A comparison of mark-recapture distance-sampling methods applied to aerial surveys of eastern grey kangaroos

Aerial surveys of kangaroos (Macropus spp.) in Queensland are used to make economically important judgements on the levels of viable commercial harvest. Previous analysis methods for aerial kangaroo surveys have used both mark-recapture methodologies and conventional distance-sampling analyses. Conventional distance sampling has the disadvantage that detection is assumed to be perfect on the transect line, while mark-recapture methods are notoriously sensitive to problems with unmodelled heterogeneity in capture probabilities. We introduce three methodologies for combining together mark-recapture and distance-sampling data, aimed at exploiting the strengths of both methodologies and overcoming the weaknesses. Of these methods, two are based on the assumption of full independence between observers in the mark-recapture component, and this appears to introduce more bias in density estimation than it resolves through allowing uncertain trackline detection. Both of these methods give lower density estimates than conventional distance sampling, indicating a clear failure of the independence assumption. The third method, termed point independence, appears to perform very well, giving credible density estimates and good properties in terms of goodness-of-fit and percentage coefficient of variation. Estimated densities of eastern grey kangaroos range from 21 to 36 individuals km-2, with estimated coefficients of variation between 11% and 14% and estimated trackline detection probabilities primarily between 0.7 and 0.9.

Monitoring the ungulate prey of the Komodo dragon Varanus komodoensis: distance sampling or faecal counts?

Monitoring the abundances of prey is important for informing the management of threatened and endangered predators. We evaluated the usefulness of faecal counts and distance sampling for monitoring the abundances of rusa deer Rusa timorensis, feral pig Sus scrofa and water buffalo Bubalus bubalis, the three key prey of the Komodo dragon Varanus komodoensis, at 11 sites on five islands in and around Komodo National Park, eastern Indonesia. We used species-specific global detection functions and cluster sizes (i.e. multiple covariates distance sampling) to estimate densities of rusa deer and feral pig, but there were too few observations to estimate densities of water buffalo. Rusa deer densities varied from from 2.5 to 165.5 deer/km2 with coefficients of variation (CVs) of 15-105%. Feral pig densities varied from 0.0 to 25.2 pigs/km 2 with CVs of 25-106%. There was a positive relationship between estimated faecal densities and estimated population densities for both rusa deer and feral pig: the form of the relationship was non-linear for rusa deer, but there was similar support for linear and non-linear relationships for feral pig. We found that faecal counts were more useful when ungulate densities were too low to estimate densities with distance sampling. Faecal count methods were also easier for field staff to conduct than distance sampling. Because spatial and temporal variation in ungulate density is likely to influence the population dynamics of the Komodo dragon, we recommend that annual monitoring of ungulates in and around Komodo National Park be undertaken using distance sampling and faecal counts. The relationships reported here will also be useful for managers establishing monitoring programmes for feral pig, rusa deer and water buffalo elsewhere in their native and exotic ranges.

Distance software: design and analysis of distance sampling surveys for estimating population size

1. Distance sampling is a widely used technique for estimating the size or density of biological populations. Many distance sampling designs and most analyses use the software Distance. 2. We briefly review distance sampling and its assumptions, outline the history, structure and capabilities of Distance, and provide hints on its use. 3. Good survey design is a crucial prerequisite for obtaining reliable results. Distance has a survey design engine, with a built-in geographic information system, that allows properties of different proposed designs to be examined via simulation, and survey plans to be generated. 4. A first step in analysis of distance sampling data is modeling the probability of detection. Distance contains three increasingly sophisticated analysis engines for this: conventional distance sampling, which models detection probability as a function of distance from the transect and assumes all objects at zero distance are detected; multiple-covariate distance sampling, which allows covariates in addition to distance; and mark–recapture distance sampling, which relaxes the assumption of certain detection at zero distance. 5. All three engines allow estimation of density or abundance, stratified if required, with associated measures of precision calculated either analytically or via the bootstrap. 6. Advanced analysis topics covered include the use of multipliers to allow analysis of indirect surveys (such as dung or nest surveys), the density surface modeling analysis engine for spatial and habitat-modeling, and information about accessing the analysis engines directly from other software. 7. Synthesis and applications. Distance sampling is a key method for producing abundance and density estimates in challenging field conditions. The theory underlying the methods continues to expand to cope with realistic estimation situations. In step with theoretical developments, state-of- the-art software that implements these methods is described that makes the methods accessible to practicing ecologists.

A Model-Based Approach for Making Ecological Inference from Distance Sampling Data

We consider a fully model-based approach for the analysis of distance sampling data. Distance sampling has been widely used to estimate abundance (or density) of animals or plants in a spatially explicit study area. There is, however, no readily available method of making statistical inference on the relationships between abundance and environmental covariates. Spatial Poisson process likelihoods can be used to simultaneously estimate detection and intensity parameters by modeling distance sampling data as a thinned spatial point process. A model-based spatial approach to distance sampling data has three main benefits: it allows complex and opportunistic transect designs to be employed, it allows estimation of abundance in small subregions, and it provides a framework to assess the effects of habitat or experimental manipulation on density. We demonstrate the model-based methodology with a small simulation study and analysis of the Dubbo weed data set. In addition, a simple ad hoc method for handling overdispersion is also proposed. The simulation study showed that the model-based approach compared favorably to conventional distance sampling methods for abundance estimation. In addition, the overdispersion correction performed adequately when the number of transects was high. Analysis of the Dubbo data set indicated a transect effect on abundance via Akaike’s information criterion model selection. Further goodness-of-fit analysis, however, indicated some potential confounding of intensity with the detection function.

Sampling and learning the Mallows and Generalized Mallows models under the Cayley distance

[EN]The Mallows and Generalized Mallows models are compact yet powerful and natural ways of representing a probability distribution over the space of permutations. In this paper we deal with the problems of sampling and learning (estimating) such distributions when the metric on permutations is the Cayley distance. We propose new methods for both operations, whose performance is shown through several experiments. We also introduce novel procedures to count and randomly generate permutations at a given Cayley distance both with and without certain structural restrictions. An application in the field of biology is given to motivate the interest of this model.

Sampling and learning the Mallows and Weighted Mallows models under the Hamming distance

[EN]In this paper we deal with distributions over permutation spaces. The Mallows model is the mode l in use. The associated distance for permutations is the Hamming distance.

Sampling and learning the Mallows model under the Ulam distance

[EN]In this paper we deal with probability distributions over permutation spaces. The Probability model in use is the Mallows model. The distance for permutations that the model uses in the Ulam distance.

Estimating abundance of killer whales in the nearshore waters of the Gulf of Alaska and Aleutian Islands using line-transect sampling

Killer whale (Orcinus orca Linnaeus, 1758) abundance in the North Pacific is known only for a few populations for which extensive longitudinal data are available, with little quantitative data from more remote regions. Line-transect ship surveys were conducted in July and August of 2001–2003 in coastal waters of the western Gulf of Alaska and the Aleutian Islands. Conventional and Multiple Covariate Distance Sampling methods were used to estimate the abundance of different killer whale ecotypes, which were distinguished based upon morphological and genetic data. Abundance was calculated separately for two data sets that differed in the method by which killer whale group size data were obtained. Initial group size (IGS) data corresponded to estimates of group size at the time of first sighting, and post-encounter group size (PEGS) corresponded to estimates made after closely approaching sighted groups.

The influence of animal mobility on the assumption of uniform distances in aerial line-transect surveys

Line-transect distance sampling is a widely used method for estimating animal density from aerial surveys. Analysis of line-transect distance data usually relies on a requirement that the statistical distribution of distances of animal groups from the transect line is uniform. We show that this requirement is satisfied by the survey design if all other assumptions of distance sampling hold, but it can be violated by consistent survey problems such as responsive movement of the animals towards or away from the observer. We hypothesise that problems with the uniform requirement are unlikely to be encountered for immobile taxa, but might become substantial for species of high mobility. We test evidence for non-uniformity using double-observer distance data from two aerial surveys of five species with a spectrum of mobility capabilities and tendencies. No clear evidence against uniformity was found for crabeater seals or emperor penguins on the pack-ice in East Antarctica, while minor non-uniformity consistent with responsive movement up to 30 m was found for Adelie penguins. Strong evidence of either non-uniformity or a failure of the capture-recapture validating method was found for eastern grey kangaroos and red kangaroos in Queensland.

Abundance and distribution patters of Hawaiian odontocetes: focus on O'ahu

This dissertation is an assessment of the status of odontocetes in Hawaiian waters focussing on O´ahu. The work builds on available literature, and on data collected by the author and by others in Hawaiian waters. Abundance and distribution patterns of odontocetes were derived from stranding and aerial survey data. A stranding network operated by the National Marine Fisheries Service, Pacific Area Office collected 187 stranding reports throughout the main Hawaiian Islands between 1937 and 2002. These reports included 16 odontocete species. Number of stranding reports increased over time and was highest on O´ahu. Strandings occurred throughout the year. The difference in number of strandings per month was not significant. Fifteen of the 16 species reported in the stranding record for the main Hawaiian Islands were also reported by aerial survey studies of the area between 1993 and 1998. Only 7 of the species reported were detected during aerial transects around O′ahu between 1998 and 2000. Based on the stranding record, Kogia sp., melon-headed whales, striped dolphins and dwarf killer whale appear to be more common than suggested by aerial surveys. Conversely, pilot whales and bottlenose dolphins were more common, according to aerial surveys, than predicted by the stranding data. Aerial surveys of waters between 0 and 500m around the Island of O′ahu showed that the most abundant species by frequency of occurrence was the pilot whale (30% of sightings), followed by the spinner (16%) and bottlenose dolphin (14%). Because of small sample size, abundance estimates for odontocetes have a high level of uncertainty. The unavailability of a correction factor for g(0)<1, and the reduced visibility below the aircraft further reduced accuracy and increased the inherent underestimation in the data. The most abundant species according to distance sampling estimates were spotted dolphins, pilot whales, false killer whales and spinner dolphins. A natural factor shaping the ecology of odontocete populations is predation pressure both by other odontocetes and, more frequently, by sharks. An account of predation by a tiger shark on a spotted dolphin near Penguin Banks is used as an example of the potential mechanisms of predation by sharks on odontocetes.

Densidade, genética e saúde populacional como ferramentas para propor um plano de controle e erradicação de invasão biológica: o caso de Callithrix aurita (Primates) no Parque Nacional da Serra dos Órgãos, RJ, Brasil

A introdução de espécies em locais fora de sua distribuição natural é uma preocupação importante na conservação da biodiversidade. A espécie Callithrix aurita é endêmica das regiões de floresta de altitude da Mata Atlântica do Sudeste do Brasil. Os critérios mais relevantes que a enquadram como espécie ameaçada de extinção são: destruição do habitat, incapacidade de adaptação a florestas secundárias degradadas, declínio populacional, distribuição restrita e introdução de espécies exóticas invasoras. Estes critérios, aliados à evidente raridade, explicam a sua inclusão na Lista Oficial de Espécies da Fauna Brasileira Ameaçadas de Extinção. Os objetivos do trabalho são: estimar o tamanho populacional de C. aurita, C. penicillata e seus híbridos no Parque Nacional da Serra dos Órgãos, avaliar a hibridação entre as espécies por caracteres morfológicos e laboratoriais, verificar o estado de saúde e confirmar a participação de C. aurita na paternidade dos animais capturados, propor um plano de erradicação e de controle de invasão de C. penicillata no Parque. Os tamanhos populacionais das duas espécies de primatas foram estimados através do método Distance Sampling. Um total de sete sagüis foi capturado com armadilhas de captura viva para a contenção física e química e posterior realização dos procedimentos. Para o hemograma, as dosagens bioquímicas e as análises genéticas, o sangue foi recolhido em um tubo de ensaio contendo anticoagulante e mantido em temperatura de refrigeração até o momento da manipulação / processamento das amostras. Callithrix aurita parece estar bem preservada apenas na área do Parque correspondente ao trecho situado no município de Petrópolis. As análises citogenéticas e moleculares dos híbridos são uma ferramenta útil para confirmar se há ou não hibridação, identificando as espécies envolvidas e verificando se há tendência nos retrocruzamentos. Pode-se sugerir que existe uma tendência à diferenciação das espécies e identificação de indivíduos híbridos pelo padrão hematológico e bioquímico, a ser confirmada com uma amostragem maior de animais da espécie C. aurita, preferencialmente da mesma localidade e nas mesmas condições. No caso de C. aurita, as principais recomendações para sua conservação incluem pesquisas para o registro de outras populações em áreas de distribuição livres de invasão, para que se possa avaliar as chances de recuperação populacional e sobrevivência da espécie. A criação de novas Unidades de Conservação deve ser estimulada, assim como estudos mais aprofundados sobre a espécie nos locais já conhecidos de ocorrência, além de um programa seguro de criação em cativeiro.

Comunidade de mamíferos de médio e grande porte em um mosaico de fitofisionomias na Mata Atlântica no estado do Espírito Santo, Brasil

A Mata Atlântica é considerada como um dos cinco hotspots mais diversos, sendo um conjunto complexo de ecossistemas que abriga uma parcela significativa da diversidade biológica do Brasil. O Estado do Espírito Santo, localizado na região Sudeste, possuía quase 90% de sua superfície coberta por Mata Atlântica, entretanto com o processo de colonização portuguesa, ocupação do território e industrialização, restou apenas 8% da cobertura florestal original. Com toda a informação existente acerca das espécies neotropicais de mamíferos de médio e grande porte ainda há muitas lacunas no nosso conhecimento. Nesse sentido, esta dissertação foi desenvolvida em quatro capítulos com o objetivo de realizar um levantamento de dados de riqueza, composição, abundância, densidade populacional, período de atividade, distribuição e uso do hábitat por espécies de mamíferos de médio e grande porte, da Reserva Natural Vale (RNV), norte do Espírito Santo. Espera-se que as informações aqui geradas possam contribuir com o incremento no conhecimento da ecologia dos mamíferos neotropicais, bem como fornecer informações desse grupo para subsidiar as políticas e ações ambientais que visem à conservação da biodiversidade. Para este estudo foi realizado amostragens mensais no período de abril de 2013 até junho de 2014 na RNV, através de armadilhamento fotográfico (39 armadilhas fotográficas) e também transecções lineares Os registros obtidos nas39 armadilhas fotográficas resultaram em um total de 7.020 dias de monitoramento. Foram observadas 23245 fotos de 26 espécies de mamíferos de médio e grande porte. Uma maior riqueza e frequência de registros ocorreram nas armadilhas estabelecidas na região norte da RNV. A distância do recurso hídrico estava positivamente relacionada com a composição de mamíferos e a quantidade de registros de caça no presente estudo teve um efeito marginalmente negativo na frequência de registros nas regiões oeste e sul, onde apresentaram uma maior incidência de caça. Nossos resultados mostram que essas espécies não estão distribuídas uniformemente dentro da reserva, com a ocupação das mesmas tendo sido afetada por quatro principais covariáveis: (1) distância entre árvores; (2) distância da estrada; (3) distância do recurso hídrico mais próximo e (4) densidade de lianas por hectare. A detectabilidade das espécies que são consideradas cinegéticas foi afetada pelo histórico de registros de caça. A maioria das espécies registradas que tiveram uma probabilidade de ocupação alta são raras ou até mesmo localmente extintas em outras áreas de domínio da Mata Atlântica. Adicionalmente nossos dados confirmam que a RNV abriga uma fauna de mamíferos de médio e grande porte rica, incluindo grandes herbívoros, dispersores de sementes e alguns carnívoros. Embora o estudo tenha sido realizado em apenas uma área, vale lembrar que a RNV, juntamente com a ReBio Sooretama, formam o maior bloco de área protegida dentro do estado do Espírito Santo e também um dos maiores blocos de Mata de Tabuleiro. Assim, para a conservação das espécies que habitam a RNV, é preciso considerar não apenas a reserva isolada, mas todo o bloco Linhares-Sooretama, uma vez que estão conectados permitirão o incremento populacional e as trocas genéticas entre as populações. Somente desse modo será aumentada a probabilidade de sobrevivência e manutenção das espécies em longo prazo, das espécies de mamíferos de médio e grande porte

Game Vertebrate Densities in Hunted and Nonhunted Forest Sites in Manu National Park, Peru

Manu National Park of southern Peru is one of the most renowned protected areas in the world, yet large-bodied vertebrate surveys conducted to date have been restricted to Cocha Cashu Biological Station, a research station covering <0.06 percent of the 1.7Mha park. Manu Park is occupied by >460 settled Matsigenka Amerindians, 300-400 isolated Matsigenka, and several, little-known groups of isolated hunter-gatherers, yet the impact of these native Amazonians on game vertebrate populations within the park remains poorly understood. On the basis of 1495 km of standardized line-transect censuses, we present density and biomass estimates for 23 mammal, bird, and reptile species for seven lowland and upland forest sites in Manu Park, including Cocha Cashu. We compare these estimates between hunted and nonhunted sites within Manu Park, and with other Neotropical forest sites. Manu Park safeguards some of the most species-rich and highest biomass assemblages of arboreal and terrestrial mammals ever recorded in Neotropical forests, most likely because of its direct Andean influence and high levels of soil fertility. Relative to Barro Colorado Island, seed predators and arboreal folivores in Manu are rare, and generalist frugivores specializing on mature fruit pulp are abundant. The impact of such a qualitative shift in the vertebrate community on the dynamics of plant regeneration, and therefore, on our understanding of tropical plant ecology, must be profound. Despite a number of external threats, Manu Park continues to serve as a baseline against which other Neotropical forests can be gauged.

基于IGES的卷曲类工件结构光测量路径规划研究

本文通过对卷曲类工件IGES文件的分析,本文提出了一种新的基于IGES文件的测量路径规划策略。根据张量积曲面的性质,提出了一种曲面组合算法,运用了张量积曲面的性质,将曲面操作转化为多次曲线操作,将IGES文件中存储的多片曲面片组合为一整片曲面,从而为自由曲面测量路径的提取提供了数学模型。运用二次逼近原理,提出了一种B样条曲线上的等距采样算法。通过在实际系统进行实验,上述策略及算法得到了验证,并在自主开发的智能测量建模加工一体化装备中得到了应用。

An invasive-native mammalian species replacement process captured by camera trap survey random encounter models

Camera traps are used to estimate densities or abundances using capture-recapture and, more recently, random encounter models (REMs). We deploy REMs to describe an invasive-native species replacement process, and to demonstrate their wider application beyond abundance estimation. The Irish hare Lepus timidus hibernicus is a high priority endemic of conservation concern. It is threatened by an expanding population of non-native, European hares L. europaeus, an invasive species of global importance. Camera traps were deployed in thirteen 1 km squares, wherein the ratio of invader to native densities were corroborated by night-driven line transect distance sampling throughout the study area of 1652 km2. Spatial patterns of invasive and native densities between the invader’s core and peripheral ranges, and native allopatry, were comparable between methods. Native densities in the peripheral range were comparable to those in native allopatry using REM, or marginally depressed using Distance Sampling. Numbers of the invader were substantially higher than the native in the core range, irrespective of method, with a 5:1 invader-to-native ratio indicating species replacement. We also describe a post hoc optimization protocol for REM which will inform subsequent (re-)surveys, allowing survey effort (camera hours) to be reduced by up to 57% without compromising the width of confidence intervals associated with density estimates. This approach will form the basis of a more cost-effective means of surveillance and monitoring for both the endemic and invasive species. The European hare undoubtedly represents a significant threat to the endemic Irish hare.