Approximation-based feature selection and application for algae population estimation

Q. Shen and R. Jensen, 'Approximation-based feature selection and application for algae population estimation,' Applied Intelligence, vol. 28, no. 2, pp. 167-181, 2008. Sponsorship: EPSRC RONO: EP/E058388/1

Monitoring and population estimation of the European badger (Meles meles) in Northern Ireland

The estimation of animal abundance has a central role in wildlife management and research, including the role of badgers Meles meles in bovine tuberculosis transmission to cattle. This is the first study to examine temporal change in the badger population of Northern Ireland over amedium- to long-term time frame of 14-18 years by repeating a national survey first conducted during 1990-1993. A total of 212 1-km2 squares were surveyed during 2007-2008 and the number, type and activity of setts therein recorded. Badgers were widespread with 75% of squares containing at least one sett. The mean density of activemain setts,which was equivalent to badger social group density, was 0.56 (95%CI: 0.46-0.67) active main setts per km2 during 2007-2008. Social group density varied significantly among landclass groups and counties. The total number of social groups was estimated at 7,600 (95%CI: 6,200-9,000) and, not withstanding probable sources of error in estimating social group size, the total abundance of badgers was estimated to be 34,100 (95% CI: 26,200-42,000). There was no significant change in the badger population from that recorded during 1990-1993. A resource selection model provided a relative probability of sett construction at a spatial scale of 25m. Sett locations were negatively associated with elevation and positively associated with slope, aspect, soil sand content, the presence of cover, and the area of improved grassland and arable agriculture within 300 m.

Evaluation and application of microsatellites for population identification of Fraser River chinook salmon (Oncorhynchus tshawytscha)

Variation at 13 microsatellite loci was previously surveyed in approximately 7400 chinook salmon (Oncorhynchus tshawytscha) sampled from 50 localities in the Fraser River drainage in southern British Columbia. Evaluation of the utility of the microsatellite variation for population-specific stock identification applications indicated that the accuracy of the stock composition estimates generally improved with an increasing number of loci used in the estimation procedure, but an increase in accuracy was generally marginal after eight loci were used. With 10–14 populations in a simulated fishery sample, the mean error in population-specific estimated stock composition with a 50-popula-tion baseline was <1.4%. Identification of individuals to specific populations was highest for lower Fraser River and lower and North Thompson River populations; an average of 70% of the individual fish were correctly assigned to specific populations. The average error of the estimated percentage for the seven populations present in a coded-wire tag sample was 2% per population. Estimation of stock composition in the lower river commercial net fishery prior to June is of key local fishery management interest. Chinook salmon from the Chilcotin River and Nicola River drainages were important contributors to the early commercial fishery in the lower river because they comprised approximately 50% of the samples from the net fishery prior to mid April.

Studies relating to the population dynamics of the European badger (Meles meles) in Ireland

European badgers (Meles meles) are an important part of the Irish ecosystem; they are a component of Ireland’s native fauna and are afforded protection by national and international laws. The species is also a reservoir host for bovine tuberculosis (bTB) and implicated in the epidemiology of bTB in cattle. Due to this latter point, badgers have been culled in the Republic of Ireland (ROI) in areas where persistent cattle bTB outbreaks exist. The population dynamics of badgers are therefore of great pure and applied interest. The studies within this thesis used large datasets and a number of analytical approaches to uncover essential elements of badger populations in the ROI. Furthermore, a review and meta-analysis of all available data on Irish badgers was completed to give a framework from which key knowledge gaps and future directions could be identified (Chapter 1). One main finding suggested that badger densities are significantly reduced in areas of repeated culling, as revealed through declining trends in signs of activity (Chapter 2) and capture numbers (Chapter 2 and Chapter 3). Despite this, the trappability of badgers was shown to be lower than previously thought. This indicates that management programmes would require repeated long-term efforts to be effective (Chapter 4). Mark-recapture modelling of a population (sample area: 755km2) suggested that mean badger density was typical of continental European populations, but substantially lower than British populations (Chapter 4). Badger movement patterns indicated that most of the population exhibited site fidelity. Long-distance movements were also recorded, the longest of which (20.1km) was the greatest displacement of an Irish badger currently known (Chapter 5). The studies presented in this thesis allows for the development of more robust models of the badger population at national scales (see Future Directions). Through the use of large-scale datasets future models will facilitate informed sustainable planning for disease control.

Population Mobility Dynamics Estimated from Mobile Telephony Data

In the last decade, mobile phones and mobile devices using mobile cellular telecommunication network connections have become ubiquitous. In several developed countries, the penetration of such devices has surpassed 100 percent. They facilitate communication and access to large quantities of data without the requirement of a fixed location or connection. Assuming mobile phones usually are in close proximity with the user, their cellular activities and locations are indicative of the user's activities and movements. As such, those cellular devices may be considered as a large scale distributed human activity sensing platform. This paper uses mobile operator telephony data to visualize the regional flows of people across the Republic of Ireland. In addition, the use of modified Markov chains for the ranking of significant regions of interest to mobile subscribers is investigated. Methodology is then presented which demonstrates how the ranking of significant regions of interest may be used to estimate national population, results of which are found to have strong correlation with census data.

Smartphone and GPS technology for freeroaming dog population surveillance -a methodological study (Studio metodologico sull’applicazione di smartphone e tecnologia GPS alla sorveglianza delle popolazioni di cani vaganti)

Free-roaming dogs (FRD) represent a potential threat to the quality of life in cities from an ecological, social and public health point of view. One of the most urgent concerns is the role of uncontrolled dogs as reservoirs of infectious diseases transmittable to humans and, above all, rabies. An estimate of the FRD population size and characteristics in a given area is the first step for any relevant intervention programme. Direct count methods are still prominent because of their non-invasive approach, information technologies can support such methods facilitating data collection and allowing for a more efficient data handling. This paper presents a new framework for data collection using a topological algorithm implemented as ArcScript in ESRI® ArcGIS software, which allows for a random selection of the sampling areas. It also supplies a mobile phone application for Android® operating system devices which integrates Global Positioning System (GPS) and Google Maps™. The potential of such a framework was tested in 2 Italian regions. Coupling technological and innovative solutions associated with common counting methods facilitate data collection and transcription. It also paves the way to future applications, which could support dog population management systems.

Population growth and development of two species of Cladocera, Moina micrura and Diaphanosoma birgei, in laboratory

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

A framework for progressively improving small area population estimates

The paper presents a framework for small area population estimation that enables users to select a method that is fit for the purpose. The adjustments to input data that are needed before use are outlined, with emphasis on developing consistent time series of inputs. We show how geographical harmonization of small areas, which is crucial to comparisons over time, can be achieved. For two study regions, the East of England and Yorkshire and the Humber, the differences in output and consequences of adopting different methods are illustrated. The paper concludes with a discussion of how data, on stream since 1998, might be included in future small area estimates.

Population growth and development of two species of Cladocera, Moina micrura and Diaphanosoma birgei, in laboratory

O objetivo do presente trabalho foi testar a influência de quatro dietas alimentares sobre o crescimento populacional, desenvolvimento, comprimento total, peso seco e valor nutricional de duas espécies zooplanctônicas, Moina micrura and Diaphanosoma birgei, com os seguintes tratamentos alimentares: somente alga (A), alga + vitaminas (AV), alga + ração (AR) e alga + ração + vitaminas (ARV). O pico de crescimento para as duas espécies estudadas ocorreu mais rápido no tratamento AV. em geral, o tratamento AV para M. micrura mostrou melhores resultados para taxa intrínseca, fecundidade, desenvolvimento embrionário e pós-embrionário. Já a longevidade e número total de desovas apresentaram melhores resultados no tratamento AR (p < 0,05). Para D. birgei, os melhores resultados foram obtidos nos tratamentos contendo ração e vitamina (p < 0,05). A maior porcentagem de proteínas e lipídeos para os dois cladóceros ocorreu nos tratamentos contendo ração, já o carboidrato foi maior no tratamento contendo somente alga (p < 0,05). em geral, as dietas contendo ração e vitamina apresentaram os melhores resultados para o desenvolvimento dos cladóceros, com qualidade de água adequada para cultivo, podendo ser utilizadas em culturas com altas concentrações em laboratório.

Méthodes de rééchantillonnage en méthodologie d'enquête

Le sujet principal de cette thèse porte sur l'étude de l'estimation de la variance d'une statistique basée sur des données d'enquête imputées via le bootstrap (ou la méthode de Cyrano). L'application d'une méthode bootstrap conçue pour des données d'enquête complètes (en absence de non-réponse) en présence de valeurs imputées et faire comme si celles-ci étaient de vraies observations peut conduire à une sous-estimation de la variance. Dans ce contexte, Shao et Sitter (1996) ont introduit une procédure bootstrap dans laquelle la variable étudiée et l'indicateur de réponse sont rééchantillonnés ensemble et les non-répondants bootstrap sont imputés de la même manière qu'est traité l'échantillon original. L'estimation bootstrap de la variance obtenue est valide lorsque la fraction de sondage est faible. Dans le chapitre 1, nous commençons par faire une revue des méthodes bootstrap existantes pour les données d'enquête (complètes et imputées) et les présentons dans un cadre unifié pour la première fois dans la littérature. Dans le chapitre 2, nous introduisons une nouvelle procédure bootstrap pour estimer la variance sous l'approche du modèle de non-réponse lorsque le mécanisme de non-réponse uniforme est présumé. En utilisant seulement les informations sur le taux de réponse, contrairement à Shao et Sitter (1996) qui nécessite l'indicateur de réponse individuelle, l'indicateur de réponse bootstrap est généré pour chaque échantillon bootstrap menant à un estimateur bootstrap de la variance valide même pour les fractions de sondage non-négligeables. Dans le chapitre 3, nous étudions les approches bootstrap par pseudo-population et nous considérons une classe plus générale de mécanismes de non-réponse. Nous développons deux procédures bootstrap par pseudo-population pour estimer la variance d'un estimateur imputé par rapport à l'approche du modèle de non-réponse et à celle du modèle d'imputation. Ces procédures sont également valides même pour des fractions de sondage non-négligeables.

L’illusion des signaux pénaux : l’effet tendancieux de l’impunité différentielle

Réalisé sous la co-direction de Pierre Tremblay

Estimativa populacional e uso do hábitat do boto-cinza (Sotalia guianensis) no litoral sul do Rio Grande do Norte

Four areas are known as of frequent usage by Guiana dolphins (Sotalia guianensis) in the south coast of Rio Grande do Norte state, northeast Brazil: Tabatinga, Pipa, Lagoa de Guaraíras and Baia Formosa. This extension of 40 km of shoreline is under increasing anthropogenic impacts due to continuous development of the coastal areas and vessel traffic. The objective of this study was to investigate aspects of population biology and habitat use of the population of Sotalia guianensis in the south coast of Rio Grande do Norte. It was applied the photo-identification technique and posterior methods of capture-recapture for population estimation (POPAN extension in MARK). The distribution, movement and site fidelity of the dolphins were analyzed trough the geographic information system (GIS) and group characteristics and behavior trough non-parametric statistics. Field work was conducted on board a 10m motor vessel from March 2008 to March 2009. Photo-identification effort was 329h with 113h of direct observation of the dolphins. The population estimatives for each area: Tabatinga: 75 (63-92); Pipa 105 (88-129); Lagoa de Guaraíras: 27 (18-54) e Baia Formosa: 112 (89-129) individuals. Total population estimative was: 223 (192 a 297). High site fidelity was detected for only part of the population (<15%) as low site fidelity and transients individuals were also detected (>20%). It was observed frequent movements between Tabatinga, Lagoa de Guaraíras and Pipa, but not Baía Formosa. This suggests a division in two communities along this shore extension: one in Pipa and other in Baía Formosa. Group size was small, most groups with up to 10 dolphins. The areas were use intensively, only in Lagoa de Guaraíras dolphins were not seen in all field trips. Lagoa de Guaraíras is an area used by small groups exclusively for foraging. In Tabatinga and Pipa dolphins concentrated close to the shore, in the inner sector of the area and the main activity is also foraging. Significant larger groups were seen in socializing behavior but there was no difference in group size between the inner and external sectors of the area. The presence of calves and juveniles were significant greater in the inner areas of Tabatinga and Pipa, confirming the hypothesis that these beaches are also used for parental care. In Baia Formosa dolphins concentrated in the outer sector and foraging was also predominant. Significant larger groups were seen in the outer sector, mainly engaged in mixed behaviors of travel/foraging, possibly in some kind of group foraging. Calves and juveniles were significant more present in the outer sector where group size was also larger. In general there was no difference in area usage and period of the day. Sotalia guianensis has characteristics that make the species vulnerable to human activities such as small population concentrated in patches of suitable habitats restrict to coastal areas. We hope that this study bring new information for the species and help for the adequate management of the area in order to assure the presence of the dolphins as well as its behavior pattern and gene flow betweencommunities.

Plankton richness and abundance in several different hydrological situations in lakes lateral to a river: a case study in the mouth zone of a tributary into a tropical reservoir.

A descriptive analysis of the responses of plankton from lakes lateral to a river in its mouth zone into a tropical reservoir to water level variations is presented. Three situations were reported: 1) a comparison of species richness and diversity and of algae population abundance in prolonged drought and in periods of connection of lakes to the river, 2) the spatial distribution of abundance and richness of Rotifera species in four isolated water bodies formed by fragmentation of a lateral lake during a period of prolonged drought and in the same areas during a period of integrity as an ecosystem, 3) the variability of total zooplankton and Cladocera densities at the end of the isolation period of a lateral lake and after the recovery of connection with the river and in a year of continuous connection with the lotic ecosystem. Various idiosyncrasies were observed in connected lateral lakes, like the surface hydrologic connectivity, a primary factor in species richness modifcations and a secondary controlling factor of plankton abundance. Underground hydrologic connectivity, through the river[forward arrow] lake water fux during the high-water period and lake [forward arrow] river during drought period, appears to have an important role in richness and abundance variations of planktonic populations in the lake isolated from the river.

Distribuição e tamanho populacional do papagaio-de-cara-roxa Amazona brasiliensis no estado de São Paulo

The Red-tailed Amazon Amazona brasiliensis is one of most threatened psitacid in the world. In the state of São Paulo, SE Brazil, it is restricted to a narrow coastal zone. The total population of A. brasiliensis has been estimated to be around 4,000 birds, but no detailed information is known for São Paulo. We studied the population status and mapped the distribution of A. brasiliensis in the state of São Paulo. Simultaneous censuses were carried out in three main islands (Cananéia, Ilha do Cardoso and Ilha Comprida) with A. brasiliensis populations in 2003 and 2004. We searched the parrots in an area of 1413.28 km2 and visited 69 sites. Amazona brasiliensis were recorded in 55 localities and 12 sleeping roosts. Our census estimated a population of at least 1,221 parrots in the stronghold of their distribution in the state of São Paulo. The highest number of parrots were recorded outside the main protected areas in the region (64% of the population), which may threaten the future of this population. Urban growing is the main threat for the population of São Paulo, and the creation of protected areas in Cananéia and Comprida island is critical for the future of the A. brasiliensis in the area.