BreakTrans: uncovering the genomic architecture of gene fusions

Producing gene fusions through genomic structural rearrangements is a major mechanism for tumor evolution. Therefore, accurately detecting gene fusions and the originating rearrangements is of great importance for personalized cancer diagnosis and targeted therapy. We present a tool, BreakTrans, that systematically maps predicted gene fusions to structural rearrangements. Thus, BreakTrans not only validates both types of predictions, but also provides mechanistic interpretations. BreakTrans effectively validates known fusions and discovers novel events in a breast cancer cell line. Applying BreakTrans to 43 breast cancer samples in The Cancer Genome Atlas identifies 90 genomically validated gene fusions. BreakTrans is available at http://bioinformatics.mdanderson.org/main/BreakTrans     

The role of nuclear architecture in genomic instability and ageing

Eukaryotes come in many shapes and sizes, yet one thing that they all seem to share is a decline in vitality and health over time--a process known as ageing. If there are conserved causes of ageing, they may be traced back to common biological structures that are inherently difficult to maintain throughout life. One such structure is chromatin, the DNA-protein complex that stabilizes the genome and dictates gene expression. Studies in the budding yeast Saccharomyces cerevisiae have pointed to chromatin reorganization as a main contributor to ageing in that species, which raises the possibility that similar processes underlie ageing in more complex organisms.     

The genetic architecture of domestication in the chicken: effects of pleiotropy and linkage

The extent of pleiotropy and epistasis in quantitative traits remains equivocal. In the case of pleiotropy, multiple quantitative trait loci are often taken to be pleiotropic if their confidence intervals overlap, without formal statistical tests being used to ascertain if these overlapping loci are statistically significantly pleiotropic. Additionally, the degree to which the genetic correlations between phenotypic traits are reflected in these pleiotropic quantitative trait loci is often variable, especially in the case of antagonistic pleiotropy. Similarly, the extent of epistasis in various morphological, behavioural and life-history traits is also debated, with a general problem being the sample sizes required to detect such effects. Domestication involves a large number of trade-offs, which are reflected in numerous behavioural, morphological and life-history traits which have evolved as a consequence of adaptation to selective pressures exerted by humans and captivity. The comparison between wild and domestic animals allows the genetic analysis of the traits that differ between these population types, as well as being a general model of evolution. Using a large F(2) intercross between wild and domesticated chickens, in combination with a dense SNP and microsatellite marker map, both pleiotropy and epistasis were analysed. The majority of traits were found to segregate in 11 tight 'blocks' and reflected the trade-offs associated with domestication. These blocks were shown to have a pleiotropic 'core' surrounded by more loosely linked loci. In contrast, epistatic interactions were almost entirely absent, with only six pairs identified over all traits analysed. These results give insights both into the extent of such blocks in evolution and the development of domestication itself.     

The role of pleiotropy in the maintenance of sex in yeast

In facultatively sexual species, lineages that reproduce asexually for a period of time can accumulate mutations that reduce their ability to undergo sexual reproduction when sex is favorable. We propagated Saccharomyces cerevisiae asexually for approximately 800 generations, after which we measured the change in sexual fitness, measured as the proportion of asci observed in sporulation medium. The sporulation rate in cultures propagated asexually at small population size declined by 8%, on average, over this time period, indicating that the majority of mutations that affect sporulation rate are deleterious. Interestingly, the sporulation rate in cultures propagated asexually at large population size improved by 11%, on average, indicating that selection on asexual function effectively eliminated most of the mutations deleterious to sporulation ability. These results suggest that pleiotropy between mutations' effects on asexual fitness and sexual fitness was predominantly positive, at least for the mutations accumulated in this experimental evolution study. A positive correlation between growth rate and sporulation rate among lines also provided evidence for positive pleiotropy. These results demonstrate that, at least under certain circumstances, selection acting on asexual fitness can help to maintain sexual function.     

The quantitative genetics of two life history trade-offs in the yellow dung fly in abundant and limited food environments

The trade-offs between body size and development time and between egg size and egg number (clutch size) are central to life history theory, but evidence for them, particularly in terms of genetic correlations, is equivocal. For the yellow dung fly Scathophaga stercoraria (Diptera: Scathophagidae), we investigated variation in phenotypic and genetic variances and covariances, i.e. heritabilities and genetic correlations, of these life history traits (plus diapause) in benign and stressful larval field or adult laboratory food environments. We found both trade-offs to be weak, as evidenced by low phenotypic and genetic correlations, but stronger in the food limited environments. Broad sense heritabilities were generally significant for all traits considered, whereas the narrow sense heritabilities for egg and clutch size were nil. With regard to the question of how environmental stress affects heritabilities, we found a whole range of responses within one single species depending on the traits considered. All three possible patterns occurred, i.e. increased h² due to increased V_G or decreased decreased h² due to increased and no change in h² due to increased V_G and V_P. These can be explained by the particular ecological circumstances yellow dung flies face in their natural environment. Nevertheless, the majority of patterns was consistent with the idea that stressful conditions amplify phenotypic differences between genotypes. Such variable responses of traits even within one organism underscores the complexity of this issue and may well explain the multiple patterns found in various organisms.Co-ordinating editor: Leimar     

The genomic and physiological basis of life history variation in a butterfly metapopulation

Unravelling the mechanisms underlying variation in life history traits is of fundamental importance for our understanding of adaptation by natural selection. While progress has been made in mapping fitness-related phenotypes to genotypes, mainly in a handful of model organisms, functional genomic studies of life history adaptations are still in their infancy. In particular, despite a few notable exceptions, the genomic basis of life history variation in natural populations remains poorly understood. This is especially true for the genetic underpinnings of life history phenotypes subject to diversifying selection driven by ecological dynamics in patchy environments--as opposed to adaptations involving strong directional selection owing to major environmental changes, such as latitudinal gradients, extreme climatic events or transitions from salt to freshwater. In this issue of Molecular Ecology,Wheat et al. (2011) now make a significant leap forward by applying the tools of functional genomics to dispersal-related life history variation in a butterfly metapopulation. Using a combination of microarrays, quantitative PCR and physiological measurements, the authors uncover several metabolic and endocrine factors that likely contribute to the observed life history phenotypes. By identifying molecular candidate mechanisms of fitness variation maintained by dispersal dynamics in a heterogeneous environment,they also begin to address fascinating interactions between the levels of physiology, ecology and evolution.     

The role of epistasis in the manifestation of heterosis: a systems-oriented approach

Heterosis is widely used in breeding, but the genetic basis of this biological phenomenon has not been elucidated. We postulate that additive and dominance genetic effects as well as two-locus interactions estimated in classical QTL analyses are not sufficient for quantifying the contributions of QTL to heterosis. A general theoretical framework for determining the contributions of different types of genetic effects to heterosis was developed. Additive x additive epistatic interactions of individual loci with the entire genetic background were identified as a major component of midparent heterosis. On the basis of these findings we defined a new type of heterotic effect denoted as augmented dominance effect di* that comprises the dominance effect at each QTL minus half the sum of additive x additive interactions with all other QTL. We demonstrate that genotypic expectations of QTL effects obtained from analyses with the design III using testcrosses of recombinant inbred lines and composite-interval mapping precisely equal genotypic expectations of midparent heterosis, thus identifying genomic regions relevant for expression of heterosis. The theory for QTL mapping of multiple traits is extended to the simultaneous mapping of newly defined genetic effects to improve the power of QTL detection and distinguish between dominance and overdominance.     

Adaptive dynamics of Lotka-Volterra systems with trade-offs: the role of interspecific parameter dependence in branching

We determine the adaptive dynamics of a general Lotka-Volterra system containing an intraspecific parameter dependency--in the form of an explicit functional trade-off between evolving parameters--and interspecific parameter dependencies--arising from modelling species interactions. We develop expressions for the fitness of a mutant strategy in a multi-species resident environment, the position of the singular strategy in such systems and the non-mixed second-order partial derivatives of the mutant fitness. These expressions can be used to determine the evolutionary behaviour of the system. The type of behaviour expected depends on the curvature of the trade-off function and can be interpreted in a biologically intuitive manner using the rate of acceleration/deceleration of the costs implicit in the trade-off function. We show that for evolutionary branching to occur we require that one (or both) of the traded-off parameters includes an interspecific parameter dependency and that the trade-off function has weakly accelerating costs. This could have important implications for understanding the type of mechanisms that cause speciation. The general theory is motivated by using adaptive dynamics to examine evolution in a predator-prey system. The applicability of the general theory as a tool for examining specific systems is highlighted by calculating the evolutionary behaviour in a three species (prey-predator-predator) system.     

Dietary effects on life history traits in a terrestrial isopod: the importance of evaluating maternal effects and trade-offs

Studies of life history aim to explain patterns in the evolution of reproductive investment, growth, and survival. Trade-offs between traits are a fundamental component of life history theory. In herbivorous arthropods life history traits are often responsive to variation in numerous environmental factors, especially diet quality. Using three artificial diets under controlled laboratory conditions, we examined changes in life history traits (i.e. growth rate, offspring number, offspring size, incubation period), trade-offs between traits, and maternal effect on the growth rate of offspring, in the common woodlouse (terrestrial isopod), Porcellio laevis. The high protein diet had significant impacts on offspring production, triggering a smaller-sized offspring, and demonstrating a trade-off between these last two traits. The high carbohydrate diet seldom exerted a significant effect on incubation period. The quality of dietary items evidently has important consequences on the life history of the mother and, thus, on offspring growth; the directions of these effects, however, were opposite. Mothers fed diets with high protein concentrations presented significant maternal effects, measured as offspring growth rate during later ontogeny. Our results support the notion that protein, rather than carbohydrate, concentrations in the diet limit herbivorous arthropods, and have significant consequences on life history traits, as was seen for P. laevis. Clearly, the change in phenotypic correlations between incubation period and offspring number from negative to positive is an empirical demonstration of the context dependence of life history trait trade-offs.     

Assessing the role of tandem repeats in shaping the genomic architecture of great apes

Background

Ancestral reconstructions of mammalian genomes have revealed that evolutionary breakpoint regions are clustered in regions that are more prone to break and reorganize. What is still unclear to evolutionary biologists is whether these regions are physically unstable due solely to sequence composition and/or genome organization, or do they represent genomic areas where the selection against breakpoints is minimal.

Methodology and Principal Findings

Here we present a comprehensive study of the distribution of tandem repeats in great apes. We analyzed the distribution of tandem repeats in relation to the localization of evolutionary breakpoint regions in the human, chimpanzee, orangutan and macaque genomes. We observed an accumulation of tandem repeats in the genomic regions implicated in chromosomal reorganizations. In the case of the human genome our analyses revealed that evolutionary breakpoint regions contained more base pairs implicated in tandem repeats compared to synteny blocks, being the AAAT motif the most frequently involved in evolutionary regions. We found that those AAAT repeats located in evolutionary regions were preferentially associated with Alu elements.

Significance

Our observations provide evidence for the role of tandem repeats in shaping mammalian genome architecture. We hypothesize that an accumulation of specific tandem repeats in evolutionary regions can promote genome instability by altering the state of the chromatin conformation or by promoting the insertion of transposable elements.     

The role of population size, pleiotropy and fitness effects of mutations in the evolution of overlapping gene functions

Sheltered from deleterious mutations, genes with overlapping or partially redundant functions may be important sources of novel gene functions. While most partially redundant genes originated in gene duplications, it is much less clear why genes with overlapping functions have been retained, in some cases for hundreds of millions of years. A case in point is the many partially redundant genes in vertebrates, the result of ancient gene duplications in primitive chordates. Their persistence and ubiquity become surprising when it is considered that duplicate and original genes often diversify very rapidly, especially if the action of natural selection is involved. Are overlapping gene functions perhaps maintained because of their protective role against otherwise deleterious mutations? There are two principal objections against this hypothesis, which are the main subject of this article. First, because overlapping gene functions are maintained in populations by a slow process of "second order" selection, population sizes need to be very high for this process to be effective. It is shown that even in small populations, pleiotropic mutations that affect more than one of a gene''s functions simultaneously can slow the mutational decay of functional overlap after a gene duplication by orders of magnitude. Furthermore, brief and transient increases in population size may be sufficient to maintain functional overlap. The second objection regards the fact that most naturally occurring mutations may have much weaker fitness effects than the rather drastic "knock-out" mutations that lead to detection of partially redundant functions. Given weak fitness effects of most mutations, is selection for the buffering effect of functional overlap strong enough to compensate for the diversifying force exerted by mutations? It is shown that the extent of functional overlap maintained in a population is not only independent of the mutation rate, but also independent of the average fitness effects of mutation. These results are discussed with respect to experimental evidence on redundant genes in organismal development.     

The role of epistasis on the evolution of recombination in host-parasite coevolution

Antagonistic coevolution between hosts and parasites is known to affect selection on recombination in hosts. The Red Queen Hypothesis (RQH) posits that genetic shuffling is beneficial for hosts because it quickly creates resistant genotypes. Indeed, a large body of theoretical studies have shown that for many models of the genetic interaction between host and parasite, the coevolutionary dynamics of hosts and parasites generate selection for recombination or sexual reproduction. Here we investigate models in which the effect of the host on the parasite (and vice versa) depend approximately multiplicatively on the number of matched alleles. Contrary to expectation, these models generate a dynamical behavior that strongly selects against recombination/sex. We investigate this atypical behavior analytically and numerically. Specifically we show that two complementary equilibria are responsible for generating strong linkage disequilibria of opposite sign, which in turn causes strong selection against sex. The biological relevance of this finding stems from the fact that these phenomena can also be observed if hosts are attacked by two parasites that affect host fitness independently. Hence the role of the Red Queen Hypothesis in natural host parasite systems where infection by multiple parasites is the rule rather than the exception needs to be reevaluated.     

The role of life history and behavior in explaining unionid mussel distributions

The São Paulo shelf ranges from ~23°S to 25°S, comprising nearly 622 km of shoreline. This region sustains historical landings of the tropical arrow squid Doryteuthis plei. As in other coleoid cephalopods, the broodstock dies following spawning and the continuance of the population relies exclusively upon the survival of the paralarvae, which are very sensitive to oceanographic conditions. As a first step towards the understanding of paralarval transport, the shelf area was evaluated in terms of retention/dispersion potential. A Lagrangian particle-tracking Individual-Based Model was set up using a 3D Princeton Ocean Model model forced with in situ data obtained from July 2009 to July 2011. Neutrally buoyant particles were released every first day of every month in the model, and tracked for 30 days. The retention potential was high for particles released from the bottom all over the study area from the coast to the shelf break (200 m isobath). Offshore losses showed a marked seasonality. Regarding inshore losses, the percentage of particles beached was constant year round and smaller than offshore losses, being higher south of 24°S. Simulation results seem to agree with present knowledge of the reproductive behaviour of the species in the region.     

From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria

The rapid increase in published genomic sequences for bacteria presents the first opportunity to reconstruct evolutionary events on the scale of entire genomes. However, extensive lateral gene transfer (LGT) may thwart this goal by preventing the establishment of organismal relationships based on individual gene phylogenies. The group for which cases of LGT are most frequently documented and for which the greatest density of complete genome sequences is available is the gamma-Proteobacteria, an ecologically diverse and ancient group including free-living species as well as pathogens and intracellular symbionts of plants and animals. We propose an approach to multigene phylogeny using complete genomes and apply it to the case of the gamma-Proteobacteria. We first applied stringent criteria to identify a set of likely gene orthologs and then tested the compatibilities of the resulting protein alignments with several phylogenetic hypotheses. Our results demonstrate phylogenetic concordance among virtually all (203 of 205) of the selected gene families, with each of the exceptions consistent with a single LGT event. The concatenated sequences of the concordant families yield a fully resolved phylogeny. This topology also received strong support in analyses aimed at excluding effects of heterogeneity in nucleotide base composition across lineages. Our analysis indicates that single-copy orthologous genes are resistant to horizontal transfer, even in ancient bacterial groups subject to high rates of LGT. This gene set can be identified and used to yield robust hypotheses for organismal phylogenies, thus establishing a foundation for reconstructing the evolutionary transitions, such as gene transfer, that underlie diversity in genome content and organization.     

Deriving the genomic tree of life in the presence of horizontal gene transfer: conditioned reconstruction

The horizontal gene transfer (HGT) being inferred within prokaryotic genomes appears to be sufficiently massive that many scientists think it may have effectively obscured much of the history of life recorded in DNA. Here, we demonstrate that the tree of life can be reconstructed even in the presence of extensive HGT, provided the processes of genome evolution are properly modeled. We show that the dynamic deletions and insertions of genes that occur during genome evolution, including those introduced by HGT, may be modeled using techniques similar to those used to model nucleotide substitutions that occur during sequence evolution. In particular, we show that appropriately designed general Markov models are reasonable tools for reconstructing genome evolution. These studies indicate that, provided genomes contain sufficiently many genes and that the Markov assumptions are met, it is possible to reconstruct the tree of life. We also consider the fusion of genomes, a process not encountered in gene sequence evolution, and derive a method for the identification and reconstruction of genome fusion events. Genomic reconstructions of a well-defined classical four-genome problem, the root of the multicellular animals, show that the method, when used in conjunction with paralinear/logdet distances, performs remarkably well and is relatively unaffected by the recently discovered big genome artifact.     

Variable life history of a cyclopoid copepod: the role of food availability

Populations of the copepod Cyclops vicinus in two Danish lakes differed in their life cycles. In Lake Væng C. vicinus was absent during summer, whereas in Lake Søbygård it continued producing distinct cohorts throughout summer. A comparison between the lakes showed that in the lake where C. vicinus was absent during summer, food limitation generally existed. In contrast, abundance of C. vicinus during summer in Lake Søbygård always coincided with available resources sufficient for the whole life cycle. Thus, summer diapause of C. vicinus is suggested to be a strategy to avoid food limitation. Avoidance of fish predation does not seem substantially to influence life cycles.     

Early evolutionary history and genomic features of gene duplicates in the human genome

Background

Human gene duplicates have been the focus of intense research since the development of array-based and targeted next-generation sequencing approaches in the last decade. These studies have primarily concentrated on determining the extant copy-number variation from a population-genomic perspective but lack a robust evolutionary framework to elucidate the early structural and genomic characteristics of gene duplicates at emergence and their subsequent evolution with increasing age.

Results

We analyzed 184 gene duplicate pairs comprising small gene families in the draft human genome with 10 % or less synonymous sequence divergence. Human gene duplicates primarily originate from DNA-mediated events, taking up genomic residence as intrachromosomal copies in direct or inverse orientation. The distribution of paralogs on autosomes follows random expectations in contrast to their significant enrichment on the sex chromosomes. Furthermore, human gene duplicates exhibit a skewed gradient of distribution along the chromosomal length with significant clustering in pericentromeric regions. Surprisingly, despite the large average length of human genes, the majority of extant duplicates (83 %) are complete duplicates, wherein the entire ORF of the ancestral copy was duplicated. The preponderance of complete duplicates is in accord with an extremely large median duplication span of 36 kb, which enhances the probability of capturing ancestral ORFs in their entirety. With increasing evolutionary age, human paralogs exhibit declines in (i) the frequency of intrachromosomal paralogs, and (ii) the proportion of complete duplicates. These changes may reflect lower survival rates of certain classes of duplicates and/or the role of purifying selection. Duplications arising from RNA-mediated events comprise a small fraction (11.4 %) of all human paralogs and are more numerous in older evolutionary cohorts of duplicates.

Conclusions

The degree of structural resemblance, genomic location and duplication span appear to influence the long-term maintenance of paralogs in the human genome. The median duplication span in the human genome far exceeds that in C. elegans and yeast and likely contributes to the high prevalence of complete duplicates relative to structurally heterogeneous duplicates (partial and chimeric). The relative roles of regulatory sequence versus exon-intron structure changes in the acquisition of novel function by human paralogs remains to be determined.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1827-3) contains supplementary material, which is available to authorized users.