Distinguishing intraspecific from interspecific variation in the leopard frog species complex

In an era of unprecedented biodiversity loss, the need for standardized practices to describe biological variation is becoming increasingly important. As with all scientific endeavors, species delimitation needs to be explicit, testable, and refutable. A fundamental task in species delimitation is distinguishing within-species variation from among-species variation. Many species that are distributed across large geographic areas exhibit levels of genetic variation that are as great or greater than those that exist between well-defined sympatric species. Here, we provide a workflow to distinguish between intra- and interspecific genetic variation and apply the workflow to a taxonomically problematic group of frogs (the Rana pipiens complex, or leopard frogs) that are widely distributed across Mexico and Central America. Our workflow makes use of recent advancements that pair genome-scale datasets with model-based species delimitation methods, while emphasizing the need for positive evide..., Samples: 25 species (+ 8 undescribed species) of leopard frogs (n=510) and 4 species of outgroup frogs (n=17); total number of samples = 527
Sequencing: ddRAD for all samples (demultiplexed fastq files available on SRA, accession number: PRJNA1233814)
Bioinformatics assembly: iPyrad 
Analyses: Phylogenetic tree reconstruction (RAxML-ng), population genetic structure (admixture), species delimitation (HHSD), landscape genomics (GDM and MMRR), and gene flow (FEEMS), , # Distinguishing intraspecific from interspecific variation in the leopard frog species complex

This repository contains data files for:

**Chambers EA, Lara-Tufiño JD, Campillo-García G, Cisneros-Bernal AY, Dudek Jr. DJ, León-Règagnon V, Townsend JH, Flores-Villela O, & Hillis DM. (XXX) Distinguishing species boundaries from geographic variation. *XXX*, [DOI](LINKTODOI).**

This paper provides a suggested framework for testing whether genetic variation arises through species boundaries or intraspecific geographic variation and focuses on species in the leopard frog species complex (*Rana pipiens*) in Mexico and Central America. All raw data and input files can be found on Dryad, and raw, demultiplexed fastqs can be found on SRA (BioProject PRJNA1233814). All scripts can also be found on GitHub [here](https://github.com/eachambers/pantherana).

## DRYAD FILES: DATA FILES

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### Naming Conventions

* **METHOD**: File or directory names contain \"rana_n-1\" or \"pooled\" to denote pooled ...,