Pest control and animal welfare

Abstract

Step some 30 years back in time. Rabbits had been a problem but appeared to be under control after years of astute use of rabbiters and dogs. One of the last batches of possums was being released into our forests for fun and fur. Deer were in numbers only sufficient to accommodate the hunters; there was the odd goat shoot, with organised culling in some areas; but by and large we were not overrun with animal pests. I do not recall that feral cats were a problem back then either.     

A reserve for feral sheep on Pitt Island,Chatham group,New Zealand

Abstract

A scientific reserve of 200 ha has been created on Pitt Island, Chatham Islands for some 300 sheep from a flock of merino origin which has been feral for about 70 years. The reserve has a history of burning-off, and of grazing by cattle, sheep, and pigs. Transects have been established to follow changes in the vegetation. Although the original sheep were white, about 90% of the feral sheep have pigmented fleeces. Self-shedding of the wool is common in the population. The contribution that feral mammals can make to genetic conservation, and the problems that they pose to other conservation priorities, are discussed.     

Parasites of the feral sheep of Pitt Island,Chatham group

Abstract

Samples from the feral and domestic sheep on Pitt Island were examined for parasites. The feral sheep had never been treated against parasites, and most were due for extermination. The domestic sheep were examined by way of comparison. The sheep ked (Melophagus ovinus) and the chorioptic mange mite (Chorioptes bovis) were found on feral but not domestic sheep. The sheep body louse (Damalinia ovis) was found on domestic but not feral sheep. Lung nodules and liver lesions, presumed to be caused by parasites, were significantly more prevalent in domestic than in feral sheep. The prevalence of Cysticercus tenuicollis cysts and Sarcocystis spp. macrocysts was similar in feral and domestic sheep. The species of intestinal nematode and their relative abundance in feral sheep were similar to those in mainland sheep. Fewer feral sheep were found to have antibodies to Toxoplasma gondii when compared with other breeds; the proportion with antibodies to Sarcocystis ovicanis differed little from that in the mainland flocks, however. The data are compared with information from the Campbell Island feral sheep flock.     

Pest problems: The view of the Animal Health Board

Abstract

The national perspective that the Animal Health Board (AHB) brings to this forum is, of course, the control and, if possible, the eradication of bovine Tb from New Zealand. Our interest in pest management is in the wild and feral animals which are known to be vector/reservoirs of the disease. In this case the most notable and significant is the possum.     

Transferrin gene frequencies of feral and domestic goats in New Zealand

Abstract

Blood plasma from three populations of feral goats (Capra hircus L.) and from five domestic breeds was analysed by polyacrylamide gel electrophoresis. The albumin locus was monomorphic in all samples. The macroglobulin locus was variable but lacked resolution on the gel. The transferrin (Tf) locus was polymorphic. The only two Tf alleles observed (Tf A and Tf B) did not vary from those described by other authors. Gene frequencies of the two Tf alleles showed that one feral population could be distinguished from the other two. Gene frequencies of domestic breeds were variable and showed no definitive pattern. Domestic breed type could not be recognised in the feral populations on the basis of transferrin analysis alone.     

Home ranges of introduced mammalian carnivores at Trounson Kauri Park,Northland, New Zealand

Abstract

At Trounson Kauri Park, we monitored the movements of 21 feral cats (Felis catus), 11 stoats (Mustela erminea) and one male ferret (Mustelafuro). In feral cats, the average minimum home range was 446 ha (±82 SE) for 14 males, significantly larger than the average minimum of 117 ha (±40 SE) for seven females. In stoats the average minimum home range was 107 ha (±20 SE), for nine males compared with 81 ha (±31 SE) for two females. The single male ferret had a minimum home range of 197 ha. Adult male feral cats lived on apparently separate, non‐overlapping home ranges; females occupied exclusive home ranges which were overlapped by adult males; home ranges of sub‐adult male feral cats overlapped those of other sub‐adult male, adult male and female feral cats. The home ranges of two neighbouring male stoats overlapped, although their core ranges did not; both these and the ferret's home ranges overlapped those of the neighbouring feral cats. The feral cats were often located in cover in pastureland or near the edge of larger tracts of forest within their home ranges; stoats near waterways in the larger tracts of forest; and the ferret near the forest/pasture margins of Trounson Kauri Park. Our results suggest that control devices targeting all these species should be set at a minimum spacing of 800 m in order to put the majority of the resident and immigrant predators at risk.     

Use of Feral Cats in Psychotherapy

ABSTRACT

Animal-assisted therapy typically involves the use of domesticated, well controlled animals that are trained to permit approach behavior and interaction by patients. This report describes the use of undomesticated, feral cats as adjuncts to psychotherapy. This approach provides advantages not attainable when domesticated pets are used. Case examples are provided to illuminate the various applications of this unique therapeutic technique.     

Distribution and population development of introduced Ring-necked Parakeets Psittacula krameri in Britain between 1983 and 1998

Capsule Of the three subpopulations, only the one west of London was increasing, with little spread.

Aims To investigate the distribution and population dynamics of feral Ring-necked Parakeets in Great Britain.

Methods County bird report records (from 1983–95) were collated and analysed to determine distribution and population trends. Roost counts were undertaken monthly from September 1996 to September 1998 to determine minimum population counts and trends.

Results The parakeets were distributed in three subpopulations: west of London, southeast London and in Thanet, Kent. The total population increased during the period, with little spread, except for a slight westward range expansion. Flock size did not increase, and population growth was only apparent from maximum counts at communal roosts. The roosts were largest in the early autumn when, in each of the three years, minimum total population counts were obtained. The west of London population was large and growing, while the southeast London and Thanet populations were smaller and not increasing. The yearly total population counts were 1508, 1880 and 2060.

Conclusion The population is still relatively small and range expansion is slow, suggesting that agricultural areas are not yet threatened by this potential pest species.     

Genomic duplication problems for unrooted gene trees

Background

Discovering the location of gene duplications and multiple gene duplication episodes is a fundamental issue in evolutionary molecular biology. The problem introduced by Guigó et al. in 1996 is to map gene duplication events from a collection of rooted, binary gene family trees onto theirs corresponding rooted binary species tree in such a way that the total number of multiple gene duplication episodes is minimized. There are several models in the literature that specify how gene duplications from gene families can be interpreted as one duplication episode. However, in all duplication episode problems gene trees are rooted. This restriction limits the applicability, since unrooted gene family trees are frequently inferred by phylogenetic methods.

Results

In this article we show the first solution to the open problem of episode clustering where the input gene family trees are unrooted. In particular, by using theoretical properties of unrooted reconciliation, we show an efficient algorithm that reduces this problem into the episode clustering problems defined for rooted trees. We show theoretical properties of the reduction algorithm and evaluation of empirical datasets.

Conclusions

We provided algorithms and tools that were successfully applied to several empirical datasets. In particular, our comparative study shows that we can improve known results on genomic duplication inference from real datasets.

     

Filling the Ark: Animal Welfare in Disasters

ABSTRACT

Populations of feral domestic cats and free-roaming, owned cats have increased throughout the United States, affecting wildlife and public health and warranting attention from a variety of management agencies. The contentious issue of feral cat management requires a greater understanding of public attitudes towards cats and preferences. We used an anonymous internet survey of randomly selected Athens-Clarke County, Georgia households to identify general public perceptions of domestic cats and preferences for cat management. We examined factors that may influence attitudes towards cats, and management including: knowledge about cats, experiences with cats and demographic variables. Results indicate that more residents have positive experiences with feral cats than negative, cat owners have greater knowledge of cats than non-cat owners, and animal welfare or conservation organization membership has a significant effect on attitudes towards cats. A majority of survey respondents agreed that more effective feral cat management is needed yet did not approve of trap-neuter-release (TNR) legislation recently passed in Athens-Clarke County. Logistic regression revealed that residents' attitudes were found to be more important than experiences or knowledge in supporting cat management legislation. Cat sanctuaries were found to be the most acceptable option to reduce feral cat populations (56%), followed by TNR (49%) and capturing and euthanizing cats (44%).     

Feral sheep and cattle and royal albatrosses on Campbell Island; population trends and habitat changes

Abstract

Sheep farming on Campbell Island began in 1895 and ended in 1931. The sheep population peaked at 8500 in 1910; only 1000 feral sheep were counted in 1961, but by 1969 there were 3000. The island was divided with a fence in 1970 and the sheep on the northern half were shot. Sheep continued to increase south of the fence, from 2088 in 1969 to 2521 in 1971 and, after a decline to 2400 in 1976, to 2861 in 1977. Breeding pairs of royal albatrosses numbered 2278 in 1958, 4344 in 1969, 5336 in 1976, and 4906 in 1977 - the first time the breeding population of this normally biennial breeder had been counted in two consecutive years. The number of feral cattle decreased from 20 in 1971 to 11 in 1977. These population trends are discussed in the context of changes to the flora in grazed and stock-free areas.     

Signal enrichment with strain-level resolution in metagenomes using topological data analysis

Background

A metagenome is a collection of genomes, usually in a micro-environment, and sequencing a metagenomic sample en masse is a powerful means for investigating the community of the constituent microorganisms. One of the challenges is in distinguishing between similar organisms due to rampant multiple possible assignments of sequencing reads, resulting in false positive identifications. We map the problem to a topological data analysis (TDA) framework that extracts information from the geometric structure of data. Here the structure is defined by multi-way relationships between the sequencing reads using a reference database.

Results

Based primarily on the patterns of co-mapping of the reads to multiple organisms in the reference database, we use two models: one a subcomplex of a Barycentric subdivision complex and the other a Čech complex. The Barycentric subcomplex allows a natural mapping of the reads along with their coverage of organisms while the Čech complex takes simply the number of reads into account to map the problem to homology computation. Using simulated genome mixtures we show not just enrichment of signal but also microbe identification with strain-level resolution.

Conclusions

In particular, in the most refractory of cases where alternative algorithms that exploit unique reads (i.e., mapped to unique organisms) fail, we show that the TDA approach continues to show consistent performance. The Čech model that uses less information is equally effective, suggesting that even partial information when augmented with the appropriate structure is quite powerful.

     

A three dimensional visualisation approach to protein heavy-atom structure reconstruction

Background

A commonly recurring problem in structural protein studies, is the determination of all heavy atom positions from the knowledge of the central α-carbon coordinates.

Results

We employ advances in virtual reality to address the problem. The outcome is a 3D visualisation based technique where all the heavy backbone and side chain atoms are treated on equal footing, in terms of the C_α coordinates. Each heavy atom is visualised on the surfaces of a different two-sphere, that is centered at another heavy backbone and side chain atoms. In particular, the rotamers are visible as clusters, that display a clear and strong dependence on the underlying backbone secondary structure.

Conclusions

We demonstrate that there is a clear interdependence between rotameric states and secondary structure. Our method easily detects those atoms in a crystallographic protein structure which are either outliers or have been likely misplaced, possibly due to radiation damage. Our approach forms a basis for the development of a new generation, visualization based side chain construction, validation and refinement tools. The heavy atom positions are identified in a manner which accounts for the secondary structure environment, leading to improved accuracy.

     

A novel algorithm for alignment of multiple PPI networks based on simulated annealing

Background

To infer gene regulatory networks (GRNs) from gene-expression data is still a fundamental and challenging problem in systems biology. Several existing algorithms formulate GRNs inference as a regression problem and obtain the network with an ensemble strategy. Recent studies on data driven dynamic network construction provide us a new perspective to solve the regression problem.

Results

In this study, we propose a data driven dynamic network construction method to infer gene regulatory network (D3GRN), which transforms the regulatory relationship of each target gene into functional decomposition problem and solves each sub problem by using the Algorithm for Revealing Network Interactions (ARNI). To remedy the limitation of ARNI in constructing networks solely from the unit level, a bootstrapping and area based scoring method is taken to infer the final network. On DREAM4 and DREAM5 benchmark datasets, D3GRN performs competitively with the state-of-the-art algorithms in terms of AUPR.

Conclusions

We have proposed a novel data driven dynamic network construction method by combining ARNI with bootstrapping and area based scoring strategy. The proposed method performs well on the benchmark datasets, contributing as a competitive method to infer gene regulatory networks in a new perspective.

     

Relevance of attributional and consequential information for environmental product labelling

Purpose

Considering the general agreement in the literature that environmental labelling should be based on consequential modelling, while all actually implemented environmental labelling schemes are based on attributional modelling, we investigate the arguments for this situation as provided in the literature, and whether a dual label, representing on the same label the attributional and consequential results for the same product, can be a relevant solution or at least contribute to a more informed discussion.

Methods

We developed a dual label for three hypothetical, comparable products and presented this for a small test audience, asking three questions, namely “Which product would you choose?”, “Was the attributional information useful?” and “Would you accept to have only the attributional information?”

Results and discussion

From this small pilot exercise, it appears that informed consumers may have a strong preference for consequential information and that the main problem in communicating consequential results is that they are perceived as less trustworthy and more uncertain due to the fact that the consequences are located in the future. It thus appears important to build into a consequential label some increased level of guarantee of future good behaviour.

Conclusions

We propose to apply the above questions to a more statistically representative audience to confirm or refute the findings of this little test exercise.

     

Evaluation of iophenoxic acid and rhodamine B for marking feral ferrets (Mustela furo)

Abstract

The blood marker iophenoxic acid, and the fluorescent dye rhodamine B, were evaluated as means of assessing bait consumption in the ferret, Mustela furo. Iophenoxic acid was elevated above baseline concentrations for a minimum of 28 days after dosing, indicating that it is a suitable medium‐term marker. Rhodamine B marked ferrets for a maximum of 7 days, and would therefore have limited operational use with feral ferrets. Iophenoxic acid was used in a field trial to assess the effectiveness of a newly developed baiting strategy for control of wild ferrets. All 21 ferrets captured after field baiting with iophenoxic acid had elevated levels of serum iodine, indicating that the newly developed baiting strategy is highly effective for marking ferrets.     

Foods of feral house cats (Felis catus L.) in forest of the Orongorongo Valley,Wellington

Abstract

The foods of feral house cats in forest in the Orongorongo Valley, Wellington, were studied over 3 years and related to the availability of prey. Some cats were trapped, tagged, and released, and could be identified individually by coat colour and pattern. The number of cats, estimated from live-trapping and sightings, was stable during the study. Examination of 677 scats revealed that mammals (rat, rabbit, opossum, mouse, and stoat, in descending order of importance) formed the bulk of the diet by weight. Remains of birds occurred in 12% of scats, but birds were estimated to form only 4.5% by weight of the diet. Insect fragments were present in many scats; wetas (Orthoptera), cicadas (Hemiptera), and beetles (Colcoptera) were important seasonally. Although eaten in large numbers, they contributed very little by weight to the diet. Populations of rats, rabbits, and opossums were fairly stable during the study; mice were abundant for most of the first 18 months, but were scarce in the last year. The literature on the food habits of feral house cats is reviewed; it emphasises that cats are primarily predators of small mammals (rodents and lagomorphs). Predation by feral cats can be important in holding rat and rabbit populations at low densities and in reducing seasonal fluctuations in their numbers. Cats can also exert heavy predation pressure on low-density mouse populations. Although the cats now eat few birds, they may have been responsible for reducing the numbers of some forest birds in the past.     

Feral cats on Stewart Island; their foods,and their effects on kakapo

Abstract

The foods of feral house cats (Felis catus) on Stewart Island were determined by examining 229 scats collected during surveys of the distribution and numbers of kakapo (Strigops habroptilus), an endangered ground-parrot species. Rats occurred in 93% of the scats, birds in 44. 1%, wetas (large orthopterans) in 26.2%, and lizards in 24.0%. Twelve (70.6%) of the 17 species of birds were native. Kakapo remains were found in 6 (5.1%) of the 118 scats collected from areas where kakapo have been recorded.     

Inline index helped in cleaning up data contamination generated during library preparation and the subsequent steps

Background

High-throughput sequencing involves library preparation and amplification steps, which may induce contamination across samples or between samples and the environment.

Methods

We tested the effect of applying an inline-index strategy, in which DNA indices of 6 bp were added to both ends of the inserts at the ligation step of library prep for resolving the data contamination problem.

Results

Our results showed that the contamination ranged from 0.29 to 1.25% in one experiment and from 0.83 to 27.01% in the other. We also found that contamination could be environmental or from reagents besides cross-contamination between samples.

Conclusions

Inline-index method is a useful experimental design to clean up the data and address the contamination problem which has been plaguing high-throughput sequencing data in many applications.

     

Relationships Between Cat Lovers and Feral Cats in Rome

ABSTRACT

The aim of this study was to assess the relationships between cat lovers and feral cats in Rome. One hundred and fifty-eight cats from 3 populations were observed for 1108 hours of data collection: some demographic characteristics of the colonies were investigated, together with the behavior of cat lovers (those who fed and cared for the cats). The quantity of food eaten and uneaten by the cats was recorded, and the cost to support each colony calculated. The quantity of food provided ranged from 20.47 to 264 kg/month. The mean quantity of food eaten/day by each cat in the study areas never surpassed 130.4 g. In total, the quantity of food wasted ranged from 522 g to 34.05 kg/month. The results of this study can help public administrations decide on how to allocate funds for the management of feral cats. Indeed, they provide statistics on the individual food intake/cat/day, as well as information on the type of collaboration one should expect from cat lovers. In addition, this study outlines advantages and limits of the “Roman model” where the Public Veterinary Services (PVS) and associations of cat lovers cooperate to manage feral cats.