Developmental system drift and flexibility in evolutionary trajectories

Antagonism of LIN-17/Frizzled and LIN-18/Ryk in nematode vulva induction reveals evolutionary alterations in core developmental pathways

Most diversity in animals and plants results from the modification of already existing structures. Many organ systems, for example, are permanently modified during evolution to create developmental and morphological diversity, but little is known about the evolution of the underlying developmental mechanisms. The theory of developmental systems drift proposes that the development of conserved morphological structures can involve large-scale modifications in their regulatory mechanisms. We test this hypothesis by comparing vulva induction in two genetically tractable nematodes, Caenorhabditis elegans and Pristionchus pacificus. Previous work indicated that the vulva is induced by epidermal growth factor (EGF)/RAS and WNT signaling in Caenorhabditis and Pristionchus, respectively. Here, we show that the evolution of vulva induction involves major molecular alterations and that this shift of signaling pathways involves a novel wiring of WNT signaling and the acquisition of novel domains in otherwise conserved receptors in Pristionchus vulva induction. First, Ppa-LIN-17/Frizzled acts as an antagonist of WNT signaling and suppresses the ligand Ppa-EGL-20 by ligand sequestration. Second, Ppa-LIN-18/Ryk transmits WNT signaling and requires inhibitory SH3 domain binding motifs, unknown from Cel-LIN-18/Ryk. Third, Ppa-LIN-18/Ryk signaling involves Axin and β-catenin and Ppa-axl-1/Axin is epistatic to Ppa-lin-18/Ryk. These results confirm developmental system drift as an important theory for the evolution of organ systems and they highlight the significance of protein modularity in signal transduction and the dynamics of signaling networks.

Diversity of biological form in animals can be generated by the modification of already existing developmental and morphological structures. One major challenge in evolutionary biology is to identify the molecular and genetic changes associated with such morphological modifications. A decade ago, the theory of developmental systems drift was proposed arguing that large-scale changes in regulatory mechanisms can underlie the development of conserved morphological structures. Our work supports this hypothesis by comparing the development of the egg-laying organ between Caenorhabditis elegans and Pristionchus pacificus, two nematode species that have significantly different mechanisms of vulva induction despite their morphological similarity. Our studies in P. pacificus reveal major molecular alterations of signaling pathways that involve first, a novel wiring and second, the acquisition of novel protein domains in otherwise conserved receptors in WNT signaling. We show that all Wnt signaling molecules analyzed are conserved in sequence, but crucial receptor molecules have acquired novel small peptides that allow new regulatory linkages. The independent evolution of small protein domains in otherwise conserved proteins increases the evolutionary freedom of signaling pathways and developmental networks. Thus, our analysis of a developmental process that follows developmental system drift highlights the significance of protein modularity in signal transduction.

Evolution of pleiotropy: epistatic interaction pattern supports a mechanistic model underlying variation in genotype-phenotype map

The genotype-phenotype (GP) map consists of developmental and physiological mechanisms mapping genetic onto phenotypic variation. It determines the distribution of heritable phenotypic variance on which selection can act. Comparative studies of morphology as well as of gene regulatory networks show that the GP map itself evolves, yet little is known about the actual evolutionary mechanisms involved. The study of such mechanisms requires exploring the variation in GP maps at the population level, which presently is easier to quantify by statistical genetic methods rather than by regulatory network structures. We focus on the evolution of pleiotropy, a major structural aspect of the GP map. Pleiotropic genes affect multiple traits and underlie genetic covariance between traits, often causing evolutionary constraints. Previous quantitative genetic studies have demonstrated population-level variation in pleiotropy in the form of loci, at which genotypes differ in the genetic covariation between traits. This variation can potentially fuel evolution of the GP map under selection and/or drift. Here, we propose a developmental mechanism underlying population genetic variation in covariance and test its predictions. Specifically, the mechanism predicts that the loci identified as responsible for genetic variation in pleiotropy are involved in trait-specific epistatic interactions. We test this prediction for loci affecting allometric relationships between traits in an advanced intercross between inbred mouse strains. The results consistently support the prediction. We further find a high degree of sign epistasis in these interactions, which we interpret as an indication of adaptive gene complexes within the diverged parental lines.

Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole

The authors screen for compounds that show synergistic antifungal activity when combined with the widely-used fungistatic drug fluconazole. Chemogenomic profiling explains the mode of action of synergistic drugs and allows the prediction of additional drug synergies.

The authors screen for compounds that show synergistic antifungal activity when combined with the widely-used fungistatic drug fluconazole. Chemogenomic profiling explains the mode of action of synergistic drugs and allows the prediction of additional drug synergies.

Chemical screens with a library enriched for known drugs identified a diverse set of 148 compounds that potentiated the action of the antifungal drug fluconazole against the fungal pathogens Cryptococcus neoformans, Cryptococcus gattii and Candida albicans, and the model yeast Saccharomyces cerevisiae, often in a species-specific manner.

Chemogenomic profiles of six confirmed hits in S. cerevisiae revealed different modes of action and enabled the prediction of additional synergistic combinations; three-way synergistic interactions exhibited even stronger synergies at low doses of fluconazole.

The synergistic combination of fluconazole and the antidepressant sertraline was active against fluconazole-resistant clinical fungal isolates and in an in vivo model of Cryptococcal infection.

Rising fungal infection rates, especially among immune-suppressed individuals, represent a serious clinical challenge (Gullo, 2009). Cancer, organ transplant and HIV patients, for example, often succumb to opportunistic fungal pathogens. The limited repertoire of approved antifungal agents and emerging drug resistance in the clinic further complicate the effective treatment of systemic fungal infections. At the molecular level, the paucity of fungal-specific essential targets arises from the conserved nature of cellular functions from yeast to humans, as well as from the fact that many essential yeast genes can confer viability at a fraction of wild-type dosage (Yan et al, 2009). Although only ∼1100 of the ∼6000 genes in yeast are essential, almost all genes become essential in specific genetic backgrounds in which another non-essential gene has been deleted or otherwise attenuated, an effect termed synthetic lethality (Tong et al, 2001). Genome-scale surveys suggest that over 200 000 binary synthetic lethal gene combinations dominate the yeast genetic landscape (Costanzo et al, 2010). The genetic buffering phenomenon is also manifest as a plethora of differential chemical–genetic interactions in the presence of sublethal doses of bioactive compounds (Hillenmeyer et al, 2008). These observations frame the difficulty of interdicting network functions in eukaryotic pathogens with single agent therapeutics. At the same time, however, this genetic network organization suggests that judicious combinations of small molecule inhibitors of both essential and non-essential targets may elicit additive or synergistic effects on cell growth (Sharom et al, 2004; Lehar et al, 2008). Unbiased screens for drugs that synergistically enhance a specific bioactive effect, but which are not themselves individually active—termed a syncretic combination—are one means to substantially elaborate chemical space (Keith et al, 2005). Indeed, compounds that enhance the activity of known agents in model yeast and cancer cell line systems have been identified both by focused small molecule library screens and by computational methods (Borisy et al, 2003; Lehar et al, 2007; Nelander et al, 2008; Jansen et al, 2009; Zinner et al, 2009).

To extend the stratagem of chemical synthetic lethality to clinically relevant fungal pathogens, we screened a bioactive library of known drugs for synergistic enhancers of the widely used fungistatic drug fluconazole against the clinically relevant pathogens C. albicans, C. neoformans and C. gattii, as well as the genetically tractable budding yeast S. cerevisiae. Fluconazole is an azole drug that inhibits lanosterol 14α-demethylase, the gene product of ERG11, an essential cytochrome P450 enzyme in the ergosterol biosynthetic pathway (Groll et al, 1998). We identified 148 drugs that potentiate the antifungal action of fluconazole against the four species. These syncretic compounds had not been previously recognized in the clinic as antifungal agents, and many acted in a species-specific manner, often in a potent fungicidal manner.

To understand the mechanisms of synergism, we interrogated six syncretic drugs—trifluoperazine, tamoxifen, clomiphene, sertraline, suloctidil and L-cycloserine—in genome-wide chemogenomic profiles of the S. cerevisiae deletion strain collection (Giaever et al, 1999). These profiles revealed that membrane, vesicle trafficking and lipid biosynthesis pathways are targeted by five of the synergizers, whereas the sphingolipid biosynthesis pathway is targeted by L-cycloserine. Cell biological assays confirmed the predicted membrane disruption effects of the former group of compounds, which may perturb ergosterol metabolism, impair fluconazole export by drug efflux pumps and/or affect active import of fluconazole (Kuo et al, 2010; Mansfield et al, 2010). Based on the integration of chemical–genetic and genetic interaction space, a signature set of deletion strains that are sensitive to the membrane active synergizers correctly predicted additional drug synergies with fluconazole. Similarly, the L-cycloserine chemogenomic profile correctly predicted a synergistic interaction between fluconazole and myriocin, another inhibitor of sphingolipid biosynthesis. The structure of genetic networks suggests that it should be possible to devise higher order drug combinations with even greater selectivity and potency (Sharom et al, 2004). In an initial test of this concept, we found that the combination of a non-synergistic pair drawn from the membrane active and sphingolipid target classes exhibited potent three-way synergism with a low dose of fluconazole. Finally, the combination of sertraline and fluconazole was active in a G. mellonella model of Cryptococcal infection, and was also efficacious against fluconazole-resistant clinical isolates of C. albicans and C. glabrata.

Collectively, these results demonstrate that the combinatorial redeployment of known drugs defines a powerful antifungal strategy and establish a number of potential lead combinations for future clinical assessment.

Resistance to widely used fungistatic drugs, particularly to the ergosterol biosynthesis inhibitor fluconazole, threatens millions of immunocompromised patients susceptible to invasive fungal infections. The dense network structure of synthetic lethal genetic interactions in yeast suggests that combinatorial network inhibition may afford increased drug efficacy and specificity. We carried out systematic screens with a bioactive library enriched for off-patent drugs to identify compounds that potentiate fluconazole action in pathogenic Candida and Cryptococcus strains and the model yeast Saccharomyces. Many compounds exhibited species- or genus-specific synergism, and often improved fluconazole from fungistatic to fungicidal activity. Mode of action studies revealed two classes of synergistic compound, which either perturbed membrane permeability or inhibited sphingolipid biosynthesis. Synergistic drug interactions were rationalized by global genetic interaction networks and, notably, higher order drug combinations further potentiated the activity of fluconazole. Synergistic combinations were active against fluconazole-resistant clinical isolates and an in vivo model of Cryptococcus infection. The systematic repurposing of approved drugs against a spectrum of pathogens thus identifies network vulnerabilities that may be exploited to increase the activity and repertoire of antifungal agents.

Distinct functional constraints partition sequence conservation in a cis-regulatory element

Different functional constraints contribute to different evolutionary rates across genomes. To understand why some sequences evolve faster than others in a single cis-regulatory locus, we investigated function and evolutionary dynamics of the promoter of the Caenorhabditis elegans unc-47 gene. We found that this promoter consists of two distinct domains. The proximal promoter is conserved and is largely sufficient to direct appropriate spatial expression. The distal promoter displays little if any conservation between several closely related nematodes. Despite this divergence, sequences from all species confer robustness of expression, arguing that this function does not require substantial sequence conservation. We showed that even unrelated sequences have the ability to promote robust expression. A prominent feature shared by all of these robustness-promoting sequences is an AT-enriched nucleotide composition consistent with nucleosome depletion. Because general sequence composition can be maintained despite sequence turnover, our results explain how different functional constraints can lead to vastly disparate rates of sequence divergence within a promoter.

Comparison between genome sequences of different species is a powerful tool in modern biology because important features are maintained by natural selection and are therefore conserved. However, some important sequences within genomes evolve considerably faster than others. One possible explanation is that they encode little or no function. Alternatively, they may evolve under different constraints that permit sequence turnover while maintaining function. Here we report that the promoter of the unc-47 gene of C. elegans contains two discrete elements. One has a highly conserved sequence that determines the spatial expression pattern. Another shows no sequence conservation, but it makes expression of the gene robust, that is, consistent between individuals and resilient to environmental challenges. Remarkably, multiple unrelated sequences are capable of promoting robust expression. Nucleotide composition of these sequences suggests that open chromatin may play a role in conferring robustness of gene expression. Because general sequence composition and therefore expression robustness can be maintained despite sequence turnover, our results offer an explanation of how rapidly diverging promoter elements can nevertheless remain functionally conserved.

Divergent mechanisms specify chordate motoneurons: evidence from ascidians

Ascidians are members of the vertebrate sister group Urochordata. Their larvae exhibit a chordate body plan, which forms by a highly accelerated embryonic strategy involving a fixed cell lineage and small cell numbers. We report a detailed analysis of the specification of three of the five pairs of motoneurons in the ascidian Ciona intestinalis and show that despite well-conserved gene expression patterns and embryological outcomes compared with vertebrates, key signalling molecules have adopted different roles. We employed a combination of cell ablation and gene manipulation to analyse the function of two signalling molecules with key roles in vertebrate motoneuron specification that are known to be expressed equivalently in ascidians: the inducer Sonic hedgehog, produced ventrally by the notochord and floorplate; and the inhibitory BMP2/4, produced on the lateral/dorsal side of the neural plate. Our surprising conclusion is that neither BMP2/4 signalling nor the ventral cell lineages expressing hedgehog play crucial roles in motoneuron formation in Ciona. Furthermore, BMP2/4 overexpression induced ectopic motoneurons, the opposite of its vertebrate role. We suggest that the specification of motoneurons has been modified during ascidian evolution, such that BMP2/4 has adopted a redundant inductive role rather than a repressive role and Nodal, expressed upstream of BMP2/4 in the dorsal neural tube precursors, acts as a motoneuron inducer during normal development. Thus, our results uncover significant differences in the mechanisms used for motoneuron specification within chordates and also highlight the dangers of interpreting equivalent expression patterns as indicative of conserved function in evo-devo studies.

Ninety years of Drosophila melanogaster hybrids

Within 10 years of the beginning of experimental genetic research on Drosophila melanogaster, in 1919, A. H. Sturtevant discovered its sibling species, D. simulans. He hybridized the two species and made fundamental discoveries about the genetic basis of hybrid incompatibility. The complete sterility of surviving F(1) hybrids frustrated Sturtevant and his vision of comprehensively exploring the genetics of interspecific differences. But over the next 90 years, a combination of clever genetic tricks and close observation of natural variation has led to a wealth of discovery using these and other hybrids of D. melanogaster and D. simulans, resulting in an advanced understanding of speciation and the evolution of morphology, gene regulation, and behavior.

In the Light of Evolution: A Reevaluation of Conservation in the CO-FT Regulon and Its Role in Photoperiodic Regulation of Flowering Time

In order to maximize reproductive success, plants have evolved different strategies to control the critical developmental shift marked by the transition to flowering. As plants have adapted to diverse environments across the globe, these strategies have evolved to recognize and respond to local seasonal cues through the induction of specific downstream genetic pathways, thereby ensuring that the floral transition occurs in favorable conditions. Determining the genetic factors involved in controlling the floral transition in many species is key to understanding how this trait has evolved. Striking genetic discoveries in Arabidopsis thaliana (Arabidopsis) and Oryza sativa (rice) revealed that similar genes in both species control flowering in response to photoperiod, suggesting that this genetic module could be conserved between distantly related angiosperms. However, as we have gained a better understanding of the complex evolution of these genes and their functions in other species, another possibility must be considered: that the genetic module controlling flowering in response to photoperiod is the result of convergence rather than conservation. In this review, we show that while data clearly support a central role of FLOWERING LOCUS T (FT) homologs in floral promotion across a diverse group of angiosperms, there is little evidence for a conserved role of CONSTANS (CO) homologs in the regulation of these loci. In addition, although there is an element of conserved function for FT homologs, even this component has surprising complexity in its regulation and evolution.

Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners

Background

Allotetraploids carry pairs of diverged homoeologs for most genes. With the genome doubled in size, the number of putative interactions is enormous. This poses challenges on how to coordinate the two disparate genomes, and creates opportunities by enhancing the phenotypic variation. New combinations of alleles co-adapt and respond to new environmental pressures. Three stages of the allopolyploidization process - parental species divergence, hybridization, and genome duplication - have been well analyzed. The last stage of evolutionary adjustments remains mysterious.

Results

Homoeolog-specific retention and use were analyzed in Arabidopsis suecica (As), a species derived from A. thaliana (At) and A. arenosa (Aa) in a single event 12,000 to 300,000 years ago. We used 405,466 diagnostic features on tiling microarrays to recognize At and Aa contributions to the As genome and transcriptome: 324 genes lacked Aa contributions and 614 genes lacked At contributions within As. In leaf tissues, 3,458 genes preferentially expressed At homoeologs while 4,150 favored Aa homoeologs. These patterns were validated with resequencing. Genes with preferential use of Aa homoeologs were enriched for expression functions, consistent with the dominance of Aa transcription. Heterologous networks - mixed from At and Aa transcripts - were underrepresented.

Conclusions

Thousands of deleted and silenced homoeologs in the genome of As were identified. Since heterologous networks may be compromised by interspecies incompatibilities, these networks evolve co-biases, expressing either only Aa or only At homoeologs. This progressive change towards predominantly pure parental networks might contribute to phenotypic variability and plasticity, and enable the species to exploit a larger range of environments.

Insights into species divergence and the evolution of hermaphroditism from fertile interspecies hybrids of Caenorhabditis nematodes

The architecture of both phenotypic variation and reproductive isolation are important problems in evolutionary genetics. The nematode genus Caenorhabditis includes both gonochoristic (male/female) and androdioecious (male/hermaprodite) species. However, the natural genetic variants distinguishing reproductive mode remain unknown, and nothing is known about the genetic basis of postzygotic isolation in the genus. Here we describe the hybrid genetics of the first Caenorhabditis species pair capable of producing fertile hybrid progeny, the gonochoristic Caenorhabditis sp. 9 and the androdioecious C. briggsae. Though many interspecies F(1) arrest during embryogenesis, a viable subset develops into fertile females and sterile males. Reciprocal parental crosses reveal asymmetry in male-specific viability, female fertility, and backcross viability. Selfing and spermatogenesis are extremely rare in XX F(1), and almost all hybrid self-progeny are inviable. Consistent with this, F(1) females do not express male-specific molecular germline markers. We also investigated three approaches to producing hybrid hermaphrodites. A dominant mutagenesis screen for self-fertile F(1) hybrids was unsuccessful. Polyploid F(1) hybrids with increased C. briggsae genomic material did show elevated rates of selfing, but selfed progeny were mostly inviable. Finally, the use of backcrosses to render the hybrid genome partial homozygous for C. briggsae alleles did not increase the incidence of selfing or spermatogenesis relative to the F(1) generation. These hybrid animals were genotyped at 23 loci, and significant segregation distortion (biased against C. briggsae) was detected at 13 loci. This, combined with an absence of productive hybrid selfing, prevents formulation of simple hypotheses about the genetic architecture of hermaphroditism. In the near future, this hybrid system will likely be fruitful for understanding the genetics of reproductive isolation in Caenorhabditis.

Mechanisms driving neural crest induction and migration in the zebrafish and Xenopus laevis

The neural crest is an evolutionary adaptation, with roots in the formation of mesoderm. Modification of neural crest behavior has been is critical for the evolutionary diversification of the vertebrates and defects in neural crest underlie a range of human birth defects. There has been a tremendous increase in our knowledge of the molecular, cellular, and inductive interactions that converge on defining the neural crest and determining its behavior. While there is a temptation to look for simple models to explain neural crest behavior, the reality is that the system is complex in its circuitry. In this review, our goal is to identify the broad features of neural crest origins (developmentally) and migration (cellularly) using data from the zebrafish (teleost) and Xenopus laevis (tetrapod amphibian) in order to illuminate where general mechanisms appear to be in play, and equally importantly, where disparities in experimental results suggest areas of profitable study.

Evolutionary variation in gene expression is associated with dimorphism in eusocial vespid wasps

Phenotypic diversity is frequently generated by differences in gene expression. In this study, we addressed the relationship between homology in gene expression and phenotype among four species of eusocial wasps. Specifically, we investigated the evolution of caste-specific and sex-specific gene expression patterns associated with caste polyphenisms and sexual dimorphisms. We also identified several genes with functions relevant to their phenotype-specific roles. Our results suggest that gene expression profiles associated with caste polyphenisms may evolve rapidly relative to those associated with sexes. Thus, caste-biased genes may undergo less regulatory constraint or be subject to greater neutral variation in expression than sex-biased genes.

Evolution of transcription networks--lessons from yeasts

That regulatory evolution is important in generating phenotypic diversity was suggested soon after the discovery of gene regulation. In the past few decades, studies in animals have provided a number of examples in which phenotypic changes can be traced back to specific alterations in transcriptional regulation. Recent advances in DNA sequencing technology and functional genomics have stimulated a new wave of investigation in simple model organisms. In particular, several genome-wide comparative analyses of transcriptional circuits across different yeast species have been performed. These studies have revealed that transcription networks are remarkably plastic: large scale rewiring in which target genes move in and out of regulons through changes in cis-regulatory sequences appears to be a general phenomenon. Transcription factor substitution and the formation of new combinatorial interactions are also important contributors to the rewiring. In several cases, a transition through intermediates with redundant regulatory programs has been suggested as a mechanism through which rewiring can occur without a loss in fitness. Because the basic features of transcriptional regulation are deeply conserved, we speculate that large scale rewiring may underlie the evolution of complex phenotypes in multi-cellular organisms; if so, such rewiring may leave traceable changes in the genome from which the genetic basis of functional innovation can be detected.

Functional regulatory divergence of the innate immune system in interspecific Drosophila hybrids

In order to investigate divergence of immune regulation among Drosophila species, we have engaged in a study of innate immune function in F1 hybrids of Drosophila melanogaster and D. simulans. If pathways have diverged between the species such that incompatibilities have arisen between interacting components of the immune network, we expect the hybrids to display dysregulation of immune genes. We have quantified gene induction in hybrid and parental flies in response to bacterial infection. These results show that although the hybrids do not suffer widespread immune breakdown, they show significantly different regulation of many immune genes relative to the parents. We examine this divergence in terms of additivity and expression differences among genes, observing distinct patterns of dysregulation among functional groups within the pathways of the innate immune system. The functional groups most sensitive to misexpression in the hybrids are the downstream components of the network, indicative of some propagation of dysregulation throughout the immune pathways. Interestingly, this dysregulation does not appear to associate with phenotypic differences in bacterial load after infection in hybrids, possibly highlighting some robustness of function of the innate immune response to perturbations like hybridization.

Arabidopsis and relatives as models for the study of genetic and genomic incompatibilities

The past few years have seen considerable advances in speciation research, but whether drift or adaptation is more likely to lead to genetic incompatibilities remains unknown. Some of the answers will probably come from not only studying incompatibilities between well-established species, but also from investigating incipient speciation events, to learn more about speciation as an evolutionary process. The genus Arabidopsis, which includes the widely used Arabidopsis thaliana, provides a useful set of model species for studying many aspects of population divergence. The genus contains both self-incompatible and incompatible species, providing a platform for studying the impact of mating system changes on genetic differentiation. Another important path to plant speciation is via formation of polyploids, and this can be investigated in the young allotetraploid species A. arenosa. Finally, there are many cases of intraspecific incompatibilities in A. thaliana, and recent progress has been made in discovering the genes underlying both F(1) and F(2) breakdown. In the near future, all these studies will be greatly empowered by complete genome sequences not only for all members of this relatively small genus, but also for many different individuals within each species.

Hybrid incompatibility genes: remnants of a genomic battlefield?

Hybrid incompatibility (including sterility, lethality, and less extreme negative effects) interests evolutionary biologists because of its role in speciation as a reproductive isolating barrier. It also has unusual genetic properties, being mainly due to interactions between at least two genes. Recent studies have identified some of the interacting genes that underlie hybrid incompatibility. These genes represent a wide array of functions, including those involved in oxidative respiration, nuclear trafficking, DNA-binding, and plant defense. Accumulating evidence suggests genomic conflict frequently drives the divergence causing incompatibilities in hybrids. The evidence bearing on this genomic conflict hypothesis is assessed and ways to test it conclusively are suggested.

Cryptic intraspecific variation in sex determination in Caenorhabditis elegans revealed by mutations

Sex determination mechanisms (SDMs) show striking diversity and appear to evolve rapidly. Although interspecific comparisons and studies of ongoing major transitions in sex determination (such as the establishment of new sex chromosomes) have shed light on how SDMs evolve, comparatively little attention has been paid to intraspecific variation with less drastic effects. In this study, I used mutant strains carrying a temperature-sensitive sex determination mutation, along with a second null mutation, in different wild genetic backgrounds to uncover hidden variation in the SDM of the model nematode Caenorhabditis elegans. I then used quantitative trait locus (QTL) mapping to begin to investigate its genetic basis. I identified several QTLs, and although this variation apparently involved genotype-by-temperature interactions, QTL effects were generally consistent across temperatures. These QTLs collectively and individually explained a relatively large fraction of the variance in tail morphology (a sexually dimorphic trait), and two QTLs contained no genes known to be involved in somatic sex determination. These results show the existence of within-species variation in sex determination in this species, and underscore the potential for microevolutionary change in this important developmental pathway.

Molecular evidence for increased regulatory conservation during metamorphosis, and against deleterious cascading effects of hybrid breakdown in Drosophila

Background

Speculation regarding the importance of changes in gene regulation in determining major phylogenetic patterns continues to accrue, despite a lack of broad-scale comparative studies examining how patterns of gene expression vary during development. Comparative transcriptional profiling of adult interspecific hybrids and their parental species has uncovered widespread divergence of the mechanisms controlling gene regulation, revealing incompatibilities that are masked in comparisons between the pure species. However, this has prompted the suggestion that misexpression in adult hybrids results from the downstream cascading effects of a subset of genes improperly regulated in early development.

Results

We sought to determine how gene expression diverges over development, as well as test the cascade hypothesis, by profiling expression in males of Drosophila melanogaster, D. sechellia, and D. simulans, as well as the D. simulans (♀) × D. sechellia (♂) male F1 hybrids, at four different developmental time points (3rd instar larval, early pupal, late pupal, and newly-emerged adult). Contrary to the cascade model of misexpression, we find that there is considerable stage-specific autonomy of regulatory breakdown in hybrids, with the larval and adult stages showing significantly more hybrid misexpression as compared to the pupal stage. However, comparisons between pure species indicate that genes expressed during earlier stages of development tend to be more conserved in terms of their level of expression than those expressed during later stages, suggesting that while Von Baer's famous law applies at both the level of nucleotide sequence and expression, it may not apply necessarily to the underlying overall regulatory network, which appears to diverge over the course of ontogeny and which can only be ascertained by combining divergent genomes in species hybrids.

Conclusion

Our results suggest that complex integration of regulatory circuits during morphogenesis may lead to it being more refractory to divergence of underlying gene regulatory mechanisms - more than that suggested by the conservation of gene expression levels between species during earlier stages. This provides support for a 'developmental hourglass' model of divergence of gene expression in Drosophila resulting in a highly conserved pupal stage.

Looking at the origin of phenotypic variation from pattern formation gene networks

This article critically reviews some widespread views about the overall functioning of development. Special attention is devoted to views in developmental genetics about the superstructure of developmental gene networks. According to these views gene networks are hierarchic and multilayered. The highest layers partition the embryo in large coarse areas and control downstream genes that subsequently subdivide the embryo into smaller and smaller areas. These views are criticized on the bases of developmental and evolutionary arguments. First, these views, although detailed at the level of gene identities, do not incorporate morphogenetic mechanisms nor do they try to explain how morphology changes during development. Often, they assume that morphogenetic mechanisms are subordinate to cell signaling events. This is in contradiction to the evidence reviewed herein. Experimental evidence on pattern formation also contradicts the view that developmental gene networks are hierarchically multilayered and that their functioning is decodable from promoter analysis. Simple evolutionary arguments suggest that, indeed, developmental gene networks tend to be non-hierarchic. Re-use leads to extensive modularity in gene networks while developmental drift blurs this modularity. Evolutionary opportunism makes developmental gene networks very dependent on epigenetic factors.

Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same

Regulatory regions with similar transcriptional output often have little overt sequence similarity, both within and between genomes. Although cis- and trans-regulatory changes can contribute to sequence divergence without dramatically altering gene expression outputs, heterologous DNA often functions similarly in organisms that share little regulatory sequence similarities (e.g. human DNA in fish), indicating that trans-regulatory mechanisms tend to diverge more slowly and can accommodate a variety of cis-regulatory configurations. This capacity to 'tinker' with regulatory DNA probably relates to the complexity, robustness and evolvability of regulatory systems, but cause-and-effect relationships among evolutionary processes and properties of regulatory systems remain a topic of debate. The challenge of understanding the concrete mechanisms underlying cis-regulatory evolution - including the conservation of function without the conservation of sequence - relates to the challenge of understanding the function of regulatory systems in general. Currently, we are largely unable to recognize functionally similar regulatory DNA.

Genetic architecture and postzygotic reproductive isolation: evolution of Bateson-Dobzhansky-Muller incompatibilities in a polygenic model

The Bateson-Dobzhansky-Muller model predicts that postzygotic isolation evolves due to the accumulation of incompatible epistatic interactions, but few studies have quantified the relationship between genetic architecture and patterns of reproductive divergence. We examined how the direction and magnitude of epistatic interactions in a polygenic trait under stabilizing selection influenced the evolution of hybrid incompatibilities. We found that populations evolving independently under stabilizing selection experienced suites of compensatory allelic changes that resulted in genetic divergence between populations despite the maintenance of a stable, high-fitness phenotype. A small number of loci were then incompatible with multiple alleles in the genetic background of the hybrid and the identity of these incompatibility loci changed over the evolution of the populations. For F(1) hybrids, reduced fitness evolved in a window of intermediate strengths of epistatic interactions, but F(2) and backcross hybrids evolved reduced fitness across weak and moderate strengths of epistasis due to segregation variance. Strong epistatic interactions constrained the allelic divergence of parental populations and prevented the development of reproductive isolation. Because many traits with varying genetic architectures must be under stabilizing selection, our results indicate that polygenetic drift is a plausible hypothesis for the evolution of postzygotic reproductive isolation.

Making the right connections: biological networks in the light of evolution

Our understanding of how evolution acts on biological networks remains patchy, as is our knowledge of how that action is best identified, modelled and understood. Starting with network structure and the evolution of protein-protein interaction networks, we briefly survey the ways in which network evolution is being addressed in the fields of systems biology, development and ecology. The approaches highlighted demonstrate a movement away from a focus on network topology towards a more integrated view, placing biological properties centre-stage. We argue that there remains great potential in a closer synergy between evolutionary biology and biological network analysis, although that may require the development of novel approaches and even different analogies for biological networks themselves.

Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved

Genomic analyses have shown that adjacent genes are often coexpressed. However, it remains unclear whether the observed coexpression is a result of functional organization or a consequence of adjacent active chromatin or transcriptional read-through, which may be free of selective biases. Here, we compare temporal expression profiles of one-to-one orthologs in conserved or divergent genomic positions in two genetically distant nematode species-Caenorhabditis elegans and C. briggsae-that share a near-identical developmental program. We find, for all major patterns of temporal expression, a substantive amount of gene expression divergence. However, this divergence is not random: Genes that function in essential developmental processes show less divergence than genes whose functions are not required for viability. Coexpression of gene neighbors in either species is highly divergent in the other, in particular when the neighborhood is not conserved. Interestingly, essential genes appear to maintain their expression profiles despite changes in neighborhoods suggesting exposure to stronger selection. Our results suggest that a significant fraction of the coexpression observed among gene neighbors may be accounted for by neutral processes, and further that these may be distinguished by comparative gene expression analyses.

Regulatory divergence in Drosophila melanogaster and D. simulans, a genomewide analysis of allele-specific expression

Species-specific regulation of gene expression contributes to the development and maintenance of reproductive isolation and to species differences in ecologically important traits. A better understanding of the evolutionary forces that shape regulatory variation and divergence can be developed by comparing expression differences among species and interspecific hybrids. Once expression differences are identified, the underlying genetics of regulatory variation or divergence can be explored. With the goal of associating cis and/or trans components of regulatory divergence with differences in gene expression, overall and allele-specific expression levels were assayed genomewide in female adult heads of Drosophila melanogaster, D. simulans, and their F1 hybrids. A greater proportion of cis differences than trans differences were identified for genes expressed in heads and, in accordance with previous studies, cis differences also explained a larger number of species differences in overall expression level. Regulatory divergence was found to be prevalent among genes associated with defense, olfaction, and among genes downstream of the Drosophila sex determination hierarchy. In addition, two genes, with critical roles in sex determination and micro RNA processing, Sxl and loqs, were identified as misexpressed in hybrid female heads, potentially contributing to hybrid incompatibility.

Major disruption of gene expression in hybrids between young sympatric anadromous and resident populations of brook charr (Salvelinus fontinalis Mitchill)

Genome-wide analyses of the transcriptome have suggested that male-biased genes are the first targets of genomic incompatibilities (g.i.) in inter-specific hybrids. However, those studies have almost invariably focused on Drosophila species that diverged at least 0.9 Ma, and with sterile male hybrids. Here, we use microarrays to analyse patterns of gene expression in very closely related (divergence <12,000 years), sympatric, but ecologically divergent anadromous and resident populations of brook charr (Salvelinus fontinalis) and their F(1) hybrids. Our results show a dramatic breakdown of gene expression patterns in hybrids compared with their parental relatives. Several disrupted genes are related to energetic metabolism, immune response, osmoregulation and protection against oxidative stress, and none has sex-biased functions. Besides, pure individuals show no expression differences at most of the genes disrupted in hybrids, which may suggest the operation of some form of stabilizing selection. Taken together, these results both confirm the idea that perturbations of regulatory networks represent a significant source of g.i. and support the suggestion that developmental pathways can diverge through time without any manifest change in the phenotypic outcome. While the role of other evolutionary forces (e.g. genetic drift) cannot be ruled out, this study suggests that ecological selective processes may provide the initial driving force behind disruption of gene expression in inter-specific hybrids.

Differential recruitment of limb patterning genes during development and diversification of beetle horns

The origins of novel complex phenotypes represent one of the most fundamental, yet largely unresolved, issues in evolutionary biology. Here we explore the developmental genetic regulation of beetle horns, a class of traits that lacks obvious homology to traits in other insects. Furthermore, beetle horns are remarkably diverse in their expression, including sexual dimorphisms, male dimorphisms, and interspecific differences in location of horn expression. At the same time, beetle horns share aspects of their development with that of more traditional appendages. We used larval RNA interference-mediated gene function analysis of 3 cardinal insect appendage patterning genes, dachshund, homothorax, and Distal-less, to investigate their role in development and diversification of beetle horns within and between species. Transcript depletion of all 3 patterning genes generated phenotypic effects very similar to those documented in previous studies that focused on general insect development. In addition, we found that Distal-less and homothorax, but not dachshund, regulate horn expression in a species-, sex-, body region-, and body size-dependent manner. Our results demonstrate differential co-option of appendage patterning genes during the evolution and radiation of beetle horns. Furthermore, our results illustrate that regulatory genes whose functions are otherwise highly conserved nevertheless retain the capacity to acquire additional functions, and that little phylogenetic distance appears necessary for the evolution of sex- and species-specific differences in these functions.

Divergence in gene regulation at young life history stages of whitefish (Coregonus sp.) and the emergence of genomic isolation

BACKGROUND

The evolution of barriers to reproduction is of key interest to understand speciation. However, there may be a current bias towards studying intrinsic postzygotic isolation in old species pairs as compared to the emergence of barriers to gene flow through adaptive divergence. This study evaluates the relative importance of both processes in the evolution of genomic isolation in incipient species of whitefish (Coregonus clupeaformis) for which preliminary data suggest that postzygotic isolation emerges with intrinsic factors acting at embryo stages but also due to extrinsic factors during adult life.

RESULTS

Gene expression data were screened using cDNA microarrays to identify regulatory changes at embryo and juvenile stages that provide evidence for genomic divergence at the underlying genetic factors. A comparison of different life history stages shows that 16-week old juvenile fish have 14 times more genes displaying significant regulatory divergence than embryos. Furthermore, regulatory changes in juvenile fish match patterns in adult fish suggesting that gene expression divergence is established early in juvenile fish and persists throughout the adult phase. Comparative analyses with results from previous studies on dwarf-normal species pairs show that at least 26 genetic factors identified in juvenile fish are candidate traits for adaptive divergence in adult fish. Eight of these show parallel directions of gene expression divergence independent of tissue type or age of the fish. The latter are associated with energy metabolism, a complex trait known to drive adaptive divergence in dwarf and normal whitefish.

CONCLUSION

Although experimental evidence suggests the existence of genetic factors that cause intrinsic postzygotic isolation acting in embryos, the analysis presented here provided few candidate genes in embryos, which also corroborate previous studies showing a lack of ecological divergence between sympatric dwarf and normal whitefish at the larval stage. In contrast, gene expression divergence in juveniles can be linked to adaptive traits and seems to be driven by positive selection. The results support the idea that adaptive differentiation may be more important in explaining the emergence of barriers to gene flow in an early phase of speciation by providing a broad genomic basis for extrinsic postzygotic isolation rather than intrinsic barriers.

Distinct developmental mechanisms underlie the evolutionary diversification of Drosophila sex combs

Similar selective pressures can lead to independent origin of similar morphological structures in multiple evolutionary lineages. Developmental mechanisms underlying convergent evolution remain poorly understood. In this report, we show that similar sex comb morphology in closely related Drosophila species is produced by different cellular mechanisms. The sex comb is a recently evolved, male-specific array of modified bristles derived from transverse bristle rows found on the first thoracic legs in both sexes. "Longitudinal" sex combs oriented along the proximo-distal leg axis evolved independently in several Drosophila lineages. We show that in some of these lineages, sex combs originate as one or several transverse bristle rows that subsequently rotate 90 degrees and align to form a single longitudinal row. In other species, bristle cells that make up the sex combs arise in their final longitudinal orientation. Thus, sex combs can develop through either sex-specific patterning of bristle precursor cells or male-specific morphogenesis of sexually monomorphic precursors. Surprisingly, the two mechanisms produce nearly identical morphology in some species. Phylogenetic analysis shows that each of these mechanisms has probably evolved repeatedly in different Drosophila lineages, suggesting that selection can recruit different cellular processes to produce similar functional solutions.

Plasticity and errors of a robust developmental system in different environments

Many developmental processes generate invariant phenotypes in a wide range of ecological conditions. Such robustness to environmental variation is a fundamental biological property, yet its extent, limits, and adaptive significance have rarely been assessed empirically. Here we tested how environmental variation affects vulval formation in Caenorhabditis nematodes. In different environments, a correct vulval pattern develops with high precision, but rare deviant patterns reveal the system's limits and how its mechanisms respond to environmental challenges. Key features of the apparent robustness are functional redundancy among vulval precursor cells and tolerance to quantitative variation in Ras, Notch, and Wnt pathway activities. The observed environmental responses and precision of vulval patterning vary within and between Caenorhabditis species. These results highlight the complex response of developmental systems to the environment and illustrate how a robust and invariant phenotype may result through cellular and molecular processes that are highly plastic--across environments and evolution.

Dynamics of hybrid incompatibility in gene networks in a constant environment

After an ancestral population splits into two allopatric populations, different mutations may fix in each. When pairs of mutations are brought together in a hybrid offspring, epistasis may cause reduced fitness. Such pairs are known as Bateson-Dobzhansky-Muller (BDM) incompatibilities. A well-known model of BDM incompatibility due to Orr suggests that the fitness load on hybrids should initially accelerate, and continue to increase as the number of potentially incompatible substitutions increases (the "snowball effect"). In the gene networks model, which violates a key assumption of Orr's model (independence of fixation probabilities), the snowball effect often does not occur. Instead, we describe three possible dynamics in a constant environment: (1) Stabilizing selection can constrain two allopatric populations to remain near-perfectly compatible. (2) Despite constancy of environment, punctuated evolution may obtain; populations may experience rare adaptations asynchronously, permitting incompatibility. (3) Despite stabilizing selection, developmental system drift may permit genetic change, allowing two populations to drift in and out of compatibility. We reinterpret Orr's model in terms of genetic distance. We extend Orr's model to the finite loci case, which can limit incompatibility. Finally, we suggest that neutral evolution of gene regulation in nature, to the point of speciation, is a distinct possibility.

Chapter 4. New model systems for the study of developmental evolution in plants

The number of genetically tractable plant model systems is rapidly increasing, thanks to the decreasing cost of sequencing and the wide amenability of plants to stable transformation and other functional approaches. In this chapter, I discuss emerging model systems from throughout the land plant phylogeny and consider how their unique attributes are contributing to our understanding of development, evolution, and ecology. These new models are being developed using two distinct strategies: in some cases, they are selected because of their close relationship to the established models, while in others, they are chosen with the explicit intention of exploring distantly related plant lineages. Such complementary approaches are yielding exciting new results that shed light on both micro- and macroevolutionary processes in the context of developmental evolution.

Chapter 3. Caenorhabditis nematodes as a model for the adaptive evolution of germ cells

A number of major adaptations in animals have been mediated by alteration of germ cells and their immediate derivatives, the gametes. Here, several such cases are discussed, including examples from echinoderms, vertebrates, insects, and nematodes. A feature of germ cells that make their development (and hence evolution) distinct from the soma is the prominent role played by posttranscriptional controls of mRNA translation in the regulation of proliferation and differentiation. This presents a number of special challenges for investigation of the evolution of germline development. Caenorhabditis nematodes represent a particularly favorable system for addressing these challenges, both because of technical advantages and (most importantly) because of natural variation in mating system that is rooted in alterations of germline sex determination. Recent studies that employ comparative genetic methods in this rapidly maturing system are discussed, and likely areas for future progress are identified.

Cell biology and evolution: molecular modules link it all?

Classical studies comparing developing embryos have suggested the importance of modified cell biological processes in the evolution of new phenotypes. Here, I revisit this connection focusing on embryonic development, in particular nematode embryogenesis. I compare phenotypic differences in nematode embryogenesis in two basic cell biological processes, the cell cycle and the localization of the first division axis. The analysis of these and other processes shows that, at the cell biological level, exhaustive variation is found that does not necessarily translate into morphological differences. Modern molecular analyses have led to a view in which molecular complexes, made up of groups of proteins, or modules, that are working together, are responsible for the proper execution of cell biological programs. I discuss how this modular architecture could facilitate the phenotypic changes observed in cell biological processes. Ultimately, understanding the connection between cellular behavior and phenotypic outcome will further elucidate the mechanisms responsible for phenotypic evolution.

On the origins of novelty in development and evolution

The origin of novel traits is what draws many to evolutionary biology, yet our understanding of the mechanisms that underlie the genesis of novelty remains limited. Here I review definitions of novelty including its relationship to homology. I then discuss how ontogenetic perspectives may allow us to move beyond current roadblocks in our understanding of the mechanics of innovation. Specifically, I explore the roles of canalization, plasticity and threshold responses during development in generating a reservoir of cryptic genetic variation free to drift and accumulate in natural populations. Environmental or genetic perturbations that exceed the buffering capacity of development can then release this variation, and, through evolution by genetic accommodation, result in rapid diversification, recurrence of lost phenotypes as well as the origins of novel features. I conclude that, in our quest to understand the nature of innovation, the nature of development deserves to take center stage.

The evolution of genetic networks by non-adaptive processes

Although numerous investigators assume that the global features of genetic networks are moulded by natural selection, there has been no formal demonstration of the adaptive origin of any genetic network. This Analysis shows that many of the qualitative features of known transcriptional networks can arise readily through the non-adaptive processes of genetic drift, mutation and recombination, raising questions about whether natural selection is necessary or even sufficient for the origin of many aspects of gene-network topologies. The widespread reliance on computational procedures that are devoid of population-genetic details to generate hypotheses for the evolution of network configurations seems to be unjustified.