O bagre cego de Iporanga, Pimelodella kronei, da região do Parque Estadual Turístico do Alto Ribeira-PETAR, SP, foi o primeiro peixe troglóbio descoberto e descrito no Brasil e um dos mais estudados até hoje. Populações de bagres cegos atribuídas a essa espécie foram encontradas, até o momento, em cavernas do Sistema das Areias (Areias de Cima - localidade-tipo e abrigando a maior população conhecida -, Areias de Baixo e Ressurgência das Areias da Água Quente, esta aparentemente com uma população periférica), na Caverna Córrego Seco, na Ressurgência de Bombas e em cavernas do Sistema Alambari (caverna Alambari de Cima - população aparentemente extinta -, e Abismo do Gurutuva). Os bagres cegos do Sistema Areias foram excessivamente coletados na década de 1970, o que teria provocado um declínio populacional acentuado, registrado por Trajano (1987) 10 anos mais tarde. O presente estudo aborda a ecologia de P. kronei, com ênfase na população das Areias, utilizando métodos comparáveis aos de Trajano (op. cit.), para fins de monitoramento. Os aspectos analisados nas Areias foram: tamanho da população, crescimento individual e deslocamentos no habitat, a partir de marcação e recaptura individual; estrutura da população em termos de distribuição das freqüências de tamanhos (comprimento-padrão), peso e fator de condição (isométrico e alométrico); troglomorfismos (graus de redução de olhos e de pigmentação melânica). Complementarmente, exemplares das Areias, Bombas, Córrego Seco e Gurutuva foram comparados quanto à morfometria. A população de P. kronei das Areias mostrou evidências de estabilidade através da recuperação da estrutura de peso e comprimento-padrão. Assim como observado para outras espécies de siluriformes troglóbios, o crescimento individual é altamente heterogêneo, com casos de crescimento negativo. Os parâmetros da equação de Von Bertallanfy revelaram valores superiores aos de Trajano (1987), resultando em uma longevidade média de 15-20 anos. Os bagres estudados na Areias de Cima mostraram tendência de deslocamentos rio acima, em direção ao ponto mais distal no Córrego Grande (mais próximo à entrada de alimento externo), provavelmente para alimentação e reprodução. É possível que existam diferenças entre a população de Bombas e as demais localidades, sendo necessária uma investigação mais aprofundada, com métodos mais discriminatórios. / The blind catfish from Iporanga, Pimelodella kronei, from Parque Estadual Turístico do Alto Ribeira- PETAR, SP, was the first troglobitic fish discovered and described in Brazil. It is also one of the most investigated species so far. Populations of blind catfish attributed to this species have been found in caves belonging to the Areias System (Areias de Cima - type-locality, sheltering the largest known population - , Areias de Baixo and Ressurgence of Areias of Águas Quente, which apparently shows a peripherical population), besides Córrego Seco Cave, Bombas Ressurgence and caves of the Alambari System (Alambari de Cima - an apparently extinct population - , and Gurutuva). The blind catfish of Areias system were over-collected during the 1970s, which may have led to an accentuated population decline, as recorded by Trajano (1987) ten years later. The present study focus on the ecology of P. kronei, with emphasis on the Areias population, by using methods comparable to those by Trajano (op. cit.) for monitoring purposes. The aspects studied in the Areias caves were: population size, individual growth and movements in the habitat, based on individual marking and recapture; population structure in terms of distribution of size (standard length), weight and condition factor (isometric and alometric) frequencies; troglomorphism (levels of eye reduction and melanic pigmentation). In addition, samples from Areias, Bombas, Córrego Seco and Gurutuva were morphometrically compared. The P. kronei population of Areias showed evidence of stability through the regain of the size and weight structure. Like the observed for other troglobitic siluriforms, the individual growth in P. kronei is highly heterogeneous, with frequent cases of negative growth. The parameters of the Von Bertallanfy equation calculated were higher than those by Trajano (1987), resulting in a higher expected longevity - 15 to 20 years. The blind catfish from Areias presented a tendency to move upstream, approaching the distal end of Córrego Grande (closer to the input of epigean nutrients), probably for feeding and reproduction. There may be some differences in the Bombas populations of other locations, to be investigated using more discriminatory methods.

Orientador: Ricardo Jannini Sawaya / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-23T04:29:37Z (GMT). No. of bitstreams: 1 Rodrigues_MuriloGuimaraes_D.pdf: 4926681 bytes, checksum: 057f2c8aa9c7d1baaa30995a12a9c858 (MD5) Previous issue date: 2013 / Resumo: A ecologia de populações investiga os fatores que levam a variação das taxas vitais e, consequentemente, no número de indivíduos. Isso inclui testar hipóteses sobre aspectos da história de vida das espécies e entender os fatores que podem modular a dinâmica populacional. No entanto, a obtenção de dados para testar hipóteses pode ser difícil para populações que apresentam probabilidades de detecção < 1, como anfíbios e répteis. A marcação e recaptura é amplamente usada para estimar a detecção e inferir aspectos de dinâmica populacional e testar hipóteses ecológicas. Neste trabalho empregamos a teoria de marcação e recaptura para testar hipóteses relacionadas à ecologia e conservação de populações de anfíbios e répteis. Utilizamos o programa MARK para implementar modelos de populações abertas e fechadas incorporando a probabilidade de detecção dos indivíduos, para obter estimativas de sobrevivência, e outros parâmetros populacionais usando máxima verossimilhança. Organizamos esta tese em quatro capítulos. Iniciamos enfatizando a importância da probabilidade de detecção, além de simular cenários hipotéticos para demonstrar a relação entre esforço de campo, tamanho ótimo amostral e viés amostral. Em seguida comparamos o efeito de duas técnicas de marcação, o corte de artelhos e o implante de microchips, sobre a sobrevivência individual do sapo ferreiro, Hypsiboas faber. No terceiro capítulo estimamos a sobrevivência e o crescimento populacional da jararaca-ilhoa, Bothrops insularis incorporando emigração temporária aos modelos. Além do estudo de taxas vitais e de dinâmica nas populações, a alocação de energia e suas consequências na sobrevivência individual podem ser testadas com modelos de marcação e recaptura. Assim, no quarto e último capítulo consideramos dois caracteres sexuais presentes no sistema de acasalamento dos lagartos, o tamanho da mandíbula e a coloração chamativa, para comparar as estimativas de sobrevivência entre machos e fêmeas do lagarto cauda de chicote, Cnemidophorus cf. ocellifer. . De forma geral, observamos que a probabilidade de detecção individual nos sistemas estudados foi baixa e condizente com a detecção de vertebrados em ambientes tropicais. Além disso, a inclusão de covariáveis na investigação de parâmetros vitais e no processo de detecção é fundamental para o melhor entendimento dos fatores que explicam a dinâmica de uma população. Especificamente observamos que: (i) demonstramos que as taxas que não incorporam a detecção são enviesadas em relação às estimativas que consideram a detecção, (ii) as estimativas de sobrevivência foram similares em indivíduos de Hypsiboas faber marcados com ablação de artelhos e microchips , (iii) Bothrops insularis apresentou baixa probabilidade de sobrevivência anual e crescimento populacional anual negativo. Por fim, (iv) machos maiores do lagarto Cnemidophorus cf. ocellifer apresentaram sobrevivência mensal menor do que machos menores, mas o oposto foi observado para as fêmeas / Abstract: Population ecology aims to search for factors that lead to variation in vital rates and consequently, in the number of individuals. This includes testing hypotheses about natural history traits and threats to populations. However, obtaining data to test hypotheses is challenging because following individuals in the field can be difficult, especially for amphibians and reptiles, where detection probabilities are often < 1. Mark-recapture methods are widely used to estimate detection probabilities and to test ecological hypothesis. Here we used mark-recapture methods to test hypotheses related to ecology and conservation of amphibian and reptile populations. We implemented open- and closed-population models in Program MARK, to account for detection probabilities and to calculate survival estimates and other population parameters. We organized this dissertation into four chapters. In the first chapter we emphasize the importance of considering detection probabilities besides simulating hypothetical scenarios to show the relationship between field effort, sample size and precision. In the second chapter we used a Cormack-Jolly-Seber model to compare the effect of two amphibian marking techniques, toeclipping and PIT tagging, on survival in the blacksmith tree frog, Hypsiboas faber. In the third chapter our goal was to estimate survival and population growth of the golden lancehead, Bothrops insularis accounting for temporary emigration using Pollock's Robust Design. Besides the study of vital rates and population dynamics, energy allocation and its consequences for survival are testable with mark-recapture models. Thus, in the last chapter we used two traits from the lizard mating system, namely jaw size and courtship coloration, to compare survival estimates between males and females of the whiptail lizard, Cnemidophorus cf. ocellifer. In summary we observed that detection probability on the studied populations were low and similar to other vertebrate populations from the tropics. However, including covariates in estimation models of vital rates and detection is important to obtain more accurate results to explain population dynamics. Specifically we conclude that (i) return rates were biased low in relation to survival estimates that account for detectability, (ii) the estimates of survival were similar between toe-clipped and PIT tagged individuals of Hypsiboas faber, (iii) Bothrops insularis showed low survival probability and negative annual population growth. And (iv) larger Cnemidophorus cf. ocellifer males showed lower monthly survival probability than smaller males but the opposite was found for females / Doutorado / Ecologia / Doutor em Ecologia

Developing appropriate management plans for species at risk requires information about their population structure and abundance. For most cetacean populations, few reliable population estimates are available and even fewer distributions have been mapped. Accurate abundance estimates can be determined from capture-recapture data if assumptions are met, however this can be difficult when the animal in question demonstrates both strong site fidelity and large-scale migrations, and different models can result in dramatically different results. I explored these issues by examining a 15-year dataset (1992-2006) of photo-identifications of humpback whales (Megaptera novaeangliae) in British Columbia (BC), Canada. I used multiple capture-recapture models to compare how the definition of population and variation in effort affected estimates of population size, and I explored means to correct for these biases. I also considered stock structure by examining individual breeding ground destinations, movement, and localized site-fidelity within BC. Across the six models considered, the BC humpback whale abundance in 2006 ranged between 1,428 and 3,856 individuals. The Lincoln-Petersen estimate (1,428-1,892) likely best described the number of humpback whales in BC during summer 2006. The effort-standardized Jolly-Seber model (1,970-2,331) is more representative of the larger population of humpback whales that uses or passes through BC over multiple years. Ultimately, selecting the best estimation model requires defining the ‘population’ of interest and accounting for spatial and temporal distribution of sampling effort. British Columbia provides feeding habitat and a potential migratory corridor for whales that breed in the northeastern Pacific Ocean. Forty-four percent of the 1,986 humpback whales considered were sighted in BC in more than one year. Identifications were highest from May to October, with a peak in September, but humpback whales were present in BC in all months of the year. Whales showed strong site fidelity with a median re-sighting distance of 75 km between years, and a maximum re-sighting distance that ranged from 0.41 km to 842 km. Matching rate within BC decreased as a function of north-south distance, though no clear north-south boundary could be established. Stock structure of humpback whales in British Columbia is complex and should be considered in managing this population. / Science, Faculty of / Zoology, Department of / Graduate

Background: Parasite evolution is hypothesized to select for levels of parasite virulence that maximise transmission success. When host population densities fluctuate, low levels of virulence with limited impact on the host are expected, as this should increase the likelihood of surviving periods of low host density. We examined the effects of Morogoro arenavirus on the survival and recapture probability of multimammate mice (Mastomys natalensis) using a seven-year capture-mark-recapture time series. Mastomys natalensis is the natural host of Morogoro virus and is known for its strong seasonal density fluctuations. Results: Antibody presence was negatively correlated with survival probability (effect size: 5-8% per month depending on season) but positively with recapture probability (effect size: 8%). Conclusions: The small negative correlation between host survival probability and antibody presence suggests that either the virus has a negative effect on host condition, or that hosts with lower survival probability are more likely to obtain Morogoro virus infection, for example due to particular behavioural or immunological traits. The latter hypothesis is supported by the positive correlation between antibody status and recapture probability which suggests that risky behaviour might increase the probability of becoming infected.

Master of Science / Department of Biology / Brett K. Sandercock / Cattle-grazing is a dominant land use in the United States, with more than 300 million hectares of land grazed each year. The habitat changes facilitated by cattle grazing can influence resource availability and habitat selection for associated wildlife. To investigate the potential for changes in traditional livestock management to restore native grassland and riparian habitat, we evaluated biological community responses to winter-grazing and livestock exclusion at the Kansas Army Ammunition Plant in southeastern Kansas. In grassland habitats, we combined winter-grazing by domestic cattle and discontinued fertilization in an attempt to restore pastures dominated by tall fescue to native tallgrass prairie and improve habitat for grassland-breeding birds. We observed a decrease in tall fescue and an increase in native, warm-season grasses in winter-grazed pastures compared to fertilized, year-round grazed pastures. Grassland-breeding bird responses to winter-grazing were species-specific. Dickcissels preferred winter-grazed pastures, while Eastern Meadowlarks and Grasshopper Sparrows tended to prefer year-round grazed pastures. Dickcissels were negatively correlated with the presence of cattle during the breeding season and the abundance of tall fescue. Grasshopper Sparrows were negatively correlated with native, warm-season grass abundance and visual obstruction, but were positively correlated with forb abundance. Henslow’s Sparrows and Common Yellowthroats were detected breeding in low numbers on pastures that had been winter-grazed for five years. Our results suggest that winter-grazing and discontinued fertilization of agricultural grasslands can direct semi-natural plant communities toward tallgrass prairie and benefit some grassland-breeding birds. In riparian habitats, livestock were excluded from 1996 to 2005. We measured bird community responses in grazed and ungrazed sites using baseline data collected in 1996-97 and post-treatment data collected in 2004-05. Riparian bird community data were analyzed using robust design mark-recapture models that allowed us to evaluate changes in bird species richness while accounting for differences in detectability among species. We detected increases in species richness in both ungrazed and grazed treatments. We observed few differences in community vital rates between treatments; however, we did detect differences in guild responses. The changes observed within both grazed and ungrazed riparian bird communities were likely influenced by regional fluctuations in species richness and composition.

Noninvasive methods for monitoring wildlife species have revolutionized the way population parameters, such as population density and survival and recruitment rates, are estimated while accounting for imperfect detection using capture-recapture models. Reliable estimates of these parameters are vital information required for making sound conservation decisions; however to date, noninvasive sampling methods have been of limited use for a vast number of species which are difficult to identify to the individual level–a general requirement of capture-recapture models. Capture-recapture models that utilize partial identity information have only recently been introduced and have not been extended to most types of noninvasive sampling scenarios in a manner that uses the spatial location where noninvasive samples were collected to further inform complete identity (i.e. spatial partial identity models). Herein, I extend the recently introduced spatial partial identity models to the noninvasive methods of remote cameras for species that are difficult to identify from photographs and DNA from hair or scat samples. The ability of these novel models to improve parameter estimation and extend study design options are investigated and the methods are made accessible to applied ecologists via statistical software. This research has the potential to greatly improve wildlife conservation decisions by improving our knowledge of parameters related to population structure and dynamics that inform those decisions. Unfortunately, many species of conservation concern (e.g., Florida panthers, Andean bears) are managed without having the necessary information on population status or trends, largely a result of the cost and difficulty of studying species in decline and because of the difficulty of applying statistical models to sparse data, which can produce imprecise and biased estimates of population parameters. By leveraging partial identity information in noninvasive samples, the models I developed will improve these parameter estimates and allow noninvasive methods to be used for more species, leading to more informed conservation decisions, and a more efficient allocation of conservation resources across species and populations. / Ph. D.

From 2006-2011, four population reintroduction techniques were applied to three sites within a reach of the upper Clinch River in Virginia designated suitable for population restoration of the federally endangered oyster mussel (Epioblasma capsaeformis). These techniques were: 1) translocation of adults (Site 1), 2) release of laboratory-propagated sub-adults (Site 1), 3) release of 8-week old laboratory-propagated juveniles (Site 2), and 4) release of stream-side infested host fishes (Site 3). Demographic data were collected in 2011 and 2012 by systematic quadrat and capture-mark-recapture sampling to assess reintroduction success, evaluate reintroduction techniques, and compare survey approaches for monitoring freshwater mussels. Estimates of abundance and density of translocated adults ranged from 450-577 individuals and 0.09-0.11/m2 in 2011, and 371-645 individuals and 0.07-0.13/m2 in 2012. Estimates of abundance and density of laboratory-propagated sub-adults ranged from 1,678-1,943 individuals and 0.33-0.38/m2 in 2011, and 1,389-1,700 individuals and 0.27-0.33/m2 in 2012. Additionally, three recruits were collected at Site 1. No E. capsaeformis were collected at Sites 2 and 3. Capture-mark-recapture sampling produced similar mean point estimates as systematic quadrat sampling, but with typically more precision. My results indicated that the release of larger individuals (>10 mm) is the most effective technique for restoring populations of E. capsaeformis, and that systematic quadrat and capture-mark-recapture sampling have useful applications in population monitoring that are dependent on project objectives. Systematic quadrat sampling is recommended when the objective is to simply estimate and detect trends in population size for species of moderate to larger densities (>0.2/m2). Capture-mark-recapture sampling should be used when objectives include assessing a reintroduced population of endangered species or at low density, obtaining precise estimates of population demographic parameters, or estimating population size for established species of low to moderate density (0.1-0.2/m2). The ability to grow endangered juveniles to larger sizes in captivity requires improving grow-out culture methods of laboratory-propagated individuals. A laboratory experiment was conducted to investigate the effects of temperature (20-28 C) on growth and survival of laboratory-propagated juveniles of the Cumberlandian combshell (Epioblasma brevidens), E. capsaeformis, and the wavyrayed lampmussel (Lampsilis fasciola) in captivity. Results indicated that 26 C is the optimum temperature to maximize growth of laboratory-propagated juveniles in small water-recirculating aquaculture systems. Growing endangered juveniles to larger sizes will improve survival in captivity and after release into the wild. As a result, hatcheries can reduce the time that juveniles spend in captivity and thus increase their overall production and enhance the likelihood of success of mussel population recovery efforts by federal and state agencies, and other partners. / Master of Science

The demographic characteristics of American eels (Anguilla rostrata) are believed to vary with latitude and distance inland from the ocean; eels are generally thought to increase in length, age, and the proportion of females in inland and more northerly areas. Understanding this variation is necessary for the sound management of eels, but investigations into characteristics on a broad scale within drainages are scarce. Eels in the Potomac River drainage, Virginia, were sampled over a two-year period in both near-coastal and inland areas to describe characteristics in each area as well as to understand drainage-wide patterns. Inland data resulted from sampling in the Shenandoah River drainage and near-coastal data resulted from sampling tributaries to the lower Potomac River. Movement and growth were also investigated in inland areas. Eels from the Shenandoah River drainage were significantly longer (median = 763 mm TL) and older (median = 11.5) than those found in the Potomac River tributary sites (median = 142 mm TL; median = 2.0, respectively). Both total length and age increased with increasing distance inland and sex ratio shifted from varying ratios of males:females in Potomac River tributaries to all females in the Shenandoah River drainage. Movements confirmed through mark-recapture over periods ranging up to one year were short, generally <100 m, with the longest detected movement being 1.5 km. Recapture rates were low and may be due either to low sampling efficiency, long-distance movements, or a combination of these factors. Growth and 95% confidence interval from five eels recaptured after approximately one year was 43.0 +/- 29.7 mm/year. CPUE decreased with increasing distance inland, confirming information reported by others for Virginia streams. / Master of Science

In conjunction with Cambrex, a biomedical company that utilizes horseshoe crabs for the production of Limulus Amoebocyte Lysate (LAL), a study was conducted to investigate movement patterns and population distributions of horseshoe crabs to increase understanding of mid-Atlantic horseshoe crab populations. In addition, areas of the shoreline of Tom's Cove, Assateague Island, Virginia were investigated as possible locations for annual spawning surveys. Twelve thousand five hundred horseshoe crabs were tagged and released in Chincoteague, Virginia and Ocean City, Maryland as part of a movement study; 431 (3.45%) were reported as resights. The mean distance between site of release and site of recapture for all resighted crabs was 68.3 km; maximum distance moved was 493.7 km. During 1999-2004, demographic data were collected from horseshoe crabs harvested in Chincoteague, VA and Ocean City, MD. The proportion of females (p < 0.0001) and juveniles (p < 0.0001) sampled varied from year-to-year, but no trends were observed. This study also showed that a greater proportion of females were observed in the juvenile cohort sampled compared to the adults sampled (p < 0.0001). The spawning survey revealed that spawning activity in Tom's Cove varied between years. On May 30th, 2003, 1,192 horseshoe crabs were observed spawning on the northern shoreline of Tom's Cove. The maximum number of horseshoe crabs observed spawning in the same area in 2004 was 94. This study provides no evidence for isolated subpopulations in Chincoteague, VA or Ocean City, MD. It also shows that horseshoe crab sex and age ratios fluctuate annually, therefore requiring a long time series of data to detect trends. / Master of Science

Cougars (Puma concolor) are difficult to census due to their large home ranges, low densities, and cryptic nature. The conventional “gold-standard” method for estimating cougar abundance entails the capture and radio-tagging of individuals in a study area in an attempt to acquire a direct enumeration of animals in the population. While this method provides an accurate abundance estimate, it is logistically challenging and prohibitively expensive. Noninvasive survey techniques may offer the ability to both accurately and inexpensively monitor cougar populations. While noninvasive techniques have been used on cougar populations, there remain questions on their accuracy and comparative efficacy. We estimated the density of a cougar population in Northwest Wyoming using direct enumeration, and used this estimate as a reference with which to evaluate the accuracy and cost-effectiveness of three types of noninvasive surveys performed between 2010 and 2014. The noninvasive methods included two annual mark- recapture sessions of: 1) remote camera trapping, 2) winter hair-collection transects, and 3) scat detection dog surveys. We GPS tracked 13 adult cougars (males = 5, females = 8) over 3 annual periods (Sep 2010 – Sep 2013). We used proportional home range overlap to determine density in a 1,570 km2 area. The average density was 0.82 cougars/100 km2 (± 0.10 SD; n = 3 years). The remote camera surveys produced a mean density of 0.60 cougars/100 km2 (n = 2 years; relative SD = 56.5%). The scat detection dog surveys produced an average density of 2.41 cougars/100 km2 (n = 2 years; relative SD = 12.6%). The winter transects failed to produce a sample size large enough for an abundance estimate. Due to the inclusion of non-adults in the scat sampling, and the fact that the reference estimate was essentially a minimum count of adults, we believe that the scat-based estimate was more accurate than the lower estimate produced by remote cameras. Additional analysis indicated that individual identification of cougars in photographs may not be reliable, challenging the validity of photo-based abundance estimates of cougars. On a cost-per-detection basis, scat detection dogs were the most cost effective method (scat detection dogs = $341; remote cameras = $3,241; winter transects = $7,627).