James Hanken | Harvard University (original) (raw)
Papers by James Hanken
System Naturae 250 – The Linnaean Ark, 2010
Imagine an electronic page for each species of organism on Earth, available everywhere by single ... more Imagine an electronic page for each species of organism on Earth, available everywhere by single access on command. The page contains the scienti c name of the species, a pictorial or genomic presentation of the primary type specimen on which its name is based, and a summary of its diagnostic traits. The page opens out directly or by linking to other databases, such as ARKive, Ecoport, GenBank and MorphBank. It comprises a summary of everything known about the species' genome, proteome, geographical distribution, phylogenetic position, habitat, ecological relationships and, not least, its perceived practical importance for humanity…. The page is inde nitely expansible. Its contents are continuously peer reviewed and updated with new information. All the pages together form an encyclopedia, the content of which is the totality of comparative biology. E. O. Wilson (2003) Human activities pose an ever-growing threat to biological diversity (Thuiller 2007). Population growth, global climate change, and other environmental perturbations heighten the urgency with which we must discover, formally describe, understand, and protect the world's species of living organisms. At the same time, the general public shows increasing interest in biodiversity and support for efforts to preserve it. In an attempt to respond to both of these imperatives, in May 2007 representatives of several of the world's leading natural history institutions, with initial nancial support from two major private philanthropies, have joined together to create the Encyclopedia of Life (EOL). The EOL will dynamically synthesize biodiversity knowledge about all known species, including their taxonomy, geographic distribution, specimens in collections, genetics, evolutionary history, morphology, behavior, ecological relationships, and importance for human well-being, and distribute this information freely through the Internet. It will serve as a primary resource for a wide audience that includes scientists, natural resource managers, conservationists, teachers, and students around
Cranial skeletal morphology, ontogeny and variation are examined in five species of Thorim, a gen... more Cranial skeletal morphology, ontogeny and variation are examined in five species of Thorim, a genus of diminutive plethodontid salamanders that are among the smallest, extant, tailed tetrapods. The akull of adult 'Thhoriu ~ is characterized by: (1) limited development or absence of several ossified clemrnts and dentition; (2) increased inter- and intraspecifir variability; (3) novel morphological ronfigurations of the braincase and jaw suspensorium. Posthatching cranial mineralization in all spccies or 'Thorzus is truncated precociously with respect to that typical of larger and more generalized plethodontid genera, such as Pseudoeurycea. These features implicate paedomorphosis as a predominant mechanism responsihle for the evolution of decreased size in Thorim from larger plethodontid ancestors. lntcrspecific differences in cranial morphology are evident; species may be characterized by greater or lesser degrees of truncated development. However, there is no consistent re...
Direct development is a widespread alternate reproductive mode in living amphibians that is chara... more Direct development is a widespread alternate reproductive mode in living amphibians that is characterized by evolutionary loss of the free-living, aquatic larval stage. Courtship, mating, and oviposition occur on land, and the terrestrial egg hatches as a fully formed, miniature adult. While it is the most common reproductive mode in urodeles, development outside the reproductive tract of the female that proceeds directly to a terrestrial hatchling occurs in only a single lineage, the lungless salamanders of the family Plethodontidae. Evolution of direct development in plethodontids has contributed importantly to the extraordinary evolutionary success of this speciose, geographically widespread, and morphologically and ecologically diverse taxon. Developmental consequences and correlates include increased egg size and embryonic development time, loss of larval structures and ontogenetic repatterning, and altered pattern formation in organogenesis. Evolutionary and phylogenetic conse...
Development, 1998
Variation in segment number is an important but neglected feature of vertebrate evolution. Some v... more Variation in segment number is an important but neglected feature of vertebrate evolution. Some vertebrates have as few as six trunk vertebrae, while others have hundreds. We examine this phenomenon in relation to recent models of evolution and development. Surprisingly, differences in vertebral number are foreshadowed by different somite counts at the tailbud stage, thought to be a highly conserved (phylotypic) stage. Somite number therefore violates the ‘developmental hourglass’ model. We argue that this is because somitogenesis shows uncoupling or dissociation from the conserved positional field encoded by genes of the zootype. Several other systems show this kind of dissociation, including limbs and feathers. Bmp-7 expression patterns demonstrate dissociation in the chick pharyngeal arches. This makes it difficult to recognise a common stage of pharyngeal development or ‘pharyngula’ in all species. Rhombomere number is more stable during evolution than somite number, possibly be...
Biodiversity Information Science and Standards, 2018
As curators of biodiversity data in natural science collections, we are deeply concerned with dat... more 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 are in the collections, where are they and where are they from. Some research uses aggregate data across collections, which involves exchange of data using standard vocabularies. Some research uses require accurate georeferences, collecting dates, and current identifications. It is well understood that the costs of data capture and data quality improvement increase with increasing time from the original observation. These factors point towards two engineering principles for software that is intended to maintain or enhance data quality: build small modular data quality tests that can be easily assembled in suites to assess the fitness of u...
Proceedings of the National Academy of Sciences, 2020
Developmental novelties often underlie the evolutionary origins of key metazoan features. The anu... more 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 and a hypochord. The coccyx forms by fusion of caudal vertebrae and has evolved repeatedly across vertebrates. However, the contribution of an ossifying hypochord to the coccyx in anurans is unique among vertebrates and remains a developmental enigma. Here, we focus on the developmental changes that lead to the anuran urostyle, with an emphasis on understanding the ossifying hypochord. We find that the coccyx and hypochord have two different developmental histories: First, the development of the coccyx initiates before metamorphic climax whereas the ossifying hypochord undergoes rapid ossification and hypertrophy; second, thyroid hormone di...
Journal of anatomy, Jan 25, 2016
Nearly two thirds of the approximately 700 species of living salamanders are lungless. These spec... more 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 is presumably little need for an atrial septum in lungless salamanders due to the absence of pulmonary veins and the presence of a single source of mixed blood flowing into the heart, but whether lungless salamanders possess an atrial septum and whether the sinoatrial aperture is located in the left or right atrium are unresolved; authors have stated opposing claims since the late 1800s. Here, we use micro-computed tomography (μ-CT) imaging, gross dissection and histological reconstruction to compare cardiac morphology among lungless plethodontid salamanders (Plethodontidae), salamanders with lungs, and the convergently lungless species O...
Royal Society Open Science, 2016
Bones of the cranial vault appear to be highly conserved among tetrapod vertebrates. Moreover, bo... more 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 birds, thereby challenging this view. In the mouse, the frontal is derived from cranial neural crest (CNC) but the parietal is derived from mesoderm, placing the CNC–mesoderm boundary at the suture between these bones. In the chicken, this boundary is located within the frontal. This difference and related data have led several recent authors to suggest that bones of the avian cranial vault are misidentified and should be renamed. To elucidate this apparent conflict, we fate-mapped CNC and mesoderm in axolotl to reveal the contributions of these two embryonic cell populations to the cranial vault in a urodele amphibian. The CNC–mesoderm bounda...
eLife, Jan 19, 2016
Vertebrate neck musculature spans the transition zone between head and trunk. The extent to which... more Vertebrate neck musculature spans the transition zone between head and trunk. The extent to which the cucullaris muscle is a cranial muscle allied with the gill levators of anamniotes or is instead a trunk muscle is an ongoing debate. Novel computed tomography datasets reveal broad conservation of the cucullaris in gnathostomes, including coelacanth and caecilian, two sarcopterygians previously thought to lack it. In chicken, lateral plate mesoderm (LPM) adjacent to occipital somites is a recently identified embryonic source of cervical musculature. We fate-map this mesoderm in the axolotl (Ambystoma mexicanum), which retains external gills, and demonstrate its contribution to posterior gill-levator muscles and the cucullaris. Accordingly, LPM adjacent to the occipital somites should be regarded as posterior cranial mesoderm. The axial position of the head-trunk border in axolotl is congruent between LPM and somitic mesoderm, unlike in chicken and possibly other amniotes.
PloS one, 2016
The Indian Purple frog, Nasikabatrachus sahyadrensis, occupies a basal phylogenetic position amon... more 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 these shifts in habits and habitats, and especially the internal remodeling of the cranial and postcranial skeleton, are unknown. Using a nearly complete metamorphic series from free-living larva to metamorph, we describe the postembryonic skeletal ontogeny of this ancient and unique monotypic lineage. The torrent-dwelling larva possesses a dorsoventrally flattened body and a head with tiny dorsal eyes, robust lower and upper jaw cartilages, well-developed trabecular horns, and a definable gap between the trabecular horns and the tip of the snout. Unlike tadpoles of many other frogs, those of Nasikabatrachus retain larval mouthparts into lat...
The Bulletin of zoological nomenclature., 1988
The purpose of this application is to conserve the specific name pennatulus Cope, 1869 for the Me... more The purpose of this application is to conserve the specific name pennatulus Cope, 1869 for the Mexican salamander Thorius pennatulus. The name first appeared (about one month earlier) as pennatribus , probably due to a spelling error.
Integrative and Comparative Biology
The pharyngeal−arch skeleton is a hallmark of vertebrates. In basal taxa, it supports the gills a... more 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 result has since been confirmed in additional species. Yet, the evolution and extent of neural crest contributions to the pharyngeal skeleton is incompletely understood. In this study, we fate map neural crest in the axolotl, Ambystoma mexicanum, using transplantations from GFP−transgenic donors into wild−type hosts. We found that neural crest does not contribute to all elements of the pharyngeal skeleton: the ventral midline element basibranchial 2 was never labeled. Based on this result we also constructed a fate map of cranial mesoderm. Our results positively demonstrate for the first time a mesodermal contribution to the pharyngeal skelet...
Evolution & Development, 2015
General and comparative endocrinology, Jan 5, 2015
Direct-developing frogs lack, wholly or in part, a wide range of larval features found in metamor... more Direct-developing frogs lack, wholly or in part, a wide range of larval features found in metamorphosing species and form adult-specific features precociously, during embryogenesis. Most information on thyroid regulation of direct development relies on hormone manipulations; the ontogeny of many thyroid axis components has not been fully described. This analysis examines differentiation of the median eminence of the hypothalamus and production of thyroid-stimulating hormone (TSH) by the pituitary of the direct-developing frog Eleutherodactylus coqui. The median eminence is established two-thirds of the way through embryogenesis. Cells immunoreactive to human TSHβ antibodies are first detected during embryogenesis and quantitative changes in TSHβ-IR cells resemble those in metamorphosing amphibians. Formation of the median eminence of the hypothalamus and TSHβ production by the pituitary precede or coincide with morphological changes during embryogenesis that occur during metamorphos...
System Naturae 250 – The Linnaean Ark, 2010
Imagine an electronic page for each species of organism on Earth, available everywhere by single ... more Imagine an electronic page for each species of organism on Earth, available everywhere by single access on command. The page contains the scienti c name of the species, a pictorial or genomic presentation of the primary type specimen on which its name is based, and a summary of its diagnostic traits. The page opens out directly or by linking to other databases, such as ARKive, Ecoport, GenBank and MorphBank. It comprises a summary of everything known about the species' genome, proteome, geographical distribution, phylogenetic position, habitat, ecological relationships and, not least, its perceived practical importance for humanity…. The page is inde nitely expansible. Its contents are continuously peer reviewed and updated with new information. All the pages together form an encyclopedia, the content of which is the totality of comparative biology. E. O. Wilson (2003) Human activities pose an ever-growing threat to biological diversity (Thuiller 2007). Population growth, global climate change, and other environmental perturbations heighten the urgency with which we must discover, formally describe, understand, and protect the world's species of living organisms. At the same time, the general public shows increasing interest in biodiversity and support for efforts to preserve it. In an attempt to respond to both of these imperatives, in May 2007 representatives of several of the world's leading natural history institutions, with initial nancial support from two major private philanthropies, have joined together to create the Encyclopedia of Life (EOL). The EOL will dynamically synthesize biodiversity knowledge about all known species, including their taxonomy, geographic distribution, specimens in collections, genetics, evolutionary history, morphology, behavior, ecological relationships, and importance for human well-being, and distribute this information freely through the Internet. It will serve as a primary resource for a wide audience that includes scientists, natural resource managers, conservationists, teachers, and students around
Cranial skeletal morphology, ontogeny and variation are examined in five species of Thorim, a gen... more Cranial skeletal morphology, ontogeny and variation are examined in five species of Thorim, a genus of diminutive plethodontid salamanders that are among the smallest, extant, tailed tetrapods. The akull of adult 'Thhoriu ~ is characterized by: (1) limited development or absence of several ossified clemrnts and dentition; (2) increased inter- and intraspecifir variability; (3) novel morphological ronfigurations of the braincase and jaw suspensorium. Posthatching cranial mineralization in all spccies or 'Thorzus is truncated precociously with respect to that typical of larger and more generalized plethodontid genera, such as Pseudoeurycea. These features implicate paedomorphosis as a predominant mechanism responsihle for the evolution of decreased size in Thorim from larger plethodontid ancestors. lntcrspecific differences in cranial morphology are evident; species may be characterized by greater or lesser degrees of truncated development. However, there is no consistent re...
Direct development is a widespread alternate reproductive mode in living amphibians that is chara... more Direct development is a widespread alternate reproductive mode in living amphibians that is characterized by evolutionary loss of the free-living, aquatic larval stage. Courtship, mating, and oviposition occur on land, and the terrestrial egg hatches as a fully formed, miniature adult. While it is the most common reproductive mode in urodeles, development outside the reproductive tract of the female that proceeds directly to a terrestrial hatchling occurs in only a single lineage, the lungless salamanders of the family Plethodontidae. Evolution of direct development in plethodontids has contributed importantly to the extraordinary evolutionary success of this speciose, geographically widespread, and morphologically and ecologically diverse taxon. Developmental consequences and correlates include increased egg size and embryonic development time, loss of larval structures and ontogenetic repatterning, and altered pattern formation in organogenesis. Evolutionary and phylogenetic conse...
Development, 1998
Variation in segment number is an important but neglected feature of vertebrate evolution. Some v... more Variation in segment number is an important but neglected feature of vertebrate evolution. Some vertebrates have as few as six trunk vertebrae, while others have hundreds. We examine this phenomenon in relation to recent models of evolution and development. Surprisingly, differences in vertebral number are foreshadowed by different somite counts at the tailbud stage, thought to be a highly conserved (phylotypic) stage. Somite number therefore violates the ‘developmental hourglass’ model. We argue that this is because somitogenesis shows uncoupling or dissociation from the conserved positional field encoded by genes of the zootype. Several other systems show this kind of dissociation, including limbs and feathers. Bmp-7 expression patterns demonstrate dissociation in the chick pharyngeal arches. This makes it difficult to recognise a common stage of pharyngeal development or ‘pharyngula’ in all species. Rhombomere number is more stable during evolution than somite number, possibly be...
Biodiversity Information Science and Standards, 2018
As curators of biodiversity data in natural science collections, we are deeply concerned with dat... more 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 are in the collections, where are they and where are they from. Some research uses aggregate data across collections, which involves exchange of data using standard vocabularies. Some research uses require accurate georeferences, collecting dates, and current identifications. It is well understood that the costs of data capture and data quality improvement increase with increasing time from the original observation. These factors point towards two engineering principles for software that is intended to maintain or enhance data quality: build small modular data quality tests that can be easily assembled in suites to assess the fitness of u...
Proceedings of the National Academy of Sciences, 2020
Developmental novelties often underlie the evolutionary origins of key metazoan features. The anu... more 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 and a hypochord. The coccyx forms by fusion of caudal vertebrae and has evolved repeatedly across vertebrates. However, the contribution of an ossifying hypochord to the coccyx in anurans is unique among vertebrates and remains a developmental enigma. Here, we focus on the developmental changes that lead to the anuran urostyle, with an emphasis on understanding the ossifying hypochord. We find that the coccyx and hypochord have two different developmental histories: First, the development of the coccyx initiates before metamorphic climax whereas the ossifying hypochord undergoes rapid ossification and hypertrophy; second, thyroid hormone di...
Journal of anatomy, Jan 25, 2016
Nearly two thirds of the approximately 700 species of living salamanders are lungless. These spec... more 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 is presumably little need for an atrial septum in lungless salamanders due to the absence of pulmonary veins and the presence of a single source of mixed blood flowing into the heart, but whether lungless salamanders possess an atrial septum and whether the sinoatrial aperture is located in the left or right atrium are unresolved; authors have stated opposing claims since the late 1800s. Here, we use micro-computed tomography (μ-CT) imaging, gross dissection and histological reconstruction to compare cardiac morphology among lungless plethodontid salamanders (Plethodontidae), salamanders with lungs, and the convergently lungless species O...
Royal Society Open Science, 2016
Bones of the cranial vault appear to be highly conserved among tetrapod vertebrates. Moreover, bo... more 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 birds, thereby challenging this view. In the mouse, the frontal is derived from cranial neural crest (CNC) but the parietal is derived from mesoderm, placing the CNC–mesoderm boundary at the suture between these bones. In the chicken, this boundary is located within the frontal. This difference and related data have led several recent authors to suggest that bones of the avian cranial vault are misidentified and should be renamed. To elucidate this apparent conflict, we fate-mapped CNC and mesoderm in axolotl to reveal the contributions of these two embryonic cell populations to the cranial vault in a urodele amphibian. The CNC–mesoderm bounda...
eLife, Jan 19, 2016
Vertebrate neck musculature spans the transition zone between head and trunk. The extent to which... more Vertebrate neck musculature spans the transition zone between head and trunk. The extent to which the cucullaris muscle is a cranial muscle allied with the gill levators of anamniotes or is instead a trunk muscle is an ongoing debate. Novel computed tomography datasets reveal broad conservation of the cucullaris in gnathostomes, including coelacanth and caecilian, two sarcopterygians previously thought to lack it. In chicken, lateral plate mesoderm (LPM) adjacent to occipital somites is a recently identified embryonic source of cervical musculature. We fate-map this mesoderm in the axolotl (Ambystoma mexicanum), which retains external gills, and demonstrate its contribution to posterior gill-levator muscles and the cucullaris. Accordingly, LPM adjacent to the occipital somites should be regarded as posterior cranial mesoderm. The axial position of the head-trunk border in axolotl is congruent between LPM and somitic mesoderm, unlike in chicken and possibly other amniotes.
PloS one, 2016
The Indian Purple frog, Nasikabatrachus sahyadrensis, occupies a basal phylogenetic position amon... more 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 these shifts in habits and habitats, and especially the internal remodeling of the cranial and postcranial skeleton, are unknown. Using a nearly complete metamorphic series from free-living larva to metamorph, we describe the postembryonic skeletal ontogeny of this ancient and unique monotypic lineage. The torrent-dwelling larva possesses a dorsoventrally flattened body and a head with tiny dorsal eyes, robust lower and upper jaw cartilages, well-developed trabecular horns, and a definable gap between the trabecular horns and the tip of the snout. Unlike tadpoles of many other frogs, those of Nasikabatrachus retain larval mouthparts into lat...
The Bulletin of zoological nomenclature., 1988
The purpose of this application is to conserve the specific name pennatulus Cope, 1869 for the Me... more The purpose of this application is to conserve the specific name pennatulus Cope, 1869 for the Mexican salamander Thorius pennatulus. The name first appeared (about one month earlier) as pennatribus , probably due to a spelling error.
Integrative and Comparative Biology
The pharyngeal−arch skeleton is a hallmark of vertebrates. In basal taxa, it supports the gills a... more 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 result has since been confirmed in additional species. Yet, the evolution and extent of neural crest contributions to the pharyngeal skeleton is incompletely understood. In this study, we fate map neural crest in the axolotl, Ambystoma mexicanum, using transplantations from GFP−transgenic donors into wild−type hosts. We found that neural crest does not contribute to all elements of the pharyngeal skeleton: the ventral midline element basibranchial 2 was never labeled. Based on this result we also constructed a fate map of cranial mesoderm. Our results positively demonstrate for the first time a mesodermal contribution to the pharyngeal skelet...
Evolution & Development, 2015
General and comparative endocrinology, Jan 5, 2015
Direct-developing frogs lack, wholly or in part, a wide range of larval features found in metamor... more Direct-developing frogs lack, wholly or in part, a wide range of larval features found in metamorphosing species and form adult-specific features precociously, during embryogenesis. Most information on thyroid regulation of direct development relies on hormone manipulations; the ontogeny of many thyroid axis components has not been fully described. This analysis examines differentiation of the median eminence of the hypothalamus and production of thyroid-stimulating hormone (TSH) by the pituitary of the direct-developing frog Eleutherodactylus coqui. The median eminence is established two-thirds of the way through embryogenesis. Cells immunoreactive to human TSHβ antibodies are first detected during embryogenesis and quantitative changes in TSHβ-IR cells resemble those in metamorphosing amphibians. Formation of the median eminence of the hypothalamus and TSHβ production by the pituitary precede or coincide with morphological changes during embryogenesis that occur during metamorphos...
BioScience, Aug 2014
There is an emerging consensus that undergraduate biology education in the United States is at a ... more 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.