Phylogenomics of bivalvia using ultraconserved elements (UCEs) reveal new topologies for Pteriomorphia and Imparidentia

Despite significant advances in phylogenetics over the past decades, the
deep relationships within Bivalvia (phylum Mollusca) remain inconclusive.
Previous efforts based on morphology or several genes have failed to
resolve many key nodes in the phylogeny of Bivalvia. Advances have been
made recently using transcriptome data, but the phylogenetic relationships
within Bivalvia historically lacked consensus, especially within
Pteriomorphia and Imparidentia. Here, we inferred the relationships of key
lineages within Bivalvia using matrices generated from specifically
designed ultraconserved elements (UCEs) with 16 available genomic
resources and 85 newly sequenced specimens from 55 families. Our new
probes (Bivalve UCE 2k v.1) for target sequencing captured an average of
849 UCEs with 1085-bp in mean length from in vitro experiments. Our
results introduced novel schemes from six major clades (Protobranchina,
Pteriomorphia, Palaeoheterodonta, Archiheterodonta, Anomalodesmata and
Imparidentia), though some inner nodes were poorly resolved, such as
paraphyletic Heterodonta in some topologies potentially due to
insufficient taxon sampling. The resolution increased when analyzing
specific matrices for Pteriomorphia and Imparidentia. We recovered three
Pteriomorphia topologies different from previously published trees, with
the strongest support for ((Ostreida + (Arcida + Mytilida)) + (Pectinida +
(Limida + Pectinida))). Limida were nested within Pectinida, warranting
further studies. For Imparidentia, our results strongly supported the new
hypothesis of (Galeommatida + (Adapedonta + Cardiida)), while the possible
non-monophyly of Lucinida was inferred but poorly supported. Overall, our
results provide important insights into the phylogeny of Bivalvia and show
that target enrichment sequencing of UCEs can be broadly applied to study
both deep and shallow phylogenetic relationships.