Here we describe large clades that differ in some metadata with respect to the rest of the tree clades of the tree. Specifically we investigate clades that differ wrt. the variants of the mosaic variants of the genes mtr and penA, minimum inhibitory concentration (MIC) (categorized into levels high and low) levels, and sex distribution,

Full tree with metadata

The annotated tree shows that most of the mosaic variant of mtr cluster in distict parts of the tree. Variants of penA that are related to high MIC also make up distinct clusters. The distribution of sex (M/F) does not display any obvious large scale patterns, but when zooming in on smaller cluseters (< 50 isolates) there are many clades that display higher fractions of females F/(F+M).

Interactive version of the phylogeny with metadata

Clades

The pictures below shows clades (see interactive plot) we deem important based on and for which we will estimate the effective population size dynamics.

MTR clusters in the upper part of the tree under node 11506. The estimated time of the most recent common ancestor (TMRCA) of this clade is around 1978.

mtr clade High MIC mosaic another High MIC mosaic High MIC non-mosaic

The PenA MIC values make up three distict clusters. The first picture shows a clade with an estimated high MIC that carries a mosaic penA gene variant. The estimated tmrca of this clade around 1959.The second clade´s tmrca is around 1976, and has the same MIC and penA mosaic profile, but includes a sub-group with different form of mosaic pen-A (denoted semi-mosaic in the figure in dark blue) The third clade´s tmrca is approximately 1940 show a clade with high MIC, but non-mosaic penA profile.

Population dynamcis in the clades

All of the clades grew in the period 1980-2010. After 2010 the effective population size falls for all the clades define by penA variants, while mtr continues growing or alternatively stablizes. The effective population size in the tree as a whole is shown below. The clades from above are highlighted.

Full phylogeny and effective population size of the global tree

The high effective population (with very high uncertainty from the confidence intervals) size from 1770-1800 is a result of the long basal branches which probably displays a lack of sequences that represent the divergence that happened in this time period. From 1810-2010 the effective population size have been steadily growing, with a pronounced decrease since 2010.