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Three Nuclear Protein-Coding Genes Corroborate a Recent Genes Genet. Syst. (2021) 96, p. 1–12 Molecular phylogeny of Branchiopoda 1 Three nuclear protein-coding genes corroborate a recent phylogenomic model of the Branchiopoda (Crustacea) and provide estimates of the divergence times of the major branchiopodan taxa Taro Uozumi1,2, Keisuke Ishiwata1,2, Mark J. Grygier3,4, La-orsri Sanoamuang5 and Zhi-Hui Su1,2* 1Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan 2JT Biohistory Research Hall, Takatsuki, Osaka 569-1125, Japan 3Lake Biwa Museum, Kusatsu, Shiga 525-0001, Japan 4Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202301, Taiwan 5Applied Taxonomic Research Center and International College, Khon Kaen University, Khon Kaen 40002, Thailand (Received 24 August 2020, accepted 18 October 2020; J-STAGE Advance published date: 14 March 2021) The class Branchiopoda (Crustacea) shows great diversity in morphology and lifestyle among its constituent higher-level taxa: Anostraca, Notostraca, Laevicau- data, Spinicaudata, Cyclestherida and Cladocera. The phylogenetic relationships among these taxa have long been controversial. We sequenced three orthologous nuclear genes that encode the catalytic subunit of DNA polymerase delta and the largest and second-largest subunits of RNA polymerase II in the expectation that the amino acid sequences encoded by these genes might be effective in clarify- ing branchiopod phylogeny and estimating the times of divergence of the major branchiopodan taxa. The results of phylogenetic analyses based on these amino acid sequences support the monophyly of Branchiopoda and provide strong molec- ular evidence in support of the following phylogenetic relationships: (Anostraca, (Notostraca, (Laevicaudata, (Spinicaudata, (Cyclestherida, Cladocera))))). Within Cladocera, comparison of the nucleotide sequences of these same genes shows Ctenopoda to be the sister group of Haplopoda + Anomopoda. Three statistical tests based on the present amino acid sequence data—the approximately unbiased test, Kishino–Hasegawa test and weighted Shimodaira–Hasegawa test—tend to refute most of the previous molecular phylogenetic studies on Branchiopoda, which have placed Notostraca differently than here; however, our results corroborate those of one recent phylogenomic study, thus confirming the effectiveness of these three genes to investigate relationships among branchiopod higher taxa. Diver- gence time estimates calibrated on the basis of fossil evidence suggest that the first divergence of extant branchiopods occurred about 534 Ma during the early Cambrian period and that diversification within the extant branchiopod lineages started in or after the late Permian. Key words: Branchiopoda, molecular phylogeny and evolution, chronology of cladogenesis, DNA polymerase gene, RNA polymerase gene Edited by Junko Kusumi INTRODUCTION * Corresponding author. [email protected] DOI: https://doi.org/10.1266/ggs.20-00046 The class Branchiopoda (Crustacea) is a relatively Copyright: ©2021 The Author(s). This is small, primarily freshwater taxon comprising about an open access article distributed under 1,120 described species (Adamowicz and Purvis, 2005; the terms of the Creative Commons BY 4.0 Brendonck et al., 2008; Forró et al., 2008; Ahyong et al., International (Attribution) License (https://creativecommons.org/ licenses/by/4.0/legalcode), which permits the unrestricted distri- 2011). Branchiopods display a wide diversity of morphol- bution, reproduction and use of the article provided the original ogy and lifestyle (Olesen, 2009) and comprise six main source and authors are credited. groups: Anostraca (fairy shrimps); Notostraca (tadpole 2 T. UOZUMI et al. shrimps); Laevicaudata, Spinicaudata and Cyclestherida rently considered by many to be the clade most closely (clam shrimps); and Cladocera (water fleas). Laevicau- related to Hexapoda (Regier et al., 2010; von Reumont data, Spinicaudata and Cyclestherida were previously et al., 2012; Oakley et al., 2013; Schwentner et al., 2018; classified together as ‘Conchostraca’, but that grouping Lozano-Fernandez et al., 2019; Noah et al., 2020), but is now recognized as paraphyletic (Olesen and Richter, Branchiopoda has also been considered to be the sis- 2013). All non-cladocerans (fairy shrimps, tadpole ter group of Hexapoda (Glenner et al., 2006; Lozano- shrimps and clam shrimps) live in inland freshwaters or Fernandez et al., 2019). For a review of this topic, see salt lakes and are generally known as “large branchio- Giribet and Edgecombe (2012). pods”. Although they share characteristics such as many In recent years, many investigations of branchiopod serially similar phyllopodous trunk limbs (Olesen, 2009), phylogeny and evolution have been conducted, based morphological and molecular analyses suggest that “large on analyses of both morphological and molecular data branchiopods” are paraphyletic (see Olesen and Richter, (Hanner and Fugate, 1997; Olesen, 1998, 2000; Negrea 2013). About half of the known species of Branchiopoda et al., 1999; Taylor et al., 1999; Spears and Abele, 2000; are cladocerans, some of which are marine. The Cladoc- Braband et al., 2002; deWaard et al., 2006; Stenderup et era are further divided into four subgroups, Anomopoda, al., 2006; Richter et al., 2007; Olesen, 2009; Schwentner Ctenopoda, Haplopoda and Onychopoda (Calman, 1909; et al., 2018; Luchetti et al., 2019). Relationships among Fryer, 1987; Walossek, 1993; Olesen et al., 1997; Olesen, the higher-level taxa, especially the phylogenetic posi- 1998, 2004; Negrea et al., 1999). tions of Notostraca and Cyclestherida and the phylogeny The systematics of Branchiopoda has recently received within Cladocera, have long been disputed (Stenderup much attention, not only because of interest in the intrin- et al., 2006; Richter et al., 2007; Olesen, 2009) (see Fig. sic diversity within the group, but also on account of bran- 1). Nonetheless, morphological analyses have succeeded chiopods’ possible importance for understanding the origin in providing a model of branchiopod sister-group relations and evolution of insects (Hexapoda). Molecular system- and phylogeny, namely (Anostraca, (Notostraca, (Laevi- atics has greatly changed our traditional understanding caudata, (Spinicaudata, (Cyclestherida, Cladocera))))) of arthropod phylogeny by revealing that Crustacea and (Richter et al., 2007; Olesen, 2009) (Fig. 1A). Hexapoda form a common clade (Pancrustacea), which As for molecular evidence, mitochondrial 12S rRNA is now widely accepted among zoologists; for a review, data supported Notostraca as the sister group to Laevi- see Giribet and Edgecombe (2019). Among crustaceans, caudata (Braband et al., 2002) (Fig. 1D), whereas maxi- either Remipedia or Remipedia + Cephalocarida is cur- mum likelihood (ML) analysis and Bayesian inference A Haplopoda B Haplopoda Anomopoda Cladocera Anomopoda Cladocera Ctenopoda Ctenopoda Cyclestherida Cyclestherida Spinicaudata Spinicaudata Laevicaudata Notostraca Notostraca Laevicaudata Anostraca Anostraca C Haplopoda D Haplopoda Anomopoda Cladocera Anomopoda Cladocera Ctenopoda Ctenopoda Cyclestherida Cyclestherida Notostraca Spinicaudata Spinicaudata Notostraca Laevicaudata Laevicaudata Anostraca Anostraca Fig. 1. Phylogenetic hypotheses of Branchiopoda based on morphological and molecular analyses. A, mainly based on morphological studies (Richter et al., 2007; Olesen, 2009; see also Olesen and Richter, 2013) and sup- ported by a recent phylogenomic study (Schwentner et al., 2018); B, C and D, based on various molecular markers with different analytical methods as described in the Introduction (for B: deWaard et al., 2006; Stenderup et al., 2006; Richter et al., 2007; for C: Stenderup et al., 2006; for D: Braband et al., 2002). Molecular phylogeny of Branchiopoda 3 based on mitochondrial 16S rRNA and nuclear 28S rRNA branchiopod representing all six higher taxa to address data supported Notostraca as the sister group to Cycles- the questions raised above. Phylogenetic analyses were therida + Cladocera (Stenderup et al., 2006) (Fig. 1C) and conducted based on the inferred aa sequences of the maximum parsimony analysis supported Notostraca as encoded proteins, and previously proposed phylogenetic the sister group to Spinicaudata + Cyclestherida + Cla- hypotheses were evaluated statistically. In addition, the docera (Stenderup et al., 2006) (Fig. 1B). This last phy- divergence times of branchiopod lineages were estimated logeny (Fig. 1B) was also supported by an analysis based based on fossil calibration points including a recently dis- on six molecular loci (COI, 16S rRNA, 18S rRNA, EF-1 covered early spinicaudatan fossil (Gueriau et al., 2016). alpha, 12S rRNA and 28S rRNA) (deWaard et al., 2006), but when the same authors restricted their analysis to MATERIALS AND METHODS only three of these loci (COI, 16S rRNA and 18S rRNA), four of the large branchiopod taxa, Anostraca, Notostraca, Taxonomic sampling The nucleotide sequences Laevicaudata and Spinicaudata, were clustered into one reported here have been deposited in the DDBJ/EMBL/ clade. In the analyses of Richter et al. (2007), who used GenBank nucleotide sequence databases with accession sequence data from six loci and 65 morphological char- numbers LC532181–LC532216 as shown in Supplemen- acters, the morphological data supported a sister-group tary Table S1. relationship between Notostraca and Diplostraca (= Lae- Supplementary Table S1 lists all the taxa used in this vicaudata + Spinicaudata
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