Mark-recapture methods use repeated captures of individually identifiable animals to provide estimates of properties of populations. Different models allow estimates to be obtained for population size and rates of processes governing population dynamics. State-space models consist of two linked processes evolving simultaneously over time. The state process models the evolution of the true, but unknown, states of the population. The observation process relates observations on the population to these true states. Mark-recapture models specified within a state-space framework allow population dynamics models to be embedded in inference ensuring that estimated changes in the population are consistent with assumptions regarding the biology of the modelled population. This overcomes a limitation of current mark-recapture methods. Two alternative approaches are considered. The "conditional" approach conditions on known numbers of animals possessing capture history patterns including capture in the current time period. An animal's capture history determines its state; consequently, capture parameters appear in the state process rather than the observation process. There is no observation error in the model. Uncertainty occurs only through the numbers of animals not captured in the current time period. An "unconditional" approach is considered in which the capture histories are regarded as observations. Consequently, capture histories do not influence an animal's state and capture probability parameters appear in the observation process. Capture histories are considered a random realization of the stochastic observation process. This is more consistent with traditional mark-recapture methods. Development and implementation of particle filtering techniques for fitting these models under each approach are discussed. Simulation studies show reasonable performance for the unconditional approach and highlight problems with the conditional approach. Strengths and limitations of each approach are outlined, with reference to Soay sheep data analysis, and suggestions are presented for future analyses.

The topic of badgers in the UK is often a contentious one, dividing opinions and sparking political debate. On one hand, badgers represent an important part of the British ecosystem but on the other a wildlife reservoir of disease implicated in the transmission of bovine tuberculosis (TB) to livestock in the UK. This has prompted strong interest in their population dynamics and epidemiology. Using data from a long-term study of a naturally infected badger population in Woodchester Park, Gloucestershire, this thesis explores a range of capture-mark-recapture (CMR) models to further understand disease and demographic processes. The first section examines long term population dynamics, simultaneously estimating demographic rates alongside their drivers using integrated population models (IPMs). The findings provide new insight into badger demography, highlighting density-dependent mechanisms, vulnerabilities to changing climate and disease prevalence and subsequently how multi-factorial analyses are required to explain fluctuating badger populations. The following sections use multistate models to answer pertinent questions regarding individual disease dynamics, revealing rates of TB infection, progression and disease-induced mortality. A key finding was sex-differences in disease response, with males more susceptible to TB infection. After applying a survival trajectory analysis we suggest sex differences are due to male immune defence deficiencies. A comparative analysis demonstrated similarities between epidemiological processes at Woodchester Park to an unconnected population of badgers from a vaccine study, supporting its continued use as a model population. The final study in this thesis constructs an IPM to estimate disease and population dynamics and in doing so uncovers disease-state recruitment allocation rates, demographic and population estimates of badgers in varying health-states and predicts future dynamics. This model aims to encapsulate the more commonly held notion of populations as dynamic entities with numerous co-occurring processes, opening up avenues for future analyses within both the badger-TB system and possible extensions to other wildlife reservoir populations.

Η εργασία αυτή αποσκοπούσε στη μελέτη της πληθυσμιακής και συμπεριφορικής οικολογίας σε δύο είδη τριτώνων που διαβιούν συμπάτρια σε ένα εποχικό τέλμα στο όρος Χελμός κατά την αναπαραγωγική τους περίοδο. Εφαρμόστηκε η μέθοδος της σύλληψης-επανασύλληψης ατόμων με τη χρήση παθητικών πομπών (PIT-tags). Χρησιμοποιήθηκε η μέθοδος εφαρμογής και επιλογής μοντέλων για την εκτίμηση του μεγέθους των πληθυσμών, της αναλογίας φύλων και των πιθανοτήτων επιβίωσης και επανασύλληψης των ατόμων, για την εξέταση του προτύπου μετανάστευσης των ατόμων προς το τέλμα, καθώς και για τη συσχέτιση των πιο πάνω παραμέτρων με περιβαλλοντικές μεταβλητές (θερμοκρασία νερου και εδάφους). Έγινε συγκριτική αξιολόγηση σωματικών μετρήσεων (μήκος και βάρος ατόμων) και διερευνήθηκε η μεταβολή στο χρόνο της κάθε μιας από τις πιο πάνω παραμέτρους ανά είδος και φύλο. Με γενετικές αναλύσεις με τη χρήση μικροδορυφορικών δεικτών προσπαθήσαμε να εκτιμήσουμε τη γενετική ποικιλομορφία (αριθμό αλληλομόρφων) των δύο πληθυσμών, να εξετάσουμε αν βρίσκονται σε ισορροπία Hardy-Weinberg και αν έχουν περάσει από φαινόμενα στενωπού. Η εκτίμηση για τον πληθυσμό του είδους I. alpestris είναι 1032 άτομα και του είδους L. vulgaris 306 άτομα. Οι αναλογίες αρσενικών:θηλυκών ατόμων είναι 1:1 και 2:7, αντίστοιχα. Λόγω ανεπάρκειας των δεδομένων, η εφαρμογή και επιλογή μοντέλων πραγματοποιήθηκε μόνο στο είδος I. alpestris. Η μέση ελάχιστη θερμοκρασία εδάφους είχε ισχυρή επίδραση στις πιθανότητες μετανάστευσης προς το τέλμα. Το ποσοστό ατόμων που εισέρχονταν στο τέλμα μεταβαλλόταν στο χρόνο, αλλά ήταν παρόμοιο για τα δύο φύλα. Η φαινομενική επιβίωση των αρσενικών ατόμων ήταν μικρότερη από την αντίστοιχη των θηλυκών, ενδεχομένως επειδή τα αρσενικά άτομα παραμένουν μέσα στο τέλμα για μικρότερο χρονικό διάστημα. Η σύγκριση του μέσου σωματικού μεγέθους και του μέσου σωματικού βάρους των ατόμων που συλλαμβάναμε σε κάθε δειγματοληψία έδειξε ότι στο είδος I. alpestris άτομα μεγαλύτερα σε μέγεθος και βάρος βρίσκονται στο τέλμα νωρίτερα στην αναπαραγωγική περίοδο. Προς το τέλος της αναπαραγωγικής περιόδου ο πληθυσμός αποτελούνταν από μικρότερα και ελαφρύτερα άτομα, ενώ το πρότυπο αυτό δεν παρατηρήθηκε στο είδος L. vulgaris. Οι γενετικές αναλύσεις αποκάλυψαν μειωμένα επίπεδα γενετικής ποικιλότητας, ειδικά στο είδος L. vulgaris, ο πληθυσμός του οποίου ενδεχομένως να έχει υποστεί φαινόμενα στενωπού, ενώ υποδεικνύουν την ανάγκη λήψης μέτρων προστασίας. / Our purpose was the study of the population and behavioural ecology of two syntopic newts at a temporary pond in Helmos mountain during their breeding period. We performed a capture-recapture experiment using Passive Integrated Transponders (PIT-tags). We fitted models to our data in order to estimate population sizes, sex ratios, apparent survival and probabilities of capture and to examine the patterns of migration into the pond. Water and ground temperature were used as covariates in the analyses in order to determine their effect on the above parameters. Measurements of length and weight were used to investigate for inter- and intra-population variability. Microsatellite DNA analyses were performed to assess the genetic structure of the two populations and to check for the occurrence of genetic bottlenecks. Population size estimates were 1032 individuals for I. alpestris and 306 individuals for L. vulgaris. Male: female ratios were 1:1 and 2:7 respectively. Due to sparseness of data, models were fitted to the I. alpestris data only. The probabilities of individuals entering the pond in each sampling interval were greatly affected by the mean minimum ground temperature for that interval. The percentage of individuals entering the pond varied with time, but was roughly the same for both sexes. Apparent survival of males was lower than that of females, probably due to the fact that males spent less time in the pond. Comparisons of mean body size and weight of individuals caught in each sampling occasion showed that in I. alpestris larger and heavier individuals entered the pond early in the breeding period. As the period drew to its end, smaller and lighter individuals comprised the sampled population. This was not observed in L. vulgaris. Genetic analyses revealed reduced levels of genetic variation relative to other conspecific populations, particularly for L. vulgaris, suggesting that genetic bottlenecks might have occurred, and call for specific conservation measures

An island subspecies endemic to the remote St Kilda archipelago, Apodemus sylvaticus hirtensis is considered of national importance but has been little studied, despite its inclusion in the criteria for the islands’ designation as a World Heritage Site. This study expands our knowledge of the core ecology of the mice; distribution, morphology, age structure, breeding phenology, population density, range size, survival and fecundity are all described and quantified using data collected from 4462 captures of 787 individuals between 2009-2012 on three sites (Carn Mor, Glen Bay & Village Bay), 1-2km apart on the main island of Hirta. Morphological analysis confirmed the reputed gigantism the mice, with maximum body weights of 60g for males and 50.5g for a non-gravid female both being approximately double that of a mainland specimen (the heaviest gravid female caught weighed 56g). Sexual dimorphism was evident, with males >1 year old being 8.7% heavier than females on average. Significant geographical variation in size was also found; mice on the seabird breeding colony of Carn Mor were heavier, longer and in better condition than mice elsewhere. Mice were observed to have a well-defined breeding season between April and September, shorter than on the mainland, with most individuals not breeding until their second year and very few surviving two winters. No geographical differences were found in the proportion of adult mice more than a year old that were in breeding condition at any given time, although there were significant geographical differences in the proportion of individuals in breeding condition for ‘young adult’ mice entering their first spring and sub adult mice in the autumn of the year in which they were. Spatially explicit capture-recapture (SECR) methods were used to quantify population densities free from ad hoc methods of trapping area estimation. Temporal variation in population size typical of temperate small mammals was found, with densities as low as 2 mice/ha in spring, increasing through summer and autumn with juvenile recruitment until reaching a peak at the beginning of winter of up to 50 mice/ha. Geographical variation was again observed, with frequent significant differences between trapping sites and an overall trend of highest population densities on the seabird breeding site. Mean individual range sizes varied between 0.3-3.0ha and were largest in Village Bay and in males in breeding condition. Pradel robust design recruitment models were used to quantify monthly survival (0.67-1.00) and fecundity (0.03- 0.41) and overall rate of population change (0.81-1.52) between sessions. Survival varied little between grids outside of the breeding season, but tended to be greater in Carn Mor than Village Bay during the summer. Fecundity rates varied little between years and grids, with one exception where increased summer fecundity followed a severe winter decline on Carn Mor. The possible role of differences in the quality of the food supply (in particular the seabird breeding colony and spatial variation in sheep grazing pressure) on creating geographical variation in body size, condition, breeding phenology, density and population dynamics are discussed in detail, as is the overall pattern of insular traits found in the mice.

Experiments based on the method of mark-recapture can be used for estimation of the abundance of natural populations, for monitoring dispersion of groups or individual specimens within a population using group or individual marking. Semiaquatic bugs (Heteroptera: Gerromorpha) were marked and recaptured many times in the field during research, individual marking was much less used since marking of small insects is difficult. The aim of this work is to develop a method of individual marking of semiaquatic bugs so that it would meet conditions such as durability, legibility and non affecting health of the marked specimen. Semiaquatic bugs of Aquarius paludum, Gerris lacustris, Limnoporus rufoscutellatus (Gerridae) and Velia caprai (Veliidae) species were selected as experimental organisms. Partial aims of this thesis were to try using this method to describe the abundance of the monitored population and to monitor dispersion of the selected species, both at lotic (V. caprai) and lentic habitats (water striders, family Gerridae). A new method of individual marking of semiaquatic bugs was developed on the basis of modifications of the commonly used methods. After a series of tests and in-field research, this method proved to be suitable as it met the essential conditions for marking insects. The abundance of the monitored population was estimated and dispersion of the selected species (V. caprai) in running water was described by using this method. The partial aims of this thesis were met, too. It was confirmed that individuals of the V. caprai species move between the monitored areas along the water course. This inclination to move is greater than tendency to remain in the place of release. The gained data also show conclusively higher rate of movement of V. caprai specimens in the upstream direction, compared to the downstream. The tendency of V. caprai to travel larger distance upstream than downstream, is significant too. No statistically relevant difference in either direction of the water course (up or down) in the surpassed altitude difference was confirmed. The differences in the monitored phenomena between the sexes and generations were compared as well. The differences, however, were not significant. A movement of the adults of the water cricket Velia caprai thus can be characterized as an upstream migration, common in insects of lotic habtitats. A part of the study taking place in still waters showed, that G. lacustris specimens move on the surface of the pond, but not to a larger degree than they remain in place. On the other hand, A. paludum specimens were proved to move away from the place of release rather than remaining in that place. These also overcome greater distance than G. lacustris specimens.

Submitted by Renata Lopes (renatasil82@gmail.com) on 2017-04-04T13:56:38Z No. of bitstreams: 1 alanrobertocepile.pdf: 1842538 bytes, checksum: edec2001e2b492b3123f078c0365d91d (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2017-04-04T15:38:05Z (GMT) No. of bitstreams: 1 alanrobertocepile.pdf: 1842538 bytes, checksum: edec2001e2b492b3123f078c0365d91d (MD5) / Made available in DSpace on 2017-04-04T15:38:05Z (GMT). No. of bitstreams: 1 alanrobertocepile.pdf: 1842538 bytes, checksum: edec2001e2b492b3123f078c0365d91d (MD5) Previous issue date: 2008-04-09 / A marcação-recaptura por meio de foto-identificação vem sendo utilizada a bastante tempo, tendo iniciado na década de 40 do século passado com animais terrestres. Sua aplicação aos mamíferos marinhos da ordem cetacea iniciou-se no final da década de 70 e desde então vem sendo usada e amplamente aprimorada. Este técnica permite tomar conhecimento de inúmeros aspectos da biologia e ecologia dos animais fotografados, entre eles a estimativa populacional e aspectos comportamentais. O capítulo I deste estudo teve como objetivo estimar a população de botos cinza (Sotalia guianensis) de Regência, ES, através do método de marcação-recaptura utilizando a técnica de foto-identificação, utilizando estimadores probabilísticos para populações fechadas amplamente usados para cetáceos em todo mundo, como Lincoln-Petersen, Schnabel e Schumacher-Echmeyer, e a criação do primeiro catálogo de identificação da espécie no estado do Espírito Santo. Foram identificados 16 indivíduos sendo 7 reavistados. A população variou de acordo com o estimador utilizado, ficando entre 81 (Schnabel) e 141 indivíduos (Lincoln-Petersen). O capítulo II objetivou conhecer o padrão de atividade de S. guianensis de Regência, principalmente em relação a parâmetros ambientais e ao comportamento oportunista de perseguição às traineiras em busca de alimento descartado pelas embarcações. / Mark-recapture by photo-identification it comes being used a long time and started in 40’s of last century with terrestrial animals. The application of this method with marine mammals of cetacea order started in 70’s and has been used and widely improved. This technique allow to know some informations about biology and ecology of the animals captured, some of them, population size estimates and behavior. The objective of chapter I of this study was the estimate of population size of estuarine dolphin, Sotalia guianensis, in Regência, ES, through the mark-recapture method by photo-identification technique, using probabilistic estimators to closed populations widely used to estimate cetaceans populations in all the world, like Lincoln-Petersen, Schnabel and Scumacher-Eschmeyer, and make the first identification catalogue for the species in the Espírito Santo state. It was identified 16 dolphins and 7 resighted. The population varied as estimator used, between 81 (Schnabel) and 141 (LincolnPetersen). The objective of chapter II was to know the activity patterns of S. guianensis in Regência, mostly in relation of ambiental parameters and oportunistic trawler following behavior, in order to gain some food discarded by fishing boats.

In aquatic systems refuge habitats increase resistance to drying events and are necessary for maintaining populations in disturbed environments. However, reduced water availability and altered flow regimes threaten the existence and function of these habitats. To test refuge function I conducted a capture-mark-recapture (CMR) study, integrating citizen science angler sampling into fisheries-independent methods. The objectives of this study were twofold: 1) To determine the contribution of citizen science anglers to improving CMR research, and 2.) to quantify apparent survival of Florida Largemouth Bass, Micropterus salmoides floridanus, in a coastal refuge habitat across multiple years of drying severity. The inclusion of angler sampling was determined to be an effective and feasible method for increasing capture probability. Apparent survival of Florida Bass varied among hydrologic periods with lowest survival when marshes functionally dried (< 10 cm). Overall mortality from drying events increased with the duration of marsh drying upstream.

In this thesis, the life history and population biology of an endemic and declining California butterfly, Speyeria adiaste clemencei (Comstock, 1925) is described from Chews Ridge, Monterey Co., CA. S. a. clemencei can be successfully reared on commercially available Viola spp., facilitating captive rearing for restoration. Larvae of S. adiaste can be distinguished morphologically from sympatric S. callippe and S. coronis larvae based upon coloration of the dorsal and dorsolateral scoli, head capsule coloration, and coloration of setae, facilitating identification in the field. Adequate access to nectar sources throughout the flight period, especially during drought years, as well as host plant density and distribution, are critical aspects for maintaining viable S. a. clemencei populations. To gain a better understanding of its population biology, three seasons of weekly Pollard walk counts and two seasons of mark recapture (MR) were conducted. The population declined during the study period, which may be associated with decreasing rainfall. MR estimates were very strongly correlated with weekly Pollard walk counts. Differences in habitat use between the sexes were observed, with males showing a slight preference for ridge over meadow plots, whereas females preferred meadow plots containing Viola host plants. Analysis of survival and dispersal indicated this species is relatively short-lived with low dispersal ability, two traits associated with its life history that have important implications for re-colonization dynamics and population structure.

Recent improvements in genetic analyses have paved the way in using molecular data to answer questions regarding evolutionary history, genetic structure, and demography. Key deer are a federally endangered subspecies assumed to be genetically unique (based on one allozyme study), homogeneous, and have a female-biased population of approximately 900 deer. I used 985bp of the mitochondrial cytochrome b gene and 12 microsatellite loci to test two hypotheses: 1) if the Moser Channel is a barrier to gene flow, I should expect that Key deer are differentiated and have reduced diversity compared to mainland deer and (2) if isolation on islands leads to a higher probability of extinction, I should expect that Key deer exhibit a small population size and a high risk of extinction. My results indicate that Key deer are genetically isolated from mainland white-tailed deer and that there is a lack of genetic substructure between islands. While Key deer exhibit reduced levels of genetic diversity compared to their mainland counterparts, they contain enough diversity of which to uniquely identify individual deer. Based on genetic identification, I estimated a census size of around 1,000 individuals with a heavily skewed female-biased adult sex ratio. Furthermore, I combined genetic and contemporary demographic data to generate a species persistence model of the Key deer. Sensitivity tests within the population viability analysis brought to light the importance of fetal sex ratio and female survival as the primary factors at risk of driving the subspecies to extinction.

As urban areas expand, agricultural lands become increasingly important habitat for many species. Compared to some types of agricultural land-use, ranchlands provide vast expanses of minimally modified habitat that support many threatened and endangered species. Conservation biologists can promote ecologically sound management approaches by quantifying the effects of agricultural practices on resident species. I examined the effects of pasture management, cattle grazing, and landscape characteristics on both adult and larval treefrogs in a ranchland in south-central Florida. I experimentally determined optimal deployment of artificial treefrog shelters constructed of polyvinylchloride (PVC) pipe to efficiently sample adult treefrogs (Chapter 1). Seventy-two shelters were hung on oak trees (Quercus virginiana) and cabbage palm trees (Sabal palmetto) with smooth trunks or boots (residual palm fronds), at all possible combinations of three heights (2, 3, and 4 m), four compass directions (N, S, E, and W) and two water levels (with or without 10 cm). Shelter residence was completely dominated by the Squirrel Treefrog, Hyla squirella (N = 65). Significantly fewer H. squirella were found in shelters on palms with boots than on smooth palms or oak trees (0.29 ± 0.21 [mean ± 1 SE hereinafter] versus 1.3 ± 0.21 and 1.1 ± 0.21, respectively), and shelters with water had slightly more H. squirella than those without (1.5 ± 0.19 versus 0.88 ± 0.19, respectively). Orientation and height did not affect the number of treefrogs encountered; thus, the optimal protocol is to deploy shelters on either smooth palms or oak trees, with water, at 2 m height for easy sampling, and in random compass orientations. I used this protocol to sample H. squirella in woodlots surrounding twelve wetlands and examined how time, frog stage and sex, and landscape features influenced treefrog survival, recapture and site fidelity (Chapter 2). I deployed 15 shelters/ha of woodlot within a 100 m buffer around each wetland. I sampled shelters three times during the fall breeding season, removed all shelters to force frogs to overwinter in natural refugia, and replaced shelters for the final spring sampling. During sampling periods, I sexed, measured, and individually marked each frog using visual implant elastomer (VIE) tags. I used Program MARK to build linear models that included either gender group (female, male or juvenile) or life history stage (adult, juvenile) and either time (sampling interval 1, 2, or 3) or season (fall, spring). I used the most informative model as a null model to assess effects of landscape covariates on survival and recapture. Females had higher survival than either males or juveniles, for which estimates were similar (0.867 vs 0.741 and 0.783, respectively). Survival did not vary over time, although there was some support for an effect of season, with lower survival during the final over-wintering period than in the fall intervals (relative variable importance: group = 0.730; stage = 0.134; time = 0.200; season = 0.310). Adults had higher recapture rates than juveniles (average recapture 0.214 vs 0.102), and recapture for both stages varied over time, with highest recapture in sampling interval two (relative variable importance: group = 0.262; stage = 0.514; time = 0.513; season = 0.229). Hyla squirella was extremely site loyal; no individuals moved between sampling sites, and 95% of recaptured individuals were in their original shelter. Strong terrestrial site fidelity calls into question the traditional "ponds as patches" metapopulation view of treefrog population dynamics. Area of woodlot within 250 m was the most important landscape variable in explaining additional variation in both survival and recapture. Frogs had higher survival and lower recapture in larger woodlots, indicating that intact, contiguous woodlots are higher quality habitat than more fragmented woodlots. Neither survival nor recapture varied with wetland grazing treatments or between pasture types. Finally, I experimentally assessed the effects of cattle grazing and pasture management on larval H. squirella. I selected four wetlands: two in semi-natural pastures (SN) and two in intensively managed pastures (IM). One wetland in each pasture type was fenced so that it was released from cattle grazing (R). I collected three clutches of H. squirella eggs (Clutches A, B, and C) and reared tadpoles in the laboratory until Gosner stage 25. In each wetland, I deployed a total of 50 tadpoles from each clutch into 105 L pens constructed of plastic laundry baskets and mesh window screening. Clutch significantly affected tadpole survival, with Clutch A having the highest percent survival, followed by Clutch B and finally Clutch C (41.66, 32.11 - 53.95 [mean, 95% confidence limits hereinafter]; 9.00, 6.76 - 11.88; 2.89, 2.02 - 4.01, respectively). Wetland type also affected survival, with SN wetlands supporting significantly higher survival than IM wetlands (SN-R: 53.95, 32.88 - 88.13; SN-G: 18.95, 11.30 - 31.36 vs IM-R: 7.32, 4.13 - 12.49; IM-G: 1.09, 0.29 - 2.39). Genetic variation in survival confirms the potential for H. squirella to adapt to rangeland management, but extremely low survival of some clutches indicates that few clutches may be able to survive in low quality wetlands, such as IM-G wetlands. Higher survival in SN pasture wetlands suggest this is a superior habitat and future management objectives should conserve semi-natural pastures and limit further modification of intensively managed pastures, including removing woodlots near wetlands.