Animal populations (Estimates)

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Predicting farm level animal populations using environmental and socioeconomic variables

Predicting farm level animal populations using environmental and socioeconomic variables

We have constructed a model that predicts the presence and absence as well as the numbers of livestock units and cattle at the farm level in New Zealand. While wildlife ecology uses similar models for conservation and research purposes, the use of modelled or inaccurate point estimates of animal populations for biosecurity operations (rather than when preparing for a disease outbreak) may introduce systematic error which could increase the number of properties affected by, and the eventual cost of a fast moving animal disease. Predictions were accurate at a wide spatial scale (3km zones or administrative regions) and our model allows us to explore uncertainty around a point estimate in animal numbers at the farm level by incorporating farm population posterior distribution estimates in disease simulators. Future work will further refine the modelling approach to improve its internal validity and provide external validation of the model using data collected from the field to fully assess the precision of the estimates of livestock numbers and of cattle on farms and to test the extensibility of the derived covariates to predict farm level counts on an unrelated spatial farms database (FarmsOnLine). While probabilities of presence and distributions of animal counts are useful in exotic disease preparedness and disease spread simulation modelling, when faced with the already considerable uncertainty inherent early in a disease outbreak response the decision maker requires the most accurate and correct information to make high quality decisions. Every reasonable effort must be made to strengthen data linkages between existing animal population data sources by aligning data collection efforts undertaken by government and industry and by the use of a single, national farm identifier.

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Identifying social learning in animal populations : A new ‘option bias’ method

Identifying social learning in animal populations : A new ‘option bias’ method

Methodology/Principal Findings: We present a solution to this problem, in the form of a new means of identifying social learning in animal populations. The method is based on the well-established premise of social learning research, that - when ecological and genetic differences are accounted for - social learning will generate greater homogeneity in behaviour between animals than expected in its absence. Our procedure compares the observed level of homogeneity to a sampling distribution generated utilizing randomization and other procedures, allowing claims of social learning to be evaluated according to consensual standards. We illustrate the method on data from groups of monkeys provided with novel two- option extractive foraging tasks, demonstrating that social learning can indeed be distinguished from unlearned processes and asocial learning, and revealing that the monkeys only employed social learning for the more difficult tasks. The method is further validated against published datasets and through simulation, and exhibits higher statistical power than conventional inferential statistics.

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Spatial Modeling of Detection and Abundance from Count Surveys of Animal Populations

Spatial Modeling of Detection and Abundance from Count Surveys of Animal Populations

The goals of stream fish surveys include assessment of the distribution of fish, determining the factors that influence fish density, and estimation of population size. In general the whole pop- ulation of a unit is not observed on a single pass and therefore to achieve these goals through statistical modeling, we also require information about the probability of detection of individual fish (Thompson, 2002). This is provided by using a two-stage sampling design, in which the first stage is the selection of the units from the stream, and the second stage involves making indepen- dent, repeated passes of the survey units. When the survey is conducted using snorkel dives, this requires a sequence of independent dive counts to be made of the population of fish in each of the units selected in the first stage. A possible approach to estimating abundance and detection probability for each unit is to assume a binomial model for the unit counts, and use either method of moments or maximum likelihood estimators (Johnson and Kotz, 1969). This method requires us to assume that the fish population is closed to births and deaths, immigration and emigration over the course of the survey, but this is reasonable when the repeated passes are made in quick succession as is generally the case in these types of surveys. However, estimation of both binomial parameters (population size and detection probability) from a single sample of counts can be highly unstable, with small changes in the data producing large shifts in the estimates of abundance and detection probability. Although more stable estimators exist, e.g., Carroll and Lombard (1985) and Olkin et al. (1981), they are not without problems of their own, particularly for the sparse data that results when population density is low in a unit (Casella, 1986).

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Modelling zoonotic diseases with treatment in both human and animal populations

Modelling zoonotic diseases with treatment in both human and animal populations

(iii) The infected animals I(T) is remove with a death rate c or by human predation before they can possibly reproduce. However, both the infected I(T) and susceptible S(T) ani- mals populations contribute to the population growth towards the carrying capacity K. (iv) Susceptible animals S(T) become infected through contact with an infected animals I(T)

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The effect of animal movement on line transect estimates of abundance

The effect of animal movement on line transect estimates of abundance

Line transect sampling is a distance sampling method for estimating the abundance of wild animal populations. One key assumption of this method is that all animals are detected at their initial location. Animal movement independent of the transect and observer can thus cause substantial bias. We present an analytic expression for this bias when detection with- in the transect is certain (strip transect sampling) and use simulation to quantify bias when detection falls off with distance from the line (line transect sampling). We also explore the non-linear relationship between bias, detection, and animal movement by varying detect- ability and movement type. We consider animals that move in randomly orientated straight lines, which provides an upper bound on bias, and animals that are constrained to a home range of random radius. We find that bias is reduced when animal movement is constrained, and bias is considerably smaller in line transect sampling than strip transect sampling pro- vided that mean animal speed is less than observer speed. By contrast, when mean animal speed exceeds observer speed the bias in line transect sampling becomes comparable with, and may exceed, that of strip transect sampling. Bias from independent animal move- ment is reduced by the observer searching further perpendicular to the transect, searching a shorter distance ahead and by ignoring animals that may overtake the observer from be- hind. However, when animals move in response to the observer, the standard practice of searching further ahead should continue as the bias from responsive movement is often greater than that from independent movement.

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Impacts of Seed and Pollen Flow on Population Genetic Structure for Plant Genomes With Three Contrasting Modes of Inheritance

Impacts of Seed and Pollen Flow on Population Genetic Structure for Plant Genomes With Three Contrasting Modes of Inheritance

The classical island and one-dimensional stepping-stone models of population genetic structure devel- oped for animal populations are extended to hermaphrodite plant populations to study the behavior of biparentally inherited nuclear genes and organelle genes with paternal and maternal inheritance. By substituting appropriate values for effective population sizes and migration rates of the genes concerned into the classical models, expressions for genetic differentiation and correlation in gene frequency between populations can be derived. For both models, differentiation for maternally inherited genes at migration- drift equilibrium is greater than that for paternally inherited genes, which in turn is greater than that for biparentally inherited nuclear genes. In the stepping-stone model, the change of genetic correlation with distance is influenced by the mode of inheritance of the gene and the relative values of long- and short- distance migration by seed and pollen. In situations where it is possible to measure simultaneously F st for

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The genomes and history of domestic animals

The genomes and history of domestic animals

livestock animal. Gene(s) that control similar traits in a human or mouse, are then cloned and sequenced in the animal. The mutations (e.g. point mutations) are determined in these genes in livestock animal populations, and an associative analysis is conducted, which reveals the relationship (or lack thereof) between the animal's phenotype and specific nucleotide substitution(s). If an association of this sort is observed, then the gene that influences a particular trait in the animal's genome was identified correctly. Obviously, this approach has a number of drawbacks, namely: a) it "works" only for genes with similar functions in different species, and; b) generally, mutations in regulatory regions of genes are not detected by this approach because they might be located outside the cloned region. Nevertheless, with the help of the candidate gene search technique, important genes have been identified as such the gene influencing the increase in muscle mass in cattle [2]. On the linkage map of the cattle, this trait is mapped (among other locations) to a locus on chromosome 2. This locus corresponds to region 2q31-22 in the human genome, which, among other genes, contains MSTN gene. The knock out of the Mstn gene in the mouse genome significantly increases muscle mass. As a result, MSTN was chosen as a "candidate gene". After sequencing of the MSTN gene in cattle, mutations segregating with the muscle mass trait had been found.

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Molecular surveillance for drug resistant Plasmodium falciparum in clinical and subclinical populations from three border regions of Burma/Myanmar: cross sectional data and a systematic review of resistance studies

Molecular surveillance for drug resistant Plasmodium falciparum in clinical and subclinical populations from three border regions of Burma/Myanmar: cross sectional data and a systematic review of resistance studies

Consistent with the a priori hypothesis, the preva- lence of elevated pfmdr1 CN was higher among isolates obtained from active screening participants than from isolates obtained from febrile clinical patients. Resist- ance surveillance currently relies on samples obtained from clinically symptomatic malaria patients; contain- ment efforts may need to more aggressively target sub- clinical infections that could serve as a reservoir for the spread of drug resistance if future studies validate an as- sociation between subclinical infection and resistance alleles. However, there are several reasons to approach this finding with caution. First, to the authors’ knowledge this is the first study to evaluate pfmdr1 CN in a predom- inantly asymptomatic population. Zhong et al. [54] found no difference between symptomatic and asymp- tomatic study volunteers in Kenya in the frequency of pfmdr1 point mutations, or of the K76T mutation of pfcrt. Second, consistent with Zhong et al. the current study found no difference in K76T mutation prevalence between screening and clinical participants, though prevalence of wild-type pfcrt was low in each region and results may be confounded by ongoing CQ drug pressure as described above. Third, a robust empirically derived conceptual model is lacking to adequately capture the complex interactions between transmission intensity, host immunity, drug pressure, fitness cost, compensatory mutations, clonality of infection, de-amplification [27,55] and other factors expected to influence the relative prevalence of resistant and wild-type parasites in clinical and asymptomatic infections. Clonality of infection is likely to play an important role, as described above, but the prevalence of monoclonal infection in Myanmar is poorly quantified. A single study from central Myanmar documented mono-infection in 32% of clinical isolates [56], but the relevance of these data to asymptomatic populations in border regions is unclear. The final reason to interpret with caution the association between sub- clinical infection and genetic resistance is the high vari- ance of pfmdr1 CN estimates found among screening participants that led to the exclusion of 55% of samples. Future studies are needed to validate the accuracy of pfmdr1 CN estimates based on filter-paper blood samples collected from subclinical populations. Despite these caveats, findings presented here highlight the need to conduct additional studies on the contribution of sub- clinical infection to the epidemiology of drug-resistant malaria.

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Variance components for susceptibility to Mycobacterium bovis infection in dairy and beef cattle

Variance components for susceptibility to Mycobacterium bovis infection in dairy and beef cattle

The genetic variance of susceptibility to bTB in environ- ments with different bTB prevalence levels has not pre- viously been documented. The pattern of genetic variances of susceptibility to bTB in environments with different bTB prevalence levels, estimated using an ani- mal linear mixed model, was similar to the trend in gen- etic variances estimated for somatic cell score in environments with different herd average somatic cell scores [38] (i.e. it was least in the most extreme environ- ments). However, the genetic variance pattern observed in the present study was in direct contrast to the pattern of genetic variance estimates reported for Johne’s disease in Dutch Holstein-Friesian cows [39], which increased with herd prevalence for Johne’s disease. Nonetheless, the pattern in genetic variance for susceptibility to bTB when estimated with a threshold animal model in the present study was similar to that observed for Johne’s disease [39] and herd prevalence (Table 3). Estimates of variance components in the different prevalence groups were similar to those reported by van Hulzen et al. [39], using a linear model, with the exception of the very high prevalence environment. An inverse relationship existed between estimates of genetic variance and heritability using the linear model across the different prevalence groups, while one would expect a positive relationship [37]. This could be due to the fewer animals in the more extreme environmental categories or selection/culling. To ensure that there was no impact of the estimation algo- rithm on estimates of the variance components, the zeros and ones in the high prevalence environment were switched and variance components re-estimated using the linear model; this did not impact the estimated variance components. Although heritability estimates differed be- tween the threshold animal model and the linear model estimates transformed to the liability scale, the heritability of susceptibility to bTB in the very high prevalence herds (>0.75) was always greatest, regardless of the model used.

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The limits of mean field heterozygosity estimates under spatial extension in simulated plant populations

The limits of mean field heterozygosity estimates under spatial extension in simulated plant populations

Understanding the evolutionary process is increasingly requiring in the integration of sources of data that are typically beyond classical population genetics models [1]. One such example is the inclusion of spatial extension. Classical population genetics approaches typically use a simplified mean-field approach in which individuals of a population or subpopulation conceptually occupy the same space, and are therefore subject to the same conditions and pressures, and purely random mating occurs. Along with other simplifying assumptions such as non-overlapping generations and constant population sizes, such populations behave in tractable ways that can be described through deterministic approaches leading to features such as Hardy- Weinberg equilibria [2] and the Wright-Fisher model [3]. The predictions of such models provide a useful starting point for evolutionary studies, for instance in establishing whether there has been significant deviation from neutrality indicative of selection. However, Mayr [4] observed that it was surprising how little classical population genetics has contributed to the understanding of one of the most important processes in evolution, speciation. This is because a mean-field based model is essentially based on an anagenic evolutionary system, rather than a cladogenic one [5]. The evolutionary differentiation of populations, which ultimately leads to speciation, requires different selective environments.

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RNA-Seq Alignment to Individualized Genomes Improves Transcript Abundance Estimates in Multiparent Populations

RNA-Seq Alignment to Individualized Genomes Improves Transcript Abundance Estimates in Multiparent Populations

For many genes, estimates of transcript abundance are relatively unaffected by alignment strategy. For example, 75% of expressed genes in CAST (n = 8980/ 11,964) have gene abundance estimates that differ by ,10% after align- ment to NCBIM37 and CAST, and most (n = 6855/ 11,964) differ by ,5%. The subset of genes most sensitive to align- ment method in real data consists primarily of closely related gene families and protein-coding genes with retrotransposed pseudogenes. Our simulations confirmed that pseudogenes can act as “read sinks” that shunt significant numbers of reads away from the protein-coding parent gene. Pseudogenes have long been considered functionless evolutionary relics; how- ever, recent evidence suggests that some are actively tran- scribed and play critical roles in gene regulation (Zheng and Gerstein 2007; Muro et al. 2011; Poliseno 2012). There is not a clear delineation among gene, gene family, and pseu- dogene, and we feel that it is better to obtain accurate read alignments than to mask regions of low genomic mappability in the reference or apply a post hoc filtering based on gene annotations. After an individual’s genetic variation is included in the alignment, particularly in the parent gene, many of these reads will align uniquely to the parent gene and be weighted accordingly by the EM algorithm (Figure S4 and Figure S5).

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Studies on Stevia (Stevia rebaudiana)

Studies on Stevia (Stevia rebaudiana)

Significant differences were identified, where cultigen, or in this study 72 elite half-sib lines was significant for majority of the traits estimated. This comes as no surprise, as these lines were selected for superior performance of yield or various desirable glycosides. Plant breeders prefer a diverse population for long term breeding gains, due to wide base of genes. Further evaluations should be conducted within specific populations, to develop phenotypic screening techniques for high glycoside compounds. New technology such as high-throughput phenotyping could likely assist in screening methods that could save resources in expensive glycoside testing via HPLC-MS where limitations in glycoside sampling exist due to cost. Correlations between glycosides and yield were generally low, however a significant correlation was found for rebaudioside C, which may suggest selection for yield and rebaudioside C may occur simultaneously. However, the correlation although significant was not high. Therefore, more evidence would be needed to support this finding.

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A Spatial Statistical Model for Landscape Genetics

A Spatial Statistical Model for Landscape Genetics

pendent and identically distributed among individuals. The global set of sampled individuals is viewed as rep- As a consequence, they do not make use of spatial coor- resentative of one or several panmictic populations sepa- dinates of sampled individuals, except in some ad hoc rated by geographic borders across space. Our modeling postprocessing schemes like those consisting of drawing strategy is hierarchical in the sense that we first specify by hand the spatial convex hull of each inferred popula- how the populations are spatially organized and then tion. Hence these methods cannot objectively identify we specify the statistical genetic properties of each popu- the spatial location of genetic discontinuities between lation conditionally on this spatial organization.

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Modelling environmental changes in the Udzungwa Mountains of Tanzania through impact assessment on rainforest mammals

Modelling environmental changes in the Udzungwa Mountains of Tanzania through impact assessment on rainforest mammals

Environmental changes and anthropogenic pressures are eroding biodiversity at unprecedented rates, with negative impact on the survival and fecundity of animal species (Millenium Ecosystem Assessment 2005, Ceballos et al. 2015, Urban 2015). Modifications and degradation in the extent and spatial configuration of habitats can in fact reduce population size and growth rates, elevating the chance of extinction of populations and species (Ronald Pulliam 1988, Naeem et al. 1999, Acevedo-Whitehouse & Duffus 2009). Assessing the impact that such natural and human-induced factors have on the distribution and dynamics of selected species is therefore crucial to plan for adequate conservation actions and, in turn, to better predict the effects on species of the current environmental conditions. As the number of species threatened with extinction is way larger that our capacity to effectively protect them with the limited resources available to conservation (Myers et al. 2000), it is widely acknowledged that efforts may be more proficiently focused on species that are known to be intensively subjected to environmental changes, habitat loss and over- exploitation. Such species are indeed highly representative of dysfunctions in the ecosystems (Bridgewater 2016).

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Microbial Loop Populations: Their Abundances and Trophodynamics in the Gulf of Aqaba, Red Sea

Microbial Loop Populations: Their Abundances and Trophodynamics in the Gulf of Aqaba, Red Sea

The relationship between heterotrophic nanoflagellates and bacterial populations of these marine protectorates can be further illustrated from the data in table (2). Here it is shown that the number of bacteria that may be caught per flagellate per hour is high in spring (110, 50 and 5 at sites 1, 2 and 3, respectively) and low in summer (10, 5, and 1 for the three sites respectively). Fenchel (1982) calculated the maximum ingestion rate as being 27-254 bacteria/flagellate/hour and Sherr et al. (1983) found ingestion rates of 10-75 bacteria/flagellate/hour. Thus, the flagellate population of Ras Mohammed and Nabq protectorates could be able to maintain themselves with these ingestion rates of 10-110 bacteria/ flagellate/hour and 5-50 bacteria/flagellate/hour, Table 2. A comparison of the bacterial, total nanoflagellates (TNAN), heterotrophic nanoflagellates (HNAN) and filter- feeding ciliate populations with estimates of the clearance rates and potential rates of food capture by these flagellates and ciliates during spring and summer 2007 at Ras Mohammed (R.M.), Nabq (N.) and Abu Galoum (A.G.) protectorates

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Mitigating amphibian disease: strategies to maintain wild populations and control chytridiomycosis

Mitigating amphibian disease: strategies to maintain wild populations and control chytridiomycosis

Conservation biologists should prepare for more active management of amphibian disease on a scale ranging from host to habitat, and varying in approach from medical to ecological. Under development are periodic physical or chemical treatments and methods to limit infectious zoospores in the environment resulting in reduced disease spread or reduced pathogen prevalence or infection intensities. Managing for both abiotic and biotic habitat characteristics may be critical given that healthy microcrustacean communities may actively pre- date Bd zoospores and reduce transmission. Altering amphibian density through culling may not be effective. Refugia where threatened and susceptible species persist must be actively targeted for conservation since they contain the remnants of within-species diversity and potential sources for population recovery, as well as space for potential managed relocation. If recovered or re-colonized populations have evolved increased disease resistance as with other wildlife epizootics [203,204], studying them may reveal new mechanisms for reducing the impact of the disease and suggest strategies for increasing the disease resistance of captive-bred frogs prior to reintroduction. Assisted selection within captive amphibian colonies has long-term potential. Attenuated Bd or an avirulent strain could be used as a live vaccine, and perhaps in wild populations after ameliorating the risks of evolving greater virulence. Molecular advances illuminating virulence mechanisms may enable genetic modification of Bd and immunogenetics studies may reveal avenues for enhancing immune responses to Bd

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Orthogonal Estimates of Variances for Additive, Dominance, and Epistatic Effects in Populations

Orthogonal Estimates of Variances for Additive, Dominance, and Epistatic Effects in Populations

For plant and animal breeders and evolutionary geneti- cists, a meaningful partition of the variance is such that estimates can be interpreted in the classical terms, as variances of breeding values, dominant deviations, epistatic deviations, and so on (Hill et al. 2008). A nonorthogonal partition may lead to the erroneous conclusion that assortative mating and inclusion of dominance and/or epistasis can yield higher ge- netic gains as opposed to the consideration of additivity and random mating. For instance, Muñoz et al. (2014) concluded that dominance accounted for 39% of the total genetic vari- ance when they used a nonorthogonal partition, vs. 24% when they used the orthogonal partition in Vitezica et al. (2013).

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Shifting suitability for malaria vectors across Africa with warming climates

Shifting suitability for malaria vectors across Africa with warming climates

Finally, I calculated human populations living within the potential distributions of these competent malaria vectors across sub-Saharan Africa based on the LandScan database [29,30], a 1 km resolution summary of present-day human population distributions globally. It should be noted that I make the explicit assumption of stability of human population distributions – although future popu- lation projections are available [38], they are overly coarse spatially to be greatly informative in this analysis, so this point remains as a future challenge for improvement. For each greenhouse gas emissions scenario, I averaged the results of the two climate models to yield single estimates of future potential distribution under that scenario. Inter- secting the model predictions with the Landscan dataset, I calculated present-day numbers of people living in areas coinciding with potential distributional areas of each mosquito species, and present-day numbers of people liv- ing in areas converting from unsuitable to suitable or vice versa.

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Estimates of the Southern Ocean general circulation improved by animal borne instruments

Estimates of the Southern Ocean general circulation improved by animal borne instruments

equipped with conductivity-temperature-depth sensors in the Southern Ocean for both biological and physical oceanographic studies. A calibrated collection of seal-derived hydrographic data is now available, consisting of more than 165,000 pro fi les. The value of these hydrographic data within the existing Southern Ocean observing system is demonstrated herein by conducting two state estimation experiments, differing only in the use or not of seal data to constrain the system. Including seal-derived data substantially modi fi es the estimated surface mixed- layer properties and circulation patterns within and south of the Antarctic Circumpolar Current. Agreement with independent satellite observations of sea ice concentration is improved, especially along the East Antarctic shelf. Instrumented animals ef fi ciently reduce a critical observational gap, and their contribution to monitoring polar climate variability will continue to grow as data accuracy and spatial coverage increase. Citation: Roquet, F., et al. (2013), Estimates of the Southern Ocean general circulation improved by animal-borne instruments, Geophys. Res. Lett., 40, doi:10.1002/ 2013GL058304.

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The influence of instantaneous variation on estimates of coral reef fish populations and communities

The influence of instantaneous variation on estimates of coral reef fish populations and communities

We undertook a sampling program that was expected to reduce the number of possible variables influencing the fish populations, such that we measured the instan- taneous within-site (transect) variability as closely as possible. Consequently, the surveys were conducted by experienced observers, during 1 season at the calmest time of year, on days with calm and sunny conditions and during midday neap tides. These factors have been hypothesized to influence survey results (Helfman 1986, Galzin 1987, Thompson & Mapstone 2002, Williams et al. 2006); therefore, methods and sampling design were specifically developed to minimize these potential effects. From 2 to 7 December 2004, fish censuses were conducted independently by 5 different observers (TRM, NAJG, PC, JHB, and NVCP), each ob- server completing 3 census passes of each transect. In most cases, consecutive passes of a transect were completed serially with only a few minutes between transects, such that the time between samples was ap- proximately the time required to complete a transect (approximately 20 min). Thus, each transect was sur- veyed 15 times, 45 passes of transects were made per management area, and 90 passes were made in total during 2004 (Table 1). Identical censuses were carried out during October to December 1992 and February to May 2003 by TRM in 4 sites within each area.

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