Raeymaekers et al-MolEcol-2012 D vs Gst

Sheet 1: microsatellite data (6 loci) of 28 lowland and upland samples collected in 2004. Sheet 2: microsatellite data (14 loci) of 18 lowland and upland samples collected in 2004. Sheet 3: microsatellite data (6 loci) of 21 upland samples collected in 2002

DataSheet_1_Genome diversity of Leishmania aethiopica.zip

Leishmania aethiopica is a zoonotic Old World parasite transmitted by Phlebotomine sand flies and causing cutaneous leishmaniasis in Ethiopia and Kenya. Despite a range of clinical manifestations and a high prevalence of treatment failure, L. aethiopica is one of the most neglected species of the Leishmania genus in terms of scientific attention. Here, we explored the genome diversity of L. aethiopica by analyzing the genomes of twenty isolates from Ethiopia. Phylogenomic analyses identified two strains as interspecific hybrids involving L. aethiopica as one parent and L. donovani and L. tropica respectively as the other parent. High levels of genome-wide heterozygosity suggest that these two hybrids are equivalent to F1 progeny that propagated mitotically since the initial hybridization event. Analyses of allelic read depths further revealed that the L. aethiopica - L. tropica hybrid was diploid and the L. aethiopica - L. donovani hybrid was triploid, as has been described for other interspecific Leishmania hybrids. When focusing on L. aethiopica, we show that this species is genetically highly diverse and consists of both asexually evolving strains and groups of recombining parasites. A remarkable observation is that some L. aethiopica strains showed an extensive loss of heterozygosity across large regions of the nuclear genome, which likely arose from gene conversion/mitotic recombination. Hence, our prospection of L. aethiopica genomics revealed new insights into the genomic consequences of both meiotic and mitotic recombination in Leishmania.</p

Microsatellite genotypes and host phenotypes

The worksheet “microsatellite genotypes” contains data from individual parasites (S. mansoni larvae) collected in Senegal, genotyped with nine microsatellite loci combined in a single multiplex: L46951, smd25, smd28 and smd89 (Durand et al., 2000); CA11-1 and S9-1 (Blair et al., 2001); smd11, smd43 and sdma28 (Curtis et al., 2001). This dataset represents 1692 parasites from 63 human hosts with at least five out of the nine loci successfully amplified. The worksheet “host phenotypes” contains host phenotypic data from the 63 human hosts. The host variables include gender, village*, liver morbidity (IP score), bladder morbidity (UBS score), Schistosoma mansoni infection intensity (epg**), Schistosoma haematobium infection intensity (ep 10ml**) and circulating anodic antigen (CAA) concentrations (picogram of CAA per mL). village* : Pakh (code 200), Ndieumeul (code 501), Diokhor Takh (code 502) epg**: number of eggs per gram of faeces; ep10ml**: number of eggs per 10 ml of urine

R script written for some of the analyses

This is an R script that was written for some of the analysis, namely: 1) hierarchical f-statistics 2) tests for inbreeding with multilocus heterozygosity and 3) tests for family structure with relatedness estimate

Microsatellite data from parasites

This data consists genotypes obtained from Schistosoma mansoni parasites that were type at nine microsatellite markers. Each locus (e.g. L46951) is coded by 6 digits (e.g. 169175). Each allele is coded by 3 digits (e.g. 169)

Human host data

Village: location where human host lived. Host: population number that was assigned to the human host. HostIdentifier: code that is linked with that host. SamplingTime: time when parasites were sampled (e.g. Aug-09 or 09-Aug means that parasites were sampled from this host in August 2009. Age: age of the human host. EPG: eggs per gram of feces, i.e. a measure of infection intensity. CoInfectionWithShaematobium: 1 = when human host was coinfected with Schistosoma haematobium, 0 = when human host was NOT coinfected

Pairwise <i>F</i>_ST estimates between <i>Schistosoma mansoni</i> samples from Mali and Senegal.

<p>Kokry = short for Kokry-Bozo. Rtoll = short for Richard Toll.</p><p>* = significant for permutation of genotypes among villages at the nominal level of 0.05.</p><p>** = significant for permutation of genotypes among villages at the nominal level of 0.001 (i.e. Bonferroni corrected). na = not applicable.</p><p>Estimates were obtained for microsatellite dataset DMS1 (below diagonal) and DMS2 (above diagonal). Note that samples with less than 10 parasites were not included to avoid biased estimation, and that samples from Richard Toll from 1993 and 1994 were pooled.</p

<i>Schistosoma mansoni</i> genetic diversity as estimated at a partial fragment of the cytochrome c oxidase subunit 1 gene.

<p>N_seq: number of sequences. N_hap: number of unique haplotypes. N_pol: number of polymorphic sites. <i>h</i>: haplotype diversity. <i>Π</i>: nucleotide diversity. SD: standard deviation.</p><p>Genetic diversity was estimated for samples obtained from Senegal and eight other African countries (see <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003998#pntd.0003998.t001" target="_blank">Table 1</a> for details on data collection). Sequences that were sampled in other countries than Senegal were pooled per country.</p

Bayesian clustering analysis with STRUCTURE using microsatellite markers.

<p>Each barplot shows the probability on the y-axis (0.0–1.0) of an individual parasite being assigned to a given number of clusters <i>K</i> (<i>K</i> = 2, 3 or 4) for microsatellite dataset DMS1 (a) and DMS2 (b). Individual parasites are aligned along the x-axis, and grouped according to the location and year of sampling (1–14). Parasites are assigned either to one cluster (each cluster is represented by a different color) or to multiple clusters if their genotypes were admixed (indicated by multiple colors). The optimal <i>K—</i>value (<i>K</i> = 4 for DMS1 and <i>K</i> = 3 for DMS2) was determined by the maximum LnP(D), which is the log likelihood of the observed genotype distribution in <i>K</i> clusters.</p

Pairwise <i>F</i>_ST estimates between <i>Schistosoma mansoni</i> samples from Mali and Senegal.

<p>Kokry = short for Kokry-Bozo. Rtoll = short for Richard Toll.</p><p>* = significant for permutation of genotypes among villages at the nominal level of 0.05.</p><p>** = significant for permutation of genotypes among villages at the nominal level of 0.001 (i.e. Bonferroni corrected). na = not applicable.</p><p>Estimates were obtained for microsatellite dataset DMS1 (below diagonal) and DMS2 (above diagonal). Note that samples with less than 10 parasites were not included to avoid biased estimation, and that samples from Richard Toll from 1993 and 1994 were pooled.</p