SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization

Many tumors are composed of genetically divergent cell subpopulations. We report SubcloneSeeker, a package capable of exhaustive identification of subclone structures and evolutionary histories with bulk somatic variant allele frequency measurements from tumor biopsies. We present a statistical framework to elucidate whether specific sets of mutations are present within the same subclones, and the order in which they occur. We demonstrate how subclone reconstruction provides crucial information about tumorigenesis and relapse mechanisms; guides functional study by variant prioritization, and has the potential as a rational basis for informed therapeutic strategies for the patient. SubcloneSeeker is available at: https://github.com/yiq/SubcloneSeeker.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0443-x) contains supplementary material, which is available to authorized users.     

HeatMapper: powerful combined visualization of gene expression profile correlations, genotypes, phenotypes and sample characteristics

Background  

Accurate interpretation of data obtained by unsupervised analysis of large scale expression profiling studies is currently frequently performed by visually combining sample-gene heatmaps and sample characteristics. This method is not optimal for comparing individual samples or groups of samples. Here, we describe an approach to visually integrate the results of unsupervised and supervised cluster analysis using a correlation plot and additional sample metadata.     

Family-Level Divergences in the Stinging Wasps (Hymenoptera: Aculeata), with Correlations to Angiosperm Diversification

Diversification in insects has often been linked to the evolution of angiosperms. The majority of studies reporting this link, however, have been done on herbivorous insects. It remains unclear if the diversification of angiosperms was also influential in the diversification of species-rich, carnivorous insect groups. Here we investigate the timing of the origin and diversification in the stinging wasps (Hymenoptera: Aculeata). We employ a Bayesian Markov chain Monte Carlo relaxed clock approach to estimate divergence times for 13 wasp families and eight superfamilies. Divergence times are calibrated with 12 fossils representing groups in various lineages. Our results indicate that many of the modern aculeate families originated during the Cretaceous and in concert with the diversification of angiosperms. This similarity between diversification ages in wasps and in angiosperms may be due to an increased habitat complexity and prey diversity that early angiosperm forests provided.     

Species with more volatile population dynamics are differentially impacted by weather

Climatic variation has been invoked as an explanation of population dynamics for a variety of taxa. Much work investigating the link between climatic forcings and population fluctuation uses single-taxon case studies. Here, we conduct comparative analyses of a multi-decadal dataset describing population dynamics of 50 co-occurring butterfly species at 10 sites in Northern California. Specifically, we explore the potential commonality of response to weather among species that encompass a gradient of population dynamics via a hierarchical Bayesian modelling framework. Results of this analysis demonstrate that certain weather conditions impact volatile, or irruptive, species differently as compared with relatively stable species. Notably, precipitation-related variables, including indices of the El Niño Southern Oscillation, have a more pronounced impact on the most volatile species. We hypothesize that these variables influence vegetation resource availability, and thus indirectly influence population dynamics of volatile taxa. As one of the first studies to show a common influence of weather among taxa with similar population dynamics, the results presented here suggest new lines of research in the field of biotic–abiotic interactions.     

The significance of wing pattern diversity in the Lycaenidae: mate discrimination by two recently diverged species

Closely related species of lycaenid butterflies are determinable, in part, by subtle differences in wing pattern. We found that female wing patterns can act as an effective mate‐recognition signal in some populations of two recently diverged species. In field experiments, we observed that males from a Lycaeides idas population and an alpine population of L. melissa preferentially initiate courtship with conspecific females. A morphometric study indicated that at least two wing pattern elements were important for distinguishing the two species: hindwing spots and orange crescent‐shaped pattern elements called aurorae. We deceived male L. idas into initiating courtship with computer generated paper models of heterospecific females when these pattern elements were manipulated, indicating that the wing pattern elements that define the diversity of this group can be effective mate recognition signals.     

HYBRID SPECIATION AND INDEPENDENT EVOLUTION IN LINEAGES OF ALPINE BUTTERFLIES

The power of hybridization between species to generate variation and fuel adaptation is poorly understood despite long‐standing interest. There is, however, increasing evidence that hybridization often generates biodiversity, including via hybrid speciation. We tested the hypothesis of hybrid speciation in butterflies occupying extreme, high‐altitude habitats in four mountain ranges in western North America with an explicit, probabilistic model, and genome‐wide DNA sequence data. Using this approach, in concert with ecological experiments and observations and morphological data, we document three lineages of hybrid origin. These lineages have different genome admixture proportions and distinctive trait combinations that suggest unique and independent evolutionary histories.     

A nonlinear relationship between genetic diversity and productivity in a polyphagous seed beetle

There has been a renewed interest in the effects of genetic diversity on population-level and community-level processes. Many of these studies have found non-additive, positive effects of diversity, but these studies have rarely examined ecological mechanisms by which diverse populations increase productivity. We used the seed beetle Callosobruchus maculatus (Coleoptera: Chrysomelidae) to study genetic diversity in insect host preference and fecundity and its effects on total productivity and resource use. We created genetically distinct lineages that varied in host preference and fecundity and then assembled groups consisting of one, three, five, or all ten lineages. We found that lineages with intermediate diversity had the highest productivity, though resource use did not change in diverse groups. In addition, lineages showed substantial plasticity in host preference when preference was assayed either individually or in groups, and productivity was much lower in groups than predicted by individual assays. These results highlight the interplay of genetic diversity, resource variation, and phenotypic plasticity in determining the ecological consequences of genetic diversity. In addition, when plasticity modifies a population’s response to population density, this may create a complex interaction between genetic diversity and density, influencing selective pressures on the population and potentially maintaining genetic diversity across generations.