Phylogenetic diversification of immunoglobulin genes and the antibody repertoire

Immunoglobulins are encoded by a large multigene system that undergoes somatic rearrangement and additional genetic change during the development of immunoglobulin-producing cells. Inducible antibody and antibody-like responses are found in all vertebrates. However, immunoglobulin possessing disulfide-bonded heavy and light chains and domain-type organization has been described only in representatives of the jawed vertebrates. High degrees of nucleotide and predicted amino acid sequence identity are evident when the segmental elements that constitute the immunoglobulin gene loci in phylogenetically divergent vertebrates are compared. However, the organization of gene loci and the manner in which the independent elements recombine (and diversify) vary markedly among different taxa. One striking pattern of gene organization is the "cluster type" that appears to be restricted to the chondrichthyes (cartilaginous fishes) and limits segmental rearrangement to closely linked elements. This type of gene organization is associated with both heavy- and light-chain gene loci. In some cases, the clusters are "joined" or "partially joined" in the germ line, in effect predetermining or partially predetermining, respectively, the encoded specificities (the assumption being that these are expressed) of the individual loci. By relating the sequences of transcribed gene products to their respective germ-line genes, it is evident that, in some cases, joined-type genes are expressed. This raises a question about the existence and/or nature of allelic exclusion in these species. The extensive variation in gene organization found throughout the vertebrate species may relate directly to the role of intersegmental (V<==>D<==>J) distances in the commitment of the individual antibody-producing cell to a particular genetic specificity. Thus, the evolution of this locus, perhaps more so than that of others, may reflect the interrelationships between genetic organization and function.      

Dynamics of microsatellite divergence under stepwise mutation and proportional slippage/point mutation models

Recently Kruglyak, Durrett, Schug, and Aquadro showed that microsatellite equilibrium distributions can result from a balance between polymerase slippage and point mutations. Here, we introduce an elaboration of their model that keeps track of all parts of a perfect repeat and a simplification that ignores point mutations. We develop a detailed mathematical theory for these models that exhibits properties of microsatellite distributions, such as positive skewness of allele lengths, that are consistent with data but are inconsistent with the predictions of the stepwise mutation model. We use our theoretical results to analyze the successes and failures of the genetic distances (delta(mu))(2) and D(SW) when used to date four divergences: African vs. non-African human populations, humans vs. chimpanzees, Drosophila melanogaster vs. D. simulans, and sheep vs. cattle. The influence of point mutations explains some of the problems with the last two examples, as does the fact that these genetic distances have large stochastic variance. However, we find that these two features are not enough to explain the problems of dating the human-chimpanzee split. One possible explanation of this phenomenon is that long microsatellites have a mutational bias that favors contractions over expansions.     

Characterization of the Arabidopsis TU8 Glucosinolate Mutation,an Allele of TERMINAL FLOWER2

Glucosinolates are a group of defense-related secondary metabolites found in Arabidopsis and other cruciferous plants. Levels of leaf glucosinolates are regulated during plant development and increase in response to mechanical damage or insect feeding. The Arabidopsis TU8 mutant has a developmentally altered leaf glucosinolate profile: aliphatic glucosinolate levels drop off more rapidly, consistent with the early senescence of the mutant, and the levels of two indole glucosinolates are uniformly low. In TU8 seeds, four long-chain aliphatic glucosinolates have significantly increased levels, whereas the indolyl-3-methyl glucosinolate level is significantly reduced relative to wild type. Genetic mapping and DNA sequencing identified the TU8 mutation as tfl2-6, a new allele of TERMINAL FLOWER2 (TFL2), the only Arabidopsis homolog of animal HETEROCHROMATIN PROTEIN1 (HP1). TU8 (tfl2-6) has other previously identified tfl2 phenotypes, including an early transition to flowering, altered meristem structure, and stunted leaves. Analysis of two additional alleles, tfl2-1 and tfl2-2, showed glucosinolate profiles similar to those of line TU8 (tfl2-6).     

Dinucleotide repeats in the Drosophila and human genomes have complex,length-dependent mutation processes

We use methods of maximum likelihood estimation to fit several microsatellite mutation models to the observed length distribution of dinucletoide repeats in the Drosophila and human genomes. All simple models are rejected by this procedure. Two new models, one with quadratic and another with piecewise linear slippage rates, have the best fits and agree with recent experimental studies by predicting that long microsatellites have a bias toward contractions.     

Selective mapping: a strategy for optimizing the construction of high-density linkage maps

Historically, linkage mapping populations have consisted of large, randomly selected samples of progeny from a given pedigree or cell lines from a panel of radiation hybrids. We demonstrate that, to construct a map with high genome-wide marker density, it is neither necessary nor desirable to genotype all markers in every individual of a large mapping population. Instead, a reduced sample of individuals bearing complementary recombinational or radiation-induced breakpoints may be selected for genotyping subsequent markers from a large, but sparsely genotyped, mapping population. Choosing such a sample can be reduced to a discrete stochastic optimization problem for which the goal is a sample with breakpoints spaced evenly throughout the genome. We have developed several different methods for selecting such samples and have evaluated their performance on simulated and actual mapping populations, including the Lister and Dean Arabidopsis thaliana recombinant inbred population and the GeneBridge 4 human radiation hybrid panel. Our methods quickly and consistently find much-reduced samples with map resolution approaching that of the larger populations from which they are derived. This approach, which we have termed selective mapping, can facilitate the production of high-quality, high-density genome-wide linkage maps.     

Above- and below-ground impacts of introduced predators in seabird-dominated island ecosystems

Predators often exert multi-trophic cascading effects in terrestrial ecosystems. However, how such predation may indirectly impact interactions between above- and below-ground biota is poorly understood, despite the functional importance of these interactions. Comparison of rat-free and rat-invaded offshore islands in New Zealand revealed that predation of seabirds by introduced rats reduced forest soil fertility by disrupting sea-to-land nutrient transport by seabirds, and that fertility reduction in turn led to wide-ranging cascading effects on belowground organisms and the ecosystem processes they drive. Our data further suggest that some effects on the belowground food web were attributable to changes in aboveground plant nutrients and biomass, which were themselves related to reduced soil disturbance and fertility on invaded islands. These results demonstrate that, by disrupting across-ecosystem nutrient subsidies, predators can indirectly induce strong shifts in both above- and below-ground biota via multiple pathways, and in doing so, act as major ecosystem drivers.     

Plant triacylglycerols as feedstocks for the production of biofuels

Triacylglycerols produced by plants are one of the most energy-rich and abundant forms of reduced carbon available from nature. Given their chemical similarities, plant oils represent a logical substitute for conventional diesel, a non-renewable energy source. However, as plant oils are too viscous for use in modern diesel engines, they are converted to fatty acid esters. The resulting fuel is commonly referred to as biodiesel, and offers many advantages over conventional diesel. Chief among these is that biodiesel is derived from renewable sources. In addition, the production and subsequent consumption of biodiesel results in less greenhouse gas emission compared to conventional diesel. However, the widespread adoption of biodiesel faces a number of challenges. The biggest of these is a limited supply of biodiesel feedstocks. Thus, plant oil production needs to be greatly increased for biodiesel to replace a major proportion of the current and future fuel needs of the world. An increased understanding of how plants synthesize fatty acids and triacylglycerols will ultimately allow the development of novel energy crops. For example, knowledge of the regulation of oil synthesis has suggested ways to produce triacylglycerols in abundant non-seed tissues. Additionally, biodiesel has poor cold-temperature performance and low oxidative stability. Improving the fuel characteristics of biodiesel can be achieved by altering the fatty acid composition. In this regard, the generation of transgenic soybean lines with high oleic acid content represents one way in which plant biotechnology has already contributed to the improvement of biodiesel.     

Direct and indirect effects of rats: does rat eradication restore ecosystem functioning of New Zealand seabird islands?

Introduced rats (Rattus spp.) can affect island vegetation structure and ecosystem functioning, both directly and indirectly (through the reduction of seabird populations). The extent to which structure and function of islands where rats have been eradicated will converge on uninvaded islands remains unclear. We compared three groups of islands in New Zealand: islands never invaded by rats, islands with rats, and islands on which rats have been controlled. Differences between island groups in soil and leaf chemistry and leaf production were largely explained by burrow densities. Community structure of woody seedlings differed by rat history and burrow density. Plots on islands with high seabird densities had the most non-native plant species. Since most impacts of rats were mediated through seabird density, the removal of rats without seabird recolonization is unlikely to result in a reversal of these processes. Even if seabirds return, a novel plant community may emerge.