Flexible hidden Markov models for behaviour-dependent habitat selection

Background There is strong incentive to model behaviour-dependent habitat selection, as this can help delineate critical habitats for important life processes and reduce bias in model parameters. For this purpose, a two-stage modelling approach is often taken: (i) classify behaviours with a hidden Markov model (HMM), and (ii) fit a step selection function (SSF) to each subset of data. However, this approach does not properly account for the uncertainty in behavioural classification, nor does it allow states to depend on habitat selection. An alternative approach is to estimate both state switching and habitat selection in a single, integrated model called an HMM-SSF. Methods We build on this recent methodological work to make the HMM-SSF approach more efficient and general. We focus on writing the model as an HMM where the observation process is defined by an SSF, such that well-known inferential methods for HMMs can be used directly for parameter estimation and state classification. We extend the model to include covariates on the HMM transition probabilities, allowing for inferences into the temporal and individual-specific drivers of state switching. We demonstrate the method through an illustrative example of plains zebra (Equus quagga), including state estimation, and simulations to estimate a utilisation distribution. Results In the zebra analysis, we identified two behavioural states, with clearly distinct patterns of movement and habitat selection (“encamped” and “exploratory”). In particular, although the zebra tended to prefer areas higher in grassland across both behavioural states, this selection was much stronger in the fast, directed exploratory state. We also found a clear diel cycle in behaviour, which indicated that zebras were more likely to be exploring in the morning and encamped in the evening. Conclusions This method can be used to analyse behaviour-specific habitat selection in a wide range of species and systems. A large suite of statistical extensions and tools developed for HMMs and SSFs can be applied directly to this integrated model, making it a very versatile framework to jointly learn about animal behaviour, habitat selection, and space use.Publisher PDFPeer reviewe

Apports des traçages artificiel et naturel à la connaissance des circulations et des zones de recharge en région semi-aride: cas de l'Atlas de Beni Mellal (Maroc)

Pour mieux comprendre les modalités d'alimentation des sources de l'Atlas, des campagnes de coloration et d'analyses isotopiques ont été effectuées sur l'ensemble des sources. La disparité des circulations, la variabilité des vitesses et des taux de restitution, révèlent un aquifère complexe ou à plusieurs entrées. La majorité des écoulements convergent vers la source de Ain Asserdoune qui constitue une zone d'abaissement d'axe de plis. L'étude isotopique montre la variation des teneurs en 180 avec l'altitude des zones de recharge des différents exutoires et avec la saison. Les gradients définis autorisent la détermination de l'altitude moyenne des impluviums des systèmes jusqu'alors mal connus, en particulier celui de l'exutoire principal du massif, Ain Asserdoune.The chalky massif of Beni-Mellal, which supplies many springs, spreads over a 365 km2 area of 500 to 2400 meters elevation (average altitude, 1200 m). Rainfall in this sector varies between 400 mm and 700 mm/year. All springs emerge along the major coastal fault giving the Liassic massif overthrushing the Cenozoic lands of piemont. The most important is Ain Asserdoune spring with an average discharge of about 1.1 m3/s. The mainly chalky and dolomitic formations are very fractured according to preferential directions (N150-180 and N50-70) and show some karstification features at the surface. Some tracing experiments with fluorescein allowed the delimitation of the boundaries of the intake area of Ain Asserdoune Basin and the determination of the groundwater flow velocity. Two types of flow were identified with fast (100 to 231 m/h) and slow circulation (< 100 m/h). Most of circulations converge towards the spring of Ain Asserdoune (fig. 1) with an important intake area. This convergence results from an axis lowering. The variability of the circulation axes, the velocity and the rate of restitution suggest either a complex aquifer or an aquifer with several inputs.Two water samplings (the first for the Beni Mellal Atlas) were carriet out in March and in September 1993 on the several springs, in order to study the variations of the oxygen-18 isotope. The oxygen-18 contents range between - 5.5 per thousand and - 7.7 per thousand (table 2). The most depleted waters directly exit from the Liassic aquifer or emerge at high altitudes; those which are richer in oxygen-18 emerge at the level of foothills, either from the Tertiary or from Liassic scales. The relationship between the oxygen-18 and the H-2 content of some samples indicates that the points are aligned along the world meteoric line (Craig, 1961). Even if the waters of Dir (piemont) springs are slighly evaporated because they partly originate in seeping Liassic waters, oxygen-18 content is probably mainly controlled by an altitude effect. Oxygen-18 data for local precipitations are not available; however, a local relationship between oxygen-18 content and mean recharge altitude was etablished for eleven (11) springs with small recharge areas whose mean altitude may be estimated from topography and geology. Oxygen 18 ratio is very well correlated to recharge average elevation for spring samples ( [delta]per thousand (O - 18)=- 3 - 0,0026 x altitude, r=0,96, fig. 3), when it is not for autumn samples. This gradient is very close to the regional relationship proposed by Marce (1975) and Kabbaj et al. (1978) (slope: 3 per thousand in oxygen-18 per 1,000 m ). This difference is attributed to the seasonal variations in the origin of water that feeds the springs. In the high water season, the whole basin area contributes to the recharge. In contrast, during low water period, water mainly originates from altitudes higher than the mean altitude of the basin, probably with a longer transit time. The seasonal variations are particularly marked for the Dir (piemont) springs (with a lower flux and intake area range of 800 to 1,200 m). They are weaker for the Lias springs and even non-existent for the main spring of the massif, Ain Asserdoune. In this latter case, the smoothing (- 7.6 per thousand and - 7.5 per thousand) of seasonal variation (which is also observed for temperature: 15.5 to 16°C ) gives evidence of important water reserves. A mean recharge altitude higher than 1,700 m may be proposed for Ain Asseroune. Based on this analysis, some emergences which in the part were assigned to the same hydrologic system can now be discriminated. On the other hand, with a similar value of oxygen-18 ratio, rather distant springs can be considered as belonging to the same hydrogeological Atlasic unit. So the relationship which was quantified (slope: 2.6 per thousand in oxygen-18 per 1,000 m) is usable for the whole Atlasic range on account of regionaly similar weather. The methodology selected in this work corroborates the results obtained by hydrometric analysis concerning the very important groundwater reserves in the Beni Mellal aquifer

General models in min-max continous location

In this paper, a class of min-max continuous location problems is discussed. After giving a complete characterization of th stationary points, we propose a simple central and deep-cut ellipsoid algorithm to solve these problems for the quasiconvex case. Moreover, an elementary convergence proof of this algorithm and some computational results are presented

The elementary events underlying force generation in neuronal lamellipodia

We have used optical tweezers to identify the elementary events underlying force generation in neuronal lamellipodia. When an optically trapped bead seals on the lamellipodium membrane, Brownian fluctuations decrease revealing the underlying elementary events. The distribution of bead velocities has long tails with frequent large positive and negative values associated to forward and backward jumps occurring in 0.1–0.2 ms with varying amplitudes up to 20 nm. Jump frequency and amplitude are reduced when actin turnover is slowed down by the addition of 25 nM Jasplakinolide. When myosin II is inhibited by the addition of 20 μM Blebbistatin, jump frequency is reduced but to a lesser extent than by Jasplainolide. These jumps constitute the elementary events underlying force generation

An Abp1-Dependent Route of Endocytosis Functions when the Classical Endocytic Pathway in Yeast Is Inhibited

Clathrin-mediated endocytosis (CME) is a well characterized pathway in both yeast and mammalian cells. An increasing number of alternative endocytic pathways have now been described in mammalian cells that can be both clathrin, actin, and Arf6- dependent or independent. In yeast, a single clathrin-mediated pathway has been characterized in detail. However, disruption of this pathway in many mutant strains indicates that other uptake pathways might exist, at least for bulk lipid and fluid internalization. Using a combination of genetics and live cell imaging, here we show evidence for a novel endocytic pathway in S. cerevisiae that does not involve several of the proteins previously shown to be associated with the ‘classic’ pathway of endocytosis. This alternative pathway functions in the presence of low levels of the actin-disrupting drug latrunculin-A which inhibits movement of the proteins Sla1, Sla2, and Sac6, and is independent of dynamin function. We reveal that in the absence of the ‘classic’ pathway, the actin binding protein Abp1 is now essential for bulk endocytosis. This novel pathway appears to be distinct from another described alternative endocytic route in S. cerevisiae as it involves at least some proteins known to be associated with cortical actin patches rather than being mediated at formin-dependent endocytic sites. These data indicate that cells have the capacity to use overlapping sets of components to facilitate endocytosis under a range of conditions