Daniel Barker

What do we need to know about speciation

Speciation has been a major focus of evolutionary biology research in recent years, with many important advances. However, some of the traditional organising principles of the subject area no longer provide a satisfactory framework, such as the classification of speciation mechanisms by geographical context into allopatric, parapatric and sympatry classes. Therefore, we have asked where speciation research should be directed in the coming years. Here, we present a distillation of questions about the mechanisms of speciation, the genetic basis of speciation and the relationship between speciation and diversity. Our list of topics is not exhaustive; rather we aim to promote discussion on research priorities and on the common themes that underlie disparate speciation processes.

Drosophila chemoreceptor gene evolution: selection, specialization and genome size

Chemoperception plays a key role in adaptation and speciation in animals, and the senses of olfaction and gustation are mediated by gene families which show large variation in repertoire size among species. In Drosophila, there are around 60 loci of each type and it is thought that ecological specialization influences repertoire size, with increased pseudogenization of loci. Here, we analyse the size of the gustatory and olfactory repertoires among the genomes of 12 species of Drosophila. We find that repertoire size varies substantially and the loci are evolving by duplication and pseudogenization, with striking examples of lineage‐specific duplication. Selection analyses imply that the majority of loci are subject to purifying selection, but this is less strong in gustatory loci and in loci prone to duplication. In contrast to some other studies, we find that few loci show statistically significant evidence of positive selection. Overall genome size is strongly correlated with the proportion of duplicated chemoreceptor loci, but genome size, specialization and endemism may be interrelated in their influence on repertoire size.

Evolutionary History of Vegetative Reproduction in Porpidia s.l. (Lichen-Forming Ascomycota)

The evolutionary history of gains and losses of vegetative reproductive propagules (soredia) in Porpidia s.l., a group of lichen-forming ascomycetes, was clarified using Bayesian Markov chain Monte Carlo (MCMC) approaches to monophyly tests and a combined MCMC and maximum likelihood approach to ancestral character state reconstructions. The MCMC framework provided confidence estimates for the reconstructions of relationships and ancestral character states, which formed the basis for tests of evolutionary hypotheses. Monophyly tests rejected all hypotheses that predicted any clustering of reproductive modes in extant taxa. In addition, a nearest-neighbor statistic could not reject the hypothesis that the vegetative reproductive mode is randomly distributed throughout the group. These results show that transitions between presence and absence of the vegetative reproductive mode within Porpidia s.l. occurred several times and independently of each other. Likelihood reconstructions of ancestral character states at selected nodes suggest that--contrary to previous thought--the ancestor to Porpidia s.l. already possessed the vegetative reproductive mode. Furthermore, transition rates are reconstructed asymmetrically with the vegetative reproductive mode being gained at a much lower rate than it is lost. A cautious note has to be added, because a simulation study showed that the ancestral character state reconstructions were highly dependent on taxon sampling. However, our central conclusions, particularly the higher rate of change from vegetative reproductive mode present to absent than vice versa within Porpidia s.l., were found to be broadly independent of taxon sampling.

The evolution of nitrogen fixation in cyanobacteria

MOTIVATION Fixed nitrogen is an essential requirement for the biosynthesis of cellular nitrogenous compounds. Some cyanobacteria can fix nitrogen, contributing significantly to the nitrogen cycle, agriculture and biogeochemical history of Earth. The rate and position on the species phylogeny of gains and losses of this ability, as well as of the underlying nif genes, are controversial. RESULTS We use probabilistic models of trait evolution to investigate the presence and absence of cyanobacterial nitrogen-fixing ability. We estimate rates of change on the species phylogeny, pinpoint probable changes and reconstruct the state and nif gene complement of the ancestor. Our results are consistent with a nitrogen-fixing cyanobacterial ancestor, repeated loss of nitrogen fixation and vertical descent, with little horizontal transfer of the genes involved. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

Maximum soil organic carbon storage in Midwest U.S. cropping systems when crops are optimally nitrogen-fertilized

Nitrogen fertilization is critical to optimize short-term crop yield, but its long-term effect on soil organic C (SOC) is uncertain. Here, we clarify the impact of N fertilization on SOC in typical maize-based (Zea mays L.) Midwest U.S. cropping systems by accounting for site-to-site variability in maize yield response to N fertilization. Within continuous maize and maize-soybean [Glycine max (L.) Merr.] systems at four Iowa locations, we evaluated changes in surface SOC over 14 to 16 years across a range of N fertilizer rates empirically determined to be insufficient, optimum, or excessive for maximum maize yield. Soil organic C balances were negative where no N was applied but neutral (maize-soybean) or positive (continuous maize) at the agronomic optimum N rate (AONR). For continuous maize, the rate of SOC storage increased with increasing N rate, reaching a maximum at the AONR and decreasing above the AONR. Greater SOC storage in the optimally fertilized continuous maize system than in the optimally fertilized maize-soybean system was attributed to greater crop residue production and greater SOC storage efficiency in the continuous maize system. Mean annual crop residue production at the AONR was 22% greater in the continuous maize system than in the maize-soybean system and the rate of SOC storage per unit residue C input was 58% greater in the monocrop system. Our results demonstrate that agronomic optimum N fertilization is critical to maintain or increase SOC of Midwest U.S. cropland.

Signatures of selection and sex‐specific expression variation of a novel duplicate during the evolution of the Drosophila desaturase gene family

The tempo and mode of evolution of loci with a large effect on adaptation and reproductive isolation will influence the rate of evolutionary divergence and speciation. Desaturase loci are involved in key biochemical changes in long‐chain fatty acids. In insects, these have been shown to influence adaptation to starvation or desiccation resistance and in some cases act as important pheromones. The desaturase gene family of Drosophila is known to have evolved by gene duplication and diversification, and at least one locus shows rapid evolution of sex‐specific expression variation. Here, we examine the evolution of the gene family in species representing the Drosophila phylogeny. We find that the family includes more loci than have been previously described. Most are represented as single‐copy loci, but we also find additional examples of duplications in loci which influence pheromone blends. Most loci show patterns of variation associated with purifying selection, but there are strong signatures of diversifying selection in new duplicates. In the case of a new duplicate of desat1 in the obscura group species, we show that strong selection on the coding sequence is associated with the evolution of sex‐specific expression variation. It seems likely that both sexual selection and ecological adaptation have influenced the evolution of this gene family in Drosophila.

Evolution of a complex locus : exon gain, loss and divergence at the Gr39a locus in Drosophila

Background Gene families typically evolve by gene duplication followed by the adoption of new or altered gene functions. A different way to evolve new but related functions is alternative splicing of existing exons of a complex gene. The chemosensory gene families of animals are characterised by numerous loci of related function. Alternative splicing has only rarely been reported in chemosensory loci, for example in 5 out of around 120 loci in Drosophila melanogaster. The gustatory receptor gene Gr39a has four large exons that are alternatively spliced with three small conserved exons. Recently the genome sequences of eleven additional species of Drosophila have become available allowing us to examine variation in the structure of the Gr39a locus across a wide phylogenetic range of fly species. Methodology/Principal Findings We describe a fifth exon and show that the locus has a complex evolutionary history with several duplications, pseudogenisations and losses of exons. PAML analyses suggested that the whole gene has a history of purifying selection, although this was less strong in exons which underwent duplication. Conclusions/Significance Estimates of functional divergence between exons were similar in magnitude to functional divergence between duplicated genes, suggesting that exon divergence is broadly equivalent to gene duplication.

4273π: Bioinformatics education on low cost ARM hardware

BackgroundTeaching bioinformatics at universities is complicated by typical computer classroom settings. As well as running software locally and online, students should gain experience of systems administration. For a future career in biology or bioinformatics, the installation of software is a useful skill. We propose that this may be taught by running the course on GNU/Linux running on inexpensive Raspberry Pi computer hardware, for which students may be granted full administrator access.ResultsWe release 4273π, an operating system image for Raspberry Pi based on Raspbian Linux. This includes minor customisations for classroom use and includes our Open Access bioinformatics course, 4273π Bioinformatics for Biologists. This is based on the final-year undergraduate module BL4273, run on Raspberry Pi computers at the University of St Andrews, Semester 1, academic year 2012-2013.Conclusions4273π is a means to teach bioinformatics, including systems administration tasks, to undergraduates at low cost.

Response to Comments on "On the Regulation of Populations of Mammals, Birds, Fish, and Insects"

The technical comments by Getz and Lloyd-Smith, Ross, and Doncaster focus on specific aspects of our analysis and estimation and do not demonstrate any results opposing our key conclusion—that, contrary to what was previously believed, the relation between a populations growth rate (pgr) and its density is generally concave.

Models incorporating chromatin modification data identify functionally important p53 binding sites

Genome-wide prediction of transcription factor binding sites is notoriously difficult. We have developed and applied a logistic regression approach for prediction of binding sites for the p53 transcription factor that incorporates sequence information and chromatin modification data. We tested this by comparison of predicted sites with known binding sites defined by chromatin immunoprecipitation (ChIP), by the location of predictions relative to genes, by the function of nearby genes and by analysis of gene expression data after p53 activation. We compared the predictions made by our novel model with predictions based only on matches to a sequence position weight matrix (PWM). In whole genome assays, the fraction of known sites identified by the two models was similar, suggesting that there was little to be gained from including chromatin modification data. In contrast, there were highly significant and biologically relevant differences between the two models in the location of the predicted binding sites relative to genes, in the function of nearby genes and in the responsiveness of nearby genes to p53 activation. We propose that these contradictory results can be explained by PWM and ChIP data reflecting primarily biophysical properties of protein–DNA interactions, whereas chromatin modification data capture biologically important functional information.