DOI: 10.5061/dryad.405g1
title: Data from: The phylogenetic origins and evolutionary history of holocentric chromosomes

description: In eukaryotes, we can recognize two kinds of chromosomes, based on the
 location of the kinetochores. The majority of eukaryotes have monocentric
 chromosomes, in which kinetochoric activity is concentrated in a single
 locus. In several unrelated eukaryotic lineages, chromosomes are
 holocentric, having diffuse centromeric / kinetochoric activity along the
 length of the chromosome. Whether holocentric chromosomes are derived or
 ancestral is still under debate. This study uses the phylogenetic tree
 from Time Tree of Life project, comprising more than 50,000 sampled
 species, to reconstruct the evolution of holocentry. Asymmetrical
 two-state Markov (Mk2) models were compared with BiSSE models to assess
 sensitivity of our conclusions to possible effects of holocentry on
 lineage diversification rates. Our analyses based on Mk2 and BiSSE models
 inferred that the rate of transition from holocentric to monocentric
 chromosomes is two orders of magnitude higher than the reverse direction.
 The ancestral state of all eukaryotes is ambiguous depending on the model,
 inferred to be either monocentric (Mk2) or holocentric (BiSSE). Whatever
 the direction, the multiple transitions and high diversity of centromere
 organization across the tree of life are what we would expect if there are
 selective advantages to both chromosome types. Understanding those
 selective advantages is key to understanding how genetic information is
 organized and transmitted from one generation to the next, and why these
 major evolutionary transitions in centromere organization have occurred in
 the first place.
description: TimetreeOfLife2015Downloaded 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: 835-845Character State Coding Holocentric vs. MonocentricThis 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.lista_JMC_ME2.csvR codes in R mark down formatIn this file are found all R codes used for the analyses.Holocentric-Ancestral_Character-Estimation2.RmdCharacter State Coding Holocentric vs. Monocentric Description UPDATEDThis 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.lista_JMC_ME2.csvR codes in R mark down format UPDATEDIn this file are found all R codes used for the analyses.Holocentric-Ancestral_Character-Estimation2.RmdSupplementary Figure 1SUP. 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.