@article{taylor_allf_hopkins_irwin_jewell_nevo_nichols_rodríguez valerón_evans_sörensen_et al._2023, title={Nature's chefs: Uniting the hidden diversity of food making and preparing species across the tree of life}, volume={73}, ISSN={0006-3568 1525-3244}, url={http://dx.doi.org/10.1093/biosci/biad026}, DOI={10.1093/biosci/biad026}, abstractNote={
 There may be no such thing as a free meal, but many species have evolved mechanisms for other species to consume the literal fruits of their labors. In the present article, inspired by a chef's recognition that such species are “nature's chefs,” we consider food-making species from the plant, animal, and fungal kingdoms, which produce food or mimic food to increase their own fitness. We identify three ways that species can produce or prepare meals—as food, drinks, or lures—and further distinguish between those providing an honest meal and those deceiving consumers with food mimics. By considering these species holistically, we highlight new hypotheses about the ecology and evolution of the widespread phenomenon of organisms that produce food for other organisms. We find surprising and useful generalities and exceptions among species as different as apple trees and anglerfish by examining species interactions across taxa, systems, and disciplines.}, number={6}, journal={BioScience}, publisher={Oxford University Press (OUP)}, author={Taylor, Brad W and Allf, Bradley and Hopkins, Skylar R and Irwin, Rebecca E and Jewell, Michelle and Nevo, Omer and Nichols, Lauren M and Rodríguez Valerón, Nabila and Evans, Joshua D and Sörensen, Pia M and et al.}, year={2023}, month={Apr}, pages={408–421} }
 @article{mckenney_nichols_alvarado_hardy_kemp_polmanteer_shoemaker_dunn_2023, title={Sourdough starters exhibit similar succession patterns but develop flour-specific climax communities}, volume={11}, ISSN={["2167-8359"]}, DOI={10.7717/peerj.16163}, abstractNote={The microbial fermentation behind sourdough bread is among our oldest technologies, yet there are many opportunities for sourdough science to learn from traditional bakers. We analyzed 16S rRNA sequences in R to assess the bacterial community structure and performance of 40 starters grown from 10 types of flour over 14 days, and identified six distinct stages of succession. At each stage, bacterial taxa correlate with determinants of bread quality including pH, rise, and aromatic profile. Day 1 starter cultures were dominated by microorganisms commonly associated with plants and flour, and by aromas similar to toasted grain/cereal. Bacterial diversity peaked from days 2–6 as taxa shifted from opportunistic/generalist bacteria associated with flour inputs, toward specialized climax bacterial communities (days 10–14) characterized by acid-tolerant taxa and fruity (p < 3.03e−03), sour (p < 1.60e−01), and fermented (p < 1.47e−05) aromas. This collection of traits changes predictably through time, regardless of flour type, highlighting patterns of bacterial constraints and dynamics that are conserved across systems and scales. Yet, while sourdough climax communities exhibit similar markers of maturity (i.e., pH ≤ 4 and enriched in Lactobacillus (mean abundance 48.1%), Pediococcus (mean abundance 22.7%), and/or Gluconobacter (mean abundance 19.1%)), we also detected specific taxa and aromas associated with each type of flour. Our results address important ecological questions about the relationship between community structure and starter performance, and may enable bakers to deliberately select for specific sourdough starter and bread characteristics.}, journal={PEERJ}, author={Mckenney, Erin A. and Nichols, Lauren M. and Alvarado, Samuel and Hardy, Shannon and Kemp, Kristen and Polmanteer, Rachael and Shoemaker, April and Dunn, Robert R.}, year={2023}, month={Oct} }
 @article{dunn_burger_carlen_koltz_light_martin_munshi-south_nichols_vargo_yitbarek_et al._2022, title={A Theory of City Biogeography and the Origin of Urban Species}, url={https://doi.org/10.3389/fcosc.2022.761449}, DOI={10.3389/fcosc.2022.761449}, abstractNote={Many of the choices humans make with regard to infrastructure, urban planning and other phenomena have impacts that will last thousands of years. This can readily be seen in modern cities in which contemporary streets run along street grids that were laid out thousands of years prior or even in which ancient viaducts still play a role. However, rarely do evolutionary biologists explicitly consider the future of life likely to be associated with the decisions we are making today. Here, we consider the evolutionary future of species in cities with a focus on the origin of lineages and species. We do so by adjusting evolutionary predictions from the theory of island biogeography so as to correspond to the unique features of cities as islands. Specifically, the species endemic to cities tend to be associated with the gray habitats in cities. Those habitats tend to be dominated by human bodies, pet bodies and stored food. It is among such species where the origin of new lineages is most likely, although most research on evolution in cities has focused on green habitats. We conclude by considering a range of scenarios for the far future and their implications for the origin of lineages and species.}, author={Dunn, Robert R. and Burger, Joseph Robert and Carlen, Elizabeth J. and Koltz, Amanda M. and Light, Jessica E. and Martin, Ryan A. and Munshi-South, Jason and Nichols, Lauren M. and Vargo, Edward L. and Yitbarek, Senay and et al.}, year={2022} }
 @misc{frank_amato_trautwein_maia_liman_nichols_schwenk_breslin_dunn_2022, title={The evolution of sour taste}, volume={289}, ISSN={["1471-2954"]}, url={http://dx.doi.org/10.1098/rspb.2021.1918}, DOI={10.1098/rspb.2021.1918}, abstractNote={The evolutionary history of sour taste has been little studied. Through a combination of literature review and trait mapping on the vertebrate phylogenetic tree, we consider the origin of sour taste, potential cases of the loss of sour taste, and those factors that might have favoured changes in the valence of sour taste—from aversive to appealing. We reconstruct sour taste as having evolved in ancient fish. By contrast to other tastes, sour taste does not appear to have been lost in any major vertebrate taxa. For most species, sour taste is aversive. Animals, including humans, that enjoy the sour taste triggered by acidic foods are exceptional. We conclude by considering why sour taste evolved, why it might have persisted as vertebrates made the transition to land and what factors might have favoured the preference for sour-tasting, acidic foods, particularly in hominins, such as humans.}, number={1968}, journal={PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES}, author={Frank, Hannah E. R. and Amato, Katie and Trautwein, Michelle and Maia, Paula and Liman, Emily R. and Nichols, Lauren M. and Schwenk, Kurt and Breslin, Paul A. S. and Dunn, Robert R.}, year={2022}, month={Feb} }
 @article{calvert_madden_nichols_haddad_lahne_dunn_mckenney_2021, title={A review of sourdough starters: ecology, practices, and sensory quality with applications for baking and recommendations for future research}, volume={5}, url={https://doi.org/10.7717/peerj.11389}, DOI={10.7717/peerj.11389}, abstractNote={The practice of sourdough bread-making is an ancient science that involves the development, maintenance, and use of a diverse and complex starter culture. The sourdough starter culture comes in many different forms and is used in bread-making at both artisanal and commercial scales, in countries all over the world. While there is ample scientific research related to sourdough, there is no standardized approach to using sourdough starters in science or the bread industry; and there are few recommendations on future directions for sourdough research. Our review highlights what is currently known about the microbial ecosystem of sourdough (including microbial succession within the starter culture), methods of maintaining sourdough (analogous to land management) on the path to bread production, and factors that influence the sensory qualities of the final baked product. We present new hypotheses for the successful management of sourdough starters and propose future directions for sourdough research and application to better support and engage the sourdough baking community.}, journal={PEERJ}, author={Calvert, Martha D. and Madden, Anne A. and Nichols, Lauren M. and Haddad, Nick M. and Lahne, Jacob and Dunn, Robert R. and McKenney, Erin A.}, year={2021}, month={May} }
 @article{fitzgerald_stuble_nichols_diamond_wentworth_pelini_gotelli_sanders_dunn_penick_2021, title={Abundance of spring- and winter-active arthropods declines with warming}, volume={12}, ISSN={["2150-8925"]}, url={https://doi.org/10.1002/ecs2.3473}, DOI={10.1002/ecs2.3473}, abstractNote={.}, number={4}, journal={ECOSPHERE}, author={Fitzgerald, Jacquelyn L. and Stuble, Katharine L. and Nichols, Lauren M. and Diamond, Sarah E. and Wentworth, Thomas R. and Pelini, Shannon L. and Gotelli, Nicholas J. and Sanders, Nathan J. and Dunn, Robert R. and Penick, Clint A.}, year={2021}, month={Apr} }
 @article{webster_mcfarland_gebert_oliverio_nichols_dunn_hartmann_fierer_2021, title={Structure and Functional Attributes of Bacterial Communities in Premise Plumbing Across the United States}, volume={55}, ISSN={["1520-5851"]}, DOI={10.1021/acs.est.1c03309}, abstractNote={Microbes that thrive in premise plumbing can have potentially important effects on human health. Yet, how and why plumbing-associated microbial communities vary across broad spatial scales remain undetermined. We characterized the bacterial communities in 496 showerheads collected from across the continental United States. The overall community structure, determined by 16S rRNA gene amplicon sequencing, revealed high levels of bacterial diversity. Although a large fraction of the observed variation in community composition could not be explained, differences in bacterial community composition were associated with water supply (private well water vs public municipal water), water source (groundwater vs surface water), and associated differences in water chemistry (pH and chlorine). Most notably, showerheads in homes supplied with public water had higher abundances of Blastomonas, Mycobacterium, and Porphyrobacter, while Pseudorhodoplanes, Novosphingobium, and Nitrospira were more abundant in those receiving private well water. We conducted shotgun metagenomic analyses on 92 of these samples to assess differences in genomic attributes. Public water-sourced showerheads had communities enriched in genes related to lipid and xenobiotic metabolisms, virulence factors, and antibiotic resistance. In contrast, genes associated with oxidative stress and membrane transporters were over-represented in communities from private well water-sourced showerheads compared to those supplied by public water systems. These results highlight the broad diversity of bacteria found in premise plumbing across the United States and the role of the water source and treatment in shaping the microbial community structure and functional potential.}, number={20}, journal={ENVIRONMENTAL SCIENCE & TECHNOLOGY}, author={Webster, Tara M. and McFarland, Alexander and Gebert, Matthew J. and Oliverio, Angela M. and Nichols, Lauren M. and Dunn, Robert R. and Hartmann, Erica M. and Fierer, Noah}, year={2021}, month={Oct}, pages={14105–14114} }
 @article{mesquita_nichols_gebert_vanderburgh_bocksberger_lester_kalan_dieguez_mccarthy_agbor_et al._2021, title={Structure of Chimpanzee Gut Microbiomes across Tropical Africa}, volume={6}, ISSN={["2379-5077"]}, url={https://doi.org/10.1128/mSystems.01269-20}, DOI={10.1128/mSystems.01269-20}, abstractNote={Gut microbial communities are drivers of primate physiology and health, but the factors that influence the gut microbiome in wild primate populations remain largely undetermined. We report data from a continent-wide survey of wild chimpanzee gut microbiota and highlight the effects of genetics, vegetation, and potentially even tool use at different spatial scales on the chimpanzee gut microbiome, including bacteria, archaea, and eukaryotic parasites. ABSTRACT Understanding variation in host-associated microbial communities is important given the relevance of microbiomes to host physiology and health. Using 560 fecal samples collected from wild chimpanzees (Pan troglodytes) across their range, we assessed how geography, genetics, climate, vegetation, and diet relate to gut microbial community structure (prokaryotes, eukaryotic parasites) at multiple spatial scales. We observed a high degree of regional specificity in the microbiome composition, which was associated with host genetics, available plant foods, and potentially with cultural differences in tool use, which affect diet. Genetic differences drove community composition at large scales, while vegetation and potentially tool use drove within-region differences, likely due to their influence on diet. Unlike industrialized human populations in the United States, where regional differences in the gut microbiome are undetectable, chimpanzee gut microbiomes are far more variable across space, suggesting that technological developments have decoupled humans from their local environments, obscuring regional differences that could have been important during human evolution. IMPORTANCE Gut microbial communities are drivers of primate physiology and health, but the factors that influence the gut microbiome in wild primate populations remain largely undetermined. We report data from a continent-wide survey of wild chimpanzee gut microbiota and highlight the effects of genetics, vegetation, and potentially even tool use at different spatial scales on the chimpanzee gut microbiome, including bacteria, archaea, and eukaryotic parasites. Microbial community dissimilarity was strongly correlated with chimpanzee population genetic dissimilarity, and vegetation composition and consumption of algae, honey, nuts, and termites were potentially associated with additional divergence in microbial communities between sampling sites. Our results suggest that host genetics, geography, and climate play a far stronger role in structuring the gut microbiome in chimpanzees than in humans.}, number={3}, journal={MSYSTEMS}, author={Mesquita, Clifton P. Bueno and Nichols, Lauren M. and Gebert, Matthew J. and Vanderburgh, Caihong and Bocksberger, Gaelle and Lester, Jack D. and Kalan, Ammie K. and Dieguez, Paula and McCarthy, Maureen S. and Agbor, Anthony and et al.}, year={2021}, month={Jun} }
 @article{madden_lahue_gordy_little_nichols_calvert_dunn_smukowski heil_2021, title={Sugar‐seeking insects as a source of diverse bread‐making yeasts with enhanced attributes}, volume={39}, ISSN={0749-503X 1097-0061}, url={http://dx.doi.org/10.1002/yea.3676}, DOI={10.1002/yea.3676}, abstractNote={Insects represent a particularly interesting habitat in which to search for novel yeasts of value to industry. Insect‐associated yeasts have the potential to have traits relevant to modern food and beverage production due to insect–yeast interactions, with such traits including diverse carbohydrate metabolisms, high sugar tolerance, and general stress tolerance. Here, we consider the potential value of insect‐associated yeasts in the specific context of baking. We isolated 63 yeast strains from 13 species of hymenoptera from the United States, representing 37 yeast species from 14 genera. Screening for the ability to ferment maltose, a sugar important for bread production, resulted in the identification of 13 strains of Candida, Lachancea, and Pichia species. We assessed their ability to leaven dough. All strains produced baked loaves comparable to a commercial baking strain of Saccharomyces cerevisiae. The same 13 strains were also grown under various sugar and salt conditions relevant to osmotic challenges experienced in the manufacturing processes and the production of sweet dough. We show that many of these yeast strains, most notably strains of Lachancea species, grow at a similar or higher rate and population size as commercial baker's yeast. We additionally assessed the comparative phenotypes and genetics of insect‐associated S. cerevisiae strains unable to ferment maltose and identified baking‐relevant traits, including variations in the HOG1 signaling pathway and diverse carbohydrate metabolisms. Our results suggest that non‐conventional yeasts have high potential for baking and, more generally, showcase the success of bioprospecting in insects for identifying yeasts relevant for industrial uses.}, number={1-2}, journal={Yeast}, publisher={Wiley}, author={Madden, Anne A. and Lahue, Caitlin and Gordy, Claire L. and Little, Joy L. and Nichols, Lauren M. and Calvert, Martha D. and Dunn, Robert R. and Smukowski Heil, Caiti}, year={2021}, month={Nov}, pages={108–127} }
 @article{landis_oliverio_mckenney_nichols_kfoury_biango-daniels_shell_madden_shapiro_sakunala_et al._2021, title={The diversity and function of sourdough starter microbiomes}, volume={10}, ISSN={2050-084X}, url={http://dx.doi.org/10.7554/eLife.61644}, DOI={10.7554/eLife.61644}, abstractNote={Humans have relied on sourdough starter microbial communities to make leavened bread for thousands of years, but only a small fraction of global sourdough biodiversity has been characterized. Working with a community-scientist network of bread bakers, we determined the microbial diversity of 500 sourdough starters from four continents. In sharp contrast with widespread assumptions, we found little evidence for biogeographic patterns in starter communities. Strong co-occurrence patterns observed in situ and recreated in vitro demonstrate that microbial interactions shape sourdough community structure. Variation in dough rise rates and aromas were largely explained by acetic acid bacteria, a mostly overlooked group of sourdough microbes. Our study reveals the extent of microbial diversity in an ancient fermented food across diverse cultural and geographic backgrounds.}, journal={eLife}, publisher={eLife Sciences Publications, Ltd}, author={Landis, Elizabeth A and Oliverio, Angela M and McKenney, Erin A and Nichols, Lauren M and Kfoury, Nicole and Biango-Daniels, Megan and Shell, Leonora K and Madden, Anne A and Shapiro, Lori and Sakunala, Shravya and et al.}, year={2021}, month={Jan} }
 @article{vecchi_kossi adakpo_dunn_nichols_penick_sanders_rebecchi_guidetti_2021, title={The toughest animals of the Earth versus global warming: Effects of long-term experimental warming on tardigrade community structure of a temperate deciduous forest}, volume={6}, ISSN={["2045-7758"]}, url={https://doi.org/10.1002/ece3.7816}, DOI={10.1002/ece3.7816}, abstractNote={Abstract Understanding how different taxa respond to global warming is essential for predicting future changes and elaborating strategies to buffer them. Tardigrades are well known for their ability to survive environmental stressors, such as drying and freezing, by undergoing cryptobiosis and rapidly recovering their metabolic function after stressors cease. Determining the extent to which animals that undergo cryptobiosis are affected by environmental warming will help to understand the real magnitude climate change will have on these organisms. Here, we report on the responses of tardigrades within a five‐year‐long, field‐based artificial warming experiment, which consisted of 12 open‐top chambers heated to simulate the projected effects of global warming (ranging from 0 to 5.5°C above ambient temperature) in a temperate deciduous forest of North Carolina (USA). To elucidate the effects of warming on the tardigrade community inhabiting the soil litter, three community diversity indices (abundance, species richness, and Shannon diversity) and the abundance of the three most abundant species (Diphascon pingue, Adropion scoticum, and Mesobiotus sp.) were determined. Their relationships with air temperature, soil moisture, and the interaction between air temperature and soil moisture were tested using Bayesian generalized linear mixed models. Despite observed negative effects of warming on other ground invertebrates in previous studies at this site, long‐term warming did not affect the abundance, richness, or diversity of tardigrades in this experiment. These results are in line with previous experimental studies, indicating that tardigrades may not be directly affected by ongoing global warming, possibly due to their thermotolerance and cryptobiotic abilities to avoid negative effects of stressful temperatures, and the buffering effect on temperature of the soil litter substrate.}, journal={ECOLOGY AND EVOLUTION}, author={Vecchi, Matteo and Kossi Adakpo, Laurent and Dunn, Robert R. and Nichols, Lauren M. and Penick, Clint A. and Sanders, Nathan J. and Rebecchi, Lorena and Guidetti, Roberto}, year={2021}, month={Jun} }
 @article{dunn_wilson_nichols_gavin_2021, title={Toward a Global Ecology of Fermented Foods}, volume={8}, ISSN={["1537-5382"]}, url={http://dx.doi.org/10.1086/716014}, DOI={10.1086/716014}, abstractNote={The control of microbes in food has been as important to human societies as the domestication of plants and animals. The direct or indirect management of microbes has been critical to food safety, ensuring nutrient availability, and developing desired sensory characteristics in food. Fermentation is more universal than is agriculture inasmuch as it is practiced by agricultural societies, pastoralists, and hunter-gatherers. In addition, fermentation likely predates agriculture, potentially by hundreds of thousands of years. However, we lack a general approach to understanding of (a) when and why technologies associated with fermentation emerged and (b) how those technologies and the microbes associated with them diverged once they emerged. Here we offer a framework for the study of the diversification of fermented foods in and among human societies. In developing this framework, we draw heavily from research on language and more generally cultural diversification.}, journal={CURRENT ANTHROPOLOGY}, author={Dunn, Robert R. and Wilson, John and Nichols, Lauren M. and Gavin, Michael C.}, year={2021}, month={Aug} }
 @article{balbin_hull_guest_nichols_dunn_thakur_2020, title={Antimicrobial resistance and virulence factors profile of Salmonella spp. and Escherichia coli isolated from different environments exposed to anthropogenic activity}, volume={22}, ISSN={["2213-7173"]}, url={http://dx.doi.org/10.1016/j.jgar.2020.05.016}, DOI={10.1016/j.jgar.2020.05.016}, abstractNote={The study aimed to identify the antimicrobial resistance (AMR) determinants and virulence factors in Salmonella spp. and Escherichia coli recovered from different anthropogenic areas in North Carolina. Soil samples were collected from different anthropogenic areas, urban and natural. The minimum inhibitory concentration (MIC) was determined by using the broth microdilution method. Whole-genome sequencing (WGS) and analysis were done to identify the AMR determinants and virulence factors. A higher prevalence of Salmonella spp. and E. coli was detected in the urban environment. The Salmonella spp. isolates showed resistance to sulfisoxazole and streptomycin, whereas E. coli was resistant to sulfisoxazole, cefoxitin and ampicillin. Salmonella serotypes Schwarzengrund and Mississippi were identified based on WGS analysis. Aminoglycoside resistance genes and IncFIB and IncFIC(FII) plasmids were detected among Salmonella spp. In general, E. coli was predominated by isolates from phylogroups B1, B2 and D. The multidrug transporter mdfA gene was detected in most of the E. coli from both the urban (100%) and natural (84.5%) environments. The FosA7 gene was detected in an isolate from a residential yard. The pCoo and pB171 plasmids were detected in an urban environment; col(156) and pHN7A8 plasmids were detected in natural environments. The detection of AMR determinants and virulence factors in these bacteria is significant in understanding the occurrence and even the development of AMR. The presence of these determinants in different anthropogenic areas suggests the need to conduct longitudinal studies for comparing the profile of pathogens across different environments.}, journal={JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE}, author={Balbin, Michelle M. and Hull, Dawn and Guest, Chloe and Nichols, Lauren and Dunn, Robert and Thakur, Siddhartha}, year={2020}, month={Sep}, pages={578–583} }
 @article{dunn_amato_archie_arandjelovic_crittenden_nichols_2020, title={The Internal, External and Extended Microbiomes of Hominins}, volume={8}, ISSN={["2296-701X"]}, url={https://doi.org/10.3389/fevo.2020.00025}, DOI={10.3389/fevo.2020.00025}, abstractNote={The social structure of primates has recently been shown to influence the composition of their microbiomes. What is less clear is how primate microbiomes might in turn influence their social behavior, either in general or with particular reference to hominins. Here we use a comparative approach to understand how microbiomes of hominins have, or might have, changed since the last common ancestor (LCA) of chimpanzees and humans, roughly six million years ago. We focus on microbiomes associated with social evolution, namely those hosted or influenced by stomachs, intestines, armpits, and food fermentation. In doing so, we highlight the potential influence of microbiomes in hominin evolution while also offering a series of hypotheses and questions with regard to evolution of human stomach acidity, the factors structuring gut microbiomes, the functional consequences of changes in armpit ecology, and whether Homo erectus was engaged in fermentation. We conclude by briefly considering the possibility that hominin social behavior was influenced by prosocial microbes whose fitness was favored by social interactions among individual hominins.}, journal={FRONTIERS IN ECOLOGY AND EVOLUTION}, author={Dunn, Robert R. and Amato, Katherine R. and Archie, Elizabeth A. and Arandjelovic, Mimi and Crittenden, Alyssa N. and Nichols, Lauren M.}, year={2020}, month={Feb} }
 @article{dunn_amato_archie_arandjelovic_crittenden_nichols_2020, title={The Internal, External and Extended Microbiomes of Hominins (vol 8, 25, 2020)}, volume={8}, ISSN={["2296-701X"]}, DOI={10.3389/fevo.2020.00236}, abstractNote={Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States, Centre for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark, Department of Anthropology, Northwestern University, Evanston, IL, United States, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Department of Anthropology, University of Nevada, Las Vegas, Las Vegas, NV, United States}, journal={FRONTIERS IN ECOLOGY AND EVOLUTION}, author={Dunn, Robert R. and Amato, Katherine R. and Archie, Elizabeth A. and Arandjelovic, Mimi and Crittenden, Alyssa N. and Nichols, Lauren M.}, year={2020}, month={Aug} }
 @article{just_nichols_dunn_2019, title={Appendix A from Human indoor climate preferences approximate specific geographies}, url={https://doi.org/10.6084/m9.figshare.7824269.v1}, DOI={10.6084/m9.figshare.7824269.v1}, author={Just, Michael G. and Nichols, Lauren M. and Dunn, Robert R.}, year={2019} }
 @article{just_nichols_dunn_2019, title={Human indoor climate preferences approximate specific geographies}, volume={6}, ISSN={["2054-5703"]}, url={https://doi.org/10.1098/rsos.180695}, DOI={10.1098/rsos.180695}, abstractNote={Human engineering of the outdoors led to the development of the indoor niche, including home construction. However, it is unlikely that domicile construction mechanics are under direct selection for humans. Nonetheless, our preferences within indoor environments are, or once were, consequential to our fitness. The research of human homes does not usually consider human evolution, and, therefore, we are without previous predictions about indoor climate preference. We worked with citizen scientists to collect indoor climate data from homes (n = 37) across the USA. We then compared these data to recent global terrestrial climate data (0.5° grid cells, n = 67 420) using a climate dissimilarity index. We also compared some climate-related physiological parameters (e.g. thermoneutral zone (TNZ)) between humans and a selection of non-human primates. On average, our study homes were most similar in climate to the outdoor conditions of west central Kenya. We found that the indoor climates of our study homes largely matched the TNZ of humans and other primates. Overall, we identified the geographical distribution of the global outdoor climate that is most similar to the interiors of our study homes and summarized study home indoor climate preferences.}, number={3}, journal={ROYAL SOCIETY OPEN SCIENCE}, author={Just, Michael G. and Nichols, Lauren M. and Dunn, Robert R.}, year={2019}, month={Mar} }
 @article{gebert_delgado-baquerizo_oliverio_webster_nichols_honda_chan_adjemian_dunn_fierer_2018, title={Ecological Analyses of Mycobacteria in Showerhead Biofilms and Their Relevance to Human Health}, volume={9}, ISSN={["2150-7511"]}, url={https://doi.org/10.1128/mBio.01614-18}, DOI={10.1128/mBio.01614-18}, abstractNote={Bacteria thrive in showerheads and throughout household water distribution systems. While most of these bacteria are innocuous, some are potential pathogens, including members of the genus Mycobacterium that can cause nontuberculous mycobacterial (NTM) lung infection, an increasing threat to public health. We found that showerheads in households across the United States and Europe often harbor abundant mycobacterial communities that vary in composition depending on geographic location, water chemistry, and water source, with households receiving water treated with chlorine disinfectants having particularly high abundances of certain mycobacteria. The regions in the United States where NTM lung infections are most common were the same regions where pathogenic mycobacteria were most prevalent in showerheads, highlighting the important role of showerheads in the transmission of NTM infections. ABSTRACT Bacteria within the genus Mycobacterium can be abundant in showerheads, and the inhalation of aerosolized mycobacteria while showering has been implicated as a mode of transmission in nontuberculous mycobacterial (NTM) lung infections. Despite their importance, the diversity, distributions, and environmental predictors of showerhead-associated mycobacteria remain largely unresolved. To address these knowledge gaps, we worked with citizen scientists to collect showerhead biofilm samples and associated water chemistry data from 656 households located across the United States and Europe. Our cultivation-independent analyses revealed that the genus Mycobacterium was consistently the most abundant genus of bacteria detected in residential showerheads, and yet mycobacterial diversity and abundances were highly variable. Mycobacteria were far more abundant, on average, in showerheads receiving municipal water than in those receiving well water and in U.S. households than in European households, patterns that are likely driven by differences in the use of chlorine disinfectants. Moreover, we found that water source, water chemistry, and household location also influenced the prevalence of specific mycobacterial lineages detected in showerheads. We identified geographic regions within the United States where showerheads have particularly high abundances of potentially pathogenic lineages of mycobacteria, and these “hot spots” generally overlapped those regions where NTM lung disease is most prevalent. Together, these results emphasize the public health relevance of mycobacteria in showerhead biofilms. They further demonstrate that mycobacterial distributions in showerhead biofilms are often predictable from household location and water chemistry, knowledge that advances our understanding of NTM transmission dynamics and the development of strategies to reduce exposures to these emerging pathogens. IMPORTANCE Bacteria thrive in showerheads and throughout household water distribution systems. While most of these bacteria are innocuous, some are potential pathogens, including members of the genus Mycobacterium that can cause nontuberculous mycobacterial (NTM) lung infection, an increasing threat to public health. We found that showerheads in households across the United States and Europe often harbor abundant mycobacterial communities that vary in composition depending on geographic location, water chemistry, and water source, with households receiving water treated with chlorine disinfectants having particularly high abundances of certain mycobacteria. The regions in the United States where NTM lung infections are most common were the same regions where pathogenic mycobacteria were most prevalent in showerheads, highlighting the important role of showerheads in the transmission of NTM infections.}, number={5}, journal={MBIO}, author={Gebert, Matthew J. and Delgado-Baquerizo, Manuel and Oliverio, Angela M. and Webster, Tara M. and Nichols, Lauren M. and Honda, Jennifer R. and Chan, Edward D. and Adjemian, Jennifer and Dunn, Robert R. and Fierer, Noah}, year={2018} }
 @article{ryan_adamson_aktipis_andersen_austin_barnes_beasley_bedell_briggs_chapman_et al._2018, title={The role of citizen science in addressing grand challenges in food and agriculture research}, volume={285}, ISSN={0962-8452 1471-2954}, url={http://dx.doi.org/10.1098/rspb.2018.1977}, DOI={10.1098/rspb.2018.1977}, abstractNote={The power of citizen science to contribute to both science and society is gaining increased recognition, particularly in physics and biology. Although there is a long history of public engagement in agriculture and food science, the term ‘citizen science’ has rarely been applied to these efforts. Similarly, in the emerging field of citizen science, most new citizen science projects do not focus on food or agriculture. Here, we convened thought leaders from a broad range of fields related to citizen science, agriculture, and food science to highlight key opportunities for bridging these overlapping yet disconnected communities/fields and identify ways to leverage their respective strengths. Specifically, we show that (i) citizen science projects are addressing many grand challenges facing our food systems, as outlined by the United States National Institute of Food and Agriculture, as well as broader Sustainable Development Goals set by the United Nations Development Programme, (ii) there exist emerging opportunities and unique challenges for citizen science in agriculture/food research, and (iii) the greatest opportunities for the development of citizen science projects in agriculture and food science will be gained by using the existing infrastructure and tools of Extension programmes and through the engagement of urban communities. Further, we argue there is no better time to foster greater collaboration between these fields given the trend of shrinking Extension programmes, the increasing need to apply innovative solutions to address rising demands on agricultural systems, and the exponential growth of the field of citizen science.}, number={1891}, journal={Proceedings of the Royal Society B: Biological Sciences}, publisher={The Royal Society}, author={Ryan, S. F. and Adamson, N. L. and Aktipis, A. and Andersen, L. K. and Austin, R. and Barnes, L. and Beasley, M. R. and Bedell, K. D. and Briggs, S. and Chapman, B. and et al.}, year={2018}, month={Nov}, pages={20181977} }
 @article{diamond_chick_penick_nichols_cahan_dunn_ellison_sandersk_gotelli_2017, title={Heat tolerance predicts the importance of species interaction effects as the climate changes}, volume={57}, ISSN={["1557-7023"]}, url={http://dx.doi.org/10.1093/icb/icx008}, DOI={10.1093/icb/icx008}, abstractNote={SYNOPSIS
Few studies have quantified the relative importance of direct effects of climate change on communities versus indirect effects that are mediated thorough species interactions, and the limited evidence is conflicting. Trait-based approaches have been popular in studies of climate change, but can they be used to estimate direct versus indirect effects? At the species level, thermal tolerance is a trait that is often used to predict winners and losers under scenarios of climate change. But thermal tolerance might also inform when species interactions are likely to be important because only subsets of species will be able to exploit the available warmer climatic niche space, and competition may intensify in the remaining, compressed cooler climatic niche space. Here, we explore the relative roles of the direct effects of temperature change and indirect effects of species interactions on forest ant communities that were heated as part of a large-scale climate manipulation at high- and low-latitude sites in eastern North America. Overall, we found mixed support for the importance of negative species interactions (competition), but found that the magnitude of these interaction effects was predictable based on the heat tolerance of the focal species. Forager abundance and nest site occupancy of heat-intolerant species were more often influenced by negative interactions with other species than by direct effects of temperature. Our findings suggest that measures of species-specific heat tolerance may roughly predict when species interactions will influence responses to global climate change.}, number={1}, journal={INTEGRATIVE AND COMPARATIVE BIOLOGY}, author={Diamond, Sarah E. and Chick, Lacy and Penick, Clint A. and Nichols, Lauren M. and Cahan, Sara Helms and Dunn, Robert R. and Ellison, Aaron M. and Sandersk, Nathan J. and Gotelli, Nicholas J.}, year={2017}, month={Jul}, pages={112–120} }
 @article{diamond_nichols_pelini_penick_barber_cahan_dunn_ellison_sanders_gotelli_2016, title={Climatic warming destabilizes forest ant communities}, volume={2}, ISSN={2375-2548}, url={http://dx.doi.org/10.1126/sciadv.1600842}, DOI={10.1126/sciadv.1600842}, abstractNote={A field-based climate warming experiment reveals a loss of dynamical community stability due to altered species interactions. How will ecological communities change in response to climate warming? Direct effects of temperature and indirect cascading effects of species interactions are already altering the structure of local communities, but the dynamics of community change are still poorly understood. We explore the cumulative effects of warming on the dynamics and turnover of forest ant communities that were warmed as part of a 5-year climate manipulation experiment at two sites in eastern North America. At the community level, warming consistently increased occupancy of nests and decreased extinction and nest abandonment. This consistency was largely driven by strong responses of a subset of thermophilic species at each site. As colonies of thermophilic species persisted in nests for longer periods of time under warmer temperatures, turnover was diminished, and species interactions were likely altered. We found that dynamical (Lyapunov) community stability decreased with warming both within and between sites. These results refute null expectations of simple temperature-driven increases in the activity and movement of thermophilic ectotherms. The reduction in stability under warming contrasts with the findings of previous studies that suggest resilience of species interactions to experimental and natural warming. In the face of warmer, no-analog climates, communities of the future may become increasingly fragile and unstable.}, number={10}, journal={Science Advances}, publisher={American Association for the Advancement of Science (AAAS)}, author={Diamond, Sarah E. and Nichols, Lauren M. and Pelini, Shannon L. and Penick, Clint A. and Barber, Grace W. and Cahan, Sara Helms and Dunn, Robert R. and Ellison, Aaron M. and Sanders, Nathan J. and Gotelli, Nicholas J.}, year={2016}, month={Oct}, pages={e1600842} }
 @article{lucky_savage_nichols_castracani_shell_grasso_mori_dunn_2014, title={Ecologists, educators, and writers collaborate with the public to assess backyard diversity in The School of Ants Project}, volume={5}, ISSN={["2150-8925"]}, url={http://dx.doi.org/10.1890/es13-00364.1}, DOI={10.1890/es13-00364.1}, abstractNote={Citizen science can generate data that would not exist otherwise while increasing public scientific literacy. However, the quality and use of citizen science data have been criticized in the recent ecological literature. We need an approach that advances eco-evolutionary understanding, achieves education goals and incorporates public participation into as many aspects of the scientific process as possible. We collaborated with public participants to make new discoveries about the distribution and ecology of ants while informing the next studies that participants and scientists might perform together. We implemented the School of Ants (SoA) program in which participants sample ants that are identified by taxonomic experts. Using a comprehensive framework that meets the needs of multiple agents, we also developed outreach materials about ant biology, collaborated with educators to incorporate SoA into classroom science, and launched an international SoA module in Italy. In the first 17 months, SoA volunteers collected ants at 500 unique sites across the USA-including all 50 states and Washington, D.C. To address concerns about the validity of citizen scientist-derived data, we conducted a ground truthing trial that confirmed that trained and untrained volunteers were equally effective at collecting ants. Data from SoA samples indicate that ant diversity varies across wide geographic scales and that there can be high levels of native ant diversity where people live. SoA volunteers collected 7 exotic and 107 native ant species. Although exotic ants were common, ants native to North America occurred in ∼70% of all sites. Many of the ants common in backyards were species that tend to be very poorly studied. For example, citizen scientists documented a range extension of more than 2000 miles for the Asian Needle Ant, Pachycondyla chinensis. Using SoA data as a starting point, we collaborated with a science writer to produce a free, interactive iBook about the common ants in North America; the book included distribution maps such as that for P. chinensis informed by participant collections. Moving forward, we plan to leverage this existing framework to address more complex ecological and evolutionary questions in partnership with our public participants.}, number={7}, journal={ECOSPHERE}, author={Lucky, Andrea and Savage, Amy M. and Nichols, Lauren M. and Castracani, Cristina and Shell, Leonora and Grasso, Donato A. and Mori, Alessandra and Dunn, Robert R.}, year={2014}, month={Jul} }
 @article{pelini_diamond_nichols_stuble_ellison_sanders_dunn_gotelli_2014, title={Geographic differences in effects of experimental warming on ant species diversity and community composition}, url={https://scholarworks.uvm.edu/casfac/81}, author={Pelini, S. L. and Diamond, S. E. and Nichols, L. M. and Stuble, K. L. and Ellison, A. M. and Sanders, N. J. and Dunn, R. R. and Gotelli, N. J.}, year={2014} }
 @article{diamond_nichols_mccoy_hirsch_pelini_sanders_ellison_gotelli_dunn_2012, title={A physiological trait-based approach to predicting the responses of species to experimental climate warming}, volume={93}, ISSN={["1939-9170"]}, url={http://dx.doi.org/10.1890/11-2296.1}, DOI={10.1890/11-2296.1}, abstractNote={Physiological tolerance of environmental conditions can influence species-level responses to climate change. Here, we used species-specific thermal tolerances to predict the community responses of ant species to experimental forest-floor warming at the northern and southern boundaries of temperate hardwood forests in eastern North America. We then compared the predictive ability of thermal tolerance vs. correlative species distribution models (SDMs) which are popular forecasting tools for modeling the effects of climate change. Thermal tolerances predicted the responses of 19 ant species to experimental climate warming at the southern site, where environmental conditions are relatively close to the ants' upper thermal limits. In contrast, thermal tolerances did not predict the responses of the six species in the northern site, where environmental conditions are relatively far from the ants' upper thermal limits. Correlative SDMs were not predictive at either site. Our results suggest that, in environments close to a species' physiological limits, physiological trait-based measurements can successfully forecast the responses of species to future conditions. Although correlative SDMs may predict large-scale responses, such models may not be accurate for predicting site-level responses.}, number={11}, journal={ECOLOGY}, author={Diamond, Sarah E. and Nichols, Lauren M. and McCoy, Neil and Hirsch, Christopher and Pelini, Shannon L. and Sanders, Nathan J. and Ellison, Aaron M. and Gotelli, Nicholas J. and Dunn, Robert R.}, year={2012}, month={Nov}, pages={2305–2312} }
 @article{sultan_horgan-kobelski_nichols_riggs_waples_2012, title={A resurrection study reveals rapid adaptive evolution within populations of an invasive plant}, url={http://dx.doi.org/10.1111/j.1752-4571.2012.00287.x}, DOI={10.1111/j.1752-4571.2012.00287.x}, abstractNote={The future spread and impact of an introduced species will depend on how it adapts to the abiotic and biotic conditions encountered in its new range, so the potential for rapid evolution subsequent to species introduction is a critical, evolutionary dimension of invasion biology. Using a resurrection approach, we provide a direct test for change over time within populations in a species' introduced range, in the Asian shade annual Polygonum cespitosum. We document, over an 11‐year period, the evolution of increased reproductive output as well as greater physiological and root‐allocational plasticity in response to the more open, sunny conditions found in the North American range in which the species has become invasive. These findings show that extremely rapid adaptive modifications to ecologically‐important traits and plastic expression patterns can evolve subsequent to a species' introduction, within populations established in its introduced range. This study is one of the first to directly document evolutionary change in adaptive plasticity. Such rapid evolutionary changes can facilitate the spread of introduced species into novel habitats and hence contribute to their invasive success in a new range. The data also reveal how evolutionary trajectories can differ among populations in ways that can influence invasion dynamics.}, author={Sultan, Sonia E. and Horgan-Kobelski, Tim and Nichols, Lauren M. and Riggs, Charlotte E. and Waples, Ryan K.}, year={2012} }
 @article{burt_dunn_nichols_sanders, title={Interactions in a warmer world: effects of experimental warming, conspecific density, and herbivory on seedling dynamics}, url={http://citeseerx.ist.psu.edu/viewdoc/summarydoi%3D10.1.1.1081.2988}, author={Burt, Melissa A and Dunn, Robert R and Nichols, Lauren M and Sanders, Nathan J} }