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Wu, Y., Wang, Y., Jiang, K., Chen, X. & Hanken, J. (2009). Homoplastic evolution of external colouration in Asian stout newts ( Pachytriton) inferred from molecular phylogeny.— Zoologica Scripta, 39, 9–22. The Asian stout newts of the genus Pachytriton (Salamandridae) inhabit montane streams in south-eastern China. Despite their abundance in the pet trade, the phylogeny and systematics of this genus are poorly understood. Colouration is often used to delimit species under the assumption that consistent chromatic differences characterize independent evolutionary lineages. We present the first phylogenetic study of Pachytriton that incorporates 2.35 kb of mitochondrial DNA (ND2, cyt b) and 1.2 kb of nuclear sequence data (RAG-1) along with morphometric characters to infer evolutionary relationships and patterns of colour evolution among the three described species: Pachytriton brevipes, Pachytriton labiatus and Pachytriton archospotus. Our results support the monophyly of Pachytriton and recover P. archospotus as the sister taxon to P. brevipes. Monophyly of P. labiatus is significantly rejected: south-western populations are sister to the group of P. brevipes plus P. archospotus, whereas north-eastern populations nest with P. brevipes. The two geographic units are further separated by multivariate morphological analyses. South-western P. labiatus is the type species; misidentification of north-eastern populations as P. labiatus results from their similar colouration. An unspotted, dark brown dorsum is the likely ancestral state for the genus, whereas black-spotted colouration characterized the common ancestor of P. brevipes, P. archospotus, and north-eastern P. labiatus and was secondarily lost in the latter group. Homoplastic evolution and intraspecific variation render colour pattern in Pachytriton an unreliable character for delimiting species boundaries. North-eastern populations of P. labiatus are declining as the result of human collection and habitat destruction and are in urgent need of conservation protection. [ABSTRACT FROM AUTHOR]

Focuses on the evolution of miniaturization in animals. Contribution of miniaturization on evolutionary success; Relation between miniaturization and survival of the species; Disadvantages of miniaturization.

Analyzes the consequences and mechanistic bases of direct development of amphibians which could provide insights into the evolutionary opportunities and constraints conferred by the ancestral metamorphic ontogeny. What is involved in the direct development of in the anuran genus Eleutherodactylus; Detailed information on the evolutionary derived alternate modes.

There is widespread recognition of a recent coming together of developmental and evolutionary biology in the study of problems of mutual interest. Contemporary studies into the development and evolution of the head largely comprise two parallel approaches, or research strategies the model systems approach and the comparative approach. The two strategies share the same general goal—greater understanding of cranial development and evolution—but typically emphasize different problems, ask different questions, and employ different methods, reflecting the contrasting backgrounds and biases of each group of investigators, there has been relatively little true synthesis. Each strategy is making important and valid contributions, but both have limitations. Resolution of many fundamental and long-standing problems in cranial development and evolution will require a combined approach that incorporates the technical and conceptual strengths of each discipline. [ABSTRACT FROM PUBLISHER]

Embryos of different species of vertebrate share a common organisation and often look similar. Adult differences among species become more apparent through divergence at later stages. Some authors have suggested that members of most or all vertebrate clades pass through a virtually identical, conserved stage. This idea was promoted by Haeckel, and has recently been revived in the context of claims regarding the universality of developmental mechanisms. Thus embryonic resemblance at the tailbud stage has been linked with a conserved pattern of developmental gene expression – the zootype. Haeckel’s drawings of the external morphology of various vertebrates remain the most comprehensive comparative data purporting to show a conserved stage. However, their accuracy has been questioned and only a narrow range of species was illustrated. In view of the current widespread interest in evolutionary developmental biology, and especially in the conservation of developmental mechanisms, re-examination of the extent of variation in vertebrate embryos is long overdue. We present here the first review of the external morphology of tailbud embryos, illustrated with original specimens from a wide range of vertebrate groups. We find that embryos at the tailbud stage – thought to correspond to a conserved stage – show variations in form due to allometry, heterochrony, and differences in body plan and somite number. These variations foreshadow important differences in adult body form. Contrary to recent claims that all vertebrate embryos pass through a stage when they are the same size, we find a greater than 10-fold variation in greatest length at the tailbud stage. Our survey seriously undermines the credibility of Haeckel’s drawings, which depict not a conserved stage for vertebrates, but a stylised amniote embryo. In fact, the taxonomic level of greatest resemblance among vertebrate embryos is below the subphylum. The wide variation in morphology among vertebrate embryos is difficult to reconcile with the idea of a phyogenetically-conserved tailbud stage, and suggests that at least some developmental mechanisms are not highly constrained by the zootype. Our study also highlights the dangers of drawing general conclusions about vertebrate development from studies of gene expression in a small number of laboratory species. [ABSTRACT FROM AUTHOR]

Epithelially expressed type II collagen is thought to play a prominent role in the embryonic patterning and differentiation of the vertebrate skull, primarily on the basis of data derived from amniotes. We describe the spatiotemporal distribution of type II collagen in the embryonic head of the African clawed frog, Xenopus laevis, using whole-mount and serial-section immunohistochemical analysis. We studied embryos spanning Nieuwkoop and Faber (1967) stages 21-39, a period including cranial neural crest cell migration and ending immediately before the onset of neurocranial chondrogenesis. Xenopus displays a transient expression of type II collagen beginning at least as early as stage 21; staining is most intense and widespread at stages 33/34 and 35/36 and subsequently diminishes. Collagen-positive areas include the ventrolateral surface of the brain, sensory vesicles, notochord, oropharynx, and integument. This expression pattern is similar, but not identical, to that reported for the mouse and two bird species (Japanese quail, domestic fowl); thus epithelially expressed type II collagen appears to be a phylogenetically widespread feature of vertebrate cranial development. Consistent with the proposed role of type II collagen in mediating neurocranial differentiation, most collagen-positive areas lie adjacent to subsequent sites of chondrogenesis in the neurocranium but not the visceral skeleton. However, much of the collagen is expressed after the migration of cranial neural crest, including presumptive chondrogenic crest, seemingly too late to pattern the neurocranium by entrapment of these migrating cells. [ABSTRACT FROM AUTHOR]

Terrestrialization, the evolution of non-aquatic oviposition, and miniaturization, the evolution of tiny adult body size, are recurring trends in amphibian evolution, but the relationships among the traits that characterize these phenomena are not well understood. Furthermore, these traits have been identified as possible “key innovations” that are predicted to increase rates of speciation in those lineages in which they evolve. We examine terrestrialization and miniaturization in sub-Saharan puddle frogs (Phrynobatrachidae) in a phylogenetic context to investigate the relationship between adaptation and diversification through time. We use relative dating techniques to ascertain if character trait shifts are associated with increased diversification rates, and we evaluate the likelihood that a single temporal event can explain the evolution of those traits. Results indicate alternate reproductive modes evolved independently in Phrynobatrachus at least seven times, including terrestrial deposition of eggs and terrestrial, non-feeding larvae. These shifts towards alternate reproductive modes are not linked to a common temporal event. Contrary to the “key innovations” hypothesis, clades that exhibit alternate reproductive modes have lower diversification rates than those that deposit eggs aquatically. Adult habitat, pedal webbing and body size have no effect on diversification rates. Though these traits putatively identified as key innovations for Phrynobatrachus do not seem to be associated with increased speciation rates, they may still provide opportunities to extend into new niches, thus increasing overall diversity., Organismic and Evolutionary Biology

The article discusses research which examined the developmental and genetic basis of lung loss in plethodontid salamanders. Topics explored include the morphological features of the incipient lung that form in plethodontid embryos, the initial morphogenetic events observed in the salamader specie Plethodon cinereus, and the gene expression patterns that offered insights on evolutionary lung loss.

The YesWorkflow McPhillips et al. 2015b, McPhillips et al. 2015a toolkit was designed to annotate data curation workflows in conventional scripts (e.g., Python, R, Java) but it can also be used to annotate YAML-based Kurator workflow configuration files. From just a file that has been annotated by YesWorkflow, YesWorkflow is able to render a top-level graphical view of the workflow structure (prospective provenance), including system inputs and outputs, actors, connections among those actors, and expected data to be passed on those connections. YesWorkflow also supports dynamic analysis and reporting on the results of the workflow (retrospective provenance) at various levels of granularity (e.g., at the actor level, script level, data level, record level, file level, function level), provided that it has been configured at each. YesWorkflow includes an @Log annotation, which describes the semantic structure of a log message within some actor in the workflow and allows the log message to be linked to the actor within which it was created, and for parts of that log message to be linked to the data passed between actors. YesWorkflow can be used to analyze the log messages after a run of the workflow and construct a store of facts, which can be queried and reasoned upon to make statements about the evolving paths taken by particular data elements through the workflow and assertions made about those data elements within the workflow. Provenance, like other metadata, appears to be rarely actionable or immediately useful for those who are expected to provide it. However, by refactoring and integrating runtime observables generated from retrospective provenance and context information from prospective provenance analysis into hybrid queries, we show how both elements can yield hybrid visualizations that reveal "the plot" of the whole execution. In this way, a comprehensive workflow graph and a customizable data lineage report are made actionable for a workflow run with meaningful provenance artifacts. Queries run on a set of facts extracted from log messages by YesWorkflow after a workflow run, in combination with the facts extracted from the annotated workflow itself, allow for powerful visualizations of the retrospective provenance of a workflow run and of particular data records within a branching workflow. [ABSTRACT FROM AUTHOR]

Since its ratification as a TDWG standard in 2009, data publishers have had to struggle with the essential step of mapping fields in working databases to the terms in Darwin Core Wieczorek et al. 2012 in order to publish and share data using that standard. Doing so requires a good understanding of both the data set and Darwin Core. The accumulated knowledge about these mappings constitutes what we call the "Darwin Cloud." We will explore the nature of data mapping challenges and the potential for semi-automated solutions to them. Specifically, we will look at the "Darwinizer" actor and its usage in related workflows within the Kurator data quality framework and the implications for communitymanaged vocabularies. [ABSTRACT FROM AUTHOR]