Two reciprocally monophyletic mtDNA lineages elucidate the taxonomic status of Mountain gazelles (Gazella gazella)

Mountain gazelles (Gazella gazella) rank among the most critically endangered mammals on the Arabian Peninsula. Past conservation efforts have been plagued by confusion about the phylogenetic relationship among various ‘phenotypically discernable’ populations, and even the question of species boundaries was far from being certain. This lack of knowledge has had a direct impact on conservation measures, especially ex situ breeding programmes, hampering the assignment of captive stocks to potential conservation units. Here, we provide a phylogenetic framework, based on the analysis of mtDNA sequences (360 bp cytochrome b and 213 bp Control Region) of 126 individuals collected from the wild throughout the Arabian Peninsula and from captive stocks. Our analyses revealed two reciprocally monophyletic genetic lineages within the presumed species Gazella gazella: one ‘northern clade’ on the Golan Heights (Israel/Syrian border) and one genetically diverse larger clade from the rest of the Arabian Peninsula including the Arava Valley (Negev, Israel). Applying the Strict Phylogenetic Species Concept (sensu Mishler & Theriot, 2000 Mishler, B. D. and Theriot, E. C. 2000. “The phylogenetic species concept (sensu Mishler and Theriot): monophyly, apomorphy, and phylogenetic species concepts”. In Species Concepts and Phylogenetic Theory. A Debate, Edited by: Wheeler, Q. D. and Meier, R. 44–54. Columbia University Press, NY.  [Google Scholar]) allows assigning species status to these two major clades.     

Admixture in Mexico City: implications for admixture mapping of Type 2 diabetes genetic risk factors

Admixture mapping is a recently developed method for identifying genetic risk factors involved in complex traits or diseases showing prevalence differences between major continental groups. Type 2 diabetes (T2D) is at least twice as prevalent in Native American populations as in populations of European ancestry, so admixture mapping is well suited to study the genetic basis of this complex disease. We have characterized the admixture proportions in a sample of 286 unrelated T2D patients and 275 controls from Mexico City and we discuss the implications of the results for admixture mapping studies. Admixture proportions were estimated using 69 autosomal ancestry-informative markers (AIMs). Maternal and paternal contributions were estimated from geographically informative mtDNA and Y-specific polymorphisms. The average proportions of Native American, European and, West African admixture were estimated as 65, 30, and 5%, respectively. The contributions of Native American ancestors to maternal and paternal lineages were estimated as 90 and 40%, respectively. In a logistic model with higher educational status as dependent variable, the odds ratio for higher educational status associated with an increase from 0 to 1 in European admixture proportions was 9.4 (95%, credible interval 3.8–22.6). This association of socioeconomic status with individual admixture proportion shows that genetic stratification in this population is paralleled, and possibly maintained, by socioeconomic stratification. The effective number of generations back to unadmixed ancestors was 6.7 (95% CI 5.7–8.0), from which we can estimate that genome-wide admixture mapping will require typing about 1,400 evenly distributed AIMs to localize genes underlying disease risk between populations of European and Native American ancestry. Sample sizes of about 2,000 cases will be required to detect any locus that contributes an ancestry risk ratio of at least 1.5.     

Monitoring Rarity: The Critically Endangered Saharan Cheetah as a Flagship Species for a Threatened Ecosystem

Deserts are particularly vulnerable to human impacts and have already suffered a substantial loss of biodiversity. In harsh and variable desert environments, large herbivores typically occur at low densities, and their large carnivore predators occur at even lower densities. The continued survival of large carnivores is key to healthy functioning desert ecosystems, and the ability to gather reliable information on these rare low density species, including presence, abundance and density, is critical to their monitoring and management. Here we test camera trap methodologies as a monitoring tool for an extremely rare wide-ranging large felid, the critically endangered Saharan cheetah (Acinonyx jubatus hecki). Two camera trapping surveys were carried out over 2–3 months across a 2,551km² grid in the Ti-n-hağğen region in the Ahaggar Cultural Park, south central Algeria. A total of 32 records of Saharan cheetah were obtained. We show the behaviour and ecology of the Saharan cheetah is severely constrained by the harsh desert environment, leading them to be more nocturnal, be more wide-ranging, and occur at lower densities relative to cheetah in savannah environments. Density estimates ranged from 0.21–0.55/1,000km², some of the lowest large carnivore densities ever recorded in Africa, and average home range size over 2–3 months was estimated at 1,583km². We use our results to predict that, in order to detect presence of cheetah with p>0.95 a survey effort of at least 1,000 camera trap days is required. Our study identifies the Ahaggar Cultural Park as a key area for the conservation of the Saharan cheetah. The Saharan cheetah meets the requirements for a charismatic flagship species that can be used to “market” the Saharan landscape at a sufficiently large scale to help reverse the historical neglect of threatened Saharan ecosystems.     

Conservation in Saudi Arabia; moving from strategy to practice

Conservation in the Kingdom of Saudi Arabia is relatively young, yet have made considerable gains in conservation through strategic proclamation and reintroductions. Changes in land use, illegal hunting and competition with domestic stock has decimated the native ungulates, meaning that the survival of the native ungulate species is now completely dependent on protected area network. The challenge is to sustain this network to make meaningful conservation impact into the future. We review the status of ungulate conservation in Saudi Arabia and highlight that the conservation strategy is well developed. The major challenge faced in conservation in Saudi Arabia now is to implement what has been sanctioned.     

Growth and final product formation by <Emphasis Type="Italic">Bifidobacterium infantis</Emphasis> in aerated fermentations

Fermentation conditions were developed to allow Bifidobacterium infantis to grow in the presence of air. Batch fermentations in TPYG medium, starting from anoxic conditions followed by the application of low airflow rates [0.02–0.1 air volume, per liquid media volume, per minute (vvm)], were analyzed for growth, oxygen uptake, and product formation by the bacterium. Under all aerated fermentations, B. infantis showed high aerotolerance, with a maximum oxygen-specific consumption rate of 0.34 mmol oxygen per gram dry cell weight per hour in the presence of 0.06 vvm. Similar growth yields were obtained under oxic and anoxic conditions (0.11–0.13 and 0.11 g dry cell weight per mmol glucose, respectively). Oxygen also influenced metabolite formation since lactate production and its molar relation to acetate increased and formate decreased with aeration rate. Under anoxic conditions, a maximum concentration of 8.1 mM lactate and an acetate/lactate ratio of 3.5:1 were obtained, while under oxic conditions the lactate concentration increased more than two-fold and the acetate/lactate molar ratio decreased to 1.5:1. The possibility of balancing acetate/lactate molar ratios for organoleptic purposes as well as for obtaining good growth under microaerated conditions was demonstrated.     

Habitat use of the endangered golden‐rumped sengi Rhynchocyon chrysopygus

The endangered golden‐rumped sengi are found only in Arabuko‐Sokoke Forest with 395.4 km² of forest habitat, and perhaps in a few isolated forest and thicket fragments of total area less than 30 km² all within central coastal Kenya. Understanding its habitat use is an important requirement to develop better conservation measures for the species and its remaining forest habitat. A more reliable method for monitoring its status is also needed. We used the Bayesian occupancy modelling with camera trap data and habitat mapping to characterise the species habitat use in the Arabuko‐Sokoke Forest. The species uses 328 km² (95% CI: 289–364 km²) of Arabuko‐Sokoke Forest habitat, and its site use increases with distance from forest edge, with the highest site use in the Cynometra thicket (0.93; 95% CI: 0.82–1). Its use of the mixed forest habitat has been significantly reduced following years of logging of Afzelia quanzensis. We recommend the use of modelled occupancy, interpreted as the proportion of area used by the species, to monitor the species status. Occupancy models account for detection probability, and heterogeneity in site use and detection can be incorporated. Estimated territory sizes can be combined to obtain abundance estimates.     

Characterization of the polyurethanolytic activity of two Alicycliphilus sp. strains able to degrade polyurethane and N-methylpyrrolidone

Two bacterial strains (BQ1 and BQ8) were isolated from decomposed soft foam. These were selected for their capacity to grow in a minimal medium (MM) supplemented with a commercial surface-coating polyurethane (PU) (Hydroform) as the carbon source (MM-PUh). Both bacterial strains were identified as Alicycliphilus sp. by comparative 16S rRNA gene sequence analysis. Growth in MM-PUh showed hyperbolic behavior, with BQ1 producing higher maximum growth (17.8 +/- 0.6 mg.ml(-1)) than BQ8 (14.0 +/- 0.6 mg.ml(-1)) after 100 h of culture. Nuclear magnetic resonance, Fourier transform infrared (IR) spectroscopy, and gas chromatography-mass spectrometry analyses of Hydroform showed that it was a polyester PU type which also contained N-methylpyrrolidone (NMP) as an additive. Alicycliphilus sp. utilizes NMP during the first stage of growth and was able to use it as the sole carbon and nitrogen source, with calculated K(s) values of about 8 mg.ml(-1). Enzymatic activities related to PU degradation (esterase, protease, and urease activities) were tested by using differential media and activity assays in cell-free supernatants of bacterial cultures in MM-PUh. Induction of esterase activity in inoculated MM-PUh, but not that of protease or urease activities, was observed at 12 h of culture. Esterase activity reached its maximum at 18 h and was maintained at 50% of its maximal activity until the end of the analysis (120 h). The capacity of Alicycliphilus sp. to degrade PU was demonstrated by changes in the PU IR spectrum and by the numerous holes produced in solid PU observed by scanning electron microscopy after bacterial culture. Changes in the PU IR spectra indicate that an esterase activity is involved in PU degradation.