Making genetic biodiversity measurable : a review of statistical multivariate methods to study variability at gene level

Measures of agro-ecosystems genetic variability are essential to sustain scientific-based actions and policies tending to protect the ecosystem services they provide. To build the genetic variability datum it is necessary to deal with a large number and different types of variables. Molecular marker data is highly dimensional by nature, and frequently additional types of information are obtained, as morphological and physiological traits. This way, genetic variability studies are usually associated with the measurement of several traits on each entity. Multivariate methods are aimed at finding proximities between entities characterized by multiple traits by summarizing information in few synthetic variables. In this work we discuss and illustrate several multivariate methods used for different purposes to build the datum of genetic variability. We include methods applied in studies for exploring the spatial structure of genetic variability and the association of genetic data to other sources of information. Multivariate techniques allow the pursuit of the genetic variability datum, as a unifying notion that merges concepts of type, abundance and distribution of variability at gene level.

Time lapse sea-bed photos (benthos) with associated current meter data from ROBIO lander deployments during Discovery cruise D297

A baited imaging lander was deployed six times in the Nazare Canyon at depths from 909 to 4361 m during August 2005 to investigate the demersal scavenging fishes. Species observed and lander-derived abundance estimates were similar to previous data from the Porcupine Seabight and abyssal plain, north-east Atlantic Ocean.

Multibeam and seismic survey, physical oceanography, and sea-bottom videos from the Bay of Biscay

We report the northernmost and deepest known occurrence of deep-water pycnodontine oysters, based on two surveys along the French Atlantic continental margin to the La Chapelle continental slope (2006) and the Guilvinec Canyon (2008). The combined use of multibeam bathymetry, seismic profiling, CTD casts and a remotely operated vehicle (ROV) made it possible to describe the physical habitat and to assess the oceanographic control for the recently described species Neopycnodonte zibrowii. These oysters have been observed in vivo in depths from 540 to 846 m, colonizing overhanging banks or escarpments protruding from steep canyon flanks. Especially in the Bay of Biscay, such physical habitats may only be observed within canyons, where they are created by both long-term turbiditic and contouritic processes. Frequent observations of sand ripples on the seabed indicate the presence of a steady, but enhanced bottom current of about 40 cm/s. The occurrence of oysters also coincides with the interface between the Eastern North Atlantic Water and the Mediterranean Outflow Water. A combination of this water mass mixing, internal tide generation and a strong primary surface productivity may generate an enhanced nutrient flux, which is funnelled through the canyon. When the ideal environmental conditions are met, up to 100 individuals per m² may be observed. These deep-water oysters require a vertical habitat, which is often incompatible with the requirements of other sessile organisms, and are only sparsely distributed along the continental margins. The discovery of these giant oyster banks illustrates the rich biodiversity of deep-sea canyons and their underestimation as true ecosystem hotspots.

Spatiotemporal monitoring of water quality in coral reefs of Tayrona National Natural Park, Colombian Caribbean, 2011-2013

Tayrona National Natural Park (TNNP; 11°17' - 11°22' N and 73°53' - 74°12' W) is a hotspot of coral reef biodiversity in the Colombian Caribbean, located between the city of Santa Marta (>455,000 inhabitants) and several smaller river mouths (Rio Piedras, Mendihuaca, Guachaca). The region experiences a strong seasonal variation in physical parameters (temperature, salinity, wind, and water currents) due to alternating dry seasons with coastal upwelling and rainy seasons. Here, a range of water quality parameters relevant for coral reef functioning is provided. Water quality was measured directly above local coral reefs (~10 m water depth) by a monthly monitoring for up to 25 months in the four TNNP bays (Chengue, Gayraca, Neguanje, and Cinto) and at sites with different degree of exposition to winds, waves and water currents (exposed vs. sheltered sites) within each bay. The water quality parameters include: inorganic nutrient (nitrate, nitrite and soluble reactive phosphorus), chlorophyll a, particulate organic carbon and nitrogen concentrations (with a replication of n=3) as well as oxygen availability, biological oxygen demand, seawater pH, and water clarity (with a replication of n=4). This is by far the most comprehensive coral reefs water quality dataset for the region. A detailed description of the methods can be found within the referenced publications.

(Table 1) 40Ar/39Ar plateau and isochron ages for basalts from the Réunion hotspot track

Concordant plateau and isochron ages were calculated from 40Ar/39Ar incremental heating experiments on volcanic rocks recovered by drilling at four Leg 115 sites and two industry wells along the volcanic lineament connecting Reunion Island to the Deccan flood basalts, western Indian Ocean. The new ages provide unequivocal evidence that volcanic activity migrated southward along this sequence of linear ridges. The geometry and age distribution of volcanism are most compatible with origin above a stationary hotspot centered beneath Reunion. The hotspot became active with rapid eruption of the Deccan flood basalts, western India, and subsequent volcanic products record the northward motion of the Indian and African plates over the hotspot through Tertiary time. The radiometric ages are in general accord with basal biostratigraphic age estimates, although some adjustments in current magnetobiostratigraphic time scales may be required.

Web-based Biodiversity Citizen Science Database (assembled 2012)

The collective impact of humans on biodiversity rivals mass extinction events defining Earth's history, but does our large population also present opportunities to document and contend with this crisis? We provide the first quantitative review of biodiversity-related citizen science to determine whether data collected by these projects can be, and are currently being, effectively used in biodiversity research. We find strong evidence of the potential of citizen science: within projects we sampled (n = 388), ~1.3 million volunteers participate, contributing up to US Dollar 2.5 billion in-kind annually. These projects exceed most federally-funded studies in spatial and temporal extent, and collectively they sample a breadth of taxonomic diversity. However, only 12% of the 388 projects surveyed obviously provide data to peer-reviewed scientific articles, despite the fact that a third of these projects have verifiable, standardized data that are accessible online. Factors influencing publication included project spatial scale and longevity and having publically available data, as well as one measure of scientific rigor (taxonomic identification training). Because of the low rate at which citizen science data reach publication, the large and growing citizen science movement is likely only realizing a small portion of its potential impact on the scientific research community. Strengthening connections between professional and non-professional participants in the scientific process will enable this large data resource to be better harnessed to understand and address global change impacts on biodiversity.