Gump South Pacific Research Station

Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities.

ABSTRACTVery high resolution (VHR) airborne data enable detection and physical measurements of individual coral reef colonies. The bathymetric LiDAR system, as an active remote sensing technique, accurately computes the coral reef ecosystem’s surface and reflectance using a single green wavelength at the decimetre scale over 1-to-100 km2 areas. A passive multispectral camera mounted on an airborne drone can build a blue-green-red (BGR) orthorectified mosaic at the centimetre scale over 0.01-to-0.1 km2 areas. A combination of these technologies is used for the first time here to map coral reef ecological state at the submeter scale. Airborne drone BGR values (0.03 m pixel size) serve to calibrate airborne bathymetric LiDAR surface and intensity data (0.5 m pixel size). A classification of five ecological states is then mapped through an artificial neural network (ANN). The classification was developed over a small area (0.01 km2) in the lagoon of Moorea Island (French Polynesia) at VHR (0.5 m pixel size) and then extended to the whole lagoon (46.83 km2). The ANN was first calibrated with 275 samples to determine the class of coral state through LiDAR-based predictors; then, the classification was validated through 135 samples, reaching a satisfactory performance (overall accuracy = 0.75).

The Genomic Observatories Metadatabase (GeOMe, http://www.geome-db.org/) is an open access repository for geographic and ecological metadata associated with biosamples and genetic data. Whereas public databases have served as vital repositories for nucleotide sequences, they do not accession all the metadata required for ecological or evolutionary analyses. GeOMe fills this need, providing a user-friendly, web-based interface for both data contributors and data recipients. The interface allows data contributors to create a customized yet standard-compliant spreadsheet that captures the temporal and geospatial context of each biosample. These metadata are then validated and permanently linked to archived genetic data stored in the National Center for Biotechnology Information’s (NCBI’s) Sequence Read Archive (SRA) via unique persistent identifiers. By linking ecologically and evolutionarily relevant metadata with publicly archived sequence data in a structured manner, GeOMe sets a gold standard for data management in biodiversity science.

Abstract DNA is the most elemental level of biodiversity, drives the process of speciation, and underpins other levels of biodiversity, including functional traits, species and ecosystems. Until recently biodiversity indicators have largely overlooked data from the molecular tools that are available for measuring variation at the DNA level. More direct analysis of trends in genetic diversity are now feasible and are ready to be incorporated into biodiversity monitoring. This chapter explores the current state-of-the-art in genetic monitoring, with an emphasis on new molecular tools and the richness of data they provide to supplement existing approaches. We also briefly consider proxy approaches that may be useful for many-species, global scale monitoring cases.

The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms.An international group of 64 scientists first published the call for a global network of Genomic Observatories in January 2012. The vision for such a network was expanded in a subsequent paper and developed over a series of meetings in Bremen (Germany), Shenzhen (China), Moorea (French Polynesia), Oxford (UK), Pacific Grove (California, USA), Washington (DC, USA), and London (UK). While this community-building process continues, here we express our mutual intent to establish the GOs Network formally, and to describe our shared vision for its future. The views expressed here are ours alone as individual scientists, and do not necessarily represent those of the institutions with which we are affiliated.

In addition to their nuclear genome, the vast majority of eukaryotes harbour cytoplasmic genomes, e.g. in mitochondria or chloroplasts. In the majority of cases, these cytoplasmic genomes are transmitted maternally only, leading to selective pressures divergent from those that act on nuclear genes. In particular, cytoplasmic genes, which reduce the fitness of males that carry them, but have no fitness effect in females, are believed to be selectively neutral. Here, we go a step further and argue that in outbreeding populations (i.e. populations with inbreeding avoidance), 'spiteful' cytoplasmic elements that reduce the number of offspring produced by males are in fact selected for. We study this process by means of a stochastic model, analysing both the probability of spread and the impact that such a spiteful cytotype can have on population dynamics. Our results demonstrate that the probability of spread of the spiteful cytotype can be several times higher in outbreeding than in panmictic populations. Spread and fixation of the spiteful cytotype can lead to different qualitative effects on the population dynamics, including extinction, decreased or increased stable population size. We discuss our results in respect to cytoplasmically induced male infertility and cytoplasmic incompatibility.