Selection of ultraconserved elements
We expanded our genomic sampling by constructing the (to our knowledge)
first UCE probe set for mollusks. We used seven published bivalve and
gastropod genomes (Table S2), with the ampullariid gastropod P.
canaliculata (Sun et al., 2019) as reference, to detect shared UCEs
using PHYLUCE v. 1.6.8 (Faircloth et al., 2012; Faircloth, 2016, 2017).
Upon obtaining candidate UCEs, we masked repetitive elements and low
complexity regions with RepeatMasker v.4.0.9 (Smith et al.
2019), and merged the results for each genome in a table with commands
of PHYLUCE. We retained UCEs with a minimum length of 100 bp (the length
of our probes) that were retrieved from 7, 6 or 5 of the genomes,
respectively. Subsequently, candidate UCEs were mapped to our previously
retained ORFs with Yass to examine potential overlaps and if
so, the involved UCEs were discarded. We also mapped UCEs onto one
another to avoid the inclusion of multiple UCEs with similar sequences.