Phylogenetic Signal Dissection of Heterogeneous 28S and 16S RRNA Genes in Spinicaudata (Branchiopoda, Diplostraca)

Overview

Journal Genes (Basel)

Publisher MDPI

Date 2021 Nov 27

PMID 34828311

Citations 1

Authors

Xiaoyan Sun

Jinhui Cheng

Affiliations

Soon will be listed here.

Abstract

It is still a challenge to reconstruct the deep phylogenetic relationships within spinicaudatans, and there are several different competing hypotheses regarding the interrelationships among Eocyzicidae, Cyzicidae s. s., Leptestheriidae, and Limnadiidae of the Suborder Spinicaudata. In order to explore the source of the inconsistencies, we focus on the sequence variation and the structure model of two rRNA genes based on extensive taxa sampling. The comparative sequence analysis revealed heterogeneity across species and the existence of conserved motifs in all spinicaudatan species. The level of intraspecific heterogeneity differed among species, which suggested that some species might have undergone a relaxed concerted evolution with respect to the gene. The Bayesian analyses were performed on nuclear (, ) and mitochondrial (, ) genes. Further, we investigated compositional heterogeneity between lineages and assessed the potential for phylogenetic noise compared to signal in the combined data set. Reducing the non-phylogenetic signals and application of optimal rRNA model recovered a topology congruent with inference from the transcriptome data, whereby Limnadiidae was placed as a sister group to Leptestheriidae + Eocyzicidae with high support (topology I). Tests of alternative hypotheses provided implicit support for four competing topologies, and topology I was the best.

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References

Gutell R, Cannone J, Shang Z, Du Y, Serra M . A story: unpaired adenosine bases in ribosomal RNAs. J Mol Biol. 2000; 304(3):335-54. DOI: 10.1006/jmbi.2000.4172. View

Springer M, Debry R, Douady C, Amrine H, Madsen O, de Jong W . Mitochondrial versus nuclear gene sequences in deep-level mammalian phylogeny reconstruction. Mol Biol Evol. 2001; 18(2):132-43. DOI: 10.1093/oxfordjournals.molbev.a003787. View

Sonnenberg R, Nolte A, Tautz D . An evaluation of LSU rDNA D1-D2 sequences for their use in species identification. Front Zool. 2007; 4:6. PMC: 1805435. DOI: 10.1186/1742-9994-4-6. View

Schwentner M, Timms B, Bastrop R, Richter S . Phylogeny of Spinicaudata (Branchiopoda, Crustacea) based on three molecular markers--an Australian origin for Limnadopsis. Mol Phylogenet Evol. 2009; 53(3):716-25. DOI: 10.1016/j.ympev.2009.07.021. View

Swain T, Taylor D . Structural rRNA characters support monophyly of raptorial limbs and paraphyly of limb specialization in water fleas. Proc Biol Sci. 2003; 270(1518):887-96. PMC: 1691322. DOI: 10.1098/rspb.2002.2297. View

Buckley T, Simon C, Flook P, Misof B . Secondary structure and conserved motifs of the frequently sequenced domains IV and V of the insect mitochondrial large subunit rRNA gene. Insect Mol Biol. 2000; 9(6):565-80. DOI: 10.1046/j.1365-2583.2000.00220.x. View

Higgs P . RNA secondary structure: physical and computational aspects. Q Rev Biophys. 2001; 33(3):199-253. DOI: 10.1017/s0033583500003620. View

Bik H, Fournier D, Sung W, Bergeron R, Thomas W . Intra-genomic variation in the ribosomal repeats of nematodes. PLoS One. 2013; 8(10):e78230. PMC: 3795665. DOI: 10.1371/journal.pone.0078230. View

Gillespie J, Yoder M, Wharton R . Predicted secondary structure for 28S and 18S rRNA from Ichneumonoidea (Insecta: Hymenoptera: Apocrita): impact on sequence alignment and phylogeny estimation. J Mol Evol. 2005; 61(1):114-37. DOI: 10.1007/s00239-004-0246-x. View

10.

Pisani D, Feuda R, Peterson K, Smith A . Resolving phylogenetic signal from noise when divergence is rapid: a new look at the old problem of echinoderm class relationships. Mol Phylogenet Evol. 2011; 62(1):27-34. DOI: 10.1016/j.ympev.2011.08.028. View

11.

Shimodaira H, Hasegawa M . CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics. 2001; 17(12):1246-7. DOI: 10.1093/bioinformatics/17.12.1246. View

12.

Townsend J, Su Z, Tekle Y . Phylogenetic signal and noise: predicting the power of a data set to resolve phylogeny. Syst Biol. 2012; 61(5):835-49. DOI: 10.1093/sysbio/sys036. View

13.

Nesnidal M, Helmkampf M, Bruchhaus I, Hausdorf B . Compositional heterogeneity and phylogenomic inference of metazoan relationships. Mol Biol Evol. 2010; 27(9):2095-104. DOI: 10.1093/molbev/msq097. View

14.

Rokas A, Carroll S . Frequent and widespread parallel evolution of protein sequences. Mol Biol Evol. 2008; 25(9):1943-53. DOI: 10.1093/molbev/msn143. View

15.

Rogers D . Spinicaudata Catalogus (Crustacea: Branchiopoda). Zool Stud. 2020; 59:e45. PMC: 7736771. DOI: 10.6620/ZS.2020.59-45. View

16.

Hartmann S, Vision T . Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?. BMC Evol Biol. 2008; 8:95. PMC: 2359737. DOI: 10.1186/1471-2148-8-95. View

17.

Reuter J, Mathews D . RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics. 2010; 11:129. PMC: 2984261. DOI: 10.1186/1471-2105-11-129. View

18.

Sun X, Cheng J . Characterization of the complete mitochondrial genome of Chinese Triops granarius and implications for species delimitation. Int J Biol Macromol. 2019; 135:734-744. DOI: 10.1016/j.ijbiomac.2019.05.208. View

19.

Lartillot N, Lepage T, Blanquart S . PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics. 2009; 25(17):2286-8. DOI: 10.1093/bioinformatics/btp368. View

20.

Crease T . The complete sequence of the mitochondrial genome of Daphnia pulex (Cladocera: Crustacea). Gene. 1999; 233(1-2):89-99. DOI: 10.1016/s0378-1119(99)00151-1. View