Hydroacoustics for density and biomass estimations in aquaculture ponds

The use of hydroacoustics is currently being studied and developed as a promising non-intrusive methodology to monitor and manage fish stocks in aquaculture farms. The main objective of this study was to develop an acoustic method for the estimation of fish density and biomass in inland aquaculture farms and test the accuracy and precision of the estimates with real data provided by the company. The study was conducted in sea bass (Dicentrarchus labrax) production ponds located in Seville (Southern Spain). A Simrad EK60 echosounder with two split-beam circular transducers operating simultaneously at 200 kHz was used for hydroacoustic surveys. Two different hydroacoustic designs were considered: central trajectories and zigzag trajectories. The accuracy and precision of the estimates were examined in order to select the best sampling design. Due to a non-homogeneous fish distribution in the pond caused by the avoidance behaviour, as a response to the sampling disturbance presented by fish, acoustic density and biomass were corrected by applying sampling theory according to the probability of fish detection. When density and biomass were corrected, the estimates became highly accurate and precise with respect to real data, which confirms that the proposed method is adequate. Similarly, acoustic estimates of fish weight were highly in agreement with real data, due to the use of specific equations developed “in situ” for the study. Although no significant differences were recorded in the density and biomass estimates with regard to the trajectory used (central vs. zigzag), it was observed that the most accurate agreement and precision were always obtained in central trajectories. Therefore, central design is proposed as the most appropriate design for hydroacoustic measurements in inland ponds. The results obtained in this study provide estimates of density and biomass that accurately match the real data, supporting the use of hydroacoustics as a potentially valid tool to manage inland aquaculture farms

Managing kangaroo grazing for the conservation of grassland and grassy woodland fauna

Large mammalian grazers are ecosystem engineers that alter the resources available to other species through selective consumption of plant matter, redistribution of nutrients and trampling. While some level of grazing is considered critical for maintaining species diversity, alteration to natural grazing regimes can have a severe impact on native biodiversity. Restoration of grazing regimes which promote conservation of biodiversity is a priority in many protected areas. However, the ability to achieve this goal is limited by a lack of understanding of what ‘appropriate’ grazing regimes for conservation of biodiversity are. In south-eastern Australia, high intensity grazing by the native eastern grey kangaroo (Macropus giganteus) has been linked to the decline of multiple taxa. While efforts to manage the impact of kangaroo grazing on other taxa have been undertaken, the effectiveness of these interventions are limited by a lack of knowledge of what constitutes optimal grazing levels. In this thesis, I used kangaroo population counts, tree canopy cover maps, ground vegetation structure, and reptile and birds counts to investigate the relationship between kangaroos, grass structure, and fauna. I found that: 1) there was a strong negative relationship between the abundance of kangaroos and grass structure (Paper I); 2) high intensity kangaroo grazing had a negative effect on the reptile community (Paper I); 3) birds with similar traits favoured similar grazing intensities, with different grazing intensities favoured by different trait groups (Paper II); 4) the occurrence of a threatened grassland reptile, the striped legless lizard (Delma impar) was positively related to fine scale grass complexity, and negatively related to kangaroo density at the broad scale (Paper III); 5) kangaroos selected forage habitat away from roads, in areas with a high cover of short grass (Paper IV); and 6) line transect sampling undertaken from vehicles driven along tracks can provide an accurate method to survey the kangaroo population provided knowledge of kangaroo distribution relative to tracks is known and accounted for (Paper V). My investigation into the relationships between kangaroos, grass structure and fauna indicated that grass structure has a strong effect on many reptiles and birds, and that intervention may be needed to change kangaroo habitat selection in a way that mimics natural foraging patterns in order to promote optimal vegetation structures for the conservation of native biodiversity. Therefore, to preserve a full-complement of species in these grassy habitats, I recommend that: 1) management of grazing is based on direct measures of grass structure, not herbivore abundance, 2) the extent and duration of intense grazing is limited; and 3) grazing pressure is rotated to create mosaics of different levels of grass structure in space and time. In making these recommendations, I emphasise that management of grazing by kangaroos will be necessary for ongoing conservation of biodiversity in grasslands and grassy woodland and that further research is needed on how to manage kangaroo grazing patterns for the conservation of biodiversity in grasslands and grassy woodlands in south-eastern Australia

Accounting for animal density gradients using independent information in distance sampling surveys

Distance sampling is extensively used for estimating animal density or abundance. Conventional methods assume that location of line or point transects is random with respect to the animal population, yet transects are often placed along linear features such as roads, rivers or shorelines that do not randomly sample the study region, resulting in biased estimates of abundance. If it is possible to collect additional data that allow an animal density gradient with respect to the transects to be modelled, we show how to extend the conventional distance sampling likelihood to give asymptotically unbiased estimates of density for the covered area. We illustrate the proposed methods using data for a kangaroo population surveyed by line transects laid along tracks, for which the true density is known from an independent source, and the density gradient with respect to the tracks is estimated from a sample of GPS collared animals. For this example, density of animals increases with distance from the tracks, so that detection probability is overestimated and density underestimated if the non-random location of transects is ignored. When we account for the density gradient, there is no evidence of bias in the abundance estimate. We end with a list of practical recommendations to investigators conducting distance sampling surveys where density gradients could be an issue

Accounting for animal density gradients using independent information in distance sampling surveys

Distance sampling is extensively used for estimating animal density or abundance. Conventional methods assume that location of line or point transects is random with respect to the animal population, yet transects are often placed along linear features such as roads, rivers or shorelines that do not randomly sample the study region, resulting in biased estimates of abundance. If it is possible to collect additional data that allow an animal density gradient with respect to the transects to be modelled, we show how to extend the conventional distance sampling likelihood to give asymptotically unbiased estimates of density for the covered area. We illustrate the proposed methods using data for a kangaroo population surveyed by line transects laid along tracks, for which the true density is known from an independent source, and the density gradient with respect to the tracks is estimated from a sample of GPS collared animals. For this example, density of animals increases with distance from the tracks, so that detection probability is overestimated and density underestimated if the non-random location of transects is ignored. When we account for the density gradient, there is no evidence of bias in the abundance estimate. We end with a list of practical recommendations to investigators conducting distance sampling surveys where density gradients could be an issue

Standardised methods for collaborative long-term monitoring and management of cetaceans in Wales

Monitoring long terms trends of species abundance is a fundamental requirement for effective conservation. Surveying wildlife creates a baseline to measure changes in the population and to detect and manage specific abiotic and biotic threats. However, long term monitoring is not always effective or achievable because of insufficient finances, resources, planning or limited project focus. Establishing a collaborative network of scientists to bring together similar research may provide the solution as seen with networks on seagrass, aquatic macrophytes and avian populations. Frequently there are many organisations working in isolation using multiple approaches on similar species. This case study specifically investigates the social barriers leading to a lack of collaborative efforts in cetacean monitoring in Wales where there are four organisations independently undertaking systematic long-term monitoring. Here, I produce, trial and analyse a simple low-cost standardised methodology that could be used for long-term monitoring by multiple organisations and review the potential of a collaborative acoustics project to enable simple comparisons of encounter rates for cetaceans Wales-wide. An online questionnaire to stakeholders revealed that primary barriers to collaborative research were personality differences and funding competition; participants indicated that the re-establishment of a marine mammal working group by Natural Resources Wales would enable development of personal relationships and fair access to resources. Similar working groups have been established in terrestrial and aquatic ecology which have attempted to overcome the challenges in effective long-term monitoring. It is anticipated that this research could be duplicated to other species to assess any barriers and solutions to collaborative working and establish more cohesive long-term monitoring strategies in ecology

ABUNDANCE, DENSITY, AND OPINIONS ABOUT COLUMBIAN BLACK-TAILED DEER, WHIDBEY ISLAND, WASHINGTON

Obtaining reliable knowledge is the first step towards properly managing wildlife species. Columbian black-tailed deer (Odocoileus hemionus columbianus) on Whidbey Island, Washington have not been the subject of study, and little is known about the population, or the opinion of resident’s of Whidbey Island towards the deer population. However, wildlife managers suggest deer on the island may be overabundant or over social carrying capacity. Given the lack of empirical knowledge about the deer population or human opinions towards deer on Whidbey Island, I designed research to determine the abundance and density of Columbian black-tailed deer on Whidbey Island, and the opinions of Whidbey Island residents and deer hunters towards deer. I used road-based spotlight sampling analyzed with distance analysis to estimate the abundance and density. The population of deer on Whidbey Island is estimated to be 2,744.5 deer (6.2 deer/km2). The density of deer varied regionally from 4 deer/km2 in the south, to 10.5 deer/km2 in the central section. To determine public opinion of the deer population, I designed a mail-back survey focused on the respondent’s interactions with deer, their perception of the acceptability of the deer population size and their level of support for increasing hunting opportunity on the island. I also conducted a phone survey of hunters who reported hunting deer on Whidbey Island to determine their opinions on the deer population size and trend. The public opinion survey indicated the deer population across the island was moderately acceptable, and there was some support for increasing hunting, but the predominant concern was maintaining public safety with increased hunting. The hunter survey indicated the deer population across the island was somewhat increasing and hunters would prefer the population to remain stable. The public and hunter opinion surveys did not indicate perception among respondents of the varying deer densities across Whidbey Island. Road-based spotlight sampling analyzed in a distance analysis framework can be useful for estimating population size and density of Columbian black-tailed deer and represents the first population estimates for Columbian black-tailed deer on Whidbey Island

Ecology and conservation of large-bodied avian frugivores of Luzon, Philippines

Avian frugivores across Southeast Asia, and in the Philippines in particular, are seriously threatened owing to massive loss of habitat and direct exploitation through hunting and the pet trade. Their declines may have dire consequences for wider ecological processes as many frugivores are also seed dispersers. Conservation programmes in the Philippines are crippled by a lack of knowledge on the status, abundance and ecology of frugivores which extend to other endemic species in the country. This PhD identified factors that influenced frugivore community composition as well as drivers of frugivore distribution across Luzon, the largest island in the Philippines. It also developed cost-effective methods for gathering baseline ecological data to inform conservation measures for frugivores and other little-known species over large geographical areas. This included a way of correcting for the bias caused by non-random transect placement in a study site which is often the case during bird surveys in the tropics. Twenty-five species of pigeons, parrots and hornbills were surveyed using distance sampling along nearly 500 km of line transects at 14 sites across the island of Luzon. I documented surprisingly few reliable disappearances of frugivores from individual forest patches – in fact this and other fieldwork since 2000 has increased the known extent of occurrence of several species. However, green racquet-tail Prioniturus luconensis may have suffered a real range contraction. More alarming was the absence of large parrots from most sites with apparently intact habitat surveyed. Even where present, large parrots exhibited lower densities than related species in similar habitat in Southeast Asia. For six species, including four of six parrots, the largest estimates of population in any reserve in Luzon numbered < 1000 individuals, and nearly one-third of all iii populations in reserves were < 100. At minimum viable population (MVPs) of 500, frugivore communities in all but 2–3 of the largest reserves are not expected to remain intact. Although seed dispersers may fare better than seed predators (large parrots), a major collapse of frugivore communities may occur across Luzon, with serious implications for ecosystem functioning. The Philippines comprise islands of different origins, climate and habitat, a situation which is expected to produce a biogeographically complex set of animal and plant communities, which themselves are influenced by anthropogenic actions. I explored similarities between frugivore communities across 24 sites in Luzon using non-metric multidimensional scaling and attempted to explain site differences in terms of a series of geographical, habitat, and disturbance predictors using Mantel tests. In both analyses using species presence/absence and densities, sites/species did not seem to ordinate simply according to region. Consistent outliers included three sites in West Luzon and two in Central Luzon, and, in terms of species, several large rare parrots and pigeons. The strongest correlates of site dissimilarity were differences in altitude and several human disturbance measures, including path width, canopy closure and a ‘human impact index’ (reflecting human pressures and forest management). While Luzon’s frugivore communities have been no doubt shaped by natural biogeographical processes, their effects have been largely obscured by anthropogenic environmental degradation. There is an urgent need to understand better the drivers of frugivore species distribution in order to develop appropriate conservation management strategies. To identify precise habitat associations of 18 avian frugivores, the presence/absence of each species along 400 m long segments of 213 transects was examined in relation to vegetation structure and composition, measured at 1227 plots, using generalised linear mixed models (the 24 sites were entered as a random factor). Individual frugivore species showed unique patterns of iv association with habitat variables but five species were high-altitude specialists while six preferred lowland sites. Another six species strongly preferred primary forest while one thrives in disturbed forest with the attendant increase in food availability. I then ran generalised additive mixed models (GAMMs) to identify any non-linearities in responses of species to habitat features. Relationships with habitat variables were on the whole simple linear or quadratic for the majority of species, suggesting that there were gains to be had in improving habitat right along the disturbance gradient. Precise and accurate estimates of wildlife population density and sizes are essential to evidence effective conservation programmes. Line transect distance sampling is a robust method in that variability in detectability due to distance from the transect line, but many conservation studies cannot, by necessity, be based on random transect placement, but instead use transects along existing trails. This study estimates the bias in abundance estimates due to non-random placement of transects along hunter trails (path width 100cm) as compared with random paths (especially cut transects). Path types were similar in altitude, but differed in terms of tree girths, slope, canopy covers, and presence of crops. Hunter trails yielded lowest densities and encounter rates for nine of 12 species and lowest effective strip width for seven of 12 species. Highest densities and encounter rates were along random paths for seven of 12 species. Differences in density across trail types were driven by differences in encounter rates rather than differences in detectability. Density estimates calculated from surveys which used non-random transects should be upwardly corrected by on average 90% (18-187%). In fragmented forests where random placement of transects is not always possible, this method of correction will allow species density estimates from sampling along hunter trails and access roads to be adjusted. v Top on the list of research and conservation priorities arising from this PhD would be to map the remaining populations of the Luzon-endemic Green Racquet-tail, Luzon Racquet-tail and Flame-breasted Fruit-dove and to formulate conservation intervention measures for these threatened/near-threatened species taking into account habitat preferences and threats to the species. Forest and reserve management programmes and policies in the Philippines and elsewhere in the tropics would greatly benefit from empirical data on species occurrence and accurate estimates of population abundance using methods described in the study. Sound ecological research by local biologists/ecologists must be encouraged to further our understanding of species requirements, species tolerance to disturbance, and viability of populations, especially of the many unique and/or threatened species in the Philippines and the wider SE Asia region

Estimating abundance of African great apes

All species and subspecies of African great apes are listed by the International Union for the Conservation of Nature as endangered or critically endangered, and populations continue to decline. As human populations and industry expand into great ape habitat, efficient, reliable estimators of great ape abundance are needed to inform conservation status and land-use planning, to assess adverse and beneficial effects of human activities, and to help funding agencies and donors make informed and efficient contributions. Fortunately, technological advances have improved our ability to sample great apes remotely, and new statistical methods for estimating abundance are constantly in development. Following a brief general introduction, this thesis reviews established and emerging approaches to estimating great ape abundance, then describes new methods for estimating animal density from photographic data by distance sampling with camera traps, and for selecting among models of the distance sampling detection function when distance data are overdispersed. Subsequent chapters quantify the effect of violating the assumption of demographic closure when estimating abundance using spatially explicit capture–recapture models for closed populations, and describe the design and implementation of a camera trapping survey of chimpanzees at the landscape scale in Kibale National Park, Uganda. The new methods developed have generated considerable interest, and allow abundances of multiple species, including great apes, to be estimated from data collected during a single photographic survey. Spatially explicit capture–recapture analyses of photographic data from small study areas yielded accurate and precise estimates of chimpanzee abundance, and this combination of methods could be used to enumerate great apes over large areas and in dense forests more reliably and efficiently than previously possible."This work was supported by a St Leonard’s College Scholarship from the University of St Andrews, and the Max Planck Institute for Evolutionary Anthropology." -- Fundin