Tools for amphibian research
Enhancing resources, training, collaboration, and diversity within the community of researchers using non-traditional research organisms.
Tools
Our goal is create open-access tools that enable researchers to investigate a range of questions in molecular, organismal, and evolutionary biology while maintaining a firm commitment to biological diversity in research organisms.
Behavior
Home security cameras for ectotherm behavior
Reliably capturing transient animal behavior in the field and laboratory remains a logistical and financial challenge, especially for small ectotherms. Here, we present a camera system that is affordable, accessible, and suitable to monitor small, cold-blooded animals historically overlooked by commercial camera traps, such as small amphibians.
This setup is published in Goolsby et al, Home security cameras as a tool for behavior observations and science equity. Preprint DOI: 10.1101/2023.04.17.537238
You can find instructions for the setup in multiple languages on our GitHub and instructions on adjusting the focus of Wyze cameras in this protocol.
A simple phototaxis assay for aquatic larvae
Phototaxis assays are utilized throughout neuroscience research to measure exploratory behaviors and visual capabilities. Here we detail a simple and low cost phototaxis assay for aquatic larvae. This assay is useful for behavior assays in laboratory settings and undergraduate teaching laboratories where student can gather data in real time in a relatively-high throughput manner.
This assay is published in Butler et al., Tadpoles rely on different sensory modalities for communication throughout development. Preprint DOI: 10.1101/2022.10.18.512729
This assay was used in a Course Undergraduate Research Experience (CURE) and published with all students as coauthors in Adebogun GT, et al. 2023. PMID: 36824381.
Poison frog tadpole ethogram
Tadpoles display a rich array of behaviors. This ethogram was developed and illustrated by Dr. Julie Butler and is available as supplementary materials in Butler et al., Tadpoles rely on different sensory modalities for communication throughout development. Preprint DOI: 10.1101/2022.10.18.512729
Functional genomics
Tissue-specific expression of plasmid DNA
Expressing exogenous genes with temporal and spatial specificity is a challenge with unusual research organisms. Here we detail how to express exogenous genes from the electroporation of plasmids into the brain and muscle of poison frog tadpoles. This protocol is useful for expressing fluorescent reporters and other genes of interest.
This protocol is published in Delia, et al. 2023. Tissue-specific in vivo transformation of plasmid DNA in Neotropical tadpoles using electroporation. PMID: 37590232.
Using morpholinos to knockdown proteins
Knocking down the abundance of proteins of interest is important for functionally testing their role in biological processes. Here we detail how to use morpholinos to knockdown protein abundance in tadpole brain tissue. We also present a relatively inexpensive semi-quantitive dot blot method for assessing protein knockdown. This manuscript is currently in revision, but the protocol is already available on protocols.io. Ludington SC, Butler JM, Golde C, O'Connell LA. 2023.
Genomes
Frog genomes
Brilliant thighed poison frog (Allobates femoralis)
Behavior: flexible parental care, territorial males, social tadpoles
Physiology: not chemically defended
Status: NCBI GCA_033576535.1
Publication: writing in progress
Fleischmann's glass frog (Hyalinobatrachium fleischmanni)
Behavior: male parental care via egg guarding
Physiology: ventral transparency
Status: available on Data Dryad
Publication: writing in progress
Golden mantella (Mantella aurantiaca)
Behavior: group living seasonal breeders
Physiology: chemically defended
Status: NCBI PRJNA974478
Publication: writing in progress, which will include annotation
Diablito poison frog (Oophaga sylvatica)
Behavior: female parental care, begging tadpoles, territorial males
Physiology: chemically defended, polymorphic coloration
Status: NCBI GCA_033576555.1
Publication: writing in progress
Golden poison frog (Phyllobates terribilis)
Behavior: male parental care, tadpoles show high behavioral plasticity
Physiology: chemically defended with batrachotoxin, bright coloration
Status: sequencing complete, currently annotating
Publication: coming after assembly completion
Mimetic poison frog (Ranitomeya imitator)
Behavior: biparental and monogamous adults, begging and aggressive tadpoles
Physiology: chemically defended, Müllarian mimic
Status: NCBI GCA_032444005.1, GenomeArk
Publication: in concert with evolution of monogamy study
Zimmerman's poison frog (Ranitomeya variabilis)
Behavior: male parental care, aggressive tadpoles
Physiology: chemically defended, polymorphic coloration
Status: sequencing in progress
Publication: in concert with evolution of monogamy study
Other animal genomes
Threadfin butterflyfish (Chaetodon auriga)
Behavior: monogamous, no parental care
Physiology: corallivore
Status: sequencing ongoing
Publication: in concert with evolution of monogamy study
Cheveron butterflyfish (Chaetodon trifascialis)
Behavior: polygamous, no parental care
Physiology: corallivore
Status: annotation in progress. GenomeArk.
Publication: in concert with evolution of monogamy study
King quail (Coturnix chinensis)
Behavior: monogamous
Physiology: polymorphic coloration, used in aviculture
Status: annotation in progress. GenomeArk.
Publication: in concert with evolution of monogamy study
Wolf spider (Hogna lenta)
Behavior: burrowing, female parental care
Physiology: moms do not eat during parental care
Status: complete, upload to NCBI will start soon
Publication: will start writing soon
Common blue tongue skink (Tiliqua scincoides)
Behavior: polygamous, long lived
Physiology: live bearing, blue tongue
Status: NCBI PRJNA1061193; GenomeArk
Publication: in concert with evolution of monogamy study
Finstripe goatfish (Upeneus taeniopterus)
Behavior: lives in reefs
Physiology: possesses hallucinogenic compounds that induce nightmares
Status: complete, upload to NCBI will start soon
Publication: will start writing soon
Other resources
Chemical ecology in the classroom
We developed a Course Undergraduate Research Experience (CURE) utilizing Caenorhabditis elegans chemotaxis assays to test how ant compounds are detected by heterospecific nervous systems. These experiments can be conducted in an undergraduate laboratory course, where new insights into interspecies interactions can be generated through genuine research experiences in a classroom setting.
This assay is used in BIO161: Organismal Biology Lab and has resulted in several peer-reviewed publications with all students as coauthors. PMIDs: 38596360, 37008729, 32550506
Growing up frog skin microbes
Frog skin microbes are critical for many host physiological process and can also protect the host from disease. How to grow up skin microbes from terrestrial frogs is detailed in Caty SN, et al. A toxic environment selects for specialist microbiome in poison frogs. Preprint DOI: 10.1101/2024.01.10.574901v1
Staging guide for poison frog tadpoles
Staging guide for Ranitomeya imitator tadpoles. Published as supplementary materials in Butler JM, et al. Tadpoles rely on different sensory modalities for communication throughout development. Preprint DOI: 10.1101/2022.10.18.512729