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Patterns and drivers of genetic diversity among Felidae species
No full textSince the late Pleistocene, species in the order Carnivora have experienced a drastic reduction in their populations and distributions. However, the global genetic diversity patterns among terrestrial carnivores have not been investigated. Using felid species as model, we characterized the genetic variation within their populations among continents, between tropical and non-tropical regions, and in relation to human activities. We then evaluated how species traits influence the observed patterns of interspecific genetic diversity. Through data collected from 135 population genetic studies conducted on 28 wild felid species (70% of the described species), data analyses using GLMM modelling showed that the populations in Africa and South America have significantly higher heterozygosity and allelic richness than those in other continents. The Asiatic lions have the least genetic diversity compared to other felids in the world. Threatened species have significantly lower genetic diversity compared to low-risk species as predicted. However, genetic diversity was not related to species body mass or geographic range. We found generation length to be an important variable explaining genetic diversity variation, in which species with short generation length have reduced genetic diversity. Furthemore, the combination of generation length, habitat and home range size captures the variation in heterozygosity significantly better. Species dependent on closed-habitat and with large home range size have reduced heterozygosity compared to their counterparts. Our results allow to identify priority felid species vulnerable to loss of genetic diversity for further conservation studies, and provide an insight into the possible genetic consequences of the late Pleistocene extinctions
Parameterization of the AquaCrop model for simulating table grapes growth and water productivity in an arid region of Mexico
No full textCurrently, the AquaCrop model has been widely tested for many fruit/grain crops; root and tuber crops; leafy vegetables, or forage crops, but is restricted to annual herbaceous species, while deciduous crops have received less if no attention. In this context, this study aims to test for the first time the ability of the AquaCrop model to simulate canopy cover (CC), actual evapotranspiration (ETa), total soil water content (TWC), biomass (B) and fruit yield (FY) of table grapes vineyards (Vitis vinifera L., cvs. Perlette and Superior) at the Costa de Hermosillo, Sonora in Northwest Mexico. Observed weather and soil physical parameters, with measured crop parameters from an experiment conducted during 2005 were used to develop climate, soil and crop input files for AquaCrop and for calibrating the model. While collected data during the 2006 growing season were used to validate the model. The model adequately simulated CC, ETa and TWC during 2005 and 2006. The Root Mean Square Error (RMSE) between observed and measured CC, ETa and TWC were 5.18%, 0.46 mm/day and 10.11 mm during 2005, and 8.82%, 0.84 mm/day and 9.1 mm during 2006, respectively. The good accuracy of simulations of CC, ETa and TWC by the model have been confirmed by additional statistical parameters like the coefficient of determination (R-2), The Mean Bias Error (MBE), the Willmott's index of agreement (d) and the Nash-Sutcliffe Efficiency (NSE). For the B and FY simulations, the results showed that the model correctly reproduced the B and FY with NRMSE value of 8.8%. The estimated average value of FY (14.56 t/ha) for both seasons are in the range of the potential yield (14-18 t/ha) of table grapes in the irrigated Costa de Hermosillo in northwest Mexico. After the validation of the AquaCrop model, it was used to evaluate the irrigation scheduling by the farmer as well as to assess the water productivity computed as the ratio of crop production to crop water use. The results showed that, the recommended irrigation by the model was about 547 mm and 509 mm, which it is about half of that applied by the farmer (1006 mm and 929 mm) during 2005 and 2006, respectively. This large difference, which represents approximately 54% and 57% of the irrigation supply, is lost through deep percolation and could be saved without vegetation suffering from water stress while maintaining the same yield. The high loss of water by percolation affects significantly the water productivity (WP), which decreases from 3.22 to 1.74 kg/m(3) if we consider the transpiration (WPTr), and the sum of ETa and Percolation (WPETa+Pr) for WP computations, respectively. Consequently, the AquaCrop model can be used as an operational tool by decision makers and growers to improve irrigation management. This is of crucial importance in arid and semi-arid regions where water is becoming increasingly scarce
Multilocus phylogeny of African striped grass mice (Lemniscomys) : stripe pattern only partly reflects evolutionary relationships
No full textMurine rodents are one of the most evolutionary successful groups of extant mammals. They are also important for human as vectors and reservoirs of zoonoses and agricultural pests. Unfortunately, their fast and relatively recent diversification impedes our understanding of phylogenetic relationships and species limits of many murine taxa, including those with very conspicuous phenotype that has been frequently used for taxonomic purposes. One of such groups are the striped grass mice (genus Lemniscomys), distributed across sub-Saharan Africa in 11 currently recognized species. These are traditionally classified into three morphological groups according to different pelage colouration on the back: (a) L. barbarus group (three species) with several continuous pale longitudinal stripes; (b) L. striatus group (four species) with pale stripes diffused into short lines or dots; and (c) L. griselda group (four species) with a single mid-dorsal black stripe. Here we reconstructed the most comprehensive molecular phylogeny of the genus Lemniscomys to date, using the largest currently available multi-locus genetic dataset of all but two species. The results show four main lineages (=species complexes) with the distribution corresponding to the major biogeographical regions of Africa. Surprisingly, the four phylogenetic lineages are only in partial agreement with the morphological classification, suggesting that the single-stripe and/or multi-striped phenotypes evolved independently in multiple lineages. Divergence dating showed the split of Lemniscomys and Arvicanthis genera at the beginning of Pleistocene; most of subsequent speciation processes within Lemniscomys were affected by Pleistocene climate oscillations, with predominantly allopatric diversification in fragmented savanna biome. We propose taxonomic suggestions and directions for future research of this striking group of African rodents
Mangrove ecological services at the forefront of coastal change in the French overseas territories
No full textMangroves are located at the land-sea interface and are therefore confronted with human settlement in the coastal areas and associated pressures and uses. This unique habitat provides important ecosystem services to coastal communities worldwide, but the global decline of their surface area and their degradation over the past decades has put coastal communities even more at risk from the effects of climate change. This paper aims to present the first ecosystem services valuation of the mangroves of the French overseas Territories. We provide the economic value of mangroves for coastal protection, carbon sequestration, water purification and fish biomass production. We coupled a geospatial analysis of mangrove's distribution with the characterisation of land artificialisation behind mangroves. Then we developed a vulnerability index based on multiple indicators of exposure to environmental and anthropogenic stressors, mangroves' sensitivity to pressures, and mangroves' adaptive capacity to adjust their production functions accordingly. We estimated the monetary value of regulation and support services provided by mangroves in French overseas territories to be on average EUR 1.6 billion annually, 60% of which is carbon sequestration, 28% coastal protection, 7% water purification and 6% fish biomass production. When considering mangroves services without the vulnerability adjustment, the total value for those services would reach EUR 2 billion per year. Although much of the spatio-temporal variability in mangrove functioning could not be considered given the spatial scale of our study, these results demonstrate the value and socio-economic importance of mangroves to face and adapt from the effects of coastal change, at local and national scales, but also highlight the loss of services due to their vulnerability. This paper emphasises on the value of ecosystem services provided by mangroves to face coastal change so that a service-based approach to conservation would plead for increased national investment into their protection
Changes in the equatorial mode of the Tropical Atlantic in terms of the Bjerknes Feedback Index
No full textOne of the main modes of sea surface temperature variability in the Tropical Atlantic is the Atlantic Equatorial Mode or Atlantic Nino. The region of largest interannual variability, where the Atlantic Cold Tongue forms, is also a region of consistent biases in climate models. In this study, we investigate the interannual variability of the Tropical Atlantic and its changes in the recent decades in terms of the Bjerknes Feedback Index (I-BJ) in a set of seven ocean reanalyses for the periods 1980-1999 and 2000-2010. Differences were observed among the reanalyses regarding their representation of each term of the Bjerknes Feedback, particularly regarding zonal surface currents, leading to differences in dynamical damping and the zonal advective feedback. However, a consistent negative index (damped) is observed in all reanalysis, with the thermocline feedback being the dominant positive term and thermal damping the dominant negative term. Warming trends are observed in sea surface temperatures in the cold tongue region in all reanalyses, as well as a decrease in interannual variability. These in turn are associated with a weakening in the Bjerknes Feedback in the early XXI century, indicated by a stronger and negative index. This results from a stronger thermal damping and weaker thermocline feedback, associated with a weaker response of equatorial zonal thermocline slope to equatorial zonal wind stress. Despite the spread among the reanalysis, the results obtained are consistent with previous studies
A timed tally counter for microscopic examination of thick blood smears in malaria studies
No full textBackground Despite many technological advances for malaria parasite detection (e.g. high resolution image acquisition), microscopic reading of thick blood smear (TBS) remains the gold standard. Even though available in low technology environment, the microscopy of TBS is slow and time consuming. Moreover microscopy may induce errors at many levels and has no quality control. Methods A electronic extension of the mechanical tally counter is proposed. In addition to the counting process it includes the process of counting itself that relies on the time elapsed between two successive pressures of the counting button leading to a timed tally counter (TTC). The microscopist performs the reading with the specific instruction starting by counting, in each high power fields, leucocytes first and then parasites. The time-stamp of all pressures of counting buttons are recorded along with the nature of the count. The data are recorded internally in CSV format and are exportable. The detection of HPFs locations and leukocyte/parasite counts per HPFs is performed through a hidden semi-Markov model (with outliers) allowing both to take into account the known distribution of leukocyte per HPFs (using a negative binomial distribution) and the pauses and hesitation of the microscopist during the reading. Parameters are estimated via the expectation-maximization algorithm. Hyper-parameters are calibrated using expert annotations. Forward/backward recursions are used to obtain the HPFs locations. Results This approach provides richer data at no extra cost. It has been demonstrated that the method can derive parasites per HPF, leukocytes per HPF, and parasite/leukocyte ratio with robust non-parametric confidence intervals. Moreover a direct digital data entry leads to a less expensive process and decreased time-consuming and error-prone manual data entry. Lastly the TTC allows detecting possible protocol break during reading and prevents the risk of fraud. Discussion and conclusion Introducing a programmed digital device in the data acquisition of TBS reading gives the opportunity to develop easily new (possible adaptive) reading protocols that will be easily followed by the reader since they will be embedded directly in the device. With the TTC the reader only has to read HPFs, counting leukocytes first and parasites second, and the counter will beep when the protocol is completed
Diffracted wavefield decomposition and multidimensional site effects in the Argostoli valley, Greece
No full textEffects of seismic ground motion induced by surface geology and geometry are known to be associated with the generation of a substantial proportion of surface waves. As a consequence, surface waves significantly contribute to ground-motion variability and site amplification. There is a growing body of literature recognizing that an understanding of physical patterns of the wavefield crossing a site is the key aspect to characterize and quantify them. However, this task remains technically challenging due to the complexity of such effects as well as the limitations of geophysical investigations, especially in case of small sedimentary valleys. The present study attempts to investigate the waves propagating across two 2-D dense seismic arrays from a number of earthquakes and explore the extent to which they are contributing to the multidimensional site effects. The arrays were deployed in the small-size, shallow alluvial valley of Koutavos-Argostoli, located in Cephalonia Island, Greece, and consisted of three-component velocimeters with interstation distances ranging from 5 to 160 m. A set of 46 earthquakes, with magnitudes between 2 and 5 and epicentral distances up to 200 km, was analysed by using an advanced seismic array processing technique, MUSIQUE. The phase velocity, backazimuth and energy of the dominant waves crossing the array were extracted, and their identification as Love or prograde/retrograde Rayleigh waves was obtained. The results clearly indicate a predominance of scattered surface waves (up to 60 per cent of total energy), mainly from the closest valley edges, above the fundamental frequency (similar to 1.5 Hz) of the valley. Love waves dominate the low-frequency wavefield (<3 Hz) while Rayleigh waves dominate some high-frequency bands. An excellent consistency is observed, in a given frequency range, among the dominance of the type of diffracted surface waves, group velocities estimated from the ground velocity structure and site amplification. The outcomes of this research provide a better understanding of the contribution of edge-diffracted surface waves and the 2-D/3-D site amplification at small and shallow alluvium valleys like Argostoli. The method applied here can be used to calibrate and validate 3-D models for simulating seismic ground motion
Evolution of Retisol impacted by artificial drainage : what can we learn from stable Fe isotope ratios ?
No full textIron oxides are one of the most reactive mineral phases in soils. As a consequence, their transformations can considerably affect the dynamics of the adsorbed elements and of the associated soil ecosystem services. Understanding the dynamics of Fe oxides in soils is therefore a key issue for the evolution of soil and associated ecosystem services. A potentially powerful tool to study the transformations of Fe-oxides in soil is stable Fe isotopes. However, there are still important gaps in our knowledge of Fe isotope fractionations. In order to examine the Fe isotope fractionations related to each process occurring in soils, we focused on a drainage-influenced sequence of Retisols, a soil type characterized by clay translocation and subsequent degradation by redox processes inducing a strong spatial Fe segregation in contrasted soil volumes. We combined the isotopic approach at the scale of a bulk horizon and at the scale of the different soil volumes, with mineralogical analyses and mass balance calculations in order to investigate the consequences of the drainage on Fe isotope fractionation. We showed that while there were no Fe isotope fractionations at the profile scale, Fe isotopic signatures varied significantly among soil volumes (delta Fe-56 values from -0.49 +/- 0.05 to 0.29 +/- 0.06 parts per thousand). These variations suggest that redox processes are the main mechanisms responsible for the Fe redistribution among the volumes, and particularly that Fe accumulation during Mn oxide precipitation makes a significant contribution to Fe isotopic fractionation, during these Retisol differentiation. In contrast, drainage-induced eluviation does not result in further Fe isotope fractionations in soil volumes in these Retisols. The isotopic signatures of the different mineral phases present in the volumes were calculated using the mass balance approach and suggest that the iron oxides (goethite, ferrihydrite) have delta Fe-56 values close to 0 parts per thousand, while the clay minerals are enriched in heavy Fe isotopes and the Mn oxides in light Fe isotopes. This study provides insight into the dynamics of Fe minerals in hydromorphic soils and offers a new perspective on stable Fe isotope fractionation in soils
Noble gas magmatic signature of the Andean Northern Volcanic Zone from fluid inclusions in minerals
No full textTrace volatile elements like He are key for understanding the mantle source signature of magmas and to better constrain the relative roles of subduction and crustal processes to the variability of along-arc chemical and isotopic signatures of magmatic fluids. Here we report on noble gas abundances and isotopic data of Fluid Inclusions (FIs) in eruptive products and/or fumarolic gases from the Colombia-Ecuador segment of Andean Northern Volcanic Zone (NVZ). FIs in olivine phenocrysts from Ecuador (El Reventador, Cotopaxi and Tungurahua) yield air-normalized corrected He-3/He-4 ratios of 7.0-7.4 R-A, within the MORB range (8 +/- 1 R-A). With exception of the Cotopaxi lavas (opx = 50 km at the Ecuadorian arc segment) may factor largely into the variability recorded on our data set. The first CO2/He-3 ratios obtained in FIs from Andean rocks support the hypothesis of increasing crustal contamination from Colombia to Ecuador, concomitant with increasing crustal thicknesses under the respective arc regions
Stable mercury concentrations of tropical tuna in the south western Pacific ocean : An 18-year monitoring study
No full textGlobal anthropogenic mercury (Hg) emissions to the atmosphere since industrialization are widely considered to be responsible for a significant increase in surface ocean Hg concentrations. Still unclear is how those inputs are converted into toxic methylmercury (MeHg) then transferred and biomagnified in oceanic food webs. We used a unique long-term and continuous dataset to explore the temporal Hg trend and variability of three tropical tuna species (yellowfin, bigeye, and skipjack) from the southwestern Pacific Ocean between 2001 and 2018 (n - 590). Temporal trends of muscle nitrogen (delta N-15) and carbon (delta C-13) stable isotope ratios, amino acid (AA) delta N-15 values and oceanographic variables were also investigated to examine the potential influence of trophic, biogeochemical and physical processes on the temporal variability of tuna Hg concentrations. For the three species, we detected significant inter-annual variability but no significant long-term trend for Hg concentrations. Inter-annual variability was related to the variability in tuna sampled lengths among years and to tuna muscle delta N-15 and delta C-13 values. Complementary AA- and model-estimated phytoplankton delta N-15 values suggested the influence of baseline processes with enhanced tuna Hg concentrations observed when dinitrogen fixers prevail, possibly fuelling baseline Hg methylation and/or MeHg bioavailability at the base of the food web. Our results show that MeHg trends in top predators do not necessary capture the increasing Hg concentrations in surface waters suspected at the global oceanic scale due to the complex and variable processes governing Hg deposition, methylation, bioavailability and biomagnification. This illustrates the need for long-term standardized monitoring programs of marine biota worldwide