Bayesian skyline plot of the population growth of the subtype F cluster.

<p>The black line represents the median estimate of the effective number of infections through time (logarithmic scale) and the shaded area represents the 95% HPD credibility interval. The horizontal axis represents calendar years.</p

Maximum likelihood tree of near full-length genome sequences of viruses of the subtype F cluster.

<p>F1 subsubtype references are included in the analysis, with country of sample collection indicated with the ISO two-letter country code. The tree is rooted with an F2 subsubtype sequence. Only bootstrap values ≥80% are shown.</p

Distribution of viruses of the subtype F cluster sequenced by us according to city of sample collection.

<p>Distribution of viruses of the subtype F cluster sequenced by us according to city of sample collection.</p

Maximum clade credibility tree of PR-RT sequences of the subtype F Western European cluster and Galician subcluster.

<p>Nodes supported by PP = 1 and PP = 0.95–0.99 are marked with filled and unfilled circles, respectively. Colors of terminal and internal branches represent sampling locations and most probable locations of the corresponding nodes, respectively, according to the legend on the right. For the nodes corresponding to the Galician subcluster and the Western European cluster, the posterior probabilities for the most probable locations and the tMRCAs are indicated above the subtending branches (95% HPD intervals are in parentheses).</p

Maximum likelihood trees of sequences from databases belonging to the Western European subtype F cluster.

<p>The trees correspond to genome segments in (a) p17^gag (HXB2 positions 790–1185), (b) p24^gag (HXB2 positions 1575–2042), (c) reverse transcriptase (HXB2 positions 2637–3278), (d) <i>env</i> V3 region (HXB2 positions 6709–7448), and (e) <i>nef</i> (HXB2 positions 8797–9417). References for the subtype F cluster are near full-length genome sequences obtained by us, with names beginning with X, P or VA, with ‘i’ ending denoting those derived from cultured isolates. Database viruses branching in the subtype F cluster are in bold type. Countries of sample collection of database viruses are indicated with the ISO two-letter codes: BE, Belgium; BR: Brazil; CH, Switzerland; ES, Spain; FR, France; GB, United Kingdom. Cities of sample collection of database viruses of the subtype F cluster, when known, are in parentheses. Only bootstrap values ≥70% are shown.</p