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Dunn RR, Kirby KR, Bowern C, Ember CR, Gray RD, McCarter J, Kavanagh PH, Trautwein M, Nichols LM, Gavin MC, Botero C. Climate, climate change and the global diversity of human houses. Evol Hum Sci 2024; 6:e24. [PMID: 38689895 PMCID: PMC11058517 DOI: 10.1017/ehs.2024.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/20/2023] [Accepted: 11/02/2023] [Indexed: 05/02/2024] Open
Abstract
Globally, human house types are diverse, varying in shape, size, roof type, building materials, arrangement, decoration and many other features. Here we offer the first rigorous, global evaluation of the factors that influence the construction of traditional (vernacular) houses. We apply macroecological approaches to analyse data describing house features from 1900 to 1950 across 1000 societies. Geographic, social and linguistic descriptors for each society were used to test the extent to which key architectural features may be explained by the biophysical environment, social traits, house features of neighbouring societies or cultural history. We find strong evidence that some aspects of the climate shape house architecture, including floor height, wall material and roof shape. Other features, particularly ground plan, appear to also be influenced by social attributes of societies, such as whether a society is nomadic, polygynous or politically complex. Additional variation in all house features was predicted both by the practices of neighouring societies and by a society's language family. Collectively, the findings from our analyses suggest those conditions under which traditional houses offer solutions to architects seeking to reimagine houses in light of warmer, wetter or more variable climates.
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Affiliation(s)
- Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC 27695, USA
| | - Kathryn R. Kirby
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada M5S 3B2
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Study of Human History, Jena, Germany
| | - Claire Bowern
- Department of Linguistics, Yale University, New Haven, CT 06520-8366, USA
| | - Carol R. Ember
- Human Relations Area Files at Yale University, New Haven, CT 06511, USA
| | - Russell D. Gray
- School of Psychology, University of Auckland, Auckland 1010, New Zealand
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Joe McCarter
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY 10024, USA
| | - Patrick H. Kavanagh
- Department of Human Dimensions of Natural Resources, Colorado State University, Fort Collins, CO 80523-1480, USA
| | - Michelle Trautwein
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA
| | - Lauren M. Nichols
- Department of Applied Ecology, North Carolina State University, Raleigh, NC 27695, USA
| | - Michael C. Gavin
- School of Psychology, University of Auckland, Auckland 1010, New Zealand
- Department of Human Dimensions of Natural Resources, Colorado State University, Fort Collins, CO 80523-1480, USA
| | - Carlos Botero
- Department of Integrative Biology, University of Texas, Austin, TX 78712USA
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Kuthyar S, Diaz J, Avalos-Villatoro F, Maltecca C, Tiezzi F, Dunn RR, Reese AT. Domestication shapes the pig gut microbiome and immune traits from the scale of lineage to population. J Evol Biol 2023; 36:1695-1711. [PMID: 37885134 DOI: 10.1111/jeb.14227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 08/22/2023] [Accepted: 08/29/2023] [Indexed: 10/28/2023]
Abstract
Animal ecology and evolution have long been known to shape host physiology, but more recently, the gut microbiome has been identified as a mediator between animal ecology and evolution and health. The gut microbiome has been shown to differ between wild and domestic animals, but the role of these differences for domestic animal evolution remains unknown. Gut microbiome responses to new animal genotypes and local environmental change during domestication may promote specific host phenotypes that are adaptive (or not) to the domestic environment. Because the gut microbiome supports host immune function, understanding the effects of animal ecology and evolution on the gut microbiome and immune phenotypes is critical. We investigated how domestication affects the gut microbiome and host immune state in multiple pig populations across five domestication contexts representing domestication status and current living conditions: free-ranging wild, captive wild, free-ranging domestic, captive domestic in research or industrial settings. We observed that domestication context explained much of the variation in gut microbiome composition, pathogen abundances and immune markers, yet the main differences in the repertoire of metabolic genes found in the gut microbiome were between the wild and domestic genetic lineages. We also documented population-level effects within domestication contexts, demonstrating that fine scale environmental variation also shaped host and microbe features. Our findings highlight that understanding which gut microbiome and immune traits respond to host genetic lineage and/or scales of local ecology could inform targeted interventions that manipulate the gut microbiome to achieve beneficial health outcomes.
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Affiliation(s)
- Sahana Kuthyar
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Jessica Diaz
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | | | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, North Carolina, USA
| | - Francesco Tiezzi
- Department of Agriculture, Food, Environment and Forestry, University of Florence, Florence, Italy
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA
| | - Aspen T Reese
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
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3
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Soghigian J, Sither C, Justi SA, Morinaga G, Cassel BK, Vitek CJ, Livdahl T, Xia S, Gloria-Soria A, Powell JR, Zavortink T, Hardy CM, Burkett-Cadena ND, Reeves LE, Wilkerson RC, Dunn RR, Yeates DK, Sallum MA, Byrd BD, Trautwein MD, Linton YM, Reiskind MH, Wiegmann BM. Phylogenomics reveals the history of host use in mosquitoes. Nat Commun 2023; 14:6252. [PMID: 37803007 PMCID: PMC10558525 DOI: 10.1038/s41467-023-41764-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 09/08/2023] [Indexed: 10/08/2023] Open
Abstract
Mosquitoes have profoundly affected human history and continue to threaten human health through the transmission of a diverse array of pathogens. The phylogeny of mosquitoes has remained poorly characterized due to difficulty in taxonomic sampling and limited availability of genomic data beyond the most important vector species. Here, we used phylogenomic analysis of 709 single copy ortholog groups from 256 mosquito species to produce a strongly supported phylogeny that resolves the position of the major disease vector species and the major mosquito lineages. Our analyses support an origin of mosquitoes in the early Triassic (217 MYA [highest posterior density region: 188-250 MYA]), considerably older than previous estimates. Moreover, we utilize an extensive database of host associations for mosquitoes to show that mosquitoes have shifted to feeding upon the blood of mammals numerous times, and that mosquito diversification and host-use patterns within major lineages appear to coincide in earth history both with major continental drift events and with the diversification of vertebrate classes.
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Affiliation(s)
- John Soghigian
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Charles Sither
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Silvia Andrade Justi
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, Suitland, MD, USA
- One Health Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Department of Entomology, Smithsonian Institution National Museum of Natural History, Washington, DC, USA
| | - Gen Morinaga
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Brian K Cassel
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Christopher J Vitek
- Center for Vector-Borne Diseases, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Todd Livdahl
- Department of Biology, Clark University, Worcester, MA, USA
| | - Siyang Xia
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Andrea Gloria-Soria
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Department of Entomology, Center for Vector Biology & Zoonotic Diseases, The Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | - Jeffrey R Powell
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Thomas Zavortink
- Bohart Museum of Entomology, University of California, Davis, CA, USA
| | | | - Nathan D Burkett-Cadena
- Florida Medical Entomology Laboratory, Institute of Food and Agricultural Sciences, University of Florida, Vero Beach, FL, USA
| | - Lawrence E Reeves
- Florida Medical Entomology Laboratory, Institute of Food and Agricultural Sciences, University of Florida, Vero Beach, FL, USA
| | - Richard C Wilkerson
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, Suitland, MD, USA
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - David K Yeates
- Australian National Insect Collection, CSIRO National Collections and Marine Infrastructure, Canberra, ACT, Australia
| | - Maria Anice Sallum
- Departamento de Epidemiologia, Faculdade de Saude Publica, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Brian D Byrd
- College of Health and Human Sciences, School of Health Sciences, Western Carolina University, Cullowhee, NC, USA
| | - Michelle D Trautwein
- Entomology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, CA, USA
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Center, Suitland, MD, USA
- One Health Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Department of Entomology, Smithsonian Institution National Museum of Natural History, Washington, DC, USA
| | - Michael H Reiskind
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Brian M Wiegmann
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA.
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McKenney EA, Nichols LM, Alvarado S, Hardy S, Kemp K, Polmanteer R, Shoemaker A, Dunn RR. Sourdough starters exhibit similar succession patterns but develop flour-specific climax communities. PeerJ 2023; 11:e16163. [PMID: 37810791 PMCID: PMC10559884 DOI: 10.7717/peerj.16163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/01/2023] [Indexed: 10/10/2023] Open
Abstract
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.
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Affiliation(s)
- Erin A. McKenney
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, United States
- North Carolina Museum of Natural Sciences, Raleigh, North Carolina, United States
| | - Lauren M. Nichols
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, United States
| | - Samuel Alvarado
- Department of Biology, University of West Florida, Pensacola, Florida, United States
- Biotechnology Program, North Carolina State University, Biotechnology-based Sequencing-based Undergraduate Research Experience (BITSURE), Raleigh, North Carolina, United States
| | - Shannon Hardy
- The Exploris School, Raleigh, North Carolina, United States
| | - Kristen Kemp
- Moore Square Middle School, Raleigh, North Carolina, United States
| | | | | | - Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, United States
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Aizpurua O, Dunn RR, Hansen LH, Gilbert MTP, Alberdi A. Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data. Crit Rev Biotechnol 2023:1-19. [PMID: 37731336 DOI: 10.1080/07388551.2023.2254933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/27/2023] [Indexed: 09/22/2023]
Abstract
Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.
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Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - M T P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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6
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Meiklejohn KA, Scheible MKR, Boggs LM, Dunn RR, Ricke DO. Using FastID to analyze complex SNP mixtures from indoor dust. J Forensic Sci 2023; 68:768-779. [PMID: 37009755 DOI: 10.1111/1556-4029.15246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/10/2023] [Accepted: 03/20/2023] [Indexed: 04/04/2023]
Abstract
Forensically relevant single nucleotide polymorphisms (SNPs) can provide valuable supplemental information to short tandem repeats (STRs) for investigative leads, and genotyping can now be streamlined using massively parallel sequencing (MPS). Dust is an attractive evidence source, as it accumulates on undisturbed surfaces, often is overlooked by perpetrators, and contains sufficient human DNA for analysis. To assess whether SNPs genotyped from indoor dust using MPS could be used to detect known household occupants, 13 households were recruited and provided buccal samples from each occupant and dust from five predefined indoor locations. Thermo Fisher Scientific Precision ID Identity and Ancestry Panels were utilized for SNP genotyping, and sequencing was completed using Illumina® chemistry. FastID, a software developed to permit mixture analysis and identity searching, was used to assess whether known occupants could be detected from associated household dust samples. A modified "subtraction" method was also used in FastID to estimate the percentage of alleles in each dust sample contributed by known and unknown occupants. On average, 72% of autosomal SNPs were recovered from dust samples. When using FastID, (a) 93% of known occupants were detected in at least one indoor dust sample and could not be excluded as contributors to the mixture, and (b) non-contributor alleles were detected in 54% of dust samples (29 ± 11 alleles per dust sample). Overall, this study highlights the potential of analyzing human DNA present in indoor dust to detect known household occupants, which could be valuable for investigative leads.
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Affiliation(s)
- Kelly A Meiklejohn
- Department of Population Health and Pathobiology, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Melissa K R Scheible
- Department of Population Health and Pathobiology, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Laura M Boggs
- Department of Population Health and Pathobiology, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Robert R Dunn
- Department of Applied Ecology, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Darrell O Ricke
- Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, Massachusetts, USA
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7
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McKenney EA, Hale AR, Anderson J, Larsen R, Grant C, Dunn RR. Hidden diversity: comparative functional morphology of humans and other species. PeerJ 2023; 11:e15148. [PMID: 37123005 PMCID: PMC10135406 DOI: 10.7717/peerj.15148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/09/2023] [Indexed: 05/02/2023] Open
Abstract
Gastrointestinal (GI) morphology plays an important role in nutrition, health, and epidemiology; yet limited data on GI variation have been collected since 1885. Here we demonstrate that students can collect reliable data sets on gut morphology; when they do, they reveal greater morphological variation for some structures in the GI tract than has been documented in the published literature. We discuss trait variability both within and among species, and the implications of that variability for evolution and epidemiology. Our results show that morphological variation in the GI tract is associated with each organ's role in food processing. For example, the length of many structures was found to vary significantly with feeding strategy. Within species, the variability illustrated by the coefficients of variation suggests that selective constraints may vary with function. Within humans, we detected significant Pearson correlations between the volume of the liver and the length of the appendix (t-value = 2.5278, df = 28, p = 0.0174, corr = 0.4311) and colon (t-value = 2.0991, df = 19, p = 0.0494, corr = 0.4339), as well as between the lengths of the small intestine and colon (t-value = 2.1699, df = 17, p = 0.0445, corr = 0.4657), which are arguably the most vital organs in the gut for nutrient absorption. Notably, intraspecific variation in the small intestine can be associated with life history traits. In humans, females demonstrated consistently and significantly longer small intestines than males (t-value15 = 2.245, p = 0.0403). This finding supports the female canalization hypothesis, specifically, increased female investment in the digestion and absorption of lipids.
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Affiliation(s)
- Erin A. McKenney
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States of America
- North Carolina Museum of Natural Sciences, Raleigh, NC, United States of America
| | - Amanda R. Hale
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States of America
- SNA International for the Defense POW/MIA Accounting Agency, Joint Base Pearl Harbor-Hickam, HI, United States of America
| | - Janiaya Anderson
- Department of Psychology, North Carolina State University, Raleigh, NC, United States of America
| | - Roxanne Larsen
- Office of Curricular Affairs, Duke University School of Medicine, Durham, NC, United States of America
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, United States of America
| | - Colleen Grant
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States of America
| | - Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States of America
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Gibb H, Bishop TR, Leahy L, Parr CL, Lessard J, Sanders NJ, Shik JZ, Ibarra‐Isassi J, Narendra A, Dunn RR, Wright IJ. Ecological strategies of (pl)ants: Towards a world-wide worker economic spectrum for ants. Funct Ecol 2023; 37:13-25. [PMID: 37056633 PMCID: PMC10084388 DOI: 10.1111/1365-2435.14135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 06/22/2022] [Indexed: 11/30/2022]
Abstract
Current global challenges call for a rigorously predictive ecology. Our understanding of ecological strategies, imputed through suites of measurable functional traits, comes from decades of work that largely focussed on plants. However, a key question is whether plant ecological strategies resemble those of other organisms.Among animals, ants have long been recognised to possess similarities with plants: as (largely) central place foragers. For example, individual ant workers play similar foraging roles to plant leaves and roots and are similarly expendable. Frameworks that aim to understand plant ecological strategies through key functional traits, such as the 'leaf economics spectrum', offer the potential for significant parallels with ant ecological strategies.Here, we explore these parallels across several proposed ecological strategy dimensions, including an 'economic spectrum', propagule size-number trade-offs, apparency-defence trade-offs, resource acquisition trade-offs and stress-tolerance trade-offs. We also highlight where ecological strategies may differ between plants and ants. Furthermore, we consider how these strategies play out among the different modules of eusocial organisms, where selective forces act on the worker and reproductive castes, as well as the colony.Finally, we suggest future directions for ecological strategy research, including highlighting the availability of data and traits that may be more difficult to measure, but should receive more attention in future to better understand the ecological strategies of ants. The unique biology of eusocial organisms provides an unrivalled opportunity to bridge the gap in our understanding of ecological strategies in plants and animals and we hope that this perspective will ignite further interest. Read the free Plain Language Summary for this article on the Journal blog.
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Affiliation(s)
- Heloise Gibb
- Department of Environment and Genetics and Centre for Future LandscapesLa Trobe UniversityBundooraVic.Australia
| | - Tom R. Bishop
- School of BiosciencesCardiff UniversityCardiffUK
- Department of Zoology and EntomologyUniversity of PretoriaPretoriaSouth Africa
| | - Lily Leahy
- Department of Environment and Genetics and Centre for Future LandscapesLa Trobe UniversityBundooraVic.Australia
| | - Catherine L. Parr
- Department of Zoology and EntomologyUniversity of PretoriaPretoriaSouth Africa
- Department of Earth, Ocean and Ecological SciencesUniversity of LiverpoolLiverpoolUK
| | | | - Nathan J. Sanders
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMIUSA
| | - Jonathan Z. Shik
- Section for Ecology and Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | | | - Ajay Narendra
- Department of Biological SciencesMacquarie UniversityNSWAustralia
| | - Robert R. Dunn
- Department of Applied EcologyNorth Carolina State UniversityRaleighNCUSA
| | - Ian J. Wright
- Department of Biological SciencesMacquarie UniversityNSWAustralia
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNSWAustralia
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9
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Winnicki MH, Dunn RR, Winther-Jensen M, Jess T, Allin KH, Bruun HH. Does childhood exposure to biodiverse greenspace reduce the risk of developing asthma? Sci Total Environ 2022; 850:157853. [PMID: 35940273 DOI: 10.1016/j.scitotenv.2022.157853] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/13/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
The prevalence of inflammatory diseases is increasing in populations throughout the industrialized world. An increasing proportion of human populations grow up and live in urban areas, probably with reduced exposure to biodiversity, including diverse soil biotas. Decreased exposure to microorganisms from natural environments, in particular in early childhood, has been hypothesized to hamper development of the human immune system and lead to increasing risks of inflammatory diseases, such as asthma. We investigated 40,249 Danish individuals born 1995-2015. Percentage greenspace was assessed in a 2 km buffer around home addresses of individuals. The Danish Biodiversity Map, charting occurrence density of red-listed animals, plants and macrofungi, was used as a proxy for multi-taxon biodiversity. For asthma defined broadly, we found no evidence of decreasing risk of developing asthma with higher levels of biodiversity, while greenspace exposure was associated with higher risk of asthma. In contrast, exposure to total and biodiverse greenspace was associated with reduced risk of developing severe asthma. Exposure to farmland, which in Denmark is heavily industrialized cropland, also showed association with elevated risk of developing asthma, even at relatively low agricultural landcover. In the subset of children growing up in highly urbanized settings, we found high exposures to urban greenspace to be associated with reduced risk of developing asthma. Our results lend limited support to the hypothesis that childhood exposure to biodiverse environments reduces the risk of acquiring inflammatory diseases later in life. However, access to urban greenspace, such as parks, which typically harbour low levels of biodiversity, seems to reduce asthma risk, potentially through exposure to common soil microbiota. Our results suggest that effects of biodiversity exposure on human health is set by a balance between ecosystem services and disservices and that biodiversity conservation is best motivated with other arguments than reduction of risks from inflammatory diseases.
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Affiliation(s)
- Martin Holm Winnicki
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; Section for Data, Biostatistics and Pharmacoepidemiology, Center for Clinical Research and Prevention, Bispebjerg Frederiksberg Hospital, Copenhagen, Denmark
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Matilde Winther-Jensen
- Section for Data, Biostatistics and Pharmacoepidemiology, Center for Clinical Research and Prevention, Bispebjerg Frederiksberg Hospital, Copenhagen, Denmark
| | - Tine Jess
- Center for Molecular Prediction of Inflammatory Bowel Disease, Department of Clinical Medicine, Aalborg University, A.C. Meyers Vænge 15A, 2450 Copenhagen, Denmark; Department of Gastroenterology & Hepatology, Aalborg University Hospital, 9100 Aalborg, Denmark
| | - Kristine Højgaard Allin
- Center for Molecular Prediction of Inflammatory Bowel Disease, Department of Clinical Medicine, Aalborg University, A.C. Meyers Vænge 15A, 2450 Copenhagen, Denmark; Department of Gastroenterology & Hepatology, Aalborg University Hospital, 9100 Aalborg, Denmark
| | - Hans Henrik Bruun
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark.
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10
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Kass JM, Guénard B, Dudley KL, Jenkins CN, Azuma F, Fisher BL, Parr CL, Gibb H, Longino JT, Ward PS, Chao A, Lubertazzi D, Weiser M, Jetz W, Guralnick R, Blatrix R, Lauriers JD, Donoso DA, Georgiadis C, Gomez K, Hawkes PG, Johnson RA, Lattke JE, MacGown JA, Mackay W, Robson S, Sanders NJ, Dunn RR, Economo EP. The global distribution of known and undiscovered ant biodiversity. Sci Adv 2022; 8:eabp9908. [PMID: 35921404 PMCID: PMC9348798 DOI: 10.1126/sciadv.abp9908] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/21/2022] [Indexed: 05/26/2023]
Abstract
Invertebrates constitute the majority of animal species and are critical for ecosystem functioning and services. Nonetheless, global invertebrate biodiversity patterns and their congruences with vertebrates remain largely unknown. We resolve the first high-resolution (~20-km) global diversity map for a major invertebrate clade, ants, using biodiversity informatics, range modeling, and machine learning to synthesize existing knowledge and predict the distribution of undiscovered diversity. We find that ants and different vertebrate groups have distinct features in their patterns of richness and rarity, underscoring the need to consider a diversity of taxa in conservation. However, despite their phylogenetic and physiological divergence, ant distributions are not highly anomalous relative to variation among vertebrate clades. Furthermore, our models predict that rarity centers largely overlap (78%), suggesting that general forces shape endemism patterns across taxa. This raises confidence that conservation of areas important for small-ranged vertebrates will benefit invertebrates while providing a "treasure map" to guide future discovery.
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Affiliation(s)
- Jamie M. Kass
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| | - Benoit Guénard
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kenneth L. Dudley
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| | - Clinton N. Jenkins
- Department of Earth and Environment and Kimberly Green Latin American and Caribbean Center, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | - Fumika Azuma
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| | - Brian L. Fisher
- Entomology, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Catherine L. Parr
- School of Environmental Sciences, University of Liverpool, Liverpool L69 3GP, UK
- Department of Zoology and Entomology, University of Pretoria, Pretoria 0028, South Africa
- School of Animal, Plant, and Environmental Sciences, University of the Witwatersrand, Johannesburg, Wits 2050, South Africa
| | - Heloise Gibb
- Department of Ecology, Environment and Evolution, and Center for Future Landscapes, La Trobe University, Bundoora, Victoria 3086, Australia
| | - John T. Longino
- School of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Philip S. Ward
- Department of Entomology and Nematology, University of California, Davis, Davis, CA 95616, USA
| | - Anne Chao
- Institute of Statistics, National Tsing Hua University, Hsin-Chu 30043, Taiwan
| | - David Lubertazzi
- Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Michael Weiser
- Department of Biology and Geographical Ecology Group, University of Oklahoma, Norman, OK 73019, USA
| | - Walter Jetz
- Center for Biodiversity and Global Change and Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
| | - Robert Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Rumsaïs Blatrix
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | - David A. Donoso
- Departamento de Biología, Escuela Politécnica Nacional, Quito, Ecuador
| | - Christos Georgiadis
- Section of Zoology–Marine Biology, Department of Biology, National and Kapodistrian University of Athens, Zografou 15772, Greece
| | | | - Peter G. Hawkes
- AfriBugs CC, 341 27th Avenue, Villieria, Pretoria, Gauteng Province 0186, South Africa
- Department of Biological Sciences, University of Venda, Thohoyandou, Limpopo Province, South Africa
| | - Robert A. Johnson
- School of Life Sciences, Arizona State University, Tempe, AZ 852787-4501, USA
| | - John E. Lattke
- Department of Zoology, Universidade Federal do Paraná, Curitiba, CEP 81531-980, PR, Brazil
| | - Joe A. MacGown
- Department of Molecular Biology, Biochemistry, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | - William Mackay
- Biodiversity Collections, Department of Biological Sciences, University of Texas, El Paso, TX, 79968, USA
| | - Simon Robson
- College of Science and Engineering, Central Queensland University, Townsville, QLD 4812, Australia
| | - Nathan J. Sanders
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC 27607, USA
| | - Evan P. Economo
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA 02138, USA
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11
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Tonione MA, Bi K, Dunn RR, Lucky A, Portik DM, Tsutsui ND. Phylogeography and population genetics of a widespread cold-adapted ant, Prenolepis imparis. Mol Ecol 2022; 31:4884-4899. [PMID: 35866574 DOI: 10.1111/mec.16624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 11/30/2022]
Abstract
As species arise, evolve, and diverge, they are shaped by forces that unfold across short and long time scales and at both local and vast geographic scales. It is rare, however, to be able document this history across broad sweeps of time and space in a single species. Here, we report the results of a continental-scale phylogenomic analysis across the entire range of a widespread species. We analyzed sequences of 1,402 orthologous Ultraconserved Element (UCE) loci from 75 individuals to identify population genetic structure and historical demographic patterns across the continent-wide range of a cold-adapted ant, the winter ant, Prenolepis imparis. We recovered five well-supported, genetically isolated clades representing lineages that diverged from 8.2-2.2 million years ago. These include: 1) an early diverging lineage located in Florida, 2) a lineage that spans the southern United States, 3) populations that extend across the midwestern and northeastern United States, 4) populations from the western United States, and 5) populations in southwestern Arizona and Mexico. Population genetic analyses revealed little or no gene flow among these lineages, but patterns consistent with more recent gene flow among populations within lineages, and localized structure with migration in the western United States. High support for five major geographic lineages and lack of evidence of contemporary gene flow indicate in situ diversification across the species' range, producing relatively ancient lineages that persisted through subsequent climate change and glaciation during the Quaternary.
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Affiliation(s)
- Maria Adelena Tonione
- Department of Environmental Science, Policy, and Management, 130 Mulford Hall, #3114, University of California-, 94720-3114, Berkeley, CA, USA
| | - Ke Bi
- Museum of Vertebrate Zoology, University of California, Berkeley, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA.,Computational Genomics Resource Laboratory (CGRL), California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, David Clark Labs, Box 7617, Raleigh, NC 27695, USA
| | - Andrea Lucky
- Entomology and Nematology Department, University of Florida, 32608, Gainesville, FL, USA
| | - Daniel M Portik
- California Academy of Sciences, 94118, San Francisco, CA, USA
| | - Neil Durie Tsutsui
- Department of Environmental Science, Policy, and Management, 130 Mulford Hall, #3114, University of California-, 94720-3114, Berkeley, CA, USA
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12
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Allf BC, Cooper CB, Larson LR, Dunn RR, Futch SE, Sharova M, Cavalier D. Citizen Science as an Ecosystem of Engagement: Implications for Learning and Broadening Participation. Bioscience 2022; 72:651-663. [PMID: 35769502 PMCID: PMC9236874 DOI: 10.1093/biosci/biac035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The bulk of research on citizen science participants is project centric, based on an assumption that volunteers experience a single project. Contrary to this assumption, survey responses (n = 3894) and digital trace data (n = 3649) from volunteers, who collectively engaged in 1126 unique projects, revealed that multiproject participation was the norm. Only 23% of volunteers were singletons (who participated in only one project). The remaining multiproject participants were split evenly between discipline specialists (39%) and discipline spanners (38% joined projects with different disciplinary topics) and unevenly between mode specialists (52%) and mode spanners (25% participated in online and offline projects). Public engagement was narrow: The multiproject participants were eight times more likely to be White and five times more likely to hold advanced degrees than the general population. We propose a volunteer-centric framework that explores how the dynamic accumulation of experiences in a project ecosystem can support broad learning objectives and inclusive citizen science.
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Affiliation(s)
- Bradley C Allf
- Department of Forestry and Environmental Resources, Raleigh, North Carolina, United States
| | - Caren B Cooper
- Department of Forestry and Environmental Resources, Raleigh, North Carolina, United States
| | - Lincoln R Larson
- North Carolina State University, Raleigh, North Carolina, United States
| | - Robert R Dunn
- Department of Applied Ecology, Raleigh, North Carolina, United States
| | | | - Maria Sharova
- Thriving Earth Exchange, an initiative of the American Geophysical Union, Washington, DC
| | - Darlene Cavalier
- Arizona State University and the founder of SciStarter, Tempe, Arizona
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13
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Alberdi A, Andersen SB, Limborg MT, Dunn RR, Gilbert MTP. Disentangling host-microbiota complexity through hologenomics. Nat Rev Genet 2022; 23:281-297. [PMID: 34675394 DOI: 10.1038/s41576-021-00421-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2021] [Indexed: 02/07/2023]
Abstract
Research on animal-microbiota interactions has become a central topic in biological sciences because of its relevance to basic eco-evolutionary processes and applied questions in agriculture and health. However, animal hosts and their associated microbial communities are still seldom studied in a systemic fashion. Hologenomics, the integrated study of the genetic features of a eukaryotic host alongside that of its associated microbes, is becoming a feasible - yet still underexploited - approach that overcomes this limitation. Acknowledging the biological and genetic properties of both hosts and microbes, along with the advantages and disadvantages of implemented techniques, is essential for designing optimal studies that enable some of the major questions in biology to be addressed.
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Affiliation(s)
- Antton Alberdi
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Sandra B Andersen
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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14
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Svenningsen CS, Bowler DE, Hecker S, Bladt J, Grescho V, Dam NM, Dauber J, Eichenberg D, Ejrnæs R, Fløjgaard C, Frenzel M, Frøslev TG, Hansen AJ, Heilmann‐Clausen J, Huang Y, Larsen JC, Menger J, Nayan NLBM, Pedersen LB, Richter A, Dunn RR, Tøttrup AP, Bonn A. Flying insect biomass is negatively associated with urban cover in surrounding landscapes. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
| | - Diana E. Bowler
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Friedrich Schiller University Jena Institute of Biodiversity Jena Germany
- Department of Ecosystem Services Helmholtz Centre for Environmental Research – UFZ Leipzig Germany
| | - Susanne Hecker
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Ecosystem Services Helmholtz Centre for Environmental Research – UFZ Leipzig Germany
| | - Jesper Bladt
- Department of Bioscience – Biodiversity and Conservation Aarhus University Aarhus Denmark
| | - Volker Grescho
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Ecosystem Services Helmholtz Centre for Environmental Research – UFZ Leipzig Germany
| | - Nicole M. Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Friedrich Schiller University Jena Institute of Biodiversity Jena Germany
| | - Jens Dauber
- Thünen‐Institute of Biodiversity Braunschweig Germany
| | - David Eichenberg
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Ecosystem Services Helmholtz Centre for Environmental Research – UFZ Leipzig Germany
| | - Rasmus Ejrnæs
- Department of Bioscience – Biodiversity and Conservation Aarhus University Aarhus Denmark
| | - Camilla Fløjgaard
- Department of Bioscience – Biodiversity and Conservation Aarhus University Aarhus Denmark
| | - Mark Frenzel
- Department of Community Ecology Helmholtz Centre for Environmental Research – UFZ Halle Germany
| | - Tobias G. Frøslev
- Centre for GeoGenetics GLOBE Institute University of Copenhagen Copenhagen Denmark
| | - Anders J. Hansen
- Centre for GeoGenetics GLOBE Institute University of Copenhagen Copenhagen Denmark
| | - Jacob Heilmann‐Clausen
- Centre for Macroecology, Evolution and Climate GLOBE Institute University of Copenhagen Copenhagen Denmark
| | - Yuanyuan Huang
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Ecosystem Services Helmholtz Centre for Environmental Research – UFZ Leipzig Germany
| | - Jonas C. Larsen
- Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Juliana Menger
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Ecosystem Services Helmholtz Centre for Environmental Research – UFZ Leipzig Germany
- Coordenação de Biodiversidade Instituto Nacional de Pesquisas da Amazônia Manaus Brazil
| | - Nur L. B. M. Nayan
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Ecosystem Services Helmholtz Centre for Environmental Research – UFZ Leipzig Germany
| | - Lene B. Pedersen
- Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Anett Richter
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Ecosystem Services Helmholtz Centre for Environmental Research – UFZ Leipzig Germany
- Thünen‐Institute of Biodiversity Braunschweig Germany
| | - Robert R. Dunn
- Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- Department of Applied Ecology North Carolina State University Raleigh North Carolina USA
| | - Anders P. Tøttrup
- Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Aletta Bonn
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Friedrich Schiller University Jena Institute of Biodiversity Jena Germany
- Department of Ecosystem Services Helmholtz Centre for Environmental Research – UFZ Leipzig Germany
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15
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Dunn RR, Burger JR, Carlen EJ, Koltz AM, Light JE, Martin RA, Munshi-South J, Nichols LM, Vargo EL, Yitbarek S, Zhao Y, Cibrián-Jaramillo A. A Theory of City Biogeography and the Origin of Urban Species. Front Conserv Sci 2022. [DOI: 10.3389/fcosc.2022.761449] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
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.
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16
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Beasley DE, Monsur M, Hu J, Dunn RR, Madden AA. The bacterial community of childcare centers: potential implications for microbial dispersal and child exposure. Environ Microbiome 2022; 17:8. [PMID: 35246271 PMCID: PMC8895594 DOI: 10.1186/s40793-022-00404-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Bacterial communities within built environments reflect differences in sources of bacteria, building design, and environmental contexts. These communities impact the health of their occupants in many ways. Children interact with the built environment differently than do adults as a result of their unique behaviors, size, and developmental status. Consequently, understanding the broader bacterial community to which children are exposed will help inform public health efforts and contribute to our growing understanding of the bacterial community associated with childcare centers. METHODS We sampled childcare centers to survey the variation in bacterial community composition across five surfaces found inside and outside twelve classrooms and six centers using 16S rRNA marker gene amplicon sequencing. We then correlated these bacterial community analyses of surfaces with environmental and demographic measures of illumination and classroom occupant density. RESULTS The childcare environment was dominated by human-associated bacteria with modest input from outdoor sources. Though the bacterial communities of individual childcare centers differed, there was a greater difference in the bacterial community within a classroom than among centers. Surface habitats-fomites-within the classroom, did not differ in community composition despite differing proximity to likely sources of bacteria, and possible environmental filters, such as light. Bacterial communities did correlate with occupant density and differed significantly between high and low usage surfaces. CONCLUSIONS Our results suggest built environments inhabited by young children are similar to functionally equivalent built environments inhabited by adults, despite the different way young children engage with their environment. Ultimately, these results will be useful when further interrogating microbial dispersal and human exposure to microorganisms in built environments that specifically cater to young children.
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Affiliation(s)
- D E Beasley
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, 27695, USA.
- Department of Biology, Geology and Environmental Science, University of Tennessee Chattanooga, Chattanooga, TN, 37403, USA.
| | - M Monsur
- College of Design, North Carolina State University, Raleigh, NC, 27695, USA
- Department of Landscape Architecture, Texas Tech University, Lubbock, TX, 79409, USA
| | - J Hu
- College of Design, North Carolina State University, Raleigh, NC, 27695, USA
| | - R R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, 27695, USA
| | - A A Madden
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, 27695, USA
- The Microbe Institute, Everett, MA, 02149, USA
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17
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Abstract
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.
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Affiliation(s)
- Hannah E. R. Frank
- Department of Crop and Soil Sciences North Carolina State University, Raleigh, USA
| | - Katie Amato
- Department of Anthropology, Northwestern University, Evanston, IL, USA
| | - Michelle Trautwein
- Entomology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, USA
| | - Paula Maia
- Department of Anthropology, Northwestern University, Evanston, IL, USA
| | - Emily R. Liman
- Department of Biological Sciences, Section of Neurobiology, University of Southern California, Los Angeles, CA, USA
| | - Lauren M. Nichols
- Department of Applied Ecology, North Carolina State University, Raleigh, USA
| | - Kurt Schwenk
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Paul A. S. Breslin
- Department of Nutritional Sciences, Rutgers The State University of New Jersey, New Brunswick, NJ, USA,Monell Chemical Senses Center, Philadelphia, PA, USA
| | - Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, USA,Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
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18
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La Richelière F, Muñoz G, Guénard B, Dunn RR, Economo EP, Powell S, Sanders NJ, Weiser MD, Abouheif E, Lessard JP. Warm and arid regions of the world are hotspots of superorganism complexity. Proc Biol Sci 2022; 289:20211899. [PMID: 35135345 PMCID: PMC8832517 DOI: 10.1098/rspb.2021.1899] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Biologists have long been fascinated by the processes that give rise to phenotypic complexity of organisms, yet whether there exist geographical hotspots of phenotypic complexity remains poorly explored. Phenotypic complexity can be readily observed in ant colonies, which are superorganisms with morphologically differentiated queen and worker castes analogous to the germline and soma of multicellular organisms. Several ant species have evolved 'worker polymorphism', where workers in a single colony show quantifiable differences in size and head-to-body scaling. Here, we use 256 754 occurrence points from 8990 ant species to investigate the geography of worker polymorphism. We show that arid regions of the world are the hotspots of superorganism complexity. Tropical savannahs and deserts, which are typically species-poor relative to tropical or even temperate forests, harbour the highest densities of polymorphic ants. We discuss the possible adaptive advantages that worker polymorphism provides in arid environments. Our work may provide a window into the environmental conditions that promote the emergence of highly complex phenotypes.
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Affiliation(s)
- Frédérique La Richelière
- Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montreal, Canada, H4B 1R6,Department of Biology, McGill University, 1205 Docteur Penfield, Montreal, Canada, H3A 1B1
| | - Gabriel Muñoz
- Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montreal, Canada, H4B 1R6
| | - Benoit Guénard
- School of Biological Sciences, University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, People's Republic of China
| | - Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, 3510 Thomas Hall, Raleigh, NC, 27695, USA
| | - Evan P. Economo
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Scott Powell
- Department of Biological Sciences, George Washington University, Washington, DC, USA
| | - Nathan J. Sanders
- Department of Ecology and Evolutionary Biology, 1105 North University Ave Biological Sciences Building, University of Michigan Ann Arbor, MI 48109-1085, USA
| | - Michael D. Weiser
- Geographical Ecology Group, Department of Biology, University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
| | - Ehab Abouheif
- Department of Biology, McGill University, 1205 Docteur Penfield, Montreal, Canada, H3A 1B1
| | - Jean-Philippe Lessard
- Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montreal, Canada, H4B 1R6
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19
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Madden AA, Lahue C, Gordy CL, Little JL, Nichols LM, Calvert MD, Dunn RR, Smukowski Heil C. Sugar-seeking insects as a source of diverse bread-making yeasts with enhanced attributes. Yeast 2021; 39:108-127. [PMID: 34687090 DOI: 10.1002/yea.3676] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/08/2021] [Accepted: 10/17/2021] [Indexed: 11/10/2022] Open
Abstract
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.
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Affiliation(s)
- Anne A Madden
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA.,The Microbe Institute, Everett, Massachusetts, USA
| | - Caitlin Lahue
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA.,University of North Carolina Chapel-Hill, Chapel Hill, North Carolina, USA
| | - Claire L Gordy
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Joy L Little
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Lauren M Nichols
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA
| | - Martha D Calvert
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA.,Department of Food Science and Technology, Virginia Tech, Blacksburg, Virginia, USA
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA
| | - Caiti Smukowski Heil
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
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20
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Webster TM, McFarland A, Gebert MJ, Oliverio AM, Nichols LM, Dunn RR, Hartmann EM, Fierer N. Structure and Functional Attributes of Bacterial Communities in Premise Plumbing Across the United States. Environ Sci Technol 2021; 55:14105-14114. [PMID: 34606240 DOI: 10.1021/acs.est.1c03309] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
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.
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Affiliation(s)
- Tara M Webster
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado 80309, United States
| | - Alexander McFarland
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Matthew J Gebert
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado 80309, United States
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80302, United States
| | - Angela M Oliverio
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado 80309, United States
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80302, United States
| | - Lauren M Nichols
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina 27607, United States
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina 27607, United States
- Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen 1050, Denmark
| | - Erica M Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado 80309, United States
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80302, United States
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21
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Sheard JK, Rahbek C, Dunn RR, Sanders NJ, Isaac NJB. Long-term trends in the occupancy of ants revealed through use of multi-sourced datasets. Biol Lett 2021; 17:20210240. [PMID: 34665990 PMCID: PMC8526175 DOI: 10.1098/rsbl.2021.0240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/29/2021] [Indexed: 11/12/2022] Open
Abstract
We combined participatory science data and museum records to understand long-term changes in occupancy for 29 ant species in Denmark over 119 years. Bayesian occupancy modelling indicated change in occupancy for 15 species: five increased, four declined and six showed fluctuating trends. We consider how trends may have been influenced by life-history and habitat changes. Our results build on an emerging picture that biodiversity change in insects is more complex than implied by the simple insect decline narrative.
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Affiliation(s)
- Julie K. Sheard
- Center for Macroecology, Evolution and Climate, University of Copenhagen, Universitetsparken 15, Copenhagen 2100, Denmark
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, University of Copenhagen, Universitetsparken 15, Copenhagen 2100, Denmark
- Center for Global Mountain Biodiversity, GLOBE Institute, University of Copenhagen, Universitetsparken 15, Copenhagen 2100, Denmark
- Institute of Ecology, Peking University, Beijing 100871, People's Republic of China
- Department of Life Sciences, Imperial College London, Ascot SL5 7PY, UK
- Danish Institute for Advanced Study, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
| | - Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Nathan J. Sanders
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Nick J. B. Isaac
- UK Centre for Ecology and Hydrology, Crowmarsh Gifford, Maclean Building, Wallingford OX10 8BB, UK
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22
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23
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Liu S, Westbury MV, Dussex N, Mitchell KJ, Sinding MHS, Heintzman PD, Duchêne DA, Kapp JD, von Seth J, Heiniger H, Sánchez-Barreiro F, Margaryan A, André-Olsen R, De Cahsan B, Meng G, Yang C, Chen L, van der Valk T, Moodley Y, Rookmaaker K, Bruford MW, Ryder O, Steiner C, Bruins-van Sonsbeek LGR, Vartanyan S, Guo C, Cooper A, Kosintsev P, Kirillova I, Lister AM, Marques-Bonet T, Gopalakrishnan S, Dunn RR, Lorenzen ED, Shapiro B, Zhang G, Antoine PO, Dalén L, Gilbert MTP. Ancient and modern genomes unravel the evolutionary history of the rhinoceros family. Cell 2021; 184:4874-4885.e16. [PMID: 34433011 DOI: 10.1016/j.cell.2021.07.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/16/2021] [Accepted: 07/23/2021] [Indexed: 12/27/2022]
Abstract
Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (∼16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.
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Affiliation(s)
- Shanlin Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark.
| | - Michael V Westbury
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Nicolas Dussex
- Centre for Palaeogenetics, Svante Arrhenius vag 20C, Stockholm 10691, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm 10405, Sweden; Department of Zoology, Stockholm University, Stockholm 10691, Sweden
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
| | - Mikkel-Holger S Sinding
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Peter D Heintzman
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø 9037, Norway
| | - David A Duchêne
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Joshua D Kapp
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Johanna von Seth
- Centre for Palaeogenetics, Svante Arrhenius vag 20C, Stockholm 10691, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm 10405, Sweden; Department of Zoology, Stockholm University, Stockholm 10691, Sweden
| | - Holly Heiniger
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
| | - Fátima Sánchez-Barreiro
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Ashot Margaryan
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Remi André-Olsen
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17121 Solna, Sweden
| | - Binia De Cahsan
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Guanliang Meng
- China National Genebank, BGI Shenzhen, Shenzhen 518083, China
| | - Chentao Yang
- China National Genebank, BGI Shenzhen, Shenzhen 518083, China
| | - Lei Chen
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Tom van der Valk
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Yoshan Moodley
- Department of Zoology, University of Venda, Thohoyandou 0950, Republic of South Africa
| | - Kees Rookmaaker
- Editor of the Rhino Resource Center, Utrecht, the Netherlands
| | - Michael W Bruford
- School of Biosciences, Sir Martin Evans Building, Cardiff University, Cardiff CF10 3AX, UK; Sustainable Places Research Institute, Cardiff University, Cardiff CF10 3BA, UK
| | - Oliver Ryder
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, San Diego, CA 92027, USA
| | - Cynthia Steiner
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, San Diego, CA 92027, USA
| | | | - Sergey Vartanyan
- N.A. Shilo North-East Interdisciplinary Scientific Research Institute, Far East Branch, Russian Academy of Sciences (NEISRI FEB RAS), Magadan 685000, Russia
| | - Chunxue Guo
- China National Genebank, BGI Shenzhen, Shenzhen 518083, China
| | - Alan Cooper
- South Australian Museum, Adelaide, SA 5000, Australia
| | - Pavel Kosintsev
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia; Ural Federal University, Yekaterinburg, Russia
| | - Irina Kirillova
- Institute of Geography, Russian Academy of Sciences, Moscow 119017, Russia
| | - Adrian M Lister
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain; Centre Nacional d'Anàlisi Genòmica, Centre for Genomic Regulation (CNAG-CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Shyam Gopalakrishnan
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Robert R Dunn
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark; Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Eline D Lorenzen
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 96050, USA
| | - Guojie Zhang
- China National Genebank, BGI Shenzhen, Shenzhen 518083, China; Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Pierre-Olivier Antoine
- Institut des Sciences de l'Évolution, Université Montpellier, CNRS, IRD, EPHE, Montpellier 34095, France
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius vag 20C, Stockholm 10691, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm 10405, Sweden; Department of Zoology, Stockholm University, Stockholm 10691, Sweden.
| | - M Thomas P Gilbert
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark; Norwegian University of Science and Technology (NTNU) University Museum, Trondheim 7012, Norway.
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24
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Demi LM, Taylor BW, Reading BJ, Tordoff MG, Dunn RR. Understanding the evolution of nutritive taste in animals: Insights from biological stoichiometry and nutritional geometry. Ecol Evol 2021; 11:8441-8455. [PMID: 34257909 PMCID: PMC8258225 DOI: 10.1002/ece3.7745] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/04/2021] [Accepted: 05/11/2021] [Indexed: 12/21/2022] Open
Abstract
A major conceptual gap in taste biology is the lack of a general framework for understanding the evolution of different taste modalities among animal species. We turn to two complementary nutritional frameworks, biological stoichiometry theory and nutritional geometry, to develop hypotheses for the evolution of different taste modalities in animals. We describe how the attractive tastes of Na-, Ca-, P-, N-, and C-containing compounds are consistent with principles of both frameworks based on their shared focus on nutritional imbalances and consumer homeostasis. Specifically, we suggest that the evolution of multiple nutritive taste modalities can be predicted by identifying individual elements that are typically more concentrated in the tissues of animals than plants. Additionally, we discuss how consumer homeostasis can inform our understanding of why some taste compounds (i.e., Na, Ca, and P salts) can be either attractive or aversive depending on concentration. We also discuss how these complementary frameworks can help to explain the evolutionary history of different taste modalities and improve our understanding of the mechanisms that lead to loss of taste capabilities in some animal lineages. The ideas presented here will stimulate research that bridges the fields of evolutionary biology, sensory biology, and ecology.
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Affiliation(s)
- Lee M. Demi
- Department of Applied EcologyNorth Carolina State UniversityRaleighNCUSA
| | - Brad W. Taylor
- Department of Applied EcologyNorth Carolina State UniversityRaleighNCUSA
| | | | | | - Robert R. Dunn
- Department of Applied EcologyNorth Carolina State UniversityRaleighNCUSA
- Center for Evolutionary HologenomicsUniversity of CopenhagenCopenhagenDenmark
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25
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Vecchi M, Kossi Adakpo L, Dunn RR, Nichols LM, Penick CA, Sanders NJ, Rebecchi L, Guidetti R. The toughest animals of the Earth versus global warming: Effects of long-term experimental warming on tardigrade community structure of a temperate deciduous forest. Ecol Evol 2021; 11:9856-9863. [PMID: 34306668 PMCID: PMC8293726 DOI: 10.1002/ece3.7816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/10/2021] [Accepted: 06/02/2021] [Indexed: 12/05/2022] Open
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.
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Affiliation(s)
- Matteo Vecchi
- Department of Biological and Environmental ScienceUniversity of JyvaskylaJyvaskylaFinland
| | | | - Robert R. Dunn
- Department of Applied EcologyNorth Carolina State UniversityRaleighNCUSA
- Center for Evolutionary HologenomicsUniversity of CopenhagenCopenhagenDenmark
| | - Lauren M. Nichols
- Department of Applied EcologyNorth Carolina State UniversityRaleighNCUSA
| | - Clint A. Penick
- Department of Ecology, Evolution, and Organismal BiologyKennesaw State UniversityKennesawGAUSA
| | - Nathan J. Sanders
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMIUSA
| | - Lorena Rebecchi
- Department of Life SciencesUniversity of Modena and Reggio EmiliaModenaItaly
| | - Roberto Guidetti
- Department of Life SciencesUniversity of Modena and Reggio EmiliaModenaItaly
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26
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Cooper CB, Hawn CL, Larson LR, Parrish JK, Bowser G, Cavalier D, Dunn RR, Haklay M(M, Gupta KK, Jelks NO, Johnson VA, Katti M, Leggett Z, Wilson OR, Wilson S. Inclusion in citizen science: The conundrum of rebranding. Science 2021. [DOI: 10.1126/science.abi6487] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Does replacing the term “citizen science” do more harm than good?
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Affiliation(s)
- Caren B. Cooper
- The list of author affilations is available in the supplementary materials
| | - Chris L. Hawn
- The list of author affilations is available in the supplementary materials
| | - Lincoln R. Larson
- The list of author affilations is available in the supplementary materials
| | - Julia K. Parrish
- The list of author affilations is available in the supplementary materials
| | - Gillian Bowser
- The list of author affilations is available in the supplementary materials
| | - Darlene Cavalier
- The list of author affilations is available in the supplementary materials
| | - Robert R. Dunn
- The list of author affilations is available in the supplementary materials
| | | | - Kaberi Kar Gupta
- The list of author affilations is available in the supplementary materials
| | | | - Valerie A. Johnson
- The list of author affilations is available in the supplementary materials
| | - Madhusudan Katti
- The list of author affilations is available in the supplementary materials
| | - Zakiya Leggett
- The list of author affilations is available in the supplementary materials
| | - Omega R. Wilson
- The list of author affilations is available in the supplementary materials
| | - Sacoby Wilson
- The list of author affilations is available in the supplementary materials
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27
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Calvert MD, Madden AA, Nichols LM, Haddad NM, Lahne J, Dunn RR, McKenney EA. A review of sourdough starters: ecology, practices, and sensory quality with applications for baking and recommendations for future research. PeerJ 2021; 9:e11389. [PMID: 34026358 PMCID: PMC8117929 DOI: 10.7717/peerj.11389] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/12/2021] [Indexed: 01/13/2023] Open
Abstract
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.
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Affiliation(s)
- Martha D Calvert
- Department of Food Science and Technology, Virginia Polytechnic Institute and State University (Virginia Tech), Blackburg, VA, United States of America.,Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States of America
| | - Anne A Madden
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States of America
| | - Lauren M Nichols
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States of America
| | - Nick M Haddad
- Kellogg Biological Station and Department of Integrative Biology, Michigan State University, Hickory Corners, MI, United States of America
| | - Jacob Lahne
- Department of Food Science and Technology, Virginia Polytechnic Institute and State University (Virginia Tech), Blackburg, VA, United States of America
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States of America.,Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | - Erin A McKenney
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States of America
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28
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Fitzgerald JL, Stuble KL, Nichols LM, Diamond SE, Wentworth TR, Pelini SL, Gotelli NJ, Sanders NJ, Dunn RR, Penick CA. Abundance of spring‐ and winter‐active arthropods declines with warming. Ecosphere 2021. [DOI: 10.1002/ecs2.3473] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Jacquelyn L. Fitzgerald
- Plant Biology and Conservation Northwestern University Evanston Illinois60201USA
- Negaunee Institute for Plant Conservation Science & Action Chicago Botanic Garden Glencoe Illinois60022USA
- Department of Applied Ecology North Carolina State University Raleigh North Carolina27695USA
| | | | - Lauren M. Nichols
- Department of Applied Ecology North Carolina State University Raleigh North Carolina27695USA
| | - Sarah E. Diamond
- Department of Biology Case Western Reserve University Cleveland Ohio44106USA
| | - Thomas R. Wentworth
- Department of Plant and Microbial Biology North Carolina State University Raleigh North Carolina27695USA
| | - Shannon L. Pelini
- Department of Biological Sciences Bowling Green State University Bowling Green Ohio43403USA
| | | | - Nathan J. Sanders
- Environmental Program Rubenstein School of Environment and Natural Resources University of Vermont Burlington Vermont05405USA
| | - Robert R. Dunn
- Department of Applied Ecology North Carolina State University Raleigh North Carolina27695USA
- Center for Evolutionary Hologenomics University of Copenhagen CopenhagenDK‐2100Denmark
| | - Clint A. Penick
- Department of Ecology, Evolution & Organismal Biology Kennesaw State University Kennesaw Georgia30144USA
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29
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Svenningsen CS, Frøslev TG, Bladt J, Pedersen LB, Larsen JC, Ejrnæs R, Fløjgaard C, Hansen AJ, Heilmann-Clausen J, Dunn RR, Tøttrup AP. Detecting flying insects using car nets and DNA metabarcoding. Biol Lett 2021; 17:20200833. [PMID: 33784872 PMCID: PMC8086955 DOI: 10.1098/rsbl.2020.0833] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Monitoring insects across space and time is challenging, due to their vast taxonomic and functional diversity. This study demonstrates how nets mounted on rooftops of cars (car nets) and DNA metabarcoding can be applied to sample flying insect richness and diversity across large spatial scales within a limited time period. During June 2018, 365 car net samples were collected by 151 volunteers during two daily time intervals on 218 routes in Denmark. Insect bulk samples were processed with a DNA metabarcoding protocol to estimate taxonomic composition, and the results were compared to known flying insect richness and occurrence data. Insect and hoverfly richness and diversity were assessed across biogeographic regions and dominant land cover types. We detected 15 out of 19 flying insect orders present in Denmark, with high proportions of especially Diptera compared to Danish estimates, and lower insect richness and diversity in urbanized areas. We detected 319 species not known for Denmark and 174 species assessed in the Danish Red List. Our results indicate that the methodology can assess the flying insect fauna at large spatial scales to a wide extent, but may be, like other methods, biased towards certain insect orders.
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Affiliation(s)
| | | | - Jesper Bladt
- Department of Bioscience-Biodiversity and Conservation, Aarhus University, Aarhus, Denmark
| | - Lene Bruhn Pedersen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Colling Larsen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Ejrnæs
- Department of Bioscience-Biodiversity and Conservation, Aarhus University, Aarhus, Denmark
| | - Camilla Fløjgaard
- Department of Bioscience-Biodiversity and Conservation, Aarhus University, Aarhus, Denmark
| | | | - Jacob Heilmann-Clausen
- Centre for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Anders P Tøttrup
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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30
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Landis EA, Oliverio AM, McKenney EA, Nichols LM, Kfoury N, Biango-Daniels M, Shell LK, Madden AA, Shapiro L, Sakunala S, Drake K, Robbat A, Booker M, Dunn RR, Fierer N, Wolfe BE. The diversity and function of sourdough starter microbiomes. eLife 2021; 10:e61644. [PMID: 33496265 PMCID: PMC7837699 DOI: 10.7554/elife.61644] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022] Open
Abstract
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.
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Affiliation(s)
| | - Angela M Oliverio
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulderUnited States
- Cooperative Institute for Research in Environmental Sciences, University of ColoradoBoulderUnited States
| | - Erin A McKenney
- Department of Applied Ecology, North Carolina State UniversityRaleighUnited States
- North Carolina Museum of Natural SciencesRaleighUnited States
| | - Lauren M Nichols
- Department of Applied Ecology, North Carolina State UniversityRaleighUnited States
| | - Nicole Kfoury
- Department of Chemistry, Tufts UniversityMedfordUnited States
| | | | - Leonora K Shell
- Department of Applied Ecology, North Carolina State UniversityRaleighUnited States
| | - Anne A Madden
- Department of Applied Ecology, North Carolina State UniversityRaleighUnited States
| | - Lori Shapiro
- Department of Applied Ecology, North Carolina State UniversityRaleighUnited States
| | | | - Kinsey Drake
- Department of Biology, Tufts UniversityMedfordUnited States
| | - Albert Robbat
- Department of Chemistry, Tufts UniversityMedfordUnited States
| | - Matthew Booker
- Department of History, North Carolina State UniversityRaleighUnited States
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State UniversityRaleighUnited States
- Danish Natural History Museum, University of CopenhagenCopenhagenDenmark
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulderUnited States
- Cooperative Institute for Research in Environmental Sciences, University of ColoradoBoulderUnited States
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Andersen B, Frisvad JC, Dunn RR, Thrane U. A Pilot Study on Baseline Fungi and Moisture Indicator Fungi in Danish Homes. J Fungi (Basel) 2021; 7:jof7020071. [PMID: 33498446 PMCID: PMC7909426 DOI: 10.3390/jof7020071] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/08/2021] [Accepted: 01/18/2021] [Indexed: 11/29/2022] Open
Abstract
In many complaint cases regarding bad indoor environments, there is no evidence of visible fungal growth. To determine if the problems are fungi-related, dust sampling is the method of choice among building surveyors. However, there is a need to differentiate between species belonging to a normal, dry indoor environment and species belonging to a damp building envelope. The purposes of this pilot study were to examine which fungal species are present in problem-free Danish homes and to evaluate different detection and identification methods. Analyses showed that the fungal diversity outside was different from the diversity inside and that the composition of fungal species growing indoors was different compared to those found as spores, both indoors and outdoors. Common for most homes were Pseudopithomyceschartarum, Cladosporiumallicinum and Alternaria sect. Infectoriae together with Botrytis spp., Penicilliumdigitatum and Pen. glabrum. The results show that ITS sequencing of dust samples is adequate if supported by thorough building inspections and that food products play as large a role in the composition of the baseline spora as the outdoor air and surrounding vegetation. This pilot study provides a list of baseline fungal species found in Danish homes with a good indoor environment.
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Affiliation(s)
- Birgitte Andersen
- Division of Energy Efficiency, Indoor Climate and Sustainability of Buildings, Department of the Built Environment, Aalborg University, A.C. Meyers Vænge 15, DK-2450 Copenhagen SV, Denmark
- Correspondence: ; Tel.: +45-9940-2312
| | - Jens C. Frisvad
- Section for Synthetic Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, DK-2800 Kongens Lyngby, Denmark;
| | - Robert R. Dunn
- Department of Applied Ecology, Campus Box 7617, NC State University Campus, Raleigh, NC 27695-7617, USA;
| | - Ulf Thrane
- Wood and Biomaterials, Building and Construction, Danish Technological Institute, Gregersensvej 1, DK-2630 Taastrup, Denmark;
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Sanders D, Grunden A, Dunn RR. A review of clothing microbiology: the history of clothing and the role of microbes in textiles. Biol Lett 2021; 17:20200700. [PMID: 33435848 PMCID: PMC7876606 DOI: 10.1098/rsbl.2020.0700] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022] Open
Abstract
Humans have worn clothing for thousands of years, and since its invention, clothing has evolved from its simple utilitarian function for survival to become an integral part of society. While much consideration has been given to the broad environmental impacts of the textile and laundering industries, little is known about the impact wearing clothing has had on the human microbiome, particularly that of the skin, despite our long history with clothing. This review discusses the history of clothing and the evolution of textiles, what is and is not known about microbial persistence on and degradation of various fibres, and what opportunities for the industrial and environmental application of clothing microbiology exist for the future.
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Affiliation(s)
- Deaja Sanders
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Amy Grunden
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC 27695, USA
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Halawani O, Dunn RR, Grunden AM, Smith AA. Bacterial exposure leads to variable mortality but not a measurable increase in surface antimicrobials across ant species. PeerJ 2020; 8:e10412. [PMID: 33344078 PMCID: PMC7719289 DOI: 10.7717/peerj.10412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 11/02/2020] [Indexed: 11/20/2022] Open
Abstract
Social insects have co-existed with microbial species for millions of years and have evolved a diversity of collective defenses, including the use of antimicrobials. While many studies have revealed strategies that ants use against microbial entomopathogens, and several have shown ant-produced compounds inhibit environmental bacterial growth, few studies have tested whether exposure to environmental bacteria represents a health threat to ants. We compare four ant species’ responses to exposure to Escherichia coli and Staphylococcus epidermidis bacteria in order to broaden our understanding of microbial health-threats to ants and their ability to defend against them. In a first experiment, we measure worker mortality of Solenopsis invicta, Brachymyrmex chinensis, Aphaenogaster rudis, and Dorymyrmex bureni in response to exposure to E. coli and S. epidermidis. We found that exposure to E. coli was lethal for S. invicta and D. bureni, while all other effects of exposure were not different from experimental controls. In a second experiment, we compared the antimicrobial ability of surface extracts from bacteria-exposed and non-exposed S. invicta and B. chinensis worker ants, to see if exposure to E. coli or S. epidermidis led to an increase in antimicrobial compounds. We found no difference in the inhibitory effects from either treatment group in either species. Our results demonstrate the susceptibility to bacteria is varied across ant species. This variation may correlate with an ant species’ use of surface antimicrobials, as we found significant mortality effects in species which also were producing antimicrobials. Further exploration of a wide range of both bacteria and ant species is likely to reveal unique and nuanced antimicrobial strategies and deepen our understanding of how ant societies respond to microbial health threats.
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Affiliation(s)
- Omar Halawani
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Amy M Grunden
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Adrian A Smith
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Research & Collections, North Carolina Museum of Natural Sciences, Raleigh, NC, USA
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Lahue C, Madden AA, Dunn RR, Smukowski Heil C. History and Domestication of Saccharomyces cerevisiae in Bread Baking. Front Genet 2020; 11:584718. [PMID: 33262788 PMCID: PMC7686800 DOI: 10.3389/fgene.2020.584718] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/13/2020] [Indexed: 11/30/2022] Open
Abstract
The yeast Saccharomyces cerevisiae has been instrumental in the fermentation of foods and beverages for millennia. In addition to fermentations like wine, beer, cider, sake, and bread, S. cerevisiae has been isolated from environments ranging from soil and trees, to human clinical isolates. Each of these environments has unique selection pressures that S. cerevisiae must adapt to. Bread dough, for example, requires S. cerevisiae to efficiently utilize the complex sugar maltose; tolerate osmotic stress due to the semi-solid state of dough, high salt, and high sugar content of some doughs; withstand various processing conditions, including freezing and drying; and produce desirable aromas and flavors. In this review, we explore the history of bread that gave rise to modern commercial baking yeast, and the genetic and genomic changes that accompanied this. We illustrate the genetic and phenotypic variation that has been documented in baking strains and wild strains, and how this variation might be used for baking strain improvement. While we continue to improve our understanding of how baking strains have adapted to bread dough, we conclude by highlighting some of the remaining open questions in the field.
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Affiliation(s)
- Caitlin Lahue
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States
| | - Anne A. Madden
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States
| | - Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Caiti Smukowski Heil
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
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Dunn RR, Amato KR, Archie EA, Arandjelovic M, Crittenden AN, Nichols LM. Corrigendum: The Internal, External and Extended Microbiomes of Hominins. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Grantham NS, Reich BJ, Laber EB, Pacifici K, Dunn RR, Fierer N, Gebert M, Allwood JS, Faith SA. Global forensic geolocation with deep neural networks. J R Stat Soc Ser C Appl Stat 2020. [DOI: 10.1111/rssc.12427] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Dunn RR. The history and future of the wild life in cities. Curr Biol 2020. [DOI: 10.1016/j.cub.2020.05.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Allwood JS, Fierer N, Dunn RR, Breen M, Reich BJ, Laber EB, Clifton J, Grantham NS, Faith SA. Use of standardized bioinformatics for the analysis of fungal DNA signatures applied to sample provenance. Forensic Sci Int 2020; 310:110250. [DOI: 10.1016/j.forsciint.2020.110250] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 03/11/2020] [Indexed: 01/30/2023]
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Riley NG, Goller CC, Leggett ZH, Lewis DM, Ciccone K, Dunn RR. Catalyzing rapid discovery of gold-precipitating bacterial lineages with university students. PeerJ 2020; 8:e8925. [PMID: 32322441 PMCID: PMC7164421 DOI: 10.7717/peerj.8925] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/16/2020] [Indexed: 12/11/2022] Open
Abstract
Intriguing and potentially commercially useful microorganisms are found in our surroundings and new tools allow us to learn about their genetic potential and evolutionary history. Engaging students from different disciplines and courses in the search for microbes requires an exciting project with innovative but straightforward procedures and goals. Here we describe an interdisciplinary program to engage students from different courses in the sampling, identification and analysis of the DNA sequences of a unique yet common microbe, Delftia spp. A campus-wide challenge was created to identify the prevalence of this genus, able to precipitate gold, involving introductory level environmental and life science courses, upper-level advanced laboratory modules taken by undergraduate students (juniors and seniors), graduate students and staff from the campus. The number of participants involved allowed for extensive sampling while undergraduate researchers and students in lab-based courses participated in the sample processing and analyses, helping contextualize and solidify their learning of the molecular biology techniques. The results were shared at each step through publicly accessible websites and workshops. This model allows for the rapid discovery of Delftia presence and prevalence and is adaptable to different campuses and experimental questions.
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Affiliation(s)
- Noah G Riley
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Carlos C Goller
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Biotechnology Program (BIT), North Carolina State University, Raleigh, NC, USA
| | - Zakiya H Leggett
- Department of Forestry and Environmental Resources (FER), North Carolina State University, Raleigh, NC, USA
| | - Danica M Lewis
- North Carolina State University Libraries, North Carolina State University, Raleigh, NC, USA
| | - Karen Ciccone
- North Carolina State University Libraries, North Carolina State University, Raleigh, NC, USA
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA.,University of Copenhagen, Natural History Museum of Denmark, Copenhagen, Denmark.,German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Germany
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40
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Dunn RR, Amato KR, Archie EA, Arandjelovic M, Crittenden AN, Nichols LM. The Internal, External and Extended Microbiomes of Hominins. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00025] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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41
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McDonald BW, Perkins T, Dunn RR, McDonald J, Cole H, Feranec RS, Kays R. High variability within pet foods prevents the identification of native species in pet cats' diets using isotopic evaluation. PeerJ 2020; 8:e8337. [PMID: 32002325 PMCID: PMC6982418 DOI: 10.7717/peerj.8337] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 12/03/2019] [Indexed: 11/30/2022] Open
Abstract
Domestic cats preying on wildlife is a frequent conservation concern but typical approaches for assessing impacts rely on owner reports of prey returned home, which can be biased by inaccurate reporting or by cats consuming prey instead of bringing it home. Isotopes offer an alternative way to quantify broad differences in animal diets. By obtaining samples of pet food from cat owners we predicted that we would have high power to identify cats feeding on wild birds or mammals, given that pet food is thought to have higher C isotope values, due to the pervasive use of corn and/or corn by-products as food ingredients, than native prey. We worked with citizen scientists to quantify the isotopes of 202 cat hair samples and 239 pet food samples from the US and UK. We also characterized the isotopes of 11 likely native prey species from the southeastern US and used mixing models to assess the diet of 47 cats from the same region. Variation in C and N isotope values for cat food was very high, even within the same brand/flavor, suggesting that pet food manufacturers use a wide range of ingredients, and that these may change over time. Cat food and cat hair from the UK had lower C values than the US, presumably reflecting differences in the amount of corn used in the food chains of the two countries. This high variation in pet food reduced our ability to classify cats as hunters of native prey, such that only 43% of the animals could be confidently assigned. If feral or free ranging cats were considered, this uncertainty would be even higher as pet food types would be unknown. Our results question the general assumption that anthropogenic foods always have high C isotope values, because of the high variability we documented within one product type (cat food) and between countries (US vs. UK), and emphasize the need to test a variety of standards before making conclusions from isotope ecology studies.
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Affiliation(s)
- Brandon W McDonald
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States of America.,North Carolina Museum of Natural Sciences, Raleigh, NC, United States of America
| | - Troi Perkins
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States of America.,North Carolina Museum of Natural Sciences, Raleigh, NC, United States of America
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States of America.,Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Jennifer McDonald
- Center for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
| | - Holly Cole
- Center for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
| | | | - Roland Kays
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States of America.,North Carolina Museum of Natural Sciences, Raleigh, NC, United States of America
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Reese AT, Madden AA, Joossens M, Lacaze G, Dunn RR. Influences of Ingredients and Bakers on the Bacteria and Fungi in Sourdough Starters and Bread. mSphere 2020; 5:e00950-19. [PMID: 31941818 PMCID: PMC6968659 DOI: 10.1128/msphere.00950-19] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 12/17/2019] [Indexed: 12/19/2022] Open
Abstract
Sourdough starters are naturally occurring microbial communities in which the environment, ingredients, and bakers are potential sources of microorganisms. The relative importance of these pools remains unknown. Here, bakers from two continents used a standardized recipe and ingredients to make starters that were then baked into breads. We characterized the fungi and bacteria associated with the starters, bakers' hands, and ingredients using 16S and internal transcribed spacer (ITS) rRNA gene amplicon sequencing and then measured dough acidity and bread flavor. Starter communities were much less uniform than expected, and this variation manifested in the flavor of the bread. Starter communities were most similar to those found in flour but shared some species with the bakers' skin. While humans likely contribute microorganisms to the starters, the reverse also appears to be true. This bidirectional exchange of microorganisms between starters and bakers highlights the importance of microbial diversity on bodies and in our environments as it relates to foods.IMPORTANCE Sourdough starters are complex communities of yeast and bacteria which confer characteristic flavor and texture to sourdough bread. The microbes present in starters can be sourced from ingredients or the baking environment and are typically consistent over time. Herein, we show that even when the recipe and ingredients for starter and bread are identical, different bakers around the globe produce highly diverse starters which then alter bread acidity and flavor. Much of the starter microbial community comes from bread flour, but the diversity is also associated with differences in the microbial community on the hands of bakers. These results indicate that bakers may be a source for yeast and bacteria in their breads and/or that bakers' jobs are reflected in their skin microbiome.
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Affiliation(s)
- Aspen T Reese
- Society of Fellows, Harvard University, Cambridge, Massachusetts, USA
| | - Anne A Madden
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA
| | - Marie Joossens
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Science, Ghent University, Ghent, Belgium
| | - Guylaine Lacaze
- Puratos Center for Bread Flavour, Puratos Corporation, Vith, Belgium
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA
- Center for Macroecology, Evolution, and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
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Zhang YM, Vitone TR, Storer CG, Payton AC, Dunn RR, Hulcr J, McDaniel SF, Lucky A. From Pavement to Population Genomics: Characterizing a Long-Established Non-native Ant in North America Through Citizen Science and ddRADseq. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00453] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Lucas JM, Madden AA, Penick CA, Epps MJ, Marting PR, Stevens JL, Fergus DJ, Dunn RR, Meineke EK. Azteca ants maintain unique microbiomes across functionally distinct nest chambers. Proc Biol Sci 2019; 286:20191026. [PMID: 31387509 DOI: 10.1098/rspb.2019.1026] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The microbiome of built structures has considerable influence over an inhabitant's well-being, yet the vast majority of research has focused on human-built structures. Ants are well-known architects, capable of constructing elaborate dwellings, the microbiome of which is underexplored. Here, we explore the bacterial and fungal microbiomes in functionally distinct chambers within and outside the nests of Azteca alfari ants in Cecropia peltata trees. We predicted that A. alfari colonies (1) maintain distinct microbiomes within their nests compared to the surrounding environment, (2) maintain distinct microbiomes among nest chambers used for different functions, and (3) limit both ant and plant pathogens inside their nests. In support of these predictions, we found that internal and external nest sampling locations had distinct microbial communities, and A. alfari maintained lower bacterial richness in their 'nurseries'. While putative animal pathogens were suppressed in chambers that ants actively inhabited, putative plant pathogens were not, which does not support our hypothesis that A. alfari defends its host trees against microbial antagonists. Our results show that ants influence microbial communities inside their nests similar to studies of human homes. Unlike humans, ants limit the bacteria in their nurseries and potentially prevent the build-up of insect-infecting pathogens. These results highlight the importance of documenting how indoor microbiomes differ among species, which might improve our understanding of how to promote indoor health in human dwellings.
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Affiliation(s)
- Jane M Lucas
- Department of Soil and Water Systems, University of Idaho, Moscow, ID 83844, USA
| | - Anne A Madden
- Department of Applied Ecology, North Carolina State University, Raleigh, NC 27695, USA
| | - Clint A Penick
- The Biomimicry Center, Arizona State University, Tempe, AZ 85287, USA
| | - Mary Jane Epps
- Department of Biology, Mary Baldwin University, Staunton, VA 24401, USA
| | - Peter R Marting
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | | | - Daniel J Fergus
- Department of Applied Ecology, North Carolina State University, Raleigh, NC 27695, USA
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC 27695, USA.,Natural History Museum, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Emily K Meineke
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138, USA
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Schuttler SG, Stevenson K, Kays R, Dunn RR. Children's attitudes towards animals are similar across suburban, exurban, and rural areas. PeerJ 2019; 7:e7328. [PMID: 31372320 PMCID: PMC6659664 DOI: 10.7717/peerj.7328] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/19/2019] [Indexed: 11/20/2022] Open
Abstract
The decline in the number of hours Americans spend outdoors, exacerbated by urbanization, has affected people’s familiarity with local wildlife. This is concerning to conservationists, as people tend to care about and invest in what they know. Children represent the future supporters of conservation, such that their knowledge about and feelings toward wildlife have the potential to influence conservation for many years to come. Yet, little research has been conducted on children’s attitudes toward wildlife, particularly across zones of urbanization. We surveyed 2,759 4–8th grade children across 22 suburban, exurban, and rural schools in North Carolina to determine their attitudes toward local, domestic, and exotic animals. We predicted that children who live in rural or exurban areas, where they may have more direct access to more wildlife species, would list more local animals as “liked” and fewer as “scary” compared to children in suburban areas. However, children, regardless of where they lived, provided mostly non-native mammals for open-ended responses, and were more likely to list local animals as scary than as liked. We found urbanization to have little effect on the number of local animals children listed, and the rankings of “liked” animals were correlated across zones of urbanization. Promising for conservation was that half of the top “liked” animals included species or taxonomic groups containing threatened or endangered species. Despite different levels of urbanization, children had either an unfamiliarity with and/or low preference for local animals, suggesting that a disconnect between children and local biodiversity is already well-established, even in more rural areas where many wildlife species can be found.
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Affiliation(s)
| | - Kathryn Stevenson
- Department of Parks, Recreation and Tourism Management, North Carolina State University, Raleigh, NC, USA
| | - Roland Kays
- North Carolina Museum of Natural Sciences, Raleigh, NC, USA.,Department of Forestry & Environmental Resources, North Carolina State University, Raleigh, NC, USA
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA.,Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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Leong M, Dunn RR, Trautwein MD. Biodiversity and socioeconomics in the city: a review of the luxury effect. Biol Lett 2019; 14:rsbl.2018.0082. [PMID: 29743266 PMCID: PMC6012690 DOI: 10.1098/rsbl.2018.0082] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 04/18/2018] [Indexed: 12/25/2022] Open
Abstract
The ecological dynamics of cities are influenced not only by geophysical and biological factors, but also by aspects of human society. In cities around the world, a pattern of higher biodiversity in affluent neighbourhoods has been termed ‘the luxury effect'. The luxury effect has been found globally regarding plant diversity and canopy or vegetative cover. Fewer studies have considered the luxury effect and animals, yet it has been recognized in the distributions of birds, bats, lizards and indoor arthropods. Higher socioeconomic status correlates with higher biodiversity resulting from many interacting factors—the creation and maintenance of green space on private and public lands, the tendency of both humans and other species to favour environmentally desirable areas, while avoiding environmental burdens, as well as enduring legacy effects. The luxury effect is amplified in arid cities and as neighbourhoods age, and reduced in tropical areas. Where the luxury effect exists, benefits of urban biodiversity are unequally distributed, particularly in low-income neighbourhoods with higher minority populations. The equal distribution of biodiversity in cities, and thus the elimination of the luxury effect, is a worthy societal goal.
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Affiliation(s)
- Misha Leong
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, CA, USA
| | - Robert R Dunn
- Department of Applied Ecology and Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, USA .,Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Denmark.,The German Centre for Integrative Biodiversity Research (iDiv), Liepzig, Germany
| | - Michelle D Trautwein
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, CA, USA
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Madden AA, Epps MJ, Fukami T, Irwin RE, Sheppard J, Sorger DM, Dunn RR. The ecology of insect-yeast relationships and its relevance to human industry. Proc Biol Sci 2019; 285:rspb.2017.2733. [PMID: 29563264 DOI: 10.1098/rspb.2017.2733] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 02/28/2018] [Indexed: 01/03/2023] Open
Abstract
Many species of yeast are integral to human society. They produce many of our foods, beverages and industrial chemicals, challenge us as pathogens, and provide models for the study of our own biology. However, few species are regularly studied and much of their ecology remains unclear, hindering the development of knowledge that is needed to improve the relationships between humans and yeasts. There is increasing evidence that insects are an essential component of ascomycetous yeast ecology. We propose a 'dispersal-encounter hypothesis' whereby yeasts are dispersed by insects between ephemeral, spatially disparate sugar resources, and insects, in turn, obtain the benefits of an honest signal from yeasts for the sugar resources. We review the relationship between yeasts and insects through three main examples: social wasps, social bees and beetles, with some additional examples from fruit flies. Ultimately, we suggest that over the next decades, consideration of these ecological and evolutionary relationships between insects and yeasts will allow prediction of where new yeast diversity is most likely to be discovered, particularly yeasts with traits of interest to human industry.
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Affiliation(s)
- Anne A Madden
- Department of Applied Ecology, North Carolina State University, David Clark Labs, 100 Brooks Avenue, Raleigh, NC 27607, USA
| | - Mary Jane Epps
- Department of Biology, Mary Baldwin University, 101 East Frederick Street, Staunton, VA 24401, USA
| | - Tadashi Fukami
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA
| | - Rebecca E Irwin
- Department of Applied Ecology, North Carolina State University, David Clark Labs, 100 Brooks Avenue, Raleigh, NC 27607, USA
| | - John Sheppard
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, 400 Dan Allen Drive, Raleigh, NC 27606, USA
| | - D Magdalena Sorger
- Department of Applied Ecology, North Carolina State University, David Clark Labs, 100 Brooks Avenue, Raleigh, NC 27607, USA.,Research & Collections, North Carolina Museum of Natural Sciences, 11 West Jones Street, Raleigh, NC 27601, USA
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, David Clark Labs, 100 Brooks Avenue, Raleigh, NC 27607, USA.,Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, 2100 Copenhagen Ø, Denmark.,German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
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Affiliation(s)
- DeAnna E. Beasley
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, TN 37403
| | | | - Alison Fowler
- Department of Applied Ecology, North Carolina State University, Raleigh, NC 27695
| | - Kirsten Keleher
- 3North Carolina School of Science and Mathematics, Durham, NC
| | - Margarita M. López-Uribe
- Department of Entomology, Center for Pollinator Research, Penn State University, State College, PA 16802
| | - Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC 27695
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Lau MK, Ellison AM, Nguyen A, Penick C, DeMarco B, Gotelli NJ, Sanders NJ, Dunn RR, Helms Cahan S. Draft Aphaenogaster genomes expand our view of ant genome size variation across climate gradients. PeerJ 2019; 7:e6447. [PMID: 30881761 PMCID: PMC6417409 DOI: 10.7717/peerj.6447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 01/10/2019] [Indexed: 11/30/2022] Open
Abstract
Given the abundance, broad distribution, and diversity of roles that ants play in many ecosystems, they are an ideal group to serve as ecosystem indicators of climatic change. At present, only a few whole-genome sequences of ants are available (19 of >16,000 species), mostly from tropical and sub-tropical species. To address this limited sampling, we sequenced genomes of temperate-latitude species from the genus Aphaenogaster, a genus with important seed dispersers. In total, we sampled seven colonies of six species: Aphaenogaster ashmeadi, Aphaenogaster floridana, Aphaenogaster fulva, Aphaenogaster miamiana, Aphaenogaster picea, and Aphaenogaster rudis. The geographic ranges of these species collectively span eastern North America from southern Florida to southern Canada, which encompasses a latitudinal gradient in which many climatic variables are changing rapidly. For the six genomes, we assembled an average of 271,039 contigs into 47,337 scaffolds. The Aphaenogaster genomes displayed high levels of completeness with 96.1% to 97.6% of Hymenoptera BUSCOs completely represented, relative to currently sequenced ant genomes which ranged from 88.2% to 98.5%. Additionally, the mean genome size was 370.5 Mb, ranging from 310.3 to 429.7, which is comparable to that of other sequenced ant genomes (212.8-396.0 Mb) and flow cytometry estimates (210.7-690.4 Mb). In an analysis of currently sequenced ant genomes and the new Aphaenogaster sequences, we found that after controlling for both spatial autocorrelation and phylogenetics ant genome size was marginally correlated with sample site climate similarity. Of all examined climate variables, minimum temperature, and annual precipitation had the strongest correlations with genome size, with ants from locations with colder minimum temperatures and higher levels of precipitation having larger genomes. These results suggest that climate extremes could be a selective force acting on ant genomes and point to the need for more extensive sequencing of ant genomes.
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Affiliation(s)
| | | | - Andrew Nguyen
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Vermont, Burlington, VT, USA
| | - Clint Penick
- The Biomimicry Center, Arizona State University, Tempe, AZ, USA
| | | | | | - Nathan J. Sanders
- Environmental Program, Rubenstein School of Environment and Natural Resources, University of Vermont, Burlington, VT, USA
| | - Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Sara Helms Cahan
- Department of Biology, University of Vermont, Burlington, VT, USA
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