Journal Articles and Book Chapters: Present - 2010

Wu, Y.K., et al., 2013. Significance of pre-Quaternary climate change for montane species diversity: Insights from Asian salamanders (Salamandridae: Pachytriton). Molecular Phylogenetics and Evolution , 66 , pp. 380-390.Abstract

Despite extensive focus on the genetic legacy of Pleistocene glaciation, impacts of earlier climatic change on biodiversity are poorly understood. Because amphibians are highly sensitive to variations in precipitation and temperature, we use a genus of Chinese montane salamanders (Salamandridae: Pachytriton) to study paleoclimatic change in East Asia, which experienced intensification of its monsoon circulation in the late Miocene associated with subsequent Pliocene warming. Using both nuclear and mitochondrial DNA sequences, we reconstruct the species tree under a coalescent model and demonstrate that all major lineages originated before the Quaternary. Initial speciation within the genus occurred after the summer monsoon entered a stage of substantial intensification. Heavy summer precipitation established temporary water connectivity through overflows between adjacent stream systems, which may facilitate geographic range expansion by aquatic species such as Pachytriton. Species were formed in allopatry likely through vicariant isolation during or after range expansion. To evaluate the influence of Pliocene warming on these cold-adapted salamanders, we construct a novel temperature buffer-zone model, which suggests widespread physiological stress or even extinction during the warming period. A significant deceleration of species accumulation rate is consistent with Pliocene range contraction, which affected P. granulosus and P. archospotus the most because they lack large temperature buffer zones. In contrast, demographic growth occurred in species for which refugia persist. The buffer-zone model reveals the Huangshan Mountain as a potential climatic refugium, which is similar to that found for other East Asian organisms. Our approach can incorporate future climatic data to evaluate the potential impact of ongoing global warming on montane species (particularly amphibians) and to predict possible population declines. (C) 2012 Elsevier Inc. All rights reserved.

Wu, Y.K., Wang, Y.Z. & Hanken, J., 2012. Comparative Osteology of the Genus Pachytriton (Caudata: Salamandridae) from Southeastern China. Asian Herpetological Research , 3 , pp. 83-102.Abstract

Osteological evidence provides invaluable insights into patterns of amphibian biodiversity. In small montane streams of southeastern China, an endemic genus of salamanders (Pachytriton) displays remarkable aquatic specializations, many of which are reflected in skeletal morphology, but these specializations remain to be studied in an integrated perspective. Attempts to fully resolve the taxonomy within the genus also can benefit from knowledge of internal morphology. We present a detailed description of the adult skeleton of P. brevipes, P. inexpectatus and P. archospotus by analyzing both cleared-and-stained and radiographed specimens in a comparative framework. Compared to terrestrial and amphibious salamanders, the most distinctive osteological features of Pachytriton include a modified hyobranchial apparatus, a reduced frontosquamosal arch, and deep neural and haemal arches of the caudal vertebrae. The hyobranchial apparatus of P. archospotus is distinctly different from that of congeners and likely secondarily derived. Patterns of interspecific variation suggest that northeastern P. inexpectatus is more closely related to P. brevipes than it is to southwestern P. inexpectatus, thereby reinforcing results from earlier molecular phylogenetic analyses. We advocate assigning northeastern P. inexpectatus to P. brevipes.

Dou, L., et al., 2012. Kurator: A Kepler Package for Data Curation Workflows. Proceedings of the International Conference on Computational Science, Iccs 2012 , 9 , pp. 1614-1619.Abstract

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.

Wheeler, Q.D., et al., 2012. Mapping the biosphere: exploring species to understand the origin, organization and sustainability of biodiversity. Systematics and Biodiversity , 10 , pp. 1-20.Abstract

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.

Wu, Y.K., Wang, Y.Z. & Hanken, J., 2012. New species of Pachytriton (Caudata: Salamandridae) from the Nanling Mountain Range, southeastern China. Zootaxa , pp. 1-16.Abstract

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.

Wake, D.B., et al., 2012. Taxonomic status of the enigmatic salamander Cryptotriton adelos (Amphibia: Plethodontidae) from northern Oaxaca, Mexico, with observations on its skull and postcranial skeleton. Zootaxa , pp. 67-70. PDF
Zimkus, B.M., et al., 2012. Terrestrialization, Miniaturization and Rates of Diversification in sub-Saharan Frogs (Anura: Phrynobatrachidae). Plos One , 7 , pp. 1-11 e35118.Abstract

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.

Kerney, R.R., et al., 2011. Do Larval Traits Re-Evolve? Evidence from the Embryogenesis of a Direct-Developing Salamander, Plethodon cinereus. Evolution , 66 , pp. 252-262.Abstract

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.

Gross, J., et al., 2011. Molecular anatomy of the developing limb bud in the coqui frog, Eleutherodactylus coqui. Developmental Biology , 356 , pp. 248-248. PDF
Meegaskumbura, M., et al., 2010. Taruga (Anura: Rhacophoridae), a new gnus of foam-nesting tree frogs endemic to Sri Lanka. Cey. J. Sci. (Bio. Sci.) , 39 , pp. 75-94. PDF
Hanken, J., 2010. The Encyclopedia of Life: a new digital resource for taxonomy. In A. Polaszek, ed. Systema Naturae 250: The Linnaean Ark. Boca Raton. Boca Raton: Taylor & Francis, pp. 127-135.
Constable, H., et al., 2010. VertNet: A new model for biodiversity data sharing. PLoS Biology , 8 , pp. e1000309. PDF
Kerney, R., Gross, J.B. & Hanken, J., 2010. Early cranial patterning in the direct-developing frog Eleutherodactylus coqui revealed through gene expression. Evolution & Development , 12 , pp. 373-382.Abstract

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.K., et al., 2010. Homoplastic evolution of external colouration in Asian stout newts (Pachytriton) inferred from molecular phylogeny. Zoologica Scripta , 39 , pp. 9-22.Abstract

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.

Wu, Y.K., et al., 2010. A new newt of the genus Cynops (Caudata: Salamandridae) from Fujian Province, southeastern China. Zootaxa , pp. 42-52.Abstract

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.

Wu, Y.K., Jiang, K. & Hanken, J., 2010. A new species of newt of the genus Paramesotriton (Salamandridae) from southwestern Guangdong, China, with a new northern record of P. longliensis from western Hubei. Zootaxa , pp. 45-58.Abstract

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.

Kerney, R., Hall, B.K. & Hanken, J., 2010. Regulatory elements of Xenopus col2a1 drive cartilaginous gene expression in transgenic frogs. International Journal of Developmental Biology , 54 , pp. 141-150.Abstract

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.