The type and number of the samples included in the study.

<p>VL: visceral leishmaniasis; CL: cutaneous leishmaniasis; CanL: canine leishmaniasis.</p

Phylogenetic tree based on the alignment of the amplified section of the ITS1 region of 42 Turkish <i>Leishmania</i> isolates and international reference strains (for <i>L. tropica</i> MHOM/IL/1990/LRC-L590 and MHOM/IL/1996/LRC-L691; for <i>L. major</i> MHOM/IL/2000/LRC-L779; <i>for L. infantum/chagasi</i> MHOM/XX/1999/LRC-L774).

<p>REF*: ITS1 sequences for <i>L. infantum</i> MHOM/TN/1980/IPT1; for <i>L. donovani</i> MHOM/IN/1980/DD8; for <i>L. major</i> MHOM/TM/1973/5ASKH were taken from Talmi-Frank et al. <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002205#pntd.0002205-TalmiFrank2" target="_blank">[47]</a> and included the tree. (VL: visceral isolates; CL: cutaneous isolates; CanL: dog isolates).</p

The Turkey map showing the location and the number of samples in province level.

<p>The Turkey map showing the location and the number of samples in province level.</p

The representative figure of two peaks obtained in some samples.

<p>The representative figure of two peaks obtained in some samples.</p

The working chart of the present study.

<p>1: Optimization; 2: Diagnosis; 3: Species identification.</p

Factorial correspondence analysis (FCA) of the 76 <i>L. donovani</i> complex strains studied.

<p>CY, Cyprus; ET, Ethiopia; GR, Greece; IN, India; KE, Kenya; LK, Sri Lanka; PT, Portugal; SD, Sudan; SP, Spain; TR, Turkey; Populations designated as MON-1 (red squares) and non MON-1 (orange and brown squares) include respectively <i>L. infantum</i> MON-1 strains from Greece, Turkey, Spain and Portugal and <i>L. infantum</i> non MON-1 strains from Spain, Portugal, France and Italy, corresponding to previous analyses <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001507#pntd.0001507-Kuhls2" target="_blank">[18]</a>, <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001507#pntd.0001507-Kuhls3" target="_blank">[21]</a>; populations designated as IN1 (India 1), IN3 (India 3) and LK (Sri Lanka) (yellow squares); SD/ET (Sudan/Ethiopia) (pink squares); KE/IN2 (Kenya/India 2) (blue squares) compose the <i>L. donovani</i> genetic group, as detected previously <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001507#pntd.0001507-Alam1" target="_blank">[16]</a>, <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001507#pntd.0001507-Alam2" target="_blank">[17]</a>, <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001507#pntd.0001507-Kuhls2" target="_blank">[18]</a>, <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001507#pntd.0001507-Kuhls3" target="_blank">[21]</a>; <i>L. infantum</i> non MON-1 strains from Turkey and Cyprus are designated as TR (dark purple squares) and CY (light purple squares), respectively. The MON-37 clone of CD44 strain from Cyprus groups with the other CY non MON-1 strains. The TR/CY strains are placed between the <i>L. infantum</i> MON-1 and non MON-1 populations and the hybrid strain EP59 from Turkey between the TR non MON-1 and MON-1 populations. The BUCK strain is placed very close to the TR non MON-1 strains, as previously described <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001507#pntd.0001507-Kuhls2" target="_blank">[18]</a>, <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001507#pntd.0001507-Kuhls3" target="_blank">[21]</a>.</p

<i>K26</i>-PCR confirms that CUK1, CUK2 and EP59 strains belong to the <i>L. donovani</i> complex.

<p>Lanes: M, 100 bp DNA ladder; CH35 (MON-37, 700 bp); PM1 (MON-1, 626 bp); SC23 (MON-38, 515 bp); CUK1 (MON-309, 480 bp); CUK2 (MON-309, 480 bp); HUSSEN (MON-31, 430 bp); EP59 (MON-308, 385 bp); BUCK (MON-78, 385 bp). Strains CUK3, CUK4, CUK7 and CUK 10 gave identical results to CUK1 and CUK2 (not shown).</p

Estimated population structure of the 76 <i>L. donovani s.l.</i> strains as inferred by STRUCTURE.

<p>MLMT profiles are based on variations in 14 microsatellite markers. Each strain is represented by a single vertical line divided into K colours, where K is the number of populations assumed. Each colour represents one population and the length of the coloured segments shows the strain's estimated proportion of membership in that population. Strains with mixed memberships to the different populations are represented by different coloured segments in the vertical bar, which are proportional to the membership coefficient. <b>A.</b> When the likelihood of population number is calculated according to Evanno et al. <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001507#pntd.0001507-Evanno1" target="_blank">[28]</a>, the derived graph for ΔK shows a peak at K = 2 indicating the existence of two main populations in the studied strain set. However, eight populations are observed based on a log-likelihood plot, which plateaus at K = 8. At K = 8, all Turkish non MON-1 strains group with MON-37 strains from Cyprus, forming the TR/CY non MON-1 population. Bar plots for K = 3 and K = 4 are also shown to help determine ancestral populations. <b>B.</b> When the <i>L. infantum</i> non MON-1 & TR/CY non MON-1 strains are re-analysed separately the log-likelihood plot plateaus at K = 5, while the ΔΚ graph shows a major peak at K = 2 and a minor one at K = 5. At K = 5 a split of the TR/CY non MON-1 population was observed.</p

Characteristics of the 76 <i>Leishmania</i> strains used in this study.

<p>The non MON-1 strains from Turkey as well as the Cyprian canine isolate clone 1 analysed herein are presented in bold.</p><p>VL, visceral leishmaniasis; CL, cutaneous leishmaniasis; PKDL, post Kala Azar dermal leishmaniasis; CanL, canine leishmaniasis.</p><p>*Only one of the three MON-37 clones (cl.1) isolated from the parent CD44 strain was further analyzed;</p><p>**Hybrid strain; CY, Cyprus; ET, Ethiopia; GR, Greece; IN, India; KE, Kenya; LK, Sri Lanka; PT, Portugal; SD, Sudan; SP, Spain; TR, Turkey; n.d., not defined.</p

Midpoint rooted Neighbor-joining tree for the 76 <i>L. donovani</i> complex strains analysed.

<p>This midpoint rooted tree was inferred from Dps-distances calculated for the MLMT data (14 microsatellite markers) of our sample set. The tree leaves are coloured according to the populations defined by structure analysis (<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001507#pntd-0001507-g002" target="_blank">Fig. 2</a>). Bootstrap values (1000 re-samplings) above 50% are indicated at key nodes. The EP59 strain was excluded from this analysis due to its hybrid profile.</p