Identifying the
founder of a group and the patterns
of evolutionary descent
The following description of eBURST focuses on groups identified using the stringent
default setting, where all STs must be a single locus variant (SLV) of at least
one other ST in the group, and eBURST produce a diagram where all STs in the
group are linked (a clonal complex). The use of eBURST with the more relaxed
group definition of 5/7 shared alleles is discussed later.
The primary founder of
a group is defined as the ST that differs
from the largest number of other STs at
only a single locus (i.e. the ST that
has the greatest number of single-locus
variants; SLVs). This method of assigning
the primary founder takes account of the
way in which clones emerge and diversify
(Figure 1A); the initial diversification
of the founding genotype of a clonal complex
will result in variants of the founder
that differ at only one of the seven loci
(i.e., SLVs of the founder). If two STs
have the same number of associated SLVs,
the one with the greatest number of double-locus
variants (DLVs) is selected as the founding
ST. In such cases the confidence in the
assignment of the primary founder will
be low, as reflected in the bootstrap
values (see
also here).
Note that the assignment
of the founding ST does not take into
account the number of isolates of each
ST; this makes the procedure relatively
robust to sampling bias. In many cases,
however, the predicted primary founder
will also be the most prevalent ST within
the group. Together with strong bootstrap
support, this can provide added confidence
in the assignment of the primary founder.
The average distance of each ST to all
other STs in the eBURST group is also
calculated by eBURST v3 and the primary
founder is likely to be the ST with the
minimum average distance to all other
STs.
The eBURST diagrams display
the patterns of descent within each group
from the predicted founding ST (Figure
1B). The initial version of BURST placed
the founder centrally and positioned SLVs
and DLVs of the founder within concentric
rings, whereas eBURST uses lines to show
the radial links from the founder to each
of its SLVs. A second difference is that
only SLV links are shown in eBURST, and
DLVs of the founder will therefore only
be linked if the intermediate SLV on the
path from the founder to the DLV is present
in the input data. All isolates that are
directly linked on a eBURST diagram will
therefore differ at only a single locus
and the cluster of linked STs should represent
a clonal complex. A DLV of the predicted
primary founder of a group will not be
included if the linking SLV has not been
sampled and using the stringent (conservative)
default group definition some STs that
might be part of the clonal complex will
therefore not be shown. In the eBURST
diagram, the circle representing the predicted
primary founder is coloured blue and the
areas of each of the circles indicate
the prevalence of the ST in the input
data (Figure 1B).

With the less stringent
group definition of 5/7 shared alleles,
more than one cluster of linked STs (clonal
complex) may be displayed in the eBURST
diagram, along with a number of unlinked
individual STs. The lack of linking between
two clusters within a single eBURST group
implies that no ST within one cluster
is a SLV of any ST in the other cluster(s).
Similarly, unlinked individual STs will
not be SLVs of any ST in the group. The
SLVs and DLVs of any ST can be displayed
on the eBURST diagram (see
also here).
Subgroups and
subgroup founders
In larger eBURST groups
there may be several STs besides the predicted
primary founder that have a number of
SLVs of their own. For example, a SLV
of the primary founder may have become
successful and diversified to produce
its own SLVs. A ST that appears to have
diversified to produce multiple SLVs is
called a subgroup founder. In the default
setting for the eBURST diagram, a ST with
at least two assigned descendent SLVs
(i.e. three SLVs in total, as the link
from the ST to its putative progenitor
is also a SLV) is defined as a subgroup
founder. In larger eBURST groups there
may be many STs with at least two assigned
descendent SLVs, and the number of descendent
SLVs that define whether a ST is shown
as a subgroup founder should be increased.
The STs that are subgroup founders, according
to the default definition of a subgroup,
or a user-defined definition, are coloured
yellow on the eBURST diagram (see examples
below). The primary founder of the group
is coloured blue. |