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Taxonomic distribution and phylogenetic utility of gender-associated mitochondrial genomes in the Unionoida (Bivalvia)

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Unionoid bivalves exhibit a great diversity in reproductive characteristics. However, the lack of a robust phylogeny severely restricts evolutionary interpretations regarding the genesis and consequences of reproductive character state diversity within the order. The apparent high fidelity of unionoidean doubly uniparental inheritance of mtDNA (DUI), where distinct female-(F) and male-(M) transmitted mtDNA genomes are present, may allow for multiple, independent mtDNA-based estimates of phylogeny and thus contribute to the generation of more robust estimates of unionoid evolutionary history. However, the current lack of knowledge regarding mtDNA transmission patterns in the Etherioidea severely ham-pers our ability to evaluate the potential of DUI for explicating unionoid phylogeny. This situation prompted us to address the following questions in this study: (1) Is DUI found in the Etherioidea? (2) What is the relative phylogenetic utility of F, M, and concatenated F + M cytochrome c oxidase subunit I (cox1) sequences for elucidating higher level unionoid evolutionary relationships? (3) What can trees derived from F and M sequence analyses tell us about the evolution of unionoid DUI and other reproductive characters? Forty-seven species representing all six families within the Unionoida were evaluated, using PCR-based methods, for the presence of DUI. Phylogenetic analyses were carried out on unionoid species for which complementary F and M cox1 DNA sequences were available as well as on a much more taxonomically inclusive F cox1 data set. We deter-mined that (1) the Etherioidea likely lacks DUI; (2) M and F + M cox1-based analyses provide better resolved estimates of unionoidean relationships than do F cox1-based analy-ses; and (3) the F and M non-concatenated cox1 inclusive phylogenetic analyses suggest the inference that (a) the presence of DUI, glochidial larvae, and endobranchous brooding are the ancestral unionoid character states, (b) both DUI and glochidial larvae were lost in the ancestral etherioidean lineage, (c) margaritiferids are closely related to unionids and exhibit a derived suite of morphological characteristics, and (d) a clarification of the evolu-tionary dynamics of unionoid DUI and other reproductive characteristics will require a ro-bust phylogeny for the order that is based on multiple data sets.
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... For each sampled population, 1 to 10 (mean = 4.8) specimens were sequenced for female (F-type) COI. PCR conditions (using the primer set LCO22me2 + HCO700dy2; Walker et al., 2006Walker et al., , 2007 were described in Froufe et al. (2016) with an annealing temperature of 50 • C. Amplified DNA templates were purified and sequenced bidirectionally using the same primers. ...
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... To amplify partial mitochondrial DNA fragments corresponding to COI and 16S rRNA genes, PCR was conducted using universal primer (LCO22me2/HCO700dy2 [33] for COI gene and 16Sar-L-myt/16Sbr-H-myt [34] for 16S rRNA gene) (S12 Table). The reaction mix for the PCR comprised 20-100ng genomic DNA, 10 mM dNTP, 10 pM of each primer, and 0.25 units of Taq DNA polymerase (Solgent Inc, Daejeon, South Korea) in a total volume of 50 μL. ...
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... Sampling was performed by wading in the lake (wearing dry-suit Whole genomic DNA was extracted from small tissue pieces preserved in 96% ethanol, using a standard high-salt protocol (Sambrook et al. 1989), from eight S. woodiana and six A. cygnea individuals. A fragment of the cytochrome oxidase c subunit I gene (COI) was amplified by PCR using universal primer modified versions, i.e., LCO22me2 and HCO700dy2 (Walker et al. 2006(Walker et al. , 2007. PCR conditions are described in Froufe et al. (2014) with an annealing temperature of 50 °C. ...
... Genomic DNA was extracted from tissue samples of the newly collected and other selected available specimens (Supporting Information 1), using a standard high-salt protocol (Sambrook, Fritsch & Maniatis, 1989) or the Jetquick tissue DNA Spin Kit (Genomed) following the manufacturer's protocol. Female lineages of mitochondrial cytochrome c oxidase subunit 1 (COI) were amplified and sequenced in both directions from all extracts using primer pair LCO22me2 + HCO700dy2 (Walker et al., 2006;Walker et al., 2007). ...
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Chapter
Unionoid bivalves have a long history of classification and reclassification. Pre-Darwin classifications were deductive and artificial, reflecting character selection and weighting. More recent classifications, which should be natural and inductive to reflect phylogeny, reveal a diversity of methodologies and results.