Jihad Abdallah

Detecting Selection in Population Trees: The Lewontin and Krakauer Test Extended

Detecting genetic signatures of selection is of great interest for many research issues. Common approaches to separate selective from neutral processes focus on the variance of FST across loci, as does the original Lewontin and Krakauer (LK) test. Modern developments aim to minimize the false positive rate and to increase the power, by accounting for complex demographic structures. Another stimulating goal is to develop straightforward parametric and computationally tractable tests to deal with massive SNP data sets. Here, we propose an extension of the original LK statistic (TLK), named TF–LK, that uses a phylogenetic estimation of the populations kinship (\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{\mathcal{F}}\) \end{document}) matrix, thus accounting for historical branching and heterogeneity of genetic drift. Using forward simulations of single-nucleotide polymorphisms (SNPs) data under neutrality and selection, we confirm the relative robustness of the LK statistic (TLK) to complex demographic history but we show that TF–LK is more powerful in most cases. This new statistic outperforms also a multinomial-Dirichlet-based model [estimation with Markov chain Monte Carlo (MCMC)], when historical branching occurs. Overall, TF–LK detects 15–35% more selected SNPs than TLK for low type I errors (P < 0.001). Also, simulations show that TLK and TF–LK follow a chi-square distribution provided the ancestral allele frequencies are not too extreme, suggesting the possible use of the chi-square distribution for evaluating significance. The empirical distribution of TF–LK can be derived using simulations conditioned on the estimated \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{\mathcal{F}}\) \end{document} matrix. We apply this new test to pig breeds SNP data and pinpoint outliers using TF–LK, otherwise undetected using the less powerful TLK statistic. This new test represents one solution for compromise between advanced SNP genetic data acquisition and outlier analyses.

Linkage disequilibrium fine mapping of quantitative trait loci: A simulation study

Recently, the use of linkage disequilibrium (LD) to locate genes which affect quantitative traits (QTL) has received an increasing interest, but the plausibility of fine mapping using linkage disequilibrium techniques for QTL has not been well studied. The main objectives of this work were to (1) measure the extent and pattern of LD between a putative QTL and nearby markers in finite populations and (2) investigate the usefulness of LD in fine mapping QTL in simulated populations using a dense map of multiallelic or biallelic marker loci. The test of association between a marker and QTL and the power of the test were calculated based on single-marker regression analysis. The results show the presence of substantial linkage disequilibrium with closely linked marker loci after 100 to 200 generations of random mating. Although the power to test the association with a frequent QTL of large effect was satisfactory, the power was low for the QTL with a small effect and/or low frequency. More powerful, multi-locus methods may be required to map low frequent QTL with small genetic effects, as well as combining both linkage and linkage disequilibrium information. The results also showed that multiallelic markers are more useful than biallelic markers to detect linkage disequilibrium and association at an equal distance.

A comparison between methods for linkage disequilibrium fine mapping of quantitative trait loci

We present a maximum likelihood method for mapping quantitative trait loci that uses linkage disequilibrium information from single and multiple markers. We made paired comparisons between analyses using a single marker, two markers and six markers. We also compared the method to single marker regression analysis under several scenarios using simulated data. In general, our method outperformed regression (smaller mean square error and confidence intervals of location estimate) for quantitative trait loci with dominance effects. In addition, the method provides estimates of the frequency and additive and dominance effects of the quantitative trait locus.

Linkage disequilibrium interval mapping of quantitative trait loci

BackgroundFor many years gene mapping studies have been performed through linkage analyses based on pedigree data. Recently, linkage disequilibrium methods based on unrelated individuals have been advocated as powerful tools to refine estimates of gene location. Many strategies have been proposed to deal with simply inherited disease traits. However, locating quantitative trait loci is statistically more challenging and considerable research is needed to provide robust and computationally efficient methods.ResultsUnder a three-locus Wright-Fisher model, we derived approximate expressions for the expected haplotype frequencies in a population. We considered haplotypes comprising one trait locus and two flanking markers. Using these theoretical expressions, we built a likelihood-maximization method, called HAPim, for estimating the location of a quantitative trait locus. For each postulated position, the method only requires information from the two flanking markers. Over a wide range of simulation scenarios it was found to be more accurate than a two-marker composite likelihood method. It also performed as well as identity by descent methods, whilst being valuable in a wider range of populations.ConclusionOur method makes efficient use of marker information, and can be valuable for fine mapping purposes. Its performance is increased if multiallelic markers are available. Several improvements can be developed to account for more complex evolution scenarios or provide robust confidence intervals for the location estimates.

Effect of Poultry Production System on Infection with Internal Parasites in “Baladi” Layer Hens of Northern West Bank, Palestine

Aims: To study the effects of poultry production systems on prevalence of internal parasites in hens of the Baladi breed in Northern West Bank, Palestine. The study is important to provide basic information essential to design appropriate parasitic control and prevention measures. Methodology: A survey study of internal parasites in Baladi layer hens was conducted in five villages of Northern West Bank, Palestine. Fecal samples were collected between September 2015 and April 2016 from 240 Baladi hens raised under four production systems (single-tier cages, double-deck cages, floor, and free range systems). The samples were examined for infection with internal parasites using the sedimentation and flotation techniques. Infection rates and their 95% confidence intervals were calculated and comparisons among production systems were performed Original Research Article Othman and Abdallah; ARRB, 16(2): 1-7, 2017; Article no.ARRB.35565 2 using logistic regression and Pearson’s Chi-square test. Results: The results showed that 102 samples (42.5%) were positive for one or more types of internal parasites. The types of detected internal parasites were nematodes (25.4% Ascaridia galli, 11.7% Heterakis gallinarum, and 3.3% Capillaria spp.), cestodes (Raillietina spp., 8.3%), and protozoa (Eimeria spp., 4.2%). Of the parasitic infections, 73.5% were nematodes, 10.8% were cestodes, 6.9% protozoa, and 8.8% were mixed species. Prevalence rates were 23.3%, 40.0%, 50.0% and 56.7% in single-tier cages, double-deck cages, floor system and the free range system, respectively. Hens raised in double-deck cages had odds ratio of infection of 1.999 (P = .08) compared to single cages, while hens raised in floor and free range systems had odds ratios 2.999 (P = .005) and 3.923 (P < .001) compared to single cage system. Conclusion: This study showed that hens reared in floor and free range systems had higher risk of parasitic infection than hens reared in cages indicating a higher need for appropriate prevention and control measures in these systems compared to cage systems.

Nutrients In situ Degradability of Almond Hulls and Cucumber Wastes from Greenhouse

Aims: Information about degradability of nutrients, effective degradability (ED) values and digestion kinetics of agricultural wastes is important for feed manufacturing industry and farmers performing feed mixing practices who currently rely on nutritive values published by research institutions. Almond hull (AH) and cucumber plant (CW) were evaluated for ruminal dry matter (DM), crude protein (CP), acid detergent fiber (ADF) and neutral detergent fiber (NDF) degradation kinetics. Methodology: Duplicate bags containing 3 g ground raw material each were incubated in the rumen of two ruminally cannulated Assaf rams for 4, 8, 16, 24, 48 and 72 h. Rate and extent of ruminal degradation were estimated. Results: Significant effects of byproduct type were observed in rapidly soluble and potentially degradable fractions, and degradation rates of DM, CP, ADF and NDF. The rapidly soluble DM, CP, ADF and NDF fractions were 16.10, 15.2, 10.64 and 14.06% for CW, and 7.21, 6.64, 6.00 and 5.62% for AH. The potentially degradable DM, CP, ADF and NDF fractions, respectively, were 55.82, 62.30, 49.40 and 55.09% for CW, and 47.61, 44.26, 46.34 and 48.53% for AH. The DM, CP, Original Research Article Omar and Abdallah; ARRB, 13(2): 1-6, 2017; Article no.ARRB.33785 2 ADF and NDF disappearance in CW were higher (P < 0.05) compared to those in AH. Similarly, the effective degradability (ED) of DM, CP, ADF and NDF in AH were higher compared to AH (P < 0.05). Conclusion: The new data presented in this study could be useful for the purposes of ration formulation and ruminants’ performance. Considering these findings, one can propose using both byproducts, together or separately as part of ruminant rations. It can be introduced in these rations as part of roughage (wheat and barley straw). CW can be incorporated in ruminant rations as part of better quality roughage (legume hay).