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New genomic methods will help assess the environmental status of marine waters

By: Dr Dan Faith, Category: Science, Date: 19 Dec 2013

Will new technology allow accurate, rapid, and cost efficient observations of the marine environment?

Mixed Marine Plankton

Peter Parks © Image Quest 3-D

A new publication by my colleagues and I discusses how new genomics approaches – and new methods for analyzing these data – opens the door to the development and application of more accurate, rapid, and cost efficient observations of the marine environment.

I became involved with this interesting group of authors as a result of a meeting associated with the Genomic Observatories Network (GO’s Network; http://www.genomicobservatories.org/). The GO’s network aims to create a global network of premier research sites working to generate genomic biodiversity observations. They are located around the globe in areas with a rich history of environmental/ecological data collection and a long-term commitment. They often promote standard data storage, access, and analyses.

Genomic Observatories is one focus of our working group on genetic diversity, within the global Biodiversity Observation Network (GEO BON). I co-lead this working group with Tet Yahara of Kyushu University. Members Dawn Field and Neil Davies have lead much of the development of Genomic Observatories.

Now, back to this paper. For me, one of the exciting angles on all this is that phylogenetic representations of genomic variation lead to a new toolbox of methods, extending my classic phylogenetic diversity (PD) measure.

In fact, my guess is that every standard index in ecology that is defined at the species level has its phylogenetic counterpart. This reflects the simple idea that we can “count-up” phylogenetic branches instead of counting up species. For example, species richness converts to quantifying how much of the tree-of-life is present (counting-up how many branches or lineages). This suggests that, even when we do not have identified species (as in many genomics applications), we can adapt standard species-level-methods. Further, phylogenetic indices such as total PD in an ecosystem seem to be good indicators of healthy ecosystem functioning. Thus, genomic technologies can assist in producing rapid and rigorous information about ecosystem functioning, often at a lower cost than traditional approaches.


Dr Dan Faith
Principal Research Scientist

More information
Sarah J. Bourlat, Angel Borja, Jack Gilbert, Martin I. Taylor, Neil Davies, Stephen B. Weisberg, John F. Griffith, Teresa Lettieri, Dawn Field, John Benzie, Frank Oliver Glöckner, Naiara Rodríguez-Ezpeleta, Daniel P. Faith, Tim P. Bean, Matthias Obst (2013). Genomics in marine monitoring: New opportunities for assessing marine health status, Marine Pollution Bulletin. 74: 19-31.

Tags biodiversity, conservation, phylogenetic,