Mitogenomics of Cladocera (Branchiopoda): Marked gene order rearrangements and independent predation roots

Shao-Lin Xu; Bo-Ping Han; Alejandro Martínez; Martin Schwentner; Diego Fontaneto; Henri J Dumont; Alexey A Kotov

doi:10.1016/j.ympev.2021.107275

Mitogenomics of Cladocera (Branchiopoda): Marked gene order rearrangements and independent predation roots

Mol Phylogenet Evol. 2021 Nov:164:107275. doi: 10.1016/j.ympev.2021.107275. Epub 2021 Jul 31.

Authors

Shao-Lin Xu¹, Bo-Ping Han², Alejandro Martínez³, Martin Schwentner⁴, Diego Fontaneto³, Henri J Dumont⁵, Alexey A Kotov⁶

Affiliations

¹ Jinan University, Department of Ecology, Guangzhou 510632, China.
² Jinan University, Department of Ecology, Guangzhou 510632, China. Electronic address: tbphan@126.com.
³ National Research Council of Italy (CNR), Water Research Institute (IRSA), Molecular Ecology Group (MEG), Largo Tonolli 50, I-28922 Verbania Pallanza, Italy.
⁴ Naturhistorisches Museum Wien (NHMW), 1140 Vienna, Austria.
⁵ Jinan University, Department of Ecology, Guangzhou 510632, China; Ghent University, Department of Biology, Ledeganckstraat 35, B-9000 Ghent, Belgium.
⁶ Laboratory of Aquatic Ecology and Invasions, A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russia.

PMID: 34339827
DOI: 10.1016/j.ympev.2021.107275

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.

Keywords: Cladocera; Gene rearrangement; Gymnomera; Metagenomic; Mitogenomes.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Bayes Theorem
Cladocera*
Gene Order
Gene Rearrangement
Genome, Mitochondrial*
Phylogeny
Predatory Behavior