locuseater and shadowboxer: programs to optimize experimental design and multiplexing strategies for genetic mark–recapture

Genetic mark–recapture requires efficient methods of uniquely identifying individuals. ‘Shadows’ (individuals with the same genotype at the selected loci) become more likely with increasing sample size, and bias harvest rate estimates. Finding loci is costly, but better loci reduce analysis costs and improve power. Optimal microsatellite panels minimize shadows, but panel design is a complex optimization process. locuseater and shadowboxer permit power and cost analysis of this process and automate some aspects, by simulating the entire experiment from panel design to harvest rate estimation.     

The effect of ocean acidification on symbiont photorespiration and productivity in Acropora formosa

Ocean acidification is expected to lower the net accretion of coral reefs yet little is known about its effect on coral photophysiology. This study investigated the effect of increasing CO₂ on photosynthetic capacity and photoprotection in Acropora formosa. The photoprotective role of photorespiration within dinoflagellates (genus Symbiodinium) has largely been overlooked due to focus on the presence of a carbon‐concentrating mechanism despite the evolutionary persistence of a Form II Rubisco. The photorespiratory fixation of oxygen produces phosphoglycolate that would otherwise inhibit carbon fixation though the Calvin cycle if it were not converted to glycolate by phosphoglycolate phosphatase (PGPase). Glycolate is then either excreted or dealt with by enzymes in the photorespiratory glycolate and/or glycerate pathways adding to the pool of carbon fixed in photosynthesis. We found that CO₂ enrichment led to enhanced photoacclimation (increased chlorophyll a per cell) to the subsaturating light levels. Light‐enhanced dark respiration per cell and xanthophyll de‐epoxidation increased, with resultant decreases in photosynthetic capacity (P_nmax) per chlorophyll. The conservative CO₂ emission scenario (A1B; 600–790 ppm) led to a 38% increase in the P_nmax per cell whereas the ‘business‐as‐usual’ scenario (A1F1; 1160–1500 ppm) led to a 45% reduction in PGPase expression and no change in P_nmax per cell. These findings support an important functional role for PGPase in dinoflagellates that is potentially compromised under CO₂ enrichment.     

Interactions between fauna and sediment control the breakdown of plant matter in river sediments

1. A substantial portion of particulate organic matter (POM) is stored in the sediment of rivers and streams. Leaf litter breakdown as an ecosystem process mediated by microorganisms and invertebrates is well documented in surface waters. In contrast, this process and especially the implication for invertebrates in subsurface environments remain poorly studied. 2. In the hyporheic zone, sediment grain size distribution exerts a strong influence on hydrodynamics and habitability for invertebrates. We expected that the influence of shredders on organic matter breakdown in river sediments would be influenced strongly by the physical structure of the interstitial habitat. 3. To test this hypothesis, the influence of gammarids (shredders commonly encountered in the hyporheos) on degradation of buried leaf litter was measured in experimental systems (slow filtration columns). We manipulated the structure of the sedimentary habitat by addition of sand to a gravel‐based sediment column to reproduce three conditions of accessible pore volume. Ten gammarids were introduced in columns together with litter bags containing alder leaves at a depth of 8 cm in sediment. Leaves were collected after 28 days to determine leaf mass loss and associated microbial activity (fungal biomass, bacterial abundance and glucosidase, xylosidase and aminopeptidase activities). 4. As predicted, the consumption of buried leaf litter by shredders was strongly influenced by the sediment structure. Effective porosity of 35% and 25% allowed the access to buried leaf litter for gammarids, whereas a lower porosity (12%) did not. As a consequence, leaf litter breakdown rates in columns with 35% and 25% effective porosity were twice as high as in the 12% condition. Microbial activity was poorly stimulated by gammarids, suggesting a low microbial contribution to leaf mass loss and a direct effect of gammarids through feeding activity. 5. Our results show that breakdown of POM in subsurface waters depends on the accessibility of food patches to shredders.     

THE FISH AND AMPHIBIAN SWIMMING TRACES UNDICHNA AND LUNICHNIUM, WITH EXAMPLES FROM THE LOWER PERMIAN OF NEW MEXICO, USA

Abstract: The ichnotaxonomy and stratigraphic, geographic and environmental distribution of fish (Undichna) and amphibian (Lunichnium) swimming traces are reviewed. The ichnospecies of Undichna consist of various combinations of sinusoidal waves of differing complexity. Some of the more complex ichnospecies are made up of elements of the simpler forms, and morphological subset relationships between them are presented. Such subset series represent potential taphoseries relationships (i.e. preservational variants that reflect, for example, undertrails), or series of minor behavioural variations. Such a system can be used to highlight that different ichnospecies occurring at a locality may be taphonomic or minor behavioural variants of each other. Caution should, therefore, be exercised before erecting new ichnospecies on the basis of limited material if its morphology is a subset of an existing ichnospecies. However, the naming of such simpler ichnospecies is valid if they represent a recurrent morphology, and it is valid to erect new ichnospecies whose morphology is not a subset of an existing ichnospecies. Specimens that demonstrate intergradation between ichnotaxa can be used to justify their synonomy. Ichnotaxonomic revisions reduce the number of ichnospecies in Undichna from 14 to nine. U. radnicensis, a highly variable ichnospecies, is synonymized with U. britannica on the basis of material from China that demonstrates they can intergrade. U. prava is a partial U. tricosta, which falls within the minimum diagnosis of U. simplicitas. U. gosiutensis is regarded as a subjective junior synonym of U. quina. U. westerbergensis, originally attributed to a ‘crossopterygian’ fish performing a tetrapod‐like gait, is reassigned as a distinct ichnospecies within Lunichnium because it demonstrates the same morphology, representing similar behaviour, albeit by a different producer. L. anceps and L. gracile are synonymized with L. rotterodium. New specimens of U. bina and L. rotterodium are also described from the Lower Permian Robledo Mountains Formation of southern New Mexico, USA.     

Ten microsatellite loci for the small red‐eyed damselfly Erythromma viridulum (Charpentier)

The small red‐eyed damselfly, Erythromma viridulum (Charpentier), is the first recorded example of a migrant damselfly establishing colonies in the British Isles. To examine the population genetic structure of E. viridulum, a partial genomic library enriched for CA microsatellite loci was constructed. Of the 42 loci tested, 19 amplified spurious bands and 13 were monomorphic, leaving 10 polymorphic loci that resolved distinct alleles within the expected size range. The number of alleles ranged between two (LIST14‐021, LIST14‐40) and eight (LIST14‐002). Observed and expected heterozygosities varied between 0.000–0.698 and 0.045–0.688, respectively.     

Hydraulic microhabitats and the distribution of macroinvertebrate assemblages in riffles

1. The influence of hydraulic conditions on the spatial distribution of macroinvertebrate assemblages was investigated in three riffles in a perennial Australian river. 2. Velocity, depth and variability of substrate roughness were measured at each of 56 macroinvertebrate sampling locations. Complex hydraulic variables (roughness Reynolds number, shear velocity, Froude number) were calculated from combinations of two or three of the directly measured variables. The biological significance of directly measured and complex hydraulic variables was determined by a combination of univariate and multivariate statistical procedures. 3. Macroinvertebrate abundance, number of taxa and community composition were significantly different between the identified roughness Reynolds number, Froude number, velocity and shear velocity microhabitats throughout the studied riffles. 4. Regression analysis showed macroinvertebrate abundance and number of taxa were negatively related to roughness Reynolds number, shear velocity, velocity and Froude number. Depth was negatively related to abundance. In general, the majority of the macroinvertebrate community preferred the areas of riffles with the lowest near‐bed turbulence. 5. Roughness Reynolds number explained more of the spatial variation in invertebrate abundance, number of taxa and community composition than the other hydraulic variables, either directly measured or calculated. Of the directly measured variables, velocity had the greatest explanatory power, which was marginally less than roughness Reynolds number and shear velocity. 6. This study demonstrated that small‐scale differences in hydraulic conditions created by combinations of velocity, depth and substrate roughness have an important role in the spatial distribution of macroinvertebrate assemblages in riffle habitats.