The genomics of mimicry: Gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system

A common goal in evolutionary biology is to discern the mechanisms that produce the astounding diversity of morphologies seen across the tree of life. Aposematic species, those with a conspicuous phenotype coupled with some form of defense, are excellent models to understand the link between vivid color pattern variations, the natural selection shaping it, and the underlying genetic mechanisms underpinning this variation. Mimicry systems in which species share a conspicuous phenotype can provide an even better model for understanding the mechanisms of color production in aposematic species, especially if comimics have divergent evolutionary histories. Here we investigate the genetic mechanisms by which mimicry is produced in poison frogs. We assembled a 6.02 Gbp genome with a contig N50 of 310 Kbp, a scaffold N50 of 390 Kbp, and 85% of expected tetrapod genes. We leveraged this genome to conduct gene expression analyses throughout development of four color morphs of R. imitator and two ..., Gene expression sample preparation:
                Samples were prepared differently for the mimic (R. imitator) and the model species (R. fantastica and R. variabilis). During the course of our work, we discovered that there were multiple groups approaching the same questions using collected samples from different species, but at slightly different timepoints. In light of this, we chose to combine our efforts into a single manuscript in an attempt at making broader inferences. We acknowledge this, and as a result, the data in this manuscript are analyzed in a manner concordant with these differences.
Ranitomeya imitator:
The initial breeding stock of Ranitomeya imitator was purchased from Understory Enterprises, LLC (Chatham, Canada). Frogs used in this project represent captive-bred individuals sourced from the following wild populations going clockwise from top left in Figure 1: Tarapoto (green-spotted), Sauce (orange-banded), Varadero (redheaded), and Baja Huallaga (yellow-striped)..., , # The genomics of mimicry: gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system

[https://doi.org/10.5061/dryad.gtht76hvp](https://doi.org/10.5061/dryad.gtht76hvp)

## Description of the data

The data in this dataset are gene count files of gene expression in the skin for individual frogs. Files are named using this scheme: \"Genus abbreviation_specific epithet_morph name_age in weeks_unique identifier.gene.counts\". So for example, file \"R_fantastica_banded_8_M15_088_L2.gene.counts\" refers to an *R. fantastica *individual of the banded population that was 8 weeks old. Files are tab-delimited and contain two columns, one for the transcript ID from our annotation, and a second of the number of counts of that particular gene. Genomic data are on the European Nucleotide Archive under accession PRJEB28312. The methods describe how data was collected and processed.

## Code

Code is available on [Zenodo.](https://zeno...