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Published Animal Genome Sequences

Figure 1

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.

Contents

This repository contains:

  • Figure1.pdf An 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.png A preview manually rendered from Figure1.pdf.
  • draw_tree.r The source code for rendering the figure.
  • Tree_tree.tre An animal phylogeny topology from Dunn et al. 2014
  • update_ncbi_records.r Script for retrieving the umber of animal species with molecular sequence data.
  • sampling.csv The data that are mapped onto the tree tips.

Execution

To render the figure from the data, run the following at the shell:

Rscript draw_tree.r

Data sources

The data in sampling.csv come from several sources.

The estimated numbers of species are drawn mostly from Appeltans et al. 2012. Where ranges were given, the average was used. The arthropod number is from Hamilton et al. 2010.

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 update_ncbi_records.r.

The numbers of published genomes are from http://wikipedia.org/wiki/List_of_sequenced_animal_genomes, which we updated.