Date: 6 November, 2018

Title: Geographic distributions, phenotypes, and phylogenetic relationships of Phalloceros (Cyprinodontiformes: Poeciliidae): insights about diversification among sympatric species pools.
Authors: Andréa T. Thomaz, Tiago P. Carvalho, Luiz R. Malabarba, L. Lacey Knowles
Contact: Andrea T Thomaz thomaz@umich.edu

Key Points:
- ddRAD data input files used to reconstruct the phylogenetic relationships in Phalloceros
- phylogenetic reconstructions in Phalloceros

Research Overview:
Estimated phylogenetic relationships based on more than 18,000 loci 
in 93 individuals (full data) or 21 individuals (subset data) 
representing 19 described species and two putative undescribed species.

Methodology:
Inputs were obtained with a ddRAD library processed with the software ipyrad (Eaton, 2014).
Specimens identification and voucher numbers are available in all files.
Further information about specimens is available in the Supplementary Material of the manuscript.
 
Evolutionary relationships were estimated under two approaches. A maximum likelihood (ML) estimate 
was obtained from RAxML v. 8.2.8 (Stamatakis, 2014) and coalescent-based approach was also used to 
estimate phylogenetic relationships using the program SVDquartets (Chifman and Kubatko, 2014) as implemented 
in PAUP* 4.0 (Swofford, 2003). Two phylogenetic trees were estimated with SVDquartets: one for the phylogenetic 
relationships estimated among individuals, and another for species lineages. Support was assessed with 1,000 
bootstrap replicates in all reconstructions. 

To infer the position of the root in Phalloceros, we extracted the SNPs from the aligned reference genome and
reconstructed the phylogenetic relationships among individuals using unlinked SNPs with SVDquartets setting 
Xiphophorus maculatus as outgroup.

Maximum likelihood ancestral state reconstructions were performed in the package ape in R with the pruned RAxML tree.

*For further information consult the manuscript.

Instrument and/or Software specifications:
ipyrad v. 0.6.17 (Eaton D.A., 2014. PyRAD: assembly of de novo RADseq loci for phylogenetic analyses. Bioinformatics 30, 1844-1849; https://github.com/dereneaton/ipyrad/blob/master/docs/index.rst)
RAxML v. 8.2.8 (Stamatakis A., 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312-1313)
SVDquartets (Chifman J, Kubatko L. 2014. Quartet inference from SNP data under the coalescent model. Bioinformatics 30, 3317-3324)
PAUP* 4.0 (Swofford D.L., 2003. PAUP*: phylogenetic analysis using parsimony and other methods, version 4.0 b10. Sinauer Associates, Sunderland)

Files contained here:
It contains 9 files:
1) Phalloceros_outgroup_uSNP.nex = input for SVDquartets reconstruction with an outgroup
2) Phalloceros_outgroup_uSNP.tre = output obtained from SVDquartets with an outgroup
3) Phalloceros_RAxML_tree = best maximum likelihood tree inferred with RAxML
4) Phalloceros_RAxML.phy = input data using full loci sequence for RAxML
5) Phalloceros_SVDind.u.snps.nex = input for SVDquartets reconstruction among individuals
6) Phalloceros_SVDind.u.snps.tre = output obtained from SVDquartets among individuals
7) Phalloceros_SVDspeciesTree.u.snps.nex = input for SVDquartets reconstruction for species tree
8) Phalloceros_SVDspeciesTree.u.snps.tre = output obtained from SVDquartets for species tree
9) UltrametricTree_AncestralCharacterReconstruction.nex = pruned RAxML tree used for ancestral state reconstruction

Related publication(s):
Andréa T. Thomaz, Tiago P. Carvalho, Luiz R. Malabarba, L. Lacey Knowles, Geographic distributions, phenotypes, and phylogenetic relationships of Phalloceros (Cyprinodontiformes: Poeciliidae): insights about diversification among sympatric species pools, Molecular Phylogenetics and Evolution, 2018, ISSN 1055-7903, https://doi.org/10.1016/j.ympev.2018.12.008

Use and Access: 
This data set is made available under a Attribution-NonCommercial 4.0 International (CC BY-NC 4.0).

To Cite Data: 
THOMAZ AT, CARVALHO TP, MALABARBA LR, KNOWLES LL, 2018. Geographic distributions, phenotypes, and phylogenetic relationships of Phalloceros (Cyprinodontiformes: Poeciliidae): insights about diversification among sympatric species pools [Data set]. University of Michigan Deep Blue Data Repository. https://doi.org/10.7302/Z2G44NJ2

Funding source:
Rackham International Research Award - University of Michigan to ATT.
Postdoctoral fellowship of PNPD-CAPES to TPC. 
CNPq (processes# 307890/2016-3 and 401204/2016-2) to LRM.