401
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Tschopp P, Duboule D. A genetic approach to the transcriptional regulation of Hox gene clusters. Annu Rev Genet 2012; 45:145-66. [PMID: 22060042 DOI: 10.1146/annurev-genet-102209-163429] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The evolution of vertebrate genomes was accompanied by an astounding increase in the complexity of their regulatory modalities. Genetic redundancy resulting from large-scale genome duplications at the base of the chordate tree was repeatedly exploited by the functional redeployment of paralogous genes via innovations in their regulatory circuits. As a paradigm of such regulatory evolution, we have extensively studied those control mechanisms at work in-cis over vertebrate Hox gene clusters. Here, we review the portfolio of genetic strategies that have been developed to tackle the intricate relationship between genomic topography and the transcriptional activities in this gene family, and we describe some of the mechanistic insights we gained by using the HoxD cluster as an example. We discuss the high heuristic value of this system in our general understanding of how changes in transcriptional regulation can diversify gene function and thereby fuel morphological evolution.
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Affiliation(s)
- Patrick Tschopp
- National Center of Competence in Research, Frontiers in Genetics, Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland
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402
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Abstract
Full limb regeneration is a property that seems to be restricted to urodele amphibians. Here we found that Polypterus, the most basal living ray-finned fish, regenerates its pectoral lobed fins with a remarkable accuracy. Pectoral Polypterus fins are complex, formed by a well-organized endoskeleton to which the exoskeleton rays are connected. Regeneration initiates with the formation of a blastema similar to that observed in regenerating amphibian limbs. Retinoic acid induces dose-dependent phenotypes ranging from inhibition of regeneration to apparent anterior-posterior duplications. As in all developing tetrapod limbs and regenerating amphibian blastema, Sonic hedgehog is expressed in the posterior mesenchyme during fin regeneration. Hedgehog signaling plays a role in the regeneration and patterning processes: an increase or reduction of fin bony elements results when this signaling is activated or disrupted, respectively. The tail fin also regenerates but, in contrast with pectoral fins, regeneration can resume after release from the arrest caused by hedgehog inhibition. A comparative analysis of fin phenotypes obtained after retinoic acid treatment or altering the hedgehog signaling levels during regeneration allowed us to assign a limb tetrapod equivalent segment to Polypterus fin skeletal structures, thus providing clues to the origin of the autopod. We propose that appendage regeneration was a common property of vertebrates during the fin to limb transition.
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403
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Pires ND, Dolan L. Morphological evolution in land plants: new designs with old genes. Philos Trans R Soc Lond B Biol Sci 2012; 367:508-18. [PMID: 22232763 PMCID: PMC3248709 DOI: 10.1098/rstb.2011.0252] [Citation(s) in RCA: 145] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The colonization and radiation of multicellular plants on land that started over 470 Ma was one of the defining events in the history of this planet. For the first time, large amounts of primary productivity occurred on the continental surface, paving the way for the evolution of complex terrestrial ecosystems and altering global biogeochemical cycles; increased weathering of continental silicates and organic carbon burial resulted in a 90 per cent reduction in atmospheric carbon dioxide levels. The evolution of plants on land was itself characterized by a series of radical transformations of their body plans that included the formation of three-dimensional tissues, de novo evolution of a multicellular diploid sporophyte generation, evolution of multicellular meristems, and the development of specialized tissues and organ systems such as vasculature, roots, leaves, seeds and flowers. In this review, we discuss the evolution of the genes and developmental mechanisms that drove the explosion of plant morphologies on land. Recent studies indicate that many of the gene families which control development in extant plants were already present in the earliest land plants. This suggests that the evolution of novel morphologies was to a large degree driven by the reassembly and reuse of pre-existing genetic mechanisms.
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Affiliation(s)
| | - Liam Dolan
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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404
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Haber MH, Benham B. Reframing the ethical issues in part-human animal research: the unbearable ontology of inexorable moral confusion. THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2012; 12:17-25. [PMID: 22881848 DOI: 10.1080/15265161.2012.699139] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Research that involves the creation of animals with human-derived parts opens the door to potentially valuable scientific and therapeutic advances, yet invokes unsettling moral questions. Critics and champions alike stand to gain from clear identification and careful consideration of the strongest ethical objections to this research. A prevailing objection argues that crossing the human/nonhuman species boundary introduces inexorable moral confusion (IMC) that warrants a restriction to this research on precautionary grounds. Though this objection may capture the intuitions of many who find this research unsettling, it relies on mistaken views of both biology and moral standing, ultimately distorting the morally relevant facts. We critically examine IMC, identify mistaken essentialist assumptions, and reframe ethical concerns. The upshot is a stronger line of objection that encourages a more inclusive and productive ethical discourse.
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405
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Fitch WT. The evolution of syntax: an exaptationist perspective. FRONTIERS IN EVOLUTIONARY NEUROSCIENCE 2011; 3:9. [PMID: 22207847 PMCID: PMC3245538 DOI: 10.3389/fnevo.2011.00009] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 12/02/2011] [Indexed: 11/14/2022]
Abstract
The evolution of language required elaboration of a number of independent mechanisms in the hominin lineage, including systems involved in signaling, semantics, and syntax. Two perspectives on the evolution of syntax can be contrasted. The “continuist” perspective seeks the evolutionary roots of complex human syntax in simpler combinatory systems used in animal communication systems, such as iteration and sequencing. The “exaptationist” perspective posits evolutionary change of function, so that systems today used for linguistic communication might previously have served quite different functions in earlier hominids. I argue that abundant biological evidence supports an exaptationist perspective, in general, and that it must be taken seriously when considering language evolution. When applied to syntax, this suggests that core computational components used today in language could have originally served non-linguistic functions such as motor control, non-verbal thought, or spatial reasoning. I outline three specific exaptationist hypotheses for spoken language. These three hypotheses each posit a change of functionality in a precursor circuit, and its transformation into a neural circuit or region specifically involved in language today. Hypothesis 1 suggests that the precursor mechanism for intentional vocal control, specifically direct cortical control over the larynx, was manual motor control subserved by the cortico-spinal tract. The second is that the arcuate fasciculus, which today connects syntactic and lexical regions, had its origin in intracortical connections subserving vocal imitation. The third is that the specialized components of Broca’s area, specifically BA 45, had their origins in non-linguistic motor control, and specifically hierarchical planning of action. I conclude by illustrating the importance of both homology (studied via primates) and convergence (typically analyzed in birds) for testing such evolutionary hypotheses.
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Affiliation(s)
- W Tecumseh Fitch
- Department of Cognitive Biology, University of Vienna Vienna, Austria
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406
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Abstract
In a model based on the wasp family Vespidae, the origin of worker behaviour, which constitutes the eusociality threshold, is not based on relatedness, therefore the origin of eusociality does not depend on inclusive fitness, and workers at the eusociality threshold are not altruistic. Instead, incipient workers and queens behave selfishly and are subject to direct natural selection. Beyond the eusociality threshold, relatedness enables 'soft inheritance' as the framework for initial adaptations of eusociality. At the threshold of irreversibility, queen and worker castes become fixed in advanced eusociality. Transitions from solitary to facultative, facultative to primitive, and primitive to advanced eusociality occur via exaptation, phenotypic accommodation and genetic assimilation. Multilevel selection characterizes the solitary to highly eusocial transition, but components of multilevel selection vary across levels of eusociality. Roles of behavioural flexibility and developmental plasticity in the evolutionary process equal or exceed those of genotype.
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Affiliation(s)
- James H Hunt
- Departments of Biology and Entomology, W M Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695, USA.
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407
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Wilson LAB. The contribution of developmental palaeontology to extensions of evolutionary theory. ACTA ZOOL-STOCKHOLM 2011. [DOI: 10.1111/j.1463-6395.2011.00539.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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408
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Doyle JJ. Phylogenetic perspectives on the origins of nodulation. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:1289-95. [PMID: 21995796 DOI: 10.1094/mpmi-05-11-0114] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Recent refinements to the phylogeny of rosid angiosperms support the conclusion that nodulation has evolved several times in the so-called N(2)-fixing clade (NFC), and provide dates for these origins. The hypothesized predisposition that enabled the evolution of nodulation occurred approximately 100 million years ago (MYA), was retained in the various lineages that radiated rapidly shortly thereafter, and was functional in its non-nodulation role for at least an additional 30 million years in each nodulating lineage. Legumes radiated rapidly shortly after their origin approximately 60 MYA, and nodulation most likely evolved several times during this radiation. The major lineages of papilionoid legumes diverged close to the time of origin of nodulation, accounting for the diversity of nodule biology in the group. Nodulation symbioses exemplify the concept of "deep homology," sharing various homologous components across nonhomologous origins of nodulation, largely due to recruitment from existing functions, notably the older arbuscular mycorrhizal symbiosis. Although polyploidy may have played a role in the origin of papilionoid legume nodules, it did not do so in other legumes, nor did the prerosid whole-genome triplication lead directly to the predisposition of nodulation.
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Affiliation(s)
- Jeff J Doyle
- Department of Plant Biology, Cornell University, Ithaca, NY, USA.
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409
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MacDougall-Shackleton SA. The levels of analysis revisited. Philos Trans R Soc Lond B Biol Sci 2011; 366:2076-85. [PMID: 21690126 DOI: 10.1098/rstb.2010.0363] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The term levels of analysis has been used in several ways: to distinguish between ultimate and proximate levels, to categorize different kinds of research questions and to differentiate levels of reductionism. Because questions regarding ultimate function and proximate mechanisms are logically distinct, I suggest that distinguishing between these two levels is the best use of the term. Integrating across levels in research has potential risks, but many benefits. Consideration at one level can help generate novel hypotheses at the other, define categories of behaviour and set criteria that must be addressed. Taking an adaptationist stance thus strengthens research on proximate mechanisms. Similarly, it is critical for researchers studying adaptation and function to have detailed knowledge of proximate mechanisms that may constrain or modulate evolutionary processes. Despite the benefits of integrating across ultimate and proximate levels, failure to clearly identify levels of analysis, and whether or not hypotheses are exclusive alternatives, can create false debates. Such non-alternative hypotheses may occur between or within levels, and are not limited to integrative approaches. In this review, I survey different uses of the term levels of analysis and the benefits of integration, and highlight examples of false debate within and between levels. The best integrative biology reciprocally uses ultimate and proximate hypotheses to generate a more complete understanding of behaviour.
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Affiliation(s)
- Scott A MacDougall-Shackleton
- Advanced Facility for Avian Research, Department of Psychology, University of Western Ontario, London, Ontario, Canada, N6A 5C2.
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410
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Brakefield PM. Evo-devo and accounting for Darwin's endless forms. Philos Trans R Soc Lond B Biol Sci 2011; 366:2069-75. [PMID: 21690125 DOI: 10.1098/rstb.2011.0007] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Evo-devo has led to dramatic advances in our understanding of how the processes of development can contribute to explaining patterns of evolutionary diversification that underlie the endless forms of animal life on the Earth. This is increasingly the case not only for the origins of evolutionary novelties that permit new functions and open up new adaptive zones, but also for the processes of evolutionary tinkering that occur within the subsequent radiations of related species. Evo-devo has time and again yielded spectacular examples of Darwin's notions of common ancestry and of descent with modification. It has also shown that the evolution of endless forms is more about the evolution of the regulatory machinery of ancient genes than the origin and elaboration of new genes. Evolvability, especially with respect to the capacity of a developmental system to evolve and to generate the variation in form for natural selection to screen, has become a pivotal focus of evo-devo. As a consequence, a balancing of the concept of endless forms in morphospace with a greater awareness of the potential for developmental constraints and bias is becoming more general. The prospect of parallel horizons opening up for the evolution of behaviour is exciting; in particular, does Sean Carroll's phrase referring to old genes learning new tricks in the evolution of endless forms apply equally as well to patterns of diversity and disparity in behavioural trait-space?
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Affiliation(s)
- Paul M Brakefield
- Department of Zoology, University Museum of Zoology Cambridge, , University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
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411
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Busch BL, Schmitz G, Rossmann S, Piron F, Ding J, Bendahmane A, Theres K. Shoot branching and leaf dissection in tomato are regulated by homologous gene modules. THE PLANT CELL 2011; 23:3595-609. [PMID: 22039213 PMCID: PMC3229137 DOI: 10.1105/tpc.111.087981] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 09/19/2011] [Accepted: 10/17/2011] [Indexed: 05/18/2023]
Abstract
Aerial plant architecture is predominantly determined by shoot branching and leaf morphology, which are governed by apparently unrelated developmental processes, axillary meristem formation, and leaf dissection. Here, we show that in tomato (Solanum lycopersicum), these processes share essential functions in boundary establishment. Potato leaf (C), a key regulator of leaf dissection, was identified to be the closest paralog of the shoot branching regulator Blind (Bl). Comparative genomics revealed that these two R2R3 MYB genes are orthologs of the Arabidopsis thaliana branching regulator REGULATOR OF AXILLARY MERISTEMS1 (RAX1). Expression studies and complementation analyses indicate that these genes have undergone sub- or neofunctionalization due to promoter differentiation. C acts in a pathway independent of other identified leaf dissection regulators. Furthermore, the known leaf complexity regulator Goblet (Gob) is crucial for axillary meristem initiation and acts in parallel to C and Bl. Finally, RNA in situ hybridization revealed that the branching regulator Lateral suppressor (Ls) is also expressed in leaves. All four boundary genes, C, Bl, Gob, and Ls, may act by suppressing growth, as indicated by gain-of-function plants. Thus, leaf architecture and shoot architecture rely on a conserved mechanism of boundary formation preceding the initiation of leaflets and axillary meristems.
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Affiliation(s)
- Bernhard L. Busch
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Gregor Schmitz
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Susanne Rossmann
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Florence Piron
- Unité de Recherche en Génomique Végétale, Unité Mixte de Recherche, Institut National de la Recherche Agronomique–Centre National de la Recherche Scientifique, 91057 Evry cedex, France
| | - Jia Ding
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Abdelhafid Bendahmane
- Unité de Recherche en Génomique Végétale, Unité Mixte de Recherche, Institut National de la Recherche Agronomique–Centre National de la Recherche Scientifique, 91057 Evry cedex, France
| | - Klaus Theres
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Address correspondence to
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412
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Moczek AP, Sultan S, Foster S, Ledón-Rettig C, Dworkin I, Nijhout HF, Abouheif E, Pfennig DW. The role of developmental plasticity in evolutionary innovation. Proc Biol Sci 2011; 278:2705-13. [PMID: 21676977 PMCID: PMC3145196 DOI: 10.1098/rspb.2011.0971] [Citation(s) in RCA: 340] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 05/24/2011] [Indexed: 11/12/2022] Open
Abstract
Explaining the origins of novel traits is central to evolutionary biology. Longstanding theory suggests that developmental plasticity, the ability of an individual to modify its development in response to environmental conditions, might facilitate the evolution of novel traits. Yet whether and how such developmental flexibility promotes innovations that persist over evolutionary time remains unclear. Here, we examine three distinct ways by which developmental plasticity can promote evolutionary innovation. First, we show how the process of genetic accommodation provides a feasible and possibly common avenue by which environmentally induced phenotypes can become subject to heritable modification. Second, we posit that the developmental underpinnings of plasticity increase the degrees of freedom by which environmental and genetic factors influence ontogeny, thereby diversifying targets for evolutionary processes to act on and increasing opportunities for the construction of novel, functional and potentially adaptive phenotypes. Finally, we examine the developmental genetic architectures of environment-dependent trait expression, and highlight their specific implications for the evolutionary origin of novel traits. We critically review the empirical evidence supporting each of these processes, and propose future experiments and tests that would further illuminate the interplay between environmental factors, condition-dependent development, and the initiation and elaboration of novel phenotypes.
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Affiliation(s)
- Armin P Moczek
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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413
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Morange M. Evolutionary developmental biology its roots and characteristics. Dev Biol 2011; 357:13-6. [PMID: 21447330 DOI: 10.1016/j.ydbio.2011.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Revised: 03/08/2011] [Accepted: 03/10/2011] [Indexed: 02/01/2023]
Abstract
The rise of evolutionary developmental biology was not the progressive isolation and characterization of developmental genes and gene networks. Many obstacles had to be overcome: the idea that all genes were more or less involved in development; the evidence that developmental processes in insects had nothing in common with those of vertebrates. Different lines of research converged toward the creation of evolutionary developmental biology, giving this field of research its present heterogeneity. This does not prevent all those working in the field from sharing the conviction that a precise characterization of evolutionary variations is required to fully understand the evolutionary process. Some evolutionary developmental biologists directly challenge the Modern Synthesis. I propose some ways to reconcile these apparently opposed visions of evolution. The turbulence seen in evolutionary developmental biology reflects the present entry of history into biology.
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Affiliation(s)
- Michel Morange
- Centre Cavaillès, USR, Ecole normale supérieure, Paris, France.
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414
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O'Connell LA, Hofmann HA. Genes, hormones, and circuits: an integrative approach to study the evolution of social behavior. Front Neuroendocrinol 2011; 32:320-35. [PMID: 21163292 DOI: 10.1016/j.yfrne.2010.12.004] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 12/03/2010] [Accepted: 12/09/2010] [Indexed: 12/23/2022]
Abstract
Tremendous progress has been made in our understanding of the ultimate and proximate mechanisms underlying social behavior, yet an integrative evolutionary analysis of its underpinnings has been difficult. In this review, we propose that modern genomic approaches can facilitate such studies by integrating four approaches to brain and behavior studies: (1) animals face many challenges and opportunities that are ecologically and socially equivalent across species; (2) they respond with species-specific, yet quantifiable and comparable approach and avoidance behaviors; (3) these behaviors in turn are regulated by gene modules and neurochemical codes; and (4) these behaviors are governed by brain circuits such as the mesolimbic reward system and the social behavior network. For each approach, we discuss genomic and other studies that have shed light on various aspects of social behavior and its underpinnings and suggest promising avenues for future research into the evolution of neuroethological systems.
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Affiliation(s)
- Lauren A O'Connell
- Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas at Austin, Austin, TX 78705, USA
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415
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Scharff C, Petri J. Evo-devo, deep homology and FoxP2: implications for the evolution of speech and language. Philos Trans R Soc Lond B Biol Sci 2011; 366:2124-40. [PMID: 21690130 PMCID: PMC3130369 DOI: 10.1098/rstb.2011.0001] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The evolution of novel morphological features, such as feathers, involves the modification of developmental processes regulated by gene networks. The fact that genetic novelty operates within developmental constraints is the central tenet of the 'evo-devo' conceptual framework. It is supported by findings that certain molecular regulatory pathways act in a similar manner in the development of morphological adaptations, which are not directly related by common ancestry but evolved convergently. The Pax6 gene, important for vision in molluscs, insects and vertebrates, and Hox genes, important for tetrapod limbs and fish fins, exemplify this 'deep homology'. Recently, 'evo-devo' has expanded to the molecular analysis of behavioural traits, including social behaviour, learning and memory. Here, we apply this approach to the evolution of human language. Human speech is a form of auditory-guided, learned vocal motor behaviour that also evolved in certain species of birds, bats and ocean mammals. Genes relevant for language, including the transcription factor FOXP2, have been identified. We review evidence that FoxP2 and its regulatory gene network shapes neural plasticity in cortico-basal ganglia circuits underlying the sensory-guided motor learning in animal models. The emerging picture can help us understand how complex cognitive traits can 'descend with modification'.
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Affiliation(s)
- Constance Scharff
- Department of Animal Behavior, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany.
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416
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He Z, Eichel K, Ruvinsky I. Functional conservation of cis-regulatory elements of heat-shock genes over long evolutionary distances. PLoS One 2011; 6:e22677. [PMID: 21799932 PMCID: PMC3143172 DOI: 10.1371/journal.pone.0022677] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 06/30/2011] [Indexed: 12/02/2022] Open
Abstract
Transcriptional control of gene regulation is an intricate process that requires precise orchestration of a number of molecular components. Studying its evolution can serve as a useful model for understanding how complex molecular machines evolve. One way to investigate evolution of transcriptional regulation is to test the functions of cis-elements from one species in a distant relative. Previous results suggested that few, if any, tissue-specific promoters from Drosophila are faithfully expressed in C. elegans. Here we show that, in contrast, promoters of fly and human heat-shock genes are upregulated in C. elegans upon exposure to heat. Inducibility under conditions of heat shock may represent a relatively simple “on-off” response, whereas complex expression patterns require integration of multiple signals. Our results suggest that simpler aspects of regulatory logic may be retained over longer periods of evolutionary time, while more complex ones may be diverging more rapidly.
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Affiliation(s)
- Zhengying He
- Department of Ecology and Evolution, Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
| | - Kelsie Eichel
- Department of Ecology and Evolution, Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
| | - Ilya Ruvinsky
- Department of Ecology and Evolution, Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
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417
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Appendage expression driven by the Hoxd Global Control Region is an ancient gnathostome feature. Proc Natl Acad Sci U S A 2011; 108:12782-6. [PMID: 21765002 DOI: 10.1073/pnas.1109993108] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The evolutionary transition of the fins of fish into tetrapod limbs involved genetic changes to developmental systems that resulted in novel skeletal patterns and functions. Approaches to understanding this issue have entailed the search for antecedents of limb structure in fossils, genes, and embryos. Comparative genetic analyses have produced ambiguous results: although studies of posterior Hox genes from homology group 13 (Hoxa-13 and Hoxd-13) reveal similarities in gene expression between the distal segments of fins and limbs, this functional homology has not been supported by genomic comparisons of the activity of their cis-regulatory elements, namely the Hoxd Global Control Region. Here, we show that cis-regulatory elements driving Hoxd gene expression in distal limbs are present in fish. Using an interspecies transgenesis approach, we find functional conservation between gnathostome Hoxd enhancers, demonstrating that orthologous sequences from tetrapods, zebrafish and skate can drive reporter gene expression in mouse limbs and zebrafish fins. Our results support the notion that some of the novelties associated with tetrapod limbs arose by modification of deeply conserved cis- and trans-acting mechanisms of Hox regulation in gnathostomes.
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418
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Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes. Nat Struct Mol Biol 2011; 18:708-14. [PMID: 21602820 DOI: 10.1038/nsmb.2059] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 03/15/2011] [Indexed: 11/09/2022]
Abstract
Many genomic alterations associated with human diseases localize in noncoding regulatory elements located far from the promoters they regulate, making it challenging to link noncoding mutations or risk-associated variants with target genes. The range of action of a given set of enhancers is thought to be defined by insulator elements bound by the 11 zinc-finger nuclear factor CCCTC-binding protein (CTCF). Here we analyzed the genomic distribution of CTCF in various human, mouse and chicken cell types, demonstrating the existence of evolutionarily conserved CTCF-bound sites beyond mammals. These sites preferentially flank transcription factor-encoding genes, often associated with human diseases, and function as enhancer blockers in vivo, suggesting that they act as evolutionarily invariant gene boundaries. We then applied this concept to predict and functionally demonstrate that the polymorphic variants associated with multiple sclerosis located within the EVI5 gene impinge on the adjacent gene GFI1.
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419
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Abstract
Although parallel and convergent evolution are discussed extensively in technical articles and textbooks, their meaning can be overlapping, imprecise, and contradictory. The meaning of parallel evolution in much of the evolutionary literature grapples with two separate hypotheses in relation to phenotype and genotype, but often these two hypotheses have been inferred from only one hypothesis, and a number of subsidiary but problematic criteria, in relation to the phenotype. However, examples of parallel evolution of genetic traits that underpin or are at least associated with convergent phenotypes are now emerging. Four criteria for distinguishing parallelism from convergence are reviewed. All are found to be incompatible with any single proposition of homoplasy. Therefore, all homoplasy is equivalent to a broad view of convergence. Based on this concept, all phenotypic homoplasy can be described as convergence and all genotypic homoplasy as parallelism, which can be viewed as the equivalent concept of convergence for molecular data. Parallel changes of molecular traits may or may not be associated with convergent phenotypes but if so describe homoplasy at two biological levels-genotype and phenotype. Parallelism is not an alternative to convergence, but rather it entails homoplastic genetics that can be associated with and potentially explain, at the molecular level, how convergent phenotypes evolve.
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Affiliation(s)
- Robert W Scotland
- Department of Plant Sciences, South Parks Road, University of Oxford, Oxford, UK.
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420
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Nakashima K, Nishino A, Horikawa Y, Hirose E, Sugiyama J, Satoh N. The crystalline phase of cellulose changes under developmental control in a marine chordate. Cell Mol Life Sci 2011; 68:1623-31. [PMID: 20972815 PMCID: PMC11114516 DOI: 10.1007/s00018-010-0556-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 10/04/2010] [Accepted: 10/04/2010] [Indexed: 10/18/2022]
Abstract
The native form of cellulose is a fibrillar composite of two crystalline phases, the triclinic I(α) and monoclinic I(β) allomorphs. Allomorph ratios are species-specific, and this gives rise to natural structural variations in cellulose crystals. However, the mechanisms contributing to crystal formation remain unknown. We show that the two crystalline phases of cellulose are tailored to distinct structures during different developmental stages of the tunicate chordate Oikopleura dioica. Larval cellulose consisting of I(α) allomorph constitutes the body cuticle fin, whereas adult cellulose consisting of I(β) allomorph frames a mucous filter-feeding device, the "house." Both structures are secreted from the epidermis in accordance with the mutually exclusive expression patterns of two distinct putative cellulose synthase genes. We discuss a possible linkage between structural variations of the crystalline phases of cellulose and the underlying evolutionary genetics of cellulose biosynthesis.
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Affiliation(s)
- Keisuke Nakashima
- Marine Genomics Unit, Okinawa Institute of Science and Technology Promotion Corporation, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0412, Japan.
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421
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Irisarri I, Vences M, San Mauro D, Glaw F, Zardoya R. Reversal to air-driven sound production revealed by a molecular phylogeny of tongueless frogs, family Pipidae. BMC Evol Biol 2011; 11:114. [PMID: 21524293 PMCID: PMC3111386 DOI: 10.1186/1471-2148-11-114] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 04/27/2011] [Indexed: 11/24/2022] Open
Abstract
Background Evolutionary novelties often appear by conferring completely new functions to pre-existing structures or by innovating the mechanism through which a particular function is performed. Sound production plays a central role in the behavior of frogs, which use their calls to delimit territories and attract mates. Therefore, frogs have evolved complex vocal structures capable of producing a wide variety of advertising sounds. It is generally acknowledged that most frogs call by moving an air column from the lungs through the glottis with the remarkable exception of the family Pipidae, whose members share a highly specialized sound production mechanism independent of air movement. Results Here, we performed behavioral observations in the poorly known African pipid genus Pseudhymenochirus and document that the sound production in this aquatic frog is almost certainly air-driven. However, morphological comparisons revealed an indisputable pipid nature of Pseudhymenochirus larynx. To place this paradoxical pattern into an evolutionary framework, we reconstructed robust molecular phylogenies of pipids based on complete mitochondrial genomes and nine nuclear protein-coding genes that coincided in placing Pseudhymenochirus nested among other pipids. Conclusions We conclude that although Pseudhymenochirus probably has evolved a reversal to the ancestral non-pipid condition of air-driven sound production, the mechanism through which it occurs is an evolutionary innovation based on the derived larynx of pipids. This strengthens the idea that evolutionary solutions to functional problems often emerge based on previous structures, and for this reason, innovations largely depend on possibilities and constraints predefined by the particular history of each lineage.
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Affiliation(s)
- Iker Irisarri
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
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422
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Badyaev AV. Origin of the fittest: link between emergent variation and evolutionary change as a critical question in evolutionary biology. Proc Biol Sci 2011; 278:1921-9. [PMID: 21490021 DOI: 10.1098/rspb.2011.0548] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In complex organisms, neutral evolution of genomic architecture, associated compensatory interactions in protein networks and emergent developmental processes can delineate the directions of evolutionary change, including the opportunity for natural selection. These effects are reflected in the evolution of developmental programmes that link genomic architecture with a corresponding functioning phenotype. Two recent findings call for closer examination of the rules by which these links are constructed. First is the realization that high dimensionality of genotypes and emergent properties of autonomous developmental processes (such as capacity for self-organization) result in the vast areas of fitness neutrality at both the phenotypic and genetic levels. Second is the ubiquity of context- and taxa-specific regulation of deeply conserved gene networks, such that exceptional phenotypic diversification coexists with remarkably conserved generative processes. Establishing the causal reciprocal links between ongoing neutral expansion of genomic architecture, emergent features of organisms' functionality, and often precisely adaptive phenotypic diversification therefore becomes an important goal of evolutionary biology and is the latest reincarnation of the search for a framework that links development, functioning and evolution of phenotypes. Here I examine, in the light of recent empirical advances, two evolutionary concepts that are central to this framework-natural selection and inheritance-the general rules by which they become associated with emergent developmental and homeostatic processes and the role that they play in descent with modification.
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Affiliation(s)
- Alexander V Badyaev
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
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423
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Zattara EE, Bely AE. Evolution of a novel developmental trajectory: fission is distinct from regeneration in the annelid Pristina leidyi. Evol Dev 2011; 13:80-95. [PMID: 21210945 DOI: 10.1111/j.1525-142x.2010.00458.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding how novelty arises has been a major focus of evolutionary developmental biology. While the origin of new genes, gene functions, and morphological features has been studied intensely, the origin of entire developmental trajectories, such as regeneration or agametic reproduction, remains poorly understood. Agametic reproduction by fission is a novel trajectory evolved numerous times among animal phyla, including Annelida, in which it is thought to arise by co-option of regeneration. To gain insight into how a novel trajectory may evolve, we investigated a relatively recent origin of fission. We performed a detailed comparison of morphogenesis during regeneration and fission in the annelid Pristina leidyi (Clitellata, Naididae), from the onset of these trajectories to the achievement of the final morphology. We find extensive similarities between fission and regeneration morphogenesis, and, of particular note, find evidence for a synapomorphy of fission and regeneration (apparently not shared with embryogenesis) in peripheral nervous system development, providing strong support for the hypothesis that fission is derived from regeneration. We also find important differences between fission and regeneration, during development of multiple organ systems. These are manifested by temporal shifts in developmental events and by the presence of elements unique to only one process. Differences are not obviously temporally clustered at the beginning, middle, or end of development but rather occur throughout, indicating that divergence has occurred along the entire developmental course of these trajectories.
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Affiliation(s)
- Eduardo E Zattara
- Biology Department, University of Maryland, College Park, MD 20742, USA
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424
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Abstract
Convergent evolution of similar phenotypic features in similar environmental contexts has long been taken as evidence of adaptation. Nonetheless, recent conceptual and empirical developments in many fields have led to a proliferation of ideas about the relationship between convergence and adaptation. Despite criticism from some systematically minded biologists, I reaffirm that convergence in taxa occupying similar selective environments often is the result of natural selection. However, convergent evolution of a trait in a particular environment can occur for reasons other than selection on that trait in that environment, and species can respond to similar selective pressures by evolving nonconvergent adaptations. For these reasons, studies of convergence should be coupled with other methods-such as direct measurements of selection or investigations of the functional correlates of trait evolution-to test hypotheses of adaptation. The independent acquisition of similar phenotypes by the same genetic or developmental pathway has been suggested as evidence of constraints on adaptation, a view widely repeated as genomic studies have documented phenotypic convergence resulting from change in the same genes, sometimes even by the same mutation. Contrary to some claims, convergence by changes in the same genes is not necessarily evidence of constraint, but rather suggests hypotheses that can test the relative roles of constraint and selection in directing phenotypic evolution.
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Affiliation(s)
- Jonathan B Losos
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA.
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425
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Fröbisch NB, Shubin NH. Salamander limb development: integrating genes, morphology, and fossils. Dev Dyn 2011; 240:1087-99. [PMID: 21465623 DOI: 10.1002/dvdy.22629] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2011] [Indexed: 11/11/2022] Open
Abstract
The development of the tetrapod limb during skeletogenesis follows a highly conservative pattern characterized by a general proximo-distal progression in the establishment of skeletal elements and a postaxial polarity in digit development. Salamanders represent the only exception to this pattern and display an early establishment of distal autopodial structures, specifically the basale commune, an amalgamation of distal carpal and tarsal 1 and 2, and a distinct preaxial polarity in digit development. This deviance from the conserved tetrapod pattern has resulted in a number of hypotheses to explain its developmental basis and evolutionary history. Here we summarize the current knowledge of salamander limb development under consideration of the fossil record to provide a deep time perspective of this evolutionary pathway and highlight what data will be needed in the future to gain a better understanding of salamander limb development specifically and tetrapod limb development and evolution more broadly.
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Affiliation(s)
- Nadia B Fröbisch
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, USA.
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426
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Espinosa-Soto C, Martin OC, Wagner A. Phenotypic robustness can increase phenotypic variability after nongenetic perturbations in gene regulatory circuits. J Evol Biol 2011; 24:1284-97. [PMID: 21443645 DOI: 10.1111/j.1420-9101.2011.02261.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Nongenetic perturbations, such as environmental change or developmental noise, can induce novel phenotypes. If an induced phenotype appears recurrently and confers a fitness advantage, selection may promote its genetic stabilization. Nongenetic perturbations can thus initiate evolutionary innovation. Genetic variation that is not usually phenotypically visible may play an important role in this process. Populations under stabilizing selection on a phenotype that is robust to mutations can accumulate such variation. After nongenetic perturbations, this variation can produce new phenotypes. We here study the relationship between a phenotype's mutational robustness and a population's potential to generate novel phenotypic variation. To this end, we use a well-studied model of transcriptional regulation circuits that are important in many evolutionary innovations. We find that phenotypic robustness promotes phenotypic variability in response to nongenetic perturbations, but not in response to mutation. Our work suggests that nongenetic perturbations may initiate innovation more frequently in mutationally robust gene expression traits.
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Affiliation(s)
- C Espinosa-Soto
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
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427
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Wake DB, Wake MH, Specht CD. Homoplasy: From Detecting Pattern to Determining Process and Mechanism of Evolution. Science 2011; 331:1032-5. [DOI: 10.1126/science.1188545] [Citation(s) in RCA: 291] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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428
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Abbasi AA. Evolution of vertebrate appendicular structures: Insight from genetic and palaeontological data. Dev Dyn 2011; 240:1005-16. [PMID: 21337665 DOI: 10.1002/dvdy.22572] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2011] [Indexed: 01/18/2023] Open
Abstract
The new body of evidence from fossils and comparative-developmental analysis of subset of appendicular patterning genes has revealed that limb elements seen in tetrapods are assembled in fish fin over evolutionary time. However, despite of deep homology in basic structure and underlying developmental system, there remains a large morphological gap between distal elements of tetrapod limb and distal fin skeleton of tetrapodomorph fish. Understanding the genetic basis of major transformations in distal-limb morphology is the next challenge for evolutionary developmental biologists. Here by integrating data from fossils, comparative-developmental and genetic studies, models are proposed describing the evolution of cis-regulatory elements as a basis for diversification of appendicular architecture. Instead of emphasizing the subset of developmental genes, for instance Hoxd genes, the focus here is on the significance of elucidating cis-regulatory elements for multiple other key molecular players of limb/fin development and genetic/molecular interactions among them, for a better understanding of the developmental and genetic basis of limb evolution.
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Affiliation(s)
- Amir Ali Abbasi
- National Center for Bioinformatics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.
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429
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Morris SC. Predicting what extra-terrestrials will be like: and preparing for the worst. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2011; 369:555-571. [PMID: 21220280 DOI: 10.1098/rsta.2010.0276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
It is difficult to imagine evolution in alien biospheres operating in any manner other than Darwinian. Yet, it is also widely assumed that alien life-forms will be just that: strange, un-nerving and probably repulsive. There are two reasons for this view. First, it is assumed that the range of habitable environments available to extra-terrestrial life is far wider than on Earth. I suggest, however, that terrestrial life is close to the physical and chemical limits of life anywhere. Second, it is a neo-Darwinian orthodoxy that evolution lacks predictability; imagining what extra-terrestrial life would look like in any detail is a futile exercise. To the contrary, I suggest that the outcomes of evolution are remarkably predictable. This, however, leads us to consider two opposites, both of which should make our blood run cold. The first, and actually extremely unlikely, is that alien biospheres will be strikingly similar to our terrestrial equivalent and that in such biospheres intelligence will inevitably emerge. The reasons for this revolve around the ubiquity of evolutionary convergence, the determinate structure of the Tree of Life and molecular inherency. But if something like a human is an inevitability, why do I also claim that the first possibility is 'extremely unlikely'? Simply because the other possibility is actually the correct answer. Paradoxically, we and our biosphere are completely alone. So which is worse? Meeting ourselves or meeting nobody?
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Affiliation(s)
- Simon Conway Morris
- Department of Earth Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EQ, UK.
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430
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Espinosa-Soto C, Martin OC, Wagner A. Phenotypic plasticity can facilitate adaptive evolution in gene regulatory circuits. BMC Evol Biol 2011; 11:5. [PMID: 21211007 PMCID: PMC3024936 DOI: 10.1186/1471-2148-11-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Accepted: 01/06/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Many important evolutionary adaptations originate in the modification of gene regulatory circuits to produce new gene activity phenotypes. How do evolving populations sift through an astronomical number of circuits to find circuits with new adaptive phenotypes? The answer may often involve phenotypic plasticity. Phenotypic plasticity allows a genotype to produce different - alternative - phenotypes after non-genetic perturbations that include gene expression noise, environmental change, or epigenetic modification. RESULTS We here analyze a well-studied model of gene regulatory circuits. A circuit's genotype encodes the regulatory interactions among circuit genes, and its phenotype corresponds to a stable gene activity pattern the circuit forms. For this model, we study how genotypes are arranged in genotype space, where the distance between two genotypes reflects the number of regulatory mutations that set those genotypes apart. Specifically, we address whether this arrangement favors adaptive evolution mediated by plasticity. We find that plasticity facilitates the origin of genotypes that produce a new phenotype in response to non-genetic perturbations. We also find that selection can then stabilize the new phenotype genetically, allowing it to become a circuit's dominant gene expression phenotype. These are generic properties of the circuits we study here. CONCLUSIONS Taken together, our observations suggest that phenotypic plasticity frequently facilitates the evolution of novel beneficial gene activity patterns in gene regulatory circuits.
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Affiliation(s)
- Carlos Espinosa-Soto
- University of Zurich, Dept. of Biochemistry, Bldg. Y27 Winterthurerstrasse 190 CH-8057 Zurich, Switzerland
- The Swiss Institute of Bioinformatics. Quartier Sorge, Batiment Genopode, 1015 Lausanne, Switzerland
| | - Olivier C Martin
- INRA, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur- Yvette, France
| | - Andreas Wagner
- University of Zurich, Dept. of Biochemistry, Bldg. Y27 Winterthurerstrasse 190 CH-8057 Zurich, Switzerland
- The Swiss Institute of Bioinformatics. Quartier Sorge, Batiment Genopode, 1015 Lausanne, Switzerland
- The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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431
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Fraser GJ, Cerny R, Soukup V, Bronner-Fraser M, Streelman JT. The odontode explosion: the origin of tooth-like structures in vertebrates. Bioessays 2010; 32:808-17. [PMID: 20730948 DOI: 10.1002/bies.200900151] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Essentially we show recent data to shed new light on the thorny controversy of how teeth arose in evolution. Essentially we show (a) how teeth can form equally from any epithelium, be it endoderm, ectoderm or a combination of the two and (b) that the gene expression programs of oral versus pharyngeal teeth are remarkably similar. Classic theories suggest that (i) skin denticles evolved first and odontode-inductive surface ectoderm merged inside the oral cavity to form teeth (the 'outside-in' hypothesis) or that (ii) patterned odontodes evolved first from endoderm deep inside the pharyngeal cavity (the 'inside-out' hypothesis). We propose a new perspective that views odontodes as structures sharing a deep molecular homology, united by sets of co-expressed genes defining a competent thickened epithelium and a collaborative neural crest-derived ectomesenchyme. Simply put, odontodes develop 'inside and out', wherever and whenever these co-expressed gene sets signal to one another. Our perspective complements the classic theories and highlights an agenda for specific experimental manipulations in model and non-model organisms.
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Affiliation(s)
- Gareth J Fraser
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.
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432
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Winchell CJ, Valencia JE, Jacobs DK. Expression of Distal-less, dachshund, and optomotor blind in Neanthes arenaceodentata (Annelida, Nereididae) does not support homology of appendage-forming mechanisms across the Bilateria. Dev Genes Evol 2010; 220:275-95. [PMID: 21116826 PMCID: PMC3005117 DOI: 10.1007/s00427-010-0346-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Accepted: 11/09/2010] [Indexed: 01/11/2023]
Abstract
The similarity in the genetic regulation of arthropod and vertebrate appendage formation has been interpreted as the product of a plesiomorphic gene network that was primitively involved in bilaterian appendage development and co-opted to build appendages (in modern phyla) that are not historically related as structures. Data from lophotrochozoans are needed to clarify the pervasiveness of plesiomorphic appendage-forming mechanisms. We assayed the expression of three arthropod and vertebrate limb gene orthologs, Distal-less (Dll), dachshund (dac), and optomotor blind (omb), in direct-developing juveniles of the polychaete Neanthes arenaceodentata. Parapodial Dll expression marks pre-morphogenetic notopodia and neuropodia, becoming restricted to the bases of notopodial cirri and to ventral portions of neuropodia. In outgrowing cephalic appendages, Dll activity is primarily restricted to proximal domains. Dll expression is also prominent in the brain. dac expression occurs in the brain, nerve cord ganglia, a pair of pharyngeal ganglia, presumed interneurons linking a pair of segmental nerves, and in newly differentiating mesoderm. Domains of omb expression include the brain, nerve cord ganglia, one pair of anterior cirri, presumed precursors of dorsal musculature, and the same pharyngeal ganglia and presumed interneurons that express dac. Contrary to their roles in outgrowing arthropod and vertebrate appendages, Dll, dac, and omb lack comparable expression in Neanthes appendages, implying independent evolution of annelid appendage development. We infer that parapodia and arthropodia are not structurally or mechanistically homologous (but their primordia might be), that Dll's ancestral bilaterian function was in sensory and central nervous system differentiation, and that locomotory appendages possibly evolved from sensory outgrowths.
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Affiliation(s)
- Christopher J. Winchell
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 621 Charles E. Young Drive South, Los Angeles, CA 90095-1606 USA
| | - Jonathan E. Valencia
- Division of Biology, California Institute of Technology, 1200 East California Boulevard; MC 156-29, Pasadena, CA 91125 USA
| | - David K. Jacobs
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 621 Charles E. Young Drive South, Los Angeles, CA 90095-1606 USA
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433
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Abstract
The beauty of the developing embryo, and the awe that it inspires, lure many scientists into the field of developmental biology. What compels cells to divide, migrate, and morph into a being with a complex body plan? Evolutionary developmental biologists hold similar fascinations, with dynamics that take place on a grander timescale. How do phenotypic traits diverge over evolutionary time? This primer illustrates how a deep understanding of the basic principles that underlie developmental biology have changed how scientists think about the evolution of body form. The primer culminates in a conversation with David Stern, PhD, and Michael Shapiro, PhD, who discuss current topics in morphological evolution, why the field should be of interest to classic developmental biologists, and what lies ahead. Developmental Dynamics 239:3497–3505, 2010. © 2010 Wiley-Liss, Inc.
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Affiliation(s)
- Julie C Kiefer
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, Utah 84132, USA.
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434
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Koyama E, Yasuda T, Minugh-Purvis N, Kinumatsu T, Yallowitz AR, Wellik DM, Pacifici M. Hox11 genes establish synovial joint organization and phylogenetic characteristics in developing mouse zeugopod skeletal elements. Development 2010; 137:3795-800. [PMID: 20978074 DOI: 10.1242/dev.053447] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Hox11 genes are essential for zeugopod skeletal element development but their roles in synovial joint formation remain largely unknown. Here, we show that the elbow and knee joints of mouse embryos lacking all Hox11 paralogous genes are specifically remodeled and reorganized. The proximal ends of developing mutant ulna and radius elements became morphologically similar and formed an anatomically distinct elbow joint. The mutant ulna lacked the olecranon that normally attaches to the triceps brachii muscle tendon and connects the humerus to the ulna. In its place, an ulnar patella-like element developed that expressed lubricin on its ventral side facing the joint and was connected to the triceps muscle tendon. In mutant knees, both tibia and fibula fully articulated with an enlarged femoral epiphyseal end that accommodated both elements, and the neo-tripartite knee joint was enclosed in a single synovial cavity and displayed an additional anterior ligament. The mutant joints also exhibited a different organization of the superficial zone of articular cartilage that normally exerts an anti-friction function. In conclusion, Hox11 genes co-regulate and coordinate the development of zeugopod skeletal elements and adjacent elbow and knee joints, and dictate joint identity, morphogenesis and anatomical and functional organization. Notably, the ulnar patella and tripartite knee joints in the mouse mutants actually characterize several lower vertebrates, including certain reptiles and amphibians. The re-emergence of such anatomical structures suggests that their genetic blueprint is still present in the mouse genome but is normally modified to the needs of the mammalian joint-formation program by distinct Hox11 function.
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Affiliation(s)
- Eiki Koyama
- Department of Orthopaedic Surgery, College of Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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435
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Skoge M, Adler M, Groisman A, Levine H, Loomis WF, Rappel WJ. Gradient sensing in defined chemotactic fields. Integr Biol (Camb) 2010; 2:659-68. [PMID: 20882228 PMCID: PMC3052262 DOI: 10.1039/c0ib00033g] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Cells respond to a variety of secreted molecules by modifying their physiology, growth patterns, and behavior. Motile bacteria and eukaryotic cells can sense extracellular chemoattractants and chemorepellents and alter their movement. In this way fibroblasts and leukocytes can find their way to sites of injury and cancer cells can home in on sites that are releasing growth factors. Social amoebae such as Dictyostelium are chemotactic to cAMP which they secrete several hours after they have initiated development. These eukaryotic cells are known to be able to sense extremely shallow gradients but the processes underlying their exquisite sensitivity are still largely unknown. In this study we determine the responses of developed cells of Dictyostelium discoideum to stable linear gradients of cAMP of varying steepness generated in 2 μm deep gradient chambers of microfluidic devices. The gradients are generated by molecular diffusion between two 80 μm deep flow-through channels, one of which is perfused with a solution of cAMP and the other with buffer, serving as continuously replenished source and sink. These low ceiling gradient chambers constrained the cells in the vertical dimension, facilitating confocal imaging, such that subcellular localization of fluorescently tagged proteins could be followed for up to 30 min without noticeable phototoxicity. Chemotactic cells enter these low ceiling chambers by flattening and elongating and then move almost as rapidly as unconstrained cells. By following the localization of activated Ras (RasGTP) using a Ras Binding Domain fused to Green Fluorescent Protein (RBD-GFP), we observed the rapid appearance of membrane associated patches at the tips of pseudopods. These patches remained associated with pseudopods while they continued to extend but were rapidly disassembled when pseudopods stalled and the cell moved past them. Likewise, fluorescence associated with localized RasGTP rapidly disappeared when the gradient was turned off. Correlation of the size and persistence of RasGTP patches with extension of pseudopods may set the rules for understanding how the signal transduction mechanisms convert a weak external signal to a strong directional bias.
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Affiliation(s)
- Monica Skoge
- Division of Biological Sciences, University of California, La Jolla, CA 92093, USA
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436
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Boisserie JR, Fisher RE, Lihoreau F, Weston EM. Evolving between land and water: key questions on the emergence and history of the Hippopotamidae (Hippopotamoidea, Cetancodonta, Cetartiodactyla). Biol Rev Camb Philos Soc 2010; 86:601-25. [DOI: 10.1111/j.1469-185x.2010.00162.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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437
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Protein evolution by molecular tinkering: diversification of the nuclear receptor superfamily from a ligand-dependent ancestor. PLoS Biol 2010; 8. [PMID: 20957188 PMCID: PMC2950128 DOI: 10.1371/journal.pbio.1000497] [Citation(s) in RCA: 159] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 08/17/2010] [Indexed: 11/19/2022] Open
Abstract
Phylogenetic reconstruction of the structure and function of the ancestor of the nuclear receptor protein family reveals how functional diversity evolves by subtle tinkering with an ancestral template. Understanding how protein structures and functions have diversified is a central goal in molecular evolution. Surveys of very divergent proteins from model organisms, however, are often insufficient to determine the features of ancestral proteins and to reveal the evolutionary events that yielded extant diversity. Here we combine genomic, biochemical, functional, structural, and phylogenetic analyses to reconstruct the early evolution of nuclear receptors (NRs), a diverse superfamily of transcriptional regulators that play key roles in animal development, physiology, and reproduction. By inferring the structure and functions of the ancestral NR, we show—contrary to current belief—that NRs evolved from a ligand-activated ancestral receptor that existed near the base of the Metazoa, with fatty acids as possible ancestral ligands. Evolutionary tinkering with this ancestral structure generated the extraordinary diversity of modern receptors: sensitivity to different ligands evolved because of subtle modifications of the internal cavity, and ligand-independent activation evolved repeatedly because of various mutations that stabilized the active conformation in the absence of ligand. Our findings illustrate how a mechanistic dissection of protein evolution in a phylogenetic context can reveal the deep homology that links apparently “novel” molecular functions to a common ancestral form. Many protein families are so diverse that it is hard to determine their ancestral functions and to understand how their derived functions evolved. The existence of so many different functions within protein families often creates the impression that complex, novel functions must have evolved repeatedly and independently. Nuclear receptors (NRs) are a large family of related proteins that regulate key biological processes in animals by binding to specific DNA sequences and triggering expression of nearby target genes. Many NRs are activated by a specific hormone or other small molecule, but some do not require a ligand, and still others are incapable of activating gene expression and so act primarily as repressors of transcription. To understand how the functional diversity of NRs evolved, we reconstructed the structural and functional characteristics of the ancient protein from which the entire family evolved, using genomic, biochemical, functional, and structural analyses in a phylogenetic framework. We show, contrary to current belief, that the ancestral NR was a ligand-activated transcriptional activator that existed in the earliest period of animal evolution. Our analysis reveals how the extraordinary functional diversity of modern receptors was generated by subtle tinkering with this ancestral template—slightly reshaping the ligand cavity, stabilizing the protein's active conformation so it no longer required a ligand, or disabling the protein's capacity to activate transcription without affecting its other properties. We predict that, when sufficient data are gathered to allow detailed evolutionary reconstructions in other protein families, it will become apparent that most protein functional diversity evolved by tinkering with ancient functions; invoking the evolution of wholesale “novelty” will seldom be necessary.
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438
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Pottin K, Hyacinthe C, Rétaux S. Conservation, development, and function of a cement gland-like structure in the fish Astyanax mexicanus. Proc Natl Acad Sci U S A 2010; 107:17256-61. [PMID: 20855623 PMCID: PMC2951400 DOI: 10.1073/pnas.1005035107] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The larvae of the fish Astyanax mexicanus transiently develop a flat and adhesive structure on the top of their heads that we have called "the casquette" (cas, meaning "hat"). We hypothesized that the cas may be a teleostean homolog of the well-studied Xenopus cement gland, despite their different positions and structures. Here we show that the cas has an ectodermal origin, secretes mucus, expresses bone morphogenic protein 4 (Bmp4) and pituitary homeobox 1/2 (Pitx1/2), is innervated by the trigeminal ganglion and serotonergic raphe neurons, and has a role in the control and the development of the larval swimming behavior. These developmental, connectivity, and behavioral functional data support a level of deep homology between the frog cement gland and the Astyanax cas and suggest that attachment organs can develop in varied positions on the head ectoderm by recruitment of a Bmp4-dependent developmental module. We also show that the attachment organs of the cichlid Tilapia mariae larvae display some of these features. We discuss the possibility that these highly diversified attachment glands may be ancestral to chordates and have been lost repetitively in many vertebrate classes.
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Affiliation(s)
- Karen Pottin
- NeD UPR2197, Centre National de la Recherche Scientifique (CNRS), Institut A. Fessard, 91198 Gif/Yvette, France
| | - Carole Hyacinthe
- NeD UPR2197, Centre National de la Recherche Scientifique (CNRS), Institut A. Fessard, 91198 Gif/Yvette, France
| | - Sylvie Rétaux
- NeD UPR2197, Centre National de la Recherche Scientifique (CNRS), Institut A. Fessard, 91198 Gif/Yvette, France
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439
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Potential genetic bases of morphological evolution in the triassic fish Saurichthys. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2010; 314:519-26. [DOI: 10.1002/jez.b.21372] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 07/24/2010] [Accepted: 07/30/2010] [Indexed: 12/22/2022]
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440
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Hashimshony T, Yanai I. Revealing developmental networks by comparative transcriptomics. Transcription 2010; 1:154-158. [PMID: 21326891 DOI: 10.4161/trns.1.3.13190] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Revised: 07/25/2010] [Accepted: 07/27/2010] [Indexed: 11/19/2022] Open
Abstract
Metazoan development relies upon the precise control of the genome's expression. This enables different cells in the animal to have different properties, despite having the same genetic material, and different animals to have different morphologies despite sharing developmental genes. However, near-identical organisms may have different overall genomic content, suggesting that the mechanisms by which evolution of the phenotype proceeds on a global level are not well understood. We review here recent works that have discovered a tremendous amount of variation between the developmental transcriptomes of both closely and distantly related organisms. It is evident that the evolution of regulatory programs occurs at a rapid rate comparable to that of other genomic processes. Distinguishing the selective pressures on each regulatory element will thus be crucial towards understanding its functional relevance. We propose that such a comparative approach is most suited to the identification of unifying principles in cell fate specification and differentiation in the animal embryo.
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Affiliation(s)
- Tamar Hashimshony
- Department of Biology; Technion-Israel Institute of Technology; Haifa, Israel
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441
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Ancestry of motor innervation to pectoral fin and forelimb. Nat Commun 2010; 1:49. [PMID: 20975699 PMCID: PMC2963806 DOI: 10.1038/ncomms1045] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Accepted: 06/30/2010] [Indexed: 02/03/2023] Open
Abstract
Motor innervation to the tetrapod forelimb and fish pectoral fin is assumed to share a conserved spinal cord origin, despite major structural and functional innovations of the appendage during the vertebrate water-to-land transition. In this paper, we present anatomical and embryological evidence showing that pectoral motoneurons also originate in the hindbrain among ray-finned fish. New and previous data for lobe-finned fish, a group that includes tetrapods, and more basal cartilaginous fish showed pectoral innervation that was consistent with a hindbrain-spinal origin of motoneurons. Together, these findings support a hindbrain–spinal phenotype as the ancestral vertebrate condition that originated as a postural adaptation for pectoral control of head orientation. A phylogenetic analysis indicated that Hox gene modules were shared in fish and tetrapod pectoral systems. We propose that evolutionary shifts in Hox gene expression along the body axis provided a transcriptional mechanism allowing eventual decoupling of pectoral motoneurons from the hindbrain much like their target appendage gained independence from the head. It was previously thought that the nerves in the pectoral fin of fish came solely from the spinal cord. Here, motoneurons in ray-finned fish are shown to also originate from the hindbrain, demonstrating that innervation was from both the hindbrain and the spinal cord in ancesteral vertebrates.
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442
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Abstract
Over the past decade, it has been discovered that disparate aspects of morphology - often of distantly related groups of organisms - are regulated by the same genetic regulatory mechanisms. Those discoveries provide a new perspective on morphological evolutionary change. A conceptual framework for exploring these research findings is termed 'deep homology'. A comparative framework for morphological relations of homology is provided that distinguishes analogy, homoplasy, plesiomorphy and synapomorphy. Four examples - three from plants and one from animals - demonstrate that homologous developmental mechanisms can regulate a range of morphological relations including analogy, homoplasy and examples of uncertain homology. Deep homology is part of a much wider range of phenomena in which biological (genes, regulatory mechanisms, morphological traits) and phylogenetic levels of homology can both be disassociated. Therefore, to understand homology, precise, comparative, independent statements of both biological and phylogenetic levels of homology are necessary.
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443
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Regulatory Factor X (RFX)-mediated transcriptional rewiring of ciliary genes in animals. Proc Natl Acad Sci U S A 2010; 107:12969-74. [PMID: 20615967 DOI: 10.1073/pnas.0914241107] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cilia were present in the last eukaryotic common ancestor (LECA) and were retained by most organisms spanning all extant eukaryotic lineages, including organisms in the Unikonta (Amoebozoa, fungi, choanoflagellates, and animals), Archaeplastida, Excavata, Chromalveolata, and Rhizaria. In certain animals, including humans, ciliary gene regulation is mediated by Regulatory Factor X (RFX) transcription factors (TFs). RFX TFs bind X-box promoter motifs and thereby positively regulate >50 ciliary genes. Though RFX-mediated ciliary gene regulation has been studied in several bilaterian animals, little is known about the evolutionary conservation of ciliary gene regulation. Here, we explore the evolutionary relationships between RFX TFs and cilia. By sampling the genome sequences of >120 eukaryotic organisms, we show that RFX TFs are exclusively found in unikont organisms (whether ciliated or not), but are completely absent from the genome sequences of all nonunikont organisms (again, whether ciliated or not). Sampling the promoter sequences of 12 highly conserved ciliary genes from 23 diverse unikont and nonunikont organisms further revealed that phylogenetic footprints of X-box promoter motif sequences are found exclusively in ciliary genes of certain animals. Thus, there is no correlation between cilia/ciliary genes and the presence or absence of RFX TFs and X-box promoter motifs in nonanimal unikont and in nonunikont organisms. These data suggest that RFX TFs originated early in the unikont lineage, distinctly after cilia evolved. The evolutionary model that best explains these observations indicates that the transcriptional rewiring of many ciliary genes by RFX TFs occurred early in the animal lineage.
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444
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Boyle MJ, Seaver EC. Expression of FoxA and GATA transcription factors correlates with regionalized gut development in two lophotrochozoan marine worms: Chaetopterus (Annelida) and Themiste lageniformis (Sipuncula). EvoDevo 2010; 1:2. [PMID: 20849645 PMCID: PMC2938726 DOI: 10.1186/2041-9139-1-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2009] [Accepted: 07/05/2010] [Indexed: 12/04/2022] Open
Abstract
Background A through gut is present in almost all metazoans, and most likely represents an ancient innovation that enabled bilaterian animals to exploit a wide range of habitats. Molecular developmental studies indicate that Fox and GATA regulatory genes specify tissue regions along the gut tube in a broad diversity of taxa, although little is known about gut regionalization within the Lophotrochozoa. In this study, we isolated FoxA and GATA456 orthologs and used whole mount in situ hybridization during larval gut formation in two marine worms: the segmented, polychaete annelid Chaetopterus, which develops a planktotrophic larva with a tripartite gut, and the non-segmented sipunculan Themiste lageniformis, which develops a lecithotrophic larva with a U-shaped gut. Results FoxA and GATA456 transcripts are predominantly restricted to gut tissue, and together show regional expression spanning most of the alimentary canal in each of these lophotrochozoans, although neither FoxA nor GATA456 is expressed in the posterior intestine of Chaetopterus. In both species, FoxA is expressed at the blastula stage, transiently in presumptive endoderm before formation of a definitive gut tube, and throughout early larval development in discrete foregut and hindgut domains. GATA456 genes are expressed during endoderm formation, and in endoderm and mesoderm associated with the midgut in each species. Several species-specific differences were detected, including an overlap of FoxA and GATA456 expression in the intestinal system of Themiste, which is instead complimentary in Chaetopterus. Other differences include additional discrete expression domains of FoxA in ectodermal trunk cells in Themiste but not Chaetopterus, and expression of GATA456 in anterior ectoderm and midgut cells unique to Chaetopterus. Conclusions This study of gene expression in a sipunculan contributes new comparative developmental insights from lophotrochozoans, and shows that FoxA and GATA456 transcription factors are part of an ancient patterning mechanism that was deployed during early evolution of the metazoan through gut. The common utilization of FoxA and GATA456 throughout gut formation by species with contrasting life history modes indicates that both genes are core components of a gut-specific gene regulatory network in spiralians. Despite a highly conserved pattern of early development, and probably similar ontogenic origins of gut tissue, there are molecular differences in gut regionalization between lophotrochozoan species.
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Affiliation(s)
- Michael J Boyle
- Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawaii, Honolulu, HI 96813, USA.
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445
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Schaack S, Gilbert C, Feschotte C. Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution. Trends Ecol Evol 2010; 25:537-46. [PMID: 20591532 DOI: 10.1016/j.tree.2010.06.001] [Citation(s) in RCA: 317] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Revised: 06/03/2010] [Accepted: 06/03/2010] [Indexed: 11/25/2022]
Abstract
Horizontal transfer is the passage of genetic material between genomes by means other than parent-to-offspring inheritance. Although the transfer of genes is thought to be crucial in prokaryotic evolution, few instances of horizontal gene transfer have been reported in multicellular eukaryotes; instead, most cases involve transposable elements. With over 200 cases now documented, it is possible to assess the importance of horizontal transfer for the evolution of transposable elements and their host genomes. We review criteria for detecting horizontal transfers and examine recent examples of the phenomenon, shedding light on its mechanistic underpinnings, including the role of host-parasite interactions. We argue that the introduction of transposable elements by horizontal transfer in eukaryotic genomes has been a major force propelling genomic variation and biological innovation.
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Affiliation(s)
- Sarah Schaack
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
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446
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Estella C, Mann RS. Non-redundant selector and growth-promoting functions of two sister genes, buttonhead and Sp1, in Drosophila leg development. PLoS Genet 2010; 6:e1001001. [PMID: 20585625 PMCID: PMC2891808 DOI: 10.1371/journal.pgen.1001001] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Accepted: 05/25/2010] [Indexed: 11/18/2022] Open
Abstract
The radically distinct morphologies of arthropod and tetrapod legs argue that these appendages do not share a common evolutionary origin. Yet, despite dramatic differences in morphology, it has been known for some time that transcription factors encoded by the Distalless (Dll)/Dlx gene family play a critical role in the development of both structures. Here we show that a second transcription factor family encoded by the Sp8 gene family, previously implicated in vertebrate limb development, also plays an early and fundamental role in arthropod leg development. By simultaneously removing the function of two Sp8 orthologs, buttonhead (btd) and Sp1, during Drosophila embryogenesis, we find that adult leg development is completely abolished. Remarkably, in the absence of these factors, transformations from ventral to dorsal appendage identities are observed, suggesting that adult dorsal fates become derepressed when ventral fates are eliminated. Further, we show that Sp1 plays a much more important role in ventral appendage specification than btd and that Sp1 lies genetically upstream of Dll. In addition to these selector-like gene functions, Sp1 and btd are also required during larval stages for the growth of the leg. Vertebrate Sp8 can rescue many of the functions of the Drosophila genes, arguing that these activities have been conserved, despite more than 500 million years of independent evolution. These observations suggest that an ancient Sp8/Dlx gene cassette was used in an early metazoan for primitive limb-like outgrowths and that this cassette was co-opted multiple times for appendage formation in multiple animal phyla.
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Affiliation(s)
- Carlos Estella
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
| | - Richard S. Mann
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
- * E-mail:
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447
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Parmentier G, Bastian FB, Robinson-Rechavi M. Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy. ACTA ACUST UNITED AC 2010; 26:1766-71. [PMID: 20519284 PMCID: PMC2894521 DOI: 10.1093/bioinformatics/btq283] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Motivation: The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we need to establish relations between ontologies describing different species. Results: We present a new algorithm, and its implementation in the software Homolonto, to create new relationships between anatomical ontologies, based on the homology concept. Homolonto uses a supervised ontology alignment approach. Several alignments can be merged, forming homology groups. We also present an algorithm to generate relationships between these homology groups. This has been used to build a multi-species ontology, for the database of gene expression evolution Bgee. Availability: download section of the Bgee website http://bgee.unil.ch/ Contact:marc.robinson-rechavi@unil.ch Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Gilles Parmentier
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
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448
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Zhu J, Zhang YT, Alber MS, Newman SA. Bare bones pattern formation: a core regulatory network in varying geometries reproduces major features of vertebrate limb development and evolution. PLoS One 2010; 5:e10892. [PMID: 20531940 PMCID: PMC2878345 DOI: 10.1371/journal.pone.0010892] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Accepted: 05/07/2010] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Major unresolved questions regarding vertebrate limb development concern how the numbers of skeletal elements along the proximodistal (P-D) and anteroposterior (A-P) axes are determined and how the shape of a growing limb affects skeletal element formation. There is currently no generally accepted model for these patterning processes, but recent work on cartilage development (chondrogenesis) indicates that precartilage tissue self-organizes into nodular patterns by cell-molecular circuitry with local auto-activating and lateral inhibitory (LALI) properties. This process is played out in the developing limb in the context of a gradient of fibroblast growth factor (FGF) emanating from the apical ectodermal ridge (AER). RESULTS We have simulated the behavior of the core chondrogenic mechanism of the developing limb in the presence of an FGF gradient using a novel computational environment that permits simulation of LALI systems in domains of varying shape and size. The model predicts the normal proximodistal pattern of skeletogenesis as well as distal truncations resulting from AER removal. Modifications of the model's parameters corresponding to plausible effects of Hox proteins and formins, and of the reshaping of the model limb, bud yielded simulated phenotypes resembling mutational and experimental variants of the limb. Hypothetical developmental scenarios reproduce skeletal morphologies with features of fossil limbs. CONCLUSIONS The limb chondrogenic regulatory system operating in the presence of a gradient has an inherent, robust propensity to form limb-like skeletal structures. The bare bones framework can accommodate ancillary gene regulatory networks controlling limb bud shaping and establishment of Hox expression domains. This mechanism accounts for major features of the normal limb pattern and, under variant geometries and different parameter values, those of experimentally manipulated, genetically aberrant and evolutionary early forms, with no requirement for an independent system of positional information.
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Affiliation(s)
- Jianfeng Zhu
- Department of Mathematics, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Yong-Tao Zhang
- Department of Mathematics, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Mark S. Alber
- Department of Mathematics, University of Notre Dame, Notre Dame, Indiana, United States of America
- Center for the Study of Biocomplexity, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Stuart A. Newman
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla, New York, United States of America
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449
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Zeller R. The temporal dynamics of vertebrate limb development, teratogenesis and evolution. Curr Opin Genet Dev 2010; 20:384-90. [PMID: 20537528 DOI: 10.1016/j.gde.2010.04.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2010] [Revised: 04/20/2010] [Accepted: 04/24/2010] [Indexed: 01/15/2023]
Abstract
Recent genetic and functional analysis of vertebrate limb development begins to reveal how the functions of particular genes and regulatory hierarchies can drastically change over time. The temporal and spatial interplay of the two instructive signalling centres are part of a larger signalling system that orchestrates limb bud morphogenesis in a rather self-regulatory manner. It appears that mesenchymal cells are specified early and subsequently, the progenitors for the different skeletal elements are expanded and determined progressively during outgrowth. Mutations and teratogens that disrupt distal progression of limb development most often cause death of the early-specified progenitors rather than altering their fates. The proliferative expansion and distal progression of paired appendage development was one of the main driving forces behind the transition from fin to limb buds during paired appendage evolution. Finally, the adaptive diversification or loss of modern tetrapod limbs in particular phyla or species appear to be a consequence of evolutionary tampering with the regulatory systems that control distal progression of limb development.
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Affiliation(s)
- Rolf Zeller
- Developmental Genetics, Department of Biomedicine, University of Basel Medical Faculty, Mattenstrasse 28, Basel, Switzerland.
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450
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de Waal FB, Ferrari PF. Towards a bottom-up perspective on animal and human cognition. Trends Cogn Sci 2010; 14:201-7. [DOI: 10.1016/j.tics.2010.03.003] [Citation(s) in RCA: 157] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Revised: 03/03/2010] [Accepted: 03/04/2010] [Indexed: 11/15/2022]
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