Data from: The phylogenetic origins and evolutionary history of holocentric chromosomes

Escudero M, Márquez-Corro JI, Hipp AL

Date Published: September 14, 2016

DOI: http://dx.doi.org/10.5061/dryad.405g1

 

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Title TimetreeOfLife2015
Downloaded 7 times
Description Downloaded from here http://www.timetree.org/book#treefiles. Hedges, S. B., Marin, J., Suleski, M., Paymer M., Kumar, S. 2015. Tree of Life Reveals Clock-Like Speciation and Diversification. Mol Biol Evol (2015) 32: 835-845
Download TimetreeOfLife2015.nwk (1.885 Mb)
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Title Character State Coding Holocentric vs. Monocentric
Downloaded 1 time
Description This is table cvs format. In the column are found species names as termed in the TimeTreeofLife2015. In the second and third column there are character state coding holocentric (1) vs. monocentric (0) for all species in the TimeTreeofLife2015. Coding in the column 3 was designed to avoid false holocentric chromosome positives and it was used for the analyses in the paper.
Download lista_JMC_ME2.csv (1.282 Mb)
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Title R codes in R mark down format
Downloaded 2 times
Description In this file are found all R codes used for the analyses.
Download Holocentric-Ancestral_Character-Estimation2.Rmd (12.05 Kb)
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Title Character State Coding Holocentric vs. Monocentric Description UPDATED
Downloaded 1 time
Description This is table cvs format. In the column are found species names as termed in the TimeTreeofLife2015. In the second and third column there are character state coding holocentric (1) vs. monocentric (0) for all species in the TimeTreeofLife2015. Coding in the column 3 was designed to avoid false holocentric chromosome positives and it was used for the analyses in the paper.
Download lista_JMC_ME2.csv (1.282 Mb)
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Title R codes in R mark down format UPDATED
Downloaded 1 time
Description In this file are found all R codes used for the analyses.
Download Holocentric-Ancestral_Character-Estimation2.Rmd (12.14 Kb)
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Title Supplementary Figure 1
Downloaded 14 times
Description SUP. FIG. 1. Phylogenetic tree of eukaryotes with 50,455 species derivate from the Time Tree of Life project. The ancestral state reconstruction of monocentric vs. holocentric chromosome based on BiSSE model is mapped on the branches using colors (blue for monocentric and red for holocentric). All groups with holocentric chromosomes are labeled in the phylogeny in red. Some representative groups of organisms with monocentric chromosomes are also indicated in blue.
Download Supplementary Figure 1.pdf (209.0 Kb)
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When using this data, please cite the original publication:

Escudero M, Márquez-Corro JI, Hipp AL (2016) The Phylogenetic Origins and Evolutionary History of Holocentric Chromosomes. Systematic Botany 41(3): 580-585. http://dx.doi.org/10.1600/036364416x692442

Additionally, please cite the Dryad data package:

Escudero M, Márquez-Corro JI, Hipp AL (2016) Data from: The phylogenetic origins and evolutionary history of holocentric chromosomes. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.405g1
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