A high-resolution flux-matrix model describes the spread of diseases in a spatial network and the effect of mitigation strategies.

Propagation of an epidemic across a spatial network of communities is described by a variant of the SIR model accompanied by an intercommunity infectivity matrix. This matrix is estimated from fluxes between communities, obtained from cell-phone tracking data recorded in the USA between March 2020 and February 2021. We apply this model to the SARS-CoV-2 pandemic by fitting just one global parameter representing the frequency of interaction between individuals. We find that the predicted infections agree reasonably well with the reported cases. We clearly see the effect of "shelter-in-place" policies introduced at the onset of the pandemic. Interestingly, a model with uniform transmission rates produces similar results, suggesting that the epidemic transmission was deeply influenced by air travel. We then study the effect of alternative mitigation policies, in particular restricting long-range travel. We find that this policy is successful in decreasing the epidemic size and slowing down the spread, but less effective than the shelter-in-place policy. This policy can result in a pulled wave of infections. We express its velocity and characterize the shape of the traveling front as a function of the epidemiological parameters. Finally, we discuss a policy of selectively constraining travel based on an edge-betweenness criterion.

Social tolerance in Octopus laqueus-A maximum entropy model.

Octopus laqueus is a small tropical octopus found in Okinawa, Japan and the greater Indo-Pacific. Octopus are often viewed as solitary animals but O. laqueus live in close proximity in the wild, and will potentially encounter one another on a regular basis, raising the possibility of social tolerance. Adopting shared den occupancy in aquaria as a potential measure of social tolerance in O. laqueus, we studied the animals' preference for shared dens over solitude. We characterized dependence of sharing preference on sex, den availability and den occupancy density. We designed two simple social tolerance assays in aquaria with a total of 45 daily measurements: (i) Pots Equal, with equal numbers of octopuses and dens and (ii) Pots Limited, with a 3:1 ratio of octopuses to dens. We found that O. laqueus will socially tolerate other individuals by sharing tanks and dens and with typically no loss to cannibalism or escape. However, animals also exhibit significant levels of social repulsion, and individuals often chose a solitary den when given the option. The patterns of den occupancy are observed to be consistent with a maximum entropy model that balances seeking shelter against avoiding other animals. The model accurately captures and predicts the data and can be generalized to other organisms and their social interactions. Overall, in O. laqueus the preference for a den is stronger than the preference to be solitary. The animals are tolerant of others with a mixture of sizes in the tank and even in a den, a reported first for octopuses outside mating. The relaxed disposition and social tolerance of O. laqueus make it a promising species to work with in the lab to explore social and potentially other behaviors in octopuses.

Experimental evidence that thermal selection shapes mitochondrial genome evolution.

Mitochondria are essential organelles, found within eukaryotic cells, which contain their own DNA. Mitochondrial DNA (mtDNA) has traditionally been used in population genetic and biogeographic studies as a maternally-inherited and evolutionary-neutral genetic marker. However, it is now clear that polymorphisms within the mtDNA sequence are routinely non-neutral, and furthermore several studies have suggested that such mtDNA polymorphisms are also sensitive to thermal selection. These observations led to the formulation of the "mitochondrial climatic adaptation" hypothesis, for which all published evidence to date is correlational. Here, we use laboratory-based experimental evolution in the fruit fly, Drosophila melanogaster, to test whether thermal selection can shift population frequencies of two mtDNA haplogroups whose natural frequencies exhibit clinal associations with latitude along the Australian east-coast. We present experimental evidence that the thermal regime in which the laboratory populations were maintained drove changes in haplogroup frequencies across generations. Our results strengthen the emerging view that intra-specific mtDNA variants are sensitive to selection, and suggest spatial distributions of mtDNA variants in natural populations of metazoans might reflect adaptation to climatic environments rather than within-population coalescence and diffusion of selectively-neutral haplotypes across populations.

Rebuilding a realistic corticostriatal "social network" from dissociated cells.

Many of the methods available for the study of cortical influences on striatal neurons have serious problems. In vivo the connectivity is so complex that the study of input from an individual cortical neuron to a single striatal cell is nearly impossible. Mixed corticostriatal cultures develop many connections from striatal cells to cortical cells, in striking contrast to the fact that only connections from cortical cells to striatal cells are present in vivo. Furthermore, interneuron populations are over-represented in organotypic cultures. For these reasons, we have developed a method for growing cortical and striatal neurons in separated compartments that allows cortical neurons to innervate striatal cells in culture. The method works equally well for acutely dissociated or cryopreserved neurons and allows a number of manipulations that are not otherwise possible. Either cortical or striatal compartments can be transfected with channel rhodopsins. The activity of both areas can be recorded in multielectrode arrays or individual patch recordings from pairs of cells. Finally, corticostriatal connections can be severed acutely. This procedure enables determination of the importance of corticostriatal interaction in the resting pattern of activity. These cultures also facilitate development of sensitive analytical network methods to track connectivity.