Habitat Earth

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california academy of sciences, food webs, marine communities, networks, real world networks

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“Habitat Earth“, the new film by the Visualization Studio at the California Academy of Sciences opened this weekend in the Morrison Planetarium. The film documents the ecological interactions that take place continually in natural systems, featuring San Francisco Bay, a northern California kelp forest, and redwood forest watersheds in the northwest of North America. I was one of the science advisers and content persons for the film and am simply in awe of the visualization team. The science is authentic and researched in detail, but most impressive is the sheer amount of data incorporated and visualized. These data range from well-known ecological stories such as the sea otter role in maintaining diversity in kelp forests, to the thousands of food web interactions from my San Francisco Bay food web dataset, to documented tracks of thousands of migrating species and human ship traffic. It’s a masterpiece of science visualization, and I was very happy to be a small part of it. Here is a short trailer to the film, narrated by Frances McDormand. In the next few posts I will link to interviews with a number of the scientists involved. In the meanwhile, enjoy the trailer and, if you are in San Francisco, please stop by and see the film in the world’s largest all-digital planetarium dome!

Modern and paleocommunity analogues

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connectance, coral reef, food webs, marine communities, modeling, Network theory, networks, paleo-food web, paleontology, real world networks, Scientific models, trophic guild, trophic level

Last week I gave a keynote presentation at the annual conference of the Geological Society of America in Vancouver. Here is the abstract, and a link to the presentation (pdf file).

ANCIENT AND MODERN COMMUNITIES AS RECIPROCAL ANALOGUES OF PERSISTENCE AND STABILITY

ROOPNARINE, Peter, Invertebrate Zoology and Geology, California Academy of Sciences, 55 Music Concourse Dr, Golden Gate Park, San Francisco, CA 94118, proopnarine@calacademy.org
Paleocommunities are spatio-temporally averaged communities structured by biotic interactions and abiotic factors. The best data on paleocommunity structures are estimates of species richness, number of biotic interactions and the topology of interactions. These provide insights into paleoecological dynamics if modern communities are used as analogs; e.g., the recent lionfish invasion of the western Atlantic is the first modern invasion of a marine ecosystem by a high trophic-level predator and serves as an analog for the invasion of paleocommunities by new predators during the Mesozoic Marine Revolution. Despite the invader’s broad diet, it targets very specific parts of the invaded food web. This will lead to non-uniform escalation on evolutionary timescales.

Theoretical ecology provides a rich framework for exploring dynamics of community persistence. Persistence–the stability of species richness and composition on geological timescales–is central to paleoecology. Ecological stability, a community’s return to stability after perturbation, is not necessary for geological persistence. However, it does dictate a community’s response to perturbation, and thus a species’ persistence or extinction. What then is the relationship between paleoecological richness/composition and ecological stability? How do communities respond to losses of species richness or ecological function? Questions of stability and diversity loss are addressed with an examination of transient responses and species deletion stability analyses of end-Permian terrestrial paleocommunities of the Karoo Basin. Transience is measured as the degree to which a perturbation is amplified over ecological time, even as a community returns asymptotically to stability. Transience during times of frequent perturbation, as during times of environmental crises, decreases the likelihood of a persistently stable community. Species deletion stability measures the dynamic response of a community to the loss of single species. It is an open question whether communities become more vulnerable or more resistant during environmental crises. That process, which has occurred repeatedly in the geological past, is important to the fate of threatened modern communities.

Ecology and the Tragedy of the Commons

Tags

real world networks, Robustness, Scientific models, tragedy of the commons

Well, it’s been quite some time since the last post, but I’ve been busy! This post is just a short notice of a new paper, just published today. The paper is part of a special issue on the Tragedy of the Commons in the journal Sustainability. My paper takes a comparative look at the Tragedy in ecological communities and human societies, and the potential of human mutualisms for avoiding tragedies. The situation is not a very hopeful one, however, given our ever-growing human population. Hardin did note this in his original essay. Finally, this paper was inspired by an earlier paper by myself and Ken Angielczyk.

Here’s a link to the paper, as well as the abstract.

Roopnarine, P. Ecology and the Tragedy of the Commons. Sustainability 2013, 5, 749-773.

Abstract

This paper develops mathematical models of the tragedy of the commons analogous to ecological models of resource consumption. Tragedies differ fundamentally from predator–prey relationships in nature because human consumers of a resource are rarely controlled solely by that resource. Tragedies do occur, however, at the level of the ecosystem, where multiple species interactions are involved. Human resource systems are converging rapidly toward ecosystem-type systems as the number of exploited resources increase, raising the probability of system-wide tragedies in the human world. Nevertheless, common interests exclusive of exploited commons provide feasible options for avoiding tragedy in a converged world.

Coral reef food webs are out!

Tags

biodiversity, coral reef, corals, food webs, marine communities, real world networks, trophic guild

The first paper dealing with our Caribbean coral reef work is finally out. This paper is really just a detailed account of the data and webs compilation, but the data are now available to all. Enjoy!

Roopnarine, Peter D. and Rachel Hertog. 2013. Detailed Food Web Networks of Three Greater Antillean Coral Reef Systems: The Cayman Islands, Cuba, and Jamaica. Dataset Papers in Ecology, Vol. 2013, Article ID 857470, 9 pages.

Abstract: Food webs represent one of the most complex aspects of community biotic interactions. Complex food webs are represented as networks of interspecific interactions, where nodes represent species or groups of species, and links are predator-prey interactions. This paper presents reconstructions of coral reef food webs in three Greater Antillean regions of the Caribbean: the Cayman Islands, Cuba, and Jamaica. Though not taxonomically comprehensive, each food web nevertheless comprises producers and consumers, single-celled and multicellular organisms, and species foraging on reefs and adjacent seagrass beds. Species are grouped into trophic guilds if their prey and predator links are indistinguishable. The data list guilds, taxonomic composition, prey guilds/species, and predators. Primary producer and invertebrate richness are regionally uniform, but vertebrate richness varies on the basis of more detailed occurrence data. Each region comprises 169 primary producers, 513 protistan and invertebrate consumer species, and 159, 178, and 170 vertebrate species in the Cayman Islands, Cuba, and Jamaica, respectively. Caribbean coral reefs are among the world’s most endangered by anthropogenic activities. The datasets presented here will facilitate comparisons of historical and regional variation, the assessment of impacts of species loss and invasion, and the application of food webs to ecosystem analyses.

The Cuban coral reef food web

Tags

biodiversity, coral reef, coral reef food web, food webs, graph, invertebrates and vertebrates, marine communities, networks, prey and predator, real world networks, sfdp

This is a rendering of the Cuban coral reef food web from our set that also includes the Cayman Islands and Jamaica. All the data will be made available very soon in an upcoming publication. This is a metanetwork, or guild-level web where nodes represent one or more species with indistinguishable prey and predator links. There is a total of 266 guilds (nodes) in the network with 3899 interactions (edges) between them. The guilds in turn encompass 860 species, including protists, macroalgae, seagrasses, invertebrates and vertebrates. Colour codes: red – primary producers; yellow – invertebrates and heterotrophic protists; magenta – vertebrates.

The web or network was rendered with Graphviz using the neato algorithm (though sfdp also produces very pleasing images). Total cpu time varied between 1-4 seconds depending on options and machine.

New paper – Networks, extinction and paleocommunity food webs

Tags

connectance, extinction, food webs, graph, link distribution, metanetwork, Network theory, networks, nonlinear, paleo-food web, power law, probability, real world networks, Robustness, simulations, trophic guild

Roopnarine, P. D. 2010. Networks, extinction and paleocommunity food webs in J. Alroy and G. Hunt, eds., Quantitative Methods in Paleobiology, The Paleontological Society Papers, 16: 143-161. (available here).

The paper is part of a volume, Quantitative Methods in Paleobiology, sponsored by The Paleontological Society. Full details are available here. The volume is also available for sale. Purchase one and support the Society!

Unbalanced food webs

Tags

extinction, food webs, modeling, Network theory, networks, paleo-food web, paleontology, real world networks, simulations

Perturbation simulations of three Karoo communities. 100 sims. per community.

A number of earlier posts have discussed food webs of the Permian–Triassic of the Karoo Basin in South Africa. This terrestrial ecosystem was subjected to the devastating end Permian mass extinction. The community which emerged in the aftermath of the extinction, the Lystrosaurus Assemblage Zone (LAZ), has been identified as having very unusual food web dynamics. This first figure compares the CEG dynamics of the end Permian Dicynodon Assemblage Zone (DAZ), LAZ, and the successive Cynognathus Assemblage Zone (CAZ). The implication is that there was a breakdown of perturbation dynamics during and/or right after the extinction episode. LAZ differs from the other communities (and in fact from every other community that we’ve studied so far!) in two ways:

1. Levels of secondary extinction can be extremely high at low peturbation levels, implying food webs of very low resistance.
2. Many species level networks or food webs (SLNs) of LAZ are nevertheless quite resistant, and resemble SLNs from the other communities. So the SLNs, or at least their dynamics, are highly variable in LAZ.

So what causes all this?

Distribution of log(low pert. sd) for random networks. Karoo communities are marked in green. LAZ occupies the extreme right.

The first question we asked ourselves was, is LAZ an unusually bad community or metanetwork, or are the other Karoo communities just exceptionally good? Our approach to addressing this was to generate 1,000 random metanetworks by randomly selecting observed guild richnesses from among our observed communities to fill the richness of a random community. A random community or metanetwork could therefore have guild richnesses that never occur together in any of the observed communities, but every guild richness of a random community is observed in at least one real Karoo community. We then simulated perturbation of 100 SLNs for each random community, and collected data on the first observation above, i.e., the variability of resistance at low levels of perturbation. As we see in the second figure, LAZ really stands out, even among the random communities! Why?

Well, in order to address that, we’ve used a number of regression models to examine the dependence of that variability on proportional guild richness. Proportional guild richness, in contrast to absolute, is the fraction of a community’s total consumer richness encompassed by a particular guild. Several guilds consistently stand out: very large amphibians, very small herbivorous amniotes, very small carnivorous/insectivorous amniotes, small carnivorous/insectivorous amniotes, carnivorous insects, and herbivorous insects. Multiple regression models demonstrate that the herbivorous guilds affect resistance variability negatively, i.e., they dampen the variability, while carnivorous guilds affect it positively! Now here’s the neat part. If we examine the sub-metanetworks of DAZ, LAZ and CAZ comprising these guilds only (see figure), we can immediately see how the communities differed with respect to these crucial guilds. Guilds with a dampening effect are shown in blue, those in red have the opposite effect (producer guilds are brown). And if you think of LAZ as being somehow imbalanced or out of whack, the figures should suggest to you some ways to “restore the balance”. I’ll discuss those in the next post.

The Network Structure of Baseball Blogs: Part 1

Tags

Network theory, networks, real world networks

Earlier in the week I read about the network structure of twitter employees’ accounts and that got me thinking about the network structure of baseball blogs….

This is very cool. Cute, interesting, of general interest, and it even mentions food webs! (Thanks to Steve W. for the link)

Dynamics and Control of Diseases in Networks with Community Structure

Tags

Network theory, networks, real world networks

The dynamics of infectious diseases spread via direct person-to-person transmission (such as influenza, smallpox, HIV/AIDS, etc.) depends on the underlying host contact network…

Different numbers of interactions in Caribbean coral reefs

Tags

connectance, coral reef, food webs, link distribution, real world networks

In-degree cumulative distributions

The last post on this topic reported that alpha vertebrate diversity differs among reef communities in the Cayman Islands, Cuba and Jamaica, with the Caymans having the greatest species richness. I also showed that if we consider the reef communities to be random draws from the gamma-level (regional) species pool, we cannot reconstruct food webs with the observed Jamaican connectance. What’s causing this? At least a partial answer is the bias in the degrees of trophic specialization in the communities. Jamaica has greater than expected connectance because it has a relatively greater proportion of generalist species, i.e. those with high in-degrees (incoming links). Interestingly, if we compare the in-degree distributions of the communities, we find no significant differences (Kolmogorov-Smirnov tests). This first figure illustrates the cumulative frequency functions of each community. While the K-S test says no difference, however, we note that there are asymmetries in the distributions, and it could well be worth decomposing these distributions into pre- and post-modal portions. They are right-skewed and relatively long-tailed.

Another way to compare the interaction or link distributions is to look at the properties of those species, present in the regional pool, that are missing from each community. The box plots at left plot the in-link distributions of “missing” vertebrates from each community. There is a clear trend, suggesting again that Jamaica is relatively poor in trophic specialists, while the Caymans are relatively rich, with Cuba in between. K-S tests fails to confirm any significance here, but sample sizes are pretty small, and there is likely a problem with test power.

A final interesting observation. Given that there are species common to two or more of the communities, we can compare the in-degree distributions of those species only. A series of paired t-tests confirm that species in Jamaica have significantly more incoming interactions than conspecifics in the Caymans and Cuba (Pr(T>t)=0.0004 and 0.0001 respectively). Can this be reconciled with the above observations? This result is telling us that if a species exists in Jamaica and elsewhere, it will have more prey resources in Jamaica! Given that we are recording only vertebrate differences among the communities, then it means that they have more vertebrate prey resources. I find this to be very odd, and I’m going to have to wrap my brain around it a bit to explain it. Might be time to decompose those distributions.