Morphometrics data on Holocene Melanopsidae of Lake Petea

The dataset includes measurements of Microcolpia parreyssii parreyssii (Philippi, 1847) and Microcolpia parreyssii sikorai (Brusina, 1903) from Holocene deposits of Lake Petea near Oradea, Romania. Additionally, the tps-files generated with the program TpsDig2 and containing pairwise x,y-coordinates describing the outlines of the digitized images are supplied. Finally, the matrix of Fourier coefficients resulting from the Fast Fourier Transform is provided.

(Tables 1+4) Sample site substratum and morphometrics and damage levels of different populations of Laternula elliptica around Antarctica

We document differences in shell damage and shell thickness in a bivalve mollusc (Laternula elliptica) from seven sites around Antarctica with differing exposures to ice movement. These range from 60% of the sea bed impacted by ice per year (Hangar Cove, Antarctic Peninsula) to those protected by virtually permanent sea ice cover (McMurdo Sound). Patterns of shell damage consistent with blunt force trauma were observed in populations where ice scour frequently occurs; damage repair frequencies and the thickness of shells correlated positively with the frequency of iceberg scour at the different sites with the highest repair rates and thicker shells at Hangar Cove (74.2% of animals damaged) compared to the other less impacted sites (less than 10% at McMurdo Sound). Genetic analysis of population structure using Amplified Fragment Length Polymorphisms (AFLPs) revealed no genetic differences between the two sites showing the greatest difference in shell morphology and repair rates. Taken together, our results suggest that L. elliptica exhibits considerable phenotypic plasticity in response to geographic variation in physical disturbance.

(Table 1) Morphometrics of narwhal (Monodon monoceros) fluke planforms

In this study, we compared the fluke geometries of male and female narwhals, which may be associated with hydrodynamic effects. Computerized tomography (CT) scanning was used to obtain data for analyses of the three-dimensional geometry of the flukes. The flukes from four narwhals (two males and two females) were obtained from aboriginal hunters in the vicinity of Broughton Island, Canada. The body lengths of the animals ranged from 2.98 to 3.60 m. Both males had erupted, upper left tusks. Standard body measurements were made including the span of the fluke (i.e., linear distance between fluke tips).

Morphometrics of seagrasses at species level, Moreton Bay, Australia determined from core samples collected in 2012-2013

Seagrass meadows are important marine carbon sinks, yet they are threatened and declining worldwide. Seagrass management and conservation requires adequate understanding of the physical and biological factors determining carbon content in seagrass sediments. Here, we identified key factors that influence carbon content in seagrass meadows across several environmental gradients in Moreton Bay, SE Queensland. Sampling was conducted in two regions: (1) Canopy Complexity, 98 sites on the Eastern Banks, where seagrass canopy structure and species composition varied while turbidity was consistently low; and (2) Turbidity Gradient, 11 locations across the entire bay, where turbidity varied among sampling locations. Sediment organic carbon content and seagrass structural complexity (shoot density, leaf area, and species specific characteristics) were measured from shallow sediment and seagrass biomass cores at each location, respectively. Environmental data were obtained from empirical measurements (water quality) and models (wave height). The key factors influencing carbon content in seagrass sediments were seagrass structural complexity, turbidity, water depth, and wave height. In the Canopy Complexity region, carbon content was higher for shallower sites and those with higher seagrass structural complexity. When turbidity varied along the Turbidity Gradient, carbon content was higher at sites with high turbidity. In both regions carbon content was consistently higher in sheltered areas with lower wave height. Seagrass canopy structure, water depth, turbidity, and hydrodynamic setting of seagrass meadows should therefore be considered in conservation and management strategies that aim to maximize sediment carbon content.

Contemporary genetic, historical genetic and morphological data sets for the Yellow-tufted Honeyeater Lichenostomus melanops

Understanding the evolutionary history of threatened populations can improve their conservation management. Re-establishment of past but recent gene flow could re-invigorate threatened populations and replenish genetic diversity, necessary for population persistence. One of the four nominal subspecies of the common yellow-tufted honeyeater, Lichenostomus melanops cassidix, is critically endangered despite substantial conservation efforts over 55 years. Using a combination of morphometric, genetic and modelling approaches we tested for its evolutionary distinctiveness and conservation merit. We confirmed that cassidix has at least one morphometric distinction. It also differs genetically from the other subspecies in allele frequencies but not phylogenetically, implying that its evolution was recent. Modelling historical distribution supported the lack of vicariance and suggested a possibility of gene flow among subspecies at least since the late Pleistocene. Multi-locus coalescent analyses indicated that cassidix diverged from its common ancestor with neighbouring subspecies gippslandicus sometime from the mid-Pleistocene to the Holocene, and that it has the smallest historical effective population size of all subspecies. It appears that cassidix diverged from its ancestor with gippslandicus through a combination of drift and local selection. From patterns of genetic subdivision on two spatial scales and morphological variation we concluded that cassidix, gippslandicus and (melanops + meltoni) are diagnosable as subspecies. Low genetic diversity and effective population size of cassidix may translate to low genetic fitness and evolutionary potential, thus managed gene flow from gippslandicus is recommended for its recovery.

Seawater carbonate chemistry and early development of the sea urchin Lytechinus variegatus in a laboratory experiment using artificial seawater

Land-based aquaculture facilities often utilize additional bicarbonate sources such as commercial sea salts that are designed to boost alkalinity in order to buffer seawater against reductions in pH. Despite these preventative measures, many facilities are likely to face occasional reductions in pH and corresponding reductions in carbonate saturation states due to the accumulation of metabolic waste products. We investigated the impact of reduced carbonate saturation states (Omega Ca, Omega Ar) on embryonic developmental rates, larval developmental rates, and echinoplutei skeletal morphometrics in the common edible sea urchin Lytechinus variegatus under high alkalinity conditions. Commercial artificial seawater was bubbled with a mixture of air and CO2 gas to reduce the carbonate saturation state. Rates of embryonic and larval development were significantly delayed in both the low and extreme low carbonate saturation state groups relative to the control at a given time. Although symmetry of overall skeletal body lengths was not affected, allometric relationships were significantly different between treatment groups. Larvae reared under ambient conditions had significantly greater postoral arm and overall body lengths relative to body lengths than larvae grown under extreme low carbonate saturation state conditions, indicating that extreme changes in the carbonate system affected not only developmental rates but also larval skeletal shape. Reduced rates of embryonic development and delayed and altered larval skeletal growth are likely to negatively impact larval culturing of L. variegatus in land-based, intensive culture situations where calcite and aragonite saturation states are lowered by the accumulation of metabolic waste products.

Seawater carbonate chemistry, mortality and hatching rate, size and mass of Clupea harengus during experiments, 2011

Due to atmospheric accumulation of anthropogenic CO2 the partial pressure of carbon dioxide (pCO2) in surface seawater increases and the pH decreases. This process known as ocean acidification might have severe effects on marine organisms and ecosystems. The present study addresses the effect of ocean acidification on early developmental stages, the most sensitive stages in life history, of the Atlantic herring (Clupea harengus L.). Eggs of the Atlantic herring were fertilized and incubated in artificially acidified seawater (pCO2 1260, 1859, 2626, 2903, 4635 µatm) and a control treatment (pCO2 480 µatm) until the main hatch of herring larvae occurred. The development of the embryos was monitored daily and newly hatched larvae were sampled to analyze their morphometrics, and their condition by measuring the RNA/DNA ratios. Elevated pCO2 neither affected the embryogenesis nor the hatch rate. Furthermore the results showed no linear relationship betweenpCO2 and total length, dry weight, yolk sac area and otolith area of the newly hatched larvae. For pCO2 and RNA/DNA ratio, however, a significant negative linear relationship was found. The RNA concentration at hatching was reduced at higher pCO2 levels, which could lead to a decreased protein biosynthesis. The results indicate that an increased pCO2 can affect the metabolism of herring embryos negatively. Accordingly, further somatic growth of the larvae could be reduced. This can have consequences for the larval fish, since smaller and slow growing individuals have a lower survival potential due to lower feeding success and increased predation mortality. The regulatory mechanisms necessary to compensate for effects of hypercapnia could therefore lead to lower larval survival. Since the recruitment of fish seems to be determined during the early life stages, future research on the factors influencing these stages are of great importance in fisheries science.

Fragilariopsis kerguelensis images from sediment core PS1768-8

Background: Light microscopic analysis of diatom frustules is widely used both in basic and applied research, notably taxonomy, morphometrics, water quality monitoring and paleo-environmental studies. In these applications, usually large numbers of frustules need to be identified and / or measured. Although there is a need for automation in these applications, and image processing and analysis methods supporting these tasks have previously been developed, they did not become widespread in diatom analysis. While methodological reports for a wide variety of methods for image segmentation, diatom identification and feature extraction are available, no single implementation combining a subset of these into a readily applicable workflow accessible to diatomists exists. Results: The newly developed tool SHERPA offers a versatile image processing workflow focused on the identification and measurement of object outlines, handling all steps from image segmentation over object identification to feature extraction, and providing interactive functions for reviewing and revising results. Special attention was given to ease of use, applicability to a broad range of data and problems, and supporting high throughput analyses with minimal manual intervention. Conclusions: Tested with several diatom datasets from different sources and of various compositions, SHERPA proved its ability to successfully analyze large amounts of diatom micrographs depicting a broad range of species. SHERPA is unique in combining the following features: application of multiple segmentation methods and selection of the one giving the best result for each individual object; identification of shapes of interest based on outline matching against a template library; quality scoring and ranking of resulting outlines supporting quick quality checking; extraction of a wide range of outline shape descriptors widely used in diatom studies and elsewhere; minimizing the need for, but enabling manual quality control and corrections. Although primarily developed for analyzing images of diatom valves originating from automated microscopy, SHERPA can also be useful for other object detection, segmentation and outline-based identification problems.

Ocean acidification and its potential effects on the early life-history of non-calcifying and calcifying echinoderm (Odontaster validus, Patiriella regularis and Arachnoides placenta) larvae, 2011

Ocean acidification, as a result of increased atmospheric CO2, has the potential to adversely affect the larval stages of many marine organisms and hence have profound effects on marine ecosystems. This is the first study of its kind to investigate the effects of ocean acidification on the early life-history stages of three echinoderms species, two asteroids and one irregular echinoid. Potential latitudinal variations on the effects of ocean acidification were also investigated by selecting a polar species (Odontaster validus), a temperate species (Patiriella regularis), and a tropical species (Arachnoides placenta). The effects of reduced seawater pH levels on the fertilization of gametes, larval survival and morphometrics on the aforementioned species were evaluated under experimental conditions. The pH levels considered for this research include ambient seawater (pH 8.1 or pH 8.2), levels predicted for 2100 (pH 7.7 and pH 7.6) and the extreme pH of 7.0, adjusted by bubbling CO2 gas into filtered seawater. Fertilization for Odontaster validus and Patiriella regularis for the predicted scenarios for 2100 was robust, whereas fertilization was significantly reduced in Arachnoides placenta. Larval survival was robust for the three species at pH 7.8, but numbers declined when pH dropped below 7.6. Normal A. placenta larvae developed in pH 7.8, whereas smaller larvae were observed for O. validus and P. regularis under the same pH treatment. Seawater pH levels below 7.6 resulted in smaller and underdeveloped larvae for all three species. The greatest effects were expected for the Antarctic asteroid O. validus but overall the tropical sand dollar A. placenta was the most affected by the reduction in seawater pH. The effects of ocean acidification on the asteroids O. validus and P. regulars, and the sand dollar A. placenta are species-specific. Several parameters, such as taxonomic differences, physiology, genetic makeup and the population's evolutionary history may have contributed to this variability. This study highlights the vulnerability of the early developmental stages and the complexity of ocean acidification. However, future research is needed to understand the effects at individual, community and ecosystem levels.

San Francisco Coastal System grain size and geochemical data for sand provenance study

Over 150 million cubic meter of sand-sized sediment has disappeared from the central region of the San Francisco Bay Coastal System during the last half century. This enormous loss may reflect numerous anthropogenic influences, such as watershed damming, bay-fill development, aggregate mining, and dredging. The reduction in Bay sediment also appears to be linked to a reduction in sediment supply and recent widespread erosion of adjacent beaches, wetlands, and submarine environments. A unique, multi-faceted provenance study was performed to definitively establish the primary sources, sinks, and transport pathways of beach sized-sand in the region, thereby identifying the activities and processes that directly limit supply to the outer coast. This integrative program is based on comprehensive surficial sediment sampling of the San Francisco Bay Coastal System, including the seabed, Bay floor, area beaches, adjacent rock units, and major drainages. Analyses of sample morphometrics and biological composition (e.g., Foraminifera) were then integrated with a suite of tracers including 87Sr/86Sr and 143Nd/144Nd isotopes, rare earth elements, semi-quantitative X-ray diffraction mineralogy, and heavy minerals, and with process-based numerical modeling, in situ current measurements, and bedform asymmetry to robustly determine the provenance of beach-sized sand in the region.