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.  bioRxiv preprint: 10.1101/2023.04.17.537238

You can find instructions for the setup in multiple languages on our GitHub.

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., Development of the visual system in social poison frog tadpoles. bioRxiv preprint: 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. Albino Xenopus tadpoles prefer dark environments compared to wild type. microPublication Biology. 10.17912/micropub.biology.000750.

protocol

Functional genomics

Tissue-specific expression of plasmid DNA

Delia J, Gaines-Richardson M, Ludington SC, Akbari N, Vasek C, Shaykevich D, O'Connell LA. 2023. Tissue-specific in vivo transformation of plasmid DNA in Neotropical tadpoles using electroporation. PLoS ONE 18(8):e0289361

protocol

Using morpholinos to knockdown proteins

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: complete, uploading to 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

Growing up frog skin microbes

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. bioRxiv preprint: 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. Development of the visual system in social poison frog tadpoles. bioRxiv preprint: 10.1101/2022.10.18.512729