The maximum non-unit eigenvalue for the Wright-Fisher model of random genetic drift incorporating selection

The largest non-unit eigenvalue λ of the transition matrix for the Wright-Fisher Markov chain model of random genetic drift is found numerically with selective advantages of genotypes taken into account. Polynomials in the selection coefficients are fitted to λ in order to summarize the behaviour of λ with varying selection. Also found are the values of the selective advantages which give rise to an acceleration to the rate of fixation of alleles. These values are compared to results for the diffusion approximation to the Wright-Fisher model.     

A random effects branch-site model for detecting episodic diversifying selection

Adaptive evolution frequently occurs in episodic bursts, localized to a few sites in a gene, and to a small number of lineages in a phylogenetic tree. A popular class of "branch-site" evolutionary models provides a statistical framework to search for evidence of such episodic selection. For computational tractability, current branch-site models unrealistically assume that all branches in the tree can be partitioned a priori into two rigid classes--"foreground" branches that are allowed to undergo diversifying selective bursts and "background" branches that are negatively selected or neutral. We demonstrate that this assumption leads to unacceptably high rates of false positives or false negatives when the evolutionary process along background branches strongly deviates from modeling assumptions. To address this problem, we extend Felsenstein's pruning algorithm to allow efficient likelihood computations for models in which variation over branches (and not just sites) is described in the random effects likelihood framework. This enables us to model the process at every branch-site combination as a mixture of three Markov substitution models--our model treats the selective class of every branch at a particular site as an unobserved state that is chosen independently of that at any other branch. When benchmarked on a previously published set of simulated sequences, our method consistently matched or outperformed existing branch-site tests in terms of power and error rates. Using three empirical data sets, previously analyzed for episodic selection, we discuss how modeling assumptions can influence inference in practical situations.     

A genetic model with mutation and selection

Two deterministic models of a multiallele population in which mutation and selection both operate are considered, and formulae for the gene frequencies are obtained. Both models are of a diploid population in which selection is additive and mutation is general; generations are discrete and nonoverlapping. In the first model, the stationary solution of the discrete equations is found. In the second, the discrete time process is approximated by a continuous time one, and the resulting differential equations are solved. The transient case for two alleles is solved explicitly, and the results are graphed. An application is given to sequences of sites.     

A deterministic genetic model for sympatric speciation by sexual selection

A deterministic haploid genetic model confirms and explores in more detail the results of our previous individual-based simulation model for sympatric speciation by sexual selection. With the deterministic model, we are able to elucidate parameter dependence by phase plane analysis. We clarify how and why sympatric speciation by sexual selection can happen in a number of ways: (1) Female preferences for or against particular types of males have different effects. Whereas the former affects how readily speciation is invoked, the latter changes the stability of speciation equilibrium. (2) When there is no cost on male ornamentations, speciation is triggered regardless of initial haplotype frequencies if sufficient female preference is provided. (3) There exists a threshold for female initial frequencies for speciation to be invoked, but male initial frequencies have little effect. (4) A small cost on female mate choice does not cancel speciation, but when large, it greatly reduces the possibility of speciation.     

The tumorigenicity of diploid and aneuploid human pluripotent stem cells

Human embryonic stem cells (HESCs) and induced pluripotent stem cells (HiPSCs) offer an immense potential as a source of cells for regenerative medicine. However, the ability of undifferentiated HESCs to produce tumors in vivo presents a major obstacle for the translation of this potential into clinical reality. Therefore, characterizing the nature of HESC-derived tumors, especially their malignant potential, is extremely important in order to evaluate the risk involved in their clinical use. Here we review recent observations on the tumorigenicity of human pluripotent stem cells. We argue that diploid, early passage, HESCs produce benign teratomas without undergoing genetic modifications. Conversely, HESCs that acquired genetic or epigenetic changes upon adaptation to in vitro culture can produce malignant teratocarcinomas. We discuss the molecular mechanisms of HESC tumorigenicity and suggest approaches to prevent tumor formation from these cells. We also discuss the differences in the tumorigenicity between mouse embryonic stem cells (MESCs) and HESCs, and suggest methodologies that may help to identify cellular markers for culture adapted HESCs.     

Effects of retinoic acid on the differentiation of THP-1 cell lines containing aneuploid or diploid chromosomes

The effects of retinoic acid on the differentiation of human monocytic leukemia cell lines containing aneuploid (THP-1-Cs5) or diploid chromosomes (THP-1-R) were studied and compared. The induction of cell adhesion to a substratum, phagocytosis of sheep red blood cells (SRBC) or IgG-coated SRBC, pinocytosis of dextran sulfate, and NBT dye reduction by the cells were examined. The occurrence of these processes was much greater in RA-treated THP-1-Cs5 cells than in RA-treated THP-1-R cells. Of all these functional activities, the most remarkable differences between the two cell types were seen for cell adhesion and phagocytosis of SRBC. Morphological changes in RA-treated THP-1-Cs5 cells were observed by light and electron microscopy. RA-treated THP-1-Cs5 cells had a moderately-developed Golgi apparatus, and abundant lysosomes, mitochondria and lipid droplets in the cytoplasm. Among various retinoids examined, RA was the strongest inducer of the differentiation of the THP-1-Cs5 cells into mature cells. These findings suggest that THP-1-Cs5 cells which contain aneuploid chromosomes are more efficiently functionally differentiated by RA than are THP-1-R cells.     

A quantitative genetic model for mixed diploid and triploid hybrid progenies in tree breeding and evolution

Interspecific hybridization has played a critical role in tree evolution and breeding. The findings of triploidy in forest trees stimulate the development of a quantitative genetic model to estimate the nature of gene action. The model is based on clonally replicated triploid progenies derived from a two-level population and individual-within-population mating design in which offspring have a double dose of alleles from the parent and a single dose of alleles from the other parent. With the same genetic assumptions of a diploid model, except non-Mendelian behavior at meiosis, and the experimental variances estimated from a linear statistical model, total genetic variances in the triploid progenies are separated into additive, dominance, and epistatic components. In addition, by combining the new model with the already existing model based on disomic expression, the partitioning of additive, dominant, and epistatic variances can be obtained for a mixed diploid/triploid F₁ progeny population. This paper provides an alternative technique to study the modes of quantitative inheritance for outcrossing, long-lived forest trees in which inbred lines cannot be easily generated. The accuracy for estimating gene action using this technique is discussed.     

A model for marker-assisted selection among single crosses with multiple genetic markers

 Trait means of marker genotypes are often inconsistent across experiments, thereby hindering the use of regression techniques in marker-assisted selection. Best linear unbiased prediction based on trait and marker data (TM-BLUP) does not require prior information on the mean effects associated with specific marker genotypes and, consequently, may be useful in applied breeding programs. The objective of this paper is to present a flanking-marker, TM-BLUP model that is applicable to interpopulation single crosses that characterize maize (Zea mays L.) breeding programs. The performance of a single cross is modeled as the sum of testcross additive and dominance effects at unmarked quantitative trait loci (QTL) and at marked QTL (MQTL). The TM-BLUP model requires information on the recombination frequencies between flanking markers and the MQTL and on MQTL variances. A tabular method is presented for calculating the conditional probability that MQTL alleles in two inbreds are identical by descent given the observed marker genotypes (G ^k _obs) at the kth MQTL. Information on identity by descent of MQTL alleles can then be used to calculate the conditional covariance of MQTL effects between single crosses given G ^k _obs. The inverse of the covariance matrix for dominance effects at unmarked QTL and MQTL can be written directly from the inverse of the covariance matrices of the corresponding testcross additive effects. In practice, the computations required in TM-BLUP may be prohibitive. The computational requirements may be reduced with simplified TM-BLUP models wherein dominance effects at MQTL are excluded, only the single crosses that have been tested are included, or information is pooled across several MQTL. Received: 22 June 1997 / Accepted: 25 February 1998     

Comparative characteristics of protein-synthesizing apparatus of diploid and aneuploid human embryo fibroblasts

The time of average polypeptide chain synthesis (tc), distribution of synthesized polypeptides according to their molecular masses, the ratio of translating and nontranslating ribosomes and polyribosomes of different size have been analyzed for diploid and aneuploid strains of fibroblasts. The magnitude of tc as well as the size of polypeptide chains synthesized were found to be similar for both kinds of fibroblasts. The relative cellular content of the translating ribosomes has been shown to decrease during the transition of cells from both strains to the stationary growth phase. The relative content of heavy polyribosomes is lower in aneuploid cells as compared with that in diploid cells. The process of translation in aneuploid fibroblasts is concluded to have no essential deviations from normal.     

Analysis of cytoplasmic and maternal effects I. A genetic model for diploid plant seeds and animals

A genetic model for modified diallel crosses is proposed for estimating variance and covariance components of cytoplasmic, maternal additive and dominance effects, as well as direct additive and dominance effects. Monte Carlo simulations were conducted to compare the efficiencies of minimum norm quadratic unbiased estimation (MINQUE) methods. For both balanced and unbalanced mating designs, MINQUE (0/1), which has 0 for all the prior covariances and 1 for all the prior variances, has similar efficiency to MINQUE(), which has parameter values for the prior values. Unbiased estimates of variance and covariance components and their sampling variances could be obtained with MINQUE(0/1) and jackknifing. A t-test following jackknifing is applicable to test hypotheses for zero variance and covariance components. The genetic model is robust for estimating variance and covariance components under several situations of no specific effects. A MINQUE(0/1) procedure is suggested for unbiased estimation of covariance components between two traits with equal design matrices. Methods of unbiased prediction for random genetic effects are discussed. A linear unbiased prediction (LUP) method is shown to be efficient for the genetic model. An example is given for a demonstration of estimating variance and covariance components and predicting genetic effects.     

A selection system for diploid and against haploid cells inSchizosaccharomyces pombe

We have isolated a mutant ofSchizosaccharomyces pombe whose growth is temperature sensitive when it is haploid but not when it is diploid. This mutant may provide a useful system for selecting nonconditional mutants which are defective in diploid formation upon conjugation.     

Fundamental theorem of natural selection and frequency-dependent selection: analysis of the matrix game diploid model

Following Ewens' interpretation about Fisher's fundamental theorem of natural selection, the matrix game model for diploid populations undergoing non-overlapping, discrete generations is investigated. The total genetic variance is decomposed and it is shown that the partial change in the mean fitness, which is equal to the additive genetic variance over the mean fitness, can be thought of as a change due only to the partial changes in the phenotypic frequencies.     

Evidence for selection in cultured diploid fibroblast strains

Single skin fibroblast cultures were established from 29 females heterozygous at the X-linked G-6-PD locus for Gd^B and an electrophoretic variant, Gd^A or Gd^A?. The cultures were transferred serially until they displayed single-enzyme phenotypes (only type A or type B enzyme) or until growth ceased. Single-enzyme phenotypes were observed in 19 instances. This occurred as early as the 4th, and as late as the 38th transfer. Ten cultures evolved A phenotypes and 9 developed B phenotypes. Possible explanations for the development of single-enzyme phenotypes include random cell-sampling during sub-culturing, selection or both. Selection occurring at least in part on the basis of X-linked loci other than G-6-PD seems most likely for those cultures which evolved rapidly to single-enzyme phenotypes, but sampling or selection or both could have played important roles in those cultures which maintained double-enzyme phenotypes for several passages and then rapidly developed single-enzyme phenotypes. In any event, the results indicate that it should not be assumed in investigations using cultivated diploid fibroblasts that the latter are generally representative of the tissue-as-a-whole from which the cultures originate.     

A random shRNA-encoding library for phenotypic selection and hit-optimization

RNA interference (RNAi) is a mechanism for inhibiting gene expression through the action of small, non-coding RNAs. Most existing RNAi libraries target single genes through canonical pathways. Endogenous microRNAs (miRNAs), however, often target multiple genes and can act through non-canonical pathways, including pathways that activate gene expression. To interrogate all possible functions, we designed, synthesized, and validated the first shRNA-encoding library that is completely random at the nucleotide level. Screening in an IL3-dependent cell line, FL5.12, yielded shRNA-encoding sequences that double cell survival upon IL3 withdrawal. Using random mutagenesis and re-screening under more stringent IL3-starvation conditions, we hit-optimized one of the sequences; a specific nucleotide change and the creation of a mismatch between the two halves of the stem both contributed to the improved potency. Our library allows unbiased selection and optimization of shRNA-encoding sequences that confer phenotypes of interest, and could be used for the development of therapeutics and tools in many fields of biology.