| Abstract | Cladocera (Crustacea: Branchiopoda) is a key group of invertebrates. Despite a long history of phylogenetic research, relationships within this group remain disputed. We here provide new insights based on 15 new mitochondrial genomes obtained from high-throughput sequencing (HTS) and 40 mitogenomes extracted from published HTS datasets. Together with 25 mitogenomes from GenBank, we generated a matrix of 80 mitogenomes, 44 of them belonging to Cladocera. We also obtained a matrix with 168 nuclear orthologous genes to further assess the phylogenetic result from mitogenomes based on published data and one new HTS data ofLeptodora. Maximum likelihood and Bayesian phylogenetic analyses recovered all Branchiopoda orders as monophyletic and supported a sister-group relationship between Anomopoda and Onychopoda, making the taxon Gymnomera paraphyletic and supporting an independent origin of predatory Haplopoda and Onychopoda. The nuclear phylogeny and topological tests also support Gymnomera as paraphyletic, and the nuclear phylogeny strongly supports a sister-group relationship between Ctenopoda and Haplopoda. We provide a fossil-calibrated time tree, congruent with a Carboniferous origin for Cladocera and a subsequent diversification of the crown group of Anomopoda, Onychopoda, and Ctenopoda, at least in the Triassic. Despite their long evolutionary history, non-Cladoceran Branchiopoda exhibited high mitogenome structural stability. On the other hand, 21 out of 24 gene rearrangements occurred within the relatively younger Cladocera. We found the differential base compositional skewness patterns between Daphnia s.s. and Ctenodaphnia, which might be related to the divergence between these taxa. We also provide evidence to support the recent finding that Spinicaudata possesses mitogenomes with inversed compositional skewness without gene rearrangement. Such a pattern has only been reported in Spinicaudata. |
| Text | 455763 2021 10.1016/j.ympev.2021.107275 cladocera Mitogenomics of Cladocera Branchiopoda marked gene order rearrangements and independent predation roots. Shao Lin Xu, Bo Ping Han, Alejandro Martinez, Martin Schwentner, Diego Fontaneto, Henri J Dumon, Alexey A Kotov 1Jinan University, Department of Ecology, Guangzhou 510632, China. 2Jinan University, Department of Ecology, Guangzhou 510632, China. Electronic address tbphan@126.com. 3National Research Council of Italy CNR , Water Research Institute IRSA , Molecular Ecology Group MEG , Largo Tonolli 50, I 28922 Verbania Pallanza, Italy. 4Naturhistorisches Museum Wien NHMW , 1140 Vienna, Austria. 5Jinan University, Department of Ecology, Guangzhou 510632, China; Ghent University, Department of Biology, Ledeganckstraat 35, B 9000, Ghent, Belgium. 6Laboratory of Aquatic Ecology and Invasions, A. N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia. Cladocera Crustacea Branchiopoda is a key group of invertebrates. Despite a long history of phylogenetic research, relationships within this group remain disputed. We here provide new insights based on 15 new mitochondrial genomes obtained from high throughput sequencing HTS and 40 mitogenomes extracted from published HTS datasets. Together with 25 mitogenomes from GenBank, we generated a matrix of 80 mitogenomes, 44 of them belonging to Cladocera. We also obtained a matrix with 168 nuclear orthologous genes to further assess the phylogenetic result from mitogenomes based on published data and one new HTS data ofLeptodora. Maximum likelihood and Bayesian phylogenetic analyses recovered all Branchiopoda orders as monophyletic and supported a sister group relationship between Anomopoda and Onychopoda, making the taxon Gymnomera paraphyletic and supporting an independent origin of predatory Haplopoda and Onychopoda. The nuclear phylogeny and topological tests also support Gymnomera as paraphyletic, and the nuclear phylogeny strongly supports a sister group relationship between Ctenopoda and Haplopoda. We provide a fossil calibrated time tree, congruent with a Carboniferous origin for Cladocera and a subsequent diversification of the crown group of Anomopoda, Onychopoda, and Ctenopoda, at least in the Triassic. Despite their long evolutionary history, non Cladoceran Branchiopoda exhibited high mitogenome structural stability. On the other hand, 21 out of 24 gene rearrangements occurred within the relatively younger Cladocera. We found the differential base compositional skewness patterns between Daphnia s.s. and Ctenodaphnia, which might be related to the divergence between these taxa. We also provide evidence to support the recent finding that Spinicaudata possesses mitogenomes with inversed compositional skewness without gene rearrangement. Such a pattern has only been reported in Spinicaudata. Published version https //www.sciencedirect.com/science/article/abs/pii/S1055790321002086 via%3Dihub cladocera 1 s2.0 S1055790321002086 main.pdf Articolo in rivista Academic Press 1095 9513 Molecular phylogenetics and evolution Online Molecular phylogenetics and evolution Online Mol. phylogenet. evol. Online Molecular phylogenetics and evolution Online diego.fontaneto FONTANETO DIEGO alejandro.martinezgarcia MARTINEZ GARCIA ALEJANDRO |
