss and re-evolution of digits in a clade of fossorial lizards (Brachymeles, Scincinae), Günter P. Wagner, Oliver W. Griffith, Philip J. Bergmann, Gaelle Bello-Hellegouarch, Tiana Kohlsdorf, Anjan Bhullar, and Cameron D. Siler
Submissions from 2017
Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems, Nathan A. Ahlgren, Yangyang Chen, David M. Needham, Alma E. Parada, Rohan Sachdeva, Vickie Trinh, Ting Chen, and Jed A. Fuhrman
Alignment-free d2∗ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences, Nathan A. Ahlgren, Jie Ren, Yang Young Lu, Jed A. Fuhrman, and Fengzhu Sun
It’s just sand between the toes: How particle size and shape variation affect running performance and kinematics in a generalist lizard, Philip J. Bergmann, Kyle J. Pettinelli, Marian E. Crockett, and Erika G. Schaper
Convergent body shapes have evolved via deterministic and historically contingent pathways in Lerista lizards, Gen Morinaga and Philip J. Bergmann
Genetic bases of fungal white rot wood decay predicted by phylogenomic analysis of correlated gene-phenotype evolution, Laszlo G. Nagy, Robert Riley, Philip J. Bergmann, Krisztina Krizsan, Francis M. Martin, Igor V. Grigoriev, Dan Cullen, and David Hibbett
Do the shuffle: Changes in Symbiodinium consortia throughout juvenile coral development, Hannah G. Reich, Deborah L. Robertson, and Gretchen Goodbody-Gringley
VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data, Jie Ren, Nathan A. Ahlgren, Yang Young Lu, Jed A. Fuhrman, and Fengzhu Sun
Prediction of virus-host infectious association by supervised learning methods, Mengge Zhang, Lianping Yang, Jie Ren, Nathan A. Ahlgren, Jed A. Fuhrman, and Fengzhu Sun
Submissions from 2016
Thermal and moisture habitat preferences do not maximize jumping performance in frogs, Allegra Mitchell and Philip J. Bergmann
Supplemental material for Reich 2016, Deborah Robertson, Hannah G. Reich, and Gretchen Goodbody-Gringley
Co-occurring Synechococcus ecotypes occupy four major oceanic regimes defined by temperature, macronutrients and iron, Jill A. Sohm, Nathan A. Ahlgren, Zachary J. Thomson, Cheryl Williams, James W. Moffett, Mak A. Saito, Eric A. Webb, and Gabrielle Rocap
Submissions from 2015
Hindlimb muscle anatomical mechanical advantage differs among joints and stride phases in basilisk lizards, Philip J. Bergmann and Meredith Hare-Drubka
Molecular Evolution of Nitrogen Assimilatory Enzymes in Marine Prasinophytes, Sohini Ghoshroy and Deborah L. Robertson
Submissions from 2014
The unique trace metal and mixed layer conditions of the costa rica upwelling dome support a distinct and dense community of Synechococcus, Nathan A. Ahlgren, Abigail Noble, Allison P. Patton, Kathryn Roache-Johnson, Laurel Jackson, Daniela Robinson, Cedar McKay, Lisa R. Moore, Mak A. Saito, and Gabrielle Rocap
Many-to-Many Mapping of Phenotype to Performance: An Extension of the F-Matrix for Studying Functional Complexity, Philip J. Bergmann and Eric J. McElroy
Submissions from 2013
Gene expression studies for the analysis of domoic acid production in the marine diatom Pseudo-nitzschia multiseries, Katie R. Boissonneault, Brooks M. Henningsen, Stephen S. Bates, Deborah L. Robertson, Sean Milton, Jerry Pelletier, Deborah A. Hogan, and David E. Housman
Tail autotomy, tail size, and locomotor performance in lizards, Eric J. McElroy and Philip J. Bergmann
Submissions from 2012
Diversity and distribution of marine Synechococcus: Multiple gene phylogenies for consensus classification and development of qPCR assays for sensitive measurement of clades in the ocean, Nathan A. Ahlgren and Gabrielle Rocap
The Evolution of Positive Allometry of Weaponry in Horned Lizards (Phrynosoma), Philip J. Bergmann and Camryn P. Berk
Vertebral evolution and the diversification of squamate reptiles, Philip J. Bergmann and Duncan J. Irschick
Spatial distribution and habitat utilization of the Zebra-tailed lizard (Callisaurus draconoides), Christopher L. Frost and Philip J. Bergmann
Molecular evolution of glutamine synthetase ii and iii in the chromalveolates, Sohini Ghoshroy and Deborah L. Robertson
Submissions from 2011
Aryl-homoserine lactone quorum sensing in stem-nodulating photosynthetic bradyrhizobia, Nathan A. Ahlgren, Caroline S. Harwood, Amy L. Schaefer, Eric Giraud, and E. Peter Greenberg
Submissions from 2010
Alternate pathways of body shape evolution translate into common patterns of locomotor evolution in two clades of lizards, Philip J. Bergmann and Duncan J. Irschick
Molecular evolution of glutamine synthetase II: Phylogenetic evidence of a non-endosymbiotic gene transfer event early in plant evolution, Sohini Ghoshroy, Manfred Binder, Aurélien Tartar, and Deborah L. Robertson
Aedes aegypti and Aedes albopictus in Bermuda: Extinction, invasion, invasion and extinction, Laran Kaplan, David Kendell, Deborah Robertson, Todd Livdahl, and Camilo Khatchikian
Characterization of three mnp genes of fomitiporia mediterranea and report of additional class ii peroxidases in the order hymenochaetales, Ingo Morgenstern, Deborah L. Robertson, and David Hibbett
Phylogenetic, structural and functional diversification of nitrate transporters in three ecologically diverse clades of mushroom-forming fungi, Jason C. Slot, Kelly N. Hallstrom, P. Brandon Matheny, Kentaro Hosaka, Gregory Mueller, Deborah L. Robertson, and David S. Hibbett
Submissions from 2009
Directional evolution of stockiness coevolves with ecology and locomotion in lizards, Philip J. Bergmann, Jay J. Meyers, and Duncan J. Irschick
Unraveling the regulation of nitrogen assimilation in the marine diatom thalassiosira pseudonana (bacillariophyceae): Diurnal variations in transcript levels for five genes involved in nitrogen assimilation, Kathryn L. Brown, Katrina I. Twing, and Deborah L. Robertson
Submissions from 2008
Hydrophobins Sc3 and Sc4 gene expression in mounds, fruiting bodies and vegetative hyphae of Schizophyllum commune, Goutami Banerjee, Deborah L. Robertson, and Thomas J. Leonard
Taxonomic identity in microbial eukaryotes: A practical approach using the testate amoeba Centropyxis to resolve conflicts between old and new taxonomic descriptions, Daniel J.G. Lahr, Philip J. Bergmann, and Sônia G.B.C. Lopes
Submissions from 2007
Systematics and biogeography of the widespread Neotropical gekkonid genus Thecadactylus (Squamata), with the description of a new cryptic species, Philip J. Bergmann and Anthony P. Russell
Submissions from 2006
Culture isolation and culture-independent clone libraries reveal new marine Synechococcus ecotypes with distinctive light and N physiologies, Nathan A. Ahlgren and Gabrielle Rocap
Measurement of Prochlorococcus ecotypes using real-time polymerase chain reaction reveals different abundances of genotypes with similar light physiologies, Nathan A. Ahlgren, Gabrielle Rocap, and Sallie W. Chisholm
Differential segmental growth of the vertebral column of the rat (Rattus norvegicus), Philip J. Bergmann, Amanda D. Melin, and Anthony P. Russell
Effects of temperature on maximum acceleration, deceleration and power output during vertical running in geckos, Phillip Bergmann and Duncan J. Irschick
Evolution of glutamine synthetase in heterokonts: Evidence for endosymbiotic gene transfer and the early evolution of photosynthesis, Deborah L. Robertson and Aurélien Tartar
Submissions from 2005
Effects of temperature on maximum clinging ability in a diurnal gecko: Evidence for a passive clinging mechanism?, Philip J. Bergmann and Duncan J. Irschick
A phylogeographically distinct and deep divergence in the widespread Neotropical turnip-tailed gecko, Thecadactylus rapicauda, D. J.C. Kronauer, P. J. Bergmann, J. M. Mercer, and A. P. Russell
Mammalian postnatal growth estimates: The influence of weaning on the choice of a comparative metric, Amanda D. Melin, Philip J. Bergmann, and Anthony P. Russell
Response of glutamine synthetase gene transcription and enzyme activity to external nitrogen sources in the diatom Skeletonema costatum (Bacillariophyceae), Misaki Takabayashi, Frances P. Wilkerson, and Deborah Robertson
Submissions from 2004
Modulated but conserved segmental growth of the original tail in Callisaurus draconoides (Phrynosomatidae) and Calotes versicolor (Agamidae), Philip J. Bergmann, Amanda M. Hobbs, Miranda L. Kavalench, and Anthony P. Russell
Submissions from 2003
Tail growth in Chamaeleo dilepis (Sauria: Chamaeleonidae): Functional implications of segmental patterns, Philip J. Bergmann, Sarah Lessard, and Anthony P. Russell
Lamella and scansor numbers in Thecadactylus rapicauda (Gekkonidae): Patterns revealed through correlational analysis and implications for systematic and functional studies, Philip J. Bergmann and Anthony P. Russell
