Tools for amphibian research

Enhancing resources, training, collaboration, and diversity within the community of researchers using non-traditional research organisms.

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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.

protocol

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.

protocol

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. 

protocol

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

 

protocol

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

protocol

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