Preparation of genomic libraries
Target enrichment was performed with genomic DNA libraries of 96 specimens (95 Coelaturini and one iridinid bivalve), i.e. 48 for continent-scale phylogenetics and 48 from six sampling localities (5-11 individuals per population) in the Malawi Basin for population genetics (Table S3). Two populations occur in the northern region, two in the southern region, one at Likoma Island and the last along the Shire River that drains Lake Malawi in the south. Genomic DNA was extracted from ~20 mg of dried tissue of the posterior or anterior adductor muscles, mantle tissue, and in case required the foot. DNA was extracted with the NucleoSpin 96 Tissue kit from Macherey-Nagel on a KingFisher Flex robot following manufacturer recommendations. DNA concentrations in the extracts were quantified with Qubit fluorometry. We sheared DNA through sonication in a Bioruptor Pico: Samples with >20 ng/µl were subjected to 20 cycles of 30s sonication, 30s pause, for those with lower DNA concentrations we used between 18 and 3 cycles depending on DNA content. The results of library fragmentation were verified with chip-based capillary electrophoresis on an Agilent BioAnalyser. Genomic libraries were prepared with the NextFlex Rapid DNA-Seq v. 2.0 kit of PerkinElmer and associated Unique Dual Indices for multiplexing.