Habitat Earth


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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!



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Late Permian community dynamics

Late Permian community dynamics

This is the second presentation that I made at the Annual Conference of the Geological Society of America in Vancouver last month. The presentation was part of a special session, “Extreme Environmental Conditions and Biotic Responses during the Permian-Triassic Boundary Crisis and Early Triassic Recovery”, co-organized my myself, Tom Algeo, Hugo Bucher and Arne Winguth. The session, spanning two days, was excellent, outstanding, and a lot of fun! I came away with the firm conviction that we are beginning to really understand the massive Permo-Triassic mass extinction, from its causes to consequences to recovery. It truly was a watershed “moment” in the history of the biosphere. The full program for both days can be found here and here. And, here is the abstract. An online copy of the presentation is available here.


ROOPNARINE, Peter, Invertebrate Zoology and Geology, California Academy of Sciences, 55 Music Concourse Dr, Golden Gate Park, San Francisco, CA 94118, proopnarine@calacademy.org and ANGIELCZYK, Kenneth D., Department of Geology, The Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605

A central question of the P/Tr extinction is the manner in which Permian ecological communities collapsed and E. Triassic ones were built. The end Permian Dicynodon Assemblage Zone (DAZ) has recently been resolved into 3 phases of the extinction spanning ~120ky, followed by the E. Triassic (Induan) Lystrosaurus Assemblage Zone (LAZ), offering an opportunity to examine the ecological dynamics of extinction and recovery in enhanced detail. We do this with 2 modelling approaches.

The first model assumes that populations exist in an energetic balance between consumption and predation. Communities are modelled as stochastic variants sampled from a space defined by species richness and functional diversity. Paleoenvironmental data from the DAZ indicate an increasingly seasonal, arid and drought-prone environment. The models were perturbed by simulated reductions of primary productivity. Results show that DAZ Phase 0 (Ph0) was a robust community resistant to low-moderate levels of perturbation with a well-defined collapse threshold. DAZ Ph1 and Ph2, however, exhibit highly variable responses and are significantly less resistant. LAZ similarly exhibits highly variable responses across minor variation of model configurations.

The second model assumes that communities are locally stable, i.e. minor perturbations are followed by asymptotic returns to equilibrium. During this return, however, communities can exhibit transient behavior during which perturbations can be greatly amplified. Amplification is likely to be important in unstable environments when the frequency of perturbations is shorter than the return time to equilibrium. Applying this model to DAZ and LAZ communities shows that the Karoo ecosystem became more limited in its responses to perturbation as the P/Tr boundary was approached, with Ph1 and Ph2 communities exhibiting very little transient behavior. LAZ in contrast exhibits increased transience.

The energetics and stability models are reconcilable in a history where the Karoo ecosystem became more ecologically stable as the extinction unfolded, yet more sensitive to cascading effects of species extinction and reductions of productivity. The Induan ecosystem was an unrecovered one, sensitive to both extinction and minor ecological disturbances.

Modern and paleocommunity analogues


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Roopnarine-04Last 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).


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.

Experimental Space


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Cayman Islands coral reef food web

Cayman Islands coral reef food web

Hi everyone, if any of you will be in the San Francisco Bay Area in the coming month, there is an exhibition at the Aggregate Space Art Gallery, featuring scientific visualizations. A couple of pieces there are from my food web work! So please stop by. Here is the gallery’s announcement:

“In their search for evidence of theories that better explain our physical reality, scientists often discover unexpected and beautiful phenomena. The researchers who created the images and videos included in “Experimental Space” did not have an art gallery in mind while they worked. Nevertheless, the images, figures, and data on view are aesthetically compelling and seductive. Through this exhibition, Aggregate Space Gallery and BAASICS bring scientific images and perspectives from the laboratory and the academic journal to the realm of art, where subjectivity trumps objectivity and ambiguity is more celebrated than demystification.

Featuring Evidence by: Erin Jarvis Alberstat, PhD candidate; Roger Anguera, Multimedia Engineer; Daniel J. Cohen, PhD; Sara M. Freeman, PhD; Luke Gilbert, PhD; Angela Kaczmarczyk, PhD candidate; Arnaud Martin, PhD; Brian Null, PhD, and Dr. Peter D. Roopnarine, PhD.”


Specimen collecting and cherry picking


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In a recent opinion piece in Slate, Ben Minteer of Arizona State University continues to raise questions of the ethical legitimacy of collecting specimens for biological research. Minteer maintains that the risk to species, where population sizes might be small enough so that collecting represents a probabilistic extinction threat, outweighs the benefits to science and conservation. Unfortunately, Minteer is expressing an opinion, not the results of a carefully weighed and conducted analysis of data or facts. This is best highlighted by his example of the recent re-discovery of a species of New Guinea bat. Minteer states, “No scientist or conservationist today would deny the importance and value of describing a new species or confirming the return of one thought lost to extinction. But scientists also have a powerful ethical responsibility to minimize any and all adverse ecological impacts of their work.” Would that the world be so easily navigated. Today there are larger threats looming to biodiversity than at any time in the past 66 million years, and every one of those threats is the result of human actions. The threat of negative ecological impacts by scientists who are trying to document, explain and ultimately sustain what remains of the natural world pales hugely when compared to the threats of habitat destruction, the over-exploitation of species, and climate change. We will face very difficult decisions in the coming decades, and information is our friend, not our enemy.

Back to Minteer though. I think that his argument amounts to cherry picking and straw men. The reason for my position is best stated in a recent blog post by my colleague at the California Academy of Sciences, Dr. Jack Dumbacher. Jack explores the discovery of that very same bat picked by Minteer as an example, and he outlines very nicely the critical nature of the work. Please read his post. I’ll end here with an excerpt: “This study highlights the value of museum specimens in modern research, and the importance of taking specimens in modern field studies. Ironically, these studies were undertaken to assess the impacts of selective logging. The biggest threat to lowland forest in PNG is due to habitat loss from logging, mining, and oil palm conversion. One of the few things that might slow habitat loss is the fact that one little poorly known female bat was recently collected there.

The legitimacy of collections for biological research



(copyright Python? via YouTube)

The April 18th issue of Science magazine included a piece by Ben Minteer of Arizona State University, and co-authors, “Avoiding (re)extinction“. The authors argued that the collection of specimens for biological research has, and may continue to place species at heightened risk of extinction, citing among other things stories such as the collection of the last remaining individuals of the Great Auk, as if those extinctions could be attributed to scientific collecting. The piece was very ill-conceived and poorly supported by evidence, basically constructing a straw man in the interest of argument (“But this is just contradiction.” “No it isn’t!”). Luiz Rocha, one of my colleagues here at the California Academy of Sciences, led a response which eventually involved 134 scientists hailing from 64 institutions around the world. Our response was published last week, also in Science. I cannot print any of the letters here, but I will include a link to our press summary.

Today is the Day of International Biodiversity


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Today the UN and other organizations recognize the critical importance and threats to biodiversity around the world. The Species Alliance is recognizing the day by airing its documentary, Call of Life, on Free Speech TV (also streamed online). The documentary is followed by short interviews of myself (Peter Roopnarine), and Stuart Pimm. Please join if you can!


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