Andrea Giometto, David R Nelson, and Andrew W Murray. 11/6/2018. “Physical interactions reduce the power of natural selection in growing yeast colonies.” PNAS, 115, 45, Pp. 11448-11453. Publisher's VersionAbstract
Microbial populations often assemble in dense populations in which proliferating individuals exert mechanical forces on the nearby cells. Here, we use yeast strains whose doubling times depend differently on temperature to show that physical interactions among cells affect the competition between different genotypes in growing yeast colonies. Our experiments demonstrate that these physical interactions have two related effects: they cause the prolonged survival of slower-growing strains at the actively-growing frontier of the colony and cause faster-growing strains to increase their frequency more slowly than expected in the absence of physical interactions. These effects also promote the survival of slower-growing strains and the maintenance of genetic diversity in colonies grown in time-varying environments. A continuum model inspired by overdamped hydrodynamics reproduces the experiments and predicts that the strength of natural selection depends on the width of the actively-growing layer at the colony frontier. We verify these predictions experimentally. The reduced power of natural selection observed here may favor the maintenance of drug-resistant cells in microbial populations and could explain the apparent neutrality of inter-clone competition within tumors.
Andrea Giometto, Florian Altermatt, and Andrea Rinaldo. 11/2017. “Demographic stochasticity and resource autocorrelation control biological invasions in heterogeneous landscapes.” Featured in the cover. Oikos, 126, 11, Pp. 1554-1563. Publisher's VersionAbstract

Classical models of biological invasions assess species spread in homogeneous landscapes by assuming constant growth rates and random local movement. Mounting evidence suggests, however, that demographic stochasticity, environmental heterogeneity and non-random movement of individuals affect considerably the spread dynamics. Here, we show that the dynamics of biological invasions are controlled by the spatial heterogeneity of the resource distribution. We show theoretically that increasing the landscape resource autocorrelation length causes a reduction in the average speed of species spread. Demographic stochasticity plays a key role in the slowdown, which is streghtened when individuals can actively move towards resources. The reduction in the front propagation speed is verified in laboratory microcosm experiments with the flagellated protist Euglena gracilis by comparing spread in habitats characterized by different resource heterogeneity. Our theoretical and experimental findings highlight the need to account for the intrinsic stochasticity of population dynamics to describe spread in spatially extended landscapes, which are inevitably characterized by heterogeneous spatial distributions of resources controlling vital rates. Our work identifies the resource autocorrelation length as a key modulator and a simple measure of landscape susceptibility to biological invasions, with implications for predicting the characters of biological invasions within naturally heterogeneous environmental corridors.

Emanuele Strano, Andrea Giometto, Saray Shay, Enrico Bertuzzo, Peter J Mucha, and Andrea Rinaldo. 10/18/2017. “The scaling structure of the global road network.” Royal Society Open Science, 4, 170590. Publisher's VersionAbstract

Because of increasing global urbanization and its immediate consequences (including changes in patterns of food demand/circulation and land-use), the next century will witness a major increase in the extent of paved roads built worldwide. Because habitat fragmentation and connectivity due to roads plays major ecological and societal roles, it is crucial to understand whether possible self-organized patterns are inherent in the global road network structure. Here, we use the largest updated database comprising all major roads on Earth, together with global urban and cropland inventories, to suggest that road length distributions within croplands are indistinguishable from urban ones except for a predictable rescaling factor. Such similarity extends to road length distributions within urban or agricultural domains of given area anywhere in the world. We find two distinct regimes for the scaling of the mean road length with the associated area, holding in general at small and at large values of the latter. In suitably large urban and cropland domains, we find that mean and total road lengths increase linearly with their domain area, differently from earlier suggestions. Scaling regimes suggest that simple and universal mechanisms regulate urban and cropland road expansion at the global scale. Our findings bear implications on global road infrastructure growth based on land-use change and on planning policies sustaining urban expansions.

Silvia Zaoli*, Andrea Giometto*, Amos Maritan, and Andrea Rinaldo. 10/3/2017. “Covariations in ecological scaling laws fostered by community dynamics.” The symbol * denotes equal contribution. Highlighted in the cover. See commentary in the same issue. Proceedings of the National Academy of Sciences, 114, 40, Pp. 10672-10677. Publisher's VersionAbstract

Scaling laws in ecology, intended both as functional relationships among ecologically-relevant quantities and the probability distributions that characterize their occurrence, have long attracted the interest of empiricists and theoreticians. Empirical evidence exists of power laws associated with the number of species inhabiting an ecosystem, their abundances and traits. Although their functional form appears to be ubiquitous, empirical scaling exponents vary with ecosystem type and resource supply rate. Although the idea that ecological scaling laws are linked had been entertained before, the full extent of macroecological pattern covariations, the role of the constraints imposed by finite resource supply and a comprehensive empirical verification are still unexplored. Here, we propose a theoretical scaling framework that predicts the linkages of several macroecological patterns related to species' abundances and body sizes. We show that such framework is consistent with the stationary state statistics of a broad class of resource-limited community dynamics models, regardless of parametrization and model assumptions. We verify predicted theoretical covariations by contrasting empirical data and provide testable hypotheses for yet unexplored patterns. We thus place the observed variability of ecological scaling exponents into a coherent statistical framework where patterns in ecology embed constrained fluctuations.

This paper was highlighted in the PNAS Cover:

See also the Commentary in the same issue:

Francesco Carrara, Andrea Giometto, Mathew Seymour, Andrea Rinaldo, and Florian Altermatt. 8/1/2015. “Inferring species interactions in ecological communities: a comparison of methods at different levels of complexity.” Methods in Ecology and Evolution, 6, 8, Pp. 895-906.Abstract


  1. Natural communities commonly contain many different species and functional groups, and multiple types of species interactions act simultaneously, such as competition, predation, commensalism or mutualism. However, experimental and theoretical investigations have generally been limited by focusing on one type of interaction at a time or by a lack of a common methodological and conceptual approach to measure species interactions.
  2. We compared four methods to measure and express species interactions. These approaches are, with increasing degree of model complexity, an extinction-based model, a relative yield model and two generalized Lotka-Volterra (LV) models. All four approaches have been individually applied in different fields of community ecology, but rarely integrated. We provide an overview of the definitions, assumptions and data needed for the specific methods and apply them to empirical data by experimentally deriving the interaction matrices among 11 protist and rotifer species, belonging to three functional groups. Furthermore, we compare their advantages and limitations to predict multispecies community dynamics and ecosystem functioning.
  3. The relative yield method is, in terms of final biomass production, the best method in predicting the 11-species community dynamics from the pairwise competition experiments. The LV model, which is considering equilibrium among the species, suffers from experimental constraints given the strict equilibrium assumption, and this may be rarely satisfied in ecological communities.
  4. We show how simulations of a LV stochastic community model, derived from an empirical interaction matrix, can be used to predict multispecies community dynamics across multiple functional groups.
  5. Our work unites available tools to measure species interactions under one framework. This improves our ability to make management-oriented predictions of species coexistence/extinction and to compare ecosystem processes across study systems.


Andrea Giometto, Marco Formentin, Andrea Rinaldo, Joel E Cohen, and Amos Maritan. 6/23/2015. “Sample and population exponents of generalized Taylor’s law.” Highlighted in the cover. Proceedings of the National Academy of Sciences, 112, 25, Pp. 7755-7760.Abstract

Taylor’s law (TL) has been verified very widely in the natural sciences, information technology, and finance. The widespread observation of TL suggests that a context-independent mechanism may be at work and stimulated the search for processes affecting the scaling of population fluctuations with population abundance. We show that limited sampling may explain why TL is often observed to have exponent b=2. Abrupt transitions in the TL exponent associated with smooth changes in the environment were recently discovered theoretically and comparable real-world transitions could harm fish populations, forests, and public health. Our study shows that limited sampling hinders the anticipation of such transitions and provides estimates for the number of samples required to reveal early warning signals of abrupt biotic change.

This paper was highlighted in the PNAS cover:

Andrea Giometto, Florian Altermatt, Amos Maritan, Roman Stocker, and Andrea Rinaldo. 6/2/2015. “Generalized receptor law governs phototaxis in the phytoplankton Euglena gracilis.” Proceedings of the National Academy of Sciences, 112, 22, Pp. 7045-7050.Abstract

Many phytoplankton species sense light and move toward or away from it. Such directed movement, called phototaxis, has major ecological implications because it contributes to the largest biomass migration on Earth, diel vertical migration of organisms responsible for roughly one-half of the global photosynthesis. We experimentally studied phototaxis for the flagellate alga Euglena gracilis by tracking algal populations over time in accurately controlled light fields. Observations coupled with formal model comparison lead us to propose a generalized receptor law governing phototaxis of phytoplankton. Such a model accurately reproduces experimental patterns resulting from accumulation and dispersion dynamics. Direct applications concern phytoplankton migrations and vertical distribution, bioreactor optimization, and the experimental study of biological invasions in heterogeneous environments.

Francesco Carrara, Andrea Giometto, Mathew Seymour, Andrea Rinaldo, and Florian Altermatt. 5/1/2015. “Experimental evidence for strong stabilizing forces at high functional diversity of aquatic microbial communities.” Ecology, 96, 5, Pp. 1340-1350.Abstract

Unveiling the mechanisms that promote coexistence in biological communities is a fundamental problem in ecology. Stable coexistence of many species is commonly observed in natural communities. Most of these natural communities, however, are composed of species from multiple trophic and functional groups, while theory and experiments on coexistence have been focusing on functionally similar species. Here, we investigated how functional diversity affects the stability of species coexistence and productivity in multispecies communities by characterizing experimentally all pairwise species interactions in a pool of 11 species of eukaryotes (10 protists and one rotifer) belonging to three different functional groups. Species within the same functional group showed stronger competitive interactions compared to among-functional group interactions. This often led to competitive exclusion between species that had higher functional relatedness, but only at low levels of species richness. Communities with higher functional diversity resulted in increased species coexistence and community biomass production. Our experimental findings and the results of a stochastic model tailored to the experimental interaction matrix suggest the emergence of strong stabilizing forces when species from different functional groups interact in a homogeneous environment. By combining theoretical analysis with experiments we could also disentangle the relationship between species richness and functional diversity, showing that functional diversity per se is a crucial driver of productivity and stability in multispecies community.

Florian Altermatt, Emanuel A Fronhofer, Aurelie Garnier, Andrea Giometto, Frederik Hammes, Jan Klecka, Delphine Legrand, Elvira Maechler, Thomas M Massie, Frank Pennekamp, Marco Plebani, Mikael Pontarp, Nicolas Schtickzelle, Virginie Thuillier, and Owen L Petchey. 2/1/2015. “Big answers from small worlds: a user's guide for protist microcosms as a model system in ecology and evolution.” Methods in Ecology and Evolution, 6, 2, Pp. 218-231.Abstract


  1. Laboratory microcosm experiments using protists as model organisms have a long tradition and are widely used to investigate general concepts in population biology, community ecology and evolutionary biology. Many variables of interest are measured in order to study processes and patterns at different spatiotemporal scales and across all levels of biological organization. This includes measurements of body size, mobility or abundance, in order to understand population dynamics, dispersal behaviour and ecosystem processes. Also, a variety of manipulations are employed, such as temperature changes or varying connectivity in spatial microcosm networks.
  2. Past studies, however, have used varying methods for maintenance, measurement, and manipulation, which hinders across-study comparisons and meta-analyses, and the added value they bring. Furthermore, application of techniques such as flow cytometry, image and video analyses, and in situ environmental probes provide novel and improved opportunities to quantify variables of interest at unprecedented precision and temporal resolution.
  3. Here, we take the first step towards a standardization of well-established and novel methods and techniques within the field of protist microcosm experiments. We provide a comprehensive overview of maintenance, measurement and manipulation methods. An extensive supplement contains detailed protocols of all methods, and these protocols also exist in a community updateable online repository.
  4. We envision that such a synthesis and standardization of methods will overcome shortcomings and challenges faced by past studies and also promote activities such as meta-analyses and distributed experiments conducted simultaneously across many different laboratories at a global scale.


Andrea Giometto, Andrea Rinaldo, Francesco Carrara, and Florian Altermatt. 1/17/2014. “Emerging predictable features of replicated biological invasion fronts.” Proceedings of the National Academy of Sciences, 111, 1, Pp. 297-301.Abstract

Biological dispersal is a key driver of several fundamental processes in nature, crucially controlling the distribution of species and affecting their coexistence. Despite its relevance for important ecological processes, however, the subject suffers an acknowledged lack of experimentation, and current assessments point at inherent limitation to predictability even in the simplest ecological settings. We show, by combining replicated experimentation on the spread of the ciliate Tetrahymena sp. with a theoretical approach based on stochastic differential equations, that information on local unconstrained movement and reproduction of organisms (including demographic stochasticity) allows reliable prediction of both the propagation speed and range of variability of invasion fronts over multiple generations.

Francesco Carrara, Andrea Rinaldo, Andrea Giometto, and Florian Altermatt. 1/2014. “Complex interaction of dendritic connectivity and hierarchical patch size on biodiversity in river-like landscapes.” The American Naturalist, 183, 1, Pp. 13-25.Abstract

Habitat fragmentation and land use changes are causing major biodiversity losses. Connectivity of the landscape or environmental conditions alone can shape biodiversity patterns. In nature, however, local habitat characteristics are often intrinsically linked to a specific connectivity. Such a link is evident in riverine ecosystems, where hierarchical dendritic structures command related scaling on habitat capacity. We experimentally disentangled the effect of local habitat capacity (i.e., the patch size) and dendritic connectivity on biodiversity in aquatic microcosm metacommunities by suitably arranging patch sizes within river-like networks. Overall, more connected communities that occupy a central position in the network exhibited higher species richness, irrespective of patch size arrangement. High regional evenness in community composition was found only in landscapes preserving geomorphological scaling properties of patch sizes. In these landscapes, some of the rarer species sustained regionally more abundant populations better tracking their own niche requirements compared to landscapes with homogeneous patch size or landscapes with spatially uncorrelated patch size. Our analysis suggests that altering the natural link between dendritic connectivity and patch size strongly affects community composition and population persistence at multiple scales. The experimental results are demonstrating a principle that can be tested in theoretical metacommunity models and eventually be projected to real riverine ecosystems.

Andrea Giometto, Florian Altermatt, Francesco Carrara, Amos Maritan, and Andrea Rinaldo. 3/19/2013. “Scaling body size fluctuations.” Proceedings of the National Academy of Sciences, 110, 12, Pp. 4646-4650.Abstract

The size of an organism matters for its metabolic, growth, mortality, and other vital rates. Scale-free community size spectra (i.e., size distributions regardless of species) are routinely observed in natural ecosystems and are the product of intra- and interspecies regulation of the relative abundance of organisms of different sizes. Intra- and interspecies distributions of body sizes are thus major determinants of ecosystems’ structure and function. We show experimentally that single-species mass distributions of unicellular eukaryotes covering different phyla exhibit both characteristic sizes and universal features over more than four orders of magnitude in mass. Remarkably, we find that the mean size of a species is sufficient to characterize its size distribution fully and that the latter has a universal form across all species. We show that an analytical physiological model accounts for the observed universality, which can be synthesized in a log-normal form for the intraspecies size distributions. We also propose how ecological and physiological processes should interact to produce scale-invariant community size spectra and discuss the implications of our results on allometric scaling laws involving body mass.

Andrea Giometto and Henrik Jeldtoft Jensen. 1/18/2012. “Connecting the microdynamics to the emergent macrovariables: Self-organized criticality and absorbing phase transitions in the deterministic lattice gas.” Physical Review E, 85, 1, Pp. 011128.Abstract

We reinvestigate the Deterministic Lattice Gas introduced as a paradigmatic model of the 1/f spectra [Phys. Rev. Lett. 64, 3103 (1990)] arising according to the self-organized criticality scenario. We demonstrate that the density fluctuations exhibit an unexpected dependence on systems size and relate the finding to effective Langevin equations. The low-density behavior is controlled by the critical properties of the gas at the absorbing state phase transition. We also show that the deterministic lattice gas is in the Manna universality class of absorbing state phase transitions. This is in contrast to expectations in the literature that suggested that the entirely deterministic nature of the dynamics would put the model in a different universality class. To our knowledge this is the first fully deterministic member of the Manna universality class.