Data for: Genetic structuring and species boundaries in the Atlantic stony coral Favia (Scleractinia, Faviidae)

Scleractinian corals are the main modern builders of coral reefs, dynamic ecosystems that are hot spots of marine biodiversity. Southern Atlantic reef corals are understudied compared to their Caribbean and Indo-Pacific counterparts and many hypotheses about their population dynamics demand further testing. We employed thousands of single nucleotide polymorphisms (SNPs) recovered via ezRAD to characterize genetic population structuring and species boundaries in the amphi-Atlantic hard coral genus Favia. Coalescent-based species delimitation (BFD* - Bayes factor delimitation) recovered F. fragum and F. gravida as separate species. Although our results agree with depth-related genetic structuring in F. fragum, they did not support incipient speciation of the “tall\" and “short” morphotypes. The preferred scenario revealed a split between two main lineages of F. gravida, one from Ascension Island and the other from Brazil. The Brazilian lineage is further divided into a species that occurs ..., DNA was extracted from tissue samples of F. fragum using the Omega E.Z.N.A Tissue DNA kit and Invitrogen PureLink Genomic DNA kit. Extractions were purified using 1.8X AmPureXP magnetic beads. DNA quality was assessed via electrophoresis in 1.5% agarose gel, ensuring that only high molecular weight DNA was carried over to the digestion step. Quantification was performed using a Qubit 2 Fluorometer and the dsDNA High Sensitivity Assay kit. Libraries were prepared following the ezRAD protocol (Toonen et al. 2013). Briefly, samples were digested using the enzyme DpnII (New England Biolabs), in 50μL reactions containing 5μL DpnII NEB 10X Buffer, 2 units of DpnII, and 200-1000ng of DNA. Digestions were incubated at 37°C for 3 hours, then heat-inactivated for 20 minutes at 65°C, purified using 1.8X AMPureXP beads, run in 1.5% agarose gels and considered successful if producing a smeared band. Library preparation began with the KAPA HyperPrep Library kit (Roche Sequencing Store) following Knap..., , # Title of dataset: **Genetic structuring and species boundaries in the Atlantic stony coral *Favia* (Scleractinia, Faviidae)**

Authors: Carolina de Lima Adam, Robert J. Toonen, David B. Carlon, Carla Zilberberg, Marcos Soares Barbeitos

Corresponding author information:

* Carolina de Lima Adam

* Current Institution address: University of Oregon

* Email: [[e-mail]](mailto:carolinaladam@gmail.c)

This README file describes the data collection and the data package accompanying the above publication.

Date of collection: *F. gravida* (Ascension Island - 6 individuals; Brazil - 47 individuals); *F. fragum* (Caribbean - 16 individuals)

## File list

1. TotalRawSNPs.vcf
2. favia_coral_20missing.vcf
3. popmap.csv
4. *.R files:

## Description of individual files

TotalRawSNPs.vcf

* Variant Call File (VCF) with raw single nucleotide polymorphisms (SNP) for each individual in the dataset
* File obtained with dDocent with the following parameters:

* ...