Testing natural selection vs. genetic drift in phenotypic evolution using quantitative trait locus data

Evolutionary biologists have long sought a way to determine whether a phenotypic difference between two taxa was caused by natural selection or random genetic drift. Here I argue that data from quantitative trait locus (QTL) analyses can be used to test the null hypothesis of neutral phenotypic evolution. I propose a sign test that compares the observed number of plus and minus alleles in the "high line" with that expected under neutrality, conditioning on the known phenotypic difference between the taxa. Rejection of the null hypothesis implies a role for directional natural selection. This test is applicable to any character in any organism in which QTL analysis can be performed.     

Genetic response from marker assisted selection in an outbred population for differing marker bracket sizes and with two identified quantitative trait loci

Effect of flanking quantitative trait loci (QTL)-marker bracket size on genetic response to marker assisted selection in an outbred population was studied by simulation of a nucleus breeding scheme. In addition, genetic response with marker assisted selection (MAS) from two quantitative trait loci on the same and different chromosome(s) was investigated. QTL that explained either 5% or 10% of phenotypic variance were simulated. A polygenic component was simulated in addition to the quantitative trait loci. In total, 35% of the phenotypic variance was due to genetic factors. The trait was measured on females only. Having smaller marker brackets flanking the QTL increased the genetic response from MAS selection. This was due to the greater ability to trace the QTL transmission from one generation to the next with the smaller flanking QTL-marker bracket, which increased the accuracy of estimation of the QTL allelic effects. Greater negative covariance between effects at both QTL was observed when two QTL were located on the same chromosome compared to different chromosomes. Genetic response with MAS was greater when the QTL were on the same chromosome in the early generations and greater when they were on different chromosomes in the later generations of MAS.     

Effect of inaccurate parameter estimates on genetic response to marker-assisted selection in an outbred population

The effect of inaccurate estimates of variance and of the location of the quantitative trait locus on the genetic response to marker-assisted selection was studied by simulation of an adult multiple ovulation and embryo transfer nucleus breeding scheme. Two genetic models were simulated for the quantitative trait locus: a total of 10 alleles or 2 distinct alleles per base parent. For both models, the locus explained either 5 or 10% of phenotypic variance. A polygenic component was simulated, and the two genetic components were summed to 35% heritability for a trait measured on females. Overestimation of variance of the quantitative trait locus had minimal effect on genetic gain for marker-assisted selection over the short term, but decreased long-term response. The long-term loss was reduced when variance of the quantitative trait locus was reestimated after four generations of marker-assisted selection. Selection for favorable alleles at a nonexistent quantitative trait locus resulted in first generation losses of 3 and 7% for postulated quantitative trait loci, explaining 5 and 10% of variance, respectively. The larger the degree of error in location, the larger was the genetic loss compared with the correct location scenario. For the largest simulated location error of 15 cM, genetic superiority of marker-assisted selection was reduced by 80% in the first generation. We concluded that studies should be undertaken to verify estimates of quantitative trait locus and location to make optimal use of marker-assisted selection.     

Normal and abnormal embryonic development of the anorectum in human embryos

A keystone of the molecular reductionist approach to cellular biology is a specific deductive strategy relating genotype to phenotype-two distinct categories. This relationship is based on the assumption that the intermediary cellular network of actively transcribed genes and their regulatory elements is deterministic (i.e., a link between expression of a gene and a phenotypic trait can always be identified, and evolution of the network in time is predetermined). However, experimental data suggest that the relationship between genotype and phenotype is nonbijective (i.e., a gene can contribute to the emergence of more than just one phenotypic trait or a phenotypic trait can be determined by expression of several genes). This implies nonlinearity (i.e., lack of the proportional relationship between input and the outcome), complexity (i.e. emergence of the hierarchical network of multiple cross-interacting elements that is sensitive to initial conditions, possesses multiple equilibria, organizes spontaneously into different morphological patterns, and is controlled in dispersed rather than centralized manner), and quasi-determinism (i.e., coexistence of deterministic and nondeterministic events) of the network. Nonlinearity within the space of the cellular molecular events underlies the existence of a fractal structure within a number of metabolic processes, and patterns of tissue growth, which is measured experimentally as a fractal dimension. Because of its complexity, the same phenotype can be associated with a number of alternative sequences of cellular events. Moreover, the primary cause initiating phenotypic evolution of cells such as malignant transformation can be favored probabilistically, but not identified unequivocally. Thermodynamic fluctuations of energy rather than gene mutations, the material traits of the fluctuations alter both the molecular and informational structure of the network. Then, the interplay between deterministic chaos, complexity, self-organization, and natural selection drives formation of malignant phenotype. This concept offers a novel perspective for investigation of tumorigenesis without invalidating current molecular findings. The essay integrates the ideas of the sciences of complexity in a biological context.     

The impact of genetic markers on selection

Genetic marker technologies, such as marker-assisted selection, parentage identification, and gene introgression can be applied to livestock selection programs. Highly saturated genetic maps are now available for cattle, swine, and sheep to provide the genetic framework for developing MAS programs. These programs rely on three phases for commercialization of the technology: the detection phase, in which quantitative trait loci are located and their effects on the phenotype measured; the evaluation phase, in which the markers are evaluated in commercial populations; and the implementation phase, in which markers are combined with phenotypic and pedigree information in genetic evaluation for predicting the genetic merit of individuals within the population. Predicting the economic impact of genetic technologies is a complex process that requires quantitative prediction and economic analysis. Evaluating the impact of these benefits across an industry can be achieved through a process in which gains from implementation of a genetic technology are assessed at the individual, enterprise, and industry levels. A pattern of annual benefits and costs can be predicted using gene flows that can be evaluated by conventional economic analysis.     

Analytical and clinical performance of an automated immunoassay system (Immulite) for estradiol in serum

Mouse strains congenic for individual quantitative trait loci (QTLs) conferring hypnotic sensitivity to ethanol were constructed by backcrossing genotypically selected ILS x ISS N2 individuals to either inbred Long Sleep (ILS) or inbred Short Sleep (ISS) mice. We used a novel "speed congenic" approach in which N2 mice were genotyped for markers flanking each of the five originally identified QTLs. Genotypic selection for ISS regions at four of the five QTLs, and for ILS/ISS at the fifth QTL, allowed rapid fixation of the genetic background. We call this strategy "QTL-Marker-Assisted Counter Selection" or QMACS. By the N4 generation, phenotypic assessments showed that in some sublines the QTL had not been captured; these sublines were discarded and positive lines split to create new replicate sublines. One QTL, on Chromosome (Chr) 8, was not confirmed. At the N8, virtually all sublines on the remaining QTLs retained the phenotypic difference between heterozygotes and ISS homozygotes. Small numbers of interim congenics were produced at the N6 and later generations in which the ILS QTL was made homozygous on the ISS background; as expected, these congenic mice showed an increased sleep time. For later backcrosses (after the N4), the parents were selected on the basis of phenotype as well as genotype. The parent-offspring correlation over all QTLs was significant, supporting the use of phenotypic selection in congenic construction.     

Developmental expression of G proteins in a migratory population of embryonic neurons

Directed neuronal migration contributes to the formation of many developing systems, but the molecular mechanisms that control the migratory process are still poorly understood. We have examined the role of heterotrimeric G proteins (guanyl nucleotide binding proteins) in regulating the migratory behavior of embryonic neurons in the enteric nervous system of the moth, Manduca sexta. During the formation of the enteric nervous system, a group of approx. 300 enteric neurons (the EP cells) participate in a precise migratory sequence, during which the undifferentiated cells populate a branching nerve plexus that lies superficially on the visceral musculature. Once migration is complete, the cells then acquire a variety of position-specific neuronal phenotypes. Using affinity-purified antisera against different G protein subtypes, we found no apparent staining for any G protein in the EP cells prior to their migration. Coincident with the onset of migration, however, the EP cells commenced the expression of one particular G protein, Go alpha. The intensity of immunostaining continued to increase as migration progressed, with Go alpha immunoreactivity being detectable in the leading processes of the neurons as well as their somata. The identity of the Go alpha-related proteins was confirmed by protein immunoblot analysis and by comparison with previously described forms of Go alpha from Drosophila. When cultured embryos were treated briefly with aluminium fluoride, a compound known to stimulate the activity of heterotrimeric G proteins, both EP cell migration and process outgrowth were inhibited. The effects of aluminium fluoride were potentiated by alpha toxin, a pore-forming compound that by itself caused no significant perturbations of migration. In preliminary experiments, intracellular injections of the non-hydrolyzable nucleotide GTP gamma-S also inhibited the migration of individual EP cells, supporting the hypothesis that G proteins play a key role in the control of neuronal motility in this system. In addition, once migration was complete, the expression of Go alpha-related proteins in the EP cells underwent a subsequent phase of regulation, so that only certain phenotypic classes among the differentiated EP cells retained detectable levels of Go alpha immunoreactivity. Thus Go may perform multiple functions within the same population of migratory neurons in the course of embryonic development.     

Role of neutrophil elastase in compression-induced spinal cord injury in rats

Myeloperoxidase (MPO) is an essential component of the oxygen-dependent microbicidal system of neutrophils and monocytes. Hereditary deficiency of MPO occurs in 1 in 2,000 to 4,000 individuals in the general population and has been generally considered an autosomal recessive trait. Previous studies have used the peroxidase activity of blood leukocytes to assess the phenotype of affected family members. Eosinophil peroxidase (EPO) also contributes to the peroxidase activity of blood leukocytes. Because EPO expression is normal in MPO-deficient subjects, eosinophil contamination can significantly contribute to peroxidase activity in leukocytes from family members of an MPO-deficient subject and thereby undermine correct interpretation of the inheritance pattern. To avoid this potential problem, we used cytochemical, immunochemical, and genetic techniques to assess the inheritance pattern of MPO deficiency in sixteen individuals from five unrelated kindreds. Each kindred had an index case with MPO deficiency and the R569W missense mutation, a genotype that causes MPO deficiency. Our analysis demonstrated that MPO deficiency was not inherited as a simple autosomal recessive trait. Most subjects were compound heterozygotes with respect to the R569W mutation and demonstrated a spectrum of phenotypes. Our data demonstrate the broad phenotypic impact of compound heterozygosity on the expression and function of a multimeric protein such as MPO.     

Population structure in Daphnia obtusa: quantitative genetic and allozymic variation

Quantitative genetic analyses for body size and for life history characters within and among populations of Daphnia obtusa reveal substantial genetic variance at both hierarchical levels for all traits measured. Simultaneous allozymic analysis on the same population samples indicate a moderate degree of differentiation: GST = 0.28. No associations between electrophoretic genotype and phenotypic characters were found, providing support for the null hypothesis that the allozymic variants are effectively neutral. Therefore, GST can be used as the null hypothesis that neutral phenotypic evolution within populations led to the observed differentiation for the quantitative traits, which I call QST. The results of this study provide evidence that natural selection has promoted diversification for body size among populations, and has impeded diversification for relative fitness. Analyses of population differentiation for clutch size, age at reproduction, and growth rate indicate that neutral phenotypic evolution cannot be excluded as the cause.     

Synthesis and antibacterial activity of U-100592 and U-100766, two oxazolidinone antibacterial agents for the potential treatment of multidrug-resistant gram-positive bacterial infections

The evolution of fitness in experimental clonal populations of vesicular stomatitis virus (VSV) has been compared under different genetic (fitness of initial clone) and demographic (population dynamics) regimes. In spite of the high genetic heterogeneity among replicates within experiments, there is a clear effect of population dynamics on the evolution of fitness. Those populations that went through strong periodic bottlenecks showed a decreased fitness in competition experiments with wild type. Conversely, mutant populations that were transferred under the dynamics of continuous population expansions increased their fitness when compared with the same wild type. The magnitude of the observed effect depended on the fitness of the original viral clone. Thus, high fitness clones showed a larger reduction in fitness than low fitness clones under dynamics with included periodic bottleneck. In contrast, the gain in fitness was larger the lower the initial fitness of the viral clone. The quantitative genetic analysis of the trait "fitness" in the resulting populations shows that genetic variation for the trait is positively correlated with the magnitude of the change in the same trait. The results are interpreted in terms of the operation of Muller's ratchet and genetic drift as opposed to the appearance of beneficial mutations.     

In vitro lymphocyte-differentiating effects of thymulin (Zn-FTS) on lymphocyte subpopulations of severely malnourished children

The success of the cardiothoracic surgery residency program in Chapel Hill is due to a number of contributing factors. The first important ingredient is the faculty. Their ability, stability, and dedication, with each faculty member developing an area of expertise, has contributed greatly to the success of our program. The second important aspect is the program design itself--all three years: the first to allow the resident time to reflect on educational priorities and do some innovative thinking; the second and third as chief resident on their respective services--for an entire, continuous year. The third and most important aspect of our program is the quality of the residents we have been able to attract--uniformly a splendid group of individuals who regularly gave more than they received and who continue to be a source of inspiration, hope, and pride for those of us who have been privileged to be their teachers.     

Needs of caregivers of clients with multiple sclerosis

In an earlier study, an in vitro evolution procedure was applied to a large population of variants of the Tetrahymena group I ribozyme to obtain individuals with a 10(5)-fold improved ability to cleave a target single-stranded DNA substrate under simulated physiological conditions. The evolved ribozymes also showed a twofold improvement, compared to the wild-type, in their ability to cleave a single-stranded RNA substrate. Here, we report continuation of the in vitro evolution process using a new selection strategy to achieve both enhanced DNA and diminished RNA-cleavage activity. Our strategy combines a positive selection for DNA cleavage with a negative selection against RNA binding. After 36 "generations" of in vitro evolution, the evolved population showed an approximately 100-fold increase in the ratio of DNA to RNA-cleavage activity. Site-directed mutagenesis experiments confirmed the selective advantage of two covarying mutations within the catalytic core of the ribozyme that are largely responsible for this modified behavior. The population of ribozymes has now undergone a total of 63 successive generations of evolution, resulting in an average of 28 mutations relative to the wild-type that are responsible for the altered phenotype.     

Nonlinear effects of chicken endogenous viruses on body weight may be responsible for maintaining these elements in a stable genetic polymorphism

The effects of presence or absence of individual endogenous virus (ev) genes on production traits was studied in a highly productive commercial layer cross. Age and BW at first egg, egg production, egg weight, and mature BW were recorded for each bird. The birds were examined for presence of ev gene fragments by Southern analysis. A general linear model was used to determine significance of effects of the 21 individual ev fragments on the individual traits and the effects of all ev fragments taken together on each of the traits. Seven significant effects were found for individual ev fragments on individual traits. Four of these involved BW at first egg, and all ev gene fragments taken together had a significant effect on BW at first egg, explaining 17% of total phenotypic variation in this trait. Significant nonlinear correlations were found between total number of ev genes and both BW at first egg and mature BW, with birds having a moderate number of ev genes showing the lowest BW. For age at first egg and egg weight, nonlinear correlations, although not significant, were consistent in sign with those found for BW, implying minimum trait magnitude at moderate number of ev genes. These effects imply that animals with intermediate numbers of ev genes will tend to be favored by commercial selection in layer flocks, whereas birds with either too many or too few ev genes will tend to be culled.(ABSTRACT TRUNCATED AT 250 WORDS)     

Evidence of discrimination against international medical graduates applying to family practice residency programs

BACKGROUND AND OBJECTIVES: The purpose of the study was to test the hypothesis that discrimination exists against international medical graduates (IMGs) applying to US family practice residency programs. METHODS: Two sets of letters were sent to 146 family practice residency programs randomly selected from the Directory of Graduate Medical Education Programs. The letters requested information and an application. All letters were identical except that the author of the first set was described as "a foreign medical graduate." The author of the second set was described as "a fourth-year medical student at the University of Nebraska Medical Center." Replies were monitored for 6 weeks after the second mailing. Response rates to each "candidate" were measured. In addition, responses were evaluated for the presence of a brochure describing the residency program, an application, cover letter, invitation for interview, eligibility criteria, and other material. RESULTS: A total of 113 programs (79%) responded. Of these, 102 responded to the fourth-year medical student and 57 responded to the IMG. Of the 46 programs replying to both candidates, only 20 provided identical mailings. Nine of the 46 programs required IMGs to meet standards that exceeded requirements set by the Educational Commission for Foreign Medical Graduates for residency training in the United States. CONCLUSIONS: A pattern of dissimilarity exists in the way family practice residency programs respond to requests for application materials, and the differences appear to depend on whether the candidate is a US medical graduate or an IMG. These results raise questions about the fairness of current methods of resident selection.     

Genetic and economic responses for within-family marker-assisted selection in dairy cattle breeding schemes

Marker-assisted selection schemes that utilize information about quantitative trait loci to preselect progeny test bulls within a family are the most practical application of quantitative trait loci results in the short-term. Technical difficulties exist for across-family marker-assisted selection using BLUP procedures. Two within-family marker-assisted selection schemes were evaluated genetically and economically using stochastic simulation for a locus that explained 5% of phenotypic variance. The genetic and economic impacts of variation in the number of offspring per bull-dam were evaluated. The top down marker-assisted selection scheme identifies sires that are heterozygous for the locus based on the granddaughter design and uses the quantitative trait locus information in the preselection of grandsons entering progeny testing. The bottom up marker-assisted selection scheme identifies sires heterozygous for a quantitative trait locus based on the daughter design and uses the information in the preselection of sons entering progeny testing. The top down scheme with one progeny per bull-dam reduced the rate of genetic gain compared with that from a breeding scheme that ignored knowledge of the quantitative trait locus. The top down scheme with reproductive performance of 3 or 40 progeny per bull-dam increased genetic gain by 1 to 2%. The bottom up scheme increased the rate of genetic gain by 1.5, 3.5, and 5% for 1, 3, and 40 progeny per bull-dam, respectively. When the top down scheme was used on the maternal path and the bottom up scheme on the paternal path, increases were 9% with 40 progeny per bull-dam. The use of reproductive technologies on bull-dams is imperative to prevent gains from marker-assisted selection being eroded by the loss in polygenic selection differential that results when more bull-dams are required to enable preselection of sons using markers.     

The shape of female mating preferences

The "shape" of a female mating preference is the relationship between a male trait and the probability of acceptance as a mating partner. The shape of preferences is important in many models of sexual selection, mate recognition, communication, and speciation, yet it has rarely been measured precisely. Here I examine preference shape for male calling song in a bushcricket (katydid). Preferences change dramatically between races of a species, from strongly directional to broadly stabilizing (but with a net directional effect). Preference shape generally matches the distribution of the male trait. This is compatible with a coevolutionary model of signal-preference evolution, although it does not rule out an alternative model, sensory exploitation. Preference shapes are shown to be genetic in origin.     

Fine-scale spatial genetic structure with nonuniform distribution of individuals

This paper presents the first theoretical study of spatial genetic structure within nonuniformly distributed continuous plant populations. A novel individual-based model of isolation by distance was constructed to simulate genetic evolution within such populations. We found larger values of spatial genetic autocorrelations in highly clumped populations than in uniformly distributed populations. Most of this difference was caused by differences in mean dispersal distances, but aggregation probably also produced a slight increase in spatial genetic structure. Using an appropriate level of approximation of the continuous distribution of individuals in space, we assessed the potential effects of density, seed and pollen dispersal, generation overlapping, and overdominance selection at an independent locus, on fine-scale genetic structure, by varying them separately in a few particular cases with extreme clumping. When selfing was allowed, all these input variables influenced both aggregation and spatial genetic structure. Most variations in spatial genetic structure were closely linked to variations in clumping and/or local density. When selfing was not allowed, spatial genetic structure was lower in most cases.     

Panic and phobic anxiety: defining phenotypes for genetic studies

OBJECTIVE: With recent advances in molecular genetics, the rate-limiting step in identifying susceptibility genes for psychiatric disorders has become phenotype definition. The success of psychiatric genetics may require the development of a "genetic nosology" that can classify individuals in terms of the heritable aspects of psychopathology. The authors' aim is to begin to apply this analysis to the anxiety disorders, focusing on panic and phobic disorders. METHOD: Two parallel traditions of defining anxiety phenotypes are reviewed: the first, more closely identified with clinical psychiatry, has identified categorical diagnoses (e.g., panic disorder and social phobia). The other, more closely identified with psychological studies of personality development, has examined dimensional traits (e.g., neuroticism) and anxious temperament (e.g., behavioral inhibition). RESULTS: The authors suggest that a genetic nosology of panic and phobic disorders may incorporate features of both traditions and discuss strategies for optimizing genetic approaches to anxiety including 1) studying phenotypic extremes, 2) identifying biological trait markers, and 3) using animal models to identify candidate loci. CONCLUSIONS: An important dividend from the effort to define the boundaries of heritable phenotypes for genetic studies of anxiety may be a refinement of the nosology of anxiety disorders.     

How should we explain variation in the genetic variance of traits?

Recent work has called attention to large differences among traits in the amount of standardized genetic variance they possess. There are four general factors which could play a role in causing this variation: mutation, elimination of deleterious variation, selection of favorable alleles, and balancing selection. Three factors could directly influence the mutational variability of traits: canalization, the mutational target size, and the timing of trait expression. Here I carry out simple tests of the importance of some of these factors using data from Drosophila melanogaster. I compiled information from the literature on the mutational and standing genetic variances in outbred populations, inferred the relative mutational target size of each trait, its a timing of expression, and used models of life history to calculate fitness sensitivities for each trait. Mutational variation seems to play an important role, as it is highly correlated with standing variance. The target size hypothesis was supported by a significant correlation between mutational variance and inferred target size. There was also a significant relationship between the timing of trait expression and mutational variance. These hypotheses are confounded by a correlation between timing and target size. The elimination and canalization hypotheses were not supported by these data, suggesting that they play a quantitatively less important role in determining overall variances. Additional information concerning the pleiotropic consequences of mutations would help to validate the fitness sensitivities used to test the elimination and canalization hypotheses.     

Evaluating applicants to emergency medicine residency programs

This article reviews the pertinent literature related to the selection process of medical students to emergency medicine residency programs. The impact that academic performance in medical school, the interview, letters of recommendation, and other achievements have on the performance of the future resident are reviewed. All articles identified by an English language MEDLINE search were reviewed by the authors as to significance to the subject. Review of relevant literature indicates that no precise correlation can be made between performance in medical school and achievements during the residency, although there seems to be a correlation between academic performance in medical school and similar performance on board certification examinations.