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.     

Analysis of rice blast resistance gene <Emphasis Type="Italic">Pi</Emphasis>-<Emphasis Type="Italic">z</Emphasis> in rice germplasm using pathogenicity assays and DNA markers

The Pi-z gene in rice confers resistance to a wide range of races of the rice blast fungus, Magnaporthe oryzae. The objective of this study was to characterize Pi-z in 111 rice germplasm accessions using DNA markers and pathogenicity assays. The existence of Pi-z in rice germplasm was detected by using four simple sequence repeat (SSR) markers (RM527, AP4791, AP5659-1, AP5659-5) closely linked to Pi-z, and was verified using pathogenicity assays with an avirulent strain (IE1k) and two virulent races (IB33 and IB49). Among 111 germplasm accessions evaluated, 73 were found to contain the Pi-z gene using both SSR markers and pathogenicity assays. The remaining 38 germplasm accessions were found to be inconsistent in their responses to the blast races IB33, IEIk and IB49 with expected SSR marker alleles, suggesting the presence of unexpected SSR alleles and additional R gene(s). These characterized germplasm can be used for genetic studies and marker-assisted breeding for improving blast resistance in rice.     

Laboratory characterization of firebrands involved in spot fires

• Introduction  

Wildfires are considered the most important disturbance in the Mediterranean Basin, and some are propagated over long distances due to lift-off and ignition of firebrands.     

Evaluation of two Indian native chicken breeds for reproduction traits and heritability of juvenile growth traits

The present study was conducted to evaluate two Indian native chicken breeds, namely, Aseel and Kadaknath for fertility, hatchability, genetic parameters of juvenile growth traits, and semen quality traits at the onset of sexual maturity. The fertility was similar in Aseel (86.96%) and Kadaknath (85.15%); however, a relatively higher hatchability was observed in Kadaknath (77.94%) than Aseel (70.74%). Heritability estimates of body weights at 4 weeks of age were almost similar in Aseel (0.37) and Kadaknath (0.39), while the estimate of body weight at 6 weeks of age was higher in Aseel (0.42) than Kadaknath (0.31). The heritability estimate of shank length at 6 weeks of age was lower in Aseel (0.16) compared to Kadaknath (0.35). The age at first egg in the flock was comparable in Aseel (148 days) and Kadaknath (150 days). Aseel breed with significantly (P ≤ 0.001) higher body weight, absolute and relative testes weights had significantly higher semen volume (P ≤ 0.05) and sperm motility (P ≤ 0.01) but had lower seminal plasma cholesterol level (P ≤ 0.05) as compared to Kadaknath. It can be concluded that there is a scope for genetic improvement of these two native breeds for juvenile growth traits since heritability estimates of these traits were relatively high.     

Leptospirosis as the most frequent infectious disease impairing productivity in small ruminants in Rio de Janeiro,Brazil

Despite the importance of small ruminants breeding in developing countries, milk/meat productivity remains unsatisfactory. Infectious diseases, such as leptospirosis, brucellosis, and small ruminant lentiviruses (SRLVs), contribute to this scenario. The objective of the present study was to determine the role of each of these diseases in the productivity of small ruminants breeding in Rio de Janeiro, Brazil. In goats, 343 samples were tested for leptospirosis, 560 for Brucella abortus, and 506 for caprine arthritis-encephalitis (CAE), whereas in sheep, 308 samples were tested for leptospirosis, 319 for B. abortus, 374 for Brucella ovis, and 278 for Maedi-Visna (MV). Regarding leptospirosis, 25.9% of goats and 47.4% sheep were seroreactive, with serovar Hardjo the most prevalent in both species. Anti-B. abortus agglutinins were found in 0.7% of all samples, exclusively in goats. In relation to SRLVs, 8.6% of goats and 3.2% of sheep samples were positive for CAE and MV, respectively. Leptospirosis was the major infectious problem in the small ruminants sampled and may contribute to impaired productivity of these animals.     

Skin and coat traits in sheep in Brazil and their relation with heat tolerance

The objective of this study was to evaluate and compare physical parameters in groups of sheep with different phenotypic characteristics in the Centre-west region of Brazil. Five groups of sheep, with nine animals per group, were selected, three groups of Santa Inês animals with different coat colours (white, brown and black), one group with crossbred animals (Santa Inês × Bergamasca) and one group with animals of the Bergamasca breed. The following traits were evaluated: coat thickness, number and length of hair, pigmentation level in the coat and the skin as well as the percentage area of sweats glands in the skin tissue, carried out by histological analysis. The number of hairs and the area of sweats glands were not significantly different between the evaluated groups. The Bergamasca breed showed low pigmentation of the skin and long hairs. The levels of pigmentation of the hair and of the skin were highly correlated. Between the Santa Inês groups, the group with white hair showed the better parameters for heat adaptation, while the brown hair group showed the lower heat adaptation when compared with another hair breed groups.     

Effect of different housing systems on fattening performance,slaughter and carcass characteristics of Akkeçi (White Goat) male kids

The aim of this study was to determine the fattening performance and the slaughter and carcass characteristics of Akkeçi (Saanen × Kilis (B₁) crossbred) male kids raised in individual crates (IC) or in group pen housing (GP). In both GP and IC groups, total 13 heads of male kids, whose initial body weights were 21.43 ± 1.03 kg and 20.61 ± 0.98 kg, respectively, evaluated for their fattening performances. After 56 days of the fattening period, the final body weights and average daily weight gains of the GP and IC kids were recorded as 30.84 ± 0.82 kg and 25.84 ± 0.76 kg; 182.42 ± 14.77 g and 92.09 ± 13.76 g, respectively (P < 0.001). Adrenal gland weights of the GP and IC groups were similar as 1.66 ± 0.25 g and 1.77 ± 0.22 g, respectively. Although, the carcass conformation of kids was similar between groups, there were significant differences between GP and IC groups for some slaughter and carcass characteristics. In general, although housing kids reared in individual crates provides opportunity to individually feed and monitor a kid, the results obtained from the individual crates in the present study were not satisfactorily from the ethological and production points of view.     

Length of productive life of sows in four pig farms in the tropics of Mexico

The objective of this study was to determine the effect of some factors on the length of productive life (LPL), the number of parities (NP), and the culling interval (CI) of sows. The information from 2003 to 2009 of 3,746 sows with LPL and NP records and 5,819 sows with CI records from the four farms of Yucatan, Mexico was used. LPL was defined as the number of days between the first farrowing and culling or death and CI as the number of days between the last farrowing and culling. To determine the effects of farm, litter size at first farrowing (LSF1) and age at first farrowing (AF1) on LPL and NP, and of farm, LSF1 and culling reason on CI general linear models were used. Means and standard errors for LPL, NP, and CI were 496.4 ± 8.42 days, 3.35 ± 0.04 parities, and 48.3 ± 0.52 days, respectively. All factors had significant effects (P < 0.05) on LPL, NP, and CI. The sows from farm 2 stayed longer (806.0 days) and had more parities (5.25) than the sows from the other farms. Sows with the smallest litters (≤8 piglets) at first farrowing stayed the least time in the farm (675.1 days) and had the fewest parities (4.49). Gilts farrowing the first time before 331 days of age stayed longer time in the farm (726.4 days) and had more parities (4.81) in comparison with 331–348 and more than 348 days age groups. With respect to CI, the sows in farm 3 stayed the longest time in the farm. Sows with more than five parities were culled sooner after their last farrowing. In conclusion, differences between farms for LPL, PN, and CI were found. Females that farrowed at a short age and those with large litters stayed longer in the herd. Old sows and those culled for reproductive reasons stayed the least time in the herd after their last farrowing.     

Evaluation of foot and mouth vaccination for yak (<Emphasis Type="Italic">Bos grunniens</Emphasis>) in Pakistan

In northern Pakistan, many farming communities rely on domestic yak (Bos grunniens) as a principle source of income. A 2006 participatory disease surveillance report from this region indicated that foot-and-mouth disease (FMD) is the most prevalent annual disease of yak. Our objectives of this study were to determine exposure levels of yak to FMD virus; implement a vaccination program based on current, regional FMD virus serotypes and subtypes; and quantify immune responses following vaccination. Blood samples were used to determine pre-vaccination exposure of animals to FMD virus by antibody presence to non-structural proteins of FMD virus using a 3-ABC trapping indirect ELISA. Vaccine used consisted of FMD serotypes ‘O’ (PanAsia-2), ‘A’ (Iran-05), and ‘Asia-1’ (Shamir), but changed later during the study to match newly circulating viruses in the country (‘O’-PanAsia-2; ‘A’-Turk-06 and Asia-1-Sindh-08). Three hundred sixty-three blood samples were tested from selected villages to determine pre-vaccination FMD virus exposure in yak with an average of 37.7%. Immune responses from initial vaccination and booster dose 30 days later showed clear protective levels (as mean percent inhibition) of antibodies against structural proteins of serotypes ‘O,’ ‘A,’ and ‘Asia-1.’ These responses remained above threshold positive level even at day 210 following initial vaccination. Results of sero-surveillance and anecdotal information of repeated FMD outbreaks demonstrate the persistence of FMD virus of yak in northern Pakistan. Laboratory results and field observations clearly indicated that yak can be protected against FMD with a good quality vaccine with FMD serotype(s) matching current, regionally circulating FMD virus.     

Modulatory function of NMDA glutamate receptor on MC<Subscript>3</Subscript>/MC<Subscript>4</Subscript> receptors agonist-induced hypophagia in neonatal meat-type chicken

Melanocortin 3 and 4 receptors (MC₃R and MC₄R) are known as the main receptors for melanocortin-induced hypophagia in mammalian and poultry. Also, central glutamatergic system has mediatory role on function of the melanocortin system in some brain areas. So, the aim of the current study was to determine the role of MC₃/MC₄ receptors agonist on food intake and its interaction with glutamatergic in 3-h food-deprived (FD₃) neonatal broilers. In experiment 1, chickens were intracerebroventricular (ICV) injected with control solution, MTII (MC₃/MC₄ receptors agonist; 2.45, 4.8 and 9.8 pmol). In experiment 2, control solution, SHU9119 (MC₃/MC₄ receptors antagonist; 0.5, 1 and 2 nmol) were ICV injected. In experiment 3, birds ICV injected with control solution, SHU9119 (0.5 nmol), MTII (9.8 pmol) and co-injection of the SHU9119 + MTII. Experiments 4–8 were similar to experiment 3, except birds injected with MK-801 (NMDA glutamate receptors antagonist, 15 nmol), CNQX (AMPA glutamate receptors antagonist; 390 nmol), AIDA (mGLUR₁ glutamate receptors antagonist; 2 nmol), LY341495 (mGLUR₂ glutamate receptors antagonist; 150 nmol) and UBP1112 (mGLUR₃ glutamate receptors antagonist; 2 nmol) instead of SHU9119. Then, cumulative food intake was recorded until 120 min after injection. According to the results, dose dependent hypophagia observed after ICV injection of the MTII (p < 0.05). ICV injection of SHU9119 significantly increased food intake in birds (p < 0.05). Co-injection of SHU9119 + MTII significantly inhibited MTII- induced hypophagia in neonatal chicks (p < 0.05). In addition, hypophagia- induced by MTII was significantly attenuated with co-injection of MTII + MK-801(p < 0.05). These results suggested MC₃ and MC₄ receptors have inhibitory role on food intake and this effect is probably mediated by NMDA glutamate receptors in neonatal chickens.