Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices

Databases of organismal traits that aggregate information from one or multiple sources can be leveraged for large-scale analyses in biology. Yet the differences among these data streams and how well they capture trait diversity have never been explored. We present the first analysis of the differences between phenotypes captured in free text of descriptive publications ('monographs') and those used in phylogenetic analyses ('matrices'). We focus our analysis on osteological phenotypes of the limbs of four extinct vertebrate taxa critical to our understanding of the fin-to-limb transition. We find that there is low overlap between the anatomical entities used in these two sources of phenotype data, indicating that phenotypes represented in matrices are not simply a subset of those found in monographic descriptions. Perhaps as expected, compared to characters found in matrices, phenotypes in monographs tend to emphasize descriptive and positional morphology, be somewhat more complex, and relate to fewer additional taxa. While based on a small set of focal taxa, these qualitative and quantitative data suggest that either source of phenotypes alone will result in incomplete knowledge of variation for a given taxon. As a broader community develops to use and expand databases characterizing organismal trait diversity, it is important to recognize the limitations of the data sources and develop strategies to more fully characterize variation both within species and across the tree of life.

Population and phylogenomic decomposition via genotyping-by-sequencing in Australian Pelargonium

Species delimitation has seen a paradigm shift as increasing accessibility of genomic-scale data enables separation of lineages with convergent morphological traits and the merging of recently diverged ecotypes that have distinguishing characteristics. We inferred the process of lineage formation among Australian species in the widespread and highly variable genus Pelargonium by combining phylogenomic and population genomic analyses along with breeding system studies and character analysis. Phylogenomic analysis and population genetic clustering supported seven of the eight currently described species but provided little evidence for differences in genetic structure within the most widely distributed group that containing P. australe. In contrast, morphometric analysis detected three deep lineages within Australian Pelargonium; with P. australe consisting of five previously unrecognized entities occupying separate geographic ranges. The genomic approach enabled elucidation of parallel evolution in some traits formerly used to delineate species, as well as identification of ecotypic morphological differentiation within recognized species. Highly variable morphology and trait convergence each contribute to the discordance between phylogenomic relationships and morphological taxonomy. Data suggest that genetic divergence among species within the Australian Pelargonium may result from allopatric speciation while morphological differentiation within and among species may be more strongly driven by environmental differences.

Synonymous and nonsynonymous distances help untangle convergent evolution and recombination

When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because different segments of the sequence alignment support different phylogenies. Similarly, convergent selective pressures at the molecular level can also lead to phylogenetic tree incongruence across the sequence alignment. Current methods for detection of phylogenetic incongruence are not equipped to distinguish between these two different mechanisms and assume that the incongruence is a result of recombination or other horizontal transfer of genetic information. We propose a new recombination detection method that can make this distinction, based on synonymous codon substitution distances. Although some power is lost by discarding the information contained in the nonsynonymous substitutions, our new method has lower false positive probabilities than the comparable recombination detection method when the phylogenetic incongruence signal is due to convergent evolution. We apply our method to three empirical examples, where we analyze: (1) sequences from a transmission network of the human immunodeficiency virus, (2) tlpB gene sequences from a geographically diverse set of 38 Helicobacter pylori strains, and (3) hepatitis C virus sequences sampled longitudinally from one patient.

Reacquisition of the lower temporal bar in sexually dimorphic fossil lizards provides a rare case of convergent evolution

Temporal fenestration has long been considered a key character to understand relationships amongst reptiles. In particular, the absence of the lower temporal bar (LTB) is considered one of the defining features of squamates (lizards and snakes). In a re-assessment of the borioteiioid lizard Polyglyphanodon sternbergi (Cretaceous, North America), we detected a heretofore unrecognized ontogenetic series, sexual dimorphism (a rare instance for Mesozoic reptiles), and a complete LTB, a feature only recently recognized for another borioteiioid, Tianyusaurus zhengi (Cretaceous, China). A new phylogenetic analysis (with updates on a quarter of the scorings for P. sternbergi) indicates not only that the LTB was reacquired in squamates, but it happened independently at least twice. An analysis of the functional significance of the LTB using proxies indicates that, unlike for T. zhengi, this structure had no apparent functional advantage in P. sternbergi, and it is better explained as the result of structural constraint release. The observed canalization against a LTB in squamates was broken at some point in the evolution of borioteiioids, whereas never re-occuring in other squamate lineages. This case of convergent evolution involves a mix of both adaptationist and structuralist causes, which is unusual for both living and extinct vertebrates.

Evolution of mammalian sound localization circuits: A developmental perspective

Localization of sound sources is a central aspect of auditory processing. A unique feature of mammals is the smooth, tonotopically organized extension of the hearing range to high frequencies (HF) above 10kHz, which likely induced positive selection for novel mechanisms of sound localization. How this change in the auditory periphery is accompanied by changes in the central auditory system is unresolved. I will argue that the major VGlut2(+) excitatory projection neurons of sound localization circuits (dorsal cochlear nucleus (DCN), lateral and medial superior olive (LSO and MSO)) represent serial homologs with modifications, thus being paramorphs. This assumption is based on common embryonic origin from an Atoh1(+)/Wnt1(+) cell lineage in the rhombic lip of r5, same cell birth, a fusiform cell morphology, shared genetic components such as Lhx2 and Lhx9 transcription factors, and similar projection patterns. Such a parsimonious evolutionary mechanism likely accelerated the emergence of neurons for sound localization in all three dimensions. Genetic analyses indicate that auditory nuclei in fish, birds, and mammals receive contributions from the same progenitor lineages. Anatomical and physiological differences and the independent evolution of tympanic ears in vertebrate groups, however, argue for convergent evolution of sound localization circuits in tetrapods (amphibians, reptiles, birds, and mammals). These disparate findings are discussed in the context of the genetic architecture of the developing hindbrain, which facilitates convergent evolution. Yet, it will be critical to decipher the gene regulatory networks underlying development of auditory neurons across vertebrates to explore the possibility of homologous neuronal populations.

Phylogeny of Mental Glands, Revisited

Mental glands and their associated delivery behaviors during courtship are unique to the plethodontid salamanders. Because previous interpretations of the evolution of these features were conducted using older phylogenetic hypotheses, we reanalyzed these traits with newer courtship descriptions and contemporary phylogenetic methods. Using Bayesian ancestral state reconstruction methods that have been developed since the first phylogenetic analyses were conducted in the mid-1990s, we reconstructed mental gland and courtship behavior evolution on a Bayesian phylogeny of the nuclear gene Rag1. The most probable ancestral condition for plethodontids was resolved as presence of a mental gland. Loss of a mental gland occurred in each subfamily and was recovered as the most probable ancestral condition for the Spelerpinae. In contrast, parsimony reconstruction recovered the presence of a mental gland in the ancestor to Spelerpinae with multiple secondary losses. We hypothesize that that absence of a mental gland is possibly ancestral in some clades (i.e., Spelerpinae) and secondary in others (e.g., paedomorphic Eurycea). The most probable ancestral form of the mental gland is likely to be the large pad-type distributed extensively in Plethodontinae and Bolitoglossinae. Desmognathans have the most unique mental glands, occurring in an anterior protrusion or bifurcated form (in Desmognathus wrighti). Fan-shaped mental glands evolved independently in Eurycea and Oedipina. Small pads arose independently in Bolitoglossinae, Plethodontinae, and Spelerpinae. Head-rubbing behavior for mental gland delivery mode was recovered as the most probable and parsimonious ancestral state for the Plethodontidae, with independent losses of this behavior in Plethodontinae and Spelerpinae. Because head-rubbing was observed in outgroups, we hypothesize that head-rubbing behavior predated mental gland evolution. Pulling, snapping, slapping, and biting behaviors evolved independently in the Plethodontinae and Spelerpinae and are not homologous with head-rubbing. All hypotheses of mental gland and courtship evolution invoke homoplasy.

Widespread flower color convergence in Solanaceae via alternate biochemical pathways

Phenotypic convergence is rampant throughout the tree of life. While recent studies have made significant progress in ascertaining the proximate mechanisms underlying convergent phenotypes, less is known about the frequency and predictability with which convergent phenotypes arise via the same or multiple pathways at the macroevolutionary scale. We investigated the proximate causes and evolutionary patterns of red flower color in the tomato family, Solanaceae, using large-scale data mining and new sequence data to reconstruct a megaphylogeny of 1341 species. We then combined spectral and anatomical data to assess how many times red flowers have evolved, the relative contribution of different pathways to independent origins of red, and whether the underlying pathway is predicted by phylogenetic relatedness. We estimated at least 30 relatively recent origins of red flowers using anthocyanins, carotenoids, or a dual production of both pigments, with significant phylogenetic signal in the use of anthocyanins and dual production, indicating that closely related red-flowered species tend to employ the same mechanism for coloration. Our study is the first to test whether developmental pathways exhibit phylogenetic signal and implies that historical contingency strongly influences the evolution of new phenotypes.

Using zebrafish in systems toxicology for developmental toxicity testing

With the high cost and the long-term assessment of developmental toxicity testing in mammals, the vertebrate zebrafish has become a useful alternative model organism for high-throughput developmental toxicity testing. Zebrafish is also very favorable for the 3R perspective in toxicology; however, the methodologies used by research groups vary greatly, posing considerable challenges to integrative analysis. In this review, we discuss zebrafish developmental toxicity testing, focusing on the methods of chemical exposure, the assessment of morphological abnormalities, housing conditions and their effects on the production of healthy embryos, and future directions. Zebrafish as a systems toxicology model has the potential to elucidate developmental toxicity pathways, and to provide a sound basis for human health risk assessments.

What does convergent evolution mean? The interpretation of convergence and its implications in the search for limits to evolution

Convergent evolution is central to the study of life's evolutionary history. Researchers have documented the ubiquity of convergence and have used this ubiquity to make inferences about the nature of limits on evolution. However, these inferences are compromised by unrecognized inconsistencies in the definitions, measures, significance tests and inferred causes of convergent evolution. I review these inconsistencies and provide recommendations for standardizing studies of convergence. A fundamental dichotomy exists between definitions that describe convergence as a pattern and those that describe it as a pattern caused by a particular process. When this distinction is not acknowledged it becomes easy to assume that a pattern of convergence indicates that a particular process has been active, leading researchers away from alternative explanations. Convergence is not necessarily caused by limits to evolution, either adaptation or constraint; even substantial amounts of convergent evolution can be generated by a purely stochastic process. In the absence of null models, long lists of examples of convergent events do not necessarily indicate that convergence or any evolutionary process is ubiquitous throughout the history of life. Pattern-based definitions of convergence, coupled with quantitative measures and null models, must be applied before drawing inferences regarding large-scale limits to evolution.

Bird embryos uncover homology and evolution of the dinosaur ankle

The anklebone (astragalus) of dinosaurs presents a characteristic upward projection, the 'ascending process' (ASC). The ASC is present in modern birds, but develops a separate ossification centre, and projects from the calcaneum in most species. These differences have been argued to make it non-comparable to dinosaurs. We studied ASC development in six different orders of birds using traditional techniques and spin-disc microscopy for whole-mount immunofluorescence. Unexpectedly, we found the ASC derives from the embryonic intermedium, an ancient element of the tetrapod ankle. In some birds it comes in contact with the astragalus, and, in others, with the calcaneum. The fact that the intermedium fails to fuse early with the tibiale and develops an ossification centre is unlike any other amniotes, yet resembles basal, amphibian-grade tetrapods. The ASC originated in early dinosaurs along changes to upright posture and locomotion, revealing an intriguing combination of functional innovation and reversion in its evolution.

Hand/foot splitting and the 're-evolution' of mesopodial skeletal elements during the evolution and radiation of chameleons

Background

One of the most distinctive traits found within Chamaeleonidae is their split/cleft autopodia and the simplified and divergent morphology of the mesopodial skeleton. These anatomical characteristics have facilitated the adaptive radiation of chameleons to arboreal niches. To better understand the homology of chameleon carpal and tarsal elements, the process of syndactyly, cleft formation, and how modification of the mesopodial skeleton has played a role in the evolution and diversification of chameleons, we have studied the Veiled Chameleon (Chamaeleo calyptratus). We analysed limb patterning and morphogenesis through in situ hybridization, in vitro whole embryo culture and pharmacological perturbation, scoring for apoptosis, clefting, and skeletogenesis. Furthermore, we framed our data within a phylogenetic context by performing comparative skeletal analyses in 8 of the 12 currently recognized genera of extant chameleons.

Results

Our study uncovered a previously underappreciated degree of mesopodial skeletal diversity in chameleons. Phylogenetically derived chameleons exhibit a ‘typical’ outgroup complement of mesopodial elements (with the exception of centralia), with twice the number of currently recognized carpal and tarsal elements considered for this clade. In contrast to avians and rodents, mesenchymal clefting in chameleons commences in spite of the maintenance of a robust apical ectodermal ridge (AER). Furthermore, Bmp signaling appears to be important for cleft initiation but not for maintenance of apoptosis. Interdigital cell death therefore may be an ancestral characteristic of the autopodium, however syndactyly is an evolutionary novelty. In addition, we find that the pisiform segments from the ulnare and that chameleons lack an astragalus-calcaneum complex typical of amniotes and have evolved an ankle architecture convergent with amphibians in phylogenetically higher chameleons.

Conclusion

Our data underscores the importance of comparative and phylogenetic approaches when studying development. Body size may have played a role in the characteristic mesopodial skeletal architecture of chameleons by constraining deployment of the skeletogenic program in the smaller and earliest diverged and basal taxa. Our study challenges the ‘re-evolution’ of osteological features by showing that ‘re-evolving’ a ‘lost’ feature de novo (contrary to Dollo’s Law) may instead be due to so called ‘missing structures’ being present but underdeveloped and/or fused to other adjacent elements (cryptic features) whose independence may be re-established under changes in adaptive selective pressure.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0464-4) contains supplementary material, which is available to authorized users.

The significance and scope of evolutionary developmental biology: a vision for the 21st century

Evolutionary developmental biology (evo-devo) has undergone dramatic transformations since its emergence as a distinct discipline. This paper aims to highlight the scope, power, and future promise of evo-devo to transform and unify diverse aspects of biology. We articulate key questions at the core of eleven biological disciplines-from Evolution, Development, Paleontology, and Neurobiology to Cellular and Molecular Biology, Quantitative Genetics, Human Diseases, Ecology, Agriculture and Science Education, and lastly, Evolutionary Developmental Biology itself-and discuss why evo-devo is uniquely situated to substantially improve our ability to find meaningful answers to these fundamental questions. We posit that the tools, concepts, and ways of thinking developed by evo-devo have profound potential to advance, integrate, and unify biological sciences as well as inform policy decisions and illuminate science education. We look to the next generation of evolutionary developmental biologists to help shape this process as we confront the scientific challenges of the 21st century.

Ultrabithorax is essential for bacteriocyte development

Symbiosis often entails the emergence of novel adaptive traits in organisms. Microbial symbionts are indispensable for diverse insects via provisioning of essential nutrients, wherein novel host cells and organs for harboring the microbes, called bacteriocytes and bacteriomes, have evolved repeatedly. Molecular and developmental mechanisms underpinning the emergence of novel symbiotic cells and organs comprise an unsolved question in evolutionary developmental biology. Here, we report that a conserved homeotic gene, Ultrabithorax, plays a pivotal role in the bacteriocyte differentiation in a hemipteran insect Nysius plebeius. During embryonic development, six pairs of aggregated presumptive bacteriocytes appear on both sides of six abdominal segments, incorporate the symbiotic bacteria at the stage of germband retraction, and fuse into a pair of lateral bacteriomes at the stage of germband flip, where bacteriocyte-associated Ultrabithorax expression coincides with the symbiont infection process. Suppression of Ultrabithorax expression by maternal RNA interference results in disappearance of the bacteriocytes and the symbiont localization therein, suggesting that Ultrabithorax is involved in differentiation of the host cells for symbiosis. Suppression of other homeotic genes abdominal-A and Antennapedia disturbs integrity and positioning of the bacteriomes, affecting the configuration of the host organs for symbiosis. Our findings unveil the molecular and developmental mechanisms underlying the bacteriocyte differentiation, which may have evolved either via cooption of the transcription factors for inducing the novel symbiotic cells, or via revival of the developmental pathway for the bacteriocytes that had existed in the ancestral hemipterans.

Repeated evolution and the impact of evolutionary history on adaptation

BACKGROUND

Whether natural selection can erase the imprint of past evolutionary history from phenotypes has been a topic of much debate. A key source of evidence that present-day selection can override historically contingent effects comes from the repeated evolution of similar adaptations in different taxa. Yet classic examples of repeated evolution are often among closely related taxa, suggesting the likelihood that similar adaptations evolve is contingent on the length of time separating taxa. To resolve this, we performed a meta-analysis of published reports of repeated evolution.

RESULTS

Overall, repeated evolution was far more likely to be documented among closely related than distantly related taxa. However, not all forms of adaptation seemed to exhibit the same pattern. The evolution of similar behavior and physiology seemed frequent in distantly related and closely related taxa, while the repeated evolution of morphology was heavily skewed towards closely related taxa. Functionally redundant characteristics-alternative phenotypes that achieve the same functional outcome-also appeared less contingent.

CONCLUSIONS

If the literature provides a reasonable reflection of the incidence of repeated evolution in nature, our findings suggest that natural selection can overcome contingent effects to an extent, but it depends heavily on the aspect of the phenotype targeted by selection.

Implications of Nubian-Like Core Reduction Systems in Southern Africa for the Identification of Early Modern Human Dispersals

Lithic technologies have been used to trace dispersals of early human populations within and beyond Africa. Convergence in lithic systems has the potential to confound such interpretations, implying connections between unrelated groups. Due to their reductive nature, stone artefacts are unusually prone to this chance appearance of similar forms in unrelated populations. Here we present data from the South African Middle Stone Age sites Uitpanskraal 7 and Mertenhof suggesting that Nubian core reduction systems associated with Late Pleistocene populations in North Africa and potentially with early human migrations out of Africa in MIS 5 also occur in southern Africa during early MIS 3 and with no clear connection to the North African occurrence. The timing and spatial distribution of their appearance in southern and northern Africa implies technological convergence, rather than diffusion or dispersal. While lithic technologies can be a critical guide to human population flux, their utility in tracing early human dispersals at large spatial and temporal scales with stone artefact types remains questionable.

Osteological Variation among Extreme Morphological Forms in the Mexican Salamander Genus Chiropterotriton (Amphibia: Plethodontidae): Morphological Evolution And Homoplasy

Osteological variation is recorded among and within four of the most distinctive species of the Mexican salamander genus Chiropterotriton. Analysis of the data is consistent with the monophyletic status of the genus and documents previously unrecorded intraspecific and interspecific variation. Most of the recorded variation involves qualitative and quantitative proportional differences, but four fixed differences constitute autapomorphic states that affirm and diagnose some species (C. dimidiatus, C. magnipes). Osteological variation in 15 characters is analyzed with respect to predictions generated from four hypotheses: 1) phylogeny, 2) adaptation to specific habitats (the four species include cave-dwelling, terrestrial, and arboreal forms), 3) size-free shape, and 4) size. High levels of intraspecific variation suggest that the characters studied are not subject to rigid functional constraints in salamanders, regardless of size. The pattern predicted by the hypothesis based on size differences seen among these four Chiropterotriton species matches most closely the observed pattern of relative skull robustness. Since size change and heterochrony are often associated in plethodontid evolution, it is likely that changes in developmental timing play a role in the morphological transitions among these morphologically diverse taxa. Webbed feet, miniaturization, body shape, and an unusual tarsal arrangement are morphologies exhibited in species of Chiropterotrition that are shown to be homoplastic with other clades of tropical plethodontids. Although extensive homoplasy in salamanders might be seen as a roadblock to unraveling phylogenetic hypotheses, the homologous developmental systems that appear to underlie such homoplasy may reveal common and consistent evolutionary processes at work.

Genetic and developmental basis for parallel evolution and its significance for hominoid evolution

Greater understanding of ape comparative anatomy and evolutionary history has brought a general appreciation that the hominoid radiation is characterized by substantial homoplasy.(1-4) However, little consensus has been reached regarding which features result from repeated evolution. This has important implications for reconstructing ancestral states throughout hominoid evolution, including the nature of the Pan-Homo last common ancestor (LCA). Advances from evolutionary developmental biology (evo-devo) have expanded the diversity of model organisms available for uncovering the morphogenetic mechanisms underlying instances of repeated phenotypic change. Of particular relevance to hominoids are data from adaptive radiations of birds, fish, and even flies demonstrating that parallel phenotypic changes often use similar genetic and developmental mechanisms. The frequent reuse of a limited set of genes and pathways underlying phenotypic homoplasy suggests that the conserved nature of the genetic and developmental architecture of animals can influence evolutionary outcomes. Such biases are particularly likely to be shared by closely related taxa that reside in similar ecological niches and face common selective pressures. Consideration of these developmental and ecological factors provides a strong theoretical justification for the substantial homoplasy observed in the evolution of complex characters and the remarkable parallel similarities that can occur in closely related taxa. Thus, as in other branches of the hominoid radiation, repeated phenotypic evolution within African apes is also a distinct possibility. If so, the availability of complete genomes for each of the hominoid genera makes them another model to explore the genetic basis of repeated evolution.

Adaptation in flower form: a comparative evodevo approach

Evolutionary developmental biology (evodevo) attempts to explain how the process of organismal development evolves, utilizing a comparative approach to investigate changes in developmental pathways and processes that occur during the evolution of a given lineage. Evolutionary genetics uses a population approach to understand how organismal changes in form or function are linked to underlying genetics, focusing on changes in gene and genotype frequencies within populations and the fixation of genotypic variation into traits that define species or evoke speciation events. Microevolutionary processes, including mutation, genetic drift, natural selection and gene flow, can provide the foundation for macroevolutionary patterns observed as morphological evolution and adaptation. The temporal element linking microevolutionary processes to macroevolutionary patterns is development: an organism's genotype is converted to phenotype by ontogenetic processes. Because selection acts upon the phenotype, the connection between evolutionary genetics and developmental evolution becomes essential to understanding adaptive evolution in organismal form and function. Here, we discuss how developmental genetic studies focused on key developmental processes could be linked within a comparative framework to study the developmental genetics of adaptive evolution, providing examples from research on two key processes of plant evodevo - floral symmetry and organ fusion - and their role in the adaptation of floral form.

Evo-devo mechanisms underlying the continuum between homology and homoplasy

The different manifestations of equivalence and similarity in structure throughout evolution suggest a continuous and hierarchical process that starts out with the origin of a morphological novelty, unit, or homologue. Once a morphological unit has originated, its properties change subsequently into variants that differ, in magnitude, from the original properties found in the common ancestor. We will look into the nature of morphological units and their degrees of modification, which will provide the starting point for restructuring the concept of "homology," keeping the use of homology as the identity of an anatomical part, and homogeny, as the specific variation of that anatomical part during evolution. We will also show that parallelism has a distinct placement within an evolutionary continuum between homology and homoplasy, whereas the phenomenon of evolutionary convergence is left outside this continuum. We will then provide some epistemological and developmental criteria to justify these distinctions, showing that there is a direct relation between the nature of these concepts and the constraints that developmental mechanisms impose on evolution. Finally, we will propose a hierarchical model that places homology, homogeny, homoplasy, and parallelism, as distinct phenomena within an evolutionary continuum.

Can systems biology help to separate evolutionary analogies (convergent homoplasies) from homologies?

Convergent evolutionary analogies (homoplasies) of many kinds occur in diverse phylogenetic clades/lineages on both the animal and plant branches of the Tree of Life. Living organisms whose last common ancestors lived millions to hundreds of millions of years ago have later converged morphologically, behaviorally or at other levels of functionality (from molecular genetics through biochemistry, physiology and other organismic processes) as a result of long term strong natural selection that has constrained and channeled evolutionary processes. This happens most often when organisms belonging to different clades occupy ecological niches, habitats or environments sharing major characteristics that select for a relatively narrow range of organismic properties. Systems biology, broadly defined, provides theoretical and methodological approaches that are beginning to make it possible to answer a perennial evolutionary biological question relating to convergent homoplasies: Are at least some of the apparent analogies actually unrecognized homologies? This review provides an overview of the current state of knowledge of important aspects of this topic area. It also provides a resource describing many homoplasies that may be fruitful subjects for systems biological research.

Mechanisms of endoderm formation in a cartilaginous fish reveal ancestral and homoplastic traits in jawed vertebrates

In order to gain insight into the impact of yolk increase on endoderm development, we have analyzed the mechanisms of endoderm formation in the catshark S. canicula, a species exhibiting telolecithal eggs and a distinct yolk sac. We show that in this species, endoderm markers are expressed in two distinct tissues, the deep mesenchyme, a mesenchymal population of deep blastomeres lying beneath the epithelial-like superficial layer, already specified at early blastula stages, and the involuting mesendoderm layer, which appears at the blastoderm posterior margin at the onset of gastrulation. Formation of the deep mesenchyme involves cell internalizations from the superficial layer prior to gastrulation, by a movement suggestive of ingressions. These cell movements were observed not only at the posterior margin, where massive internalizations take place prior to the start of involution, but also in the center of the blastoderm, where internalizations of single cells prevail. Like the adjacent involuting mesendoderm, the posterior deep mesenchyme expresses anterior mesendoderm markers under the control of Nodal/activin signaling. Comparisons across vertebrates support the conclusion that endoderm is specified in two distinct temporal phases in the catshark as in all major osteichthyan lineages, in line with an ancient origin of a biphasic mode of endoderm specification in gnathostomes. They also highlight unexpected similarities with amniotes, such as the occurrence of cell ingressions from the superficial layer prior to gastrulation. These similarities may correspond to homoplastic traits fixed separately in amniotes and chondrichthyans and related to the increase in egg yolk mass.

New developmental evidence clarifies the evolution of wrist bones in the dinosaur-bird transition

From early dinosaurs with as many as nine wrist bones, modern birds evolved to develop only four ossifications. Their identity is uncertain, with different labels used in palaeontology and developmental biology. We examined embryos of several species and studied chicken embryos in detail through a new technique allowing whole-mount immunofluorescence of the embryonic cartilaginous skeleton. Beyond previous controversy, we establish that the proximal-anterior ossification develops from a composite radiale+intermedium cartilage, consistent with fusion of radiale and intermedium observed in some theropod dinosaurs. Despite previous claims that the development of the distal-anterior ossification does not support the dinosaur-bird link, we found its embryonic precursor shows two distinct regions of both collagen type II and collagen type IX expression, resembling the composite semilunate bone of bird-like dinosaurs (distal carpal 1+distal carpal 2). The distal-posterior ossification develops from a cartilage referred to as "element x," but its position corresponds to distal carpal 3. The proximal-posterior ossification is perhaps most controversial: It is labelled as the ulnare in palaeontology, but we confirm the embryonic ulnare is lost during development. Re-examination of the fossil evidence reveals the ulnare was actually absent in bird-like dinosaurs. We confirm the proximal-posterior bone is a pisiform in terms of embryonic position and its development as a sesamoid associated to a tendon. However, the pisiform is absent in bird-like dinosaurs, which are known from several articulated specimens. The combined data provide compelling evidence of a remarkable evolutionary reversal: A large, ossified pisiform re-evolved in the lineage leading to birds, after a period in which it was either absent, nonossified, or very small, consistently escaping fossil preservation. The bird wrist provides a modern example of how developmental and paleontological data illuminate each other. Based on all available data, we introduce a new nomenclature for bird wrist ossifications.

An Evo-Devo perspective on ever-growing teeth in mammals and dental stem cell maintenance

A major challenge for current evolutionary and developmental biology research is to understand the evolution of morphogenesis and the mechanisms involved. Teeth are well suited for the investigation of developmental processes. In addition, since teeth are composed of hard-mineralized tissues, primarily apatite, that are readily preserved, the evolution of mammals is well documented through their teeth in the fossil record. Hypsodonty, high crowned teeth with shallow roots, and hypselodonty, ever-growing teeth, are convergent innovations that have appeared multiple times since the mammalian radiation 65 million years ago, in all tooth categories (incisors, canines, premolars, and molars). A shift to hypsodonty, or hypselodonty, during mammalian evolution is often, but not necessarily, associated with increasingly abrasive diet during important environmental change events. Although the evolution of hypsodonty and hypselodonty is considered to be the result of heterochrony of development, little has been known about the exact developmental mechanisms at the origin of these morphological traits. Developmental biologists have been intrigued by the mechanism of hypselodonty since it requires the maintenance of continuous crown formation during development via stem cell niche activity. Understanding this mechanism may allow bioengineered tooth formation in humans. Hypsodonty and hypselodonty are thus examples of phenotypic features of teeth that have both impacts in understanding the evolution of mammals and holds promise for human tooth bioengineering.

Sex determination in annual fishes: Searching for the master sex-determining gene in Austrolebias charrua (Cyprinodontiformes, Rivulidae)

Evolution of sex determination and differentiation in fishes involves a broad range of sex strategies (hermaphroditism, gonochorism, unisexuality, environmental and genetic sex determination). Annual fishes inhabit temporary ponds that dry out during the dry season when adults die. The embryos exhibit an atypical developmental pattern and remain buried in the bottom mud until the next rainy season. To elucidate genomic factors involved in the sex determination in annual fish, we explored the presence of a candidate sex-specific gene related to the cascade network in Austrolebias charrua. All phylogenetic analyses showed a high posterior probability of occurrence for a clade integrated by nuclear sequences (aprox. 900 bp) from both adults (male and female), with partial cDNA fragments of A. charrua from juveniles (male) and the dsx D. melanogaster gene. The expressed fragment was detected from blastula to adulthood stages showing a sexually dimorphic expression pattern. The isolated cDNA sequence is clearly related to dsx D. melanogaster gene and might be located near the top of the sex determination cascade in this species.