Cell lineage phylogenies can reveal the timing of germline segregation.

<p>Four paired samples (A-D) of somatic tissue (represented as a leaf) and germline tissue (represented as a flower) are taken from different branches of a single tree. Because plants accumulate somatic mutations as they grow, we expect a phylogeny of the 4 samples of either tissue to recapitulate the developmental histories of the cell lineages that led to those tissues. The phylogenetic relationships between somatic and germline tissues can reveal the timing of germline segregation. If the germline segregates early, then the germline tissues will group together on the tree (top phylogeny). If the germline segregates late (e.g., just before flowers form) then the germline and somatic tissue samples from each branch will group together in the tree. Intermediate timings of germline segregation will result in phylogenies with a structure intermediate between the two extremes shown here. Regardless, we expect the interrelationships among each of the 4 samples from a given tissue to recapitulate the physical structure of the tree, providing a useful positive control for difficult bioinformatics analyses. <i>Figure created with the assistance of Ella Maru Studio</i>.</p

LCPT_simulation_files

This zipfile will unzip to produce a folder which contains all the files and python script necessary to run all the simulations in the paper. Detailed instructions on how to replicate the analyses in the paper are provided in the README, and at the top of the python script in the file (open it in a text editor)

Raw CHC data

The untransformed peak areas, produced by integrating GC-MS output files in Chemstation. The data are grouped by species and caste

R script to convert branch length in divergence dates

A R script to compute the mass-corrected substitution rate and compute the divergence dates. This program convert branch length in divergence dates by computing the mass-corrected molecular rates as described in Nabholz et al. 2016. Header of the script contains useful informations

Xiphorhynchus_Rocha_2015

This dataset is used as the second working example in Nabholz et al. 201

Harrier_Oatley_2015

This dataset is used as the first working example in Nabholz et al. 201

Chronogram Calibration sets 2

Chronogram estimated using the calibration sets 2 (see table 1 of Nabholz et al. 2016

Phylogenetic tree

Phylogenetic tree of 475 species following the topology of Prum et al. (2015

Tracking the formation of species assemblages over time: phylogenetic reconstruction of patterns of colonisation and speciation

<p>Data include 1) code.zip: R code used in the study 2) passeriformes.trees: posterior trees of the New Zealand passerines 3) passeriformes.xml: BEAST input file for the New Zealand passerines.</p

Full nucleotide sequences alignment

Alignments of the 12 H-stranded protein-coding genes (i.e. all the protein-coding genes except NADH-dehydrogenase 6, ND6) for 475 specie