Extensive Linkage Disequilibrium in the Achaete-Scute Complex of Drosophila Melanogaster

We have analyzed the level of gametic association between restriction map variants in a sample of 44 X chromosomes from a natural population of Drosophila melanogaster. Of 21 pairwise tests involving 7 restriction map polymorphisms in the yellow-achaete-scute complex, 17 were found to be significant, including some between restriction sites over 80 kb apart. Three-way linkage disequilibria and their variances were also estimated for all 35 three-way comparisons between these loci. Twelve such tests were found to be significant, again spanning distances of up to 80 kb on the restriction map. Only 9 of a possible 128 haplotypes were represented in the sample and 8 of these could be linked together by changes at a single site. The strength of these associations at y-ac-sc is unusual by comparison with studies on other regions of the genome of D. melanogaster, and is consistent with the very low level of recombination which has been reported for the complex. However, our estimate of nucleotide diversity in the region is not significantly different from those made for some other loci in this species.     

The variance of sample heterozygosity

The variance of sample heterozygosity, averaged over several loci, is studied in a variety of situations. The variance depends on the sampling implicit in the mating system as well as on that explicit in the loci scored and individuals sampled. There are also effects of allelic distributions over loci and of linkage or linkage disequilibrium between pairs of loci. Results are obtained for populations in drift and mutation balance, for infinite populations undergoing mixed self and random mating, and for finite monoecious populations with or without selfing. For unlinked loci in drift/mutation balance, variances appear to be lessened more by increasing the number of loci scored than by increasing the number of individuals sampled. For infinite populations under the mixed self and random mating system, however, the reverse is true. Methods for estimating the variance of sample heterozygosity are discussed, with attention being paid to unbalanced data where not all loci are scored in all individuals.     

An anterior/posterior communication compartment border in engrailed wing discs: possible implications for Drosophila pattern formation

Our previous studies have suggested that all the known lineage compartment borders in the wing imaginal disc of Drosophila are coincident with boundaries of reduced gap junctional communication (communication compartment borders). Since engrailed discs have a disrupted anterior/posterior (A/P) lineage border (G. Morata and P. A. Lawrence, 1975, Nature (London) 255, 614-617), it was of great interest to determine if their A/P communication restriction boundary is similarly disrupted. Examination of gap-junction-mediated exchange of small fluorescent molecules between cells in the engrailed wing disc revealed a boundary of restricted communication that appeared to be identical to the wild-type A/P communication restriction boundary. This result suggests that lineage compartments are not required for the formation of A/P communication restrictions. Furthermore, we suggest that perhaps communication compartments are the domains within which information is provided for specifying the formation of lineage compartments.     

Methylation Deficiency Causes Vitamin B12-Associated Neuropathy in the Pig

Pigs were treated with N2O which is known to impair vitamin B12 function in vivo. Such pigs demonstrated an inability to gain weight, progressive ataxia, and spinal neuropathy. The ataxia was totally and the neuropathy partially preventable by dietary methionine supplementation. Methionine synthase activity was inhibited in both the liver and brain. There was a marked elevation of S-adenosylhomocysteine in the neural tissues and a concomitant failure of S-adenosylmethionine to rise and thus maintain the methylation ratio, except when supplementary dietary methionine was added. In contrast, the methylation ratio in the rat was affected to a lesser extent. The neuropathy, it is suggested, is caused by raised S-adenosylhomocysteine levels in neural tissue; as a result, the methylation ratio is inverted and S-adenosylmethionine-dependent methylation reactions are inhibited.     

Testing top‐down and bottom‐up effects on arid zone beetle assemblages following mammal reintroduction

Species extinctions and declines are occurring globally and commonly have cascading effects on ecosystems. In Australia, mammal extinctions have been extensive, particularly in arid areas, where precipitation drives ecosystems. Many ecologically extinct mammals feed on soil‐dwelling insects. However, how this top‐down pressure affected their prey and how this contrasts with the bottom‐up impacts of fluctuating precipitation remains unclear. We constructed a long‐term exclusion experiment in a multi‐species mammal reintroduction zone in semi‐arid Australia to test how top‐down (reintroduced mammals) and bottom‐up (precipitation) factors affect root‐feeding chafer beetles (Coleoptera: Melolonthinae). We used emergence traps in ten replicate 20 × 20 m plots of control, exclusion and procedural control treatments to trap chafers biannually from 2009 to 2015. Annual precipitation during this period varied from 173 to 481 mm. Mammal exclusion did not affect chafers, indicating that top‐down regulation was not important. Instead, chafer abundance, species density and biomass increased with precipitation. Chafer body size and assemblage composition were best predicted by sampling year, suggesting that random drift determined species abundances. Increased resource availability therefore favoured all species similarly. We thus found no evidence that mammal predation alters chafer populations and conclude that they may be driven primarily by bottom‐up processes. Further research should determine if the cascading effects of species loss are less important for herbivores generally than for higher level trophic groups and the role of ecosystem stability in mediating these patterns.     

Multi‐allelic exact tests for Hardy–Weinberg equilibrium that account for gender

Statistical tests for Hardy–Weinberg equilibrium are important elementary tools in genetic data analysis. X‐chromosomal variants have long been tested by applying autosomal test procedures to females only, and gender is usually not considered when testing autosomal variants for equilibrium. Recently, we proposed specific X‐chromosomal exact test procedures for bi‐allelic variants that include the hemizygous males, as well as autosomal tests that consider gender. In this study, we present the extension of the previous work for variants with multiple alleles. A full enumeration algorithm is used for the exact calculations of tri‐allelic variants. For variants with many alternate alleles, we use a permutation test. Some empirical examples with data from the 1,000 genomes project are discussed.