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.