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A participatory monitoring programme of an exceptional modification of urban soundscapes during Covid-19 containment (Data collection in progress)

Future software improvements. (PDF 110 kb)

Supplementary references. (PDF 85 kb)

Comparison with other packages. (PDF 282 kb)

Basic simulation workflow. (PDF 155 kb)

Performance assessment of SiMRivâ s optimization approach. (PDF 935 kb)

Despite being a highly studied carnivore, the Eurasian otter (Lutra lutra) still offers the opportunity to explore many aspects of its ecology and behaviour that are poorly known or have only been investigated in temperate areas. From April 2007 to October 2010, the OPA research project (Otter Project in Alentejo) was conducted in the south-central Alentejo region of Portugal, in an area of roughly 800 km2. Through the capture and subsequent radio-tracking of 16 wild Lutra lutra individuals (9 males and 7 females) for an average of 139 radio-locations per animal (about 126 days), together with the genotyping of 51 individual otters, the project aimed to provide a set of basic data on the biology and ecology of the species that were missing or limited throughout its extent of occurrence or in the Mediterranean environment. This thesis focus on some of the aspects of the referred project, such as: (1) extent of home ranges (HR) and movement patterns, including their relationships to seasonality and the availability (and its variability) of water resources; (2) genetic spatial structure, dispersal and social interactions; (3) activity rhythms; (4) habitat selection, with particular focus on the modality and frequency of use of reservoirs; (5) testing of a GPS GSM/GPRS telemetry system in riparian habitats and on free-ranging wild otters. Concerning point (1), Network K-function analyses revealed a non-uniform use of home ranges in all monitored individuals of adult size, thus showing fidelity to their annual home range (site fidelity). On average, 49 radio-locations (fixes) (corresponding to approximately 45 days of tracking) were necessary to estimate a stable home range. The estimated average linear extension of home ranges was approximately 16.8 km for females (SE = 2.8) and 38.5 km for males (SE = 2.4), or 22.5 and 92.7 Ha respectively. The maximum extension recorded was 68.1 km (78.6 km including outliers). All individuals had at least one artificial reservoir within their home ranges, representing, on average, 32% of each home range. Several measures of abundance and dispersion of water (which, in turn, also affect the dispersion of aquatic prey) were used in correlation analyses and multiple regression analyses, using Generalized Linear Models (GLM) with the extent of the monitored otters‟ home range as the response variable. The goal was to test the Resource Dispersion Hypothesis (RDH - Macdonald 1983), a hypothesis which predicts, amongst other, the extent of territories in terms of resource dispersion within them. All analyses conducted showed a general influence of abundance and dispersion on otters‟ home range size. However, the response of individuals to changes brought on by the arrival of summer drought was quite diverse. Besides sex and maturity of the animal, it was dependent on the characteristics of the main stream in which it lived and on its space use modality: animals that lived along waterways that have dried up less than the average showed smaller extents of HRs as well as those that consistently used one or a few lentic environments of limited size. Larger extents were usually associated with animals whose HRs were located in areas with high dispersion of water or with individuals which showed a less concentrated use of reservoirs. In general, it appears that the percentage of drought during the dry season determines the minimum HR size (when the otters would tend to enclose within their home ranges patches with a minimum amount of water), while during the wet season – when minimum size is already guaranteed – otters would expand their territories (home ranges) to the surrounding areas, increasing the possibilities of foraging and mating (area-minimizing strategy - Mitchell & Powell 2004, 2007). During a single night (N = 54), otters used on average 3.7 km (SD = 2.9, range: 0 - 14.3) of the annual home range, moving 2 km (SD = 2.8, range: 0 - 22.9) away from the start point of activity (always coinciding with a known resting site) and covering a cumulative distance of 8.2 km (SD = 5.2, range: 0 - 24.2), with a revisiting index ranging from 0 to 4.23 (mean = 2.44, SD = 0.91). Between two fixes of a continuous monitoring session (documented every 15 minutes), the average displacement was 183 m (SD = 355, range 0 - 4271, N = 5609), at an average speed of 712 m/h (SD = 1308; range: 0 - 16325) (N = 5904). All monitored otters (N = 19, including those tagged with GPS harnesses) showed high fidelity to the aquatic habitat, being always located (N = 10286) within a short distance from water (mean = 19 m, SD = 25, range: 0 - 521). Most of the variability observed in movement parameters was caused by interactions between sex, age and season. In particular, adult males were the most mobile category and this was especially true during the wet season, when the greater abundance of water and the return of the hydric connectivity in the previously dried watercourses led to a larger extension in their movements and expansion of home ranges, probably in an attempt to maximize reproductive opportunities. During the wet season movement parameters were generally higher in both sexes, while revisiting rates were higher in the dry season. Correlation analyses performed between movement patterns and variables concerning the dispersion and abundance of water showed that with an increase in the availability of watery sectors the otters increased the amplitude of their movements, reducing their visits to the same portions of their range; on the other side, with a greater fragmentation of the hydrography, indicated by a higher average percentage of dry sites, movements were less extensive and revisits more frequent. Such findings confirm the critical effect that the fragmentation in the availability of the water resource exerts on the biology and behaviour of otters in a Mediterranean environment. Regarding point (2), a mixed approach consisting of genetic techniques and radio-telemetry was used with the following purposes: to verify the existence of a spatial structure in the relationship between individuals of the same population; to investigate the scale of the hypothetical relationship between degree of relatedness and geographic distance; to identify events of dispersal; to verify the hypothesis of a male-biased dispersal in this species; to study the social interactions between monitored individuals. The molecular data refers to DNA extraction from 65 samples of tissue, hair, blood or fresh spraints collected during the project, which led to the genotyping of 51 individuals (28 females and 23 males). These analyses revealed that spatially closer females (N = 286 paired combinations) were more related, while the same cannot be stated for males (N = 224 paired combinations). These patterns are suggestive of male-biased dispersal. Surprisingly, the relationship between geographic distance and relatedness decreased after a threshold of about 30–40 km, suggesting the existence of isolation by distance between individuals of the study population at a fine spatial (and time) scale. The first data on dispersal by this species obtained through radio tracking techniques are presented. These data are the first from a Mediterranean area and are an addition to the only previously reported case on this species (involving a one year old male of a Scottish population marked with radio-active zinc, which dispersed 68 km). Dispersal was detected only in males (N = 4), in a sample of 7 sub-adult individuals monitored; no events of dispersion were documented in either 2 sub-adult females (F6 and F8), nor in one of the males (M4), confirming evidences about male-biased dispersal gathered through molecular analyses. The dispersal distance was on average 20 km (SD = 6), ranging from 10 to 26 km (or 34 ± 9, range: 25 - 47, when expressed as cumulative distance traveled). Possible explanations of the short dispersal distances are discussed. Interestingly, of the 4 sub-adult males of which dispersal was detected, 3 followed the same route and ended up occupying (at different times) almost the same area, although they had potentially available different parts of river catchments and directions. Still regarding the socio-spatial organization of the species, analyses of static and dynamic interactions were performed on individuals with neighbouring or overlapping home ranges. From these analyses, it appears that also in the Mediterranean study area the social organization of the species falls within the classical model of intrasexual territoriality typical of mustelids, with a polygynous breeding system. However, some discrepancies have emerged with regard to what is reported in literature. Contrary to the commonly referred solitary behaviour of the species, monitored otters showed a high degree of overlap in space and time (in some cases even sharing the same diurnal resting sites and even between a male and a female with cubs when the former was known for not being the father). By documenting a large portion of time spent together (not only during matings) by individuals of opposite sex, some flexibility in the social system of this species is highlighted. The evidence gathered confirms the idea that the sociality of a species is complex and variable, and suggests the necessity to undertake further studies on the sociality of the Eurasian otter at the individual level and fine temporal and spatial scale in diverse areas. The otters showed high levels of activity, with 45% of fixes documented as in activity and the remaining 55% at rest and the percentages rosing to 76 and 23, respectively, when considering only night fixes. The activity was, indeed, mainly nocturnal. Among the major determinants of circadian rhythms were foraging strategies (nocturnal hours are believed to present better conditions for catching the two major categories of prey: fish and red swamp crayfish), thermoregulation (to avoid extreme temperatures, both hot and cold), seasonal variability (higher activity during the wet season), age, dispersal events in young males and reproductive status in females. The onset of activity was correlated with sunset time, while the end of activity was less predictable. The hours of greatest activity were concentrated after sunset (from 21:00 to 22:00), in the middle of the night (from 2:00 to 3:00) and before dawn (around 5:00). Multiple regression analyses using generalized linear mixed-effect models (GLMM) showed a combined effect of several weather variables and micro-climatic conditions on nocturnal activity patterns. In particular, among other documented effects, extreme temperatures decrease the probability of finding an otter in activity. The same models, when applied to the width of movement undertaken by the otters, showed the influence of a smaller number of variables. It therefore seems that the decision to be active or not depends much on environmental descriptors, which may in turn regulate the activity rhythms of prey, while the choice to make a substantial move or not is mainly related to intrinsic factors such as sex, age and reproductive requirements. Such choice could also be conditioned by memory/cognitive maps related to resource location, territorial marking needs and interaction with conspecifics. Habitat selection (point 4) was analyzed on a substantial sample of radio-monitored animals through a dual methodological approach, consisting in logistic regression in generalized linear mixed-effect models (GLMM) and the more traditional method of use/availability of Neu et al. (1974). The two methods were applied both on the whole set of fixes and only on the active ones. The final model selected by the GLMM, regarding the probability of an otter visiting a specific sector (100 m) of its home range, seems to indicate that this is influenced by: the distance from the nearest known resting site (with probability decreasing the greater the distance); the type of habitat (water channels were less visited than dams, rivers and ponds), which is in turn dependent on the season (ponds are most visited during the dry season); the presence, during the dry season, of perennial pools; the distance from the site with the highest biomass of the red swamp crayfish (and, as a proxy, also of fish); the distance from the nearest dam (with probability decreasing the greater the distance); the distance from the nearest paved road (there is more chance of a site being visited the further away a road is); and the distance from home range boundaries (the farther from the boundaries, the less likely it is for an otter to visit a site). The probability of otter activity in a particular section within its home range appeared to be influenced by the same factors. However, in this model: the distance from the nearest confluence was also selected (the farther from a confluence site, the lower the probability of selection by an otter during its period of activity); increased activity was associated in decreasing order with ponds, dams and rivers, while in the first model the order was dams, rivers and ponds (it is to be noted that these three habitat types are the most selected in both models). Furthermore, there is a different order in the importance of the variables‟ effects due to slight variations in the estimates of their coefficients and some minor differences in the estimates of the coefficients of the same variables, mainly regarding to the distance from the nearest resting site, which appears greater in the first than in the second model (as expected, since the first also includes fixes during the day, when the otters are on most occasions inactive in their resting sites). All the analyses performed on habitat selection highlight a continuous use of lentic habitats by the otters throughout the year and not just during summer months as previously hypothesized in literature. Reservoirs appear to be selected in particular because of prey abundance (mainly fish, here, on average, more abundant), but, being scarce in terms of cover (therefore shelter availability), they are much less used for resting, for which otters selected streams in the majority of cases. These, however, are also used for foraging, especially for the red swamp crayfish, which is here, on average, more abundant. Ponds are used quite frequently for both activity and rest and they seem to play an important role during cubs‟ raising. The behaviour shown by monitored individuals is consistent with habitat selection already occurring at the landscape scale (second-order selection - Johnson 1980). The selection of streams (in primis) and ponds for resting seems to be due to the high availability of riparian vegetation. Results obtained here therefore highlight the need of a set of habitats for the otter in a Mediterranean context: lentic ones, which serve as main source of water and prey during the extreme summer drought, and lotic ones, richer in riparian vegetation and which therefore provide shelter and conditions for prey resilience in the intermittent isolated pools, confirming what was previously suggested by studies carried out by indirect methods (presence signs‟ surveys). A low-cost GPS GSM-GPRS system (point 5), developed by the Dutch Otterstation Foundation (Netherlands), has been tested in this project for the first time on an otter species (through the use of harnesses). This tool allowed to track animals (N = 6, 711 locations, for a mean period of 9 days and the rate of acquisition of the GPS signal 68.2%) with a high frequency (otherwise impossible based only on man-powered field work) and resulted in a good accuracy level (average error = 8.9 m, SD = 8.5). This experiment was also the first test of a GPS technology in a riparian habitat and on a fresh-water diving animal. The collection of dead animals enabled to expand the sample and to acquire some information on demographic parameters of the studied otter population as well as to perform some morphometric measurements. In particular, the population had a sex ratio of 0.8 males per one female (N = 51), broken down into 39% cubs, 39% adults and 26% sub-adult individuals (N = 40). The estimated average age was 2.2 years (SD = 2.5), with a maximum of 11 years (one female specimen). Death by anthropic causes was noticeable, the major mortality factor being represented by road accidents (62%, N = 24). Mortality events were mainly distributed in the first two months of autumn, after the summer droughts. From the morphometric measurements collected on a sample of 35 animals, the average weight of male individuals was 8.5 kg (SD = 0.9, N = 5) and that of females 6.6 kg (SD = 1.0, N = 10). Average body length was 123.6 cm (SD = 2.6) for males and 111.9 cm (DS = 3.5) for females. Estimates of otter density within individual home ranges of 5 monitored females varied from 0.23 (± 0.05) alle 0.53 (± 0.16) otters per km, depending on whether they are referred to the entire portion of the used water network or only to main rivers respectively. The number of otters captured (N = 47), in particular those equipped with intraperitoneal radio-transmitters (N = 16), together with the long-term average monitoring period per animal (401 days), were higher than those of previous studies of radio tracking of Lutra lutra. This allowed to identify a correct protocol of capture (including the testing of different trapping alarm systems), surgical implant and radio-monitoring of the species, as well as to extend the obtained inferences at a population level. The mixed approach, consisting of radio tracking and molecular techniques, combined with the collection of a fair number of deceased animals in the study area, enabled to gain a wealth of information at the individual level and for a reasonable period of time (about 3 ½ years), covering different aspects of the ecology of a population. The results here provided reveal previously unknown or little known aspects of the eco-ethology of the species, particularly in a Mediterranean environment, such as extents of home-ranges, habitat use and selection, movement and activity patterns, social interactions, dispersal, spatial structure of the relatedness between individuals and density of population. They therefore constitute a source of important information for proper management and conservation of this species in the Portuguese territory (and possibly applicable to other Mediterranean environments). Although the conservation status of otters in Portugal is reassuring, all the evidence collected during this study emphasizes that the Mediterranean populations of this species are subject to significant risks associated with their dependence on water. Different evidence on how the ecology and behaviour of the species are strongly influenced by the climatic characteristics of the Mediterranean environment and the fragmentation and high variability in the availability of the water resource caused by droughts were indeed provided. Such evidence highlight that otters are potentially affected by climate change already in the present and in many aspects of their ecology/behaviour, confirming what was recently suggested for the future distribution of the species through climate simulation models (Cianfrani et al. 2011). external referees were: prof Anna Loy (Università del Molise - Italy) and prof Sandro Lovari (Università di Siena - Italy). the PhD project was basically funded by Lorenzo Quaglietta's fellowship, with a little help from Fundaçao Luis de Molina (Evora University - Portugal).

Ecologists traditionally investigate the feeding ecology of vertebrates by visual identification of prey in their scats using a microscope. This analysis, however, presents some pitfalls, such as poor prey identification at genus/species level. DNA barcoding is an alternative to the traditional diet analysis, recently applied to investigate the diet of several vertebrates. It allows the identification of cryptic or not-recognizable prey portions basing their identification on the analysis of conserved DNA fragments. Here, we combined microscope analysis with DNA barcoding to investigate the diet of the Eurasian otter (Lutra lutra) in an area recently recolonized by the species, in the surroundings of Tarvisio, NE Italy. We collected 102 spraints and analysed all of them at microscope. A random subsample (N=50) was then analysed through DNA barcoding, via amplification of the V9 region of the SSU 18S-rDNA 18S gene. Furthermore, we assessed seasonal variation in otter diet and whether otters select certain salmonids size classes, to identify potential conflict with anglers. According to the microscope analysis, otters ate primarily fish (salmonids and European bullhead), secondarily amphibians and, more rarely, crayfish, both annually and seasonally. DNA barcoding analysis confirmed the microscope results, attributing some salmonids sequences to the brown trout (Salmo trutta). The lack of potential prey species reference sequences in the GenBank database hampered us in identifying the other taxa found in the spraints at more informative levels. Consumed salmonids and bullheads were of small size. In particular, otters selected salmonids size class of 100 mm, which is much smaller than the minimum catchable size for angling. Overall, our study confirms DNA barcoding potential for otter diet analyses, highlighting the need of additional markers to improve molecular prey identification and suggesting that otters do not constitute a significant threat to anglers in the area.

CARNEIRO, Inês Sofia Mendes - Territorial and Social Behaviour of the Pyrenean desman (Galemys pyrenaicus) assessed from Scat Deposition. Coimbra : [s.n.], 2016. Dissertação de Mestrado. Os ecossistemas aquáticos são conhecidos pela sua notável biodiversidade, contendo cerca de um terço de espécies restritas a este habitat (Charbonnel et al., 2015). No entanto, encontram-se entre os habitats mais ameaçados do mundo, devido essencialmente a actividades antropogénicas que afectam gravemente a biodiversidade aquática (Biffi et al., 2016; Charbonnel et al., 2015). Nestes casos, espécies raras de carácter endémico e de reduzido tamanho populacional são particularmente importantes para a biologia de conservação, dada a sua vulnerabilidade (Charbonnel et al., 2015; Melero, Aymerich, Luque-Larena, & Gosàlbez, 2012). Dentro das espécies aquáticas raras, Galemys pyrenaicus é um dos mamíferos Europeus menos conhecido do público em geral e dentro da comunidade científica (Charbonnel et al., 2015; Melero et al., 2012). O seu estatuto vulnerável, associado à falta de conhecimentos sobre a ecologia e comportamento da espécie, tem-se revelado um dos maiores desafios contemporâneos à conservação e gestão da mesma para muitos cientistas (Melero et al., 2012). Estudos anteriores, focados na selecção de habitat da toupeira-de-água a uma escala fina, apresentam alguns problemas como a definição de escalas grosseiras para identificação de associações ambientais finas e a falta de inferência estatística (Biffi et al., 2016; Charbonnel et al., 2015). Considerando os problemas descritos, o nosso projecto tenta complementar a informação existente sobre a selecção de habitat da toupeira-de-água usando descritores a duas diferentes escalas espaciais (micro-habitat – 0,5 m2 – e transecto - ~200-600m). Os objectivos principais deste estudo são 1) estudar os padrões que determinam quais as variáveis ambientais que mais influenciam o comportamento de deposição de excrementos por parte da toupeira-de-água, a duas escalas diferentes; e 2) perceber a importância ecológica das variáveis de habitat seleccionadas para a deposição de dejectos como “recursos-chave” para determinar a presença de toupeira-de-água. Para isso, testámos a influência das variáveis: presença de amieiro, localização nas margens ou leito, exposição do substrato, velocidade da água e a presença de musgo (variáveis ambientais e biológicas de escala fina). Também testámos a influência das variáveis: percentagem de cobertura, “spraintability”, largura do leito, velocidade da água, percentagem de “pool” e percentagem de “riffle” (variáveis ambientais e biológicas de larga escala) na abundância de dejectos de toupeira-de-água encontrados por km de transecto. Verificámos que a uma escala mais fina a toupeira- de-água depositou os seus excrementos principalmente em locais não expostos, localizados nas margens do rio, perto de locais de grande velocidade da água. Ao contrário do que era esperado, a presença de amieiro não resultou ser determinante na selecção feita pela espécie. A presença de musgo demonstrou um efeito inconsistente da variável. À escala do transecto, o uso do habitat local pela toupeira baseado na distribuição dos seus dejectos parece influenciado pela heterogeneidade de substrato. Estes resultados serão importantes para perceber quais as características de habitat mais importantes para a toupeira-de-água, o que poderá permitir inferências sobre a comunicação e organização social da espécie. Freshwater environments are known for its notable biodiversity, holding about one third of vertebrate species restricted to this ecosystem (Charbonnel et al., 2015). However, they are amongst the most threatened habitats in the world due to human activities that cause alterations of the natural river conditions and strongly affect aquatic biodiversity (Biffi et al., 2016; Charbonnel et al., 2015). In these environments, rare species with small population sizes and especially endemic species are of particular interest for conservation biology due to their vulnerability to extinction (Charbonnel et al., 2015; Melero et al., 2012). Among rare freshwater species the Pyrenean desman (Galemys pyrenaicus) is one of the less known European mammals to the general public (Charbonnel et al., 2015; Melero et al., 2012) and within the scientific community. Its vulnerable status together with an almost complete lack of knowledge regarding their ecology and behaviour has made their conservation and management a contemporary challenge for many scientists (Melero et al., 2012). Previous studies have investigated the habitat preferences of Pyrenean desman at small- site scale but they present some problems like the definition of scales too coarse to identify finer habitat associations and the lack of statistical inference (Biffi et al., 2016; Charbonnel et al., 2015). Taking into account the described problems, our project tries to complement the information existent on Pyrenean desman habitat preferences using descriptors at two different scales (small-site scale – 0,5m2 – and a larger scale - ~200-600m). The main objectives of this study were 1) to study the patterns that determine which environmental factors mostly influence the scat deposition behaviour of the Pyrenean desman at two different scales 2) to understand the ecological importance of the habitat variables selected for scat deposition as key resources for determining the Pyrenean desmans‟ presence. This was achieved by testing the influence of the variables presence of alder, bank or bed localization, substrate exposure, water speed and presence of musk (small-scale environmental and biological variables). We also tested the influence of the variables: percentage of coverage, spraintability, riverbed width, water speed, percentage of pool and percentage of riffle (large scale environmental and biological variables). We verified that at a small-site scale, Pyrenean desman preferentially selected as habitat requirements non-exposed sites, preferably at riverbanks near locations of high river flow. Contrary to what was expected, alder presence was not determinative for Pyrenean desman selection. Musk revealed inconsistent variable effect, with its significance varying a lot. At a larger scale, the use of local habitat by the Pyrenean desman appears to be driven by higher spraintability with transects with abundant emergent items and greater percentage of substrate heterogeneity preferably selected. These results will be important also to help understanding which habitat characteristics are important to the Pyrenean desman, which may draw clues on communication and social organization of the species.

Tese de mestrado, Ecologia e Gestão Ambiental, Universidade de Lisboa, Faculdade de Ciências, 2015 Submitted by Teresa Boa (tdboa@fc.ul.pt) on 2016-01-28T15:18:25Z No. of bitstreams: 1 ulfc116082_tm_Sofia_Coelho.pdf: 1062376 bytes, checksum: 6e2bca5bbbf8de335f525bdc101a65c5 (MD5) Made available in DSpace on 2016-01-28T15:18:35Z (GMT). No. of bitstreams: 1 ulfc116082_tm_Sofia_Coelho.pdf: 1062376 bytes, checksum: 6e2bca5bbbf8de335f525bdc101a65c5 (MD5) Previous issue date: 2015