23 Works

Data from: Observed forest sensitivity to climate implies large changes in 21st century North American forest growth

Noah D. Charney, Flurin Babst, Benjamin Poulter, Sydne Record, Valerie M. Trouet, David Frank, Brian J. Enquist & Margaret E. K. Evans
Predicting long-term trends in forest growth requires accurate characterisation of how the relationship between forest productivity and climatic stress varies across climatic regimes. Using a network of over two million tree-ring observations spanning North America and a space-for-time substitution methodology, we forecast climate impacts on future forest growth. We explored differing scenarios of increased water-use efficiency (WUE) due to CO2-fertilisation, which we simulated as increased effective precipitation. In our forecasts: (1) climate change negatively impacted...

Data from: Experimental evolution of an emerging plant virus in host genotypes that differ in their susceptibility to infection

Julia Hillung, José M. Cuevas, Sergi Valverde & Santiago F. Elena
This study evaluates the extent to which genetic differences among host individuals from the same species conditions the evolution of a plant RNA virus. We performed a three-fold replicated evolution experiment in which Tobacco etch potyvirus isolate At17b (TEV-At17b), adapted to Arabidopsis thaliana ecotype Ler-0, was serially passaged in five genetically heterogeneous ecotypes of A. thaliana. After 15 passages we found that evolved viruses improved their fitness, showed higher infectivity and stronger virulence in their...

Data from: On the evolutionary interplay between dispersal and local adaptation in heterogeneous environments

Andrew M. Berdahl, Colin J. Torney, Emmanuel Schertzer, Simon A. Levin & Andrew Berdahl
Dispersal, whether in the form of a dandelion seed drifting on the breeze, or a salmon migrating upstream to breed in a non-natal stream, transports genes between locations. At these locations, local adaptation modifies the gene frequencies so their carriers are better suited to particular conditions, be those of newly disturbed soil or a quiet river pool. Both dispersal and local adaptation are major drivers of population structure; however, in general, their respective roles are...

Data from: A life-cycle model of human social groups produces a u-shaped distribution in group size

Gul Deniz Salali, Harvey Whitehouse & Michael E. Hochberg
One of the central puzzles in the study of sociocultural evolution is how and why transitions from small-scale human groups to large-scale, hierarchically more complex ones occurred. Here we develop a spatially explicit agent-based model as a first step towards understanding the ecological dynamics of small and large-scale human groups. By analogy with the interactions between single-celled and multicellular organisms, we build a theory of group lifecycles as an emergent property of single cell demographic...

Data from: Draining the pool? Carbon storage and fluxes in three alpine plant communities

Mia Vedel Sørensen, Richard Strimbeck, Kristin Odden Nystuen, Rozalia Erzsebet Kapas, Brian J. Enquist & Bente Jessen Graae
Shrub communities have expanded in arctic and alpine tundra during recent decades. Changes in shrub abundance may alter ecosystem carbon (C) sequestration and storage, with potential positive or negative feedback on global C cycling. To assess potential implications of shrub expansion in different alpine plant communities, we compared C fluxes and pools in one Empetrum-dominated heath, one herb- and cryptogam-dominated meadow, and one Salix-shrub community in Central Norway. Over two growing seasons, we measured Gross...

Data from: The impact of high-order epistasis in the within-host fitness of a positive-sense plant RNA virus

Jasna Lalić & Santiago F. Elena
RNA viruses are the main source of emerging infectious diseases because of the evolutionary potential bestowed by their fast replication, large population sizes and high mutation and recombination rates. However, an equally important property, which is usually neglected, is the topography of the fitness landscape. How many fitness maxima exist and how well they are connected is especially interesting, as this determines the number of accessible evolutionary pathways. To address this question, we have reconstructed...

Data from: Courting disaster: how diversification rate affects fitness under risk

William C. Ratcliff, Peter Hawthorne & Eric Libby
Life is full of risk. To deal with this uncertainty, many organisms have evolved bet-hedging strategies that spread risk through phenotypic diversification. These rates of diversification can vary by orders of magnitude in different species. Here we examine how key characteristics of risk and organismal ecology affect the fitness consequences of variation in diversification rate. We find that rapid diversification is strongly favored when the risk faced has a wide spatial extent, with a single...

Data from: High mutation rates limit evolutionary adaptation in Escherichia coli

Kathleen Sprouffske, José Aguilar-Rodríguez, Paul Sniegowski & Andreas Wagner
Mutation is fundamental to evolution, because it generates the genetic variation on which selection can act. In nature, genetic changes often increase the mutation rate in systems that range from viruses and bacteria to human tumors. Such an increase promotes the accumulation of frequent deleterious or neutral alleles, but it can also increase the chances that a population acquires rare beneficial alleles. Here, we study how up to 100-fold increases in Escherichia coli’s genomic mutation...

Disentangling ecological and taphonomic signals in ancient food webs

Jack Shaw, Emily Coco, Kate Wootton, Dries Daems, Andrew Gillreath-Brown, Anshuman Swain & Jennifer Dunne
Analyses of ancient food webs reveal important paleoecological processes and responses to a range of perturbations throughout Earth’s history, such as climate change. These responses can inform our forecasts of future biotic responses to similar perturbations. However, previous analyses of ancient food webs rarely accounted for key differences between modern and ancient community data, particularly selective loss of soft-bodied taxa during fossilization. To consider how fossilization impacts inferences of ancient community structure we (1) analyzed...

Data from: Reconstructing Asian faunal introductions to eastern Africa from multi-proxy biomolecular and archaeological datasets

Mary E. Prendergast, Michael Buckley, Alison Crowther, Heidi Eager, Laurent Frantz, Ophélie Lebrasseur, Rainer Hutterer, Ardern Hulme-Beaman, Wim Van Neer, Katerina Douka, Margaret-Ashley Veall, Eréndira M. Quintana Morales, Verena J. Schuenemann, Ella Reiter, Richard Allen, Evangelos A. Dimopoulos, Richard M. Helm, Ceri Shipton, Ogeto Mwebi, Christiane Denys, Mark C. Horton, Stephanie Wynne-Jones, Jeffrey Fleisher, Chantal Radimilahy, Henry Wright … & Mark Horton
Human-mediated biological exchange has had global social and ecological impacts. In sub-Saharan Africa, several domestic and commensal animals were introduced from Asia in the pre-modern period; however, the timing and nature of these introductions remain contentious. One model supports introduction to the eastern African coast after the mid-first millennium CE, while another posits introduction dating back to 3000 BCE. These distinct scenarios have implications for understanding the emergence of long-distance maritime connectivity, and the ecological...

Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes

Riddhiman Dhar, Tobias Bergmiller & Andreas Wagner
Gene duplication is important in evolution, because it provides new raw material for evolutionary adaptations. Several existing hypotheses about the causes of duplicate retention and diversification differ in their emphasis on gene dosage, sub-functionalization, and neo-functionalization. Little experimental data exists on the relative importance of gene expression changes and changes in coding regions for the evolution of duplicate genes. Furthermore, we do not know how strongly the environment could affect this importance. To address these...

Data from: How chimpanzees integrate sensory information to select figs

Nathaniel J. Dominy, Justin D. Yeakel, Uttam Bhat, Lawrence Ramsden, Richard W. Wrangham & Peter W. Lucas
Figs are keystone resources that sustain chimpanzees when preferred fruits are scarce. Many figs retain a green(ish) colour throughout development, a pattern that causes chimpanzees to evaluate edibility on the basis of achromatic accessory cues. Such behaviour is conspicuous because it entails a succession of discrete sensory assessments, including the deliberate palpation of individual figs, a task that requires advanced visuomotor control. These actions are strongly suggestive of domain-specific information processing and decision-making, and they...

Data from: Microbiome sharing between children, livestock and household surfaces in western Kenya

Emily Mosites, Matt Sammons, Elkanah Otiang, Alexander Eng, Ceclia Noecher, Ohad Manor, Sarah Hilton, Samuel M. Thmbi, Clayton Onyango, Gemina Garland-Lewis, Douglas R. Call, M. Kariuki Njenga, Judith N. Wasserheit, Jennifer A. Zambriski, Judd L. Walson, Guy H. Palmer, Joel Montgomery, Elhanan Borenstein, Richard Omore, Peter M. Rabinowitz, Samuel M. Thumbi & Cecilia Noecker
The gut microbiome community structure and development are associated with several health outcomes in young children. To determine the household influences of gut microbiome structure, we assessed microbial sharing within households in western Kenya by sequencing 16S rRNA libraries of fecal samples from children and cattle, cloacal swabs from chickens, and swabs of household surfaces. Among the 156 households studied, children within the same household significantly shared their gut microbiome with each other, although we...

Data from: Highly resolved early Eocene food webs show development of modern trophic structure after the end-Cretaceous extinction

Conrad C. Labandeira & Jennifer A. Dunne
Generalities of food web structure have been identified for extant ecosystems. However, the trophic organization of ancient ecosystems is unresolved, as prior studies of fossil webs have been limited by low-resolution, high-uncertainty data. We compiled highly resolved, well-documented feeding interaction data for 700 taxa from the 48 million-year-old latest early Eocene Messel Shale, which contains a species assemblage that developed after an interval of protracted environmental and biotal change during and following the end-Cretaceous extinction....

Data from: Parasites affect food web structure primarily through increased diversity and complexity

Jennifer A. Dunne, Kevin D. Lafferty, Andrew P. Dobson, Ryan F. Hechinger, Armand M. Kuris, Neo D. Martinez, John P. McLaughlin, Kim N. Mouritsen, Robert Poulin, Karsten Reise, Daniel B. Stouffer, David W. Thieltges, Richard J. Williams & Claus Dieter Zander
Comparative research on food web structure has revealed generalities in trophic organization, produced simple models, and allowed assessment of robustness to species loss. These studies have mostly focused on free-living species. Recent research has suggested that inclusion of parasites alters structure. We assess whether such changes in network structure result from unique roles and traits of parasites or from changes to diversity and complexity. We analyzed seven highly resolved food webs that include metazoan parasite...

Data from: The causes of epistasis in genetic networks

Javier Macía, Ricard V. Solé & Santiago F. Elena
Epistasis refers to the non-additive interactions between genes in determining phenotypes. Considerable efforts have shown that, even for a given organism, epistasis may vary both in intensity and sign. Recent comparative studies supported that the overall sign of epistasis switches from positive to negative as the complexity of an organism increases, and it has been hypothesized that this change shall be a consequence of the underlying gene network properties. Why should this be the case?...

Data from: Network structure and local adaptation in coevolving bacteria-phage interactions

James Gurney, Lafi Aldakak, Alex Betts, Claire Gougat-Barbera, Timothée Poisot, Oliver Kaltz & Michael E. Hochberg
Numerous theoretical and experimental studies have investigated antagonistic coevolution between parasites and their hosts. Although experimental tests of theory from a range of biological systems are largely concordant regarding the influence of several driving processes, we know little as to how mechanisms acting at the smallest scales (individual molecular and phenotypic changes) may result in the emergence of structures at larger scales, such as coevolutionary dynamics and local adaptation. We capitalized on methods commonly employed...

Data from: Social feedback and the emergence of rank in animal society

Elizabeth A. Hobson & Simon DeDeo
Dominance hierarchies are group-level properties that emerge from the aggression of individuals. Although individuals can gain critical benefits from their position in a hierarchy, we do not understand how real-world hierarchies form. Nor do we understand what signals and decision-rules individuals use to construct and maintain hierarchies in the absence of simple cues such as size or spatial location. A study of conflict in two groups of captive monk parakeets (Myiopsitta monachus) found that a...

Data from: Hot spots become cold spots: coevolution in variable temperature environments

Alison B. Duncan, Eike Dusi, Franck Jacob, Johan Ramsayer, Michael E. Hochberg & Oliver Kaltz
Antagonistic coevolution between hosts and parasites is a key process in the genesis and maintenance of biological diversity. Whereas coevolutionary dynamics show distinct patterns under favourable environmental conditions, the effects of more realistic, variable conditions are largely unknown. We investigated the impact of a fluctuating environment on antagonistic coevolution in experimental microcosms of Pseudomonas fluorescens SBW25 and lytic phage SBWΦ2. High-frequency temperature fluctuations caused no deviations from typical coevolutionary arms-race dynamics. However, coevolution was stalled...

Data from: Implementation of complex biological logic circuits using spatially distributed multicellular consortia

Javier Macia, Romilde Manzoni, Nuria Conde, Arturo Urrios, Eulàlia De Nadal, Ricard Solé & Francesc Posas
Engineered synthetic biological devices have been designed to perform a variety of functions from sensing molecules and bioremediation to energy production and biomedicine. Notwithstanding, a major limitation of in vivo circuit implementation is the constraint associated to the use of standard methodologies for circuit design. Thus, future success of these devices depends on obtaining circuits with scalable complexity and reusable parts. Here we show how to build complex computational devices using multicellular consortia and space...

Data from: Does environmental heterogeneity drive functional trait variation? A test in montane and alpine meadows

Jordan Stark, Rebecca Lehman, Lake Crawford, Brian J. Enquist & Benjamin Blonder
While community-weighted means of plant traits have been linked to mean environmental conditions at large scales, the drivers of trait variation within communities are not well understood. Local environmental heterogeneity (such as microclimate variability), in addition to mean environmental conditions, may decrease the strength of environmental filtering and explain why communities support different amounts of trait variation. Here, we assess two hypotheses: first, that more heterogeneous local environments and second, that less extreme environments, should...

Data from: Effects of spatial scale of sampling on food web structure

Spencer A. Wood, Roly Russell, Dieta Hanson, Richard J. Williams & Jennifer A. Dunne
This study asks whether the spatial scale of sampling alters structural properties of food webs and whether any differences are attributable to changes in species richness and connectance with scale. Understanding how different aspects of sampling effort affect ecological network structure is important for both fundamental ecological knowledge and the application of network analysis in conservation and management. Using a highly resolved food web for the marine intertidal ecosystem of the Sanak Archipelago in the...

Data from: The causes of epistasis in genetic networks

Javier Macía, Ricard V. Solé & Santiago F. Elena
Epistasis refers to the non-additive interactions between genes in determining phenotypes. Considerable efforts have shown that, even for a given organism, epistasis may vary both in intensity and sign. Recent comparative studies supported that the overall sign of epistasis switches from positive to negative as the complexity of an organism increases, and it has been hypothesized that this change shall be a consequence of the underlying gene network properties. Why should this be the case?...

Registration Year

  • 2020
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  • 2011

Resource Types

  • Dataset


  • Santa Fe Institute
  • University of Arizona
  • Pompeu Fabra University
  • University of Oxford
  • Swiss Institute of Bioinformatics
  • University of Washington
  • Princeton University
  • Universitat Politècnica de València
  • University of Zurich
  • Harvard University