Which strategy is better for linkage analysis: single-nucleotide polymorphisms or microsatellites? Evaluation by identity-by-state – identity-by-descent transformation affected sib-pair method on GAW14 data

Background

The genetics of plumage of Japanese quail is of interest both from a biological standpoint, for comparative studies between avian species, and from a zootechnical standpoint, for identifying commercial selection lines or crosses. There are only few plumage mutations reported in quail, and the present work describes a new color variant "rusty" and a new feather structure "curly", and their heredity from an F1 and F2 segregation experiment.

Results

Curly feathers result from abnormal early growth caused by transient joining of follicle walls of adjacent feathers around 10 days of age, but the expression of the trait is variable. Rusty plumage color results from the replacement of the wild-type plumage pattern on the tip of the feather by a reddish coloration, but the pigmentation of the bottom part of the feather is not affected. Two lines breeding true for the curly or the rusty phenotype were developed. Both characters are determined by autosomal recessive mutations which are independent. The curly mutation has also a positive effect on body weight at 5 weeks of age.

Conclusion

The curly line is a new model which may be used for further work on the growth of the feather, and the rusty mutation is a new addition to the panel of plumage mutations available for comparative studies in poultry, and more generally among avian species.     

Land-use changes assessed by overlay or mosaic methods: Which method is best for management planning?

Environmental planning must determine management practices for a given territory based on the landscape processes that have occurred over time and their consequences. Therefore, environmental planning decisions must be based on strong empirical evidence that can be easily understood by all involved parties. Several studies have highlighted the methodological deficiencies that occur when obtaining and interpreting such issues, particularly in heterogeneous landscapes with complex interactions. In this paper, we evaluated two methodological approaches that are used in management planning, land use/cover change (LUCC) and mosaic change (MC) to compare their effectiveness and suitability for supporting decision-making. We applied these methods to the coastal landscape of São Sebastião Island, Brazil, which has undergone many changes in the last 50 years. For two years, land use/cover maps were produced using GIS and assessed according to changes in landscape elements (LUCC) and boundaries (MC). Overall, the LUCC failed to identify sets with similar structural heterogeneities in the landscape. However, the LUCC is easier for stakeholders to understand and apply than the MC. The MC method better presented the evolution of the relationship between the landscape elements and heterogeneity.     

Native or nonnative host plants: What is better for a specialist moth?

The enemy release hypothesis (ERH) predicts that the lack of natural enemies, such as herbivores, contributes to the success of nonnative plants as colonizers. Larvae of the Neotropical specialist moth Utetheisa ornatrix (Erebidae: Arctiinae) can feed on unripe seeds and leaves of both native and nonnative Crotalaria species (Fabaceae). Despite some species being able to eat nonnative plants, such behavior can impair the herbivore, as they are not adapted to the alien plant, and still contribute to the success of the nonnative species via enemy release. We tested the performance of the moth from hatching to adulthood fed on two native (C. micans and C. paulina) and two nonnative (C. pallida, C. juncea) host plants. Utetheisa ornatrix performed better (lower development time, heavier pupae and more eggs) on the native host plants than in the nonnative. However, larva performance in nonnative C. pallida was similar to that in the native host plants. Using the larval weight 7 days after hatching from the eggs as a proxy for performance in twelve Crotalaria species (five Neotropical natives, four nonnatives from Afrotropical region, and three nonnatives from India), we found similar results. Crotalaria nutritional compounds, the defensive pyrrolizidine alkaloids and Crotalaria phylogeny did not explain moth performance. Our results give some support to the ERH. The good moth performance in nonnative C. pallida may be related to its high availability as host plant for U. ornatrix, and its longer time since their introduction in Neotropics which would provide opportunity for the moth to adapt.     

Fees or refuges: which is better for the sustainable management of insect resistance to transgenic Bt corn?

The evolution of resistance in insect pests will imperil the efficiency of transgenic insect-resistant crops. The currently advised strategy to delay resistance evolution is to plant non-toxic crops (refuges) in close proximity to plants engineered to express the toxic protein of the bacterium Bacillus thuringiensis (Bt). We seek answers to the question of how to induce growers to plant non-toxic crops. A first strategy, applied in the United States, is to require Bt growers to plant non-Bt refuges and control their compliance with requirements. We suggest that an alternative strategy is to make Bt seed more expensive by instituting a user fee, and we compare both strategies by integrating economic processes into a spatially explicit, population genetics model. Our results indicate that although both strategies may allow the sustainable management of the common pool of Bt-susceptibility alleles in pest populations, for the European corn borer (Ostrinia nubilalis) one of the most serious pests in the US corn belt, the fee strategy is less efficient than refuge requirements.     

Morphological versus acoustic analysis: what is the most efficient method for sexing yelkouan shearwaters Puffinus yelkouan?

Sexing monomorphic seabirds is particularly difficult, and available methods have various disadvantages, such as seasonal non-applicability or stress induction. The yelkouan shearwater Puffinus yelkouan is a poorly studied seabird endemic to the Mediterranean basin. Ecological and biological data are needed for this species, thus necessitating the development of appropriate field methods. Here, we tested two methods for sexing yelkouan shearwaters: the classical morphological method and a new acoustic method. Morphological analysis demonstrated sexual differences in head, leg and feather measurements, with a high degree of overlap resulting in only 87.2% accuracy. In contrast, acoustic analysis showed that the highest value of the fundamental frequency (FC) and duration of the clear note of calls did not overlap between males and females. Yelkouan shearwaters can be sexed with 100% accuracy by measuring FC. If FC < 678.4 Hz, the bird is female, while if FC > 678.4 Hz, the bird is male. Other advantages of this method are its simplicity and non-invasiveness, which are particularly important for a potentially threatened species.     

A meta‐analysis of isolation by distance: relic or reference standard for landscape genetics?

Isolation by distance (IBD) has been a common measure of genetic structure among populations and is based on Euclidean distances among populations. Whereas IBD does not incorporate geographic complexity (e.g. dispersal barriers, corridors) that may better predict genetic structure, a new approach (landscape genetics) joins landscape ecology with population genetics to better model genetic structure. Should IBD be set aside or should it persist as the most simple model in landscape genetics? We evaluated the status of IBD by collecting and analyzing results of 240 IBD data sets among diverse taxa and study systems. IBD typically represented a low proportion of variance in genetic structure (mean r²=0.22) in part because many studies included relatively few populations (mean=11). The number of populations studied (N) was asymptotically related to IBD significance; a study with 9 populations has only 50% probability of significance, while one with >23 populations will have 90% probability of significance. Surprisingly, ectothermic animals were significantly (p=0.0018) more likely to have significant IBD than endotherms, which suggests a metabolic basis underlying gene flow rates. We also observed marginally significant effects on IBD significance for a) taxa in general and b) dispersal modes within actively‐dispersing endotherms. Other factors analyzed (genetic markers, genetic distances, habitats, active or passive dispersal, plant growth form) did not significantly affect IBD, likely related to typical N. For multiple reasons we conclude that IBD should continue as the simplest reference standard against which all other, more complex models should be compared in landscape genetics research.     

Huh-7 or HepG2 cells: which is the better model for studying human apolipoprotein-B100 assembly and secretion?

Apolipoprotein-B100 (apoB100) is the essential protein for the assembly and secretion of very low density lipoproteins (VLDL) from liver. The hepatoma HepG2 cell line has been the cell line of choice for the study of synthesis and secretion of human apoB-100. Despite the general use of HepG2 cells to study apoB100 metabolism, they secrete relatively dense, lipid-poor particles compared with VLDL secreted in vivo. Recently, Huh-7 cells were adopted as an alternative model to HepG2 cells, with the implicit assumption that Huh-7 cells were superior in some respects of lipoprotein metabolism, including VLDL secretion. In this study we addressed the hypothesis that the spectrum of apoB100 lipoprotein particles secreted by Huh-7 cells more closely resembles the native state in human liver. We find that Huh-7 cells resemble HepG2 cells in the effects of exogenous lipids, microsomal triglyceride transfer protein (MTP)-inhibition, and proteasome inhibitors of apoB100 secretion, recovery, and degradation. In contrast to HepG2 cells, however, MEK-ERK inhibition does not correct the defect in VLDL secretion. Huh-7 cells do not appear to offer any advantages over HepG2 cells as a general model of human apoB100-lipoprotein metabolism.     

Pesticide or wastewater: Which one is a bigger culprit for acute health symptoms among vegetable growers in Pakistan's Punjab?

Literature highlights harmful effects of pesticides and untreated wastewater use on farmers' health but none of the studies explore the magnitude of deleterious health effects simultaneously. The objective of the study is to quantify pesticide and untreated wastewater induced health symptoms among vegetable growers and to investigate which one is a bigger culprit. A sample of 830 vegetable growers was selected by stratified random sampling from three major vegetable growing districts of Pakistan's Punjab. A two stage estimation technique is employed to estimate unbiased health effects of vegetable growers after controlling for pesticide endogeneity. The results demonstrate that both untreated wastewater and pesticide quantities are responsible for acute symptoms, but comparison of their scaled coefficients indicates that wastewater is twofold responsible for acute symptoms than pesticide. To minimize these negative effects, a policy of untreated disposal of wastewater in peri-urban areas for crop production needs to be re-designed. The installation of a treatment plant by collecting pollution premium from untreated wastewater emitters seems to be the most sustainable and practically viable option. It is also observed that pesticide is contributing to farmers' acute symptoms; hence, awareness campaigns about judicious and safe use of pesticides may help to mitigate acute symptoms.     

Phylloclimate or the climate perceived by individual plant organs: what is it? How to model it? What for?

This review introduces the emergence of a new research topic, phylloclimate, located at the crossroads between ecophysiology and canopy microclimate research. Phylloclimate corresponds to the physical environment actually perceived by each individual aerial organ of a plant population, and is described by physical variables such as spectral irradiance, temperature, on-leaf water and features of around-organ air (wind speed, temperature, humidity, etc.). Knowing the actual climate in which plant organs grow may enable advances in the understanding of plant-environment interactions, as knowing surface temperature instead of air temperature enabled advances in the study of canopy development. Characterizing phylloclimate variables, using experimental work or modeling, raises many questions such as the choice of suitable space- and time-scale as well as the ability to individualize plant organs within a canopy. This is of particular importance when aiming to link phylloclimate and function-structure plant models. Finally, recent trends and challenging questions in phylloclimate research are discussed, as well as the possible applications of phylloclimate results.     

Which one of the two common reporter systems is more suitable for chemiluminescent enzyme immunoassay: alkaline phosphatase or horseradish peroxidase?

Alkaline phosphatase and horseradish peroxidase are the most commonly used reporter systems in chemiluminescent enzyme immunoassay (CLEIA). Which one, therefore, would be better when establishing a CLEIA method for a new target substance? There was no standard answer. In this study, both reporters were compared systematically including luminescence kinetics, conjugation methods, optimal condition and detection performance, using two common drugs, SD‐methoxy‐pyrimidine and enrofloxacin, as determination objects. The results revealed that there was much difference between the luminescence kinetics of the two systems. However, there was little difference between these systems when detecting the same substance, including in optimal conditions and determination of performance. Both reporters were suitable for establishing chemiluminescent enzyme immunoassays. Therefore, the choice of alkaline phosphatase or horseradish peroxidase as the reporter system in chemiluminescent enzyme immunoassays depends on availability. Conversely, these two report systems could be applied in simultaneous analysis of multicomponents due to their different optical behaviors and similar performances. But attention should be paid to conjugation method and coating buffer, which affected the luminescent intensity of different determination targets. Copyright © 2015 John Wiley & Sons, Ltd.     

Diversity indices or floristic quality index: Which one is more appropriate for comparison of forest integrity in different land uses?

Zagros forest in Iran has been heavily altered by anthropogenic disturbances such as farming, grazing and other activities. In this study, we first estimated the herbaceous plants coefficient of conservatism within this region. Forest integrity of different land uses was then assessed by common measures of plant diversity and the indices were specifically developed to estimate vegetation integrity (conservatism coefficient, floristic quality index and modified floristic quality index). As complementary approaches, some soil physiochemical properties were applied to judge forest integrity. A total of 81, 82, 88, native species were recorded in understory grazing (UG), abandoned fields (AF), and protected area (PA) land uses, respectively. Common species had higher abundance in AF land use, whereas specialized species were found in PA land use. Diversity indices and modified floristic quality index values were higher in AF land use compared to UG and PA land uses, and fisher alpha diversity index highlighted the significant differences in the plant diversity among land uses, while PA land use had high species richness with greater number of sensitive species and floristic quality index. Soils under PA land use showed the highest organic carbon, nitrogen and pH. Based on results, floristic quality index and mean coefficient of conservatism can be more informative than species-diversity measures in assessing floristic integrity and in contradiction to diversity indices, are accurate tools to determine differences in the integrity of land uses. Results indicate that PA land use have indeed progressed ecologically toward a vigorous ecosystem as observed by the development of its vegetation community.     

Influence of nitrate on uptake of ammonium by nitrogen-depleted soybean: is the effect located in roots or shoots?

In non-nodulated soybean [Glycine max (L.) Merrill cv. Ransom]plants that were subjected to 15 d of nitrogen deprivation inflowing hydroponic culture, concentrations of nitrogen declinedto 1.0 and 1.4mmol Ng^–1 dry weight in shoots and roots,respectively, and the concentration of soluble amino acids (determinedas primary amines) declined to 40µmol g^–1 dry weightin both shoots and roots. In one experiment, nitrogen was resuppliedfor 10 d to one set of nitrogen-depleted plants as 1.0 mol m^–3NH₄⁺ to the whole root system, to a second set as 0.5 mol m^–3NH₄⁺ plus 0.5 mol m^–3 NO₃^– to the whole root system,and to a third set as 1.0 mol m^–3 NH₄⁺ to one-half ofa split-root system and 1.0 mol m^–3 NO₃^– to theother half. In a second experiment, 1.0 mol m^–3 of nitrogenwas resupplied for 4 d to whole root systems in NH₄⁺ : NO₃^–ratios of 1:0, 9:1, and 1:1. Nutrient solutions were maintainedat pH 6.0. When NH₄⁺ was resupplied in combination with NO₃^– to thewhole root system in Experiment I, cumulative uptake of NH₄⁺for the 10 d of resupply was about twice as great as when NH₄⁺was resupplied alone. Also, about twice as much NH₄⁺ as NO₃^–was taken up when both ions were resupplied to the whole rootsystem. When NH₄⁺ and NO₃^– were resupplied to separatehalves of a split-root system, however, cumulative uptake ofNH₄⁺ was about half that of NO₃^–. The uptake of NH₄⁺,which is inhibited in nitrogen-depleted plants, thus is facilitatedby the presence of exogenous NO₃^–, and the stimulatingeffect of NO₃^– on uptake of NH₄⁺ appears to be confinedto processes within root tissues. In Experiment II, resupplyof nitrogen as both NH₄⁺ and NO₃^– in a ratio of either1:1 or 9:1 enhanced the uptake of NH₄⁺. The enhancement of NH₄⁺uptake was 1.8-fold greater when the NH₄⁺: NO₃^–-resupplyratio was 1:1 than when it was 9:1; however, only 1.3 timesas much NO₃^– was taken up by plants resupplied with the1 :1 exogenous ratio. The effect of NO₃^– on enhancementof uptake of NH₄⁺ apparently involves more than net uptake ofNO₃^– itself and perhaps entails an effect of NO₃^–uptake on maintenance of K⁺ availability within the plant. Theconcentration of K⁺ in plants declined slightly during nitrogendeprivation and continued to decline following resupply of nitrogen.The greatest decline in K⁺ concentration occurred when nitrogenwas resupplied as NH₄⁺ alone. It is proposed that decreasedavailability of K⁺ within the NH₄⁺-resup-plied plants inhibitedNH₄⁺ uptake through restricted transfer of amino acids fromthe root symplasm into the xylem. Key words: Ammonium, Glycine max, nitrate, nitrogen-nutrition, nitrogen stress, split-root cultures     

Where is the pulse to have the finger on? A retrospective analysis of two decades of Alpine Galliforms (Aves: Galliformes) census and game bag data in Italy

Information on the abundance of the Italian populations of black grouse (Lyrurus tetrix), Alpine rock ptarmigan (Lagopus muta helvetica) and Alpine rock partridge (Alectoris graeca saxatilis) rely only on extrapolations of local data to the national scale, since there is no national standardized survey. Consequently, their status is virtually unknown. We performed a first-ever assessment of a medium-term (1996–2014) population trend of these species using and comparing post-breeding count and bag data at hunting district scale. These data were collected from various authorities in charge of wildlife management and allowed us to test the influence of hunting policies on the estimated trends. Rock partridge showed a stable trend with numbers fluctuating between years, while there was evidence of a severe decline for rock ptarmigan. No general conclusion could be drawn for the black grouse, as we detected lack of consistency of count and bag data. Counts were greatly overdispersed as a result of an uneven count effort among hunting districts. Adding the game management authority as model covariate resulted in more robust trend estimations, suggesting a significant effect of different policies that emerged also as similar hunting pressure across species within authorities. Hunting effort variation over the time was instead negligible. Species-specific game management bias is discussed. Our results highlight the need for a survey scheme or guidelines to be applied uniformly at a national scale.     

Expression analysis of some genes regulated by retinoic acid in controls and triadimefon‐exposed embryos: is the amphibian Xenopus laevis a suitable model for gene‐based comparative teratology?

BACKGROUND: The use of nonmammal models in teratological studies is a matter of debate and seems to be justified if the embryotoxic mechanism involves conserved processes. Published data on mammals and Xenopus laevis suggest that azoles are teratogenic by altering the endogenous concentration of retinoic acid (RA). The expression of some genes (Shh, Ptch‐1, Gsc, and Msx2) controlled by retinoic acid is downregulated in rat embryos exposed at the phylotypic stage to the triazole triadimefon (FON). In order to propose X. laevis as a model for gene‐based comparative teratology, this work evaluates the expression of Shh, Ptch‐1, Gsc, and Msx2 in FON‐exposed X. laevis embryos. METHODS: Embryos, exposed to a high concentration level (500 µM) of FON from stage 13 till 17, were examined at stages 17, 27, and 47. Stage 17 and 27 embryos were processed to perform quantitative RT‐PCR. RESULTS: The developmental rate was never affected by FON at any considered stage. FON‐exposed stage 47 larvae showed the typical craniofacial malformations. A significant downregulation of Gsc was observed in FON‐exposed stage 17 embryos. Shh, Ptch‐1, Msx2 showed a high fluctuation of expression both in control and in FON‐exposed samples both at stages 17 and 27. CONCLUSION: The downregulation of Gsc mimics the effects of FON on rat embryos, showing for this gene a common effect of FON in the two vertebrate classes. The high fluctuation observed in the gene expression of the other genes, however, suggests that X. laevis at this stage has limited utility for gene‐based comparative teratology. Birth Defects Res (Part B) 92:189–194, 2011. © 2011 Wiley‐Liss, Inc.