Journal Articles and Book Chapters: Present - 2010

Ferrão, M., et al., 2020. New Species of Leaf-litter Toad of the Rhinella margaritifera Species Group (Anura: Bufonidae) from Amazonia. Copeia , 108 (4) , pp. 967-986. PDF
Ferrão, M., et al., 2020. A new species of Dendropsophus (Anura, Hylidae) from southwestern Amazonia with a green bilobate vocal sac. ZooKeys , 942 , pp. 77.Abstract
Recent studies have shown that species diversity of the South American frog genus Dendropsophus is significantly underestimated, especially in Amazonia. Herein, through integrative taxonomy a new species of Dendropsophus from the east bank of the upper Madeira River, Brazil is described. Based on molecular phylogenetic and morphological analyses, the new species is referred to the D. microcephalus species group, where it is differentiated from its congeners mainly by having a green bilobate vocal sac and an advertisement call comprising 1–4 monophasic notes emitted with a dominant frequency of 8,979–9,606 Hz. Based on intensive sampling conducted in the study area over the last ten years, the new species is restricted to the east bank of the upper Madeira River, although its geographic range is expected to include Bolivian forests close to the type locality.
Olea, G.P., et al., 2020. Descriptions of five new species of the salamander genus Chiropterotriton (Caudata: Plethodontidae) from eastern Mexico and the status of three currently recognized taxa. PeerJ , 8 (e8800). PDF
Senevirathne, G., et al., 2020. Ontogeny of the anuran urostyle and the developmental context of the evolutionary novelty. PNAS , 117 (6) , pp. 3034-3044. PDF
Maddin, H.C., et al., 2020. Development and evolution of the tetrapod skull-neck boundary. Biological Reviews , 95 , pp. 573-591.Abstract

 The origin and evolution of the vertebrate skull have been topics of intense study for more than two centuries. Whereas early theories of skull origin, such as the infl uential vertebral theory, have been largely refuted with respect to the anterior (pre-otic) region of the skull, the posterior (post-otic) region is known to be derived from the anteriormost paraxial segments, i.e. the somites. Here we review the morphology and development of the occiput in both living and extinct tetrapods, taking into account revised knowledge of skull development by augmenting historical accounts with recent data. When occipital composition is evaluated relative to its position along the neural axis, and specifi cally to the hypoglossal nerve complex, much of the apparent interspecifi c variation in the location of the skull– neck boundary stabilizes in a phylogenetically informative way. Based on this criterion, three distinct conditions are identifi ed in (i ) frogs, (ii ) salamanders and caecilians, and (iii ) amniotes. The position of the posteriormost occipital segment relative to the hypoglossal nerve is key to understanding the evolution of the posterior limit of the skull. By using cranial foramina as osteological proxies of the hypoglossal nerve, a survey of fossil taxa reveals the amniote condition to be present at the base of Tetrapoda. This result challenges traditional theories of cranial evolution, which posit translocation of the occiput to a more posterior location in amniotes relative to lissamphibians (frogs, salamanders, caecilians), and instead supports the largely overlooked hypothesis that the reduced occiput in lissamphibians is secondarily derived. Recent advances in our understanding of the genetic basis of axial patterning and its regulation in amniotes support the hypothesis that the lissamphibian occipital form may have arisen as the product of a homeotic shift in segment fate from an amniote-like condition.

Key words : skull, development, tetrapod, occiput, somites, skull– neck, homeotic transformation

Kerney, R.R., Hanken, J. & Blackburn, D.C., 2018. Early limb patterning in the direct-developing salamanderPlethodon cinereus revealed by sox9 and col2a1. Evolution & Development , 20 (3-4) , pp. 100-107. Publisher's Version kerney_et_al.2018.evoldev.w_cover.pdf
Meegaskumbura, M., et al., 2015. Patterns of reproductive-mode evolution in Old World tree frogs (Anura, Rhacophoridae). Zoologica Scripta , doi:10.1111/zsc.12121. PDF
McPhillips, T., et al., 2015. YesWorkflow: A User-Oriented, Language-Independent Tool for Recovering Workflow Information from Scripts. International Journal for Digital Curation , 10 , pp. 298-313. PDF
Sefton, E.M., Piekarski, N. & Hanken, J., 2015. Dual embryonic origin and patterning of the pharyngeal skeleton in the axolotl (Ambystoma mexicanum). Evolution & Development , 17 , pp. 175-184. PDF
Jennings, D.H., Evans, B. & Hanken, J., 2015. Development of neuroendocrine components of the thyroid axis in the direct-devoloping frog Eleutherodactylus coqui: formation of the median eminence and the onset of pituitary TSH production. Gen. Comp. Endocrinol. , 214 , pp. 62-67. PDF
Hanken, J., 2015. Is heterochrony still an effective paradigm for contemporary studies of evo-devo?. In A. C. Love, ed. Conceptual Change in Biology: Scientific and Philosophical Perspectives on Evolution and Development. Boston Studies in the Philosophy and History of Science. Berlin. Berlin: Springer-Verlag, pp. 97-110. PDF
Song, T., et al., 2014. Toward automated design, analysis, and optimization of declarative curation workflows. Internat. J. Dig. Curat. , 9 , pp. 111-122. PDF
Piekarski, N., Gross, J.B. & Hanken, J., 2014. Evolutionary innovation and conservation in the embryonic derivation of the vertebrate skull. Nature Communications , 5 , pp. 5661.Abstract

Development of the vertebrate skull has been studied intensively for more than 150 years, yet many essential features remain unresolved. One such feature is the extent to which embryonic derivation of individual bones is evolutionarily conserved or labile. We perform long-term fate mapping using GFP-transgenic axolotl and Xenopus laevis to document the contribution of individual cranial neural crest streams to the osteocranium in these amphibians. Here we show that the axolotl pattern is strikingly similar to that in amniotes; it likely represents the ancestral condition for tetrapods. Unexpectedly, the pattern in Xenopus is much different; it may constitute a unique condition that evolved after anurans diverged from other amphibians. Such changes reveal an unappreciated relation between life history evolution and cranial development and exemplify 'developmental system drift', in which interspecific divergence in developmental processes that underlie homologous characters occurs with little or no concomitant change in the adult phenotype.

Cook, J.A., et al., 2014. Natural History Collections as Emerging Resources for InnovativeEducation. Bioscience , 64 , pp. 725-734.Abstract

There is an emerging consensus that undergraduate biology education in the United States is at a crucial juncture, especially as we acknowledge the need to train a new generation of scientists to meet looming environmental and health crises. Digital resources for biology now available online provide an opportunity to transform biology curricula to include more authentic and inquiry-driven educational experiences. Digitized natural history collections have become tremendous assets for research in environmental and health sciences, but, to date, these data remain largely untapped by educators. Natural history collections have the potential to help transform undergraduate science education from passive learning into an active exploration of the natural world, including the exploration of the complex relationships among environmental conditions, biodiversity, and human well-being. By incorporating natural history specimens and their associated data into undergraduate curricula, educators can promote participatory learning and foster an understanding of essential interactions between organisms and their environments.

Rovito, S.M., et al., 2013. Adaptive radiation in miniature: the minute salamanders of the Mexican highlands (Amphibia: Plethodontidae: Thorius). Biological Journal of the Linnean Society , 109 , pp. 622-643.Abstract

The small size and apparent external morphological similarity of the minute salamanders of the genus Thorius have long hindered evolutionary studies of the group. We estimate gene and species trees within the genus using mitochondrial and nuclear DNA from nearly all named and many candidate species and find three main clades. We use this phylogenetic hypothesis to examine patterns of morphological evolution and species coexistence across central and southern Mexico and to test alternative hypotheses of lineage divergence with and without ecomorphological divergence. Sympatric species differ in body size more than expected after accounting for phylogenetic relationship, and morphological traits show no significant phylogenetic signal. Sympatric species tend to differ in a combination of body size, presence or absence of maxillary teeth, and relative limb or tail length, even when they are close relatives. Sister species of Thorius tend to occupy climatically similar environments, which suggests that divergence across climatic gradients does not drive species formation in the genus. Rather than being an example of cryptic species formation, Thorius more closely resembles an adaptive radiation, with ecomorphological divergence that is bounded by organism-level constraints.(c) 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109, 622-643.

Bloom, S., et al., 2013. Developmental origins of a novel gut morphology in frogs. Evolution & Development , 15 , pp. 213-223.Abstract

Phenotypic variation is a prerequisite for evolution by natural selection, yet the processes that give rise to the novel morphologies upon which selection acts are poorly understood. We employed a chemical genetic screen to identify developmental changes capable of generating ecologically relevant morphological variation as observed among extant species. Specifically, we assayed for exogenously applied small molecules capable of transforming the ancestral larval foregut of the herbivorous Xenopus laevis to resemble the derived larval foregut of the carnivorous Lepidobatrachus laevis. Appropriately, the small molecules that demonstrate this capacity modulate conserved morphogenetic pathways involved in gut development, including downregulation of retinoic acid (RA) signaling. Identical manipulation of RA signaling in a species that is more closely related to Lepidobatrachus, Ceratophrys cranwelli, yielded even more similar transformations, corroborating the relevance of RA signaling variation in interspecific morphological change. Finally, we were able to recover the ancestral gut phenotype in Lepidobatrachus by performing a reverse chemical manipulation to upregulate RA signaling, providing strong evidence that modifications to this specific pathway promoted the emergence of a lineage-specific phenotypic novelty. Interestingly, our screen also revealed pathways that have not yet been implicated in early gut morphogenesis, such as thyroid hormone signaling. In general, the chemical genetic screen may be a valuable tool for identifying developmental mechanisms that underlie ecologically and evolutionarily relevant phenotypic variation.

Ziermann, J.M., et al., 2013. Morphology of the cranial skeleton and musculature in the obligate carnivorous tadpole of Lepidobatrachus laevis (Anura: Ceratophryidae). Acta Zoologica , 94 , pp. 101-112.Abstract

Ziermann, J.M., Infante, C., Hanken, J. and Olsson, L. 2011. Morphology of the cranial skeleton and musculature in the obligate carnivorous tadpole of Lepidobatrachus laevis (Anura: Ceratophryidae). Acta Zoologica (Stockholm) 00:112. Lepidobatrachus laevis (Ceratophryidae: Ceratophryinae) is a bizarre frog endemic to the Chacoan desert of central South America. Its tadpole is an obligate carnivore that can catch and consume live prey nearly its own size. Morphological adaptations associated with this unique feeding mode, including the larval skull anatomy and associated cranial musculature, have only been partly described. We studied the head of Stages 2627 larvae using gross dissection, immunohistochemistry, and standard histology. Derived features of this tadpole compared to the microphagous, herbivorous larvae of most other anurans include simplified chondrocranial cartilages and very robust jaw muscles. The mm. suspensorio- et quadratoangularis do not take their origin from the processus muscularis of the palatoquadrate, as in most other tadpoles, but instead originate from the corpus of the palatoquadrate caudal to this process. The jaw levators are unusually large. The tadpole of Ceratophrys, another member of the ceratophryine clade, also consumes large animal prey, but its morphology is very different. It probably has evolved independently from a generalized, mainly herbivorous tadpole similar to the larva of Chacophrys, the third ceratophryine genus. Most specialized features of the larval head of Lepidobatrachus laevis are adaptations for megalophagyingestion of whole, very large animal prey.

Whited, J.L., et al., 2013. Pseudotyped retroviruses for infecting axolotl in vivo and in vitro. Development , 140 , pp. 1137-1146.Abstract

Axolotls are poised to become the premiere model system for studying vertebrate appendage regeneration. However, very few molecular tools exist for studying crucial cell lineage relationships over regeneration or for robust and sustained misexpression of genetic elements to test their function. Furthermore, targeting specific cell types will be necessary to understand how regeneration of the diverse tissues within the limb is accomplished. We report that pseudotyped, replication-incompetent retroviruses can be used in axolotls to permanently express markers or genetic elements for functional study. These viruses, when modified by changing their coat protein, can infect axolotl cells only when they have been experimentally manipulated to express the receptor for that coat protein, thus allowing for the possibility of targeting specific cell types. Using viral vectors, we have found that progenitor populations for many different cell types within the blastema are present at all stages of limb regeneration, although their relative proportions change with time.