Computational Ecology at MSRC

Rich Williams Head, Computational Ecology and Environmental Science Group

Computational Ecology at MSRC

Ecology: the science of the interactions between organisms and their environments There are technical problems that are particularly important in ecological research and conceptual issues central to our emerging scientific understanding of complex systems, all of which can be addressed using computational methods.

Ecological Theory/Modelling:
Fundamental rules or laws are lacking Theory is highly heterogeneous and situation-specific Global scale patterns suggest that general theory is possible Need theory that crosses the conceptual hierarchy from individual to ecosystem

Ecological Data:
Conceptual heterogeneity drives data heterogeneity High data volume is typically not an issue; collecting data is. Data is typically privately held and sharing is not always common For many, Excel is the data entry and management tool of choice

Scientific Working Practices:

Many scientists are not especially computationally savvy Data management practices are poor or non-existent Lack of code sharing and re-use leads to duplication of effort

Computational Ecology and Environmental Science Group

Long-Term Objectives Scientific Challenges Develop theoretical and computational tools and methods to advance ecology and environmental science in areas that present important global challenges. 1. Biotic feedbacks in the climate system: feedbacks on scales from global to local, including plant-animal interactions in vegetation models. 2. Biodiversity science: the distribution and abundance of species, the role of biodiversity in ecosystem function, prediction and management of invasive species 3. Microbial ecology and biogeochemistry: microbial diversity, biogeography, community composition, population dynamics and system function. 1. Data acquisition and management: sensor networks, metadata creation and management, data semantics, distributed data systems, data discovery and integration, data heterogeneity. 2. Computational modeling of complex systems: agent-based models, evolutionary models, systems with multiple spatial and temporal scales, connecting individual behaviour to system properties, languages for model specification. 3. Integrating models and data: Bayesian techniques, machine learning, optimal design of monitoring and experiments. 4. Tool usability, maintainability and extensibility

Technological Challenges

Computational Ecology and Environmental Science Group

Dr. Rich Williams, Group Head Dr. Drew Purves, Scientist

Dr Leeza Pachepsky, Post-doc Dr Robin Freeman, Post-doc

Dr Matthew Smith, Post-doc Dr Greg McInerny, Post-doc

Addressing these issues in a set of highly collaborative research projects:

Programme
Understanding Ecosystems and Biodiversity Understanding Biotic Components of Climate System

Projects
(1)Modelling cloud forest species distributions [RW w/ KU-Conabio]; (2) Modelling invasive species spread and impact [LP w/ UCSB,Cam]; (3) Modelling food webs structure and function [RW w/ SFI, Tech U Darmstadt]; (5) Advanced techniques for modelling plant and forest growth [DP w/ IES, Zurich] (1) Connecting tree physiology, plant Xylem structure to evapotranspiration and the global climate [ DP&RW w/ Cam]; (2) Understanding biogeochemical feedback on earth system [RW w/ UEA]; (3) development of a new fire model for use in earth systems modelling [DP w/ CNRS]; (4) Landscape-scale coupled biological meteorological model of Peruvian cloud forest [RW w/ Oxford U.] (1) Integrating ecological and biodiversity data [RW & RF w/ CPB] (2) System for monitoring and understand avian behaviour [RF and AB w/ Oxford] (3) Global database of forest inventory [DP] (4) Initial release of digitized Cambridge Herbarium collection, most importantly Darwins collection from voyage on The Beagle [RW w/ Cam] (1) Tools for cloud forest conservation [RW&LP w/ WCMC]; (2) Tools for optimal reserve design [LP w/ EBD, Spain]

Managing Ecological and Biodiversity Data

Tools for Environmental Management

Autonomous Monitoring of Vulnerable Habitats

Seabirds are highly vulnerable to environmental change and so are indicator species of ecosystem health This project is developing a wireless network to monitor the behaviour of the Manx Shearwater (Puffinus puffinus) The system allows real-time data analysis and reprogramming of sensors Initial results contradict much of the conventional wisdom of behaviour in nesting burrows Planned extensions include GPS tracking to monitor foraging behaviour and deployment in other systems. Collaborators: Robin Freeman (MSRC), Tim Guilford (Univ of Oxford), Chris Perrins (Univ of Oxford), Torben Weis (U. DuisburgEssen)

Skomer Island avian monitoring system

Building a global database of forest inventory data

Forests harbour around 60% of the

worlds biodiversity and around half of its terrestrial carbon. There is an urgent need to predict how forests will respond to continuing anthropogenic perturbations including increased atmospheric CO2, logging and landuse change. To aid in the development and parameterization of models to predict these responses, this project will collate millions of pre-existing field measurements of trees from national forest inventories into a coherent, user-friendly database.
Collaborators: Drew Purves (MSR), and a network of international researchers

200,000 plots

Cra Ht

Cw

Taxonomic Concepts versus Taxonomic Names in Ecological Analysis

The accurate identification of specimens is particularly important for ecological surveys of biodiversity. Taxonomic names are a significant and pervasive source of ambiguity when dealing with biodiversity data of mixed provenance. This project is designed to find out how big an effect problems in the naming of species is having on our biodiversity analyses. The project will design and implement a taxonomic concept/name resolution server, a data integration tool to integrate data sets defined using taxonomic concepts, and visualization tools for exploring the data. These tools will be used to perform comparative analyses using taxonomic names and taxonomic concepts. Collaborators: Rich Williams (MSRC), Jessie Kennedy (Napier Univ) and various biodiversity data providers.
USDA Plants & ITIS Abies lasiocarpa var. lasiocarpa var. arizonica Flora North America

Abies bifolia

Understanding and predicting forest dynamics at local to global scales

A predictive understanding of forest dynamics is urgently needed to address problems including biodiversity and climate change. This project has developed a new model for forest dynamics, which is now being parameterized for various global forests. A crucial part of this analysis is a new way to model and visualize forest canopies. These tools are being implemented within the DISCOVERY framework under development within the European Science Initiative Drew Purves (MSR); Steve Pacala (Princeton University); and others

A toolbox for spatial analysis of invasive species spread

Invasive species (species non-native to their habitat) are causing significant economic and environmental damages worldwide. Economic damage of invasive species has been estimated to $137 billion per year in the United States alone. This project will develop a toolbox for analysis and prediction spread of invasive species that incorporates the latest analytical and numerical techniques. The toolbox will create an integrated tool that will enable non-expert researchers to use computational, mathematical and statistical techniques on spatio-temporal data. Collaborators: Leeza Pachepsky (MSRC), Prof. Jonathan Levine (University of California Santa Barbara)
Drake and Lodge. 2004. Proc. R. Soc. Lond. B.

pinker.wjh.harvard.edu/photos/santa_barbara_california/pages/ice%20plant%20and%20sea.htm

Kareiva et al. 2007 Science 316: 1866-1869

The Structure and Dynamics of Complex Ecological Networks

Food webs, or networks of who eats whom in an ecosystem, have long been a central topic in ecological research and general network theory. Food webs provide a complex yet tractable description of ecosystem diversity and complexity. Computational methods are being used to study the interplay between network structure, species traits and interaction rules which lead to robust, diverse ecological networks.

Projects and Collaborators:

Rich Williams (MSRC) Entropy of degree distributions, effect of network structure on species persistence and ecosystem function.
Neo Martinez (UCSB), Uli Brose (Tech U. Darmstadt) allometric scaling of dynamical models, keystone species in complex food webs Jen Dunne (Santa Fe Institute) structural and dynamical models of the impact of early humans on food webs in the Aleutian Islands

ri ci

ni