taxonID	type	description	language	source
03F287BA8959FFF1FF680A76FC6EEA76.taxon	description	Freshwater snails were collected by scooping using handheld metal sieve scoops according to a standard protocol [18]. Collections were carried out by three trained and experienced technicians for 15 min per sampling site. Brief descriptions of all sampling sites (e. g. water depth, degree of vegetation, whether sites were temporal pools located away from the lake’s edge or were at the lake’s edge) were recorded. Te same sampling protocol was applied regardless of the environmental conditions at the sample site. Biomphalaria were initially identified to genus level based on shell morphology according to previous morphological descriptions [25] and collected into small screwcap pots containing lake water and lake vegetation for short-term (<3 h) transportation. Shortly after collection, Biomphalaria were maintained in aquaria, also containing lake water and lake vegetation, according to collection site.	en	Archer, John, Cunningham, Lucas J., Juhász, Alexandra, Jones, Sam, Reed, Amber L., Yeo, Shi Min, Mainga, Bright, Chammudzi, Priscilla, Kapira, Donales R., Lally, David, Namacha, Gladys, Makaula, Peter, LaCourse, James E., Kayuni, Sekeleghe A., Webster, Bonnie L., Musaya, Janelisa, Stothard, J. Russell (2024): Population genetics and molecular xenomonitoring of Biomphalaria freshwater snails along the southern shoreline of Lake Malawi, Malawi. Parasites & Vectors (521) 17 (1): 1-16, DOI: 10.1186/s13071-024-06546-5, URL: https://doi.org/10.1186/s13071-024-06546-5
03F287BA895EFFF6FF680B0DFACFEFD9.taxon	description	700 - bp region of the Biomphalaria mitochondrial cox 1 gene according to a standard protocol [9]. Details of all primer sequences, reaction mixes used and PCR conditions are described in Additional file 2: Tables S 1 A, S 1 B and S 1 C, respectively. All Biomphalaria cox 1 PCRs included a positive control using B. pfeifferi DNA provided by the Schistosome and Snail Resource (SSR; an open access biomedical resource) [30] and a negative control using ddH 2 O in place of template DNA. Amplicons were visualised by running 4 µl of PCR products mixed with 1.5 µl of 5 × loading buffer blue (Bioline Ltd., London, UK), stained with GelRed in a 1 % agarose gel. Te PCR products were then purified using the QIAquick PCR Purification Kit (QIAGEN Ltd.) according to the manufacturer’s instructions and Sanger sequenced in the forward direction using a dilution of the LCO _ 1490 _ FW forward primer. Sequence data were visualised, trimmed and edited as needed using Geneious Prime version 2023.01 (Biomatters Ltd., Aukland, New Zealand) before being identified using the Basic Local Alignment Search Tool (BLAST) algorithm within the National Center for Biotechnology Information (NCBI) database [31].	en	Archer, John, Cunningham, Lucas J., Juhász, Alexandra, Jones, Sam, Reed, Amber L., Yeo, Shi Min, Mainga, Bright, Chammudzi, Priscilla, Kapira, Donales R., Lally, David, Namacha, Gladys, Makaula, Peter, LaCourse, James E., Kayuni, Sekeleghe A., Webster, Bonnie L., Musaya, Janelisa, Stothard, J. Russell (2024): Population genetics and molecular xenomonitoring of Biomphalaria freshwater snails along the southern shoreline of Lake Malawi, Malawi. Parasites & Vectors (521) 17 (1): 1-16, DOI: 10.1186/s13071-024-06546-5, URL: https://doi.org/10.1186/s13071-024-06546-5
03F287BA895FFFF4FCD20B39FD5FEF19.taxon	description	to amplify only the S. mansoni ND 5 locus for Sanger sequencing [24]. Amplicons were visualised in the same manner as for the multiplex molecular xenomonitoring PCRs. Schistosoma mansoni ND 5 PCR products were purified as described above and Sanger sequenced in the forward direction using a dilution of the ND 52 forward primer. Sequence data were visualised, trimmed, edited and identified as described above. Templeton Crandall and Sing haplotype network To assess S. mansoni ND 5 diversity, we performed a haplotype analysis using all generated S. mansoni ND 5 sequence data. To do this, a MAFFT alignment was performed using sequence data within Geneious Prime (default MAFFT parameter settings). Te MAFFT alignment was then visualised, examined and edited as described above. Te alignment was then exported from Geneious Prime in Nexus file format and imported into PopART version 1.7. Within PopART, a TCS haplotype network was generated to allow examination of haplotype group structuring.	en	Archer, John, Cunningham, Lucas J., Juhász, Alexandra, Jones, Sam, Reed, Amber L., Yeo, Shi Min, Mainga, Bright, Chammudzi, Priscilla, Kapira, Donales R., Lally, David, Namacha, Gladys, Makaula, Peter, LaCourse, James E., Kayuni, Sekeleghe A., Webster, Bonnie L., Musaya, Janelisa, Stothard, J. Russell (2024): Population genetics and molecular xenomonitoring of Biomphalaria freshwater snails along the southern shoreline of Lake Malawi, Malawi. Parasites & Vectors (521) 17 (1): 1-16, DOI: 10.1186/s13071-024-06546-5, URL: https://doi.org/10.1186/s13071-024-06546-5
03F287BA895CFFF4FF680F8DFEFBEA39.taxon	description	To identify Trematoda species other than S. mansoni infecting Biomphalaria, we subjected all samples that successfully amplified only Biomphalaria and Trematoda ITS loci to a secondary singleplex PCR, again to amplify only the Biomphalaria ITS and Trematoda ITS loci. To do this, the molecular xenomonitoring PCR was repeated, but with replacement of the S. mansoni ND 5 forward and reverse primers with ddH 2 O. Amplicons were visualised in the same manner as for the multiplex molecular xenomonitoring PCRs and the approximately 1005 - bp Trematoda ITS gel band was excised using a fresh scalpel. Excised gel bands were purified using the QIAquick Gel purification kit (Qiagen Ltd.) according to manufacturer’s instructions and were then purified as described above prior to Sanger sequencing in the forward direction using a dilution of the ETTS 2 forward primer. Sequence data were visualised, trimmed and edited as needed using Geneious Prime version 2023.01 (Biomatters, Ltd.) before being identified using the BLAST algorithm within the NCBI database [31].	en	Archer, John, Cunningham, Lucas J., Juhász, Alexandra, Jones, Sam, Reed, Amber L., Yeo, Shi Min, Mainga, Bright, Chammudzi, Priscilla, Kapira, Donales R., Lally, David, Namacha, Gladys, Makaula, Peter, LaCourse, James E., Kayuni, Sekeleghe A., Webster, Bonnie L., Musaya, Janelisa, Stothard, J. Russell (2024): Population genetics and molecular xenomonitoring of Biomphalaria freshwater snails along the southern shoreline of Lake Malawi, Malawi. Parasites & Vectors (521) 17 (1): 1-16, DOI: 10.1186/s13071-024-06546-5, URL: https://doi.org/10.1186/s13071-024-06546-5
03F287BA895DFFFBFF680A7BFE7FEA99.taxon	description	Te S. mansoni ND 5 locus was successfully amplified during the secondary S. mansoni ND 5 singleplex PCR in all 20 Biomphalaria samples that had amplified all three target loci during the initial molecular xenomonitoring PCR. All 20 ND 5 amplicons were confirmed as S. mansoni through ND 5 analysis, confirming infection with S. mansoni. Te prevalence of S. mansoni infection in these 589 Biomphalaria was therefore increased from 0.17 % based on cercarial shedding to 3.4 % based on molecular xenomonitoring. Biomphalaria snails infected with S. mansoni were identified at four of the 41 (9.6 %) malacological survey sites (Fig. 5). At site 13, three of 175 collected Biomphalaria (1.7 %) were infected with S. mansoni; at site 18, two of 66 collected Biomphalaria (3 %) were infected with S. mansoni; and at site 27, five of 151 collected Biomphalaria (4 %) were infected with S. mansoni. At site 21, however, nine of 80 Biomphalaria (11.25 %) were infected with S. mansoni, the highest prevalence of Biomphalaria infections across all malacological surveillance sites. Te number of malacological surveillance sites where intestinal schistosomiasis transmission was identified was therefore increased from just one using cercarial shedding to four using molecular xenomonitoring. Te S. mansoni ND 5 TCS haplotype network is shown in Fig. 6. Two distinct clusters were formed, each comprising three unique haplotypes. One unique haplotype consisting of two S. mansoni ND 5 sequences was identified at site 13; no other haplotypes were found at this site. One unique haplotype comprising one S. mansoni ND 5 sequence was identified at site 21. Te remaining four haplotypes were present at more than one single site, with two being present at three sites (sites 18, 21 and 27). All 20 S. mansoni ND 5 sequences were uploaded to the GenBank repository (Accession numbers: PP 889740 - PP 889759). Only the Biomphalaria ITS and Trematoda ITS loci were amplified in 12 Biomphalaria DNA samples, indicating infection with non- S. mansoni trematodes. Te Trematoda ITS gel band was successfully excised and genotyped in all 12 of these samples. Of these 12 samples, six were identified as Uvulifer spp., which were all present at site 13, and the remaining six were identified as Petasiger spp., which were present at sites 18, 20, 21 and 27 (Additional file 1: Table S 2), based on ITS analysis. No genetic variation was found between any ITS sequence data for Uvulifer spp. or between any ITS sequence data for Petasiger spp. All six Uvulifer spp. ITS sequences and all six Petasiger spp. ITS sequences were uploaded to the GenBank repository (Accession numbers: PP 510464 - PP 510469 and PP 510476 - PP 501481, respectively). An example agarose gel image of the high-throughput molecular xenomonitoring PCR assay [24] is shown in Additional file 4: Figure S 1. Additional data generated during Biomphalaria molecular xenomonitoring can be found in Additional file 5: Dataset S 1, Biomphalaria molecular xenomonitoring data.	en	Archer, John, Cunningham, Lucas J., Juhász, Alexandra, Jones, Sam, Reed, Amber L., Yeo, Shi Min, Mainga, Bright, Chammudzi, Priscilla, Kapira, Donales R., Lally, David, Namacha, Gladys, Makaula, Peter, LaCourse, James E., Kayuni, Sekeleghe A., Webster, Bonnie L., Musaya, Janelisa, Stothard, J. Russell (2024): Population genetics and molecular xenomonitoring of Biomphalaria freshwater snails along the southern shoreline of Lake Malawi, Malawi. Parasites & Vectors (521) 17 (1): 1-16, DOI: 10.1186/s13071-024-06546-5, URL: https://doi.org/10.1186/s13071-024-06546-5
