Nuclear and mitochondrial phylogenomics of the Diplostomoidea and Diplostomida (Digenea, Platyhelminthes)¹

Abstract

phylogenetic studies, namely the possible placement of the Cyathocotylidae outside the 109 Diplostomoidea (Hernández-Mena et al., 2017), and the Diplostomidae as a basal lineage in the 110 order Plagiorchiida (Brabec et al., 2015). Both results originate from analysis of mtDNA, and we 111 obtained data to determine if these patterns were robust to additional taxon sampling. To decide 112 between what were likely to be conflicting topologies based on mtDNA and rDNA, we 113 employed phylogenomic analyses of ultra-conserved elements (UCEs). 114Although we set out to work on higher relationships among a small number of 115 representative specimens, we were aware that the diversity and identity of diplostomoid species 116 often differs from initial suspicions based on morphology (Blasco-Costa and Locke, 2017). We 117 therefore supported our identifications with morphological comparisons and analysis of 118 additional DNA sequences from closely related species, which led to several findings related to 119 the alpha taxonomy of the seven specimens of principal interest. 120 121 2. Materials and Methods 122 2.1 Specimen collection and identification 123

Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction

“…UCEs are among the most widely used types of phylogenomic markers, and have been used to resolve both higher level and population level phylogenetic relationships (McCormack et al 2012, Winker et al 2018. They are found throughout the tree of life, including Cnidaria, flat worms (Platyhelminthes), arachnids, insects, as well as in birds and mammals (Quattrini et al 2018, Locke et al 2018, Faircloth 2017, Moyle et al 2016, Esselstyn et al 2017. UCEs are beneficial for their ease of capture from non-model organisms.…”

“…UCEs are among the most widely used types of phylogenomic markers and have been used to resolve both higher level and population level phylogenetic relationships ( McCormack et al 2012 ; Winker et al 2018 ). They are found throughout the animal tree of life, including Cnidaria, flat worms (Platyhelminthes), arachnids, insects, as well as in birds and mammals ( Moyle et al 2016 ; Esselstyn et al 2017 ; Faircloth 2017 ; Locke et al 2018 ; Quattrini et al 2018 ; White and Braun 2019 ). UCEs are advantageous because of their ease of capture from nonmodel organisms, and they (and other probe-based approaches) can provide access to loci from degraded DNA of museum specimens ( Bi et al 2013 ; Blaimer et al 2016 ; McCormack et al 2016; Van Dam et al 2017 ).…”