Publications

2008
Parra-Olea, G., Wake, D. & Hanken, J., 2008. Pseudoeurycea tlahcuiloh. In IUCN 2012. IUCN Red List of Threatened Species. Version 2012.2. Publisher's Version
Parra-Olea, G., Wake, D. & Hanken, J., 2008. Pseudoeurycea unguidentis. In IUCN 2012. IUCN Red List of Threatened Species. Version 2012.2. Publisher's Version
Parra-Olea, G., Wake, D. & Hanken, J., 2008. Thorius dubitus. In IUCN 2012. IUCN Red List of Threatened Species. Version 2012.2. Publisher's Version
Parra-Olea, G. & Wake, D., 2008. Thorius grandis. In IUCN 2012. IUCN Red List of Threatened Species. Version 2012.2. Publisher's Version
Parra-Olea, G., et al., 2008. Thorius infernalis. In IUCN 2012. IUCN Red List of Threatened Species. Version 2012.2. Publisher's Version
Parra-Olea, G., Wake, D. & Hanken, J., 2008. Thorius insperatus. In IUCN 2012. IUCN Red List of Threatened Species. Version 2012.2. Publisher's Version
Parra-Olea, G., Wake, D. & Hanken, J., 2008. Thorius macdougalli. In IUCN 2012. IUCN Red List of Threatened Species. Version 2012.2. Publisher's Version
Parra-Olea, G., Wake, D. & Hanken, J., 2008. Thorius magnipes. In IUCN 2012. IUCN Red List of Threatened Species. Version 2012.2. Publisher's Version
Parra-Olea, G., Wake, D. & Hanken, J., 2008. Thorius minutissimus. In IUCN 2012. IUCN Red List of Threatened Species. Version 2012.2. Publisher's Version
Parra-Olea, G., Wake, D. & Hanken, J., 2008. Thorius minydemus. In IUCN 2012. IUCN Red List of Threatened Species. Version 2012.2. Publisher's Version
Parra-Olea, G., et al., 2008. Thorius narismagnus. In IUCN 2012. IUCN Red List of Threatened Species. Version 2012.2. Publisher's Version
Parra-Olea, G., Wake, D. & Hanken, J., 2008. Thorius narisovalis. In IUCN 2012. IUCN Red List of Threatened Species. Version 2012.2. Publisher's Version
Meegaskumbura, M., et al., 2008. Pickled frogs help biodiversity assessment. In S. Stuart, et al., ed. Threatened Amphibians of the World. Barcelona, Gland, Arlington. Barcelona, Gland, Arlington: Lynx Edicions, IUCN, and Conservation International, pp. 45. PDF
Blackburn, D.C., Hanken, J. & Jenkins, F.A., 2008. Concealed weapons: erectile claws in African frogs. Biology Letters , 4 , pp. 355-357.Abstract

Vertebrate claws are used in a variety of important behaviours and are typically composed of a keratinous sheath overlying the terminal phalanx of a digit. Keratinous claws, however, are rare in living amphibians; their microstructure and other features indicate that they probably originated independently from those in amniotes. Here we show that certain African frogs have a different type of claw, used in defence, that is unique in design among living vertebrates and lacks a keratinous covering. These frogs have sectorial terminal phalanges on their hind feet that become functional by cutting through the skin. In the resting state, the phalanx is subdermal and attached to a distal bony nodule, a neomorphic skeletal element, via collagen-rich connective tissue. When erected, the claw breaks free from the nodule and pierces the ventral skin. The nodule, suspended by a sheath attached to the terminal phalanx and supported by collagenous connections to the dermis, remains fixed in place. While superficially resembling the shape of claws in other tetrapods, these are the only vertebrate claws known to pierce their way to functionality.

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Zimmermann, J., et al., 2008. DNA damage in preserved specimens and tissue samples: a molecular assessment. Frontiers in Zoology , 5.Abstract

The extraction of genetic information from preserved tissue samples or museum specimens is a fundamental component of many fields of research, including the Barcode of Life initiative, forensic investigations, biological studies using scat sample analysis, and cancer research utilizing formaldehyde-fixed, paraffin-embedded tissue. Efforts to obtain genetic information from these sources are often hampered by an inability to amplify the desired DNA as a consequence of DNA damage. Previous studies have described techniques for improved DNA extraction from such samples or focused on the effect of damaging agents - such as light, oxygen or formaldehyde - on free nucleotides. We present ongoing work to characterize lesions in DNA samples extracted from preserved specimens. The extracted DNA is digested to single nucleosides with a combination of DNase I, Snake Venom Phosphodiesterase, and Antarctic Phosphatase and then analyzed by HPLC-ESI-TOF-MS. We present data for moth specimens that were preserved dried and pinned with no additional preservative and for frog tissue samples that were preserved in either ethanol, or formaldehyde, or fixed in formaldehyde and then preserved in ethanol. These preservation methods represent the most common methods of preserving animal specimens in museum collections. We observe changes in the nucleoside content of these samples over time, especially a loss of deoxyguanosine. We characterize the fragmentation state of the DNA and aim to identify abundant nucleoside lesions. Finally, simple models are introduced to describe the DNA fragmentation based on nicks and double-strand breaks.

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Kerney, R. & Hanken, J., 2008. Gene expression reveals unique skeletal patterning in the limb of the direct-developing frog, Eleutherodactylus coqui. Evolution & Development , 10 , pp. 439-448.Abstract

The growing field of skeletal developmental biology provides new molecular markers for the cellular precursors of cartilage and bone. These markers enable resolution of early features of skeletal development that are otherwise undetectable through conventional staining techniques. This study investigates mRNA distributions of skeletal regulators runx2 and sox9 along with the cartilage-dominant collagen 2(alpha)1 (col2a1) in embryonic limbs of the direct-developing anuran, Eleutherodactylus coqui. To date, distributions of these genes in the limb have only been examined in studies of the two primary amniote models, mouse and chicken. In E coqui, expression of transcription factors runx2 and sox9 precedes that of col2a1 by 0.5-1 developmental stage (approximately 12-24 h). Limb buds of E. coqui contain unique distal populations of both runx2- and sox9-expressing cells, which appear before formation of the primary limb axis and do not express col2a1. The subsequent distribution of col2a1 reveals a primary limb axis similar to that described for Xenopus laevis. Precocious expression of both runx2 and sox9 in the distal limb bud represents a departure from the conserved pattern of proximodistal formation of the limb skeleton that is central to prevailing models of vertebrate limb morphogenesis. Additionally, runx2 is expressed in the early joint capsule perichondria of the autopod and in the perichondria of long bones well before periosteum formation. The respective distributions of sox9 and col2a1 do not reveal the joint perichondria but instead are expressed in the fibrocartilage that fills each presumptive joint capsule. These distinct patterns of runx2- and sox9-expressing cells reveal precursors of chondrocyte and osteoblast lineages well before the appearance of mature cartilage and bone.

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Gross, J.B. & Hanken, J., 2008. Review of fate-mapping studies of osteogenic cranial neural crest in vertebrates. Developmental Biology , 317 , pp. 389-400.Abstract

Recent years have witnessed renewed interest in defining the embryonic cell populations that directly contribute to the bony skull. This question lies at the intersection of several important developmental, clinical and evolutionary interests. Until recently, our collective understanding of the embryonic origin of the vertebrate osteocranium has been based on a small number of reports published solely using avian models. As data gradually accumulates from other, distantly related species (e.g., mouse and frog), we can begin to evaluate long-standing assumptions regarding the behavior of osteogenic (bone-forming) neural crest cells within a wider phylogenetic and comparative context. In this review, we summarize data collected to date in three major vertebrate taxa: amphibians, birds and mammals. We highlight three largely unexplored topics within the field of osteogenic neural crest development: 1) disagreements in bone tissue origin within and across current model systems; 2) whether the pattern of neural crest cell contribution to skull bone is evolutionarily conservative or labile; and 3) how our understanding of development and morphology will benefit from fate maps using currently unexamined animal models. (C) 2008 Elsevier Inc. All rights reserved.

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Gross, J.B. & Hanken, J., 2008. Segmentation of the vertebrate skull: neural-crest derivation of adult cartilages in the clawed frog, Xenopus laevis. Integrative and Comparative Biology , 48 , pp. 681-696.Abstract

We utilize a novel, transgenic cell-labeling system to assess the embryonic derivation of cartilages in the post-metamorphic skull of anuran amphibians. Many of these cartilages form de novo at metamorphosis and have no obvious precursors within the larval skeleton. Most adult cartilages are derived from mandibular- or hyoid-stream neural crest, either individually or in combination; branchial-stream neural crest makes a modest contribution. Each stream also contributes to at least one cartilage in the middle ear or external ear. Four cartilages are composite elements; each is derived from at least two distinct cell populations. Many boundaries between adjacent neural-crest territories are cryptic insofar as they do not coincide with anatomical boundaries. The system of adult cranial segmentation revealed by these fate-mapping results differs in important respects from both the segmentation of the ontogenetically earlier larval skull and the cranial segmentation in amniotes. Most striking is the rostral inversion of neural-crest-derived cartilages in Xenopus, such that mandibular stream-derived elements are deployed caudal to those derived from the hyoid stream, which predominate anteriorly. This novel pattern of rostral segmentation may be a consequence of the complex, biphasic life history that is characteristic of most species of living amphibians, and especially anurans, in which cranial architecture is significantly reconfigured at metamorphosis. Neural-crest derivation of the vertebrate skull is not invariant; instead, embryonic derivation of individual components of the cranial skeleton may vary widely among species.

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2007
Parra, G., et al., 2007. Systematics and Conservation. In C. Gascon, et al., ed. Amphibian Conservation Action Plan. Gland and Cambridge. Gland and Cambridge: IUCN/SSC Amphibian Specialist Group, pp. 45-48. PDF
Kerney, R., et al., 2007. Cranial ontogeny in Philautus silus (Anura : Ranidae : Rhacoohorinae) reveals few similarities with other direct-developing anurans. Journal of Morphology , 268 , pp. 715-725.Abstract

Direct development has evolved in rhacophorine frogs independently from other anuran lineages, thereby offering an opportunity to assess features associated with this derived life history. Using a developmental series of the direct-developing Philautus silus (Ranidae: Rhaeophorinae) from Sri Lanka, we examine features of cranial morphology that are part of a suite of adaptations that facilitate feeding in free-living tadpoles, but have been changed or lost in other direct-developing lineages. Larval-specific upper jaw cartilages, which are absent from many non-rhacophorine direct-developing species (such as Eleutherodactylus coqui), develop in embryos of P. silus. Similarly, lower jaw cartilages initially assume a larval morphology, which is subsequently remodeled into the adult jaw configuration before hatching. However, the cartilaginous jaw suspension and hyobranchial skeleton never assume a typical larval morphology. The palatoquadrate, which suspends the lower jaw, lacks the posterior connections to the braincase found in many metamorphosing species. Unlike in metamorphosing species, bone formation in P. silus begins before hatching. However, the sequence of bone formation resembles that of metamorphosing anurans more than that of other direct developers. In particular, P. silus does not exhibit precocious ossification of the lower jaw, which is characteristic of some frogs and caecilians that lack a free-living tadpole. These data reveal some similarities between Philautus and other direct-developing anurans. However, the departure of Philautus embryos from the generalized tadpole skeletal morphology is less pronounced than that observed in other direct-developing taxa.

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