Phylogenetics of the australasian mudfishes: evolution of an eel-like body plan

The mudfish genus Neochanna (Osmeriformes: Galaxiidae) contains six species that exhibit varying degrees of morphological and ecological adaptation to life in swampy conditions. Here, we present the first molecular phylogenetic analysis (16S rRNA+cytochrome b; 1681bp) of the entire genus to (1) test for monophyly of Australian and New Zealand taxa and (2) elucidate morphological character evolution. In addition, we analyse a matrix of 21 morphological characters to test for congruence between mitochondrial DNA and morphology, and to examine total evidence under a Bayesian framework. Molecular data indicate that the diadromous Tasmanian mudfish, N. cleaveri, is sister to a clade of five non-diadromous New Zealand mudfishes. Mapping of morphological characters onto the molecular phylogeny suggests an evolutionary transition from a plesiomorphic "stream" galaxiid morphotype to a more specialised "anguilliform" galaxiid morphotype. Pelvic fins have become increasingly reduced and dorsal, anal, and caudal fins are increasingly confluent. Associated with these changes are elongated nostrils, reduced eyes, and increased anterior cranial ossification. Morphological and total evidence analyses yield similar or identical topologies, respectively. The phylogenetic distribution of diadromy in Neochanna is consistent with a single loss of this character state in New Zealand. However, the strong sister relationship (3.6% divergent; 100% bootstrap support) detected between non-diadromous N. burrowsius (South Island, NZ) and N. rekohua (Chatham Islands) indicates geologically recent dispersal across 850km of ocean. Diadromy may therefore have been retained in the common ancestor of these two mudfish species, and subsequently lost from both lineages.     

Formins in development: orchestrating body plan origami

Formins, proteins defined by the presence of an FH2 domain and their ability to nucleate linear F-actin de novo, play a key role in the regulation of the cytoskeleton. Initially thought to primarily regulate actin, recent studies have highlighted a role for formins in the regulation of microtubule dynamics, and most recently have uncovered the ability of some formins to coordinate the organization of both the microtubule and actin cytoskeletons. While biochemical analyses of this family of proteins have yielded many insights into how formins regulate diverse cytoskeletal reorganizations, we are only beginning to appreciate how and when these functional properties are relevant to biological processes in a developmental or organismal context. Developmental genetic studies in fungi, Dictyostelium, vertebrates, plants and other model organisms have revealed conserved roles for formins in cell polarity, actin cable assembly and cytokinesis. However, roles have also been discovered for formins that are specific to particular organisms. Thus, formins perform both global and specific functions, with some of these roles concurring with previous biochemical data and others exposing new properties of formins. While not all family members have been examined across all organisms, the analyses to date highlight the significance of the flexibility within the formin family to regulate a broad spectrum of diverse cytoskeletal processes during development.     

Graduality and innovation in the evolution of complex phenotypes: insights from development

The neo-Darwinian paradigm benefits from the assumption that phenotypic variation is gradual and that phenotype and genotype have a relatively simple relationship. These assumptions are historically inherited from the times of the neo-Darwinian synthesis and, consequently, do not include present understanding about development. In this study, understanding about the dynamics of pattern formation is used to explore to that extent phenotypic variation can be expected to be gradual and simply related to molecular variation. Variation in simple phenotypes seems to fit neo-Darwinian assumptions but variation in complex phenotypes does not. Instead, variation in complex phenotypes would have a tendency to relatively less gradual evolution, even at microevolutionary time scales, that would make phylogenetic reconstructions more difficult. In addition, they will have a tendency to exhibit specific trends in innovation rates over group radiations with early accelerations and late decelerations. This work also explores further consequences of these results in our understanding of phenotypic evolution.     

Polyembryony in parasitic wasps: evolution of a novel mode of development

Major developmental innovations have been associated with adaptive radiations that have allowed particular groups of organisms to occupy empty ecospace. Well-known developmental novelties associated with the conquest of new habitats include the evolution of the tetrapode limb, allowing the radiation of vertebrates into a terrestrial habitat, and formation of insect wings that permitted their dispersal into the air. However, an understanding of the evolutionary forces and molecular mechanisms behind developmental novelties still remains tenuous. A little-studied adaptive radiation in insects from the developmental perspective is the evolution of parasitism. The parasitic lifestyle has allowed parasitic insects to occupy a novel ecological niche where they have evolved a plethora of life history strategies and modes of embryogenesis, developing on or within the body of the host. One of the most striking adaptations to development within the body of the host includes polyembryonic development, where certain wasps form clonally up to 2000 embryos from a single egg. Taking advantage of well-established insect phylogeny, techniques developed in a model insect, the fruit fly, and a wealth of knowledge in comparative insect embryology, we are starting to tease apart the evolutionary events that have led to this novel mode of development in insects.     

CP12: a small nuclear-encoded chloroplast protein provides novel insights into higher-plant GAPDH evolution

Higher-plant chloroplast NAD(P)-glyceraldehyde 3-phosphate dehydrogenase (NAD(P)-GAPDH; EC 1.2.1.13) is composed of two different nuclear-encoded subunits, GAPA and GAPB, forming the highly active heterotetrameric A₂B₂ enzyme. The main difference between these two subunits is a C-terminal extension of about 30 amino acid residues of GAPB. We present cDNA clones for a nuclear-encoded chloroplast protein from pea, spinach and tobacco, which we have named CP12. The mature protein consists of only 74, 75 and 76 amino acid residues, respectively and contains two domains with significant homology to the C-terminal extension of GAPB. Affinity chromatography approaches reveal also a specific interaction between CP12 and chloroplast GAPDH. Northern blot analysis indicates that CP12 is, like plastid GAPDH, expressed in green and also in etiolated leaves. Further homology is observed between CP12 and ORF3, an open reading frame located in the hox gene cluster of Anabaena variabilis. This gene cluster encodes the subunits of the bidirectional NADP⁺-dependent [NiFeS] dehydrogenase. We propose therefore a common evolutionary origin of CP12 and higher-plant chloroplast GAPDH subunit GAPB from the cyanobacterial ORF3.     

Expression of a homeobox gene product in normal and mutant zebrafish embryos: evolution of the tetrapod body plan

An antibody was used to detect antigens in zebrafish that appear to be homologous to the frog homeodomain-containing protein XlHbox 1. These antigens show a restricted expression in the anteroposterior axis and an anteroposterior gradient in the pectoral fin bud, consistent with the distribution of XlHbox 1 protein in frog and mouse embryos. In the somitic mesoderm, a sharp anterior limit of expression coincides exactly with the boundary between somites 4 and 5, and the protein level fades out posteriorly. A similar, graded expression of the antigen is seen within the series of Rohon-Beard sensory neurons of the CNS. We also immunostained the mutant spt-1 ('spadetail'), in which the trunk mesoderm is greatly depleted and disorganized in the region of XlHbox 1 expression. The defects stem from misdirected cell movements during gastrulation, but nervertheless, newly recruited cells that partially refill the trunk mesoderm express the antigen within the normal span of the anteroposterior axis. This finding suggests that the mutation does not delete positional information required for activation of the XlHbox 1 gene.     

Two spinal cords in birds: novel insights into early avian evolution

Birds can be subdivided into two large superordinal assemblages based on differences in the dorsal horn of the spinal grey matter. Palaeognaths (i.e. ratites and tinamous), along with a few other orders of neognathous birds, exhibit the primitive dorsal horn state characteristic of other amniotes wherein cutaneous nerves form a single map of the body surface across the dorsal horn. In contrast, the vast majority of neognaths exhibit a novel, distinctly bifid dorsal horn wherein cutaneous nerves form not one, but two separate maps of the skin, each lying side-by-side. This unusual dorsal horn organization, which has been highly conserved and represents the derived state in birds, may identify a novel, major avian clade. These findings shed new light on historically problematic taxa and the early evolutionary branching sequence among living birds. Most notably, they reveal that the traditional orders Gruiformes, Columbiformes, Cuculiformes and Piciformes are unnatural assemblages. Further, in addition to palaeognaths, these findings suggest that most gruiforms, including buttonquails and mesites, as well as pigeons, cuckoos, woodpeckers and songbirds, represent ancient lineages whose ancestry predates the majority of ''modern'' birds. The phylogeny of living birds may thus be likened more to a dense bush than the traditional tree, with more than half of all living species arising from a basal side branch.     

Evolution of gene regulatory networks controlling body plan development

Evolutionary change in animal morphology results from alteration of the functional organization of the gene regulatory networks (GRNs) that control development of the body plan. A major mechanism of evolutionary change in GRN structure is alteration of cis-regulatory modules that determine regulatory gene expression. Here we consider the causes and consequences of GRN evolution. Although some GRN subcircuits are of great antiquity, other aspects are highly flexible and thus in any given genome more recent. This mosaic view of the evolution of GRN structure explains major aspects of evolutionary process, such as hierarchical phylogeny and discontinuities of paleontological change.     

The evolution of nervous system patterning: insights from sea urchin development

Recent studies of the sea urchin embryo have elucidated the mechanisms that localize and pattern its nervous system. These studies have revealed the presence of two overlapping regions of neurogenic potential at the beginning of embryogenesis, each of which becomes progressively restricted by separate, yet linked, signals, including Wnt and subsequently Nodal and BMP. These signals act to specify and localize the embryonic neural fields - the anterior neuroectoderm and the more posterior ciliary band neuroectoderm - during development. Here, we review these conserved nervous system patterning signals and consider how the relationships between them might have changed during deuterostome evolution.     

Hox, Wnt, and the evolution of the primary body axis: insights from the early-divergent phyla

   

The subkingdom Bilateria encompasses the overwhelming majority of animals, including all but four early-branching phyla: Porifera, Ctenophora, Placozoa, and Cnidaria. On average, these early-branching phyla have fewer cell types, tissues, and organs, and are considered to be significantly less specialized along their primary body axis. As such, they present an attractive outgroup from which to investigate how evolutionary changes in the genetic toolkit may have contributed to the emergence of the complex animal body plans of the Bilateria. This review offers an up-to-date glimpse of genome-scale comparisons between bilaterians and these early-diverging taxa. Specifically, we examine these data in the context of how they may explain the evolutionary development of primary body axes and axial symmetry across the Metazoa. Next, we re-evaluate the validity and evolutionary genomic relevance of the zootype hypothesis, which defines an animal by a specific spatial pattern of gene expression. Finally, we extend the hypothesis that Wnt genes may be the earliest primary body axis patterning mechanism by suggesting that Hox genes were co-opted into this patterning network prior to the last common ancestor of cnidarians and bilaterians.     

Essential roles of fibronectin in the development of the left-right embryonic body plan

Studies in Xenopus laevis suggested that cell-extracellular matrix (ECM) interactions regulate the development of the left–right axis of asymmetry; however, the identities of ECM components and their receptors important for this process have remained unknown. We discovered that FN is required for the establishment of the asymmetric gene expression pattern in early mouse embryos by regulating morphogenesis of the node, while cellular fates of the nodal cells, canonical Wnt and Shh signaling within the node were not perturbed by the absence of FN. FN is also required for the expression of Lefty 1/2 and activation of SMADs 2 and 3 at the floor plate, while cell fate specification of the notochord and the floor plate, as well as signaling within and between these two embryonic organizing centers remained intact in FN-null mutants. Furthermore, our experiments indicate that a major cell surface receptor for FN, integrin α5β1, is also required for the development of the left–right asymmetry, and that this requirement is evolutionarily conserved in fish and mice. Taken together, our studies demonstrate the requisite role for a structural ECM protein and its integrin receptor in the development of the left–right axis of asymmetry in vertebrates.     

Deuterostomes in a twist: the origins of a radical new body plan

SUMMARY Echinoderms have a unique ontogeny and adult structure, and, among Bilateria, are the phylum that has diverged most radically in appearance from the ancestral body plan. Embryology and gene expression studies suggest how this transformation may have occurred while paleontological data provide direct evidence for the order in which these events took place. Comparing echinoderm ontogeny and genetic developmental signalling patterns with those of their sister group, the hemichordates, suggests that an evolutionary switch from posterior facultative to anterior obligate larval attachment proved the critical trigger. This necessitated introduction of a phase of torsion in development to bring the mouth into a more appropriate orientation for filter feeding, which in turn rotated the axis of the developing adult 90° out of alignment with Hox and other body patterning genes. As a result the developing echinoderm rudiment came to receive a complex mosaic of anterior–posterior signalling, and extensive co-option of signalling pathways was able to take place. The fossil record shows that early (pre-radiate) echinoderms were much more hemichordate-like, with a muscular post-anal stalk and facultative attachment, and probably developed maintaining continuity with larval axes, as in hemichordates, although left-right asymmetry was more highly developed. Anterior attachment and torsion, however, were clearly part of the developmental pattern of helicoplacoids and (to a much greater extent) in subsequent pentaradiate forms.     

Reevaluation of the perianth and androecium in Caryophyllales: implications for flower evolution

The Caryophyllales have the highest diversity in androecial patterns among flowering plants with stamen numbers ranging from 1 up to 4,000. Thanks to the recent progress in reconstructing the phylogeny of core Caryophyllales, questions of floral evolution, such as the origin and diversification of the androecium, can be readdressed. Caryophyllales are unique among core eudicots in sharing an androecial ring meristem or platform with centrifugal development of stamens and petals. Stamens are basically arranged in two whorls and evolution within the clade depends on the shift of either the antesepalous or the alternisepalous whorls to an upper position on the ring meristem and the reduction of the other. Four main developmental phenomena are responsible for the high diversity in androecial patterns: (1) the sterilisation of the outermost stamens through a division of common primordia; (2) the secondary addition of stamens by a centrifugal initiation of supernumerary stamens superimposed on a lower stamen number; (3) the pairwise displacement of alternisepalous stamens to the middle of the outer sepals and their potential fusion, or as part of a pluristaminate androecium; (4) the inversed sequence, reduction and loss of antesepalous stamens. Shifts in stamen numbers depend on pressures of the calyx and carpels and changes in the number of the latter. These patterns are expressed differently in the three main evolutionary lines of core Caryophyllales and are systematically relevant: (1) A basal grade of Caryophyllales, culminating with Caryophyllaceae, Amaranthaceae, Stegnosperma and Limeum, has the antesepalous stamens initiated in upper position on the ring meristem, and alternisepalous stamens are preferentially reduced. Among the antesepalous whorl there is a progressive loss of stamens following a sequence inversed to sepal initiation. Petaloid staminodes are formed by the radial division of outer stamens. (2) The raphide-clade and Molluginaceae are characterized by alternisepalous stamens in upper position on the ring meristem, with a trend to secondary stamen multiplication, and loss of antesepalous stamens. (3) The Portulacineae share the pattern of the raphide clade, but some taxa show shifts to an upper position on the ring meristem of either antesepalous or alternisepalous stamens, linked with secondary multiplications and reduction of either whorl. Different floral characters are plotted on a recent cladogram of Caryophyllales. The data show a consistent correlation between shifting carpel and stamen numbers independent of perianth evolution. Comparative data suggest that the basic androecium of Caryophyllales consists of two whorls of five stamens, linked with an absence of petals, and the evolution of the androecium is a combination of reductions and secondary multiplications of stamens with a highly predictive systematic value.     

Conflicting processes in the evolution of body size and development time

Body size and development time of Manduca sexta are both determined by the same set of three developmental–physiological factors. These define a parameter space within which it is possible to analyse and explain how phenotypic change is associated with changes in the underlying factors. Body size and development time are determined by the identical set of underlying factors, so they are not independent, but because the mechanisms by which these factors produce each phenotype are different, the two phenotypes are only weakly correlated, and the correlation is context dependent. We use a mathematical model of this mechanism to explore the association between body size and development time and show that the correlation between these two life-history traits can be positive, zero or negative, depending entirely on where in parameter space a population is located, and on which of the underlying factors has a greater variation. The gradient within this parameter space predicts the unconstrained evolutionary trajectory under directional selection on each trait. Calculations of the gradients for body size and development time revealed that these are nearly orthogonal through much of the parameter space. Therefore, simultaneous directional selection on body size and development time can be neither synergistic nor antagonistic but leads to conflicting selection on the underlying developmental parameters.     

Turtle phylogeny: insights from a novel nuclear intron

Introns have gained considerable popularity as markers for molecular phylogenetics. However, no primers exist for a nuclear intron that amplifies across all turtles. Available data from morphology and mitochondrial DNA have not unambiguously resolved relationships within the superfamily Trionychoidea and the family Chelidae, which together form a large portion of extant turtle diversity. We tested the phylogenetic utility of a novel intron from the RNA fingerprint protein 35 (R35) as applied to these two areas of turtle systematics. We found the intron to be a single-copy locus that provides excellent resolving power for lineages among turtles, though problems with alignment made it impossible to infer deeper amniote relationships. Maximum parsimony and maximum likelihood both demonstrated the polyphyly of Trionychoidea and the reciprocal monophyly of Australian/New Guinea and South American chelid turtles. This is the first study to resolve such relationships with strong statistical support, and we suggest that R35 holds great promise for resolving additional persistent problems in the phylogeny of living turtles.     

Neocentromeres: new insights into centromere structure, disease development, and karyotype evolution

Since the discovery of the first human neocentromere in 1993, these spontaneous, ectopic centromeres have been shown to be an astonishing example of epigenetic change within the genome. Recent research has focused on the role of neocentromeres in evolution and speciation, as well as in disease development and the understanding of the organization and epigenetic maintenance of the centromere. Here, we review recent progress in these areas of research and the significant insights gained.