Methods to account for spatial autocorrelation in the analysis of species distributional data: a review

Species distributional or trait data based on range map (extent‐of‐occurrence) or atlas survey data often display spatial autocorrelation, i.e. locations close to each other exhibit more similar values than those further apart. If this pattern remains present in the residuals of a statistical model based on such data, one of the key assumptions of standard statistical analyses, that residuals are independent and identically distributed (i.i.d), is violated. The violation of the assumption of i.i.d. residuals may bias parameter estimates and can increase type I error rates (falsely rejecting the null hypothesis of no effect). While this is increasingly recognised by researchers analysing species distribution data, there is, to our knowledge, no comprehensive overview of the many available spatial statistical methods to take spatial autocorrelation into account in tests of statistical significance. Here, we describe six different statistical approaches to infer correlates of species’ distributions, for both presence/absence (binary response) and species abundance data (poisson or normally distributed response), while accounting for spatial autocorrelation in model residuals: autocovariate regression; spatial eigenvector mapping; generalised least squares; (conditional and simultaneous) autoregressive models and generalised estimating equations. A comprehensive comparison of the relative merits of these methods is beyond the scope of this paper. To demonstrate each method's implementation, however, we undertook preliminary tests based on simulated data. These preliminary tests verified that most of the spatial modeling techniques we examined showed good type I error control and precise parameter estimates, at least when confronted with simplistic simulated data containing spatial autocorrelation in the errors. However, we found that for presence/absence data the results and conclusions were very variable between the different methods. This is likely due to the low information content of binary maps. Also, in contrast with previous studies, we found that autocovariate methods consistently underestimated the effects of environmental controls of species distributions. Given their widespread use, in particular for the modelling of species presence/absence data (e.g. climate envelope models), we argue that this warrants further study and caution in their use. To aid other ecologists in making use of the methods described, code to implement them in freely available software is provided in an electronic appendix.     

Abrolhos bank reef health evaluated by means of water quality, microbial diversity, benthic cover, and fish biomass data

The health of the coral reefs of the Abrolhos Bank (Southwestern Atlantic) was characterized with a holistic approach using measurements of four ecosystem components: (i) inorganic and organic nutrient concentrations, [1] fish biomass, [1] macroalgal and coral cover and (iv) microbial community composition and abundance. The possible benefits of protection from fishing were particularly evaluated by comparing sites with varying levels of protection. Two reefs within the well-enforced no-take area of the National Marine Park of Abrolhos (Parcel dos Abrolhos and California) were compared with two unprotected coastal reefs (Sebasti?o Gomes and Pedra de Leste) and one legally protected but poorly enforced coastal reef (the "paper park" of Timbebas Reef). The fish biomass was lower and the fleshy macroalgal cover was higher in the unprotected reefs compared with the protected areas. The unprotected and protected reefs had similar seawater chemistry. Lower vibrio CFU counts were observed in the fully protected area of California Reef. Metagenome analysis showed that the unprotected reefs had a higher abundance of archaeal and viral sequences and more bacterial pathogens, while the protected reefs had a higher abundance of genes related to photosynthesis. Similar to other reef systems in the world, there was evidence that reductions in the biomass of herbivorous fishes and the consequent increase in macroalgal cover in the Abrolhos Bank may be affecting microbial diversity and abundance. Through the integration of different types of ecological data, the present study showed that protection from fishing may lead to greater reef health. The data presented herein suggest that protected coral reefs have higher microbial diversity, with the most degraded reef (Sebasti?o Gomes) showing a marked reduction in microbial species richness. It is concluded that ecological conditions in unprotected reefs may promote the growth and rapid evolution of opportunistic microbial pathogens.     

The high diversity of <Emphasis Type="Italic">Lotus corniculatus</Emphasis> endosymbionts in soils of northwest Spain

The diversity of rhizobia that establish symbiosis with Lotus corniculatus has scarcely been studied. Several species of Mesorhizobium are endosymbionts of this legume, including Mesorhizobium loti, the type species of this genus. We analysed the genetic diversity of strains nodulating Lotus corniculatus in Northwest Spain and ten different RAPD patterns were identified among 22 isolates. The phylogenetic analysis of the 16S rRNA gene showed that the isolated strains belong to four divergent phylogenetic groups within the genus Mesorhizobium. These phylogenetic groups are widely distributed worldwide and the strains nodulate L. corniculatus in several countries of Europe, America and Asia. Three of the groups include the currently described Mesorhizobium species M. loti, M. erdmanii and M. jarvisii which are L. corniculatus endosymbionts. An analysis of the recA and atpD genes showed that our strains belong to several clusters, one of them very closely related to M. jarvisii and the remanining ones phylogenetically divergent from all currently described Mesorhizobium species. Some of these clusters include L. corniculatus nodulating strains isolated in Europe, America and Asia, although the recA and atpD genes have been sequenced in only a few L. corniculatus endosymbionts. The results of this study revealed great phylogenetic diversity of strains nodulating L. corniculatus, allowing us to predict that even more diversity will be discovered as further ecosystems are investigated.     

Cutaneous metastasis of occult hepatocellular carcinoma: a case report

BACKGROUND: Skin metastases from hepatocellular carcinoma (HCC) represented only 0.8% of all known cutaneous metastases in a recent large series. The most frequent site appears to be the head, but this fact has received little attention. An accurate cytologic diagnosis is extremely difficult in patients with unknown liver dysfunction. We report the cytologic features of a face metastasis from occult HCC. CASE: A 65-year-old woman presented with a mass in the right preauricular region of 2 months' duration. Her past medical history was noncontributory. Fine needle aspiration cytology was performed. Following the cytologic diagnosis, computed tomography revealed a 6-cm mass in the right lobe of the liver, portal vein thrombosis and involvement of the superior vena cava. The smears were very cellular. The most frequent pattern was trabecular with transmural endothelization. The cells had an epithelial appearance and polyhedral shape, exhibiting distinct borders. The nuclei were centrally placed, with a prominent nucleolus. The cytoplasm was granular. There were numerous atypical bare nuclei. Subsequent staining with antihepatocyte showed positivity in most tumor cells. The final diagnosis was metastatic HCC. CONCLUSION: HCCs should be considered in the differential diagnosis of carcinomas metastatic to the face, even in the absence of liver symptoms.     

Immunogenicity and safety assessment of the Cuban recombinant hepatitis B vaccine in healthy adults.

Manufactures of biotechnological/biological products (including vaccines) frequently make changes to manufacturing processes of products both during development and after approval. In our case, a non-inferiority bridging study was carried out to demonstrate that changes in the production plant facilities of Cuban recombinant hepatitis B vaccine, Heberbiovac HB, did not affect the safety and immunogenicity of the vaccine. This controlled, randomized, doubled-blinded trial included 501 volunteers, aged between 20 and 64, who were given three doses of vaccine (20 microg HBsAg/mL) at month 0, 1, and 2. Four lots were evaluated (three corresponding to the new production facilities and a control one produced in the older facilities). One month after the third dose, were observed protective levels of anti-HBsAg in 97% of the subjects that concluded the study with a geometric mean antibody titer (GMT) of 931.18 IU/L. Normal values of body mass index (BMI), the younger ages, and being a female, were significantly related to a good antibody response. The vaccine was well tolerated. Pain at the injection site was the most commonly reported symptom. We conclude that Heberbiovac HB vaccine maintains its characteristics after the modifications carried out in the production plant facilities and both, lot obtained in previous facilities and in the new ones, are comparable in terms of safety and immunogenicity.     

Daily rhythms of leukocytes populations,biochemical and enzymatic blood parameters in a carnivorous freshwater catfish (Lophiosilurus alexandri)

The aim of this study was to investigate the daily rhythms of hematological, biochemical and enzymatic parameters of the blood of a nocturnal model of fish (Lophiosilurus alexandri) bred in the laboratory (F1). Thirty-six juveniles were stocked in six tanks of a recirculation aquaculture system for 20 days. The fish were exposed to a light:dark cycle of 12:12 h and were fed 1% of biomass twice a day with commercial diet. The daily rhythms of hematological, biochemical and enzymatic parameters were then measured at six sampling times “zeitgeber time = ZT” at four-hour intervals under light:dark 12:12 h (lights on = ZT0, at 8.00 a.m). No differences were observed to alkaline phosphatase, glucose, cortisol, aspartate aminotransferase, superoxide dismutase, total protein and hematocrit (p > 0.05). However, white blood cell count, Lymphocytes (LYN), Neutrophils (NEU), Eosinophil and Neutrophils to Lymphocytes ratio were significant different between sample times (p < 0.05). Also, a significant difference in alanine transaminase was observed, with a peak of production at nighttime. In contrast, glutathione peroxidase peaked at 8:00. Uric acid, magnesium and Calcium (Ca⁺⁺) showed statistically significant differences (p < 0.05). A significant difference was observed (p < 0.05), with a peak of albumin at 08:00 and triglycerides at 12:00, while cholesterol was low (p < 0.05) at 08:00 and higher from 12:00 to 04:00. Cosinor analysis revealed also rhythmicity to SOD, UA, Mg and Ca⁺⁺, ALB and CHO (p < 0.05). In conclusion, the time of day must be considered a key factor when using blood parameters as biomarkers for disease, health and welfare in the L. alexandri aquaculture.     

Biocontrol of grey mould by Ulocladium atrum applied at different flower and fruit stages of strawberry

Grey mould is an important disease ofstrawberries resulting from flower and fruitinfection by Botrytis cinerea Pers. Thesaprophytic fungus Ulocladium atrumPreuss is a promising biological controlagent for control of B. cinerea instrawberry and other crops. The objective ofthis research was to determine the efficacy ofU. atrum to control grey mould by asingle application of a spore suspension (2 ×10⁶ conidia/ml) at different flowerand fruit development stages. Four experimentswere carried out in 1999, two under natural andtwo under enhanced inoculum levels of B.cinerea. In each experiment, flowers and youngfruits in six distinct stages of developmentwere sprayed with either water or U.atrum suspension. U. atrum suppressedB. cinerea sporulation on petals by 15 to54%. One to four days after spraying, U.atrum was present on less than 30% of stamensand did not affect the incidence of B.cinerea on these flower parts. The efficacy ofthe U. atrum sprays in controlling greymould was low to moderate, and resulted onaverage in a reduction of 21% in diseaseincidence on ripe fruits. Low control efficacywas probably due to poor coverage with orcolonisation of stamens by U. atrumspores, and a relatively low level ofsuppression of the colonisation of flower partsby B. cinerea. Significant reductions ofgrey mould in comparison to the control(p 0.10; on average 41% reduction) werefound most frequently when the antagonist wasintroduced at late flowering or early fruitstages. Therefore, these are the most suitablestages to apply U. atrum. Further studiesare needed to improve the spray coverage andpersistence of U. atrum inoculum.     

Genetic demography of Antioquia (Colombia) and the Central Valley of Costa Rica

We report a comparative genetic characterization of two population isolates with parallel demographic histories: the Central Valley of Costa Rica (CVCR) and Antioquia (in northwest Colombia). The analysis of mtDNA, Y-chromosome and autosomal polymorphisms shows that Antioquia and the CVCR are genetically very similar, indicating that closely related parental populations founded these two isolates. In both populations, the male ancestry is predominantly European, whereas the female ancestry is mostly Amerind. In agreement with their isolation, the Amerindian mtDNA diversity of Antioquia and the CVCR is typical of ethnically-defined native populations and is markedly lower than in other Latin American populations. A comparison of linkage disequilibrium (LD) at 18 marker pairs in Antioquia and the CVCR shows that markers in LD in both populations are located at short genetic distances (相似文献   

The daily variations of airborne fungal spores in Mexico City

The daily and seasonal distribution of airborne fungal particles was recorded in a high altitude tropical zone. Sampling was carried out in the southern part of Mexico City. An Andersen air sampler was used over a period of six months. Ten minutes sampling for each set of plates was done at fixed schedule: 07:30, 14:00 and 19:00 hours. The sampler was placed 10 m above the ground. Daily variation was found to be associated with the season, weather and atmospheric stability. The highest value of mold counts (3195 CFU m⁻³) was recorded in the evening on October, a transitional month between the rainy and the dry seasons, the lowest (45 CFU m⁻³) at noon during the rainy season. Mold counts were significantly correlated with temperature, having negative signs both in the morning and at noon, and being positive in the evening. The abundance of only three genera was recorded.Cladosporium, was isolated more frequently, and its abundance at 14:00 h was of 38%;Alternaria represented 4.0%, at 14:00 h, andAspergillus 3.0% at 7:30 h. Fifteen species belonging to the latter genera were identified and most of them are considered as opportunistic molds of clinical significance.