Taller R

Ya se encuentran en la carpeta del curso tanto el tutoral de R de lo que se vio en la clase con Jonás, como el set de datos para que puedan practicar lo visto.

Lectura 23 Febrero 2015

The nested assembly of plant–animal mutualistic networks

Jordi Bascompte, Pedro Jordano, Carlos J. Melián, and Jens M. Olesen

Most studies of plant–animal mutualisms involve a small number of species. There is almost no information on the structural organization of species-rich mutualistic networks despite its potential importance for the maintenance of diversity. Here we analyze 52 mutualistic networks and show that they are highly nested; that is, the more specialist species interact only with proper subsets of those species interacting with the more generalists. This assembly pattern generates highly asymmetrical interactions and organizes the community cohesively around a central core of interactions. Thus, mutualistic networks are neither randomly assembled nor organized in compartments arising from tight, parallel specialization. Furthermore, nestedness increases with the complexity (number of interactions) of the network: for a given number of species, communities with more interactions are significantly more nested. Our results indicate a nonrandom pattern of community organization that may be relevant for our understanding of the organization and persistence of biodiversity.

Febrero 2015

Local dispersal promotes biodiversity in a real-life game of rock–paper–scissors

Benjamin Kerr, Margaret A. Riley, Marcus W. Feldman and Brendan J. M. Bohannan

One of the central aims of ecology is to identify mechanisms that maintain biodiversity. Numerous theoretical models have shown that competing species can coexist if ecological processes such as dispersal, movement, and interaction occur over small spatial scales. In particular, this may be the case for nontransitive communities, that is, those without strict competitive hierarchies. The classic non-transitive system involves a community of three competing species satisfying a relationship similar to the children’s game rock–paper–scissors, where rock crushes scissors, scissors cuts paper, and paper covers rock. Such relationships have been demonstrated in several natural systems. Some models predict that local interaction and dispersal are sufficient to ensure coexistence of all three species in such a community, whereas diversity is lost when ecological processes occur over larger scales. Here, we test these predictions empirically using a non-transitive model community containing three populations of Escherichia coli. We find that diversity is rapidly lost in our experimental community when dispersal and interaction occur over relatively large spatial scales, whereas all populations coexist when ecological processes are localized.

Lectura 3 - 18 Febrero 2015

Chemical warfare from an ecological perspective

Richard E. Lenski and Margaret A. Riley

Chemical weapons are recent acquisitions in humankind’s ever-growing arsenal of destruction. But bacteria and fungi have been practicing chemical warfare for a very long time. Among the numerous and structurally diverse antimicrobial agents that microbes produce are penicillin by the mold Penicillium notatum, many important antibiotics by streptomycetes, a wide range of bacteriocins by Escherichia coli and most other bacteria (including the food preservative, nisin, by Lactococcus lactis), and killer toxins by the yeast Saccharomyces cerevisiae.

Lectura 2 - 18 Febrero

Red Queen Hypothesis

Paul N. Pearson

It has long been debated to what extent evolution is driven by environmental change and to what extent it is driven by competitive interactions between species. A simple model that encapsulates the competitive aspect of coevolution was proposed by Leigh Van Valen in 1973 and termed the Red Queen hypothesis. Like all good scientific models, it had the effect of simplifying the issues and focusing the debate, and hence it has become an influential part of evolutionary theory.

Lectura 18 Febrero

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

J. Jeffrey Morris, Richard E. Lenski and Erik R. Zinser

Reductive genomic evolution, driven by genetic drift, is common in endosymbiotic bacteria. Genome reduction is less common in free-living organisms, but it has occurred in the numerically dominant open-ocean bacterioplankton Prochlorococcus and “Candidatus Pelagibacter,” and in these cases the reduction appears to be driven by natural selection rather than drift. Gene loss in free-living organisms may leave them dependent on cooccurring microbes for lost metabolic functions. We present the Black Queen Hypothesis (BQH), a novel theory of reductive evolution that explains how selection leads to such dependencies; its name refers to the queen of spades in the game Hearts, where the usual strategy is to avoid taking this card. Gene loss can provide a selective advantage by conserving an organism’s limiting resources, provided the gene’s function is dispensable. Many vital genetic functions are leaky, thereby unavoidably producing public goods that are available to the entire community. Such leaky functions are thus dispensable for individuals, provided they are not lost entirely from the community. The BQH predicts that the loss of a costly, leaky function is selectively favored at the individual level and will proceed until the production of public goods is just sufficient to support the equilibrium community; at that point, the benefit of any further loss would be offset by the cost. Evolution in accordance with the BQH thus generates “beneficiaries” of reduced genomic content that are dependent on leaky “helpers,” and it may explain the observed nonuniversality of prototrophy, stress resistance, and other cellular functions in the microbial world.

Lectura 11 Febrero

Evolution of microbial markets 

Gijsbert D. A. Werner, Joan E. Strassmann, Aniek B. F. Ivens, Daniel J. P. Engelmoer, Erik Verbruggen, David C. Queller, Ronald Noë, Nancy Collins Johnson, Peter Hammerstein, and E. Toby Kiers

Biological market theory has been used successfully to explain cooperative behavior in many animal species. Microbes also engage in cooperative behaviors, both with hosts and other microbes, that can be described in economic terms. However, a market approach is not traditionally used to analyze these interactions. Here, we extend the biological market framework to ask whether this theory is of use to evolutionary biologists studying microbes. We consider six economic strategies used by microbes to optimize their success in markets. We argue that an economic market framework is a useful tool to generate specific and interesting predictions about microbial interactions, including the evolution of partner discrimination, hoarding strategies, specialized versus diversified mutualistic services, and the role of spatial structures, such as flocks and consortia. There is untapped potential for studying the evolutionary dynamics of microbial systems. Market theory can help structure this potential by characterizing strategic investment of microbes across a diversity of conditions.

Lectura 09 Febrero

Microbial interactions: from networks to models

Karoline Faust and Jeroen Raes

Metagenomics and 16S pyrosequencing have enabled the study of ecosystem structure and dynamics to great depth and accuracy. Co-occurrence and correlation patterns found in these data sets are increasingly used for the prediction of species interactions in environments ranging from the oceans to the human microbiome. In addition, parallelized co-culture assays and combinatorial labelling experiments allow high-throughput discovery of cooperative and competitive relationships between species.