On the path to extinction: Inbreeding and admixture in a declining grey wolf population

Allee effects reduce the viability of small populations in many different ways, which act synergistically to lead populations towards extinction vortexes. The Sierra Morena wolf population, isolated in the south of the Iberian Peninsula and composed of just one or few packs for decades, represents a good example of how diverse threats act additively in very small populations. We sequenced the genome of one of the last wolves identified (and road‐killed) in Sierra Morena and that of another wolf in the Iberian Wolf Captive Breeding Program and compared them with other wolf and dog genomes from around the world (including two previously published genome sequences from northern Iberian wolves). The results showed relatively low overall genetic diversity in Iberian wolves, but diverse population histories including past introgression of dog genes. The Sierra Morena wolf had an extraordinarily high level of inbreeding and long runs of homozygosity, resulting from the long isolation. In addition, about one‐third of the genome was of dog origin. Despite the introgression of dog genes, heterozygosity remained low because of continued inbreeding after several hybridization events. The results thus illustrate the case of a small and isolated wolf population where the low population density may have favoured hybridization and introgression of dog alleles, but continued inbreeding may have resulted in large chromosomal fragments of wolf origin completely disappearing from the population, and being replaced by chromosomal fragments of dog origin. The latest population surveys suggest that this population may have gone extinct.     

The impact of endogenous content,replicates and pooling on genome capture from faecal samples

Target‐capture approach has improved over the past years, proving to be very efficient tool for selectively sequencing genetic regions of interest. These methods have also allowed the use of noninvasive samples such as faeces (characterized by their low quantity and quality of endogenous DNA) to be used in conservation genomic, evolution and population genetic studies. Here we aim to test different protocols and strategies for exome capture using the Roche SeqCap EZ Developer kit (57.5 Mb). First, we captured a complex pool of DNA libraries. Second, we assessed the influence of using more than one faecal sample, extract and/or library from the same individual, to evaluate its effect on the molecular complexity of the experiment. We validated our experiments with 18 chimpanzee faecal samples collected from two field sites as a part of the Pan African Programme: The Cultured Chimpanzee. Those two field sites are in Kibale National Park, Uganda (N = 9) and Loango National Park, Gabon (N = 9). We demonstrate that at least 16 libraries can be pooled, target enriched through hybridization, and sequenced allowing for the genotyping of 951,949 exome markers for population genetic analyses. Further, we observe that molecule richness, and thus, data acquisition, increase when using multiple libraries from the same extract or multiple extracts from the same sample. Finally, repeated captures significantly decrease the proportion of off‐target reads from 34.15% after one capture round to 7.83% after two capture rounds, supporting our conclusion that two rounds of target enrichment are advisable when using complex faecal samples.     

Antioxidant and Prooxidant Effects of Ascorbic Acid, Dehydroascorbic Acid and Flavonoids on LDL Submitted to Different Degrees of Oxidation

Although a high intake of antioxidants may decrease the risk of developing cardiovascular diseases, under certain circunstances they may promote free radical generation and lipid peroxidation. The objectives of the present study were to determine the antioxidant effects of ascorbic acid (AA), dehydroascorbic acid (DHA) and flavonoids on LDL submitted to different degrees of oxidation. LDL was submitted to oxidation with CuCl₂ (2.4 μM). Before or at different times after the propagation of the oxidation process, 28 μM (5 μg/ml) of either AA or DHA or 5 μg/mL flavonoids extract were added. Alpha-tocopherol, conjugated dienes, thiobarbituric acid reacting substances (TBARS) and LDL electrophoretic mobility were determined as indices of LDL oxidation. The presence of any of the three antioxidants from the onset of the incubation delayed the oxidation process. However, the addition of both DHA and flavonoids to the oxidation process when it was already initiated and alpha-tocopherol consumed, accelerated the oxidation. In contrast, AA delayed the oxidation process even when added after alpha-tocopherol was consumed. Nevertheless, it also accelerated LDL oxidation when added during the propagation phase of the oxidation process. In conclusion: although AA, DHA and flavonoids delay LDL oxidation when added before the initiation of the process, they accelerate the process if added to minimally oxidized LDL.     

Effects of grazing and topography on long-term vegetation changes in a Mediterranean ecosystem in Israel

The dynamics of Mediterranean vegetation over 28 years was studied in the Northern Galilee Mountains, Israel, in order to identify and quantify the major factors affecting it at the landscape scale. Image analysis of historical and current aerial photographs was used to produce high resolution digital vegetation maps (pixel size = 30 cm) for an area of 4 km² in the Galilee Mountains, northern Israel. GIS tools were used to produce corresponding maps of grazing regime, topographic indices and other relevant environmental factors. The effects of those factors were quantified using a multiple regression analyses. Major changes in the vegetation occurred during the period studied (1964–1992); tree cover increased from 2% in 1964 to 41% in 1992, while herbaceous vegetation cover decreased from 56% in 1964 to 24% in 1992. Grazing, topography and initial vegetation cover were found to significantly affect present vegetation patterns. Both cattle grazing and goat grazing reduced the rate of increase in tree cover, yet even intensive grazing did not halt the process. Grazing affected also the woody-herbaceous vegetation dynamics, reducing the expansion of woody vegetation. Slope, aspect, and the interaction term between these two factors, significantly affected vegetation pattern. Altogether, 56% and 72% of the variability in herbaceous and tree cover, respectively, was explained by the regression models. This study indicates that spatially explicit Mediterranean vegetation dynamics can be predicted with fair accuracy using few biologically important environmental variables.     

High-resolution species-distribution model based on systematic sampling and indirect observations

Species distribution models (SDMs) are often limited by the use of coarse-resolution environmental variables and by the number of observations required for their calibration. This is particularly true in the case of elusive animals. Here, we developed a SDM by combining three elements: a database of explanatory variables, mapped at a fine resolution; a systematic sampling scheme; and an intensive survey of indirect observations. Using MaxEnt, we developed the SDM for the population of the Asiatic wild ass (Equus hemionus), a rare and elusive species, at three spatial scales: 10, 100, and 1000 m per pixel. We used indirect observations of feces mounds. We constructed 14 layers of explanatory variables, in five categories: water, topography, biotic conditions, climatic variables and anthropogenic variables. Woody vegetation cover and slopes were found to have the strongest effect on the distribution of wild ass and were included as the main predictors in the SDM. Model validation revealed that an intensive survey of feces mounds and high-resolution predictor layers resulted in a highly accurate and informative SDM. Fine-grain (10 and 100 m) SDMs can be utilized to: (1) characterize the variables influencing species distribution at high resolution and local scale, including anthropogenic effects and geomorphologic features; (2) detect potential population activity centers; (3) locate potential corridors of movement and possible isolated habitat patches. Such information may be useful for the conservation efforts of the Asiatic wild ass. This approach could be applied to other elusive species, particularly large mammals.     

Predicting the receptive range of olfactory receptors

Although the family of genes encoding for olfactory receptors was identified more than 15 years ago, the difficulty of functionally expressing these receptors in an heterologous system has, with only some exceptions, rendered the receptive range of given olfactory receptors largely unknown. Furthermore, even when successfully expressed, the task of probing such a receptor with thousands of odors/ligands remains daunting. Here we provide proof of concept for a solution to this problem. Using computational methods, we tune an electronic nose to the receptive range of an olfactory receptor. We then use this electronic nose to predict the receptors' response to other odorants. Our method can be used to identify the receptive range of olfactory receptors, and can also be applied to other questions involving receptor–ligand interactions in non-olfactory settings.     

Enhanced Erythrocyte Adhesiveness/Aggregation in Obesity Corresponds to Low‐Grade Inflammation

Objective: Previous studies have suggested that obesity enhances the inflammatory response, producing macromolecules involved in the induction and/or maintenance of increased erythrocyte aggregation. The objectives of this study were to evaluate the correlation between inflammation markers, erythrocyte adhesiveness/aggregation, and the degree of obesity and to assess phosphatidylserine expression on erythrocyte surface membrane of obese vs. nonobese individuals. Research Methods and Procedures: Erythrocyte adhesiveness/aggregation in the peripheral venous blood was evaluated by using a new biomarker, phosphatidylserine expression was assessed by means of flow cytometry, and markers of inflammation were measured in 65 subjects: 30 obese [body mass index (BMI) = 41 ± 7.7 kg/m²] and 35 nonobese (BMI = 24 ± 2.7 kg/m²) individuals. Pearson correlations and Student's t test were performed. Results: A highly significant difference was noted in the degree of erythrocyte adhesiveness/aggregation and markers of inflammation between the study groups. BMI correlated with erythrocyte adhesiveness/aggregation (r = 0.42, p = 0.001), erythrocyte sedimentation rate (r = 0.42, p = 0.001), high‐sensitive C‐reactive protein (r = 0.55, p < 10^?4), fibrinogen (r = 0.37, p = 0.004), and white blood cell count (r = 0.45, p < 10^?4). The degree of erythrocyte adhesiveness/aggregation correlated with erythrocyte sedimentation rate (r = 0.5, p < 10^?4), high‐sensitive C‐reactive protein (r = 0.56, p < 10^?4), fibrinogen (r = 0.54, p < 10^?4), and white blood cell count (r = 0.32, p = 0.01). Discussion: Our results suggest that obesity‐related erythrocyte adhesiveness/aggregation is probably mediated through increased concentrations of adhesive macromolecules in the circulation and not necessarily through hyperlipidemia or phosphatidylserine exposure on erythrocyte's membrane.