Data curation is critical for scientific data digitization, sharing, integration, and use. This paper presents Kurator, a software package for automating data curation pipelines in the Kepler scientific workflow system. Several curation tools and services are integrated into this package as actors to enable construction of workflows to perform and document various data curation tasks. The integration of Google cloud services (e. g., Google spreadsheets), allows workflow steps to invoke human experts outside the workflow in a manner that greatly simplifies the complex data handling in distributed, multi-user curation workflows. The Kepler platform provides the modeling, execution and management ability, including a collection-oriented model of computation (COMAD), and provenance tracking and browsing for the curation package. These features not only allow workflows to be easily modeled, maintained, and evolved, but also QA/QC of curation results is facilitated through examination of provenance information recorded during workflow execution. Effectiveness of the Kurator package is demonstrated through a workflow for data curation of natural science collections.
The time is ripe for a comprehensive mission to explore and document Earth's species. This calls for a campaign to educate and inspire the next generation of professional and citizen species explorers, investments in cyber-infrastructure and collections to meet the unique needs of the producers and consumers of taxonomic information, and the formation and coordination of a multi-institutional, international, transdisciplinary community of researchers, scholars and engineers with the shared objective of creating a comprehensive inventory of species and detailed map of the biosphere. We conclude that an ambitious goal to describe 10 million species in less than 50 years is attainable based on the strength of 250 years of progress, worldwide collections, existing experts, technological innovation and collaborative teamwork. Existing digitization projects are overcoming obstacles of the past, facilitating collaboration and mobilizing literature, data, images and specimens through cyber technologies. Charting the biosphere is enormously complex, yet necessary expertise can be found through partnerships with engineers, information scientists, sociologists, ecologists, climate scientists, conservation biologists, industrial project managers and taxon specialists, from agrostologists to zoophytologists. Benefits to society of the proposed mission would be profound, immediate and enduring, from detection of early responses of flora and fauna to climate change to opening access to evolutionary designs for solutions to countless practical problems. The impacts on the biodiversity, environmental and evolutionary sciences would be transformative, from ecosystem models calibrated in detail to comprehensive understanding of the origin and evolution of life over its 3.8 billion year history. The resultant cyber-enabled taxonomy, or cybertaxonomy, would open access to biodiversity data to developing nations, assure access to reliable data about species, and change how scientists and citizens alike access, use and think about biological diversity information.
New species of amphibians are being reported at an astonishingly fast rate. These include some that have been known to the commercial pet trade for years but have not been formally described due to uncertain origin. The distinctive phenotype of "Pachytriton B" among the Chinese stout newts (also known as paddle-tailed newts) is one such example. Through examination of museum specimens, we locate a population from Mt. Mang within the Nanling Mountain Range with morphology and coloration similar to Pachytriton B. Molecular phylogenetic analyses strongly suggest that this population and Pachytriton B belong to the same species, which differs from congeners morphologically and chromatically and is described here as a new species. This species is characterized by a large and stout body, uniformly light brown dorsum, and orange spots or blotches that extend ribbon-like along the dorsolateral sides of the body. A mitochondrial genealogy suggests that the new species is the sister taxon to the group (P. brevipes + P. feii). Morphologically, this species is significantly stouter than P. feii and has significantly longer limbs than P. brevipes.
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.
Recent molecular phylogenies suggest the surprising reacquisition of posthatching metamorphosis within an otherwise direct-developing clade of lungless salamanders (family Plethodontidae). Metamorphosis was long regarded as plesiomorphic for plethodontids, yet the genus Desmognathus, which primarily includes metamorphosing species, is now nested within a much larger clade of direct-developing species. The extent to which the putative reacquisition of metamorphosis in Desmognathus represents a true evolutionary reversal is contingent upon the extent to which both larva-specific features and metamorphosis were actually lost during the evolution of direct development. In this study we analyze development of the hyobranchial skeleton, which is dramatically remodeled during salamander metamorphosis, in the direct-developing red-backed salamander, Plethodon cinereus. We find dramatic remodeling of the hyobranchial skeleton during embryogenesis in P. cinereus and the transient appearance of larva-specific cartilages. Hyobranchial development in this direct-developing plethodontid is highly similar to that in metamorphosing plethodontids (e.g., Desmognathus). The proposed reacquisition of hyobranchial metamorphosis within Desmognathus does not represent the re-evolution of a lost phenotype, but instead the elaboration of an existing developmental sequence.
The vertebrate limb demonstrates remarkable similarity in basic organization across phylogenetically disparate groups. To gain further insight into how this morphological similarity is maintained in different developmental contexts, we explored the molecular anatomy of size-reduced embryos of the Puerto Rican coqui frog, Eleutherodactylus coqui. This animal demonstrates direct development, a life-history strategy marked by rapid progression from egg to adult and absence of a free-living, aquatic larva. Nonetheless, coqui exhibits a basal anuran limb structure, with four toes on the forelimb and five toes on the hind limb. We investigated the extent to which coqui limb bud development conforms to the model of limb development derived from amniote studies. Toward this end, we characterized dynamic patterns of expression for 13 critical patterning genes across three principle stages of limb development. As expected, most genes demonstrate expression patterns that are essentially unchanged compared to amniote species. For example, we identified an EcFgf8-expression domain within the apical ectodermal ridge (AER). This expression pattern defines a putatively functional AER signaling domain, despite the absence of a morphological ridge in coqui embryos. However, two genes, EcMeis2 and EcAlx4, demonstrate altered domains of expression, which imply a potential shift in gene function between coqui frogs and amniote model systems. Unexpectedly, several genes thought to be critical for limb patterning in other systems, including EcFgf4, EcWnt3a, EcWnt7a, and EcGremlin, demonstrated no evident expression pattern in the limb at the three stages we analyzed. The absence of EcFgf4 and EcWnt3a expression during limb patterning is perhaps not surprising, given that neither gene is critical for proper limb development in the mouse, based on knockout and expression analyses. In contrast, absence of EcWnt7a and EcGremlin is surprising, given that expression of these molecules appears to be absolutely essential in all other model systems so far examined. Although this analysis substantiates the existence of a core set of ancient limb-patterning molecules, which likely mediate identical functions across highly diverse vertebrate forms, it also reveals remarkable evolutionary flexibility in the genetic control of a conserved morphological pattern across evolutionary time.
P>Genetic and developmental alterations associated with the evolution of amphibian direct development remain largely unexplored. Specifically, little is known of the underlying expression of skeletal regulatory genes, which may reveal early modifications to cranial ontogeny in direct-developing species. We describe expression patterns of three key skeletal regulators (runx2, sox9, and bmp4) along with the cartilage-dominant collagen 2 alpha 1 gene (col2a1) during cranial development in the direct-developing anuran, Eleutherodactylus coqui. Expression patterns of these regulators reveal transient skeletogenic anlagen that correspond to larval cartilages, but which never fully form in E. coqui. Suprarostral anlagen in the frontonasal processes are detected through runx2, sox9, and bmp4 expression. Previous studies have described these cartilages as missing from Eleutherodactylus cranial ontogeny. These transcriptionally active suprarostral anlagen fuse to the more posterior cranial trabeculae before they are detectable with col2a1 staining or with the staining techniques used in earlier studies. Additionally, expression of sox9 fails to reveal an early anterior connection between the palatoquadrate and the neurocranium, which is detectable through sox9 staining in Xenopus laevis embryos (a metamorphosing species). Absence of this connection validates an instance of developmental repatterning, where the larval quadratocranial commissure cartilage is lost in E. coqui. Expression of runx2 reveals dermal-bone precursors several developmental stages before their detection with alizarin red. This early expression of runx2 correlates with the accelerated embryonic onset of bone formation characteristic of E. coqui and other direct-developing anurans, but which differs from the postembryonic bone formation of most metamorphosing species. Together these results provide an earlier depiction of cranial patterning in E. coqui by using earlier markers of skeletogenic cell differentiation. These data both validate and modify previously reported instances of larval recapitulation and developmental repatterning associated with the evolution of anuran direct development.
Wu, Y., Wang, Y., Jiang, K., Chen, X. & Hanken, J. (2010). 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, cytb) 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.
A new species of fire-bellied newt, Cynops fudingensis, is described from northeastern Fujian Province, southeastern China. This species forms a well-supported clade with C. orientalis and C. orphicus based on molecular phylogenetic analysis of nucleotide sequences from mitochondrial DNA subunit two of NADH dehydrogenase and its two flanking tRNAs. Further, its genetic distance to each of the two previously described species is large. Principal-components analysis of external linear measurements differentiates the new species from C. orientalis and C. orphicus in morphological space. Geographically, C. fudingensis occupies the distribution gap between C. orientalis and C. orphicus.
We report two previously unknown populations of Asian warty newts (Salamandridae: Paramesotriton) in China. The first population, from southwestern Guangdong, is described as a new species, which is closely related to P. guangxiensis based on morphological and molecular data. The second new population, from western Hubei, is assigned to P. longliensis, which extends the known range of this species 400 km northwards. Limited genetic differentiation between P. longliensis and P. zhijinensis suggests that these two names may refer to the same (single) species.
This study characterizes regulatory elements of collagen2 alpha 7 (col2a1) in Xenopus that enable transgene expression in cartilage-forming chondrocytes. The reporters described in this study drive strong cartilage-specific gene expression, which will be a valuable tool for further investigations of Xenopus skeletal development. While endogenous col2a1 mRNA is expressed in many embryonic tissues, its expression becomes restricted to tadpole and adult chondrocytes. This chondrocyte-specific expression is recapitulated by col2a1 reporter constructs, which were tested through I-Scel meganuclease-mediated transgenesis. These constructs contain a portion of the Xenopus tropicalis col2a1 intron, which aligns to a cartilage-specific intronic enhancer that has been well characterized in mammals. Two overlapping regions of the first intron that are 1.5-Kb and 665-bp long, both of which contain this enhancer sequence, drove EGFP expression in both larval and adult chondrocytes when connected to an upstream promoter. However, neither a truncated 155-bp region that also contains the enhancer, nor a separate 347-bp intronic region that lacks it, was able to drive cartilaginous transgene expression. The two cartilage-specific transgenes are heritable in F1 progeny, which exhibit none of the background expression observed in the injected founders. This study is the first to use the I-Scel technique to characterize an enhancer element in Xenopus, and the first to generate chondrocyte-specific gene expression in a non-mammalian vertebrate. The creation of novel cartilage-specific gene expression provides a new tool for further studies of anuran skeletal development.
A new species of Asian warty newt, Paramesotriton ermizhaoi, is described from Guangxi Zhuang Autonomous Region in southern China. This species is easily distinguished from other congeners by external morphology and osteology. Phylogenetic analyses based on mitochondrial data place P. ermizhaoi as a possible sister taxon to P. hongkongensis and P. chinensis. The number of trunk vertebrae varies from 12 to 13 in the new species. The relationship between P. ermizhaoi and a potentially new Pachytriton species (Pachytriton C), and the Guangxi population of P. chinensis is briefly discussed.