Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

Biological stoichiometry provides a mechanistic theory linking cellular and biochemical features of co‐evolving biota with constraints imposed by ecosystem energy and nutrient inputs. Thus, understanding variation in biomass carbon : nitrogen : phosphorus (C : N : P) stoichiometry is a major priority for integrative biology. Among various factors affecting organism stoichiometry, differences in C : P and N : P stoichiometry have been hypothesized to reflect organismal P‐content because of altered allocation to P‐rich ribosomal RNA at different growth rates (the growth rate hypothesis, GRH). We tested the GRH using data for microbes, insects, and crustaceans and we show here that growth, RNA content, and biomass P content are tightly coupled across species, during ontogeny, and under physiological P limitation. We also show, however, that this coupling is relaxed when P is not limiting for growth. The close relationship between P and RNA contents indicates that ribosomes themselves represent a biogeochemically significant repository of P in ecosystems and that allocation of P to ribosome generation is a central process in biological production in ecological systems.

Ecological stoichiometry is the study of the balance of multiple chemical elements in ecological interactions. This paper reviews recent findings in this area and seeks to broaden the stoichiometric concept for use in evolutionary studies, in integrating ecological dynamics with cellular and genetic mechanisms, and in developing a unified means for studying diverse organisms in diverse habitats. This broader approach would then be considered``biological stoichiometry''. Evidence supporting a hypothesised connection between the C:N:P stoichiometry of an organism and its growth rate (the``growth rate hypothesis'') is reviewed. Various data indicate that rapidly growing organisms commonly have low biomass C:P and N:P ratios. Evidence is then discussed suggesting that low C:P and N:P ratios in rapidly growing organisms reflect increased allocation to P-rich ribosomal RNA (rRNA), as rapid protein synthesis by ribosomes is required to support fast growth. Indeed, diverse organisms (bacteria, copepods, fishes, others) exhibit increased RNA levels when growing actively. This implies that evolutionary processes that generate, directly or indirectly, variation in a major life history trait (specific growth rate) have consequences for ecological dynamics due to their effects on organismal elemental composition. Genetic mechanisms by which organisms generate high RNA, high growth rate phenotypes are discussed next, focusing on the structure and organisation of the ribosomal RNA genes (the``rDNA''). In particular, published studies of a variety of taxa suggest an association between growth rate and variation in the length and content of the intergenic spacer (IGS) region of the rDNA tandem repeat unit. In particular, under conditions favouring increased growth or yield, the number of repeat units (``enhancers'') increases (and the IGS increases in length), and transcription rates of rRNA increase. In addition, there is evidence in the literature that increased numbers of copies of rDNA genes are associated with increased growth and production. Thus, a combination of genetic mechanisms may be responsible for establishing the growth potential, and thus the RNA allocation and C:N:P composition, of an organism. Furthermore, various processes, during both sexual and asexual reproduction, can generate variation in the rDNA to provide the raw material for selection and to generate ecologically significant variation in C:N:P stoichiometry. This leads us to hypothesize that the continuous generation of such variation may also play a role in how species interactions develop in ecosystems under different conditions of energy input and nutrient supply.