@article{95805a52085b4e4280a83fcd0a473894,
title = "Phylogenomic analysis of the beetle suborder Adephaga with comparison of tailored and generalized ultraconserved element probe performance",
abstract = "Adephaga is the second largest suborder of beetles (Coleoptera) and they serve as important arthropod predators in both aquatic and terrestrial ecosystems. The suborder is divided into Geadephaga comprising terrestrial families and Hydradephaga for aquatic lineages. Despite numerous studies, phylogenetic relationships among the adephagan families and monophyly of the Hydradephaga itself remain in question. Here we conduct a comprehensive phylogenomic analysis of the suborder using ultraconserved elements (UCEs). This study presents the first in vitro test of a newly developed UCE probe set customized for use within Adephaga that includes both probes tailored specifically for the suborder, alongside generalized Coleoptera probes previously found to work in adephagan taxa. We assess the utility of the entire probe set, as well as comparing the tailored and generalized probes alone for reconstructing evolutionary relationships. Our analyses recovered strong support for the paraphyly of Hydradephaga with whirligig beetles (Gyrinidae) placed as sister to all other adephagan families. Geadephaga was strongly supported as monophyletic and placed sister to a clade composed of Haliplidae + Dytiscoidea. Monophyly of Dytiscoidea was strongly supported with relationships among the dytiscoid families resolved and strongly supported. Relationships among the subfamilies of Dytiscidae were strongly supported but largely incongruent with prior phylogenetic estimates for the family. The results of our UCE probe comparison showed that tailored probes alone outperformed generalized probes alone, as well as the full combined probe set (containing both types of probes), under decreased taxon sampling. When taxon sampling was increased, the full combined probe set outperformed both tailored probes and generalized probes alone. This study provides further evidence that UCE probe sets customized for a focal group result in a greater number of recovered loci and substantially improve phylogenomic analysis.",
author = "Gustafson, {Grey T.} and Baca, {Stephen M.} and Alexander, {Alana M.} and Short, {Andrew E.Z.}",
note = "Funding Information: We are very grateful to Matt Gimmel, Ji?? H?jek, Makoto Kato, Kelly Miller and Emmanuel Toussaint for providing specimens of key taxa utilized in our analyses. We also thank the University of Kansas Center for Research Computing and the Biodiversity Institute for computation resources used during this project. The authors also wish to acknowledge the use of New Zealand eScience Infrastructure (NeSI) high-performance computing facilities, consulting support and/or training services as part of this research. New Zealand's national facilities are provided by NeSI and funded jointly by NeSI's collaborator institutions and through the Ministry of Business, Innovation & Employment's Research Infrastructure programme (https://www.nesi.org.nz). We thank Michael Branstetter and two anonymous reviewers for their constructive comments on this manuscript. This work was supported in part by US National Science Foundation grant DEB-1453452 to AEZS. GTG was supported by a NIH IRACDA postdoctoral research fellowship (5K12GM063651) while conducting this work. SMB was supported by the NSF Graduate Research Fellowship (NSF0064451). All authors declare there are no conflicts of interest. Funding Information: We are very grateful to Matt Gimmel, Ji{\v r}{\'i} H{\'a}jek, Makoto Kato, Kelly Miller and Emmanuel Toussaint for providing specimens of key taxa utilized in our analyses. We also thank the University of Kansas Center for Research Computing and the Biodiversity Institute for computation resources used during this project. The authors also wish to acknowledge the use of New Zealand eScience Infrastructure (NeSI) high‐performance computing facilities, consulting support and/or training services as part of this research. New Zealand's national facilities are provided by NeSI and funded jointly by NeSI's collaborator institutions and through the Ministry of Business, Innovation & Employment's Research Infrastructure programme ( https://www.nesi.org.nz ). We thank Michael Branstetter and two anonymous reviewers for their constructive comments on this manuscript. This work was supported in part by US National Science Foundation grant DEB‐1453452 to AEZS. GTG was supported by a NIH IRACDA postdoctoral research fellowship (5K12GM063651) while conducting this work. SMB was supported by the NSF Graduate Research Fellowship (NSF0064451). All authors declare there are no conflicts of interest. Publisher Copyright: {\textcopyright} 2019 The Royal Entomological Society",
year = "2020",
month = jul,
day = "1",
doi = "10.1111/syen.12413",
language = "English (US)",
volume = "45",
pages = "552--570",
journal = "Systematic Entomology",
issn = "0307-6970",
publisher = "Wiley-Blackwell",
number = "3",
}