Improving estimates of population status and trend with superensemble models

Fishery managers must often reconcile conflicting estimates of population status and trend. Superensemble models, commonly used in climate and weather forecasting, may provide an effective solution. This approach uses predictions from multiple models as covariates in an additional “superensemble” model fitted to known data. We evaluated the potential for ensemble averages and superensemble models (ensemble methods) to improve estimates of population status and trend for fisheries. We fit four widely applicable data‐limited models that estimate stock biomass relative to equilibrium biomass at maximum sustainable yield (B/B_MSY). We combined these estimates of recent fishery status and trends in B/B_MSY with four ensemble methods: an ensemble average and three superensembles (a linear model, a random forest and a boosted regression tree). We trained our superensembles on 5,760 simulated stocks and tested them with cross‐validation and against a global database of 249 stock assessments. Ensemble methods substantially improved estimates of population status and trend. Random forest and boosted regression trees performed the best at estimating population status: inaccuracy (median absolute proportional error) decreased from 0.42 – 0.56 to 0.32 – 0.33, rank‐order correlation between predicted and true status improved from 0.02 – 0.32 to 0.44 – 0.48 and bias (median proportional error) declined from ?0.22 – 0.31 to ?0.12 – 0.03. We found similar improvements when predicting trend and when applying the simulation‐trained superensembles to catch data for global fish stocks. Superensembles can optimally leverage multiple model predictions; however, they must be tested, formed from a diverse set of accurate models and built on a data set representative of the populations to which they are applied.     

Preventing species invasion: A role for integrative taxonomy?

Integrative taxonomy, a multi‐disciplinary approach adding modern techniques to traditional morphology‐based methods (e.g. molecular and morphological criteria), can play an important role in bioinvasion research to identify introduced taxa, discover pathways of introduction and inform authorities to control and prevent future introductions. The present study is the first on introduced populations of Callosciurus, Asiatic tree squirrels, known as potentially invasive species in Europe (Italy, Belgium and France). We combined molecular (mitochondrial DNA markers: CoxI, D‐loop) and morphometric analysis on skulls, comparing them to the widest morphological and molecular datasets ever assembled for Callosciurus. Squirrels collected in Italy and Belgium share the same haplotypes and skull characteristics, but are conspicuously different from the French population in Antibes. Genetic data revealed close similarity between French squirrels and Pallas's squirrels, Callosciurus erythraeus, from Taiwan, China. Italian and Belgian squirrels formed an independent taxonomic lineage in genetic analyses, whose taxonomic rank needs further investigation. The morphological and morphometric characteristics of these 2 populations are, however, similar to known specimens assigned to Callosciurus erythraeus. These results may indicate a common origin for the populations found in Belgium and Italy. In contrast, French specimens suggest an independent introduction event of squirrels originating from Asia.     

Ultrasonographic differentiation between portal venous and parenchymal gas may be important for the prognosis of canine and feline hepatic emphysema: 37 cases

The aim of this retrospective, cross‐sectional, study was to evaluate clinical findings and outcomes for different ultrasonographic patterns of hepatic emphysema in dogs and cats. Dogs and cats with an ultrasonographic diagnosis of hepatic emphysema and a known outcome, from January 2010 to January 2018, were enrolled. The following data were recorded from medical and ultrasonographic records: ultrasonographic patterns of hepatic emphysema (parenchymal, portal venous, biliary), clinical signs, laboratory findings, and outcomes (favorable, poor). A total of 33 dogs and four cats met the inclusion criteria. Among these, 23 cases were classified as hepatic portal venous gas, 10 as parenchymal emphysema, and four as biliary emphysema. Clinical diagnosis categories were as follows: infection/sepsis (9), gastro‐intestinal disease (9), iatrogenic (9), trauma (5), and liver neoplasia (5). An increase in serum liver enzymes was significantly associated with parenchymal emphysema (P = .03). Other clinical and laboratory findings were not associated with the type of hepatic emphysema. Hepatic portal venous gas was mostly transient in patients with ultrasonographic follow‐up. The overall mortality was 40.5%. A significant difference was found between mortality by portal venous gas (21.7%) and mortality by parenchymal emphysema (90%) (P = .003). In conclusion, the ultrasonographic differentiation of hepatic emphysema between hepatic portal venous gas and parenchymal emphysema may be important for the prognosis of hepatic emphysema. The presence of parenchymal emphysema may be a poor prognostic indicator, while hepatic portal venous gas may be more benign. However, ultrasound findings should be carefully evaluated in the context of clinical findings.     

Soil pyrogenic organic matter characterisation by spectroscopic analysis: a study on combustion and pyrolysis residues

Purpose

Pyrogenic organic matter (PyOM) in the soil of a maritime pine forest in Central Italy, formed during a fire of high severity, was characterised by Fourier transform infrared (FT-IR) and ¹³C nuclear magnetic resonance (NMR). Furthermore, soil samples from burnt and unburnt sampling sites and natural charcoal collected from the ground were characterised after progressive heating under air and nitrogen atmosphere. The aim was to better understand the role fire plays on PyOM formation and oxidation.

Materials and methods

The top 10 cm of mineral soil and the above-lying charcoal particles were collected soon after the fire. Sampling was also performed on an adjacent unburnt portion of the forest. The bulk soil organic matter (SOM), its extractable fraction and charcoal particles were investigated by FT-IR and ¹³C NMR spectroscopies. They also underwent thermogravimetric analysis under air or N₂, stopping the thermal reactions at the end of the first exothermic reaction in the range 350–500 °C.

Results and discussion

The NMR investigation clearly revealed a significant enrichment in aromatic and alkyl C in the burnt soil compared to the unburnt one. Several clues led to hypothesise that SOM was not exposed to extreme heating during the fire, notwithstanding the high fire severity estimated by a vegetation-based visual scale. In the thermal treatment mimicking fire, charcoal lost much of its mass and carbon content. However, at 500 °C, it still maintained a significant recalcitrant fraction. Nitrogen concentration in the bulk soil increased after heating, particularly under air condition. This phenomenon could be due to the formation of heterocyclic nitrogen compounds in the charred material.

Conclusions

In the study area, PyOM is rich in aliphatic compounds presumably because of the understory sclerophyllous vegetation typically found in Mediterranean environments. A large fraction of the charcoal released to the soil during the fire is sensitive to oxidation by subsequent fires. On the other hand, charcoal preserves a significant fraction of C, the most recalcitrant one, with expected long residence time in soil. PyOM formed under high oxygen availability is richer in N than that formed in inert atmosphere, which might make PyOM more susceptible to biochemical degradation.

     

Clues to the genesis of a discontinuously distributed fragipan in the northern Apennines,Italy

At about 1000 m above sea level in the Vallombrosa Forest, northern Apennines, Central Italy, a dense pan that meets the diagnostic criteria for fragipans is discontinuously distributed. The unusual slope-parallel “digitate” distribution of the pan suggests that it could have formed on water-saturated soil material that moved as earthflows. Actually, several soils in the Vallombrosa Forest have buried or truncated horizons, indicating episodes of mass movement and deposition. However, the fragipan under study shows a homogeneous morphology throughout, hence not providing clues about the occurrence of episodes that have contributed to the emplacement of the parent material. Also, the physical, chemical, and mineralogical analyses of the fragipan do not reveal discontinuities that help to resolve distinct episodes of deposition. Nevertheless, discontinuities in features such as the degree of alteration of biotite grains and the amount of plasma, seen through the micromorphological investigation at 50–60 cm of the current depth, suggest the occurrence of at least two depositional events. Radiocarbon dating of large-size pieces of charcoal collected at three depths within the fragipan yielded three ages that may reflect different times of accumulation of the parent material during the last glacial period. Post-depositional micromorphological features, such as relatively undamaged clay coatings and a weak platy structure, indicate pedogenesis with the absence of intense pedoturbation.     

Determination of Ni (II) in beverages without any sample pretreatment by adsorptive stripping chronopotentiometry (AdSCP)

The purpose of this paper was to use adsorptive stripping chronopotentiometry for the determination of Ni (II) in worldwide consumed beverages without any sample pretreatment, using dimethilglyoxime (DMG) as complexing agent and a glassy carbon mercury film electrode as the working electrode. Ni (DMG)2 complex is adsorbed onto the mercury film at an electrolysis potential of -500 mV for 60 s and then reduced by a -5 microA constant cathodic current. The sensitivity of the method was studied for certified reference water and black tea in the pH range 6.5-11. At pH 9.5 in ammonia buffer, a detection limit of 0.2 microg L(-1) was achieved; the instrumental precision (expressed as rsd %) was 1.5%, and the accuracy, expressed as obtained recoveries both from certified and not certified matrixes, ranged from 93.0 to 95.5 %. The chronopotentiometric analysis executed on commercial beverages provided evidence that black tea samples were the richest source of Ni (II) (1500-3700 microg L(-1)), followed by coffee (100.0-300.5 microg L(-1)); bottled mineral water showed a Ni (II) concentration lower than 4.6 microg L(-1). Among alcoholic beverages, red wines presented the highest content of Ni (II) (55.5-105.0 microg L(-1)). Significant differences were noticed between Ni (II) levels of fermented and distillated alcoholic beverages; moreover, canned cola and beer did not show higher Ni (II) levels with respect to the glass-bottled products.     

Characterization of carrot root oil arising from supercritical fluid carbon dioxide extraction

Carrot root oil (SCO), obtained by supercritical fluid carbon dioxide (SC-CO2) extraction, was characterized and compared to a commercial carrot oil (MCO) and a virgin olive oil (VOO) (cv. Coratina). SCO showed much higher contents of carotenes, phenolics, waxes, phytosterols, and sesquiterpene and monoterpene volatiles. In SCO, the most prominent components present in the fully investigated analytical fractions (fatty acids, triglycerides, waxes, phytosterols, long-chain aliphatic alcohols, superior triterpene alcohols, and volatiles) were, respectively, linolenic acid, trilinolein, waxes C38, beta-sitosterol, campesterol and stigmasterol, 1-hexacosanol, 24-methylencycloartanol and cycloartenol, beta-caryophyllene, alpha-humulene, alpha-pinene, and sabinene. In VOO, the major constituents of the above analytical classes were, respectively, oleic acid, trilinolein, waxes C36, unsaturated volatile C6 aldehydes (trans-2-hexenal most markedly), and the same prominent sterols and superior alcohols found in SCO. In MCO, which also contained a proportion of unknown plant oil, several components showed magnitudes that were lower compared to SCO but higher with respect to VOO. The last had the aliphatic and triterpene alcohol concentration higher compared to that of both SCO and MCO. Several chemometric methods, applied to different analytical data sets, proved to be effective in grouping the three oil kinds.