Using compositional mixed-effects models to evaluate responses to amino acid supplementation in milk replacers for calves.

The consequences of supplementing Lys, Met, and Thr in milk replacers (MR) for calves have been widely studied, but scarce information exists about potential roles of other AA (whether essential or not). The effects on growth performance of supplementation of 4 different AA combinations in a mixed ration (25.4% crude protein and 20.3% fat) based on skim milk powder and whey protein concentrate were evaluated in 76 Holstein male calves (3 ± 1.7 d old). The 4 MR were as follows: CTRL with no AA supplementation; PG, supplying additional 0.3% Pro and 0.1% Gly; FY, supplying additional 0.2% Phe and 0.2% Tyr; and KMT, providing additional 0.62% Lys, 0.22% Met, and 0.61% Thr. All calves were fed the same milk allowance program and were weaned at 56 d of study. Concentrate intake was limited to minimize interference of potential differences in solid feed intake among treatments. Animals were weighed weekly, intakes recorded daily, and blood samples obtained at 2, 5, and 7 wk of study to determine serum urea and plasma AA concentrations. Plasma AA concentrations were explored using compositional data analysis, and their isometric log-ratio transformations were used to analyze their potential influence on ADG and serum urea concentration using a linear mixed-effects model. We detected no differences in calf performance and feed intake. Plasma relative concentration of the AA supplemented in the KMT and PG treatments increased in their respective treatments, and, in PG calves, a slight increase in the proportion of plasma Gly, Glu, and branched-chain AA was also observed. The proportions of plasma branched-chain AA, His, and Gln increased, and those of Thr, Arg, Lys, and Glu decreased with calves' age. A specific log-contrast balance formed by Arg, Thr, and Lys was found to be the main driver for lowering serum urea concentrations and increasing calf growth. The use of compositional mixed-effects models identified a cluster formed by the combination of Arg, Thr, and Lys, as a potential AA to optimize calf growth.

A Bayesian test for Hardy-Weinberg equilibrium of biallelic X-chromosomal markers.

The X chromosome is a relatively large chromosome, harboring a lot of genetic information. Much of the statistical analysis of X-chromosomal information is complicated by the fact that males only have one copy. Recently, frequentist statistical tests for Hardy-Weinberg equilibrium have been proposed specifically for dealing with markers on the X chromosome. Bayesian test procedures for Hardy-Weinberg equilibrium for the autosomes have been described, but Bayesian work on the X chromosome in this context is lacking. This paper gives the first Bayesian approach for testing Hardy-Weinberg equilibrium with biallelic markers at the X chromosome. Marginal and joint posterior distributions for the inbreeding coefficient in females and the male to female allele frequency ratio are computed, and used for statistical inference. The paper gives a detailed account of the proposed Bayesian test, and illustrates it with data from the 1000 Genomes project. In that implementation, a novel approach to tackle multiple testing from a Bayesian perspective through posterior predictive checks is used.

Testing for Hardy-Weinberg equilibrium at biallelic genetic markers on the X chromosome.

Testing genetic markers for Hardy-Weinberg equilibrium (HWE) is an important tool for detecting genotyping errors in large-scale genotyping studies. For markers at the X chromosome, typically the χ(2) or exact test is applied to the females only, and the hemizygous males are considered to be uninformative. In this paper we show that the males are relevant, because a difference in allele frequency between males and females may indicate HWE not to hold. The testing of markers on the X chromosome has received little attention, and in this paper we lay down the foundation for testing biallelic X-chromosomal markers for HWE. We develop four frequentist statistical test procedures for X-linked markers that take both males and females into account: the χ(2) test, likelihood ratio test, exact test and permutation test. Exact tests that include males are shown to have a better Type I error rate. Empirical data from the GENEVA project on venous thromboembolism is used to illustrate the proposed tests. Results obtained with the new tests differ substantially from tests that are based on female genotype counts only. The new tests detect differences in allele frequencies and seem able to uncover additional genotyping error that would have gone unnoticed in HWE tests based on females only.

A statistical analysis of the effect of warfare on the human secondary sex ratio.

Many factors have been hypothesized to affect the human secondary sex ratio (the annual percentage of males among all live births), among them race, parental ages, and birth order. Some authors have even proposed warfare as a factor influencing live birth sex ratios. The hypothesis that during and shortly after periods of war the human secondary sex ratio is higher has received little statistical treatment. In this paper we evaluate the war hypothesis using 3 statistical methods: linear regression, randomization, and time-series analysis. Live birth data from 10 different countries were included. Although we cannot speak of a general phenomenon, statistical evidence for an association between warfare and live birth sex ratio was found for several countries. Regression and randomization test results were in agreement. Time-series analysis showed that most human sex-ratio time series can be described by a common model. The results obtained using intervention models differed somewhat from results obtained by regression methods.

Human live birth and sperm-sex ratios compared.

The human secondary sex ratio is compared with the percentage of Y-chromosome bearing spermatozoa in human semen. Live birth sex ratio is about 51.3%, whereas the overall percentage of Y-chromosome bearing spermatozoa in our study samples was 50.3%, i.e. 1% closer to the proportion expected by Mendelian segregation. The observed difference between live birth and sperm-sex ratios was significant (P < 0.0001). A possible effect of male age on the percentage Y-bearing spermatozoa was found to be non-significant.