Optimizing the widely used nuclear protein‐coding gene primers in beetle phylogenies and their application in the genus Sasajiscymnus Vandenberg (Coleoptera: Coccinellidae)

Abstract

Advances in genomic biology and the increasing availability of genomic resources allow developing hundreds of nuclear protein‐coding (NPC) markers, which can be used in phylogenetic research. However, for low taxonomic levels, it may be more practical to select a handful of suitable molecular loci for phylogenetic inference. Unfortunately, the presence of degenerate primers of NPC markers can be a major impediment, as the amplification success rate is low and they tend to amplify nontargeted regions. In this study, we optimized five NPC fragments widely used in beetle phylogenetics (i.e., two parts of carbamoyl‐phosphate synthetase: CADXM and CADMC, Topoisomerase, Wingless and Pepck) by reducing the degenerate site of primers and the length of target genes slightly. These five NPC fragments and 6 other molecular loci were amplified to test the monophyly of the coccinellid genus Sasajiscymnus Vandenberg. The analysis of our molecular data set clearly supported the genus Sasajiscymnus may be monophyletic but confirmation with an extended sampling is required. A fossil‐calibrated chronogram was generated by BEAST, indicating an origin of the genus at the end of the Cretaceous (77.87 Myr). Furthermore, a phylogenetic informativeness profile was generated to compare the phylogenetic properties of each gene more explicitly. The results showed that COI provides the strongest phylogenetic signal among all the genes, but Pepck, Topoisomerase, CADXM and CADMC are also relatively informative. Our results provide insight into the evolution of the genus Sasajiscymnus , and also enrich the molecular data resources for further study.

Molecular phylogeny and systematics of the subgenus Oxyphortica Duda from the Oriental region (Diptera: Drosophilidae: Stegana)

“…2) and is the least informative marker. Even though this maker seems to be unsuitable for reconstruction of rapid phylogenetic radiation in our study, the marker was routinely used in species recognition and phylogenetic reconstruction (Monteiro et al, 2000;Monaghan et al, 2005;Asokan et al, 2013;Resch et al, 2014;Huang et al, 2020). Overall, our trees based on combined datasets are more effective for deep-level phylogenetic analysis (Figs 1, 2A), which have higher support than when being used separately, even when a marker possesses relatively strong phylogenetic signal.…”

“…Evaluating the contribution of each individual gene in phylogenetic inference is crucial for selecting appropriate molecular markers for inferring phylogenetic relationships at different taxonomic levels (Huang et al, 2020). Phylogenetic informativeness profiles suggest that mitochondrial loci possess much greater phylogenetic signal to resolve the species-level phylogenetic relationships (Fig.…”

Phylogenetics of Piresia (Poaceae: Bambusoideae) reveals unexpected generic relationships within Olyreae with taxonomic and biogeographic implications

“…ML analyses were performed on the same partitions as for the BI analyses using RAxML v.8.2.8.12 (Stamatakis, 2014) on the CIPRES Science Gateway v.3.3 (Miller & al., 2010) using the option “‐f a” (search for the best‐scoring ML tree and a rapid bootstrap analysis) and 1000 bootstrap replicates (Stamatakis, 2014). We did not use the indels in the ML analyses because it is not possible to specify different partitions and models in RAxML (Stamatakis, 2014; Huang & al., 2020). Bootstrap values ≥70% were considered as supported (70%–79% weak, 80%–89% moderate, and 90%–100% strong support).…”

Elmis syriaca (Kuwert, 1890) and E. zoufali (Reitter, 1910) (Coleoptera: Elmidae) confirmed as distinct species based on molecular data, morphology and geographical distribution

“…DNA barcoding was used in population studies [10][11][12] and contributed to revisions of species distribution and in descriptions of newly discovered or previously overlooked taxa [7,8,[13][14][15][16][17][18][19][20]. Besides the cytochrome C oxidase subunit I (COI) gene (the standard mitochondrial barcoding marker), various nuclear markers have been proposed as alternative or supplementary barcodes for species delineation in Coleoptera (e.g., [21][22][23][24]); however, the sole use of molecular data may be misleading, and a combined evidence approach is warranted whenever possible in order to gain insight into taxonomic and systematic relationships (e.g., [3,6,8]).…”