Numerous physiological and morphological adaptations were achieved during the transition to lungl... more 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 lungless salamanders express in the larval integument and the adult buccopharynx—principal sites of respiratory gas exchange in these species—a novel paralogue of the gene surfactant-associated protein C (SFTPC), which is a critical component of pulmonary surfactant expressed exclusively in the lung in other vertebrates. The paralogous gene appears to be found only in salamanders, but, similar to SFTPC, in lunged salamanders it is expressed only in the lung. This heterotopic gene expression, combined with predictions from structural modelling and respiratory tissue ultrastructure, suggests that lungless salamanders may produce pulmonary surfactant-like secretions outside the lungs and that the novel paralogue of SFTPC might facilitate extrapulmonary respiration in the absence of lungs. Heterotopic expression of the SFTPC paralogue may have contributed to the remarkable evolutionary radiation of lungless salamanders, which account for more than two thirds of urodele species alive today.
In this authoritative three-volume reference work, leading researchers bring together current wor... more In this authoritative three-volume reference work, leading researchers bring together current work to provide a comprehensive analysis of the comparative morphology, development, evolution, and functional biology of the skull.
In the FilteredPush (FP) and Kurator projects we have built tools for quality control of biodiver... more In the FilteredPush (FP) and Kurator projects we have built tools for quality control of biodiversity data. One of these, FP-Akka , is derived from earlier work on the Kepler Kuration package, where, to run data-curation workflows within a FilteredPush node infrastructure, code was refactored into an external service wrapper layer, a data validation logic layer, and a workflow layer that composes elements of the logic layer into actors in a record-centric workflow. The service wrapper layer and data validation layer are packaged in an FP-KurationServices library, which can be composed with Kepler Kuration workflows or with workflows written in the Akka parallelization framework. In developing and maintaining FP-Akka, we encountered multiple challenges arising from the interplay between external services and workflow components: discovery of pertinent services, technical documentation and integration of services, documentation of domain-specific details of assumptions made by the services, the wide variety of technologies used by service providers, and maintenance of our code base in the face of changing services. To find services pertinent to the data-quality needs of the science goals of US Thematic Collections Networks (TCNs)—principally, quality control of scientific names, georeferences, and collecting event dates—we have looked, ad hoc, to the usual suspects for quality data in relevant domains and have done some discovery using The Biodiversity Catalogue service registry. We also wrote a service (for name and date data concerning entomologists) in a case where shallow searching for pertinent services returned no results. Service documentation at the technical level has ranged from Web Services Description Language (WSDL) files from which we could generate code, to example response documents, to none; in the latter case, we simply coded to the observed responses of the service. Much more difficult has been domain concepts documentation, the information needed to tell what assumptions the service provider is making about questions made to the service, and what assumptions are embedded in the responses. In a simple case, such as for a service that provides information related to scientific names, are the responses from the service making nomenclatural assertions, taxonomic assertions, or a mixture of both? Also relevant to understanding of service use is how clean and authoritative is the dataset behind the service, and, when quality varies in a dataset, presence of row-level assertions about data quality. Biodiversity-related service implementations use a wide variety of exchange technologies, in effect requiring consumers to do something different for each service we interact with, thus each component in our service-wrapper layer is wholly different from the others. The combination of different technologies for services and different domain assumptions made by similar services have combined to make it difficult for us to cleanly write a layer containing our validation logic and compose this with a layer that abstracts services. Instead, we have had to bring some of the logic dealing with the differing assumptions of different services down into the service-wrapper layer. To maintain the code, we responded to both documented and silent changes to service Application Programming Interfaces (APIs). In order to detect API changes that would cause our code to fail, we have unit tests that query the services. This has created challenges for our development framework, as when a service has a transient outage, builds that run these tests fail (and, in the case of automated build systems, tend not to leave clear traces of failure causes). Our single largest challenge has not been technological, but social: to understand the domain-specific assumptions of biodiversity data service providers.
The Kurator project aims to facilitate the development, documentation, and efficient execution of... more The Kurator project aims to facilitate the development, documentation, and efficient execution of scripts and workflows for cleaning biodiversity data. Kurator tools under development and available as prototypes in the Kurator GitHub repositories ( http://github.com/kurator-org/ ) support traditional scripting as well as high-performance, actor-oriented workflow approaches to validating, annotating, and cleaning data. The Kurator-Akka framework ( http://github.com/kurator-org/kurator-akka ) makes it easy to develop and run high-performance data cleaning workflows that employ the Akka actor toolkit by shielding actor developers and workflow users alike from the complexities of the Akka API (application programming interface). Kurator-Akka actors currently can be written either in Python or Java, and workflows may be specified using a language based on YAML (YAML Ain't Markup Language) that defines how data flows between the actors at run time. A workflow can be composed from existing actors by editing a simple text file and subsequently executed by providing this file to the Kurator-Akka workflow runtime. Actors in a Kurator-Akka workflow execute concurrently in different threads, potentially yielding pipeline parallelism and thus higher throughput than is achievable in conventional scripts. Recognizing that conventional scripts written, for example, in Bash, Python or R, also represent an effective means of automating data cleaning workflows, Kurator is leading an interdisciplinary effort to develop the YesWorkflow toolkit ( http://yesworkflow.org/yw ). YesWorkflow (YW) aims to provide many of the benefits of using a scientific workflow management system without having to rewrite scripts for execution within a workflow engine. Instead, a YesWorkflow user simply adds special YesWorkflow comments to existing scripts. These comments declare how data is used and results produced, step by step, by the script. The YesWorkflow tools interpret the YW comments and produce graphical output that reveals the stages of computation and the flow of data in the script. A means for reconstructing and querying the provenance of the outputs of a script marked up with YesWorkflow annotations is currently under development. Because scripts marked up with YesWorkflow annotations may be used as actors in the Kurator-Akka framework, Kurator tools span the scripting and workflow automation paradigms. The Kurator-Validation GitHub repository ( http://github.com/kurator-org/kurator-validation ) provides example scripts, actors, workflows, and documentation that demonstrate how Kurator tools effectively integrate scripting and automated workflow approaches to cleaning biodiversity data. Using a simple Python class that wraps the WoRMS (World Register of Marine Species) web service as a starting point, documentation available in the Kurator-Validation GitHub repository demonstrate (1) how a Python script can make use of this WoRMS service class to validate names against the standard WoRMS taxonomy; (2) how to annotate this script with YesWorkflow comments so the script can be modeled, visualized and analyzed as a workflow; (3) how a Kurator-Akka actor invoking the WoRMS service class can be written in Python; and (4) how a workflow employing this actor can be specified in YAML and executed by the Kurator-Akka framework with each actor running concurrently.
Data cleaning has the potential to improve the chances for people and computers to find and use r... more Data cleaning has the potential to improve the chances for people and computers to find and use relevant data. This is true for researchers as well as for large-scale data aggregators. In the biodiversity realm, Darwin Core provides a convenient scope and framework for data cleaning tools and vocabularies. One way to address data cleaning tasks is to use workflows that act on a combination of original data, controlled vocabularies, algorithms, and services to detect inconsistencies and errors, recommend changes, and augment the original data with improvements and additions. There are advantages from the perspective of flexibility to construct such workflows from specialized, reusable "actors" -- building blocks that do specific tasks, such as provide a list of distinct values of a field in a data set. The Kurator project uses Akka, a Java-based framework to construct workflows with actors written in a variety and even in a combination of programming languages. In this presentation, we will explore the process of building actors and combining them in Akka workflows that do a variety of data cleaning and reporting tasks inspired by the VertNet process of mobilizing data from institutional data sets for large-scale aggregators such as VertNet, iDigBio, and the Global Biodiversity Information Facility. Ultimately, the goal of this work might be, given a biodiversity data set, to provide an improved version of that data set in the form of a Darwin Core archive that includes a data quality extension (not yet developed) to report what was found, what was done to it, and what could still be done to further improve it.
NEW BIOLOGICAL BOOKS 105 conclusion is-oh gosh, sorry, I was thinking of something else and canno... more NEW BIOLOGICAL BOOKS 105 conclusion is-oh gosh, sorry, I was thinking of something else and cannot tell you. Just kidding folks. This is a great little read.
We describe three new species of minute salamanders, genus Thorius, from the Sierra Madre del Sur... more 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., T. longicaudus sp. nov., and T. tlaxiacus sp. nov. are larger than T. minutissimus and possess elliptical rather than oval nostrils; T. pinicola and T. longicaudus also have longer tails. All three new species occur west of the range of T. minutissimus, which has the easternmost distribution of any member of the genus. The new species are distinguished from each other and from other named Thorius in Oaxaca by a combination of adult body size, external morphology and osteology, and by protein characters (allozymes) and differences in DNA sequences. In addition, we redescribe T. minutissimus and a related species, T. narisovalis, to further clarify the taxonomic status of Oaxacan populations and to facilitate future studies of the remaining genetically differentiated Thorius that cannot be satisfactorily assigned to any named species. Populations of all five species considered here appear to have declined dramatically over the last one or two decades and live specimens are difficult to find in nature. Thorius may be the most endangered genus of amphibians in the world. All species may go extinct before the end of this century.
Fundamental aspects of cranial anatomy in vertebrates were resolved initially well before the del... more Fundamental aspects of cranial anatomy in vertebrates were resolved initially well before the delineation and broad acceptance of Darwinian evolution, let alone modern studies of molecular genetics and cell‐lineage analysis and broad recognition of the prominent role of the embryonic neural crest. Contemporary work has validated many classical observations, yet others mandate reassessment and reevaluation of several underlying assumptions and conventions. Head segmentation is perhaps the most classical topic of all. Compelling accounts regarding the nature and extent of head segmentation abound, but the empirical base on which such accounts are grounded is surprisingly thin. We have utilized a novel transgenic line of the clawed frog, Xenopus laevis, to map neural‐crest derivation of the bony adult skull. This method circumvents technical limitations that have hindered previous studies of the embryonic origin of adult‐specific features in frogs, which form first at metamorphosis. Th...
bioRxiv (Cold Spring Harbor Laboratory), Jul 11, 2023
Taxonomic uncertainty at the species level compromises our knowledge of biodiversity, conservatio... more 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 nurse frogAllobates gasconiand infer its phylogenetic relationships. This species was described in 2002 based solely on morphology, but several characters crucial for the reliable diagnosis of species inAllobateswere not considered. Our results show thatA. gasconisensu stricto is not a member of theA. caeruleodactylusclade as previously claimed, but is a member of theA. trilineatusclade.Allobates gasconiis readily distinguished from congeners by a combination of morphological and bioacoustic characters; a revised diagnosis is provided. The type series ofA. gasconicomprises more than one species, and we exclude a paratype from lower Juruá River. The species is restricted geographically to flooded environments in the middle and upper Juruá River in Brazil and in the Ucayali River in Peru. The initial misidentification, subsequent absence of topotypic molecular and acoustic data, and the poor preservation condition of the type series have contributed to taxonomic confusion sinceA. gasconiwas first described. The descriptions of other species ofAllobatespublished more than two decades ago were based mainly on gross morphology and we recommend integrative taxonomic revisions to elucidate their systematics.
bioRxiv (Cold Spring Harbor Laboratory), Apr 8, 2022
Most frogs' diets shift between the larval and adult phases, from a filter-feeding herbivore to a... more 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 frog Lepidobatrachus laevis forgoes this metamorphic shift in feeding mode and instead consumes a bulk-feeding, carnivorous diet both as a larvae and as an adult. This unusual larval diet is enabled by the presence of an adult-like stomach in the tadpole. This study investigates the anatomy and embryonic development of the larval stomach of L. laevis and what, if any, further changes occur during metamorphosis. The histology of embryonic and metamorphic stomach development is compared to that of Xenopus tropicalis, a frog with a typical larval stomach. We find that L. laevis directly forms an adult-like stomach during embryonic development without first forming a larval-like configuration. Moreover, no additional major remodeling of the stomach occurs during metamorphosis, although the stomach does gradually and slightly increase in complexity, proliferating more glands and increasing connective tissue and muscle layers, between hatching and the end of metamorphosis. This developmental trajectory of the stomach in L. laevis corresponds with the megalophagous, carnivorous diet these frogs maintain from tadpole to adult, as well as the maintenance of active feeding throughout metamorphosis. These results will
... range 0.89-1.15). The mental gland is present in large adult males and is round to moderately... more ... range 0.89-1.15). The mental gland is present in large adult males and is round to moderately ellipti-cal (maximum dimensions: 1.0 mm wide, 1.0 mm long). The postiliac gland is prominent ex-ternally. Many specimens have ...
Numerous physiological and morphological adaptations were achieved during the transition to lungl... more 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 lungless salamanders express in the larval integument and the adult buccopharynx—principal sites of respiratory gas exchange in these species—a novel paralogue of the gene surfactant-associated protein C (SFTPC), which is a critical component of pulmonary surfactant expressed exclusively in the lung in other vertebrates. The paralogous gene appears to be found only in salamanders, but, similar to SFTPC, in lunged salamanders it is expressed only in the lung. This heterotopic gene expression, combined with predictions from structural modelling and respiratory tissue ultrastructure, suggests that lungless salamanders may produce pulmonary surfactant-like secretions outside the lungs and that the novel paralogue of SFTPC might facilitate extrapulmonary respiration in the absence of lungs. Heterotopic expression of the SFTPC paralogue may have contributed to the remarkable evolutionary radiation of lungless salamanders, which account for more than two thirds of urodele species alive today.
In this authoritative three-volume reference work, leading researchers bring together current wor... more In this authoritative three-volume reference work, leading researchers bring together current work to provide a comprehensive analysis of the comparative morphology, development, evolution, and functional biology of the skull.
In the FilteredPush (FP) and Kurator projects we have built tools for quality control of biodiver... more In the FilteredPush (FP) and Kurator projects we have built tools for quality control of biodiversity data. One of these, FP-Akka , is derived from earlier work on the Kepler Kuration package, where, to run data-curation workflows within a FilteredPush node infrastructure, code was refactored into an external service wrapper layer, a data validation logic layer, and a workflow layer that composes elements of the logic layer into actors in a record-centric workflow. The service wrapper layer and data validation layer are packaged in an FP-KurationServices library, which can be composed with Kepler Kuration workflows or with workflows written in the Akka parallelization framework. In developing and maintaining FP-Akka, we encountered multiple challenges arising from the interplay between external services and workflow components: discovery of pertinent services, technical documentation and integration of services, documentation of domain-specific details of assumptions made by the services, the wide variety of technologies used by service providers, and maintenance of our code base in the face of changing services. To find services pertinent to the data-quality needs of the science goals of US Thematic Collections Networks (TCNs)—principally, quality control of scientific names, georeferences, and collecting event dates—we have looked, ad hoc, to the usual suspects for quality data in relevant domains and have done some discovery using The Biodiversity Catalogue service registry. We also wrote a service (for name and date data concerning entomologists) in a case where shallow searching for pertinent services returned no results. Service documentation at the technical level has ranged from Web Services Description Language (WSDL) files from which we could generate code, to example response documents, to none; in the latter case, we simply coded to the observed responses of the service. Much more difficult has been domain concepts documentation, the information needed to tell what assumptions the service provider is making about questions made to the service, and what assumptions are embedded in the responses. In a simple case, such as for a service that provides information related to scientific names, are the responses from the service making nomenclatural assertions, taxonomic assertions, or a mixture of both? Also relevant to understanding of service use is how clean and authoritative is the dataset behind the service, and, when quality varies in a dataset, presence of row-level assertions about data quality. Biodiversity-related service implementations use a wide variety of exchange technologies, in effect requiring consumers to do something different for each service we interact with, thus each component in our service-wrapper layer is wholly different from the others. The combination of different technologies for services and different domain assumptions made by similar services have combined to make it difficult for us to cleanly write a layer containing our validation logic and compose this with a layer that abstracts services. Instead, we have had to bring some of the logic dealing with the differing assumptions of different services down into the service-wrapper layer. To maintain the code, we responded to both documented and silent changes to service Application Programming Interfaces (APIs). In order to detect API changes that would cause our code to fail, we have unit tests that query the services. This has created challenges for our development framework, as when a service has a transient outage, builds that run these tests fail (and, in the case of automated build systems, tend not to leave clear traces of failure causes). Our single largest challenge has not been technological, but social: to understand the domain-specific assumptions of biodiversity data service providers.
The Kurator project aims to facilitate the development, documentation, and efficient execution of... more The Kurator project aims to facilitate the development, documentation, and efficient execution of scripts and workflows for cleaning biodiversity data. Kurator tools under development and available as prototypes in the Kurator GitHub repositories ( http://github.com/kurator-org/ ) support traditional scripting as well as high-performance, actor-oriented workflow approaches to validating, annotating, and cleaning data. The Kurator-Akka framework ( http://github.com/kurator-org/kurator-akka ) makes it easy to develop and run high-performance data cleaning workflows that employ the Akka actor toolkit by shielding actor developers and workflow users alike from the complexities of the Akka API (application programming interface). Kurator-Akka actors currently can be written either in Python or Java, and workflows may be specified using a language based on YAML (YAML Ain't Markup Language) that defines how data flows between the actors at run time. A workflow can be composed from existing actors by editing a simple text file and subsequently executed by providing this file to the Kurator-Akka workflow runtime. Actors in a Kurator-Akka workflow execute concurrently in different threads, potentially yielding pipeline parallelism and thus higher throughput than is achievable in conventional scripts. Recognizing that conventional scripts written, for example, in Bash, Python or R, also represent an effective means of automating data cleaning workflows, Kurator is leading an interdisciplinary effort to develop the YesWorkflow toolkit ( http://yesworkflow.org/yw ). YesWorkflow (YW) aims to provide many of the benefits of using a scientific workflow management system without having to rewrite scripts for execution within a workflow engine. Instead, a YesWorkflow user simply adds special YesWorkflow comments to existing scripts. These comments declare how data is used and results produced, step by step, by the script. The YesWorkflow tools interpret the YW comments and produce graphical output that reveals the stages of computation and the flow of data in the script. A means for reconstructing and querying the provenance of the outputs of a script marked up with YesWorkflow annotations is currently under development. Because scripts marked up with YesWorkflow annotations may be used as actors in the Kurator-Akka framework, Kurator tools span the scripting and workflow automation paradigms. The Kurator-Validation GitHub repository ( http://github.com/kurator-org/kurator-validation ) provides example scripts, actors, workflows, and documentation that demonstrate how Kurator tools effectively integrate scripting and automated workflow approaches to cleaning biodiversity data. Using a simple Python class that wraps the WoRMS (World Register of Marine Species) web service as a starting point, documentation available in the Kurator-Validation GitHub repository demonstrate (1) how a Python script can make use of this WoRMS service class to validate names against the standard WoRMS taxonomy; (2) how to annotate this script with YesWorkflow comments so the script can be modeled, visualized and analyzed as a workflow; (3) how a Kurator-Akka actor invoking the WoRMS service class can be written in Python; and (4) how a workflow employing this actor can be specified in YAML and executed by the Kurator-Akka framework with each actor running concurrently.
Data cleaning has the potential to improve the chances for people and computers to find and use r... more Data cleaning has the potential to improve the chances for people and computers to find and use relevant data. This is true for researchers as well as for large-scale data aggregators. In the biodiversity realm, Darwin Core provides a convenient scope and framework for data cleaning tools and vocabularies. One way to address data cleaning tasks is to use workflows that act on a combination of original data, controlled vocabularies, algorithms, and services to detect inconsistencies and errors, recommend changes, and augment the original data with improvements and additions. There are advantages from the perspective of flexibility to construct such workflows from specialized, reusable "actors" -- building blocks that do specific tasks, such as provide a list of distinct values of a field in a data set. The Kurator project uses Akka, a Java-based framework to construct workflows with actors written in a variety and even in a combination of programming languages. In this presentation, we will explore the process of building actors and combining them in Akka workflows that do a variety of data cleaning and reporting tasks inspired by the VertNet process of mobilizing data from institutional data sets for large-scale aggregators such as VertNet, iDigBio, and the Global Biodiversity Information Facility. Ultimately, the goal of this work might be, given a biodiversity data set, to provide an improved version of that data set in the form of a Darwin Core archive that includes a data quality extension (not yet developed) to report what was found, what was done to it, and what could still be done to further improve it.
NEW BIOLOGICAL BOOKS 105 conclusion is-oh gosh, sorry, I was thinking of something else and canno... more NEW BIOLOGICAL BOOKS 105 conclusion is-oh gosh, sorry, I was thinking of something else and cannot tell you. Just kidding folks. This is a great little read.
We describe three new species of minute salamanders, genus Thorius, from the Sierra Madre del Sur... more 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., T. longicaudus sp. nov., and T. tlaxiacus sp. nov. are larger than T. minutissimus and possess elliptical rather than oval nostrils; T. pinicola and T. longicaudus also have longer tails. All three new species occur west of the range of T. minutissimus, which has the easternmost distribution of any member of the genus. The new species are distinguished from each other and from other named Thorius in Oaxaca by a combination of adult body size, external morphology and osteology, and by protein characters (allozymes) and differences in DNA sequences. In addition, we redescribe T. minutissimus and a related species, T. narisovalis, to further clarify the taxonomic status of Oaxacan populations and to facilitate future studies of the remaining genetically differentiated Thorius that cannot be satisfactorily assigned to any named species. Populations of all five species considered here appear to have declined dramatically over the last one or two decades and live specimens are difficult to find in nature. Thorius may be the most endangered genus of amphibians in the world. All species may go extinct before the end of this century.
Fundamental aspects of cranial anatomy in vertebrates were resolved initially well before the del... more Fundamental aspects of cranial anatomy in vertebrates were resolved initially well before the delineation and broad acceptance of Darwinian evolution, let alone modern studies of molecular genetics and cell‐lineage analysis and broad recognition of the prominent role of the embryonic neural crest. Contemporary work has validated many classical observations, yet others mandate reassessment and reevaluation of several underlying assumptions and conventions. Head segmentation is perhaps the most classical topic of all. Compelling accounts regarding the nature and extent of head segmentation abound, but the empirical base on which such accounts are grounded is surprisingly thin. We have utilized a novel transgenic line of the clawed frog, Xenopus laevis, to map neural‐crest derivation of the bony adult skull. This method circumvents technical limitations that have hindered previous studies of the embryonic origin of adult‐specific features in frogs, which form first at metamorphosis. Th...
bioRxiv (Cold Spring Harbor Laboratory), Jul 11, 2023
Taxonomic uncertainty at the species level compromises our knowledge of biodiversity, conservatio... more 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 nurse frogAllobates gasconiand infer its phylogenetic relationships. This species was described in 2002 based solely on morphology, but several characters crucial for the reliable diagnosis of species inAllobateswere not considered. Our results show thatA. gasconisensu stricto is not a member of theA. caeruleodactylusclade as previously claimed, but is a member of theA. trilineatusclade.Allobates gasconiis readily distinguished from congeners by a combination of morphological and bioacoustic characters; a revised diagnosis is provided. The type series ofA. gasconicomprises more than one species, and we exclude a paratype from lower Juruá River. The species is restricted geographically to flooded environments in the middle and upper Juruá River in Brazil and in the Ucayali River in Peru. The initial misidentification, subsequent absence of topotypic molecular and acoustic data, and the poor preservation condition of the type series have contributed to taxonomic confusion sinceA. gasconiwas first described. The descriptions of other species ofAllobatespublished more than two decades ago were based mainly on gross morphology and we recommend integrative taxonomic revisions to elucidate their systematics.
bioRxiv (Cold Spring Harbor Laboratory), Apr 8, 2022
Most frogs' diets shift between the larval and adult phases, from a filter-feeding herbivore to a... more 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 frog Lepidobatrachus laevis forgoes this metamorphic shift in feeding mode and instead consumes a bulk-feeding, carnivorous diet both as a larvae and as an adult. This unusual larval diet is enabled by the presence of an adult-like stomach in the tadpole. This study investigates the anatomy and embryonic development of the larval stomach of L. laevis and what, if any, further changes occur during metamorphosis. The histology of embryonic and metamorphic stomach development is compared to that of Xenopus tropicalis, a frog with a typical larval stomach. We find that L. laevis directly forms an adult-like stomach during embryonic development without first forming a larval-like configuration. Moreover, no additional major remodeling of the stomach occurs during metamorphosis, although the stomach does gradually and slightly increase in complexity, proliferating more glands and increasing connective tissue and muscle layers, between hatching and the end of metamorphosis. This developmental trajectory of the stomach in L. laevis corresponds with the megalophagous, carnivorous diet these frogs maintain from tadpole to adult, as well as the maintenance of active feeding throughout metamorphosis. These results will
... range 0.89-1.15). The mental gland is present in large adult males and is round to moderately... more ... range 0.89-1.15). The mental gland is present in large adult males and is round to moderately ellipti-cal (maximum dimensions: 1.0 mm wide, 1.0 mm long). The postiliac gland is prominent ex-ternally. Many specimens have ...
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Papers by James Hanken