Bayesian interval mapping of count trait loci based on zero-inflated generalized Poisson regression model

Count phenotypes with excessive zeros are often observed in the biological world. Researchers have studied many statistical methods for mapping the quantitative trait loci (QTLs) of zero-inflated count phenotypes. However, most of the existing methods consist of finding the approximate positions of the QTLs on the chromosome by genome-wide scanning. Additionally, most of the existing methods use the EM algorithm for parameter estimation. In this paper, we propose a Bayesian interval mapping scheme of QTLs for zero-inflated count data. The method takes advantage of a zero-inflated generalized Poisson (ZIGP) regression model to study the influence of QTLs on the zero-inflated count phenotype. The MCMC algorithm is used to estimate the effects and position parameters of QTLs. We use the Haldane map function to realize the conversion between recombination rate and map distance. Monte Carlo simulations are conducted to test the applicability and advantage of the proposed method. The effects of QTLs on the formation of mouse cholesterol gallstones were demonstrated by analyzing an mouse data set.     

Unique mid‐tract loss of a primary remex in male broadbills of the Southeast Asian genus Calyptomena: timing and possible implications

Female Calyptomena broadbills have 10 large primaries, whereas adult males have nine. At or before the main post‐juvenile moult, males abort what appears to be juvenile P5. This creation of row space is accompanied by a shortening of the wing tip, a development (together with tail shortening) that, as in some Neotropical suboscines, may relate to performance of exaggerated displays. Calyptomena has been linked taxonomically with Afrotropical Smithornis, the one genus of broadbills with proven display‐related modification of flight‐feathers.     

Accounting for differential migration strategies between age groups to monitor raptor population dynamics in the eastern Black Sea flyway

Migration counts can offer a cost-effective method for monitoring the state of migrant raptor populations. However, differential migration strategies between inexperienced juveniles and experienced non-juveniles are rarely accounted for when inferring population trends from raptor migration counts. Since 2011, the Batumi Raptor Count (BRC) monitors the autumn migration of more than 1 million raptors along the eastern Black Sea coast in the Republic of Georgia. We also systematically sampled age information to assess differential migration timing between age groups and estimate age-specific linear trends in abundance between 2011 and 2018 for eight focal species. In so doing we aimed (1) to reassess the global relevance of BRC counts for each species and the potential for monitoring abundance of juveniles and non-juveniles, and (2) to identify demographic changes underlying recent trends in overall abundance. We found that the mean annual passage of non-juveniles at Batumi represents at least 1% of the estimated global breeding population of five study species. As expected, counts of juveniles were more variable than counts of non-juveniles. Yet despite our short monitoring period our models had sufficient statistical power to detect changes in abundance of 10%/year or less for at least one age group in all species except Pallid Harrier Circus macrourus. Our results indicate stable abundance and demography for half of the study species. We also found strong and significant increases in the abundance of Black Kites Milvis migrans and Short-toed Eagles Circaetus gallicus that were primarily due to increasing numbers of non-juveniles. By contrast, juvenile Montagu's Harriers Circus pygargus and Booted Eagles Hieraaetus pennatus significantly decreased in abundance. The first decade of BRC surveys offers an important benchmark for monitoring raptor populations using the eastern African–Palearctic flyway in the 21st century. We discuss possible causes of the observed trends and hope our work will stimulate demographic monitoring at migration count sites.     

NucleoCounter—An efficient technique for the determination of cell number and viability in animal cell culture processes

The NucleoCounter is a novel, portable cell counting device based on the principle of fluorescence microscopy. The present work establishes its use with animal cells and checks its reliability, consistency and accuracy in comparison with other cytometric techniques. The main advantages of this technique are its ability to handle a large number of samples with a high degree of precision and its simplicity and specificity in detecting viable cells quantitatively in a heterogeneous culture. The work addresses and overcomes the problems of subjectivity, and some of the inherent sampling errors associated with using the traditional haemocytometer and Trypan Blue exclusion method. NucleoCounter offers reduced intra- and inter-observer variation as well as consistency in repetitive analysis that establishes it as an efficient and highly potential device for at-line monitoring of animal cell processes. Furthermore, since the only manual steps required are sample aspiration and mixing with two reagents, it is feasible that the whole method could be automated and brought on-line for process monitoring and control.     

The statistical analysis of the differential blood count

The differential blood count obtained by unbiased sampling mathematically follows a multinomial distribution. The variation between individuals can be formalized by a mixing distribution of the parameters of the multinomial distribution. By DIRICHLET-distributions used as mixing distributions the main phenomena of the observed data can be described, and they are useful in estimating and testing treatment effects. If the correlation between the different types of leucocytes is taken into account in an appropriate manner, univariate test procedures can be applied also.     

Use of Forest Edges by Bats in a Managed Pine Forest Landscape

ABSTRACT Forest edges often have increased species richness and abundance (edge effect) and affect spatial behaviors of species and dynamics of species interactions. Landscapes of intensively managed pine (Pinus spp.) stands are characterized by a mosaic of patches and linear forest edges. Managed pine forests are a primary landscape feature of the southeastern United States, but the effects of intensive management on bat communities are poorly understood. Insectivorous bats are important top predators in nocturnal forest food webs. We examined bat foraging behavior along forest edges and in 4 structurally distinct stand types (open-canopy pine, prethinned pine, thinned pine, and unmanaged forest) within a managed pine forest in the coastal plain of North Carolina, USA. During May-August, 2006 and 2007, we recorded echolocation calls using Pettersson D240X bat detectors linked to digital recorders at 156 sites. We also sampled nocturnal flying insects at each site using Malaise insect traps. We used negative binomial count regression models to describe bat foraging behavior relative to forest edges, stand types, and prey availability. Although some species showed affinities for certain stand types and prey items, bat activity patterns were most strongly related to forest edges. Edges were used extensively by 6 aerial-hunting bat species, but avoided by Myotis species. Forest edges function similarly to natural forest gaps, by providing foraging opportunities for aerial-hunting bat species. Therefore, the maintenance of forest edges in managed pine landscapes may enhance foraging habitat for aerial-hunting bat species.     

Blind Count Surveys of White-Tailed Deer and Population Estimates Using Bowden's Estimators

Abstract: Conducting surveys from blinds when supplemental feed (bait) has been provided has not been evaluated for estimating parameters of ungulate populations. We conducted blind count surveys of white-tailed deer (Odocoileus virginianus) in a 214-ha enclosure in central Texas, USA, in 2007 and 2008 to address 2 main objectives: 1) to evaluate a blind count survey protocol developed for use on small parcels of land, and 2) to use data collected from blind count surveys to conduct simulations to evaluate the reliability of abundance and sex ratio estimates obtained from Bowden's estimator. In each year population abundance (2007: 60; 2008: 48) and sex ratio (M:F, 2007: 0.58; 2008: 0.71) were known as were sighting frequencies of every animal. The enclosure had 5 blinds and we baited each blind with corn. We encountered many deer during surveys because there were only 2 deer in 2007 and 1 deer in 2008 that we did not view from blinds ≥1 time. To evaluate bias and precision of abundance and sex ratio estimates we conducted 10,000 bootstrap simulations. We evaluated both parameters in relation to the percentage of each population marked, number of surveys conducted from blinds, and whether surveys were conducted in the morning, evening, or both morning and evening. Also, we evaluated abundance in relation to whether we identified animals with unique marks to individual, and we evaluated sex ratio in relation to intersexual distribution of marks. Abundance estimates were less biased and more precise when we uniquely identified all marked animals and 40–70% of the population was marked. Sex ratio estimates were less biased when 40–70% of the population was marked and surveys were conducted in the morning and evening. Sex ratio estimates, however, were less precise than abundance estimates. Unbiased estimates of white-tailed deer population parameters can be obtained from blind count surveys conducted on small parcels of enclosed land and when animals are baited.     

Nitric oxide concentrations in mammary quarters during heifer mastitis

The aim of this study was to evaluate nitric oxide (NOx) concentration in infected and non-infected mammary quarters of dairy heifers before and after calving. The relationship between bacterial species and NOx concentrations, as well as correlation between NOx concentrations and postpartum somatic cell count (SCC), was assessed. Coagulase-negative staphylococci, Staphylococcus aureus and Escherichia coli were the bacteria commonly isolated during the pre- and postpartum period. Infected quarters had greater NOx concentrations than non-infected quarters before (30.81 v. 22.83 μM/ml, P < 0.05) and after (9.56 v. 5.77 μM/ml, P < 0.0001) calving. It was determined that the interaction between sampling period and infectious status had no effect on NOx concentration (P < 0.16). Infected quarters had greater SCC (log₁₀) than healthy quarters (4.95 v. 4.39; P < 0.0001). NOx concentrations, however, did not correlate with SCC (r = 0.02). In summary, changes in NOx concentration were mainly dependent on the infectious status of the quarters with variations among the bacterial species (P < 0.05).