The beak of the other finch: coevolution of genetic covariance structure and developmental modularity during adaptive evolution

The link between adaptation and evolutionary change remains the most central and least understood evolutionary problem. Rapid evolution and diversification of avian beaks is a textbook example of such a link, yet the mechanisms that enable beak''s precise adaptation and extensive adaptability are poorly understood. Often observed rapid evolutionary change in beaks is particularly puzzling in light of the neo-Darwinian model that necessitates coordinated changes in developmentally distinct precursors and correspondence between functional and genetic modularity, which should preclude evolutionary diversification. I show that during first 19 generations after colonization of a novel environment, house finches (Carpodacus mexicanus) express an array of distinct, but adaptively equivalent beak morphologies—a result of compensatory developmental interactions between beak length and width in accommodating microevolutionary change in beak depth. Directional selection was largely confined to the elimination of extremes formed by these developmental interactions, while long-term stabilizing selection along a single axis—beak depth—was mirrored in the structure of beak''s additive genetic covariance. These results emphasize three principal points. First, additive genetic covariance structure may represent a historical record of the most recurrent developmental and functional interactions. Second, adaptive equivalence of beak configurations shields genetic and developmental variation in individual components from depletion by natural selection. Third, compensatory developmental interactions among beak components can generate rapid reorganization of beak morphology under novel conditions and thus greatly facilitate both the evolution of precise adaptation and extensive diversification, thereby linking adaptation and adaptability in this classic example of Darwinian evolution.     

Bio-ontologies: current trends and future directions

In recent years, as a knowledge-based discipline, bioinformatics has been made more computationally amenable. After its beginnings as a technology advocated by computer scientists to overcome problems of heterogeneity, ontology has been taken up by biologists themselves as a means to consistently annotate features from genotype to phenotype. In medical informatics, artifacts called ontologies have been used for a longer period of time to produce controlled lexicons for coding schemes. In this article, we review the current position in ontologies and how they have become institutionalized within biomedicine. As the field has matured, the much older philosophical aspects of ontology have come into play. With this and the institutionalization of ontology has come greater formality. We review this trend and what benefits it might bring to ontologies and their use within biomedicine.     

Pathways in the emergence of developmental neuroethology: Antecedents to current views of neurobehavioral ontogeny

The historical forces that have contributed to our current views of neurobehavioral development (and thus to the fields of developmental psychobiology and neuroethology) are many and varied. Although similar statements might be made about almost any field of science, it is in particular true of this field, which represents a kind of mongrel discipline derived from at least three major sources (psychology, embryology, and neuroscience) and several more minor ones (including developmental psychology and psychiatry, psychoanalysis, education, zoology, ethology, and sociology). Although I attempt to demonstrate here how each of these sources may have influenced the emergence of a unified field of developmental psychobiology or developmental neuroethology, because the present article represents the first attempt of which I am aware to trace the history of these fields I am certain that there is considerable room for improvement, correction, and revision of the views expressed here. Accordingly, I consider this inaugural effort a kind of reconnaissance intended to trace a necessarily imperfect historic path for others to follow and improve upon. In the final analysis, I will be satisfied if this article only serves to underscore two related points: first is the value derived from historical studies of contemporary issues in development, and the second concerns the extent to which our current ideas and concepts about neurobehavioral development, ideas often considered new and contemporary, were already well known to those who came before us. The first point underscores the arguments expressed in the Introduction that the present must always be reconciled with the past, for the past is never entirely past. The second point returns full circle to an important thought expressed in the opening quotation to this article, namely, that even though our historic predecessors lacked much of the empirical facts available to us they were nonetheless able to attain a surprisingly deep understanding of neurobehavioral ontogeny. © 1992 John Wiley & Sons, Inc.     

Comparative developmental anatomy of seedlings in nine species of podostemaceae (subfamily Podostemoideae)

The developmental anatomy is described for seedlings of nine Asian and Australian species of Podostemaceae, subfamily Podostemoideae. The hypocotyl is rudimentary (except in Zeylanidium olivaceum) and does not form a primary root in any of the species examined. An adventitious root forms endogenously in the hypocotyl of six species with ribbon-like or flattened subcylindrical roots, and in Z olivaceum with foliose roots. In contrast, it forms exogenously in Hydrobryum griffithii and Synstylis micranthera with foliose roots. The juvenile root becomes flattened and dorsiventral, branches exogenously (in Polypleurum stylosum, P. wallichii and Z. lichenoides) and produces shoots endogenously (in P. stylosum, P. wallichii, S. micranthera and Z. lichenoides). The root meristem is simple, composed of surface and uniform inner cells, and is devoid of root cap initials in all species. The reduced meristem morphology of seedling roots may be primitive in the Asian-Australian Podostemoideae. A root cap or protective tissue did not form during the culture period, even in the seven species with capped adult roots, probably due to its delayed development. It was absent throughout ontogeny in the other two species. No obvious shoot apical meristem forms between the cotyledons. One to several leaves occupy the shoot apical area in species with endogenous adventitious roots, while no leaves are formed in species with exogenous roots. These differences suggest recurrent origins of foliose roots in the Asian clade. Similarities between the unique seedling morphology and mutant Arabidopsis phenotypes are discussed.     

Molecular cloning of cDNAs for auxin-induced mRNAs and developmental expression of the auxin-inducible genes

By differential hybridization, two auxin-inducible cDNA clones (SAR1 and SAR2) have been isolated from a cDNA library constructed to poly(A)⁺ mRNA from auxin-treated strawberry receptacles. Both the clones have been used as probes to study the expression of the auxin-induced genes in pollinated and unpollinated fruits of various stages of development and in different organs. A high level of auxin-induced mRNAs is found in pollinated fruits as compared to unpollinated fruits of the same age, suggesting that the expression of the auxin-induced genes is developmentally regulated and the level of auxin-induced mRNAs is regulated by endogenous auxin. Furthermore, our data on the expression of SAR1 and SAR2 genes in pollinated and unpollinated fruits revealed a positive correlation between growth of strawberry fruit and the induction of mRNA corresponding to the SAR1 and SAR2 clones. Ethylene has no effect on the expression of the auxin-induced mRNAs. SAR1 mRNA is not detected in other parts of strawberry plants whereas SAR2 mRNA is present in roots. Furthermore, mRNA corresponding to SAR1 and SAR2 is not detected in other auxin-responsive plant systems such as pea epicotyls and bean explants.     

Involvement of differential gene expression and mRNA stability in the developmental regulation of the hsp 30 gene family in heat-shocked Xenopus laevis embryos

Four complete hsp 30 genes have been isolated from Xenopus laevis: hsp 30A, hsp 30B (a pseudogene), hsp 30C, and hsp 30D. The hsp 30A and hsp 30C genes are first heat inducible at the early tailbud stage, as determined by RNase protection and RT-PCR assays. In this study, we determined by RT-PCR that the hsp 30D gene was first heat inducible (33^oC for 1 h) at the mid-tailbud stage, approximately 1 day later in development than hsp 30A and hsp 30C. Furthermore, using Northern blot analysis, we detected the presence of very low levels of hsp 30 mRNA at the heat-shocked late blastula stage. The relative levels of these pre-tailbud (PTB) hsp 30 mRNAs increased at the gastrula and neurula stage followed by a dramatic enhancement in heat shocked tail-bud and tadpole stage embryos (50- to 100- fold relative to late blastula). Interestingly, treatment of blastula or gastrula embryos at high temperatures (37^oC for 1 h) or with the protein synthesis inhibitor, cycloheximide, followed by heat shock, led to enhanced accumulation of the pre-tailbud (PTB) hsp 30 mRNAs. hsp 70, hsp 87, and actin messages were not stabilized at high temperatures or by cycloheximide treatment. Finally, hsp 30D mRNA was not detected by RT-PCR analysis of cycloheximidetreated, heat-shocked blastula stage embryos, confirming that it is not a member of the PTB hsp 30 mRNAs. This study indicates that differential gene expression and mRNA stability are involved in the regulation of hsp 30 gene expression during early Xenopus laevis development. © 1995 Wiley-Liss, Inc.     

Identification of members of the HSP30 small heat shock protein family and characterization of their developmental regulation in heat-shocked xenopus laevis embryos

In the present study we have characterized the synthesis of members of the HSP30 family during Xenopus laevis development using a polyclonal antipeptide antibody derived from the carboxyl end of HSP30C. Two-dimensional PAGE/immunoblot analysis was unable to detect any heat-inducible small HSPs in cleavage, blastula, gastrula, or neurula stage embryos. However, heat-inducible accumulation of a single protein was first detectable in early tailbud embryos with an additional 5 HSPs at the late tailbud stage and a total of 13 small HSPs at the early tadpole stage. In the Xenopus A6 kidney epithelial cell line, a total of eight heat-inducible small HSPs were detected by this antibody. Comparison of the pattern of protein synthesis in embryos and somatic cells revealed a number of common and unique heat inducible proteins in Xenopus embryos and cultured kidney epithelial cells. To specifically identify the protein product of the HSP30C gene, we made a chimeric gene construct with the Xenopus HSP30C coding sequence under the control of a constitutive promoter. This construct was microinjected into fertilized eggs and resulted in the premature and constitutive synthesis of the HSP30C protein in gastrula stage embryos. Through a series of mixing experiments, we were able to specifically identify the protein encoded by the HSP30C gene in embryos and somatic cells and to conclude that HSP30C synthesis was first heat-inducible at the early tailbud stage of development. The differential pattern of heat-inducible accumulation of members of the HSP30 family during Xenopus development suggests that these proteins may have distinct functions at specific embryonic stages during a stress response.     

Nuclear phosphoinositides and their roles in cell biology and disease

Since the late 1980s, a growing body of evidence has documented that phosphoinositides and their metabolizing enzymes, which regulate a large variety of cellular functions both in the cytoplasm and at the plasma membrane, are present also within the nucleus, where they are involved in processes such as cell proliferation, differentiation, and survival. Remarkably, nuclear phosphoinositide metabolism operates independently from that present elsewhere in the cell. Although nuclear phosphoinositides generate second messengers such as diacylglycerol and inositol 1,4,5 trisphosphate, it is becoming increasingly clear that they may act by themselves to influence chromatin structure, gene expression, DNA repair, and mRNA export. The understanding of the biological roles played by phosphoinositides is supported by the recent acquisitions demonstrating the presence in the nuclear compartment of several proteins harboring phosphoinositide-binding domains. Some of these proteins have functional roles in RNA splicing/processing and chromatin assembly. Moreover, recent evidence shows that nuclear phospholipase Cβ1 (a key phosphoinositide metabolizing enzyme) could somehow be involved in the myelodysplastic syndrome, i.e. a hematopoietic disorder that frequently evolves into an acute leukemia. This review aims to highlight the most significant and updated findings about phosphoinositide metabolism in the nucleus under both physiological and pathological conditions.     

Fluctuating asymmetry and developmental instability in evolutionary biology: past, present and future

The role of developmental instability (DI), as measured by fluctuating asymmetry (FA), in evolutionary biology has been the focus of a wealth of research for more than half a century. In spite of this long period and many published papers, our current state of knowledge reviewed here only allows us to conclude that patterns are heterogeneous and that very little is known about the underlying causes of this heterogeneity. In addition, the statistical properties of FA as a measure of DI are only poorly grasped because of a general lack of understanding of the underlying mechanisms that drive DI. If we want to avoid that this area of research becomes abandoned, more efforts should be made to understand the observed heterogeneity, and attempts should be made to develop a unifying statistical protocol. More specifically, and perhaps most importantly, it is argued here that more attention should be paid to the usefulness of FA as a measure of DI since many factors might blur this relationship. Furthermore, the genetic architecture, associations with fitness and the importance of compensatory growth should be investigated under a variety of stress situations. In addition, more focus should be directed to the underlying mechanisms of DI as well as how these processes map to the observable phenotype. These insights could yield more efficient statistical models and a unified approach to the analysis of patterns in FA and DI. The study of both DI and canalization is indispensable to obtain better insights in their possible common origin, especially because both have been suggested to play a role in both micro- and macro-evolutionary processes.     

Cloning and characterization of the murine Imitation Switch (ISWI) genes: differential expression patterns suggest distinct developmental roles for Snf2h and Snf2l

Here we report the cloning of two cDNAs, Snf2h and Snf2l, encoding the murine members of the Imitation Switch (ISWI) family of chromatin remodeling proteins. To gain insight into their function we examined the spatial and temporal expression patterns of Snf2h and Snf2l during development. In the brain, Snf2h is prevalent in proliferating cell populations whereas, Snf2l is predominantly expressed in terminally differentiated neurons after birth and in adult animals, concomitant with the expression of a neural specific isoform. Moreover, a similar proliferation/differentiation relationship of expression for these two genes was observed in the ovaries and testes of adult mice. These results are consistent with a role of Snf2h complexes in replication-associated nucleosome assembly and suggest that Snf2l complexes have distinct functions associated with cell maturation or differentiation.     

Seedling developmental anatomy of an undescribed Malaccotristicha species (Podostemaceae, subfamily Tristichoideae) with implications for body plan evolution

The seedling development of an undescribed Malaccotristicha species was observed by using seedling culture and microtomy to infer the evolution of body plan with a focus on the root, which is a developmentally leading organ of most Podostemaceae. The young seedling has a small primary shoot apical meristem and a primary root apical meristem. The shoot meristem develops into a plumular ramulus, and the root meristem, into a cylindrical radicle with no root cap. The radicle transforms to a dorsiventral, flattened, capped primary root. An adventitious root develops endogenously on the lateral side of the hypocotyl and is similar to the primary root. This is a new pattern in Podostemaceae. Comparison of this and described patterns of Podostemaceae (and the sister-group Hypericaceae) suggests that the radicle was lost in the early evolution of Podostemaceae and instead adventitious roots replaced it as a leading organ.     

Gyrodactylid developmental biology: historical review, current status and future trends

In the viviparous gyrodactylids, embryos develop one inside another within the parental uterus, a phenomenon with major implications for the biology of this species-rich group. Development occurs via two routes: first-born daughters develop at the centre of an embryo cluster in utero, whereas all other daughters develop from oocytes. The resulting offspring are, however, morphologically indistinguishable. We review here the history of gyrodactylid embryology in the context of current knowledge and, present additional cytogenetic and ultrastructural observations of embryonic development. These progenetic parasites are highly modified for viviparity; oocyte maturation and sperm storage occur in a single chamber, the Egg Cell Forming Region, and a mature oocyte passes into the uterus after the birth of the preceding, fully developed offspring. The uterus has a syncytial lining derived from anterior and posterior cap cells. These cells are the first to differentiate in the female reproductive system and may be involved in controlling development. Embryos receive nutrients via the uterus rather than from vitelline cells. Traditionally, development of the first-born daughter has been considered a form of polyembryony, although paedogenesis has also been suggested. In contrast to previous studies, we could not trace lineage of the first-born daughter to a single quiescent macromere. However, only mitotic divisions have been conclusively observed in the intraembryonic generation, indicating an asexual origin. All other daughters are formed from meiotically derived oocytes by sexual reproduction or automictic parthenogenesis. The latter may involve pre-meiotic doubling of chromosomes, but the precise mechanism and the relative proportion of sexual and parthenogenetic offspring are unknown. Exceptionally, cleavage in Gyrodactylus spp. occurs by duets rather than quartets (a pattern previously only recorded in acoels) and is characterised by extensive cell rearrangements. Blastomeres may be connected by fine cytoplasmic processes or completely disassociated and are readily redistributed by the muscular actions of the parental uterus. This process resembles 'Blastomeren-Anarchie' of rhabdocoels but without the structural support of vitelline cells. It prevents generation of early cell fate maps and indicates regulative, rather than mosaic, development. Structures such as the gut and excretory system differentiate late, and are highlighted, together with the attachment apparatus, as examples of post-embryonic differentiation. Molecular and cellular techniques are now essential to further elucidate mechanisms of gyrodactylid reproduction, which will in turn contribute to current debates with animal embryology.     

Transgenic assays for mutations and cancer: current status and future perspectives

Transgenic mouse modelling has proved to be a powerful approach to explore the various steps involved in spontaneous and induced carcinogenesis. Some of the multitude of models currently available have the potential to become a substitute for the expensive, long-term rodent bioassay to predict carcinogenicity of environmental compounds. Here, we review the progress in the development and use of transgenic mouse models specifically for the purpose of carcinogenicity and mutagenicity testing.     

Ontogeny, anatomy, and the problem of homology: Carl Gegenbaur and the American tradition of cell lineage studies

Summary In this paper we analyze Carl Gegenbaur’s conception of the relationship between embryology (“Ontogenie”) and comparative anatomy and his related ideas about homology. We argue that Gegenbaur’s conviction of the primacy of comparative anatomy and his careful consideration of caenogenesis led him to a more balanced view about the relationship between ontogeny and phylogeny than his good friend Ernst Haeckel. We also argue that Gegenbaur’s ideas about the centrality of comparative anatomy and his definitions of homology actually laid the conceptual foundations for Hans Spemann’s (1915) later analysis of homology. We also analyze Gegenbaur’s reception in the United States and how the discussions between E.B. Wilson and Edwin Conklin about the role of the “embryological criterion of homology” and the latter’s argument for an even earlier concept of cellular homology reflect the recurring theme of preformism in ontogeny, a theme that finds its modern equivalent in various genetic definitions of homology, only recently challenged by the emerging synthesis of evolutionary developmental biology. Finally, we conclude that Gegenbaur’s own careful methodological principles can serve as an important model for proponents of present day “evo-devo”, especially with respect to the integration of ontogeny with phylogeny embedded in comparative anatomy.     

Pathway databases and tools for their exploitation: benefits,current limitations and challenges

In past years, comprehensive representations of cell signalling pathways have been developed by manual curation from literature, which requires huge effort and would benefit from information stored in databases and from automatic retrieval and integration methods. Once a reconstruction of the network of interactions is achieved, analysis of its structural features and its dynamic behaviour can take place. Mathematical modelling techniques are used to simulate the complex behaviour of cell signalling networks, which ultimately sheds light on the mechanisms leading to complex diseases or helps in the identification of drug targets. A variety of databases containing information on cell signalling pathways have been developed in conjunction with methodologies to access and analyse the data. In principle, the scenario is prepared to make the most of this information for the analysis of the dynamics of signalling pathways. However, are the knowledge repositories of signalling pathways ready to realize the systems biology promise? In this article we aim to initiate this discussion and to provide some insights on this issue.     

Ascidian embryos as a model system to analyze expression and function of developmental genes

Ascidians have served as an appropriate experimental system in developmental biology for more than a century. The fertilized egg develops quickly into a tadpole larva, which consists of a small number of organs including epidermis, central nervous system with two sensory organs, endoderm and mesenchyme in the trunk, and notochord and muscle in the tail. This configuration of the ascidian tadpole is thought to represent the most simplified and primitive chordate body plan. Their embryogenesis is simple, and lineage of embryonic cells is well documented. The ascidian genome contains a basic set of genes with less redundancy compared to the vertebrate genome. Cloning and characterization of developmental genes indicate that each gene is expressed under discrete spatio-temporal pattern within their lineage. In addition, the use of various molecular techniques in the ascidian embryo system highlights its advantages as a future experimental system to explore the molecular mechanisms underlying the expression and function of developmental genes as well as genetic circuitry responsible for the establishment of the basic chordate body plan. This review is aimed to highlight the recent advances in ascidian embryology.     

Comparative anatomy and systematics of woody Saxifragaceae. Aphanopetalum Endl.

The floral and vegetative anatomy of the small Australian genus Aphanopetalum were studied. Wood is described for the first time and is characterized by predominantly solitary pores, scalariform vessel element perforation plates with low bar numbers, imperforate tracheary elements with distinctly bordered pits, sparse axial parenchyma, and a combination of homocellular and heterocellular rayS. Starch occurs in both axial and ray parenchyma of the wood. Stems possess unilacunar, one-trace nodes and the uncommon feature of an endodermis with well-defined Casparian stripS. Leaves have anomocytic stomata, a bifacial mesophyll and semicraspedodromous venation or a combination of semicraspedodromous and brochidodromous venation. The tetramerous flowers are apetalous or have minute petals. The compound, half-inferior gynoecium consists of essentially totally united carpels. The pattern of floral vascularization resembles different Saxifragaceae sensu lalo in that the compound sepal-plane and petal-plane traces give rise to staman bundles as well as sepal, petal, and carpel wall venation in their respective planes. The ventral ovarian bundles are fused into a single ventral complex that subdivides at the top of the ovary to form ventral bundles and to supply the one ovule in each locule. Vegetative and floral features provide compelling evidence to suggest that Aphanopetalum has its nearest relatives among the Saxifragaceae sensu lato rather than Cunoniaceae. The genus is probably best treated as forming its own subfamily (or family) among the saxifragaean alliance.