Species distribution modeling: a statistical review with focus in spatio-temporal issues

The use of complex statistical models has recently increased substantially in the context of species distribution behavior. This complexity has made the inferential and predictive processes challenging to perform. The Bayesian approach has become a good option to deal with these models due to the ease with which prior information can be incorporated along with the fact that it provides a more realistic and accurate estimation of uncertainty. In this paper, we first review the sources of information and different approaches (frequentist and Bayesian) to model the distribution of a species. We also discuss the Integrated Nested Laplace approximation as a tool with which to obtain marginal posterior distributions of the parameters involved in these models. We finally discuss some important statistical issues that arise when researchers use species data: the presence of a temporal effect (presenting different spatial and spatio-temporal structures), preferential sampling, spatial misalignment, non-stationarity, imperfect detection, and the excess of zeros.     

Beach recovery capabilities after El Niño 2015–2016 at Ensenada Beach,Northern Baja California

This study investigates the recovery capabilities of a single-barred beach in the Pacific Mexican coast before and after the 2015–2016 El Niño winter. Concurrent hydrodynamic and morphological data collected over a 3-year period (August 2014–2017) were analysed to determine the subaerial-subtidal volumetric exchange and cross-shore subtidal sandbar migrations, in relation to the incident wave forcing. The beach presented a seasonal seaward and landward sandbar migration cycle. The sandbar migrated offshore during the energetic waves between November and February, and onshore during the milder wave period in spring, until welding to the subaerial beach around May. The transfer of sediment towards the subaerial section continued over the summer, reaching a complete recovery by September/October. Prior to El Niño, the subaerial beach successfully recovered by the end of summer 2015 through the landward sandbar migration process. The 2015–2016 energetic winter waves caused a subaerial volume loss of ~ 140 m³ m^?1 (from October 2015 to March 2016), more than twice the amount eroded in the other winters, and the sandbar moved further offshore and to deeper depths (3–4 m) than the winter before. In addition, the energetic 2015–2016 winter waves lasted for 2 months longer than in other years, making the 2016 spring shorter. Consequently, during the onshore migration, the sandbar was unable of reaching shallow depths, and a large portion of sand remained in the subtidal beach. The subaerial beach recovered 60 and 65% of the loss in the 2016 and 2017 summers, respectively. It is concluded that the landward migration process of the sandbar during the spring is critical to ensure a full subaerial beach recovery over the mild wave period in summer. The recovery capabilities of the subaerial beach will depend on the cross-shore distance and depth where the sandbar is located, and on the duration of mild wave conditions required for the sandbar to migrate onshore.     

Low resistivity zones at contacts of igneous intrusions emplaced in organic-rich formations and their implications on fluid flow and petroleum systems: A case study in the northern Neuquén Basin,Argentina

Igneous sills and laccoliths emplaced in sedimentary basins may significantly impact petroleum systems, both positively and negatively. Igneous intrusions provide heat to maturate regionally immature organic-rich host rocks, act as fractured reservoirs hosting commercial accumulations of hydrocarbons, and form structures affecting fluid flow and trapping at different scales. Nevertheless, the petrophysical implications of igneous intrusions on their host rock are poorly known. In this study, we analyse 200 wells in the Río Grande Valley oil field, Neuquén basin, Argentina, where the main reservoirs are in fractured igneous sills. This dataset represents a globally unique possibility to characterize the igneous–host rock interaction using both wireline logs and core material. We identify a systematic Contact Low Resistivity Zone (CLRsZ) at both the upper and lower contacts of the sills emplaced in the organic-rich Vaca Muerta and Agrio Formations. We characterize the nature of these CLRsZ and their petrophysical properties by integrating resistivity and gamma ray well logs, petrographic analyses, petrophysical tests and geochemical analyses. The low resistivity signal of the CLRsZ is dominantly carried by massive-sulphide deposits, mainly pyrite, observed both in the host rock and the chilled margin of the sills. Well log images and porosity-permeability analysis on core plugs show that both the sills and their associated CLRsZ can act as carrier for fluid flow and reservoir for hydrocarbons storage. The thickness of the upper and lower CLRsZ correlates linearly with the thickness of the sill, and the volume of both the upper and lower CLRsZ represents ca. 40% with respect to the volume of their associated sill. The thickness of the CLRsZ represents ca. 13% of the thickness of contact aureole induced by the sills. In the CLRsZ, a great proportion of kerogen was transformed to hydrocarbon, so that CLRsZ were restricted to the innermost contact aureole of the sills. Our results show that the CLRsZ can have major implications on fluid flow and should be considered in reservoir models in volcanic basins hosting sills emplaced in organic-rich formations.     

Assessing the performance of a physically based hydrological model using a proxy‐catchment approach in an agricultural environment

Physically based models are useful frameworks for testing intervention strategies designed to reduce elevated sediment loads in agricultural catchments. Evaluating the success of these strategies depends on model accuracy, generally established by a calibration and evaluation process. In this contribution, the physically based SHETRAN model was assessed in two similar U.K. agricultural catchments. The model was calibrated on the Blackwater catchment (18 km²) and evaluated in the adjacent Kit Brook catchment (22 km²) using 4 years of 15 min discharge and suspended sediment flux data. Model sensitivity to changes in single and multiple combinations of parameters and sensitivity to changes in digital elevation model resolution were assessed. Model flow performance was reasonably accurate with a Nash–Sutcliffe efficiency coefficient of 0.78 in Blackwater and 0.60 in Kit Brook. In terms of event prediction, the mean of the absolute percentage of difference (μAbs_diff) between measured and simulated flow volume (Qv), peak discharge (Qp), sediment yield (Sy), and peak sediment flux (Sp) showed larger values in Kit Brook (48% [Qv], 66% [Qp], 298% [Sy], and 438% [Sp]) compared with the Blackwater catchment (30% [Qv], 41% [Qp], 106% [Sy], and 86% [Sp]). Results indicate that SHETRAN can produce reasonable flow prediction but performs less well in estimation of sediment flux, despite reasonably similar hydrosedimentary behaviour between catchments. The sensitivity index showed flow volume sensitive to saturated hydraulic conductivity and peak discharge to the Strickler coefficient; sediment yield was sensitive to the overland flow erodibility coefficient and peak sediment flux to raindrop/leaf soil erodibility coefficient. The multiparameter sensitivity analysis showed that different combinations of parameters produced similar model responses. Model sensitivity to grid resolution presented similar flow volumes for different digital elevation model resolutions, whereas event peak and duration (for both flow and sediment flux) were highly sensitive to changes in grid size.     

Isotopic and hydrochemistry spatial variation of sulfate for groundwater characterization in karstic aquifers

The Sierra Gorda aquifer is one of the most extensive of southern Spain. The main groundwater discharge is produced at its northern boundary through several high‐flow springs. In this study, stable isotopes of dissolved sulfate (δ³⁴S and δ¹⁸O) and groundwater chemistry were used to determine the origin of the sulfate and to characterize the groundwater flow. We sampled the main springs, as well as other minor outlets related to perched water tables, in order to determine the different sources of SO₄^2? (e.g., dissolution of evaporites and atmospheric deposition). The substantial difference in the amount of dissolved SO₄^2? between the springs located in its northwestern part (≈25 mg/L) and those elsewhere in the northern part (≈60 mg/L) suggests zones with separate groundwater flow systems. A third group of springs, far from the northeastern boundary of the permeable outcrops, shows higher SO₄^2? content than the rest (≈125 mg/L). The isotopic range of sulfate (?0.3‰ to 14.82‰ V‐CTD) points to several sources, including dissolution of Triassic or Miocene evaporites, atmospheric deposition, and decomposition of organic material in the soil. Among these, the dissolution of Triassic gypsum—which overlies the saturated zone as a consequence of the folds and faults that deform the aquifer—is the main source of SO₄^2? (range from 12.79‰ to 14.82‰ V‐CTD). This range is typical for Triassic gypsum. The higher karstification in the western sector, together with important differences in the saturated thickness between the western and eastern sectors, would also be due to the tectonic structure and could explain the difference in SO₄^2? contents in the water. This singular arrangement may cause a higher residence time of groundwater in the eastern sector; thus, a higher contact time with Triassic evaporitic rocks is inferred. Accordingly, the stable isotopes of SO₄^2? are found to be a valuable tool for identifying areas with different flow systems in the saturated zone of karstic aquifers, as well as for evaluating aspects such as the degree of karstification .     

Age and sources of the ore at Tharsis and Rio Tinto, Iberian Pyrite Belt, from Re-Os isotopes

Re-Os isotopes were used to constrain the source of the ore-forming elements of the Tharsis and Rio Tinto mines of the Iberian Pyrite Belt, and the timing of mineralization. The pyrite from both mines has simila]r Os and Re concentrations, ranging between 0.05–0.7 and 0.6–66 ppb, respectively. ¹⁸⁷Re/¹⁸⁸Os ratios range from about 14 to 5161. Pyrite-rich ore samples from the massive ore of Tharsis and two samples of stockwork ore from Rio Tinto yield an isochron with an age of 346 ± 26 Ma, and an initial ¹⁸⁷Os/¹⁸⁸Os ratio of about 0.69. Five samples from Tharsis yield an age of 353 ± 44 Ma with an initial ¹⁸⁷Os/¹⁸⁸Os ratio of about 0.37. A sample of massive sulfide ore from Tharsis and one from Rio Tinto lie well above both isochrons and could represent Re mobilization after mineralization. The pyrite Re-Os ages agree with the paleontological age of 350 Ma of the black shales in which the ores are disseminated. Our data do not permit us to determine whether the Re-Os isochron yields the original age of ore deposition or the age of the Hercynian metamorphism that affected the ores. However, the reasonable Re-Os age reported here indicates that the complex history of the ores that occurred after the severe metamorphic event that affected the Iberian Pyrite Belt massive sulfide deposits did not fundamentally disturb the Re-Os geochronologic system. The highly radiogenic initial Os isotopic ratio agrees with previous Pb isotopic studies. If the initial ratio is recording the initial and not the metamorphic conditions, then the data indicate that the source of the metals was largely crustal. The continental margin sediments that underlie the deposits (phyllite-quartzite group) or the volcanic rocks (volcanogenic-sedimentary complex) in which the ores occur are plausible sources for the ore-forming metals and should constrain the models for the genesis of these deposits. Received: 15 March 1999 / Accepted: 26 July 1999     

Influence of ground motion intensity on the effectiveness of tuned mass dampers

The effectiveness of Tuned Mass Dampers (TMD) on buildings subjected to moderate and high-intensity motions is analysed. First, the response of a 22-storey four-bay reinforced concrete non-linear frame with a TMD is studied for motions with different intensities. Several values of the relevant parameters are assumed in the analyses. Then, equivalent single-degree-of-freedom systems with TMDs and without them are defined and analysed under the action of ground motions with intensities associated with different return intervals at the site where the structures are located. Vulnerability curves for the systems are obtained based on the probabilities of reaching two different performance limit states. The expected annual rate of exceedance of each limit state is calculated. The results show that the effectiveness of TMDs is higher for systems with small non-linearity produced by small and moderate earthquakes, than for systems with high non-linear behaviour, generally associated with high-intensity motions. Some recommendations about the applicability of TMD are given. Copyright © 1999 John Wiley & Sons Ltd.     

Spatial spring distribution of the copepod Eurytemora affinis (Copepoda,Calanoida) in a restoring estuary,the Scheldt (Belgium)

The spatial spring distribution of Eurytemora affinis (adults and C5) in the Scheldt estuary (Belgium) brackish and freshwater reaches was studied in between 1996 and 2007. The bulk of the E. affinis population being generally situated in the brackish water reach (salinity > 0.5); we studied which environmental factors are responsible for its recent sporadic occurrence in the freshwater estuarine reach. Using PLS analysis, it is shown that its presence upstream is limited by a sufficient oxygen concentration (>4 mg l⁻¹) that is associated with temperature. Not only are the environmental conditions in the upstream zone important, but also the frequent presence of an O₂ minimum zone in the mid-estuary (O₂ min < 1.3 mg l⁻¹) seems to block the movement of the downstream E. affinis population in an upstream direction. Occasionally, the bulk of the population is however situated upstream. During these periods, high E. affinis abundance was also observed in the Durme tributary. Our findings suggest the possibility to use E. affinis as an “indicator” species of water quality, but also lead us to stress the necessity to consider conditions over the entire estuary when studying restoration effects, not exclusively in the zone of interest.