Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- and M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia)

The Unionidae represent an excellent model taxon for unravelling the drivers of freshwater diversity, but, phylogeographic studies on Southeast Asian taxa are hampered by lack of a comprehensive phylogeny and mutation rates for this fauna. We present complete female- (F) and male-type (M) mitogenomes of four genera of the Southeast Asian dade Contradentini+Rectidentini. We calculate substitution rates for the mitogenome, the 13 protein-coding genes, the two ribosomal units and three commonly used fragments (co1, nd1 and 16S) of both F- and M-mtDNA, based on a fossil-calibrated, mitogenomic phylogeny of the Unionidae. Phylogenetic analyses, including an M+F concatenated dataset, consistently recovers a monophyletic Gonideinae. Subfamily-level topology is congruent with that of a previous nuclear genomic study and with patterns in mitochondrial gene order, suggesting Unionidae F-type 2 as a synapomorphy of the Gonideinae. Our phylogeny indicates that the clades Contradentini+Rectidentini and Lamprotulini+Pseudodontini+Gonideini split in the early Cretaceous (similar to 125 Mya), and that the crown group of Contradentini+Rectidentini originated in the late Cretaceous (similar to 79 Mya). Most gonideine tribes originated during the early Palaeogene. Substitution rates were comparable to those previously published for F-type col and 16S for certain Unionidae and Margaritiferidae species (pairs).

Automated summary

The Unionidae serve as an excellent model taxon for studying freshwater diversity drivers, but the lack of a comprehensive phylogeny and mutation rates for Southeast Asian taxa hinders phylogeographic studies. By analyzing mitogenomes of several genera within the Contradentini+Rectidentini clade, researchers were able to estimate substitution rates and infer evolutionary relationships. The study revealed the early Cretaceous divergence of clades Contradentini+Rectidentini and Lamprotulini+Pseudodontini+Gonideini, with most gonideine tribes originating during the early Paleogene. Substitution rates were found to be comparable to previously published data for certain Unionidae and Margaritiferidae species.