The biogenesis of RNAs and proteins is a threat to the cell. Indeed, the act of transcription and nascent RNAs challenge DNA stability. Both RNAs and nascent proteins can also initiate the formation of toxic aggregates because of their physicochemical properties. In reviewing the literature, I show that co-transcriptional and co-translational biophysical constraints can trigger DNA instability that in turn increases the likelihood that sequences that alleviate the constraints emerge over evolutionary time. These directed genetic variations rely on the biogenesis (...) of small RNAs that are transcribed directly from challenged DNA regions or processed from the transcripts that directly or indirectly generate constraints or aggregates. These small RNAs can then target the genomic regions from which they initially originate and increase the local mutation rate of the targeted loci. This mechanism is based on molecular pathways involved in anti-parasite genome defence systems, and implies that gene expression-related biophysical constraints represent a driving force of genome evolution. Are randomly generated mutations the only source of genetic variation during evolution? This paper describes the molecular mechanisms by which co-transcriptional and co-translational biophysical constraints trigger genetic variations in targeted-genomic sequences in an RNA-depending manner. This directed-mutational process that drives genome evolution is related to antiparasite genome defence systems. (shrink)

In vertebrates it is often found that if one considers a group of genes clustered on a certain chromosome, then the homologues of those genes often form another cluster on a different chromosome. There are four explanations, not necessarily mutually exclusive, to explain how such homologous clusters appeared. Homologous clusters are expected at a low probability even if genes are distributed at random. The duplication of a subset of the genome might create homologous clusters, as would a duplication of (...) the entire genome. Alternatively, it may be adaptive for certain combinations of genes to cluster, although clearly the genes must have duplicated prior to rearrangement into clusters. Molecular phylogenetics provides a means to examine the origins of homologous clusters, although it is difficult to discriminate between the different explanations using current data. However, with more extensive sequencing and mapping of vertebrate genomes, especially those of the early diverging chordates, it should soon become possible to resolve the origins of homologous clusters. BioEssays 21:697–703, 1999. © 1999 John Wiley & Sons, Inc. (shrink)

Frequent lateral genetic transfer undermines the existence of a unique “tree of life” that relates all organisms. Vertical inheritance is nonetheless of vital interest in the study of microbial evolution, and knowing the “tree of cells” can yield insights into ecological continuity, the rates of change of different cellular characters, and the evolutionary plasticity of genomes. Notwithstanding within-species recombination, the relationships most frequently recovered from genomic data at shallow to moderate taxonomic depths are likely to reflect cellular inheritance. At (...) the same time, it is clear that several types of ‘average signals’ from whole genomes can be highly misleading, and the existence of a central tendency must not be taken as prima facie evidence of vertical descent. Phylogenetic networks offer an attractive solution, since they can be formulated in ways that mitigate the misleading aspects of hybrid evolutionary signals in genomes. But the connections in a network typically show genetic relatedness without distinguishing between vertical and lateral inheritance of genetic material. The solution may lie in a compromise between strict tree-thinking and network paradigms: build a phylogenetic network, but identify the set of connections in the network that are potentially due to vertical descent. Even if a single tree cannot be unambiguously identified, choosing a subnetwork of putative vertical connections can still lead to drastic reductions in the set of candidate vertical hypotheses. (shrink)

In fact, nearly every scientist who has written on the general subject of evolution has felt compelled to show how deftly he can skate toward the abyss of teleology without falling in.J.H. Campbell, 163Molecular biology has as its primary objective the elucidation of the coupling between genotype and phenotype. This goal has so far been pursued within a neoDarwinian theoretical framework which is relatively limited. Within this framework we can indeed understand remarkably well the mechanisms of replication and expression (...) of genes and the means by which replication and expression are regulated in cells; we know how genotype determines phenotype at the molecular level, in single cells. We are also close to an understanding of the relationship between genes and development in muticellular animals and plants. (shrink)

In fact, nearly every scientist who has written on the general subject of evolution has felt compelled to show how deftly he can skate toward the abyss of teleology without falling in.J.H. Campbell, 163Molecular biology has as its primary objective the elucidation of the coupling between genotype and phenotype. This goal has so far been pursued within a neoDarwinian theoretical framework which is relatively limited. Within this framework we can indeed understand remarkably well the mechanisms of replication and expression (...) of genes and the means by which replication and expression are regulated in cells; we know how genotype determines phenotype at the molecular level, in single cells. We are also close to an understanding of the relationship between genes and development in muticellular animals and plants. (shrink)

Like biological species, languages change over time. As noted by Darwin, there are many parallels between language evolution and biological evolution. Insights into these parallels have also undergone change in the past 150 years. Just like genes, words change over time, and language evolution can be likened to genome evolution accordingly, but what kind of evolution? There are fundamental differences between eukaryotic and prokaryotic evolution. In the former, natural variation entails the gradual accumulation (...) of minor mutations in alleles. In the latter, lateral gene transfer is an integral mechanism of natural variation. The study of language evolution using biological methods has attracted much interest of late, most approaches focusing on language tree construction. These approaches may underestimate the important role that borrowing plays in language evolution. Network approaches that were originally designed to study lateral gene transfer may provide more realistic insights into the complexities of language evolution.Editor's suggested further reading in BioEssays Linguistic evidence supports date for Homeric epics Abstract. (shrink)

Horizontal transfer (HT) is the transmission of genetic material between non‐mating species, a phenomenon thought to occur rarely in multicellular eukaryotes. However, many transposable elements (TEs) are not only capable of HT, but have frequently jumped between widely divergent species. Here we review and integrate reported cases of HT in retrotransposons of the BovB family, and DNA transposons, over a broad range of animals spanning all continents. Our conclusions challenge the paradigm that HT in vertebrates is restricted to infective long (...) terminal repeat (LTR) retrotransposons or retroviruses. This raises the possibility that other non‐LTR retrotransposons, such as L1 or CR1 elements, believed to be only vertically transmitted, can horizontally transfer between species. Growing evidence indicates that the process of HT is much more general across different TEs and species than previously believed, and that it likely shapes eukaryotic genomes and catalyses genome evolution. (shrink)

Chromosomal rearrangements frequently occur at specific places (“hot spots”) in the genome. These recombination hot spots are usually separated by 50–100 kb regions of DNA that are rarely involved in rearrangements. It is quite likely that there is a correlation between the above‐mentioned distances and the average size of DNA loops fixed at the nuclear matrix. Recent studies have demonstrated that DNA loop anchorage regions can be fairly long and can harbor DNA recombination hot spots. We previously proposed that (...) chromosomal DNA loops may constitute the basic units of genome organization in higher eukaryotes. In this review, we consider recombination between DNA loop anchorage regions as a possible source of genome evolution. (shrink)

Graphical AbstractThe fungus Neurospora comprises a novel model for testing hypotheses involving the role of sex and reproduction in eukaryotic genome evolution. Its variation in reproductive mode, lack of sex-specific genotypes, availability of phylogenetic species, and young sex-regulating chromosomes make research in this genus complementary to animal and plant models.

Balanced pools of deoxyribonucleoside triphosphates (dNTPs) are essential for DNA replication to occur with maximum fidelity. Conditions that create biased dNTP pools stimulate mutagenesis, as well as other phenomena, such as recombination or cell death. In this essay we consider the effective dNTP concentrations at replication sites under normal conditions, and we ask how maintenance of these levels contributes toward the natural fidelity of DNA replication. We focus upon two questions. (1) In prokaryotic systems, evidence suggests that replication is driven (...) by small, localized, rapidly replenished dNTP pools that do not equilibrate with the bulk dNTP pools in the cell. Since these pools cannot be analyzed directly, what indirect approaches can illuminate the nature of these replication‐active pools? (2) In eukaryotic cells, the normal dNTP pools are highly asymmetric, with dGTP being the least abundant nucleotide. Moreover, the composition of the dNTP pools changes as cells progress through the cell cycle. To what extent might these natural asymmetries contribute toward a recently described phenomenon, the differential rate of evolution of different genes in the same genome? (shrink)

Although I am a molecular immunologist from another area of that wide discipline, for many years I have had a deep fascination with the whole topic of ancestral haplotypes. After recently reading an interesting article in this journal, “Reflections on the History and Ethics of the Proper Attribution and Misappropriation of Merit” , I was impelled to act and submit this essay for publication. The title of Gans’s article points to some of my own motivations. Gans outlines how many important (...) scientific discoveries are deliberately overlooked or inappropriately cited by contemporaries, or even completely misappropriated by undeserving scientists coming soon afterwards.It was Ceppellini and co-workers .. (shrink)

Recent sequencing of the metazoan Oikopleura dioica genome has provided important insights, which challenges the current understanding of eukaryotic genome evolution. Many genomic features of O. dioica show deviation from the commonly observed trends in other eukaryotic genomes. For instance, O. dioica has a rapidly evolving, highly compact genome with a divergent intron‐exon organization. Additionally, O. dioica lacks the minor spliceosome and key DNA repair pathway genes. Even with a compact genome, O. dioica contains tandem (...) repeats, comparable to other eukaryotes, and shows lineage‐specific expansion of certain protein domains. Here, we review its genomic features in the context of current knowledge, discuss implications for contemporary biology and identify areas for further research. Analysis of the O. dioica genome suggests that non‐adaptive forces such as elevated mutation rates might influence the evolution of genome architecture. The knowledge of unique genomic features and splicing mechanisms in O. dioica may be exploited for synthetic biology applications, such as generation of orthogonal splicing systems. (shrink)

A common belief is that evolution generally proceeds towards greater complexity at both the organismal and the genomic level, numerous examples of reductive evolution of parasites and symbionts notwithstanding. However, recent evolutionary reconstructions challenge this notion. Two notable examples are the reconstruction of the complex archaeal ancestor and the intron‐rich ancestor of eukaryotes. In both cases, evolution in most of the lineages was apparently dominated by extensive loss of genes and introns, respectively. These and many other cases (...) of reductive evolution are consistent with a general model composed of two distinct evolutionary phases: the short, explosive, innovation phase that leads to an abrupt increase in genome complexity, followed by a much longer reductive phase, which encompasses either a neutral ratchet of genetic material loss or adaptive genome streamlining. Quantitatively, the evolution of genomes appears to be dominated by reduction and simplification, punctuated by episodes of complexification. (shrink)

The cryptomonads and chlorarachniophytes are two unicellular algal lineages with complex cellular structures and fascinating evolutionary histories. Both groups acquired their photosynthetic abilities through the assimilation of eukaryotic endosymbionts. As a result, they possess two distinct cytosolic compartments and four genomes—two nuclear genomes, an endosymbiont‐derived plastid genome and a mitochondrial genome derived from the host cell. Like mitochondrial and plastid genomes, the genome of the endosymbiont nucleus, or ‘nucleomorph’, of cryptomonad and chlorarachniophyte cells has been greatly reduced (...) through the combined effects of gene loss and intracellular gene transfer. This article focuses on the structure, function, origin and evolution of cryptomonad and chlorarachniophyte nucleomorph genomes in light of recent comparisons of genome sequence data from both groups. It is now possible to speculate on the reasons that nucleomorphs persist in cryptomonads and chlorarachniophytes but have been lost in all other algae with plastids of secondary endosymbiotic origin. BioEssays 29:392–402, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

Prokaryotic genomes of endosymbionts and parasites are examples of naturally evolved minimal cells, the study of which can shed light on life in its minimum form. Their diverse biology, their lack of a large set of orthologous genes and the existence of essential linage (and environmentally) specific genes all illustrate the diversity of genes building up naturally evolved minimal cells. This conclusion is reinforced by the fact that sometimes the same essential function is performed by genes from different evolutionary origins. (...) Nevertheless, all cells perform a set of life‐essential functions however different their cell machinery and environment in which they thrive. An upcoming challenge for biologists will be to discern, by studying differences and similarities in current biodiversity, how cells with reduced genomes have adapted while retaining all basic life‐supporting functions. (shrink)

The paper addresses a central problem in evolutionary biology and cognitive science; evolution of a neural based learning phenotype from a structured genotype. It describes morphogenesis of a neural network-based cognitive system, starting from a single genotype having a modulon control structure. It further shows how such a system, denoted as GALA architecture, growing its own recurrent axon connections, can further develop into various structures capable of learning in different learning modes, such as advice learning, reinforcement learning, and emotion (...) learning. The paper particularly considers the emotion learning systems and their motivational structure. A simulation experiment is provided to illustrate the theoretical issues discussed. (shrink)

The role of gene expression in evolutionary adaptation has been a subject of debate for over 40 years.cis‐regulation of transcription has been proposed to be the primary source of morphological novelty in evolution, though this is based on only a handful of examples. Recently the first genome‐wide studies of gene expression adaptation have been published, giving us an initial global view of this process. Systematic studies such as these will allow a number of key questions currently facing the (...) field of gene expression evolution to be addressed. (shrink)

Few topics have intrigued biologists as much as the evolution of sex. Understanding why sex persists despite its costs requires not just rigorous theoretical study, but also empirical data on related fundamental issues, including the nature of genetic variance for fitness, patterns of genetic interactions, and the dynamics of adaptation. The increasing feasibility of examining genomes in an experimental context is now shedding new light on these problems. Using this approach, McDonald et al. recently demonstrated that sex uncouples beneficial (...) and deleterious mutations, allowing selection to proceed more effectively with sex than without. Here we discuss the insights provided by this study, along with other recent empirical work, in the context of the major theoretical models for the evolution of sex. (shrink)

The discoveries, advancements and continuing controversies in the field of molecular evolution are reviewed. Topics summarized are (1) the evolution of the genetic code, (2) gene evolution including the demonstration of homology, estimation of sequence divergence, phylogenetic trees, the molecular clock and the origin of genes and gene families by various genetic mechanisms, and (3) eukaryotic genome evolution, including the highly repeated satellite sequences, the interspersed and potentially mobile repeated sequences and the unique sequence fraction (...) of the genome. (shrink)

Humans spend large portions of their time and energy talking to one another, yet it remains unclear whether this activity is primarily selfish or altruistic. Here, it is shown how parent‐of‐origin specific gene expression—or “genomic imprinting”—may provide an answer to this question. First, it is shown why, regarding language, only altruistic or selfish scenarios are expected. Second, it is pointed out that an individual's maternal‐origin and paternal‐origin genes may have different evolutionary interests regarding investment into language, and that this intragenomic (...) conflict may drive genomic imprinting which—as the direction of imprint depends upon whether investment into language is relatively selfish or altruistic—may be used to discriminate between these two possibilities. Third, predictions concerning the impact of various mutations and epimutations at imprinted loci on language pathologies are derived. In doing so, a framework is developed that highlights avenues for using intragenomic conflicts to investigate the evolutionary drivers of language. (shrink)

The cerebral cortex controls our most distinguishing higher cognitive functions. Human‐specific gene expression differences are abundant in the cerebral cortex, yet we have only begun to understand how these variations impact brain function. This review discusses the current evidence linking non‐coding regulatory DNA changes, including enhancers, with neocortical evolution. Functional interrogation using animal models reveals converging roles for our genome in key aspects of cortical development including progenitor cell cycle and neuronal signaling. New technologies, including iPS cells and (...) organoids, offer potential alternatives to modeling evolutionary modifications in a relevant species context. Several diseases rooted in the cerebral cortex uniquely manifest in humans compared to other primates, thus highlighting the importance of understanding human brain differences. Future studies of regulatory loci, including those implicated in disease, will collectively help elucidate key cellular and genetic mechanisms underlying our distinguishing cognitive traits. (shrink)

Despite the enormous diversity in plant form, structure and growth environment across the seed‐bearing plants (angiosperms and gymnosperms), the chloroplast genome has, with few exceptions, remained remarkably conserved. This conservation suggests the existence of universal evolutionary selection pressures associated with photosynthesis—the primary function of chloroplasts. The stark exceptions to this conservation occur in parasitic angiosperms, which have escaped the dominant model by evolving the capacity to obtain some or all of their carbon (and nutrients) from their plant hosts. The (...) consequence of this evolution to parasitism is a relaxation of the evolutionary constraints associated with the need to maintain photosynthetic function, the very function that drove early stages of the ancient symbiotic relationship that produced the contemporary chloroplast. Extreme examples of reductionism among parasitic angiosperms reveals major alterations in chloroplast function with the loss of photosynthetic capacity and, with that, massive alterations in chloroplast genome content. This review highlights emerging patterns in reported gene loss and gene retention in the chloroplast genomes of parasitic plants. Some gene losses appear to occur in the early stages of parasitic evolution, even before the loss of photosynthetic capacity, like the chlororespiratory (ndh) genes. This contrasts with unexpected gene retentions, like that of the rbcL gene responsible for photosynthetic carbon dioxide fixation, and belies current understanding of gene function. The review relates gene retention to current knowledge of protein function and gene processing that has implications to broader aspects of genome conservation in organelles. BioEssays 26:235–247, 2004. Wiley Periodicals, Inc. (shrink)

Forensic genomics now enables law enforcement agencies to undertake rapid and detailed analysis of suspect samples using a technique known as massively parallel sequencing (MPS), including information such as physical traits, biological ancestry, and medical conditions. This article discusses the implications of MPS and provides ethical analysis, drawing on the concept of joint rights applicable to genomic data, and the concept of collective moral responsibility (understood as joint moral responsibility) that are applicable to law enforcement investigations that utilize genomic data. (...) The widespread and unconstrained use of this technology without appropriate legal protections of individual moral rights and associated accountability mechanisms, could potentially not only involve violations of individual moral rights but also lead to an unacceptable shift in the balance of power between governments and the citizenry. We argue that in light of the rights of victims and the security benefits for society, there is a collective moral responsibility for individuals to submit their DNA to law enforcement and for MPS to be used where other, less invasive techniques are not effective. However, this application should be limited by legislation, including that any data obtained should be directly relevant to the investigation and should be destroyed at the conclusion of the investigation. (shrink)

Investigation of the evolution of the DNA sequences that comprise a small gene cluster in five closely related species of Drosophila shows that it evolves as a mosaic, with adjacent subregions displaying very different rates and types of evolution. It appears that local differences in the influence of selectional and mutational forces result in the formation of these distinct subregions.

“ The Origins of Genome Architecture ” by Michael Lynch (2007) may not immediately sound like a book that someone interested in the philosophy of biology would grab off the shelf. But there are three important reasons why you should read this book. Firstly, if you want to understand biological evolution, you should have at least a passing familiarity with evolutionary change at the level of the genome. This is not to say that everyone interested in (...) class='Hi'>evolution should be a geneticist or a bioinformatician, but that a working knowledge of genetic change is an essential part of the intellectual toolkit of modern evolutionary biology, even if your primary focus is the evolution of behaviour or the diversity of communities. Secondly, this book provides excellent examples of another important tool in the biologist’s intellectual toolkit, but one that is rarely explained or illustrated to such an extent: null (or neutral) models. The role null models play in testing hypotheses in evolution is a central focus of this book. Thirdly, as an accomplished work of advocacy for a strictly microevolutionary view of evolution, this book provides grist for the mill for the important debate about whether population genetic processes are the sine qua non of evolutionary explanations. (shrink)

Genome complexity is correlated with biological complexity. A recent paper by Michael Lynch proposes that evolution of complex genomic architecture was driven primarily by non‐adaptive stochastic forces, rather than by adaptive evolution.1 A general negative relationship between selection efficiency and genome complexity provides a strong support for this hypothesis. The broad capacity of this theory is both its appeal and source for criticism. BioEssays 28: 979–982, 2006. © 2006 Wiley Periodicals, Inc.

Sponges are important but often‐neglected organisms. The absence of classical animal traits (nerves, digestive tract, and muscles) makes sponges challenging for non‐specialists to work with and has delayed getting high quality genomic data compared to other invertebrates. Yet analyses of sponge genomes and transcriptomes currently available have radically changed our understanding of animal evolution. Sponges are of prime evolutionary importance as one of the best candidates to form the sister group of all other animals, and genomic data are essential (...) to understand the mechanisms that control animal evolution and diversity. Here we review the most significant outcomes of current genomic and transcriptomic analyses of sponges, and discuss limitations and future directions of sponge transcriptomic and genomic studies. (shrink)

This chapter analyzes the revolutionary impact of genomic science on the study of evolution, and addresses the issues that modern evolutionary biology has either learned or needs to grapple with in the age of genomics. It suggests that transposable elements are genomic constituents which can result in novel genes or gene functions. The chapter proposes that although epigenetic changes remain compatible with the Modern Synthesis, dissecting the details could possibly result in new insights into the dynamics of the evolutionary (...) process which are not currently considered. It shows that the nature of epistasis is increasingly gaining prominence, and offers new avenues of research into the genetic architecture of evolutionary change. (shrink)

Recent and not so recent advances in our molecular understanding of the genome make the once prevalent view of the genome as a passive container of genetic information (i.e., genes) untenable, and emphasize the importance of the internal organization and re-organization dynamics of the genome for both development and evolution. While this conclusion is by now well accepted, the construction of a comprehensive conceptual framework for studying the genome as a dynamic system, capable of self-organization (...) and adaptive behavior is still underway. This work deals with the effect of such a conceptual shift on evolutionary thought. Specifically, I try to articulate the conceptual commitments and obligations of views that privilege explanatorily or causally the genome, its dynamics and mechanisms, over genes. I refer to this class of views as belonging to ‘the genome perspective’. (shrink)

Mitochondrial genomes are clearly marked by a strong tendency towards reductive evolution. This tendency has been facilitated by the transfer of most of the essential genes for mitochondrial propogation and function to the nuclear genome. The most extreme examples of genomic simplification are seen in animal mitochondria, where there also are the greatest tendencies to codon reassignment. The reassignment of codons to amino acids different from those designated in the so called universal code is seen in part as (...) an expression of the reduction of the number of genes used by these genomes to code for tRNA species. The driving force for the reductive evolution of mitochondrial genomes is identifed with two population genetic effects which may also be operating on populations of parasites. (shrink)

The presence and role of microbes in human cancers has come full circle in the last century. Tumors are no longer considered aseptic, but implications for cancer biology and oncology remain underappreciated. Opportunities to identify and build translational diagnostics, prognostics, and therapeutics that exploit cancer's second genome—the metagenome—are manifold, but require careful consideration of microbial experimental idiosyncrasies that are distinct from host‐centric methods. Furthermore, the discoveries of intracellular and intra‐metastatic cancer bacteria necessitate fundamental changes in describing clonal evolution (...) and selection, reflecting bidirectional interactions with non‐human residents. Reconsidering cancer clonality as a multispecies process similarly holds key implications for understanding metastasis and prognosing therapeutic resistance while providing rational guidance for the next generation of bacterial cancer therapies. Guided by these new findings and challenges, this Review describes opportunities to exploit cancer's metagenome in oncology and proposes an evolutionary framework as a first step towards modeling multispecies cancer clonality. Also see the video abstract here: https://youtu.be/-WDtIRJYZSs. (shrink)

Developing ethical standards for clinical use of large-scale genome and exome sequencing has proven challenging, in part due to the inevitability of incidental or secondary findings. Policy of the American College of Medical Genetics and Genomics has evolved but remains problematic. In 2013, ACMG issued policy recommending mandatory analysis of 56 extra genes whenever sequencing was ordered for any indication, in order to ascertain positive findings in pathogenic and actionable genes. Widespread objection yielded a 2014 amendment allowing patients to (...) opt-out from analysis of the extra genes. In 2015, ACMG published the amended policy, providing that patients could opt out of the full set of extra genes, but not a subset. In 2016, ACMG enlarged the set and indicated planned expansion of the roster of extra genes to include pharmacogenetic findings. ACMG policy does not protect the respect for patient choice that prevails in other domains of clinical medicine, where informed consent allows patients to opt in to desired testing. By creating an expanding domain of genomic testing that will be routinely conducted unless patients reject the entire set of extra tests, ACMG creates an exceptional domain clinical practice that is not supported by ethics or science. (shrink)

Our understanding of genomic reorganization, the mechanics of genomic transmission to offspring during germ line formation, and how these structural changes contribute to the speciation process, and genetic disease is far from complete. Earlier attempts to understand the mechanism(s) and constraints that govern genome remodeling suffered from being too narrowly focused, and failed to provide a unified and encompassing view of how genomes are organized and regulated inside cells. Here, we propose a new multidisciplinary Integrative Breakage Model for the (...) study of genome evolution. The analysis of the high‐level structural organization of genomes (nucleome), together with the functional constrains that accompany genome reshuffling, provide insights into the origin and plasticity of genome organization that may assist with the detection and isolation of therapeutic targets for the treatment of complex human disorders. (shrink)

Honeybees display a fascinating social behavior. The structural basis for this behavior, which made the bee a model organism for the study of communication, learning and memory formation, is the tiny insect brain. Neurons of the brain communicate via messenger molecules. Among these molecules, neuropeptides represent the structurally most‐diverse group and occupy a high hierarchic position in the modulation of behavior. A recent analysis of the honeybee genome revealed a considerable number of predicted (200) and confirmed (100) neuropeptides in (...) this insect.1 Is this quantity merely the result of advanced mass spectrometric techniques and bioinformatic tools or does it reflect the expression of more of these important messenger molecules, more than known from other insects studied so far? Our analysis of the data suggests that the social behavior is by no means correlated with a specific increase in the number of neuropeptides. Indeed, the honeybee genome is likely to contain fewer neuropeptide genes, neuropeptide paralogues and neuropeptide receptor genes than the solitary fruitfly Drosophila. BioEssays 29:416–421, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

Plastids and mitochondria arose through endosymbiotic acquisition of formerly free-living bacteria. During more than a billion years of subsequent concerted evolution, the three genomes of plant cells have undergone dramatic structural changes to optimize the expression of the compartmentalized genetic material and to fine-tune the communication between the nucleus and the organelles. The chimeric composition of many multiprotein complexes in plastids and mitochondria (one part of the subunits being nuclear encoded and another one being encoded in the organellar (...) class='Hi'>genome) provides a paradigm for co-evolution at the cellular level. In this paper, we discuss the co-evolution of nuclear and organellar genomes in the context of environmental adaptation in species and populations. We highlight emerging genetic model systems and new experimental approaches that are particularly suitable to elucidate the molecular basis of co-adaptation processes and describe how nuclear-cytoplasmic co-evolution can cause genetic incompatibilities that contribute to the establishment of hybridization barriers, ultimately leading to the formation of new species. (shrink)