James Hanken

• PhD
• Managing Director at Harvard University

By using integrative taxonomy, we describe a new species of terrestrial foam-nesting frog of the genus Adenomera from white-sand forests of the Rio Negro Sustainable Development Reserve, Central Amazonia, Brazil. Within the A. andreae clade, the new species belongs to the A. simonstuarti complex where it is sister to the lineage from the lower Juru...

The impact of preserved museum specimens is transforming and increasing by three-dimensional (3D) imaging that creates high-fidelity online digital specimens. Through examples from the openVertebrate (oVert) Thematic Collections Network, we describe how we created a digitization community dedicated to the shared vision of making 3D data of specimen...

Southern Amazonia is one of the less-explored regions by anuran taxonomists. We describe a small new species of snouted treefrog, genus Scinax, from this region, from a fluvial archipelago in the Juruena River, state of Mato Grosso, Brazil. The description is based on external morphology of adults and tadpoles, advertisement call and molecular data...

Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three dis...

Taxonomic uncertainty at the species level compromises our knowledge of biodiversity, conservation, and systematics. The impact of such uncertainty is heightened in megadiverse regions such as Amazonia due to high levels of cryptic diversity. We used integrative taxonomy based on newly collected topotypical specimens to redescribe the Amazonian nur...

Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.

We use integrative taxonomy to formally describe a candidate species of nurse frog of the genus Allobates from southwestern Brazilian Amazonia. The new species nests within a clade that has been defined historically as A. gasconi, but it has an 8.8-11.0% genetic distance for 16S to samples from the type locality of A. gasconi. The new species diffe...

Taxonomic uncertainty at the species level compromises our knowledge of biodiversity, conservation and systematics. The impact of such uncertainty is heightened in megadiverse regions such as Amazonia due to high levels of cryptic diversity. We used integrative taxonomy based on newly collected topotypical specimens to redescribe the Amazonian nurs...

Modularity (segmentation), homology and heterochrony were essential concepts embraced by Gavin de Beer in his studies of the development and evolution of the vertebrate skull. While his pioneering contributions have stood the test of time, our understanding of the biological processes that underlie each concept has evolved. We assess de Beer's init...

Integration of the world's natural history collections can provide a resource for decision-makers.

Over the past three centuries, people have collected objects and specimens and placed them in natural history museums throughout the world. Taken as a whole, this global collection is the physical basis for our understanding of the natural world and our place in it, an unparalleled source of information that is directly relevant to issues as divers...

One or more members of four living amphibian clades have independently dispensed with pulmonary respiration and lack lungs, but little is known of the developmental basis of lung loss in any taxon. We use morphological, molecular, and experimental approaches to examine the Plethodontidae, a dominant family of salamanders, all of which are lungless...

Cryptic diversity is extremely common in widespread Amazonian anurans, but especially in nurse frogs of the genus Allobates . There is an urgent need to formally describe the many distinct but unnamed species, both to enable studies of their basic biology but especially to facilitate conservation of threatened environments in which many are found....

Climate change and infectious diseases continue to drive global amphibian population declines, contributing to one of the greatest vertebrate extinctions of the Anthropocene. Currently around 16% amphibian species across the world are affected by four pathogens – Batrachochytrium dendrobatidis ( Bd ), B. salamandrivorans ( Bsal ), Ranavirus and Per...

Large diversifications of species are known to occur unevenly across space and evolutionary lineages, but the relative importance of their driving mechanisms, such as climate, ecological opportunity and key evolutionary innovations (KEI), remains poorly understood. Here, we explore the remarkable diversification of rhacophorid frogs, which represen...

Most frogs' diets shift between the larval and adult phases, from a filter-feeding herbivore to a bulk-feeding carnivore. This change in diet corresponds to a biphasic mode of gut development that begins during embryogenesis and resumes at metamorphosis, when nearly the entire anatomy of the tadpole is reorganized into its adult morphology. The fro...

Recent studies have showed that several species of frogs previously thought to be widespread throughout Amazonia are species complexes with each individual species displaying smaller geographic ranges and that only a small fraction of Amazonian frogs are indeed widely distributed. Evaluating cryptic diversity within these complexes and describing a...

We describe through integrative taxonomy a new species of snouted treefrog of the genus Scinax from white-sand forests of the Rio Negro Sustainable Development Reserve in Central Amazonia, Brazil. The new species is phylogenetically related to other Scinax with striped eyes and pulsed advertisement calls. It differs from other Amazonian species mai...

Frogs are an ecologically diverse and phylogenetically ancient group of living amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus . Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis , along with draft chromosome-scale sequences of three d...

24 Although large diversifications of species occur unevenly across space and evolutionary 25 lineages, the relative importance of their driving mechanisms, such as climate, ecological 26 opportunity and key innovations, remains poorly understood. Here, we explore the 27 remarkable diversification of rhacophorid frogs, which represent six percent o...

We describe through integrative taxonomy a new Amazonian species of leaf-litter toad of the Rhinella margaritifera species group. The new species inhabits open lowland forest in southwest Amazonia in Brazil, Peru, and Bolivia. It is closely related to a Bolivian species tentatively identified as Rhinella cf. paraguayensis. Both the new species and...

Nurse frogs (Aromobatidae: Allobates) are probably the most extensively studied genus by taxonomists in Brazilian Amazonia. The southwestern portion of Amazonia is the most species-rich: as many as seven species may occur in sympatry at a single locality. In this study, we describe a new species of nurse frog from this region. The description integ...

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, t...

The genus Chiropterotriton is endemic to Mexico with a geographical distribution along the Sierra Madre Oriental, the Trans Mexican Volcanic Belt and the Sierra de Juárez. The recent use of molecular tools has shown that Mexico’s amphibian diversity is highly underestimated, including a large number of cryptic, unnamed species. Chiropterotriton has...

We demonstrate archival 3D digitization of glossy, translucent and highly detailed glass sculptures, namely the glass models of marine invertebrates made by Rudolf and Leopold Blaschka in the late 19th century. Achieving satisfactory results required optimizing well-known techniques of light and polarization control and photogrammetric processing....

A longstanding goal of evolutionary developmental biology is to document the precise mechanisms that underlie formation of, and differences among, basic body plans, organ systems and physiological functions. Another, less‐studied approach is to reveal how those mechanisms are perturbed to enable, or even mediate, the origin of novel adaptations tha...

Developmental novelties often underlie the evolutionary origins of key metazoan features. The anuran urostyle, which evolved nearly 200 MYA, is one such structure. It forms as the tail regresses during metamorphosis, when locomotion changes from an axial-driven mode in larvae to a limb-driven one in adult frogs. The urostyle comprises of a coccyx a...

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 influential 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 ante...

Amphibians form fingers without webbing by differential growth between digital and interdigital regions. Amniotes, however, employ interdigital cell death (ICD), an additional mechanism that contributes to a greater variation of limb shapes. Here, we investigate the role of environmental oxygen in the evolution of ICD in tetrapods. While cell death...

Direct development is a reproductive mode in amphibians that has evolved independently from the ancestral biphasic life history in at least a dozen anuran lineages. Most direct-developing frogs, including the Puerto Rican coquí, Eleutherodactylus coqui, lack a free-living aquatic larva and instead hatch from terrestrial eggs as miniature adults. Th...

Pseudophilautus comprises an endemic diversification predominantly associated with the wet tropical regions of Sri Lanka that provides an opportunity to examine the effects of geography and historical climate change on diversification. Using a time-calibrated multi-gene phylogeny, we analyze the tempo of diversification in the context of past clima...

Numerous physiological and morphological adaptations were achieved during the transition to lungless respiration that accompanied evolutionary lung loss in plethodontid salamanders, including those that enable efficient gas exchange across extrapulmonary tissue. However, the molecular basis of these adaptations is unknown. Here, we show that lungle...

As curators of biodiversity data in natural science collections, we are deeply concerned with data quality, but quality is an elusive concept. An effective way to think about data quality is in terms of fitness for use (Veiga 2016). To use data to manage physical collections, the data must be able to accurately answer questions such as what objects...

Direct-developing amphibians form limbs during early embryonic stages, as opposed to the later, often postembryonic limb formation of metamorphosing species. Limb patterning is dramatically altered in direct-developing frogs, but little attention has been given to direct-developing salamanders. We use expression patterns of two genes, sox9 and col2...

Numerous physiological and morphological adaptations were achieved during the transition to lungless respiration following evolutionary lung loss in plethodontid salamanders, including those that enable efficient gas exchange across extrapulmonary tissue. However, the molecular basis of these adaptations is unknown. Here we show that lungless salam...

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...

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-le...

In the Kurator project, we are developing libraries of small modules, each designed to address a particular data quality test. These libraries, which can be run on single computers or scalable architecture, can be incorporated into data management processes in the form of customizable data quality scripts. A script composed of these modules can be...

Fig. S2. Histological sections through the heart of the lunged salamander Ambystoma mexicanum at stage 57.

Fig. S3. The atrial septum of the swordtail newt, Cynops ensicauda

Fig. S1. Histological sections through the heart of the lunged salamander Ambystoma mexicanum at stage 52.

Fig. S4. Reconstruction of the atrial septum in adult Plethodon cinereus based on histological sections.

Table S1. Collection localities for plethodontid salamanders. All localities are in Massachusetts, USA.

Video S1. 3‐D histological reconstruction of the heart of the lunged salamander Ambystoma mexicanum at stage 52.

Video S2. 3‐D histological reconstruction of the heart of the lunged salamander Ambystoma mexicanum at stage 57.

Video S3. 3‐D volume rendering of the heart of an adult lungless salamander (Plethodon cinereus).

We describe three new species of minute salamanders, genus Thorius, from the Sierra Madre del Sur of Oaxaca, Mexico. Until now only a single species, T. minutissimus, has been reported from this region, although molecular data have long shown extensive genetic differentiation among geographically disjunct populations. Adult Thorius pinicola sp. nov...

Bones of the cranial vault appear to be highly conserved among tetrapod vertebrates. Moreover, bones identified with the same name are assumed to be evolutionarily homologous. However, recent developmental studies reveal a key difference in the embryonic origin of cranial vault bones between representatives of two amniote lineages, mammals and bird...

Supplementary Figure S1-Contribution of cranial neural crest streams and mesoderm to the bony skull of axolotl.

Electronic Supplementary Materials: Transplantation method details. Supplementary Table S1-Summary of the composition of the cranial vault across tetrapods.

Nearly two thirds of the approximately 700 species of living salamanders are lungless. These species respire entirely through the skin and buccopharyngeal mucosa. Lung loss dramatically impacts the configuration of the circulatory system but the effects of evolutionary lung loss on cardiac morphology have long been controversial. For example, there...

ELife digest Muscles in the head and trunk (main body) form from different parts of the embryo, and their development uses different genes. Trunk muscles are derived from somites – paired blocks of cells arranged in segments on either side of the midline (which divides the body into left and right halves). By contrast, cells that give rise to head...

The Indian Purple frog, Nasikabatrachus sahyadrensis, occupies a basal phylogenetic position among neobatrachian anurans and has a very unusual life history. Tadpoles have a large ventral oral sucker, which they use to cling to rocks in torrents, whereas metamorphs possess adaptations for life underground. The developmental changes that underlie th...

Cranial and postcranial ossification indices versus developmental (Gosner) stage in Nasikabatrachus sahyadrensis. (A) Skull. (B) Postcranial skeleton. In each comparison, ossification index equals the number of bones present at a given stage divided by the total number of bones present at the end of metamorphosis (skull, 11; postcranial skeleton, 7...

External morphological measurements of Nasikabatrachus sahyadrensis. (XLSX)

Cranial and postcranial bones of Nasikabatrachus sahyadrensis in different developmental stages. (XLSX)

Patterns of reproductive-mode evolution in Old World tree frogs (Anura, Rhacophoridae). —Zoologica Scripta, 00, 000–000. The Old World tree frogs (Anura: Rhacophoridae), with 387 species, display a remarkable diversity of reproductive modes – aquatic breeding, terrestrial gel nesting, terrestrial foam nesting and terrestrial direct development. The...

The impressive morphological diversification of vertebrates was achieved in part by innovation and modification of the pharyngeal skeleton. Extensive fate mapping in amniote models has revealed a primarily cranial neural crest derivation of the pharyngeal skeleton. Although comparable fate maps of amphibians produced over several decades have faile...

Congenital atrial septal defects (ASDs) rank among the three most common birth defects in humans. However, the proportion of ASDs with a known genetic basis is small. New methods, models and systems for studying ASD are needed to further our understanding of its etiology and to develop possible treatments. We demonstrate that salamanders offer an e...

Scientific workflow management systems offer features for composing complex com- putational pipelines from modular building blocks, executing the resulting automated workflows, and recording the provenance of data products resulting from workflow runs. Despite the advantages such features provide, many automated workflows continue to be implemented...

Heterochrony, or change in the relative timing of developmental events, has been a dominant concept in the study of the relation between evolution and development since even before the term was coined in the mid-nineteenth century. Its popularity exploded beginning in the late 1970s and 1980s as part of the resurgence of interest in Evo-devo that a...

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...

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...

Data curation is increasingly important. Our previous work on a Kepler curation package has demonstrated advantages that come from automating data curation pipelines by using workflow systems. However, manually designed curation workflows can be error-prone and inefficient due to a lack of user understanding of the workflow system, misuse of actors...

45 At a time when amphibian populations globally are in decline, the recent discoveries of large numbers of new frog species on Sri Lanka, an island from which the pathogenic chytrid fungus has not yet been reported, may seem heartening (Meegaskumbura et al. 2002). A total of 42 new species of anurans have been described since 1993, and many more s...

Electronic annotation of scientific data is very similar to annotation of documents. Both types of annotation amplify the original object, add related knowledge to it, and dispute or support assertions in it. In each case, annotation is a framework for discourse about the original object, and, in each case, an annotation needs to clearly identify i...

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 phylogenet...

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 sp...

The pharyngeal−arch skeleton is a hallmark of vertebrates. In basal taxa, it supports the gills and muscles of the pharynx, whereas in more derived groups it surrounds the larynx and trachea. That most of the pharyngeal−arch skeleton is derived from embryonic neural crest was first demonstrated in the mudpuppy in the late 19th century, and this res...

The vertebrate skull is derived from embryonic neural crest and mesoderm. These contributions have been revealed in great detail in one amniote model and to a lesser extent in other taxa. The degree to which patterns of derivation are evolutionary conserved or labile among most lineages nevertheless remains largely unknown. Amphibians are a non‐amn...

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 morphological variation as observed among extant species. Specifically, w...

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 nec...

The pharyngeal−arch skeleton is a hallmark of vertebrates. In basal taxa, it supports the gills and muscles of the pharynx, whereas in more derived groups it surrounds the larynx and trachea. That most of the pharyngeal−arch skeleton is derived from embryonic neural crest was first demonstrated in the mudpuppy in the late 19th century, and this res...

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...

Papenfuss and Wake (1987) described a new species of plethodontid salamander from northern Oaxaca, Mexico, which they named Nototriton adelos. The species was assigned to Nototriton primarily on the basis of its similarity to members of that widespread genus, which as then constituted ranged from Oaxaca, Mexico, to east-central Costa Rica. At that...

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. Th...