Extract species tree from the Ensembl Compara database

Question

[BlastedBadger]

Hi, I have a problem specific to the EnsEMBL Compara database, which is how to retrieve the species tree that was used to run TreeBest in the Compara pipeline. I am basing this question on the version 93.

In short:

Does anyone know how to proceed to extract the EnsEMBL species tree used by TreeBest?

Detailed question:

My problem is that in the description of the protein trees pipeline, it says that:

The species tree is based on the NCBI taxonomy tree (subject to some modifications depending on new datasets).

So I am unsure whether the tree that we can download manually on the species tree page is the one including the modifications. Is it the case?

In any case, I am interested in fetching it automatically. I am more at ease with SQL than object-oriented Perl, but I tried the API:

#!/usr/bin/env perl


use warnings;
use strict;

use Bio::EnsEMBL::Registry;

# Auto-configuration
Bio::EnsEMBL::Registry->load_registry_from_db(
    -host => 'ensembldb.ensembl.org',
    -user => 'anonymous',
    -port => 5306);

my $species_tree_adaptor = Bio::EnsEMBL::Registry->get_adaptor(
    'Multi', 'compara', 'SpeciesTree');

#Bio::EnsEMBL::Compara::DBSQL::SpeciesTreeAdaptor

my $species_trees = $species_tree_adaptor->fetch_all();

foreach my $tree (@{$species_trees}) {
    print $tree->toString(), "\n";
}

This code fetches something, but I think it's just some ID and label from the species_tree_root table, but I would like a newick output...

Below, I tried using directly the SpeciesTree class, but the create_species_tree does not work without any argument, and anyway, I don't see any method of this class to write a newick tree. I should maybe use SpeciesTreeNode->newick_format(), but I don't know how to get such an instance...

use Bio::EnsEMBL::Compara::Utils::SpeciesTree;
## include all available species from genome_db by default
my $species_tree = Bio::EnsEMBL::Compara::Utils::SpeciesTree->create_species_tree();
#print $species_tree->newick_format();

Additionnally, I am interested in the $species_tree->ultrametrize_from_timetree() method.

Many thanks.

[Jean-Karim Heriche]

It seems clear to me that the tree provided on GitHub is the one used by Ensembl. As far as I know, the modifications of the NCBI tree concern the inclusion of new species.

Answer 1

[Emily]

You can just download it.

[BlastedBadger]

I understand from this page that that one is not the tree used in the protein trees pipeline. Also it is a fully resolved tree, and therefore compared to the NCBI topology makes some choices regarding uncertain branching orders: for example, it differs from the TimeTree topology at those places: ((Boreoeutheria,Xenarthra),Afrotheria) VS (Boreoeutheria,(Xenarthra,Afrotheria)), or ((Glires,Tupaia),Primates) VS (Glires,(Tupaia,Primates)), among other. I am supposing EnsEMBL Compara uses the unresolved polytomic tree from NCBI to reconcile protein trees, and so I wonder, how were the polytomies resolved in the tree you link to?