LSD Software

Link to LSD software. The initial commit is the LSD version used in all of the experiments described in our publication in Systematic Biology, plus examples, readme etc. We recommend NOT using this version, as LSD is regularly updated and improved. Use instead the version available from LSD web site: http://www.atgc-montpellier.fr/LSD/

Online Appendix of Least Square Dating article (LSD, To et al. Syst Biol 2015)

This Online Appendix contains the detailed description of our algorithms and their properties, and additional figures and tables

Maximum likelihood phylogenetic tree based on 3,081 HIV-1 subtype C <i>pol</i> sequences.

<p>Maximum likelihood (PhyML) phylogenetic tree based on 1,011 nucleotide sites of <i>pol</i> gene sequence (nucleotides 2,253–3,263 of HXB2 coordinates) from 3,081 HIV-1 subtype C isolates. Sequences were isolated in the countries shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033579#pone-0033579-t002" target="_blank">Table 2</a>. Sequences are colored to their region of origin: Senegal in red, Southern African countries (South-Africa, Botswana, Malawi, Mozambique, Swaziland, Zambia and Zimbabwe) in orange, other African countries (mainly from the East) in yellow, North and South America in purple, Asia in green and Europe in blue. The branch support (aLRT) of clade A, B, C and MSM are of 73%, 76%, 82% and 99% respectively.</p

Dating the subtype C epidemic in general and MSM populations in Senegal.

<p>Coalescent based estimations (BEAST) and 95% highest posterior density (HPD) intervals of the MRCA dates of 56 HIV-1 subtype C <i>pol</i> sequences obtained from the general and the MSM population. Results are displayed for all tested substitution rate priors and molecular clock models, except for relaxed exponential with both less informative priors which provides very large 95% HPD intervals and shows convergence problems (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033579#pone.0033579.s007" target="_blank">Table S3</a> for detailed results, including substitution rate estimations).</p

Bayesian tree with timescale of 56 HIV-1 C <i>pol</i> sequences from Senegal.

<p>Maximum clade credibility tree with time scale obtained with BEAST using 1,011 nucleotide sites of <i>pol</i> gene sequences (nucleotides 2,253–3,263 of HXB2 coordinates) from 56 HIV-1 subtype C isolates from Senegal. This tree is obtained using the relaxed uncorrelated lognormal molecular clock model and moderately informative substitution rate prior (Normal: 2.5×10⁻³,7.5×10⁻⁴). Clades with posterior probabilities ≥95% are indicated by diamonds. MSM isolates are colored in red.</p

Bayesian skyride plot of HIV-1 C demographic growth in Senegal using 56 <i>pol</i> sequences.

<p>Estimates of HIV-1 C effective number of infections (<i>N_e</i>) over time from 56 Senegalese <i>pol</i> sequences using a Bayesian skyride plot in BEAST with relaxed uncorrelated lognormal molecular clock and moderately informative substitution rate prior (ucld.mean Normal: 2.5×10⁻³, 7.5×10⁻⁴). The X-axis represents the time in year. The Y-axis represents the HIV-1 effective number of infections (log₁₀ scale). The black line marks the median estimate for <i>N_e</i> and the blue shadow region displays the 95% highest posterior density (HPD) interval.</p

Numbers of HIV-1 subtype C strains from different countries that were included in this study.

<p>Numbers of HIV-1 subtype C strains from different countries that were included in this study.</p

HIV-1 subtype C strains from Senegal included in this study.

<p>HIV-1 subtype C strains from Senegal included in this study.</p

Maximum likelihood phylogenetic tree constructed from 56 HIV-1 C <i>pol</i> sequences from Senegal and 121 close relatives.

<p>Detailed maximum likelihood (PhyML) phylogenetic tree constructed using 1,011 nucleotide sites of <i>pol</i> gene sequence (nucleotides 2,253–3,263 of HXB2 coordinates) from 177 HIV-1 subtype C isolates from Senegal and close relatives (see text). Branch support values (bootstrap and aLRT) are displayed (see figure legend). Colors indicate the geographic origin and sequences were isolated in the following countries: 56 in red from Senegal, 25 in orange from Zambia, 49 in yellow from southern Africa (Botswana 6; Mozambique 5; Swaziland 2; South Africa 35; Zimbabwe 1), 12 in green from East Africa (Burundi 2; Ethiopia 9; Kenya 1; Sudan 2), 3 in blue from other African countries (DRC 1; Equatorial Guinea 1; Gabon 1) and 30 in black from European and Asian countries (Belgium 4; China 1; Germany 2; Denmark 1; Spain 5; France 1; Greece 1; Israel 1; India 1; Italia 1; Luxembourg 1; Norway 2; Portugal 2; Sweden 7).</p

Evolutionary relationships between the HIV-1 <i>env</i> genes in the eight donor/recipient pairs.

<p>The evolutionary history was inferred using the Neighbor-Joining method <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069144#pone.0069144-Boeras1" target="_blank">[38]</a>. The optimal tree with the sum of branch length = 2.01912678 is shown. The tree is drawn to scale, with branch length in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Maximum Composite Likelihood method <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069144#pone.0069144-Whitney1" target="_blank">[39]</a> and the unit is the number of base substitutions per site. Codon positions included were 1^st+2^nd+3^rd+noncoding. All positions containing gaps and missing data were eliminated from the dataset. There were a total of 230 positions in the final dataset. Phylogenetic analyses were conducted in MEGA4 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069144#pone.0069144-Redd1" target="_blank">[40]</a>. For each recipient, viruses isolated from PBMC-derived DNA (•) and plasma RNA (○) are represented, with a different color for each donor/recipient pair. Asterisks indicate branches with bootstrap values greater than 98%.</p