Diel variation in movement patterns and habitat use by the near-threatened cabrera vole in mediterranean farmland

As variações circadianas no comportamento animal e o seu impacto nas populações constituem desafios importantes em ecologia e conservação. Nesta tese documentam-se as variações circadianas no uso do habitat e padrões de movimento pelo rato de Cabrera, em habitats Mediterrânicos fragmentados. O estudo baseou-se no radio-seguimento de indivíduos em habitats dominados por herbáceas e arbustos. Os resultados indicaram que a proporção de tempo despendido em deslocações, a distância percorrida, e a selecção do tipo de vegetação, estão fortemente interrelacionados, variando consideravelmente ao longo de diferentes períodos do dia. Os ratos movimentaram-se mais frequentemente e maiores distâncias nos períodos diurnos, durante os quais as áreas dominadas por herbáceas foram usadas mais intensivamente. Durante a estação seca houve alguma tendência para a diminuição dos movimentos durante as horas mais quentes. Estes resultados são discutidos no sentido de mostrar como indicadores comportamentais podem contribuir para melhorar a gestão e conservação da espécie; ABSTRACT: Understanding the circadian variations in species behaviour and its impacts on population is a challenging topic in ecology and conservation. This thesis documents the circadian variations in habitat use and movement patterns by Cabrera voles in fragmented Mediterranean farmland. The study was based on radiotracking data of individuals living in habitat patches dominated by wet grasses and shrubs. Results indicated that the proportion of time animals spent moving, the distance moved and the selection strength of vegetation were closely linked behavioural traits, which varied considerably across the 24 hour cycle. Voles moved more frequently and over larger distances during daytime, which was when wet grasses were used more intensively. During the dry season there was some tendency for a decrease in movement activity during the hottest hours of the day. These results are used to discuss how behavioural indicators may be useful to improve conservation management of the species.

Otolith shape variation provides a marker of stock origin for north Atlantic bluefin tuna (Thunnus thynnus)

Two stocks of bluefin tuna (Thunnus thynnus) inhabit the north Atlantic; the western and eastern stocks spawn in the Gulf of Mexico and the Mediterranean Sea respectively. Trans-Atlantic movements occur outside spawning time whereas natal homing maintains stock structure. Commercial fisheries may exploit a mixed assemblage of both stocks. The incorporation of mixing rates into stock assessment is precluded by uncertainties surrounding stock discrimination. Otolith shape descriptors were used to characterise western and eastern stocks of Atlantic bluefin tuna in the present study and to estimate stock composition in catches of unknown origin. Otolith shape varied with length and between locations and years. Within a restricted size range (200-297-cm fork length (FL)) the two stocks were distinguished with an accuracy of 83%. Bayesian stock mixture analysis indicated that samples from the east Atlantic and Mediterranean were predominantly of eastern origin. The proportion assigned to the eastern stock showed slight spatial variation; however, overlapping 95% credible intervals indicated no significant difference (200-297 cm FL: central Atlantic, 73-100%; Straits of Gibraltar, 73-100%; Morocco, 50-99%; Portugal 64-100%). Otolith shape could be used in combination with other population markers to improve the accuracy of mixing rate estimates for Atlantic bluefin tuna.

ANALYSIS OF MACROINVERTEBRATE COMMUNITIES IN SEASONAL WETLANDS THROUGH TIME, ACROSS SPACE, AND USING SPECIES TRAITS

Restoration of natural wetlands may be informed by macroinvertebrate community composition. Macroinvertebrate communities of wetlands are influenced by environmental characteristics such as vegetation, soil, hydrology, land use, and isolation. This dissertation explores multiple approaches to the assessment of wetland macroinvertebrate community composition, and demonstrates how these approaches can provide complementary insights into the community ecology of aquatic macroinvertebrates. Specifically, this work focuses on macroinvertebrates of Delmarva Bays, isolated seasonal wetlands found on Maryland’s eastern shore. A comparison of macroinvertebrate community change over a nine years in a restored wetland complex indicated that the macroinvertebrate community of a rehabilitated wetlands more rapidly approximated the community of a reference site than did a newly created wetland. The recovery of a natural macroinvertebrate community in the rehabilitated wetland indicated that wetland rehabilitation should be prioritized over wetland creation and long-term monitoring may be needed to evaluate restoration success. This study also indicated that characteristics of wetland vegetation reflected community composition. The connection between wetland vegetation and macroinvertebrate community composition led to a regional assessment of predaceous diving beetle (Coleoptera: Dytiscidae) community composition in 20 seasonal wetlands, half with and half without sphagnum moss (Sphagnum spp.). Species-level identifications indicated that wetlands with sphagnum support unique and diverse assemblages of beetles. These patterns suggest that sphagnum wetlands provide habitat that supports biodiversity on the Delmarva Peninsula. To compare traits of co-occurring beetles, mandible morphology and temporal and spatial variation were measured between three species of predaceous diving beetles. Based on mandible architecture, all species may consume similarly sized prey, but prey characteristics likely differ in terms of piercing force required for successful capture and consumption. Therefore, different assemblages of aquatic beetles may have different effects on macroinvertebrate community structure. Integrating community-level and species-level data strengthens the association between individual organisms and their ecological role. Effective restoration of imperiled wetlands benefits from this integration, as it informs the management practices that both preserve biodiversity and promote ecosystem services.

Temporal variation of faecal indicator bacteria in tropical urban storm drains

Human faecal contamination poses a widespread hazard for human health. In urban areas, sewer leakage may be an important cause of faecal pollution to surface water. Faecal indicator bacteria (FIB) are the most widely used indicators to monitor surface water quality. However, assessing whether a water body is meeting water quality criteria is made difficult by the high variability of FIB concentrations over time. In this study, the variation of FIB concentration in surface water from tropical urban catchments is investigated. Eleven urban sub-catchments were sampled hourly over 24-hr and samples analysed for FIB. It was found that FIB show a diurnal pattern that is characterised by daytime FIB concentrations that are significantly higher than nighttime FIB concentrations. This observed diurnal variation of FIB closely follows that of sewer flows and contrasts with observations in rural streams where FIB concentrations are known to be low in the daytime and high during the night. Field tracer tests provide qualitative evidence of sewage exfiltration and transport to drains via preferential flow paths. The diurnal FIB variation and field tracer tests indicate the likelihood of surface water contamination due to leaking sewers. The results further suggest that contamination of surface-water drains is likely a widespread problem in tropical urban areas due to extensive drainage networks and the persistence of FIB under tropical conditions. Because of FIB variation over time, the time at which samples are collected is important in being able to capture the daily maximum and minimum FIB concentrations. The Kruskal-Wallis test shows that hourly sampling from 04:00 to 07:00 and from 12:00 to 15:00 results in significantly different FIB concentration (minimum and maximum, respectively). Furthermore, the Wilcoxon-Mann-Whitney test shows that sampling at 12:00 and 14:00 results in significantly higher FIB concentrations, while sampling at 05:00 and 04:00 or 05:00 and 06:00 results in significantly lower FIB concentrations, than sampling at other hours of the day.

Association between maternal education and objectively measured physical activity and sedentary time in adolescents

BACKGROUND: Investigating socioeconomic variation in physical activity (PA) and sedentary time is important as it may represent a pathway by which socioeconomic position (SEP) leads to ill health. Findings on the association between children's SEP and objectively assessed PA and/or sedentary time are mixed, and few studies have included international samples.

OBJECTIVE: Examine the associations between maternal education and adolescent's objectively assessed PA and sedentary time.

METHODS: This is an observational study of 12 770 adolescents (10-18 years) pooled from 10 studies from Europe, Australia, Brazil and the USA. Original PA data were collected between 1997 and 2009. The associations between maternal education and accelerometer variables were examined using robust multivariable regression, adjusted for a priori confounders (ie, body mass index, monitor wear time, season, age and sex) and regression coefficients combined across studies using random effects meta-analyses. Analyses were conducted in March 2014.

RESULTS: Adolescents of university educated mothers spent more time sedentary (9.5 min/day, p=0.005) and less time in light activity (10 min/day, p<0.001) compared with adolescents of high school educated mothers. Pooled analysis across two studies from Brazil and Portugal (analysed separately because of the different coding of maternal education) showed that children of higher educated mothers (tertiary vs primary/secondary) spent less time in moderate to vigorous PA (MVPA) (6.6 min/day, p=0.001) and in light PA (39.2 min/day: p<0.001), and more time sedentary (45.9 min/day, p<0.001).

CONCLUSIONS: Across a number of international samples, adolescents of mothers with lower education may not be at a disadvantage in terms of overall objectively measured PA.

Measurement and data transmission validity of a multi-biosensor system for real-time remote exercise monitoring among cardiac patients

Background: Remote telemonitoring holds great potential to augment management of patients with coronary heart disease (CHD) and atrial fibrillation (AF) by enabling regular physiological monitoring during physical activity. Remote physiological monitoring may improve home and community exercise-based cardiac rehabilitation (exCR) programs and could improve assessment of the impact and management of pharmacological interventions for heart rate control in individuals with AF.

Objective: Our aim was to evaluate the measurement validity and data transmission reliability of a remote telemonitoring system comprising a wireless multi-parameter physiological sensor, custom mobile app, and middleware platform, among individuals in sinus rhythm and AF.

Methods: Participants in sinus rhythm and with AF undertook simulated daily activities, low, moderate, and/or high intensity exercise. Remote monitoring system heart rate and respiratory rate were compared to reference measures (12-lead ECG and indirect calorimeter). Wireless data transmission loss was calculated between the sensor, mobile app, and remote Internet server.

Results: Median heart rate (-0.30 to 1.10 b∙min-1) and respiratory rate (-1.25 to 0.39 br∙min-1) measurement biases were small, yet statistically significant (all P≤.003) due to the large number of observations. Measurement reliability was generally excellent (rho=.87-.97, all P<.001; intraclass correlation coefficient [ICC]=.94-.98, all P<.001; coefficient of variation [CV]=2.24-7.94%), although respiratory rate measurement reliability was poor among AF participants (rho=.43, P<.001; ICC=.55, P<.001; CV=16.61%). Data loss was minimal (<5%) when all system components were active; however, instability of the network hosting the remote data capture server resulted in data loss at the remote Internet server during some trials.

Conclusions: System validity was sufficient for remote monitoring of heart and respiratory rates across a range of exercise intensities. Remote exercise monitoring has potential to augment current exCR and heart rate control management approaches by enabling the provision of individually tailored care to individuals outside traditional clinical environments.

Effects of season period, team quality, and playing time on basketball players' game-related statistics

The aim of this study was to identify within-season differences in basketball players' game-related statistics according to team quality and playing time. The sample comprised 5309 records from 198 players in the Spanish professional basketball league (2007-2008). Factor analysis with principal components was applied to the game-related statistics gathered from the official box-scores, which limited the analysis to five factors (free-throws, 2-point field-goals, 3-point field-goals, passes, and errors) and two variables (defensive and offensive rebounds). A two-step cluster analysis classified the teams as stronger (69 ± 8 winning percentage), intermediate (43 ± 5 winning percentage), and weaker teams (32 ± 5 winning percentage); individual players were classified based on playing time as important players (28 ± 4 min) or less important players (16 ± 4 min). Seasonal variation was analysed monthly in eight periods. A mixed linear model was applied to identify the effects of team quality and playing time within the months of the season on the previously identified factors and game-related statistics. No significant effect of season period was observed. A team quality effect was identified, with stronger teams being superior in terms of 2-point field-goals and passes. The weaker teams were the worst at defensive rebounding (stronger teams: 0.17 ± 0.05; intermediate teams: 0.17 ± 0.06; weaker teams: 0.15 ± 0.03; P = 0.001). While playing time was significant in almost all variables, errors were the most important factor when contrasting important and less important players, with fewer errors being made by important players. The trends identified can help coaches and players to create performance profiles according to team quality and playing time. However, these performance profiles appear to be independent of season period.

Office workers' objectively assessed total and prolonged sitting time: individual-level correlates and worksite variations

Sedentary behavior is highly prevalent in office-based workplaces; however, few studies have assessed the attributes associated with this health risk factor in the workplace setting. This study aimed to identify the correlates of office workers' objectively-assessed total and prolonged (≥ 30 min bouts) workplace sitting time. Participants were 231 Australian office workers recruited from 14 sites of a single government employer in 2012-13. Potential socio-demographic, work-related, health-related and cognitive-social correlates were measured through a self-administered survey and anthropometric measurements. Associations with total and prolonged workplace sitting time (measured with the activPAL3) were tested using linear mixed models. Worksites varied significantly in total workplace sitting time (overall mean [SD]: 79% [10%] of work hours) and prolonged workplace sitting time (42% [19%]), after adjusting for socio-demographic and work-related characteristics. Organisational tenure of 3-5 years (compared to tenure > 5 years) was associated with more time spent in total and prolonged workplace sitting time, while having a BMI categorised as obese (compared to a healthy BMI) was associated with less time spent in total and prolonged workplace sitting time. Significant variations in sitting time were observed across different worksites of the same employer and the variation remained after adjusting for individual-level factors. Only BMI and organisational tenure were identified as correlates of total and prolonged workplace sitting time. Additional studies are needed to confirm the present findings across diverse organisations and occupations.

Adding fuel to the "fire of life": energy budgets across levels of variation in ectotherms and endotherms

Energy metabolism - the "fire of life" - is the sum of the processes by which animals acquire energy, channel energy into useful functions, and dissipate energy from their bodies. Acquisition and allocation processes deal with energy mainly as a quantity, but energy is absorbed or expended over a period of time; therefore, the most relevant way to conceptualize energy budgets is with the use of rate functions. A large number of recent studies have examined co-variation in metabolic and behavioral traits among individuals. A general finding stemming from this body of work is that there is no single cause-and-effect mechanism driving these relationships, but that the direction of the effects is dynamic and shifts in different contexts and environments. However, the remarkable energetic differences between endotherms and ectotherms are an unexploited basis for achieving a further understanding of such relationships.

GENETIC VARIATION, LOCAL ADAPTATION AND POPULATION STRUCTURE IN NORTH AMERICAN RED OAK SPECIES, QUERCUS RUBRA L. AND Q. ELLIPSOIDALIS E. J. HILL

Forest trees, like oaks, rely on high levels of genetic variation to adapt to varying environmental conditions. Thus, genetic variation and its distribution are important for the long-term survival and adaptability of oak populations. Climate change is projected to lead to increased drought and fire events as well as a northward migration of tree species, including oaks. Additionally, decline in oak regeneration has become increasingly concerning since it may lead to decreased gene flow and increased inbreeding levels. This will in turn lead to lowered levels of genetic diversity, negatively affecting the growth and survival of populations. At the same time, populations at the species’ distribution edge, like those in this study, could possess important stores of genetic diversity and adaptive potential, while also being vulnerable to climatic or anthropogenic changes. A survey of the level and distribution of genetic variation and identification of potentially adaptive genes is needed since adaptive genetic variation is essential for their long-term survival. Oaks possess a remarkable characteristic in that they maintain their species identity and specific environmental adaptations despite their propensity to hybridize. Thus, in the face of interspecific gene flow, some areas of the genome remain differentiated due to selection. This characteristic allows the study of local environmental adaptation through genetic variation analyses. Furthermore, using genic markers with known putative functions makes it possible to link those differentiated markers to potential adaptive traits (e.g., flowering time, drought stress tolerance). Demographic processes like gene flow and genetic drift also play an important role in how genes (including adaptive genes) are maintained or spread. These processes are influenced by disturbances, both natural and anthropogenic. An examination of how genetic variation is geographically distributed can display how these genetic processes and geographical disturbances influence genetic variation patterns. For example, the spatial clustering of closely related trees could promote inbreeding with associated negative effects (inbreeding depression), if gene flow is limited. In turn this can have negative consequences for a species’ ability to adapt to changing environmental conditions. In contrast, interspecific hybridization may also allow the transfer of genes between species that increase their adaptive potential in a changing environment. I have studied the ecologically divergent, interfertile red oaks, Quercus rubra and Q. ellipsoidalis, to identify genes with potential roles in adaptation to abiotic stress through traits such as drought tolerance and flowering time, and to assess the level and distribution of genetic variation. I found evidence for moderate gene flow between the two species and low interspecific genetic differences at most genetic markers (Lind and Gailing 2013). However, the screening of genic markers with potential roles in phenology and drought tolerance led to the identification of a CONSTANS-like (COL) gene, a candidate gene for flowering time and growth. This marker, located in the coding region of the gene, was highly differentiated between the two species in multiple geographical areas, despite interspecific gene flow, and may play a role in reproductive isolation and adaptive divergence between the two species (Lind-Riehl et al. 2014). Since climate change could result in a northward migration of trees species like oaks, this gene could be important in maintaining species identity despite increased contact zones between species (e.g., increased gene flow). Finally I examined differences in spatial genetic structure (SGS) and genetic variation between species and populations subjected to different management strategies and natural disturbances. Diverse management activities combined with various natural disturbances as well as species specific life history traits influenced SGS patterns and inbreeding levels (Lind-Riehl and Gailing submitted).

An inter-laboratory validation of a real time PCR assay to measure host excretion of bacterial pathogens, particularly of Mycobacterium bovis

Advances in the diagnosis of Mycobacterium bovis infection in wildlife hosts may benefit the development of sustainable approaches to the management of bovine tuberculosis in cattle. In the present study, three laboratories from two different countries participated in a validation trial to evaluate the reliability and reproducibility of a real time PCR assay in the detection and quantification of M. bovis from environmental samples. The sample panels consisted of negative badger faeces spiked with a dilution series of M. bovis BCG Pasteur and of field samples of faeces from badgers of unknown infection status taken from badger latrines in areas with high and low incidence of bovine TB (bTB) in cattle. Samples were tested with a previously optimised methodology. The experimental design involved rigorous testing which highlighted a number of potential pitfalls in the analysis of environmental samples using real time PCR. Despite minor variation between operators and laboratories, the validation study demonstrated good concordance between the three laboratories: on the spiked panels, the test showed high levels of agreement in terms of positive/negative detection, with high specificity (100%) and high sensitivity (97%) at levels of 10(5) cells g(-1) and above. Quantitative analysis of the data revealed low variability in recovery of BCG cells between laboratories and operators. On the field samples, the test showed high reproducibility both in terms of positive/negative detection and in the number of cells detected, despite low numbers of samples identified as positive by any laboratory. Use of a parallel PCR inhibition control assay revealed negligible PCR-interfering chemicals co-extracted with the DNA. This is the first example of a multi-laboratory validation of a real time PCR assay for the detection of mycobacteria in environmental samples. Field studies are now required to determine how best to apply the assay for population-level bTB surveillance in wildlife.

Measuring Latency Variation in the Internet

We analyse two complementary datasets to quantify the latency variation experienced by internet end-users: (i) a large-scale active measurement dataset (from the Measurement Lab Network Diagnostic Tool) which shed light on long-term trends and regional differences; and (ii) passive measurement data from an access aggregation link which is used to analyse the edge links closest to the user. The analysis shows that variation in latency is both common and of significant magnitude, with two thirds of samples exceeding 100\,ms of variation. The variation is seen within single connections as well as between connections to the same client. The distribution of experienced latency variation is heavy-tailed, with the most affected clients seeing an order of magnitude larger variation than the least affected. In addition, there are large differences between regions, both within and between continents. Despite consistent improvements in throughput, most regions show no reduction in latency variation over time, and in one region it even increases. We examine load-induced queueing latency as a possible cause for the variation in latency and find that both datasets readily exhibit symptoms of queueing latency correlated with network load. Additionally, when this queueing latency does occur, it is of significant magnitude, more than 200\,ms in the median. This indicates that load-induced queueing contributes significantly to the overall latency variation.

Diversity and Stability in Food Webs : Impacts of Non-Equilibrium Dynamics, Topology and Variation

With progressive climate change, the preservation of biodiversity is becoming increasingly important. Only if the gene pool is large enough and requirements of species are diverse, there will be species that can adapt to the changing circumstances. To maintain biodiversity, we must understand the consequences of the various strategies. Mathematical models of population dynamics could provide prognoses. However, a model that would reproduce and explain the mechanisms behind the diversity of species that we observe experimentally and in nature is still needed. A combination of theoretical models with detailed experiments is needed to test biological processes in models and compare predictions with outcomes in reality. In this thesis, several food webs are modeled and analyzed. Among others, models are formulated of laboratory experiments performed in the Zoological Institute of the University of Cologne. Numerical data of the simulations is in good agreement with the real experimental results. Via numerical simulations it can be demonstrated that few assumptions are necessary to reproduce in a model the sustained oscillations of the population size that experiments show. However, analysis indicates that species "thrown together by chance" are not very likely to survive together over long periods. Even larger food nets do not show significantly different outcomes and prove how extraordinary and complicated natural diversity is. In order to produce such a coexistence of randomly selected species—as the experiment does—models require additional information about biological processes or restrictions on the assumptions. Another explanation for the observed coexistence is a slow extinction that takes longer than the observation time. Simulated species survive a comparable period of time before they die out eventually. Interestingly, it can be stated that the same models allow the survival of several species in equilibrium and thus do not follow the so-called competitive exclusion principle. This state of equilibrium is more fragile, however, to changes in nutrient supply than the oscillating coexistence. Overall, the studies show, that having a diverse system means that population numbers are probably oscillating, and on the other hand oscillating population numbers stabilize a food web both against demographic noise as well as against changes of the habitat. Model predictions can certainly not be converted at their face value into policies for real ecosystems. But the stabilizing character of fluctuations should be considered in the regulations of animal populations.

Shedder status— An analysis of self and non-self DNA in multiple handprints deposited by the same individuals over time

There are several studies that suggest that different people deposit different quantities of their own DNA on items they touch, i.e. some are good shedders and others are bad shedders. It is of interest to determine if individuals deposit consistent quantities of their own DNA, no matter the occasion, as well as the degree of variability among individuals. To investigate this, participants were tested for their ability to deposit DNA by placing right and left handprints on separate DNA-free glass plates at three set times during the day (morning, midday and afternoon) on four different days spaced over several weeks. Information regarding recent activities performed by the individual was recorded, along with information on gender, hand dominance and hand size. A total of 240 handprint deposits were collected from 10 individuals and analyzed for differences in DNA quantity and the type of the DNA profile obtained at different times of the day, on different days, between the two hands of the same individual, and between different individuals. Furthermore, the correlation between the deposit quantity and the ratio of self to non-self DNA in the mixed deposits was analyzed to determine if the amount of non-self DNA has an effect on overall DNA quantities obtained. In general, this study has shown that while there is substantial variation in the quantities deposited by individuals on different occasions, some clear trends were evident with some individuals consistently depositing significantly more or less DNA than others. Non-self DNA was usually deposited along with self DNA and, in most instances, was the minor component. Incidents where the non-self portion was the major component were very rare and, when observed, were associated with a poor depositor/shedder. Forensic DNA scientists need to consider the range and variability of DNA a person deposits when touching an object, the likelihood of non-self DNA being co-deposited onto the handled object of interest and the factors that may affect the relative quantity of this component within the deposit.

Criterion validity of the activPAL™ and ActiGraph for assessing children's sitting and standing time in a school classroom setting

BACKGROUND: Few studies have investigated the accuracy of the ActiGraph (AG) GTX3 accelerometer for assessing children's sitting and standing time. The activPAL (aP) has an inclinometer function that enables it to distinguish between sitting/lying and standing; however, its accuracy for assessing sitting and standing in older children is unknown. This study validated the accuracy of these devices for estimating sitting and standing time in a school classroom against a criterion measure of direct observation (DO).

FINDINGS: Forty children in grades 5-7 wore both devices while being video recorded during two school lessons. AG and aP data were simultaneously collected in 15-s epochs. Individual participant DO and aP data were recorded as total time spent sitting/lying, standing and stepping. AG data were converted into time spent sitting and standing using previously established cut-points. Compared with DO, the aP underestimated sitting time (mean bias = -1.9 min, 95 % LoA = -8.9 to 5.2 min) and overestimated standing time (mean bias = 1.8 min, 95% LoA = -9.6 to 13.3 min). The best-performing AG cut-point across both sitting and standing (<75 counts/15 s) was more accurate than the aP, underestimating sitting time (mean bias = -0.8 min, 95 % LoA = -10.5 to 9.9 min) and standing time (mean bias = -0.4 min, 95% LoA = -9.8 to 9.1 min), but was less precise as evidenced by wider LoAs and poorer correlations with DO (sitting r = 0.86 aP vs 0.80 AG; standing r = 0.78 aP vs 0.60 AG).

CONCLUSIONS: The aP demonstrated good accuracy and precision for assessing free-living sitting and standing time in classroom settings. The AG was most accurate using a cut-point of < 75 counts/15 s. Further studies should validate the monitors in settings with greater inter- and intra-individual variation in movement patterns.