Level of interest:

This paper will not only interest workers across genomics but also interest other workers on biodiversity observatories and observation networks. The paper is also of interest to those following emerging international programs, including IPBES and GEO BON.

Advice on publication: Accept after discretionary revisions (see below)

Davies et al present a well-written, strong case for a coordinated effort to develop “Genomic Observatories” (GOs). The logic is that focusing sequencing efforts in locations that are already intensively studied we can cost-effectively advance our understanding of biodiversity and ecosystem services. Davies et al describe GOs as “inter-disciplinary research sites” because they are rich in contextual data (e.g. data on environmental variables) produced by previous long-term studies. This means that the GOs can serve as “innovation incubators for ecogenomics” and can provide” a rich source of use cases (and users) for standards development”.

Discretionary Revisions

1. Davies et al appropriately discuss GOs in the context of gaps in our knowledge of biodiversity, providing some superb discussion on “dark taxa” biodiversity. Here, they could refer to the broader international initiatives that are looking at forms of observation systems for this purpose (e.g.Wheeler et al 2012).

2. The authors say “Indeed, as the ‘genomic revolution’ gains momentum we should start imagining a world where biodiversity is completely known at the genetic level, at least for some key sites on Earth.”

This is a somewhat ironic statement, with biodiversity “completely known” – but in fact only at some sites!

This highlights the key property, and possible limitation, of GOs: we find out quite a lot about some places but this may or may not inform us about broader patterns of regional/global biodiversity.

Here, it is good that the authors suggest links to GEO BON – the emerging global biodiversity observation network: “Such an initiative .. should be built in collaboration with and embedded within existing networks (e… and related initiatives (e.g., …. GEO BON[30], etc.)”.

GEO BON will support GO-type “observatories” (at genetic, species, and other levels), but it also supports use of biodiversity spatial models that extend the data collected at many different places (often for a variety of reasons), to form a biodiversity surface for all places in the region. In this “lens” approach (Andrefouet et al 2008), the time series information may come from remote sensing, rather than repeated site sampling.

So, the authors may wish to highlight these potential links between “genomic observatories” and the complementary strategies of “genomic observation networks”. Only the combination of approaches may move us towards “completely known” biodiversity. It is an interesting open question as to whether/how intensive efforts at key places will synergise with less-intensive sampling at many sites.

I note that the authors say “…we argue that genomics needs to become more of a ‘place-based’ science.” With “… a scientific paradigm shift towards sustained sequencing of site-specific complex assemblages.”

This highlights the time series at selected places approach, but genomics perhaps needs to be “place-based” also through regional-scale spatial models. Faith et al (2009) and Couve et al (2011) highlight some of the research issues in this context.

1. Davies et al say: “The foundational layer of biodiversity - genetic variation - would thus be mainstreamed into Earth Observation systems enabling predictive modelling of biodiversity dynamics and resultant impacts on ecosystems services.” And “rendering tangible benefits to society through the enhanced ecosystem services expected from a better understanding of biodiversity dynamics.” These statements may be a bit vague for many readers; the authors may wish to add expand/explain.

Competing interests: None declared.

References:

Andrefouet, S.; Costello, M.J.; Faith, D.P.; Ferrier, S.; Geller, G.N.; Höft, R.; Jürgens, N.; Lane, M.A.; Larigauderie, A.; Mace, G.; Miazza S.; Muchoney, D.; Parr, T.; Pereira, H.M.; Sayre, R.; Scholes, R.J.; Stiassny, M.L.J.; Turner, W.; Walther, B.A.; Yahara, T. The GEO Biodiversity Observation Network: Concept Document; GEO—Group on Earth Observations: Geneva, Switzerland. 2008, Available at: http://www.earthobservations.com/documents/cop/bi_geobon/ 200811_geobon_concept_document.pdf/,

Couvet,Denis, Vincent Devictor, Frederic Jiguet, Romain Julliard (2011) Scientific contributions of extensive biodiversity monitoring 334 370–377.

Faith, Daniel P., Catherine A. Lozupone, David Nipperess and Rob Knight (2009) 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. Int. J. Mol. Sci. 10, 4723-4741.

Wheeler, Q. D. S. Knapp, D. W. Stevenson, J. Stevenson, S. D. Blum, B. M. Boom, G. G. Borisy, J. L. Buizer, M. R. De Carvalho, A. Cibrian, M. J. Donoghue, V. Doyle, E. M. Gerson, C. H. Graham, P. Graves, S. J. Graves, R. P. Guralnick, A. L. Hamilton, J. Hanken, W. Law, D. L. Lipscomb, T. E. Lovejoy, H. Miller, J. S. Miller, S. Naeem, M. J. Novacek, L. M. Page, N. I. Platnick, H. Porter-Morgan, P. H. Raven, M. A. Solis, A. G. Valdecasas, S. Van Der Leeuw, A. Vasco, N. Vermeulen, J. Vogel, R. L. Walls, E. O. Wilson & J. B. Woolley (2012): Mapping the biosphere: exploring species to understand the origin, organization and sustainability of biodiversity, Systematics and Biodiversity, 10:1, 1-20

Minor issues not for publication

Re “A journal for the network, International Ecostations, should be developed to disseminate progress and explore new publishing models,”

This sentence seems odd – is this proposing a name for the journal?

Level of interest: An article of outstanding merit and interest in its field

Quality of written English: Acceptable

Statistical review: No, the manuscript does not need to be seen by a statistician.