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Groping around a familiar room in the dark, relearning to read after a brain injury, navigating a virtual landscape through an avatar: all are expressions of vicariance--when the brain substitutes one process or function for another. Alain Berthoz shows that this capacity allows humans to think creatively in an increasingly complex world.-- Provided by publisher.

We present here the hologenome theory of evolution, which considers the holobiont (the animal or plant with all of its associated microorganisms) as a unit of selection in evolution. The hologenome is defined as the sum of the genetic information of the host and its microbiota. The theory is based on four generalizations: (1) All animals and plants establish symbiotic relationships with microorganisms. (2) Symbiotic microorganisms are transmitted between generations. (3) The association between host and symbionts affects the fitness of the holobiont within its environment. (4) Variation in the hologenome can be brought about by changes in either the host or the microbiota genomes; under environmental stress, the symbiotic microbial community can change rapidly. These points taken together suggest that the genetic wealth of diverse microbial symbionts can play an important role both in adaptation and in evolution of higher organisms. During periods of rapid changes in the environment, the diverse microbial symbiont community can aid the holobiont in surviving, multiplying and buying the time necessary for the host genome to evolve. The distinguishing feature of the hologenome theory is that it considers all of the diverse microbiota associated with the animal or the plant as part of the evolving holobiont. Thus, the hologenome theory fits within the framework of the 'superorganism' proposed by Wilson and Sober.

Roland Brosch and colleagues report whole-genome sequencing of tubercle bacilli with smooth colony morphology, also known as Mycobacterium canetti and/or Mycobacterium prototuberculosis , obtained from humans with tuberculosis from geographically diverse regions. Their comparative genomic analysis with Mycobacterium tuberculosis and other M. tuberculosis complex members identifies extensive recombination and provides insights into the evolution of mycobacteria. The authors also report that tubercle bacilli with smooth colony morphology show reduced persistence and virulence compared to M. tuberculosis strains in infection experiments in mice. Global spread and limited genetic variation are hallmarks of M. tuberculosis , the agent of human tuberculosis. In contrast, Mycobacterium canettii and related tubercle bacilli that also cause human tuberculosis and exhibit unusual smooth colony morphology are restricted to East Africa. Here, we sequenced and analyzed the whole genomes of five representative strains of smooth tubercle bacilli (STB) using Sanger (4–5× coverage), 454/Roche (13–18× coverage) and/or Illumina DNA sequencing (45–105× coverage). We show that STB isolates are highly recombinogenic and evolutionarily early branching, with larger genome sizes, higher rates of genetic variation, fewer molecular scars and distinct CRISPR-Cas systems relative to M. tuberculosis . Despite the differences, all tuberculosis-causing mycobacteria share a highly conserved core genome. Mouse infection experiments showed that STB strains are less persistent and virulent than M. tuberculosis. We conclude that M. tuberculosis emerged from an ancestral STB-like pool of mycobacteria by gain of persistence and virulence mechanisms, and we provide insights into the molecular events involved.

Colonization of land by plants was a major transition on Earth, but the developmental and genetic innovations required for this transition remain unknown. Physiological studies and the fossil record strongly suggest that the ability of the first land plants to form symbiotic associations with beneficial fungi was one of these critical innovations. In angiosperms, genes required for the perception and transduction of diffusible fungal signals for root colonization and for nutrient exchange have been characterized. However, the origin of these genes and their potential correlation with land colonization remain elusive. A comprehensive phylogenetic analysis of 259 transcriptomes and 10 green algal and basal land plant genomes, coupled with the characterization of the evolutionary path leading to the appearance of a key regulator, a calcium- and calmodulin-dependent protein kinase, showed that the symbiotic signaling pathway predated the first land plants. In contrast, downstream genes required for root colonization and their specific expression pattern probably appeared subsequent to the colonization of land. We conclude that the most recent common ancestor of extant land plants and green algae was preadapted for symbiotic associations. Subsequent improvement of this precursor stage in early land plants through rounds of gene duplication led to the acquisition of additional pathways and the ability to form a fully functional arbuscular mycorrhizal symbiosis.

Convergent evolution is an important phenomenon in the history of life. Despite this, there is no common definition of convergence used by biologists. Instead, several conceptually different definitions are employed. The primary dichotomy is between patternbased definitions, where independently evolved similarity is sufficient for convergence, and process-based definitions, where convergence requires a certain process to produce this similarity. The unacknowledged diversity of definitions can lead to problems in evolutionary research. Process-based definitions may bias researchers away from studying or recognizing other sources of independently evolved similarity, or lead researchers to interpret convergent patterns as necessarily caused by a given process. Thus, pattern-based definitions are recommended. Existing measeures of convergence are reviewed, and two new measures are developed. Both are pattern based and conceptually minimal, quantifying nothing but independently evolved similarity. One quantifies the amount of phenotypic distance between two lineages that is closed by subsequent evolution; the other simply counts the number of lineages entering a region of phenotypic space. The behavior of these measures is explored in simulations; both show acceptable Type I and Type II error. The study of convergent evolution will be facilitated if researchers are explicit about working definitions of convergence and adopt a standard toolbox of convergence measures.

Significance Why do species’ ranges often end when no obvious change in the environment suggests they should? Our theory explains that there is an inherent limit to adaptation arising in any (finite) natural population and identifies the key parameters that determine this limit to a species’ range. Two observable parameters describe the threshold when adaptation fails: ( i ) the loss of fitness due to dispersal to a different environment, and ( ii ) the efficacy of selection relative to stochastic effects in finite populations. Why do species not adapt to ever-wider ranges of conditions, gradually expanding their ecological niche and geographic range? Gene flow across environments has two conflicting effects: although it increases genetic variation, which is a prerequisite for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane proposed that, when the environment varies across space, “swamping” by gene flow creates a positive feedback between low population size and maladaptation, leading to a sharp range margin. However, current deterministic theory shows that, when variance can evolve, there is no such limit. Using simple analytical tools and simulations, we show that genetic drift can generate a sharp margin to a species’ range, by reducing genetic variance below the level needed for adaptation to spatially variable conditions. Aided by separation of ecological and evolutionary timescales, the identified effective dimensionless parameters reveal a simple threshold that predicts when adaptation at the range margin fails. Two observable parameters determine the threshold: ( i ) the effective environmental gradient, which can be measured by the loss of fitness due to dispersal to a different environment; and ( ii ) the efficacy of selection relative to genetic drift. The theory predicts sharp range margins even in the absence of abrupt changes in the environment. Furthermore, it implies that gradual worsening of conditions across a species’ habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible.

A subject of extensive study in evolutionary theory has been the issue of how neutral, redundant copies can be maintained in the genome for long periods of time. Concurrently, examples of adaptive gene duplications to various environmental conditions in different species have been described. At this point, it is too early to tell whether or not a substantial fraction of gene copies have initially achieved fixation by positive selection for increased dosage. Nevertheless, enough examples have accumulated in the literature that such a possibility should be considered. Here, I review the recent examples of adaptive gene duplications and make an attempt to draw generalizations on what types of genes may be particularly prone to be selected for under certain environmental conditions. The identification of copy-number variation in ecological field studies of species adapting to stressful or novel environmental conditions may improve our understanding of gene duplications as a mechanism of adaptation and its relevance to the long-term persistence of gene duplications.

How do we understand and explain the apparent dichotomy between plasticity and robustness in the context of development? Can we identify these complex processes without resorting to 'either/or' solutions? Written by two leaders in the field, this is the first book to fully unravel the complexity of the subject, explaining that the epigenetic processes generating plasticity and robustness are in fact deeply intertwined. It identifies the different mechanisms that generate robustness and the various forms of plasticity, before considering the functional significance of the integrated mechanisms and how the component processes might have evolved. Finally, it highlights the ways in which epigenetic mechanisms could be instrumental in driving evolutionary change. Essential reading for biologists and psychologists interested in epigenetics and evolution, this book is also a valuable resource for biological anthropologists, sociobiologists, child psychologists and paediatricians.

Key Points The hypothesis that differences in gene regulation have an important role in speciation and adaptation is more than 40 years old. RNA sequencing (RNA-seq) allows measurement and comparison of gene expression levels across practically any combination of species at an unprecedented resolution. Comparative studies of gene expression levels in all species studied to date provide compelling evidence that most gene regulatory patterns evolve under evolutionary constraint. It is more difficult to infer the action of positive (directional) selection on gene regulation than the action of stabilizing selection, especially in non-model species such as humans and non-human apes, where environmental and genetic effects might be confounded. Inter-species differences in epigenetic markers can probably explain a substantial fraction of gene expression differences between species. Because a broad range of experimental manipulations are possible in model organisms, studies that focus on model species can move beyond simple comparisons of gene expression and offer deep insights into the causal relationship between regulatory changes and phenotypic evolution. Functional studies in model systems can often shed light on the adaptive phenotypes that were affected by regulatory changes between humans and other primates. Some phenotypes, however (for example, the development of language), are inherently difficult to study using model species. It might be possible to use induced pluripotent stem cells derived differentiated cells from humans and non-human primates to test functionally for the outcomes of inter-species differences in gene regulation. Gene expression levels can now be compared among species at greater resolution. Focusing on work in primates, the authors discuss the evolution of gene expression, ways of exploring mechanisms that underlie expression changes and complementary work in model organisms on the functional effects of expression changes. The hypothesis that differences in gene regulation have an important role in speciation and adaptation is more than 40 years old. With the advent of new sequencing technologies, we are able to characterize and study gene expression levels and associated regulatory mechanisms in a large number of individuals and species at an unprecedented resolution and scale. We have thus gained new insights into the evolutionary pressures that shape gene expression levels and have developed an appreciation for the relative importance of evolutionary changes in different regulatory genetic and epigenetic mechanisms. The current challenge is to link gene regulatory changes to adaptive evolution of complex phenotypes. Here we mainly focus on comparative studies in primates and how they are complemented by studies in model organisms.

The human pathogen Helicobacter pylori displays extensive genetic diversity. While H. pylori is known to evolve during infection, population dynamics inside the gastric environment have not been extensively investigated. Here we obtained gastric biopsies from multiple stomach regions of 16  H. pylori -infected adults, and analyze the genomes of 10  H. pylori isolates from each biopsy. Phylogenetic analyses suggest location-specific evolution and bacterial migration between gastric regions. Migration is significantly more frequent between the corpus and the fundus than with the antrum, suggesting that physiological differences between antral and oxyntic mucosa contribute to spatial partitioning of H. pylori populations. Associations between H. pylori gene polymorphisms and stomach niches suggest that chemotaxis, regulatory functions and outer membrane proteins contribute to specific adaptation to the antral and oxyntic mucosa. Moreover, we show that antibiotics can induce severe population bottlenecks and likely play a role in shaping the population structure of H. pylori . Helicobacter pylori , a bacterial pathogen that infects human stomachs, has high genetic diversity across hosts. Here, Ailloud et al. reveal genetic structuring of H. pylori populations among different stomach regions of individual hosts and find signals of genetic associations with stomach region.