GEO BON - a global Biodiversity Observation Network

Towards a Biodiversity Observation Network - GEO BON

The Group on Earth Observations or GEO ( ) is a partnership of more than 70 nations and 50 participating organisations. GEO is designing a Global Earth Observing System of Systems
(GEOSS) in order to improve the coordination of new and existing Earth observation data sets.

Biodiversity is one of the nine Societal Benefit Areas recognised by GEO. A Biodiversity Observation Network - GEO BON - is one of the first systems that GEO is producing for the GEOSS.

The GEO BON Implementation Plan was released on International Biodiversity Day.


Download the Detailed Implementation Plan or view the Press Release

GEO BON links to the emerging IPBES (Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services) are outlined in the "Gap analysis for the purpose of facilitating the discussions on how to improve and strengthen the science-policy interface on biodiversity and ecosystem services"

I serve on the GEO BON Steering Committee and co-lead one of the Working Groups.
The GEO BON steering committee has established eight working groups to advance the implementation of specific topics. The working group leads are indicated in parenthesis:
1.Genetics (Tet Yahara and Daniel Faith)
2.Terrestrial Species Monitoring Programmes (Henrique Pereira)
3.Terrestrial Ecosystem Monitoring (Rob Jongman)
4.Freshwater Ecosystem Monitoring (Ian Harrison)
5.Marine Ecosystem Monitoring (Jan de Leeuw and Carlo Heip)
6.Ecosystem Services (Hal Mooney)
7.In-situ / Remote-sensing Integration (Simon Ferrier)
8.Data Integration and Inter-operability: Informatics and Portals (Hannu Saarenmaa and Eamonn O Tuama)

Working Group 1: genetic/phylogenetic diversity

One of the current working groups for GEO BON is interested in global and regional scale monitoring of genetic and phylogenetic diversity (WG1).

The GEO BON Concept Document describes one important strategy for WG1:

"GEO BON will address the integration of remote sensing observations and in situ observations at the genetic level. GEO BON will use approaches that side-step the accumulation of genetic observations over time and instead rely on remotely sensed observations, over time, of changes in land/water condition. Here, spatial genetic variation models act as the “lens” for interpreting these changes. An example context is found in molecular approaches such as those used for microbes that provide patterns of genetic variation summarized as phylogenetic patterns. These patterns of genetic variation may be quantified using a measure of phylogenetic diversity or dissimilarity. The links from phylogenetic dissimilarities to environmental variables provide a basis for developing spatial models of genetic variation, as in the striking finding that global bacteria genetic diversity patterns (using 16S ribosomal RNA sequences) are strongly linked to salinity factors (Lozupone et al 2007). GEO BON will promote the use of such spatial biodiversity models as a “lens” to interpret the observed changes over time in ecosystem and habitat metrics (such as the presence or absence of particular ecosystems, their surface area, and degree of fragmentation) derived from remote sensing. GEO BON will explore the extension and standardization of these strategies."

The analysis of microbial 16s data has used phylogenetic dissimilarities and ordination models to compare samples and reveal underlying environmental factors or gradients. However, there are challenges in refining these methods for the “lens” approach in GEO BON. Some of these issues are addressed in:

Faith D.P., Lozupone C.A., Nipperess D., Knight R. The Cladistic Basis for the Phylogenetic Diversity (PD) Measure Links Evolutionary Features to Environmental Gradients and Supports Broad Applications of Microbial Ecology’s “Phylogenetic Beta Diversity” Framework. International Journal of Molecular Sciences. 2009; 10(11):4723-4741.

That paper points to robust ordination methods, developed elsewhere in ecology, that can overcome some of the current perceived difficulties in modelling 16s data in microbial ecology. For example, the GEO BON lens approach requires robust ordinations that avoid distortions such as the well-known arch or horseshoe problem. In considering a wide range of dissimilarity measures and ordination approaches, microbial workers have run head-long into this problem.

Kuczynski et al (2010) argue
“The arch effect (where samples along a single environmental gradient are misleadingly placed in an arch configuration) was prominent in the simulated data, where we know there is only a single gradient. The presence of the same effect in the soil data suggests that the pH gradient in the soil was the single driving factor in these communities”

They concluded: “Several statistical artifacts remained resistant to analysis. Although several techniques minimized the arch effect, none of the techniques we considered here eliminated it.....Resolving the arch effect so that multiple gradients can be studied remains an important challenge for the field.”
(Justin Kuczynski , Zongzhi Liu , Catherine Lozupone , Daniel McDonald , Noah Fierer &
Rob Knight (2010) Microbial community resemblance methods differ in their ability to detect biologically relevant patterns. Nature Methods 7, 813-819 doi:10.1038/nmeth.1499 )

More recently, Gonzalez and Knight (2012; Advancing analytical algorithms and pipelines for billions of microbial sequences. Current Opinion in Biotechnology 23:64–71) say:
“Another approach that can reduce certain artifacts, such as the horseshoe effect (a pattern in which the two ends of an axis attract each other due to a shared lack of the taxa in the middle, thus obscuring the gradient pattern), is to use nonlinear methods. NMDS can better preserve the highdimensional structure with few axes in some cases, although cannot fully avoid the arch effect in realistic microbial datasets. The main differences between PCoA and NMDS are that the former is based on distances, where the final configuration should match the original distances as close as possible, and the latter is based on ranks..”

The Faith et al (2009) paper referred to earlier work based on Bray Curtis type dissimilarities and hybrid multidimensional scaling (HMDS or SSH) that overcomes the arch problem and provides a robust ordination space suitable for inferring biodiversity loss through the lens approach (and ED methods).

Identifying the robust framework for ordination of 16s data addresses one challenge, but still leaves open the challenge of practical ordination algorithms for large data sets. WG1 workers are exploring approaches that are based on the robustness of Bray Curtis type dissimilarities and hybrid multidimensional scaling - but side-step the computationally-intensive ordination and work directly with the dissimilarities in ED methods. The rationale is that, for applications of the lens approach, we do not have to look at the ordination and so can use shortcuts to calculate ED biodiversity loss scores.

These strategies may assist GEO BON and programs such as the Earth Microbiome Project.

Recent presentations cover aspects of GEO BON.


 • The Group on Earth Observations Biodiversity Observation Network (GEO BON) Workshop on Essential Biodiversity Variables, February 2012, European Space Agency, Frascati, Italy.
• International workshop on global diversity assessment. Kyushu University, Japan Aug 2011.
• Invited talk "A range of phylogenetic tools and methods based on the PD measure" at Hennig XXX - the 2011 Meeting of the Willi Hennig Society, São José do Rio Preto, Brazil, August 2011. Symposium "Phylogenetics as a tool for Conservation" view talk
• Meeting of the Scientific Committee of bioGENESIS, a core project of DIVERSITAS, New York, June, 2011.  Meeting of the Scientific Committee of DIVERSITAS, Paris, March 2011.
• International Expert Meeting: Assessment of the Adequacy of Existing Observation Capabilities for the CBD 2020 Targets. Convened by the Group on Earth Observations Biodiversity Observation Network (GEO BON), In cooperation with the European Biodiversity Observation Network (EBONE), the Global Biodiversity Information Facility (GBIF), the International Union for Conservation of Nature (IUCN) and the United Nations Environment Program’s World Conservation Monitoring Centre (UNEP-WCMC). March 2011.

• INTERNATIONAL CONFERENCE ON BIODIVERSITY AND CLIMATE CHANGE, "Conserving biodiversity amidst climate change" February 1-3, 2011,Philippine International Convention Center. invited talk: "Global perspectives on climate change land/water use, and biodiversity: Strategies to better address overall biodiversity, including evolutionary history" DANIEL P. FAITH & ANNE-HELEN PRIUR-RICHARD (presented by Priur-Richard)

• 3rd Symposium on Long-Term Ecological and Biodiversity Research, Institute of Biology, University of the Philippines, Diliman, Quezon City, November 2010, Philippines.
• Biodiversity Indicators for Global Biodiversity Models workshop, October 2010, Cambridge, UK.

• Annual Meeting of the British Ecological Society, Leeds, U.K., September. Talk: "Indices for phylogenetic ecology based on the PD (phylogenetic diversity) measure". Also, Associate Editor Meeting for Methods in Ecology and Evolution
• Eco-Evolutionary Approaches to Understanding and Predicting the Response of Species Range to Climate Change, Kyushu University, Japan, August, 2010, talk: "Overview of GEO-BON and AP-BON"
• 95th Ecological Society of America meeting, Pittsburgh. Aug 2010. Co-organised symposium: "From Microbial to Conservation Biology: Exploring Phylogenetic Beta Diversity as a Theoretical Tool Uniting Disciplines" My talk: "Phylogenetic beta diversity as a tool in biodiversity conservation and monitoring (Daniel Faith, Simon Ferrier, Dan Rosauer)

• The 2010 International meeting of the Association for Tropical Biology and Conservation: “Tropical biodiversity: surviving the food, energy and climate crisis”. July 2010; Bali, Indonesia. Our symposium: “Integrating evolution, ecology and biodiversity science” My talk: "Phylogenetic diversity and a global scale biodiversity observation network, GEO BON"
• Invited speaker and Panel member at the Convention on Biological Diversity COP10 Pre-conference, Nagoya , Japan, 2010. my talk on Systematic Conservation Planning also slides from Panel discussion on targets. Complete program and talks. Also see the Recommendations from CBD-COP10 PreConference which includes my suggested recommendations regarding %targets, take-up of systematic conservation planning, and the need to address still-unknown biodiversity.
• Meeting of the Scientific Committee of DIVERSITAS, Nagoya , Japan, 2010
• Meeting of the GEO BON working group on global monitoring of genetic and phylogenetic diversity, in Asilomar, Monteray, California, USA, 2010. slides for introduction to our genetics working group
• Invited participant at the International Meeting for Promoting Asia-Pacific Biodiversity Observation Network (AP-BON), held in Tokyo, Japan, in December 2009.

Also, an invited presentation at: "Strategies in taxonomy: research in a changing world" (20-22 May 2009, Pruhonice, Czech Republic). My talk addressed one GEO BON candidate strategy: "Estimation of status of biodiversity for different places at different times changes in land/water condition (e.g. using remote sensing), integrated with spatial genetic/phylogenetic variation models as the “lens” to infer corresponding changes at the genetic/phylogenetic levels."

The described approach uses PD-dissimilarities* among samples to create models linking phylogenetic spatial variation to environmental and other gradients. We then apply standard species-level methods to create indices reflecting phylogenetic diversity losses from climate and land use change. These methods are based on the ED (environmental diversity) method, which "counts-up” species under an evolutionary model of unimodal response of features to gradients. My conference presentation concluded that these methods may serve GEO BON, by integrating phylogenetic information into a “lens” for interpreting remotely sensed changes in land condition.  

see also

"International collaborations to support a global Biodiversity Observation Network (GEO BON): research challenges ranging from microbes to a global 2010 biodiversity target"

 *background on phylogenetic or PD-dissimilarities can be found in the papers/software by Lozupone et al (UniFrac) and Ferrier et al (2007).


GEO BON publications:

Scholes. Robert J, Michele Walters, Eren Turak, Hannu Saarenmaa,Carlo HR Heip, E´amonn O´ Tuama, Daniel P Faith, Harold A Mooney,Simon Ferrier, Rob HG Jongman, Ian J Harrison, Tetsukazu Yahara and Henrique M Pereira (2012) Building a global observing system for biodiversity. Current Opinion in Environmental Sustainability.

GEO BON (2011) Adequacy of Biodiversity Observation Systems to support the CBD 2020 Targets. GEO BON Project Office.

Faith, D.P.(2011) Ecosystem services and biodiversity option values. Science published online, 10 Feb 2011.

Faith, D.P.(2011) Higher-level targets for ecosystem services and biodiversity should focus on regional capacity for effective trade-offs. Diversity 3,1-7; doi:10.3390/d3010001

Faith D.P., Lozupone C.A., Nipperess D., Knight R. The Cladistic Basis for the Phylogenetic Diversity (PD) Measure Links Evolutionary Features to Environmental Gradients and Supports Broad Applications of Microbial Ecology’s “Phylogenetic Beta Diversity” Framework. International Journal of Molecular Sciences. 2009; 10(11):4723-4741.

Read commentary: Faith, DP (2010) More Benefits from a Barometer of Life. Science Online, 24 Jun 2010

Read the Summary of our Implementation Plans, for the Fourteenth meeting of the Subsidiary Body on Scientific, Technical and Technological Advice (SBSTTA 14)10 - 21 May 2010 - Nairobi,Kenya UNEP/CBD/SBSTTA/14/INF/13

Read the Summary Report of our 1st Meeting of the GEO BON Steering Committee (Geneva, 22 – 23 June 2009)

Read the GEO Biodiversity Observation Network: Concept Document (Andrefouet, S.; Costello, M.J.; Faith, D.P. et al. (2008) The GEO Biodiversity Observation Network: Concept Document. GEO – Group on Earth Observations, Geneva, Switzerland).


Other research supporting GEO BON has developed methods for making better use of existing land classes or types, by taking into account overlap among types, and incorporating ED methods.

See the link at upper right:

"Enhancing environmental types using museum data and ED models"


Dr Dan Faith , Senior Principal Research Scientist email:danfaith8[at]
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