Maximum clade credibility tree for <i>env</i>.

<p>Both tips and internal branches are colored according to the patient in which the viral lineages are hypothesized to reside (cfr. legend on the left). For branches that cross a transmission interval, the part up to the interval is assigned to the source patients. For posterior support values for each node, we refer to <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003505#pcbi.1003505.s004" target="_blank">Figure S4</a>. The transmission intervals are represented by the grey boxes. Dashed red circles indicate the coalescent incongruences. For the AB and CD coalescent event, the posterior marginal density of the tMRCA estimate is plotted over the corresponding node in greyshade. Only a lower limit of the transmission interval is known for the AB transmission. For transmissions BC, FG, CE, CL and EK the most recent boundary of the transmission interval equals the first sampling date.</p

Violin plot representation of the <i>pol</i> and <i>env</i> within and between-host evolutionary rates.

<p>Only patients for which samples for more than one time point are available were used for the within-host analysis. The ‘within’ host label represents the HPM estimate of the mean within host evolutionary rate of all patients. Likewise, the ‘linked’ between host label marks the direct estimate of the between host evolutionary rate. For the latter, only the first available sample of each patient was used. The ‘unlinked’ between host labels denotes the rate estimates obtained with the skyride prior for the <i>pol</i> and <i>env</i> regions of the epidemiologically unlinked subtype C sequences that overlap with our clonal data sets. The means of each rate estimate are connected by a black line. Numbers between brackets indicate the fold decrease of the mean relative to the within host mean rate estimate. All rates are in units of nucleotide substitutions per site per year * 10⁻³.</p

Maximum clade credibility tree for <i>pol</i>.

<p>Both tips and internal branches are colored according to the patient in which the viral lineages are hypothesized to reside (cfr. legend on the left). For branches that cross a transmission interval, the part up to the interval is assigned to the source patients. For posterior support values for each node, we refer to <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003505#pcbi.1003505.s002" target="_blank">Figure S2</a>. The transmission intervals are represented by the grey boxes. Dashed red circles indicate the topological and coalescent incongruences. For the CD coalescent event, the posterior marginal density of the tMRCA estimate is plotted over the corresponding node in greyshade. Only a lower limit of the transmission interval is known for the AB transmission. For transmissions BC, FG, CE, CL and EK the most recent boundary of the transmission interval (almost) equals the first sampling date.</p

Evolutionary rate estimates and support for the fixed effect in the mixed effects clock model.

<p>The mean evolutionary rate and highest posterior density (HPD) intervals are expressed as the number of nucleotide substitutions (10⁻³) per site per year. The Bayes factor (BF) is computed as the posterior odds over the prior odds that the rate for the transmission branches or transmitted lineage branches is smaller than the within host-rate.</p

Maximum clade credibility tree for <i>pol</i> after exclusion of the same drug resistance associated positions as in [18].

<p>Tips and internal branches are colored according to the states' posterior probability as estimated using a non-reversible discrete asymmetric trait analysis with the patients as discrete states <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003505#pcbi.1003505-Lemey5" target="_blank">[67]</a>, <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003505#pcbi.1003505-Edwards2" target="_blank">[68]</a>. Both tips and internal branches are colored according to the patient in which the viral lineages are hypothesized to reside (cfr. legend on the left). For posterior support values for each node, we refer to <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003505#pcbi.1003505.s003" target="_blank">Figure S3</a>. The black dotted circle indicates the node responsible for the higher compatibility of the BH transition. Like the increased CD compatibility, this results from the lower evolutionary rates that lead to somewhat older divergence time estimates. A) The divergence time between the patient B and I lineages is older than the upper bound of the BI transmission interval. Following the BI host transition, BH cannot be compatible any more. B) When the B-I divergence time is estimated after its respective transmission, the viral genealogy is inferred to be incompatible with the BI transmission, and no transition into patient I is assumed. However, because the same node also represents the B-H coalescence time and this is in agreement with the compatibility constraints, the fair amount of too recent divergence time estimations for the B-I lineages results in 30% BH compatibility.</p

Molecular clock estimates and compatibility probabilities for the <i>pol</i> and <i>env</i> sequences.

<p>Compatibility is expressed as the proportion of trees in the posterior sample that is compatible with the indicated transmission event after removal of 10% as burn-in. The mean evolutionary rate and highest posterior density (HPD) intervals are expressed as the number of nucleotide substitutions (10⁻³) per site per year. The coefficient of variation represents the scaled variance in evolutionary rate among lineages. The time to the most recent common ancestor (tMRCA) represents the time since the most recent sampling date (24/03/2006), and is expressed in years.</p>1<p>The percentage of sampled genealogies with an entirely compatible coalescent history (C) are listed for the transmission histories assuming A as the original source (AB) as well as B as the original source (BA).</p>2<p>DRMs = drug resistance mutations. See <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003505#pcbi.1003505-Lemey2" target="_blank">[18]</a> for an overview of the removed positions.</p

A hypothetical transmission chain and viral genealogy for 4 patients.

<p>For each transmission event, we show an upper and lower boundary for the transmission event. The viral lineages within each each patient are represented by a particular branch color, while the transmission-associated host transitions in the viral genealogy are depicted using a color gradient. Whereas the viral genealogy is compatible with transmission from P1 to P2 and P2 to P3, independent of the number of lineages transmitted, the most recent common ancestor for the P3 and P4 lineages is too recent to be compatible with the respective transmission event.</p

NATIONAL STATEMENT OF SCIENCE INVESTMENT DRAFT: Response from Rutherford Discovery Fellowship recipients (2010-2013)

<p>This is a joint response written and co-signed by 97.5% of New Zealand’s Rutherford Discovery Fellows. We are a group of internationally recognised early- to mid-career researchers who have been selected for our innovative approaches to research across the sciences and the humanities. We work in diverse fields, spanning physical, engineering, information and communications technology, medical, molecular and environmental research through to social sciences, law and the humanities. We are based across a wide cross-section of New Zealand’s Universities and Crown Research Institutes (CRIs), and are engaged in basic, applied and near-to-market research. All of us have directly benefitted from the investments and changes that the Government has been making to the Science sector. As a result of the Rutherford Discovery Fellowship, we have chosen to return to, or to stay in, New Zealand.</p> <p> </p