Effects of the number of markers per haplotype and clustering of haplotypes on the accuracy of QTL mapping and prediction of genomic breeding values

The aim of this paper was to compare the effect of haplotype definition on the precision of QTL-mapping and on the accuracy of predicted genomic breeding values. In a multiple QTL model using identity-by-descent (IBD) probabilities between haplotypes, various haplotype definitions were tested i.e. including 2, 6, 12 or 20 marker alleles and clustering base haplotypes related with an IBD probability of > 0.55, 0.75 or 0.95. Simulated data contained 1100 animals with known genotypes and phenotypes and 1000 animals with known genotypes and unknown phenotypes. Genomes comprising 3 Morgan were simulated and contained 74 polymorphic QTL and 383 polymorphic SNP markers with an average r² value of 0.14 between adjacent markers. The total number of haplotypes decreased up to 50% when the window size was increased from two to 20 markers and decreased by at least 50% when haplotypes related with an IBD probability of > 0.55 instead of > 0.95 were clustered. An intermediate window size led to more precise QTL mapping. Window size and clustering had a limited effect on the accuracy of predicted total breeding values, ranging from 0.79 to 0.81. Our conclusion is that different optimal window sizes should be used in QTL-mapping versus genome-wide breeding value prediction.     

Hooker and islands1

Sir Joseph Dalton Hooker (1817–1911), friend and scientific confidant of Charles Darwin, lectured in 1866 on ‘Insular floras’ at the Annual Meeting of the British Association for the Advancement of Science. His interest and knowledge of islands had been aroused when he travelled to the Antarctic aboard the Erebus under Sir James Clark Ross from 1839–43. On his return, Darwin passed on to Hooker the botanical collections he had made on the Beagle voyage, including those from the Galapagos. Hooker's conclusions from these and from his own material and experiences were important to Darwin as he developed the ideas that culminated in the publication of the Origin of Species. The 1866 lecture provided a focus for subsequent and informative studies on evolution, and islands continue to provide invaluable natural laboratories for evolutionary biology and genetics. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 96 , 462–481.     

Variation in food availability influences prey‐capture method in antlion larvae

Abstract 1. Larvae of a Myrmecaelurus sp. are unique among antlions because they have two prey‐capture methods; they either ambush prey at the surface, or dig pit traps that prey fall in to. It was hypothesised that larvae will use the capture method that maximises their net rate of energy gain, which will be influenced by food availability (encounter rate) and by past energy inputs (body condition). 2. Costs were estimated by measuring resting and activity metabolic rates and determining the duration of pit maintenance at various encounter rates with ants that served as prey. Benefits were estimated from the energy gained per ant captured at different encounter rates. 3. Net energy gained was higher with a pit than without one, and was influenced more by the differences in prey capture rate between the two capture methods, and less by the differences in energy costs associated with each method. The proportion of larvae that constructed pits was higher when they were in intermediate body condition than when in good or in poor body condition. 4. Thus, the use of one capture method or the other depends on a combination of the influences of past net energy gain and the antlion’s most recent change in encounter rate with prey. Ambushing without a pit may serve as a default when physiological constraints limit the larvae’s ability to invest in pit construction and maintenance, or when larvae are sated, and saving the energy of pit construction and maintenance is worthwhile.     

Variation in stomatal characteristics over the lower surface of Commelina communis leaves

Abstract. The silicone rubber impression technique was used to measure stomatal apertures in 9 mm² sampling areas covering the entire lower surface of leaves of Commelina communis L. The data were analysed using a computer program which produced 'iso-aperture' contours illustrating local differences in mean stomatal aperture. Little consistency was seen in the iso-aperture patterns among sampling times, although the stomata were always relatively closed at the leaf tip and base. When stomata in the middle of the lamina were open, those near to the leaf margin tended to be relatively closed. In places, gradients of mean stomatal aperture were as high as 1 μm mm⁻¹. Measurements along a transect across the lower epidermis revealed no correlation of stomatal aperture with the presence of major veins in the mesophyll tissue. Variation in guard-cell size and stomatal frequency on the lower leaf surface was also analysed. The guard cells were smallest and the stomata more frequent near to the leaf margins. The significance of the results is discussed in relation to measurements of leaf conductance and models of stomatal function.     

Materials and methods for carbon dioxide and water exchange analysis§

Abstract Some of the materials which are commonly used in equipment for carbon dioxide and water exchange analysis can adsorb substantial amounts of carbon dioxide and water and, thus, may cause large experimental errors. Also presented are procedures for determining the influence of light intensity, carbon dioxide concentration, and temperature upon photosynthesis and transpiration.     

Darwin was astonished

Darwin did not approach the Galápagos with the same enthusiasm and energy as he showed at earlier places visited by the Beagle. Notwithstanding, he looked back on the five weeks the Beagle spent in the Galápagos as a time when he made observations important for the development of his evolutionary ideas. In retrospect, he was astonished at what he saw there.