Work Description

Title: Geographic distributions, phenotypes, and phylogenetic relationships of Phalloceros (Cyprinodontiformes: Poeciliidae): insights about diversification among sympatric species pools [DATA SET] Open Access Deposited

http://creativecommons.org/licenses/by-nc/4.0/
Attribute Value
Methodology
  • Inputs were obtained with a ddRAD library processed with the software ipyrad. 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.
Description
  • 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. Nine files are part of this dataset, including all input files to infer the phylogenetic reconstructions and the outputs obtained, in addition to a pruned tree used to infer the ancestral state reconstructions.
Creator
Depositor
  • thomaz@umich.edu
Contact information
Discipline
Keyword
Citations to related material
  • 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
Resource type
Last modified
  • 03/27/2019
Language
DOI
License
To Cite this Work:
Thomaz, A., Carvalho, T., Malabarba, L., Knowles, L. Geographic distributions, phenotypes, and phylogenetic relationships of Phalloceros (Cyprinodontiformes: Poeciliidae): insights about diversification among sympatric species pools [DATA SET] [Data set]. University of Michigan - Deep Blue.

Relationships

Files (Count: 10; Size: 229 MB)

Download All Files (To download individual files, select them in the “Files” panel above)

Best for data sets < 3 GB. Downloads all files plus metadata into a zip file.

Files are ready   Download Data from Globus
Best for data sets > 3 GB. Globus is the platform Deep Blue Data uses to make large data sets available.   More about Globus