Author Correction: The mid-developmental transition and the evolution of animal body plans.

An Amendment to this paper has been published and can be accessed via a link at the top of the paper.

The mid-developmental transition and the evolution of animal body plans.

Animals are grouped into ~35 'phyla' based upon the notion of distinct body plans. Morphological and molecular analyses have revealed that a stage in the middle of development--known as the phylotypic period--is conserved among species within some phyla. Although these analyses provide evidence for their existence, phyla have also been criticized as lacking an objective definition, and consequently based on arbitrary groupings of animals. Here we compare the developmental transcriptomes of ten species, each annotated to a different phylum, with a wide range of life histories and embryonic forms. We find that in all ten species, development comprises the coupling of early and late phases of conserved gene expression. These phases are linked by a divergent 'mid-developmental transition' that uses species-specific suites of signalling pathways and transcription factors. This mid-developmental transition overlaps with the phylotypic period that has been defined previously for three of the ten phyla, suggesting that transcriptional circuits and signalling mechanisms active during this transition are crucial for defining the phyletic body plan and that the mid-developmental transition may be used to define phylotypic periods in other phyla. Placing these observations alongside the reported conservation of mid-development within phyla, we propose that a phylum may be defined as a collection of species whose gene expression at the mid-developmental transition is both highly conserved among them, yet divergent relative to other species.

Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer.

The concept of germ layers has been one of the foremost organizing principles in developmental biology, classification, systematics and evolution for 150 years (refs 1 - 3). Of the three germ layers, the mesoderm is found in bilaterian animals but is absent in species in the phyla Cnidaria and Ctenophora, which has been taken as evidence that the mesoderm was the final germ layer to evolve. The origin of the ectoderm and endoderm germ layers, however, remains unclear, with models supporting the antecedence of each as well as a simultaneous origin. Here we determine the temporal and spatial components of gene expression spanning embryonic development for all Caenorhabditis elegans genes and use it to determine the evolutionary ages of the germ layers. The gene expression program of the mesoderm is induced after those of the ectoderm and endoderm, thus making it the last germ layer both to evolve and to develop. Strikingly, the C. elegans endoderm and ectoderm expression programs do not co-induce; rather the endoderm activates earlier, and this is also observed in the expression of endoderm orthologues during the embryology of the frog Xenopus tropicalis, the sea anemone Nematostella vectensis and the sponge Amphimedon queenslandica. Querying the phylogenetic ages of specifically expressed genes reveals that the endoderm comprises older genes. Taken together, we propose that the endoderm program dates back to the origin of multicellularity, whereas the ectoderm originated as a secondary germ layer freed from ancestral feeding functions.

Evolution of heat-shock protein expression underlying adaptive responses to environmental stress.

Heat-shock proteins (Hsps) and their cognates are primary mitigators of cell stress. With increasingly severe impacts of climate change and other human modifications of the biosphere, the ability of the heat-shock system to affect evolutionary fitness in environments outside the laboratory and to evolve in response is topic of growing importance. Since the last major reviews, several advances have occurred. First, demonstrations of the heat-shock response outside the laboratory now include many additional taxa and environments. Many of these demonstrations are only correlative, however. More importantly, technical advances in "omic" quantification of nucleic acids and proteins, genomewide association analysis, and manipulation of genes and their expression have enabled the field to move beyond correlation. Several consequent advances are already evident: The pathway from heat-shock gene expression to stress tolerance in nature can be extremely complex, mediated through multiple biological processes and systems, and even multiple species. The underlying genes are more numerous, diverse and variable than previously appreciated, especially with respect to their regulatory variation and epigenetic changes. The impacts and limitations (e.g., due to trade-offs) of natural selection on these genes have become more obvious and better established. At last, as evolutionary capacitors, Hsps may have distinctive impacts on the evolution of other genes and ecological consequences.

Locomotion in response to shifting climate zones: not so fast.

Although a species' locomotor capacity is suggestive of its ability to escape global climate change, such a suggestion is not necessarily straightforward. Species vary substantially in locomotor capacity, both ontogenetically and within/among populations, and much of this variation has a genetic basis. Accordingly, locomotor capacity can and does evolve rapidly, as selection experiments demonstrate. Importantly, even though this evolution of locomotor capacity may be rapid enough to escape changing climate, genetic correlations among traits (often due to pleiotropy) are such that successful or rapid dispersers are often limited in colonization or reproductive ability, which may be viewed as a trade-off. The nuanced assessment of this variation and evolution is reviewed for well-studied models: salmon, flying versus flightless insects, rodents undergoing experimental evolution, and metapopulations of butterflies. This work reveals how integration of physiology with population biology and functional genomics can be especially informative.

Heat-shock promoters: targets for evolution by P transposable elements in Drosophila.

Transposable elements are potent agents of genomic change during evolution, but require access to chromatin for insertion-and not all genes provide equivalent access. To test whether the regulatory features of heat-shock genes render their proximal promoters especially susceptible to the insertion of transposable elements in nature, we conducted an unbiased screen of the proximal promoters of 18 heat-shock genes in 48 natural populations of Drosophila. More than 200 distinctive transposable elements had inserted into these promoters; greater than 96% are P elements. By contrast, few or no P element insertions segregate in natural populations in a "negative control" set of proximal promoters lacking the distinctive regulatory features of heat-shock genes. P element transpositions into these same genes during laboratory mutagenesis recapitulate these findings. The natural P element insertions cluster in specific sites in the promoters, with up to eight populations exhibiting P element insertions at the same position; laboratory insertions are into similar sites. By contrast, a "positive control" set of promoters resembling heat-shock promoters in regulatory features harbors few P element insertions in nature, but many insertions after experimental transposition in the laboratory. We conclude that the distinctive regulatory features that typify heat-shock genes (in Drosophila) are especially prone to mutagenesis via P elements in nature. Thus in nature, P elements create significant and distinctive variation in heat-shock genes, upon which evolutionary processes may act.

Evidence-based appointment and promotion of academic faculty at the University of Chicago.

The authors report how one academic medical center (AMC) and associated nonclinical departments implemented evidence-based academic criteria and an evidence-based academic vetting process, which may be models for other institutions. In 2004-2005, The University of Chicago Division of the Biological Sciences and Pritzker School of Medicine reconceptualized its appointment, promotion, and tenure criteria to recognize all forms of scholarship as equally legitimate bases for academic tenure. The revised criteria also accommodate differences in academic effort consistent with varying clinical demands. Implementation of these criteria, however, necessitated revised practices in providing objective evidence and analysis of their satisfaction. Three complementary mechanisms now yield excellent evidence and analysis. The first, electronic forms (e-forms) comprise highly specific response items with embedded instructions, advice, and rationale. The e-forms encourage candidates and departments to provide the evidence that subsequent review needs to evaluate appointment or promotion proposals. Unexpectedly, the e-forms have been coopted as effective mechanisms for faculty development. Second, a faculty dean of academic affairs, a regular faculty member, was appointed to provide robust academic authority and perspective to the process. Third, the promotion and tenure advisory committee was restricted to evaluating academic criteria, and from considerations of institutional value. This change interposed a "firewall" between academic and institutional review. These changes have attenuated dissatisfaction with the appointments and promotions process both within and outside the AMC.

Remarkable site specificity of local transposition into the Hsp70 promoter of Drosophila melanogaster.

Heat-shock genes have numerous features that ought to predispose them to insertional mutagenesis via transposition. To elucidate the evolvability of heat-shock genes via transposition, we have exploited a local transposition technique and Drosophila melanogaster strains with EPgy2 insertions near the Hsp70 gene cluster at 87A7 to produce numerous novel EPgy2 insertions into these Hsp70 genes. More than 50% of 45 independent insertions were made into two adjacent nucleotides in the proximal promoter at positions -96 and -97, and no insertions were into a coding or 3'-flanking sequence. All inserted transposons were in inverse orientation to the starting transposon. The frequent insertion into nucleotides -96 and -97 is consistent with the DNase hypersensitivity, absence of nucleosomes, flanking GAGA-factor-binding sites, and nucleotide sequence of this region. These experimental insertions recapitulated many of the phenotypes of natural transposition into Hsp70: reduced mRNA expression, less Hsp70 protein, and decreased inducible thermotolerance. The results suggest that the distinctive features of heat-shock promoters, which underlie the massive and rapid expression of heat-shock genes upon heat shock, also are a source of evolutionary variation on which natural selection can act.

Key issues in achieving an integrative perspective on stress.

An integrative perspective on molecular mechanisms of stress resistance requires understanding of these mechanisms not just in vitro or in the model organism in the research laboratory - but in the healthy or diseased human in society,in the cultivated plant or animal in agricultural production,and in populations and species in natural communities and ecosystems. Such understanding involves careful attention to the context in which the organism normally undergoes stress,and appreciation that biological phenomena occur at diverse levels of organization (from molecule to ecosystem). Surprisingly,three issues fundamental to achieving an integrative perspective are presently unresolved: (i) Is variation in lower-level traits (nucleotide sequences, genes, gene products) seldom, commonly, or always consequential for stress resistance? (ii) Does environmental stress reduce or enhance genetic variation, which is the raw material of evolution? (iii) Is the present distribution of organisms along natural gradients of stress largely the result of organisms living where they can, or is adaptive evolution generally sufficient to overcome stress? Effective collaboration among disciplinary specialists and meta-analysis may be helpful in resolving these issues.

Thermal preconditioning and heat-shock protein 72 preserve synaptic transmission during thermal stress.

As with other tissues, exposing the mammalian CNS to nonlethal heat stress (i.e., thermal preconditioning) increases levels of heat-shock proteins (Hsps) such as Hsp70 and enhances the viability of neurons under subsequent stress. Using a medullary slice preparation from a neonatal mouse, including the site of the neural network that generates respiratory rhythm (the pre-Bötzinger complex), we show that thermal preconditioning has an additional fundamental effect, protection of synaptic function. Relative to 30 degrees C baseline, initial thermal stress (40 degrees C) greatly increased the frequency of synaptic currents recorded without pharmacological manipulation by approximately 17-fold (p < 0.01) and of miniature postsynaptic currents (mPSCs) elicited by GABA (20-fold) glutamate (10-fold), and glycine (36-fold). Thermal preconditioning (15 min at 40 degrees C) eliminated the increase in frequency of overall synaptic transmission during acute thermal stress and greatly attenuated the frequency increases of GABAergic, glutamatergic, and glycinergic mPSCs (for each, p < 0.05). Moreover, without thermal preconditioning, incubation of slices in solution containing inducible Hsp70 (Hsp72) mimicked the effect of thermal preconditioning on the stress-induced release of neurotransmitter. That preconditioning and exogenous Hsp72 can affect and preserve normal physiological function has important therapeutic implications.

Reverse transcriptional profiling: non-correspondence of transcript level variation and proximal promoter polymorphism.

BACKGROUND: Variation in gene expression between two Drosophila melanogaster strains, as revealed by transcriptional profiling, seldom corresponded to variation in proximal promoter sequence for 34 genes analyzed. Two sets of protein-coding genes were selected from pre-existing microarray data: (1) those whose expression varied significantly and reproducibly between strains, and (2) those whose transcript levels did not vary. Only genes whose regulation of expression was uncharacterized were chosen. At least one kB of the proximal promoters of 15-19 genes in each set was sequenced and compared between strains (Oregon R and Russian 2b). RESULTS: Of the many promoter polymorphisms, 89.6% were SNPs and 10.4% were indels, including homopolymer tracts, microsatellite repeats, and putative transposable element footprints. More than half of the SNPs were changes within a nucleotide class. Hypothetically, genes differing in expression between the two strains should have more proximal promoter polymorphisms than those whose expression is similar. The number, frequency, and type of polymorphism, however, were the same in both sets of genes. In fact, the promoters of six genes with significantly different mRNA expression were identical in sequence. CONCLUSION: For these genes, sequences external to the proximal promoter, such as enhancers or in trans, must play a greater role than the proximal promoter in transcriptomic variation between D. melanogaster strains.

What accounts for the wide variation in life span of genetically identical organisms reared in a constant environment?

Individual organisms show marked variability in life span, even when they are of the same genotype and are raised in a common environment protected from extrinsic hazards. This intrinsic variability of life span is thought to arise from the stochastic nature of the cellular and molecular mechanisms controlling development and ageing. In this article we review what is currently understood about the factors underlying the variability of life span and consider the implications for research that aims to improve the predictability of health in old age.

What evidence is there for the existence of individual genes with antagonistic pleiotropic effects?

Classical evolutionary theory predicts the existence of genes with antagonistic effects on longevity and various components of early-life fitness. Quantitative genetic studies have provided convincing evidence that such genes exist. However, antagonistic pleiotropic effects have rarely been attributed to individual loci. We examine several classes of longevity-assurance genes: those involved in regulation of the gonad; the insulin-like growth factor pathway; free-radical scavenging; heat shock proteins and apoptosis. We find initial evidence that antagonistic pleiotropic effects are pervasive in each of these classes of genes and in various model systems--although most studies lack explicit studies of fitness components. This is particularly true of human studies. Very little is known about the early-life fitness effects of longevity loci. Given the possible medical importance of such effects we urge their future study.

Aims of undergraduate physiology education: a view from the University of Chicago.

Physiology may play an important, if not essential role, in a liberal arts education because it provides a context for integrating information and concepts from diverse biological and extra-biological disciplines. Instructors of physiology may aid in fulfilling this role by clarifying the core concepts that physiological details exemplify. As an example, presented here are the core principles that are the basis for an undergraduate physiology course taught at the University of Chicago. The first of these is: Evolution has resulted in organisms comprising mechanisms for maintenance, growth, and reproduction, despite perturbations of the internal and external environment. Such principles necessitate a coupling of physiology to diverse disciplines (i.e., "sciomics") and provide a basis for integrating discoveries in other disciplines.

Response to natural and laboratory selection at the Drosophila hsp70 genes.

To determine whether and how laboratory and natural selection act on the hsp70 (70-Kd heat-shock protein) genes of Drosophila melanogaster, we examined hsp70 allele frequencies in two sets of populations. First, five populations reared at different temperatures for more than 20 years differentially fixed both a large insertion/deletion (indel) polymorphism at the 87A7 hsp70 cluster ("56H8"/"122") and a single nucleotide polymorphism at the 87C1 hsp70 cluster. In both cases, the 18 degrees C and 25 degrees C populations fixed one allele and the 28 degrees C populations the other, consistent with previously described evolved differences among these populations in Hsp70 expression and thermotolerance. Second, we examined 56H8 and 122 frequencies in a set of 11 populations founded from flies collected along a latitudinal transect of eastern Australia. The 56H8 allele frequencies are positively associated with latitude, consistent with maintenance of the 56H8/122 polymorphism by natural selection. Thermal extremes and average values are negatively correlated with latitude. These results suggest that natural selection imposed by temperature and thermal variability may affect hsp70 allele frequencies.

Engineering Candidate Genes in Studies of Adaptation: The Heat-Shock Protein Hsp70 in Drosophila melanogaster.

One approach to elucidating the relationships among genes, traits, performance, and fitness is to choose genes of candidate evolutionary interest whose significance is well understood from in vitro and cellular studies and to explore the consequences of manipulating these genes in whole organisms in an evolutionary context. Ongoing research on Hsp70 in Drosophila exemplifies this candidate gene approach. The heat-shock protein Hsp70 was chosen for analysis because its biochemical phenotype (i.e., molecular chaperone activity), regulation, and encoding genes are well understood. Investigation of the thermal environment of Drosophila larvae in the wild and natural Hsp70 expression establishes an ecological context for the candidate gene. Engineering of the hsp70 genes via site-specific homologous recombination, expression off of a heterologous promoter, and expression of an innocuous protein off of the hsp70 promoter show that Hsp70 can be sufficient for a significant component of inducible thermotolerance but can have deleterious consequences. Study of nonengineered variation in Hsp70 expression reveals that the genetically engineered effects have counterparts in nature. Thus, in complementary fashion, both genetic engineering and the more classical approaches of evolutionary biology each contribute essential insights to adaptation.

Hsp70 and thermal pretreatment mitigate developmental damage caused by mitotic poisons in Drosophila.

To assess the ability of the heat-inducible molecular chaperone heat-shock protein 70 (Hsp70) to mitigate a specific developmental lesion, we administered the antimicrotubule drugs vinblastine (VB) and colchicine (COL) to larvae of Drosophila engineered to express differing levels of Hsp70 after heat pretreatment (HP). VB and COL decreased survival during metamorphosis, disrupted development of the adult eye and other structures as well as their precursor imaginal disks, and induced chromosome nondisjunction in the wing imaginal disk as indicated by the somatic mutation and recombination test (SMART) assay. Hsp70-inducing HP reduced many of these effects. For the traits viability, adult eye morphology, eye imaginal disk morphology, cell death in the eye imaginal disks, and single and total mutant clone formation in the SMART assay, HP reduced the impact of VB to a greater extent in Drosophila with 6 hsp70 transgenes than in a sister strain from which the transgenes had been excised. Because the extra-copy strain has higher levels of Hsp70 than does the excision strain but is otherwise almost identical in genetic background to the excision strain, these outcomes are attributable to Hsp70. The hsp70 copy number had a variable interaction with HP and COL administration.