Sensitivity of methods for estimating breeding values using genetic markers to the number of QTL and distribution of QTL variance

The objective of this simulation study was to compare the effect of the number of QTL and distribution of QTL variance on the accuracy of breeding values estimated with genomewide markers (MEBV). Three distinct methods were used to calculate MEBV: a Bayesian Method (BM), Least Angle Regression (LARS) and Partial Least Square Regression (PLSR). The accuracy of MEBV calculated with BM and LARS decreased when the number of simulated QTL increased. The accuracy decreased more when QTL had different variance values than when all QTL had an equal variance. The accuracy of MEBV calculated with PLSR was affected neither by the number of QTL nor by the distribution of QTL variance. Additional simulations and analyses showed that these conclusions were not affected by the number of individuals in the training population, by the number of markers and by the heritability of the trait. Results of this study show that the effect of the number of QTL and distribution of QTL variance on the accuracy of MEBV depends on the method that is used to calculate MEBV.     

Migration of wild and captive‐bred Little Bustards Tetrax tetrax: releasing birds from Spain threatens attempts to conserve declining French populations

Populations of the Little Bustard Tetrax tetrax in the farmlands of Europe have declined greatly over the last century. In Western Europe, France now holds the only remaining migratory population, which currently numbers fewer than 300 displaying males. However, the movements of these birds are virtually unknown, in spite of the important implications of this information for the conservation of this species. We identified migratory movements and overwintering areas of French migratory populations, using wild individuals fitted with satellite or radio‐transmitters. Little Bustards completed their migration journey over a relatively short time period (2–5 days), with nocturnal migration flights of 400–600 km per night. All birds overwintered in Iberia. In addition, we tested the consequences of captive rearing on migratory movements. French wild adults and French captive‐bred juveniles behaved similarly with regard to migration, suggesting that hand‐raising does not alter migratory movements. However, birds originating from eggs collected in Spain and reared in western France did not migrate, suggesting a genetic component to migratory behaviour. These results therefore suggest that a conservation strategy involving the release in France of birds hatched from eggs collected in Spain may imperil the expression of migratory movements of the French population. More generally, to maintain the integrity of native populations, the introduced individuals should mimic their migratory movements and behaviour.     

Multi-scale assessment of macroinvertebrate richness and composition in Mediterranean-climate rivers

1. Similar constraints in distant, but climatically comparable, regions may be expected to yield biotic assemblages with similar attributes. Environmental factors that constrain communities at smaller scales, however, may be different between climatically similar regions. Thus, patterns observed at large scales may differ from those detected at small scales, and international comparisons should be focussed at multiple scales. 2. Mediterranean‐climate regions (MCRs) are characterized by remarkable seasonal variability in precipitation and temperature. Accordingly, rivers in these regions have seasonal and predictable floods and droughts, and temporary reaches are frequent. Present in six geographical regions of the world, MCRs have similar environmental constraints and are ideal for testing intercontinental similarities between macroinvertebrate communities. 3. We examined aquatic macroinvertebrate taxon richness and composition in MCRs at three scales: regional, reach and macrohabitat. At the regional scale, the Mediterranean Basin had the highest taxon richness at family level, and southwestern Australia the lowest. Taxonomic composition showed c. 85% similarity between the northern hemisphere MCRs of California and the Mediterranean Basin, which were followed in similarity by South Africa. The two Australian MCRs (South west and South) showed a similarity to each other of about 70% whereas the Chilean fauna was the most distinct. 4. At the reach scale, taxon richness was not significantly different between permanent and temporary reaches in any MCR, whereas taxonomic composition was significantly different among northern hemisphere MCRs. At the macrohabitat scale, taxon richness was not significantly different between lotic and lentic macrohabitats within any of the MCRs, but differences in macroinvertebrate communities were found between macrohabitats when considering regions. 5. Our results show that the strength of similarity between distant but climatically similar regions is scale‐dependent, being highest at the macrohabitat scale. Although the similarities in richness and composition at the macrohabitat scale are presumed to be universal, the seasonal predictability of drought in MCRs is expected to result in characteristic macroinvertebrate responses at the reach scale. We suggest, however, that regional evolutionary history and environmental characteristics may override this general pattern of a similar response of MCRs at different scales. The Mediterranean Basin and California, having similar historical and environmental condition, thus appeared as the most similar MCRs at all scales.     

Abundance Estimation With a Transient Model Under the Robust Design

Abstract: A common situation in capture-mark-recapture (CMR) studies on birds and other organisms is to capture individuals not belonging to the studied population only present during the short time of the capture session. Presence of such transient individuals affects demographic parameter estimation from CMR data. Methods exist to reduce biases on survival estimates in the presence of transients and have been shown to be particularly efficient within the Robust Design framework (several secondary capture sessions within a short time interval during which the studied population can be assumed closed). We present a new model to estimate population size accounting for transients. We first used simulated data to show that the method reduces positive biases due to transients. In a second step, we applied the method to a real CMR dataset on a reed warbler (Acrocephalus scirpaceus) population. Population size estimates are reduced by up to 50% when correcting for the presence of transients. Many field studies on managed animal populations use capture-recapture methodology to obtain crucial parameters of the focal population demography. The resulting data sets are used either to estimate population size ignoring the presence of transients, or to estimate vital rates, accounting for transients but overlooking abundance estimation. Our method conciliates these 2 approaches.     

Periphyton responses to invertebrate grazing and riparian canopy in three northern California coastal streams

SUMMARY. 1. Field experiments were conducted to examine the impact of grazing invertebrates on periphyton biomass in twenty-one pools across three northern California coastal streams (U.S.A.): Big Sulphur Creek, the Rice Fork of the Eel River, and Big Canyon Creek. Periphyton accrual on artificial substrate tiles was compared in each stream between two treatments: those elevated slightly above the stream bottom to reduce access by grazers (= platforms) and those placed directly on the stream bottom to allow access by grazers (=controls).
2. Crawling invertebrate grazers (cased caddisflies and snails) were numerically dominant in each stream (86% of all grazers in Big Sulphur Creek, 61% in the Rice Fork, 84% in Big Canyon Creek). Platforms effectively excluded crawling grazers, but were less effective in excluding swimming mayfly grazers (Baetidae).
3. Periphyton biomass (as AFDM) on tiles was significantly lower on controls compared to platforms for the Rice Fork, an open-canopy stream, and Big Sulphur Creek, a stream with a heterogeneous canopy. In contrast, no grazer impact was found for Big Canyon Creek, a densely shaded stream. Here, extremely low periphyton biomass occurred for both treatments throughout the 60 day study.
4. The influence of riparian canopy on periphyton growth (i.e. accrual on platforms), grazer impact on periphyton, and grazer abundance was examined for Big Sulphur Creek. As canopy increased (15–98% cover), periphyton biomass on platforms decreased. In contrast, canopy had little influence on periphyton accrual on controls; apparently, grazers could maintain low periphyton standing crops across the full range of canopy levels. The abundance of one grazer species, the caddisfly Gumaga nigricula , was highest in open, sunlit stream pools; abundance of two other prominent grazers, Helicopsyche borealis (Trichoptera) and Centroptilum convexum (Ephemeroptera), however, was unrelated to canopy.     

Functional Properties of Cloned Melanogenic Proteins

Several genes critical to the regulation of melanin production in mammals have recently been cloned and characterized. They map to the albino, brown, and slaty loci in mice, and encode proteins with similar structures and features, but with distinct catalytic capacities. The albino locus encodes tyrosinase, an enzyme with three distinct catalytic activities—tyrosine hydroxylase, 3,4-dihydroxyphenylalanine (DOPA) oxidase and DHI (5,6-dihydroxyindole) oxidase. The brown locus encodes TRP-l (tyrosinase-related protein-I), which has the same, but greatly reduced, catalytic potential. The slaty locus encodes TRP-2, another tyrosinase related-protein, which has DOPAchrome tautomerase activity. In this study we have examined the enzymatic interactions of these proteins, and their regulation by a novel melanogenic inhibitor. We observed that tyrosinase activity is more stable in the presence of TRP-l and/or TRP-2, but that the catalytic function of TRP-2 is not affected by the presence of TRP-1 or tyrosinase. Other factors also may influence melanogenesis and a unique melanogenic inhibitor suppresses tyrosinase and DOPAchrome tautomerase activities, but does not affect the spontaneous rate of DOPAchrome decarboxylation to DHI. The results demonstrate the catalytic functions of these proteins and how they stably interact within a melanogenic complex in the melanosome to regulate the quantity and quality of melanin synthesized by the melanocyte.