Assessing the Impacts of Time-to-Detection Distribution Assumptions on Detection Probability Estimation

Abundance estimates from animal point-count surveys require accurate estimates of detection probabilities. The standard model for estimating detection from removal-sampled point-count surveys assumes that organisms at a survey site are detected at a constant rate; however, this assumption can often lead to biased estimates. We consider a class of N-mixture models that allows for detection heterogeneity over time through a flexibly defined time-to-detection distribution (TTDD) and allows for fixed and random effects for both abundance and detection. Our model is thus a combination of survival time-to-event analysis with unknown-N, unknown-p abundance estimation. We specifically explore two-parameter families of TTDDs, e.g., gamma, that can additionally include a mixture component to model increased probability of detection in the initial observation period. Based on simulation analyses, we find that modeling a TTDD by using a two-parameter family is necessary when data have a chance of arising from a distribution of this nature. In addition, models with a mixture component can outperform non-mixture models even when the truth is non-mixture. Finally, we analyze an Ovenbird data set from the Chippewa National Forest using mixed effect models for both abundance and detection. We demonstrate that the effects of explanatory variables on abundance and detection are consistent across mixture TTDDs but that flexible TTDDs result in lower estimated probabilities of detection and therefore higher estimates of abundance.Supplementary materials accompanying this paper appear on-line.     

Selenium hyperaccumulation offers protection from cell disruptor herbivores

Background  

Hyperaccumulation, the rare capacity of certain plant species to accumulate toxic trace elements to levels several orders of magnitude higher than other species growing on the same site, is thought to be an elemental defense mechanism against herbivores and pathogens. Previous research has shown that selenium (Se) hyperaccumulation protects plants from a variety of herbivores and pathogens. Selenium hyperaccumulating plants sequester Se in discrete locations in the leaf periphery, making them potentially more susceptible to some herbivore feeding modes than others. In this study we investigate the protective function of Se in the Se hyperaccumulators Stanleya pinnata and Astragalus bisulcatus against two cell disrupting herbivores, the western flower thrips (Frankliniella occidentalis) and the two-spotted spider mite (Tetranychus urticae).     

Gall production on hawthorns caused by <Emphasis Type="Italic">Gymnosporangium</Emphasis> spp. in Hatay province,Turkey

Three hawthorn and related rust diseases caused by Gymnosporangium confusum on Crataegus monogyna, Gymnosporangium clavariiforme on Crataegus orientalis and Gymnosporangium sabinae on Pyrus communis were detected in Hatay province, Turkey. G. confusum was also found causing telial galls on Juniperus communis. G. confusum and G. clavariiforme produced aecial horns on overwintered galls on hawthorn twigs from May to June. The production of galls caused by Gymnosporangium on the secondary host is unusual. Portions of the nuclear ITS and LSU rDNA were sequenced for all three species of Gymnosporangium for use as a species barcode; sequences were deposited in GenBank. Sequence data from G. clavariiforme and G. sabinae matched those in GenBank; however, this is the first study to deposit sequence data from G. confusum to GenBank. The life cycles of G. confusum and G. clavariiforme are discussed along with implications for disease control.     

Characterization of the first two viruses described from wild populations of hammer orchids (Drakaea spp.) in Australia

Sequences representing the genomes of two distinct virus isolates infecting wild plants of two members of the genus Drakaea (hammer orchids) in Western Australia are described. The virus isolated from Drakaea livida has a bipartite genome of 4490 nt (RNA1) and 2905 nt (RNA2) that shares closest sequence and structural similarity to members of the genus Pecluvirus, family Virgaviridae, described from legumes in the Indian subcontinent and West Africa. However, it differs from pecluviruses by lacking a P39 protein on RNA2 and having a cysteine‐rich protein gene located 3′ of the triple gene block protein genes. It is the first peclu‐like virus to be described from Australia. The name Drakaea virus A is proposed (DVA; proposed member of the family Virgaviridae, genus unassigned). The second virus isolate was identified from Drakaea elastica, a species classed as endangered under conservation legislation. The genome sequence of this virus shares closest identity with isolates of Donkey orchid symptomless virus (DOSV; proposed member of the order Tymovirales, family and genus unassigned), a species described previously from wild Caladenia and Diuris orchids in the same region. These viruses are the first to be isolated from wild Drakaea populations and are proposed to have an ancient association with their orchid hosts.     

Influence of variety on the within-plant distribution of cassava green spider mite (Acari: Tetranychidae), and leaf anatomical characteristics and chemical components in relation to varietal resistance

The within-plant distribution of the cassava green spider mite, Mononychellus tanajoa Bondar, and the anatomical characteristics and the chemical components relating to varietal resistance of cassava, were studied using 11 cassava genotypes with varying levels of resistance for two dry seasons and one wet season. The results show that M. tanajoa aggregates on the top leaves of cassava at low levels of resistance as compared with a more even within-plant distribution at higher levels of resistance. Thus, for accurate sampling of mite populations, it might be important to consider young and old leaves, not just the young leaves, in fields containing resistant and susceptible cassava genotypes. Correlations between the anatomical characteristics and mite population density and damage scores were not consistent across months, either within or over seasons. This suggests that leaf anatomical characteristics may not be important in the varietal resistance of cassava to M. tanajoa. During the dry season, mite population density was positively correlated with leaf nitrogen, potassium and phosphorus and negatively correlated with leaf calcium and fat. Only calcium was negatively associated with mite damage at the peak of the dry season (January 1993 and 1994). Breeding cassava genotypes with high levels of leaf calcium and fat, and low levels of leaf nitrogen, potassium and phosphorus, may improve the level of resistance to M. tanajoa.     

There’s certainly a lot of hurting out there: navigating the trolley of progress down the supermarket aisle

For the past decade, supermarket chains have been positioned as the pre-eminent actor in global and national food systems. Some agri-food scholars argue that their ever-expanding transnational supply chains have established an era of stable production-consumption relations (or Food Regime), while others point to the conflicts they are encountering with governments, social movements and ‘alternative’ consumers. However, remarkably little attention has been paid to their relationship with communities and to community system sustainability. Based on fieldwork conducted in the Goulburn Valley, Australia, we argue that supermarket operations are contributing to community tensions through contestation over valued symbols and narratives about what desirable ‘progress’ looks like. We identified three interrelated points of tension being intensified by supermarket chains: whether progress is encapsulated by being an agricultural production or a modern consumption centre; whether progress should be based on a model of corporate capital or the local small business; and to what extent modern citizens can and should support community shopping instead of convenience shopping. For long-time residents, supermarkets are paradoxical actors appealing to, as well as, challenging the narrative of a community whose economic strength was based on the surrounding natural environment and local people’s endeavours. The concepts of solastalgia and structural nostalgia are relevant, with the former referring to the place-based distress experienced by residents whose local area is changing profoundly and the latter describing a process amplifying that distress. Through exploring the political paradoxes of community solastalgia, we raise new questions about supermarket authority within contemporary Food Regimes.     

Effect of the Medium Replacement Interval on the Viability,Growth and In Vitro Maturation of Isolated Caprine and Ovine Pre‐Antral Follicles

The aim of the present study was to evaluate the effects of different medium replacement intervals on the viability, antral cavity formation, growth and in vitro maturation (IVM) of oocytes from caprine and ovine pre‐antral follicles. Pre‐antral ovarian follicles (≥150 μm) were isolated from the ovarian cortex of goats and sheep and were individually cultured for 24 days using two different medium replacement intervals [2 days (T₁) or 6 days (T₂)]. Follicle development was evaluated on the basis of antral cavity formation, increases in follicular diameter and the presence of healthy cumulus oocyte complexes and fully grown oocytes. For caprine species, results showed a higher percentage (p < 0.05) of viable follicles in T₁ than T₂ from day 6 until the end of the culture. In addition, when comparing both treatments after the same culture duration, the rate of antrum formation was significantly higher in T₁ than in T₂ from day 12 onwards. Yet, in ovines, when both treatments were compared on day 24 of the culture, there were more viable follicles in T₂ than in T₁ (p < 0.05). In the caprine species, percentages of fully grown oocytes (≥110 μm) acceptable for IVM after 24 days of culture were significantly higher in normal follicles cultured in T₁ (30.0%) than in T₂ (6.7%; p < 0.05). On the other hand, in ovines, at the end of the culture, the percentage of oocytes destined for IVM was higher in T₂ than in T₁ (23.5% vs 2.9%; p < 0.05). In conclusion, under the same conditions, the frequency of medium replacement significantly affected the in vitro development of caprine and ovine pre‐antral follicles. To improve the efficiency of the culture system, the medium must be replaced every 2 and 6 days for goat and sheep pre‐antral follicles, respectively.     

The potential for zoonotic transmission of Giardia duodenalis and Cryptosporidium spp. from beef and dairy cattle in Ontario, Canada

The objective of this study was to compare the occurrence and the genotypes and species of Giardia duodenalis and Cryptosporidium spp. in beef and dairy cattle from farms in the Regional Municipality of Waterloo, Ontario, in an effort to determine the potential for zoonotic transmission from these animals. Pooled manure samples were collected from 45 dairy cattle farms and 30 beef cattle farms. The presence of Giardia cysts and Cryptosporidium oocysts was determined by immunofluorescence microscopy, while nested-PCR and DNA sequencing were used to determine genotypes and species. The overall farm prevalence was very high for both Giardia and Cryptosporidium, and was similar for dairy cattle farms (96 and 64%, respectively) and beef cattle farms (97 and 63%, respectively). However, on dairy cattle farms, G. duodenalis and Cryptosporidium spp. were detected in 44% and 6% of total pooled pen manure samples, respectively, with the occurrence of both parasites being generally higher in calves than in older animals. Most Giardia isolates were identified as either the host-adapted genotype G. duodenalis Assemblage E or the zoonotic Assemblage B. Cryptosporidium parvum and Cryptosporidium andersoni were the most frequently identified species in dairy cattle, while the non-zoonotic species Cryptosporidium ryanae and Cryptosporidium bovis were also found. On beef cattle farms, 72% and 27% of the total pooled pen manure samples were positive for Giardia and Cryptosporidium, respectively, with no obvious correlation with age. All Giardia isolates in beef cattle were identified as G. duodenalis Assemblage E, while all Cryptosporidium isolates were identified by sequence analysis as C. andersoni, although microscopic analyses, and subsequent restriction fragment length polymorphism analyses, indicated that other Cryptosporidium species were also present. The results of this study indicate that although Giardia and Cryptosporidium were identified in a higher overall percentage of the pooled beef cattle manure samples than in dairy cattle, firmly established zoonotic genotypes and species were much more common in dairy cattle than in beef cattle in this region. Dairy cattle, and especially dairy calves, may, therefore, pose a greater risk of infection to humans than beef cattle. However, these results may also provide evidence of potential zooanthroponotic transmission (human to animal).