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 clade 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 (~125 Mya), and that the crown group of Contradentini+Rectidentini originated in the late Cretaceous (~79 Mya). Most gonideine tribes originated during the early Palaeogene. Substitution rates were comparable to those previously published for F-type co1 and 16S for certain Unionidae and Margaritiferidae species (pairs).This research was developed under ConBiomics: the missing approach for the Conservation of Freshwater Bivalves Project No. NORTE-01-0145-FEDER-030286, co-financed by COMPETE 2020, Portugal 2020, and the European Union through the ERDF, and by the Portuguese Foundation for Science and Technology (FCT) through national funds, and Strategic Funding UIDB/04423/2020 and UIDP/04423/2020. FCT also supported A.G.S. (SFRH/BD/137935/2018) and S.V. (UID/AGR/04033/2019). A.Z.was supported by an Anne McLaren Research Fellowship from the University of Nottingham. I.N.B. was supported by the Ministry of Science and Higher Education of Russia (Project No. AAAA-A18-118012390161-9 and Project No. FSRU 2020-0007) and the Russian Scientific Fund (Project No. 19-04-00066)