Phylogenetic Information Content of Copepoda Ribosomal DNA Repeat Units: ITS1 and ITS2 Impact

Overview

Journal Biomed Res Int

Publisher Wiley

Specialties Biomedical Engineering
Biotechnology
General Medicine

Date 2014 Sep 13

PMID 25215300

Citations 6

Authors

Maxim V Zagoskin

Valentina I Lazareva

Andrey K Grishanin

Dmitry V Mukha

Affiliations

Soon will be listed here.

Abstract

The utility of various regions of the ribosomal repeat unit for phylogenetic analysis was examined in 16 species representing four families, nine genera, and two orders of the subclass Copepoda (Crustacea). Fragments approximately 2000 bp in length containing the ribosomal DNA (rDNA) 18S and 28S gene fragments, the 5.8S gene, and the internal transcribed spacer regions I and II (ITS1 and ITS2) were amplified and analyzed. The DAMBE (Data Analysis in Molecular Biology and Evolution) software was used to analyze the saturation of nucleotide substitutions; this test revealed the suitability of both the 28S gene fragment and the ITS1/ITS2 rDNA regions for the reconstruction of phylogenetic trees. Distance (minimum evolution) and probabilistic (maximum likelihood, Bayesian) analyses of the data revealed that the 28S rDNA and the ITS1 and ITS2 regions are informative markers for inferring phylogenetic relationships among families of copepods and within the Cyclopidae family and associated genera. Split-graph analysis of concatenated ITS1/ITS2 rDNA regions of cyclopoid copepods suggested that the Mesocyclops, Thermocyclops, and Macrocyclops genera share complex evolutionary relationships. This study revealed that the ITS1 and ITS2 regions potentially represent different phylogenetic signals.

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References

Hasegawa M, Kishino H, Yano T . Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 1985; 22(2):160-74. DOI: 10.1007/BF02101694. View

Minxiao W, Song S, Chaolun L, Xin S . Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: useful molecular markers for phylogenetic and population studies. BMC Genomics. 2011; 12:73. PMC: 3041745. DOI: 10.1186/1471-2164-12-73. View

Bergsten J . A review of long-branch attraction. Cladistics. 2021; 21(2):163-193. DOI: 10.1111/j.1096-0031.2005.00059.x. View

Vergilino R, Markova S, Ventura M, Manca M, Dufresne F . Reticulate evolution of the Daphnia pulex complex as revealed by nuclear markers. Mol Ecol. 2011; 20(6):1191-207. DOI: 10.1111/j.1365-294X.2011.05004.x. View

Mukha D, Sidorenko A . [Detection and analysis of Tetrahymena pyriformis 26S ribosomal DNA domain sequences, differing in degree of evolutionary conservation]. Mol Biol (Mosk). 1995; 29(3):529-37. View

Cui R, Schumer M, Kruesi K, Walter R, Andolfatto P, Rosenthal G . Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes. Evolution. 2013; 67(8):2166-79. DOI: 10.1111/evo.12099. View

Taylor D, Hebert P, Colbourne J . Phylogenetics and evolution of the Daphnia longispina group (Crustacea) based on 12S rDNA sequence and allozyme variation. Mol Phylogenet Evol. 1996; 5(3):495-510. DOI: 10.1006/mpev.1996.0045. View

Mukha D, Sidorenko A . [Detection of highly conservative domains in the sequence of 17S ribosomal DNA from Tetrahymena pyriformis]. Genetika. 1996; 32(11):1494-7. View

Makarenkov V . T-REX: reconstructing and visualizing phylogenetic trees and reticulation networks. Bioinformatics. 2001; 17(7):664-8. DOI: 10.1093/bioinformatics/17.7.664. View

10.

Aguilar J, Nieto Feliner G . Additive polymorphisms and reticulation in an ITS phylogeny of thrifts (Armeria, Plumbaginaceae). Mol Phylogenet Evol. 2003; 28(3):430-47. DOI: 10.1016/s1055-7903(02)00301-9. View

11.

Cornils A, Blanco-Bercial L . Phylogeny of the Paracalanidae Giesbrecht, 1888 (Crustacea: Copepoda: Calanoida). Mol Phylogenet Evol. 2013; 69(3):861-72. DOI: 10.1016/j.ympev.2013.06.018. View

12.

Machida R, Tsuda A . Dissimilarity of species and forms of planktonic Neocalanus copepods using mitochondrial COI, 12S, nuclear ITS, and 28S gene sequences. PLoS One. 2010; 5(4):e10278. PMC: 2860979. DOI: 10.1371/journal.pone.0010278. View

13.

Eyun S, Lee Y, Suh H, Kim S, Soh H . Genetic identification and molecular phylogeny of Pseudodiaptomus species (Calanoida, Pseudodiaptomidae) in Korean waters. Zoolog Sci. 2007; 24(3):265-71. DOI: 10.2108/zsj.24.265. View

14.

Castresana J . Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000; 17(4):540-52. DOI: 10.1093/oxfordjournals.molbev.a026334. View

15.

Mallet J . Hybridization as an invasion of the genome. Trends Ecol Evol. 2006; 20(5):229-37. DOI: 10.1016/j.tree.2005.02.010. View

16.

Arnason U, Spilliaert R, Palsdottir A, Arnason A . Molecular identification of hybrids between the two largest whale species, the blue whale (Balaenoptera musculus) and the fin whale (B. physalus). Hereditas. 1991; 115(2):183-9. DOI: 10.1111/j.1601-5223.1991.tb03554.x. View

17.

Carson H, Kaneshiro K, Val F . NATURAL HYBRIDIZATION BETWEEN THE SYMPATRIC HAWAIIAN SPECIES DROSOPHILA SILVESTRIS AND DROSOPHILA HETERONEURA. Evolution. 2017; 43(1):190-203. DOI: 10.1111/j.1558-5646.1989.tb04217.x. View

18.

LARKIN M, Blackshields G, Brown N, Chenna R, McGettigan P, McWilliam H . Clustal W and Clustal X version 2.0. Bioinformatics. 2007; 23(21):2947-8. DOI: 10.1093/bioinformatics/btm404. View

19.

Tamura K . Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases. Mol Biol Evol. 1992; 9(4):678-87. DOI: 10.1093/oxfordjournals.molbev.a040752. View

20.

Maior T, Sheveleva N, Sukhanova L, Timoshkin O, Kirilchik S . [Molecular-phylogenetic analysis of cyclopoids (Copepoda: Cyclopoida) from Lake Baikal and its water catchment basin]. Genetika. 2011; 46(11):1556-64. View