Association Mapping in Outbred Populations: Power and Efficiency When Genotyping Parents and Phenotyping Progeny

We develop expressions for the power to detect associations between parental genotypes and offspring phenotypes for quantitative traits. Three different “indirect” experimental designs are considered: full-sib, half-sib, and full-sib–half-sib families. We compare the power of these designs to detect genotype–phenotype associations relative to the common, “direct,” approach of genotyping and phenotyping the same individuals. When heritability is low, the indirect designs can outperform the direct method. However, the extra power comes at a cost due to an increased phenotyping effort. By developing expressions for optimal experimental designs given the cost of phenotyping relative to genotyping, we show how the extra costs associated with phenotyping a large number of individuals will influence experimental design decisions. Our results suggest that indirect association studies can be a powerful means of detecting allelic associations in outbred populations of species for which genotyping and phenotyping the same individuals is impractical and for life history and behavioral traits that are heavily influenced by environmental variance and therefore best measured on groups of individuals. Indirect association studies are likely to be favored only on purely economical grounds, however, when phenotyping is substantially less expensive than genotyping. A web-based application implementing our expressions has been developed to aid in the design of indirect association studies.     

High genetic and morphological diversity despite range contraction in the diploid Hieracium eriophorum (Asteraceae) endemic to the coastal sand dunes of south‐west France

Endemic plants inhabiting coastal sand dunes show augmented extinction risks due to the dynamic nature of dunes and strong human pressure on coastal areas. To investigate the survival strategies and threats to long‐term survival of such species, we combined genetic, morphological and biogeographical approaches, using the example of Hieracium eriophorum (Asteraceae) and its putative cryptic sister species H. prostratum, which are endemic to the longest coastal sand dune in Europe. An analysis of amplified fragment length polymorphism revealed high within‐population genetic variability, and slight isolation by distance was the only indication of genetic population structure. Thus, no signs of genetic threats to survival were found. Furthermore, genetic and morphometric data provided no evidence for the existence of two species. Therefore, we propose to synonymize H. prostratum with H. eriophorum and provide a nomenclatural overview with typification. Finally, an analysis of historical distribution records showed that, during the last 100 years, the species was lost from its range margins, where its habitat became fragmented. Taken together, our results suggest that one successful survival strategy of narrow endemics may be the achievement of large local population sizes on a small geographical scale, thus avoiding the genetic problems inherent to small and fragmented populations. Dune management policies should thus take care that the current tendencies to allow more erosion will not result in too severe fragmentation of the remaining continuous stretches of dune habitat. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 169 , 365–377.     

Metabolism of 3H- and 14C-labelled lactate in starved rats

1. [2-³H,U-¹⁴C]- or [3-³H,U-¹⁴C]-Lactate was administered by infusion or bolus injection to overnight-starved rats. Tracer lactate was injected or infused through indwelling cannulas into the aorta and blood was sampled from the vena cava (A–VC mode), or it was administered into the vena cava and sampled from the aorta (V–A mode). Sampling was continued after infusion was terminated to obtain the wash-out curves for the tracer. The activities of lactate, glucose, amino acids and water were followed. 2. The kinetics of labelled lactate in the two modes differed markedly, but the kinetics of labelled glucose were much the same irrespective of mode. 3. The kinetics of ³H-labelled lactate differed markedly from those for [U-¹⁴C]lactate. Isotopic steady state was attained in less than 1h of infusion of [³H]lactate but required over 6h for [U-¹⁴C]lactate. 4. ³H from [2-³H]lactate labels glucose more extensive than does that from [3-³H]lactate. [3-³H]Lactate also labels plasma amino acids. The distribution of ³H in glucose was determined. 5. Maximal radioactivity in ³HOH in plasma is attained in less than 1min after injection. Near-maximal radioactivity in [¹⁴C]glucose and [³H]glucose is attained within 2–3min after injection. 6. The apparent replacement rates for lactate were calculated from the areas under the specific-radioactivity curves or plateau specific radioactivities after primed infusion. Results calculated from bolus injection and infusion agreed closely. The apparent replacement rate for [³H]lactate from the A–VC mode averaged about 16mg/min per kg body wt. and that in the V–A mode about 8.5mg/min per kg body wt. The apparent rates for [¹⁴C]lactate (`rate of irreversible disposal') were 8mg/min per kg body wt. for the A–VC mode and 5.5mg/min per kg body wt. for the V–A mode. Apparent recycling of lactate carbon was 55–60% according to the A–VC mode and 35% according to the V–A mode. 7. The specific radioactivities of [U-¹⁴C]glucose at isotopic steady state were 55% and 45% that of [U-¹⁴C]lactate in the A–VC and V–A modes respectively. We calculated, correcting for the dilution of ¹⁴C in gluconeogenesis via oxaloacetate, that over 70% of newly synthesized glucose was derived from circulating lactate. 8. Recycling of ³H between lactate and glucose was evaluated. It has no significant effect on the calculation of the replacement rate, but affects considerably the areas under the wash-out curves for both [2-³H]- and [3-³H]-lactate, and calculation of mean transit time and total lactate mass in the body. Corrected for recycling, in the A–VC mode the mean transit time is about 3min, the lactate mass about 50mg/kg body wt. and the lactate space about 65% of body space. The V–A mode yields a mass and lactate space about half those with the A–VC mode. 9. The area under the wash-out curve for [¹⁴C]lactate is some 20–30 times that for [³H]lactate, and apparent carbon mass is 400–500mg/kg body wt. and presumably includes the carbon of glucose, pyruvate and amino acids, which are exchanging rapidly with that of lactate.     

The role of vocal individuality in conservation

Identifying the individuals within a population can generate information on life history parameters, generate input data for conservation models, and highlight behavioural traits that may affect management decisions and error or bias within census methods. Individual animals can be discriminated by features of their vocalisations. This vocal individuality can be utilised as an alternative marking technique in situations where the marks are difficult to detect or animals are sensitive to disturbance. Vocal individuality can also be used in cases were the capture and handling of an animal is either logistically or ethically problematic. Many studies have suggested that vocal individuality can be used to count and monitor populations over time; however, few have explicitly tested the method in this role. In this review we discuss methods for extracting individuality information from vocalisations and techniques for using this to count and monitor populations over time. We present case studies in birds where vocal individuality has been applied to conservation and we discuss its role in mammals.     

Orientation of the genetic variance-covariance matrix and the fitness surface for multiple male sexually selected traits

Stabilizing selection has been predicted to change genetic variances and covariances so that the orientation of the genetic variance-covariance matrix (G) becomes aligned with the orientation of the fitness surface, but it is less clear how directional selection may change G. Here we develop statistical approaches to the comparison of G with vectors of linear and nonlinear selection. We apply these approaches to a set of male sexually selected cuticular hydrocarbons (CHCs) of Drosophila serrata. Even though male CHCs displayed substantial additive genetic variance, more than 99% of the genetic variance was orientated 74.9 degrees away from the vector of linear sexual selection, suggesting that open-ended female preferences may greatly reduce genetic variation in male display traits. Although the orientation of G and the fitness surface were found to differ significantly, the similarity present in eigenstructure was a consequence of traits under weak linear selection and strong nonlinear (convex) selection. Associating the eigenstructure of G with vectors of linear and nonlinear selection may provide a way of determining what long-term changes in G may be generated by the processes of natural and sexual selection.     

Divergent selection and the evolution of signal traits and mating preferences

Mating preferences are common in natural populations, and their divergence among populations is considered an important source of reproductive isolation during speciation. Although mechanisms for the divergence of mating preferences have received substantial theoretical treatment, complementary experimental tests are lacking. We conducted a laboratory evolution experiment, using the fruit fly Drosophila serrata, to explore the role of divergent selection between environments in the evolution of female mating preferences. Replicate populations of D. serrata were derived from a common ancestor and propagated in one of three resource environments: two novel environments and the ancestral laboratory environment. Adaptation to both novel environments involved changes in cuticular hydrocarbons, traits that predict mating success in these populations. Furthermore, female mating preferences for these cuticular hydrocarbons also diverged among populations. A component of this divergence occurred among treatment environments, accounting for at least 17.4% of the among-population divergence in linear mating preferences and 17.2% of the among-population divergence in nonlinear mating preferences. The divergence of mating preferences in correlation with environment is consistent with the classic by-product model of speciation in which premating isolation evolves as a side effect of divergent selection adapting populations to their different environments.     

Chemotactic responses of human peripheral blood monocytes to the complement-derived peptides C5a and C5a des Arg

We examined responses of human peripheral blood polymorphonuclear leukocytes (PMN) and monocytes to the highly purified human complement-derived peptides C5a and C5a des Arg. As reported previously, C5a proved to be approximately 10- to 20-fold more potent than C5a des Arg as a chemoattractant for human PMN. C5a also was more potent than C5a des Arg in causing PMN to acquire a polarized morphology. In contrast, we found that human monocytes do not distinguish between C5a and C5a des Arg when these peptides are used as chemoattractants. In two different assay systems, both peptides acted at identical concentrations to stimulate suboptimal and optimal migration of monocytes. Human monocytes also did not distinguish between C5a and C5a des Arg when these peptides were used as inducers of polarization. Studies performed with functionally active, [125I]-labeled C5a and C5a des Arg, however, demonstrated that binding of C5a des Arg to monocytes differed from binding of C5a. Although [125I]-C5a des Arg appeared to bind to the same receptor as [125I]-C5a, binding of labeled C5a des Arg occurred with an affinity that was approximately 100-fold less than that observed with labeled C5a. These results indicate that leukocyte chemotactic and polarization responses to C5a and C5a des Arg vary, depending on the target cell type.     

A derivative of wheat germ agglutinin specifically inhibits formyl-peptide-induced polymorphonuclear leukocyte chemotaxis by blocking re-expression (or recycling) of receptors

We examined the mechanism of action of a derivative of wheat germ agglutinin (WGA-D) which specifically and irreversibly inhibits N-formyl-methionyl-leucyl-phenylalanine (FMLP)-induced polymorphonuclear leukocyte (PMN) chemotaxis. At a concentration that completely inhibited PMN chemotaxis, WGA-D had no effect on either the uptake or release of [3H]-FMLP by PMN. Similarly, WGA-D did not affect either the short-term binding to, or internalization by, PMN of a fluoresceinated FMLP analog. WGA-D did interfere, however, with the re-expression (or recycling) of FMLP receptors by PMN that had been preincubated with 1 microM FMLP for 10 min at 4 degrees C. This effect was specific for WGA-D, because it was not observed when concanavalin A was used. Scatchard plot analysis of FMLP binding to PMN after receptor re-expression demonstrated that WGA-D-treated PMN had a significant diminution in the number of high affinity receptors. WGA-D-mediated inhibition of FMLP receptor re-expression was associated with inhibition of FMLP-induced PMN chemotaxis, but had no effect on either FMLP-induced PMN superoxide anion generation or degranulation. Studies using [125I]-WGA-D demonstrated that PMN did not internalize WGA-D spontaneously. PMN did internalize [125I]-WGA-D, however, when stimulated with FMLP. Internalization of WGA-D by FMLP-stimulated PMN was rapid, dependent on the concentration of FMLP, and specific. Internalization of [125I]-WGA-D by PMN did not occur when highly purified human C5a, instead of FMLP, was used as a stimulus. Subcellular fractionation studies demonstrated that [125I]-WGA-D and [3H]-FMLP were co-internalized by PMN, and segregated to a compartment co-migrating with Golgi markers. Western blot analysis, using PMN plasma membranes, demonstrated that WGA-D bound to a single membrane glycoprotein that migrated with an apparent m.w. of 62,000. The data indicate that WGA-D, perhaps by binding to the FMLP receptor, inhibits FMLP-induced PMN chemotaxis by blocking the re-expression (or recycling) of a population of receptors required for continuous migration.     

Relationships between breeding soundness and sex drive classifications in beef bulls

Prior to use in single-sire mating trials, ninety-two beef bulls were evaluated to determine the relationships between. Breeding Soundness Examination (BSE) and sex drive assessment categories. A BSE score was given to each bull based on scrotal circumference, spermatozoal motility and morphology. Eighty bulls were classified as satisfactory potential breeders, while 12 were classified as questionable potential breeders. Each bull was exposed to two, 10 min modified libido/serving capacity tests. Sixty-nine bulls were classified as high libido and 23 were classified as medium libido. Differences in scrotal circumference and spermatozoal motility did not influence (P > 0.05) the BSE classifications. However, differences in primary, secondary and total spermatozoal abnormalities were the major factors affecting the BSE classification. Bulls classified as high libido serviced three times more (P < 0.01) during the two test periods than bulls classified as medium libido. High libido bulls were superior in all sex drive traits. However, bulls in the two libido categories did not differ (P > 0.05) in semen quality or scrotal circumference. There was no relationship (P > 0.05) between BSE and sex drive traits (r = -0.16 to 0.24).