Published Animal Genome Sequences
A phylogenetic summary of the number of published animal genomes, in relation to the numbers of described species and species with molecular data. These numbers are shown on a log scale.
This figure was originally generated for the manuscript:
Dunn, CW and JF Ryan. 2015. The Evolution of Animal Genomes. Current Opinion in Genetics and Development 35:25-32. doi:10.1016/j.gde.2015.08.006
Are we missing a published genome? Do you have better estimates on numbers of species for any of these clades? Please let us know via the issue tracker.
This repository contains:
Figure1.pdfAn animal phylogeny with the number of described species, number of species with molecular sequence data, and number of published genomes mapped to the tips.
Figure1.pngA preview manually rendered from
draw_tree.rThe source code for rendering the figure.
Tree_tree.treAn animal phylogeny topology from Dunn et al. 2014
update_ncbi_records.rScript for retrieving the umber of animal species with molecular sequence data.
sampling.csvThe data that are mapped onto the tree tips.
To render the figure from the data, run the following at the shell:
The data in
sampling.csv come from several sources.
The numbers of described species are drawn from Giga Community of Scientists 2014.
The number of species with molecular data is compiled from NCBI with the script
The numbers of published genomes are from http://wikipedia.org/wiki/List_of_sequenced_animal_genomes, which we updated.