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(sec_phylogen)=
Tskit, the tree sequence toolkit, can be used as an efficient library for very large evolutionary trees. Tskit makes it easy to deal with trees with millions of
tips, as in the example below:
:"tags": ["hide-input"]
import tskit
%%time
num_tips = 1_000_000
big_tree = tskit.Tree.generate_comb(num_tips);
print("Tree sequence takes up", big_tree.tree_sequence.nbytes / 1024**2, "Mb")
print(f"Generating a 'comb' (pectinate) tree of {num_tips} tips took:")
:::{todo} Display the million tip tree in condensed form, when tskit-dev/tskit#2372 (comment) and tskit-dev/tskit#2628 are solved :::
Calculations on these huge trees can be very efficient:
%%time
traversed_nodes = 0
for u in big_tree.nodes(order="postorder"):
traversed_nodes += 1
print(f"Postorder traversal through {traversed_nodes} nodes took:")
%%time
b1_index = big_tree.b1_index()
print(f"B1 balance index is {b1_index}. Calculation took:")
We can also read trees efficiently, e.g. in Newick format:
:::{todo} Add example of fast reading of a newick file, once tskit-dev/tskit#2187 is solved. E.g. we could say
For example, we can read in a newick format tree of XXX tips in XXX secs. In practice, this means when reading in a large tree you are mainly limited by disk access speeds :::
import tsconvert # used for reading tree sequences from different formats
# example code reading in a large file, timed
# Or read smaller trees from strings (here we create a tree spanning 1000 genomic units)
ts = tsconvert.from_newick("(A:6,((B:1,C:1):2,(D:2,E:2):1):3);", span=1000)
The "succinct tree sequence" format used by tskit can also store mutations
(and optionally a reference genome) along with the tree(s). This results in a
single unified representation of large genomic datasets, storing trees,
sequence data and metadata in a single efficient structure. Examples are given
in the section below entitled {ref}sec_phylogen_unified_structure.
As the name suggests, a tree sequence can also store and analyse a sequence of
trees along a genome (i.e. a "phylogenetic network"). This is necessary to
account for recombination between lineages, and may be important even when looking at
species-level phylogenies due to the effects of hybridization and incomplete lineage
sorting. An overview, and links to further details are given at the
{ref}end of this page <sec_phylogen_multiple_trees>.
Unlike other phylogenetic libraries, tskit is designed to efficiently store not just
single trees, but sequences of correlated trees along a genome. This means that the
library has some features not found in more standard phylogenetic libraries.
Here we focus on the {ref}sec_python_api,
introducing seven tskit concepts that may be useful to those with a background in
phylogenetics (each is linked to a separate section below):
- An evolutionary tree is always contained within a "tree sequence".
See {ref}
sec_phylogen_tree_in_sequence - The basic elements of a tree are nodes and edges, referred to by integer IDs.
See {ref}
sec_phylogen_ids - The
Treeobject in the Python API provides useful phylogenetic methods. See {ref}sec_phylogen_tree_object - Specific nodes in a tree (often the tips) are marked as "samples", meaning they are
known from data. See {ref}
sec_phylogen_samples - Nodes and edges have additional attributes, with arbitrary information stored in
metadata. See {ref}
sec_phylogen_metadata - All nodes must have a valid time, meaning trees are always directional
(i.e. "rooted"). See {ref}
sec_phylogen_node_time - "Roots" in trees have a specific definition, and a single tree can consist of
topologically independent clades (a "multiroot" tree).
See {ref}
sec_phylogen_multiroot
(sec_phylogen_tree_in_sequence)=
In tskit, all trees are stored as a "tree sequence" of correlated trees. This allows
easy extension of the library to multiple trees produced e.g. by hybridization.
In the simplest case, however, the tree sequence can contain just a single tree. This
can be obtained using the {meth}~TreeSequence.first() method.
:"tags": ["hide-input"]
# Make sensible node labels. It would be nice to roll this into tree.draw()
node_labels = {
node_object.id: node_object.metadata["name"]
for node_object in ts.nodes()
if "name" in node_object.metadata
}
tree = ts.first()
tree.draw(node_labels=node_labels) # or use draw_svg() for more options
Often you will have the tree sequence stored in a variable, such as the ts variable
used above. However, you can also obtain the tree sequence in which a tree is
contained using the {attr}Tree.tree_sequence attribute:
tree.tree_sequence # When output in a notebook, prints a summary of the tree sequence
(sec_phylogen_ids)=
The plot above labels nodes by their name, but internally the tskit library relies
heavily on integer IDs. Here's the same tree with node IDs plotted instead:
tree = ts.first()
tree.draw_svg()
Each {ref}node<sec_terminology_nodes> in a tree sequence is allocated an
integer ID starting from 0 to ts.num_nodes - 1 (IDs can be allocated in any order;
often the tips are labelled starting from 0 but this is not necessarily so, and
is not the case in the example above).
For efficiency reasons, tree traversal routines, as well as many other tskit methods,
tend to return integer IDs. You can use this ID to get specific information about the
node and its position in the tree, for example
node_id = 4
parent_id = tree.parent(node_id)
child_ids = tree.children(node_id)
print("The parent of", node_id, "is", parent_id, "and its children are", child_ids)
# or e.g. get all parents them as an array (where -1 means there is no parent)
print(f"The parents of nodes 0..{ts.num_nodes-1} are", tree.parent_array)
Other methods also exist to
{ref}examine nodes in a tree<sec_python_api_trees_node_measures>, e.g.
{meth}Tree.is_leaf, {meth}Tree.mrca for the most recent common ancestor between
2 or more nodes, etc.
Rather than refer to "branches" of a tree, tskit tends to refer to
{ref}sec_terminology_edges (the term "edge" emphasises that these can span
{ref}sec_phylogen_multiple_trees, although for tree sequences containing a single
tree, the terms are interchangeable). Like other entities in tskit, edges are referred
to by an integer ID. For instance, here is the edge above the internal node 4
node_id = 4
edge_id = tree.edge(node_id)
print("The edge above", node_id, "has ID", edge_id)
print(tree.tree_sequence.edge(edge_id))
The left and right attributes of an edge give genomic coordinates, and are
important in tree sequences that contain more than one tree.
(sec_phylogen_tree_object)=
The {class}Tree object has {ref}methods<sec_python_api_trees> to perform basic operations
on a tree such as traversing the nodes, identifying parents, children, and common
ancestors, etc. {ref}Several methods<sec_python_api_trees_node_measures_array>
also return numpy arrays for use in
{ref}efficient algorithms using numba<sec_trees_numba>
for n_id in tree.nodes(order="postorder"):
# you can also use "preorder", "levelorder", "timeasc", etc.
print(n_id)
# Or get all of them as arrays
print("Node IDs in postorder:", tree.postorder())
Various phylogenetic statistics are also available on trees, e.g
print(f"The colless imbalance index is {tree.colless_index()}")
See {ref}sec_phylogen_methods for more examples.
(sec_phylogen_samples)=
Often we are only have detailed information about specific nodes that we have sampled,
such as genomes A, B, C, D, and E in the example above. These are designated as
sample nodes, and are plotted as square nodes. The concept of
{ref}sample nodes<sec_data_model_definitions_sample> is integral
to the tskit format. They can be identified by using the
{meth}Node.is_sample and {meth}Tree.is_sample methods, or can be listed using
{meth}TreeSequence.samples or {meth}Tree.samples() (internally, the node.flags
field is used to {ref}flag up<sec_node_table_definition> which nodes are samples):
for n_id in tree.nodes():
n_is_sample = tree.is_sample(n_id)
print(f"Node {n_id} {'is' if n_is_sample else 'is not'} a sample node")
print("Sample nodes are", tree.tree_sequence.samples())
Often the sample nodes are the leaves of a tree, but this need not be the case. There are fast methods for identifying the sample nodes under an internal node in the tree, etc.
(sec_phylogen_metadata)=
Given a node ID, you can access more information about the node from a
{class}node object<tskit.Node>.
Because nodes are shared across all trees in a tree sequence, you access the
node object via the tree_sequence to which this tree belongs:
tree.tree_sequence.node(node_id) # or simply ts.node(node_id)
Attributes such as id, flags and time are always present. Arbitrary information,
such a name or e.g. bootstrap values, are stored in metadata
for n_id in tree.nodes():
print("Node", n_id, tree.tree_sequence.node(n_id).metadata.get("name", "<no name>"))
However, for large datasets, it may be more efficient to access the array of e.g.
times for all nodes, which provides direct memory access into the
{ref}tables<sec_tables> that underlie the tree sequence format:
tree.tree_sequence.nodes_time
(sec_phylogen_node_time)=
Perhaps the most noticable different between a tskit tree and the encoding of trees
in other phylogenetic libraries is that tskit does not explicitly store branch lengths.
Instead, each node has a time associated with it. Branch lengths can therefore be
found by calculating the difference between the time of a node and the time of its
parent node.
Since nodes must have a time, tskit trees aways have these (implicit) branch
lengths. To represent a tree ("cladogram") in which the branch lengths are not
meaningful, the {attr}TreeSequence.time_units of a tree sequence can be
specified as "uncalibrated" (see below)
Another implication of storing node times rather than branch lengths is that tskit
trees are always directional (i.e. they are "rooted"). The reason that tskit stores
times of nodes (rather than e.g. genetic distances between them) is to ensure temporal
consistency. In particular it makes it impossible for a node to be an ancestor of a
node in one tree, and a descendant of the same node in another tree in the tree sequence.
This is of critical importance when extending the concept of genetic ancestry to
{ref}sec_phylogen_multiple_trees along a genome.
The {attr}TreeSequence.time_units attribute stores the units in which time is
measured: if not known, this defaults to "unknown":
print("Time units are", tree.tree_sequence.time_units)
tree.draw_svg(y_axis=True)
Although branch lengths are not stored explicitly, for convenience tskit provides a
{meth}Tree.branch_length method:
print(
"The edge (i.e. branch) immediately above node",
node_id,
"has a 'length' of",
tree.branch_length(node_id),
)
:::{todo} The branch distance between two samples is also easy to calculate
NB: Turn the following in to a code cell
target_node_1 = 5
target_node_2 = 7
print(
"The branch distance between nodes",
target_node_1,
"and",
target_node_2,
"is",
# See https://github.com/tskit-dev/tskit/issues/2627 - what should be call this
# so as not to get mixed up with tree.path_length which counts the number of edges
# tree.branch_distance(target_node_1, target_node_2),
)
It is worth noting that this distance is the basis for the "genetic divergence"
between two samples in a tree. For this reason, an equivalent way to carry out the
calculation is to use {meth}TreeSequence.divergence, part of the the standard tskit
{ref}sec_stats framework, setting mode="branch" and
windows="trees". This is a more flexible approach, as it allows the distance between
multiple sets of samples in {ref}sec_phylogen_multiple_trees to be calculated
efficiently:
NB: Turn the following in to a code cell
target_node_1 = 5
target_node_2 = 7
print(
"Branch distance using built-in stats framework:"
tree.tree_sequence.divergence(([5], [7]), mode="branch", windows="trees")
)
:::
(sec_phylogen_multiroot)=
In tskit, {ref}sec_data_model_tree_roots of trees are defined with respect to the
sample nodes. In particular, if we move back in time along the tree branches from a
sample, the oldest node that we encounter is defined as a root. The ID of a root can be
obtained using {attr}Tree.root:
print("The root node of the following tree has ID", tree.root)
tree.draw_svg()
But in tskit, we can also create a single "tree" consisting of multiple unlinked
clades. In our example, we can create one of these phylogenetically unusual objects
if we remove the edge above node 4, by
{ref}editing the underlying tables<sec_tables_editing>:
# Trees & tree seqs are immutable: to change them, modify a copy of the underlying tables
tables = ts.dump_tables()
keep_edge = tables.edges.child != 4
tables.edges.replace_with(tables.edges[keep_edge])
new_ts = tables.tree_sequence() # Turn the edited tables back into a tree sequence
new_tree = new_ts.first()
new_tree.draw_svg()
Although there are two separate topologies in this plot, in tskit terminology, it is
considered a single tree, but with two roots:
print("The first tree has", len(new_tree.roots), "roots:", new_tree.roots)
This also means that if we have no topology at all (i.e. an "empty tree"), each sample is its own root.
tables.edges.clear()
erased_ts = tables.tree_sequence()
empty_tree = erased_ts.first()
print("This empty tree has", len(empty_tree.roots), "roots:", empty_tree.roots)
empty_tree.draw_svg()
The samples here are {ref}sec_data_model_tree_isolated_nodes. This may seem like a
strange corner case, but in tskit, isolated sample nodes are used to represent
{ref}sec_data_model_missing_data. This therefore represents a tree in which
relationships between the samples are not known. This could apply, for instance,
in regions of the genome where no genetic data exists, or where genetic ancestry
has not been simulated.
(sec_phylogen_methods)=
:::{todo} Demo some phylogenetic methods. e.g.
- Total branch length - demo quick calculation across multiple trees - incremental algorithm used extensively in population genetics. ("bringing tree thinking to popgen").
- KC distance
- Balance metrics
- Topology rankings (see #93) :::
(sec_phylogen_unified_structure)=
Tskit has been designed to capture both evolutionary tree topologies and the genetic
sequences that evolve along the branches of these trees. This is achieved by defining
{ref}sec_terminology_mutations_and_sites which are associated with specific positions
along the genome.
import msprime # The `msprime` package can throw mutations onto a tree sequence
mutated_ts = msprime.sim_mutations(ts, rate=3e-3, random_seed=321)
mutated_tree = mutated_ts.first()
print("Variable sites with the following IDs generated")
for site in mutated_tree.sites():
print(
f"Site ID {site.id} @ genomic position {site.position:g}:",
f"{site.ancestral_state} -> {site.mutations[0].derived_state}"
)
mutated_tree.draw_svg()
Mutations occur above nodes in a tree, with all the descendant
nodes inheriting that specific mutation (unless replaced by a subsequent
mutation at the same site). This allows genetic variation to be
{ref}efficiently represented<sec_what_is_dna_data> using the tree topology.
To obtain the genetic variation at each site across the entire genome, you can use the
{meth}TreeSequence.sites method, or (less efficiently), you can use
{meth}TreeSequence.alignments to output the
entire sequences for each sample node:
for node_id, alignment in zip(
mutated_ts.samples(),
mutated_ts.alignments(missing_data_character="."),
):
print(f"Node {node_id}: {alignment}")
(sec_phylogen_multiple_trees)=
Where tskit really shines is when the ancestry of your dataset cannot be adequately
represented by a single tree. This is a pervasive issue in genomes (even from different
species) that have undergone recombination in the past. The resulting series of
{ref}local trees<sec_what_is_local_trees> along a genome are highly correlated
(see {ref}sec_concepts).
Instead of storing each tree along a genome separately, tskit records the genomic
coordinates of each edge, which leads to enormous efficiencies in storage and
analysis. As a basic demonstration, we can repeat the edge removal example
{ref}above <sec_phylogen_multiroot>, but only remove the ancestral link above node 4
for the first half of the genome.
tables = ts.dump_tables()
edge_id_above_node_4 = ts.first().edge(4)
left_coord_for_edges = tables.edges.left
left_coord_for_edges[edge_id_above_node_4] = 50
tables.edges.left = left_coord_for_edges # reset the right coords
tables.sort()
multi_ts = tables.tree_sequence()
multi_ts.draw_svg()
For the left hand side of the genome we lack information about the ancestry of node 4, but for the right hand side we know this information. The result is to generate 2 trees in the tree sequence, which differ only in the presence of absence of a single branch. We do not have to separately store the entire tree on the right: all the edges that are shared between trees are stored only once.
The rest of the tskit tutorials will lead you through the concepts involved with
storing and analysing sequences of many correlated trees. For a simple introduction, you
might want to start with {ref}sec_what_is.