Comparative Phylogenetic Perspectives on the Evolutionary Relationships in the Brine Shrimp Artemia Leach, 1819 (Crustacea: Anostraca) Based on Secondary Structure of ITS1 Gene

Document Type: Research Article


1 College of Life Sciences and Ecology, Hainan Tropical Ocean University, Yucai Rd, Sanya 572000, China

2 Institute of Evolution and Marine Biodiversity, Ocean University of China, 5 Yushan Road, Qingdao 266003, China

3 Department of Ecology, Evolution and Behavior, University of Minnesota, MN 55108, USA


This is the first study on phylogenetic relationships in the genus Artemia Leach, 1819 using the pattern and sequence of secondary structures of internal transcribed spacer 1 (ITS1). Significant intraspecific variation in the secondary structure of ITS1 rRNA was found in Artemia tibetiana. In the phylogenetic tree based on joined primary and secondary structure sequences, Artemia urmiana and parthenogenetic populations displayed new lineages, and two New World species (Artemia franciscana and Artemia persimilis) were located in a basal clade that was not detected in previous studies. The close evolutionary relationship between A. franciscana and A. persimilis are expressively supported by the previous empirical and experimental investigation on the ability of hybridization (in natural habitats and lab conditions) and analysis on allozyme markers.


Abatzopoulos TJ, Beardmore JA, Clegg JS, Sorgeloos P. 2002b. Artemia: basic and applied biology. Kluwer Academic Publishers, Dordrecht, the Netherlands.

Abatzopoulos TJ, Kappas I, Bossier P, Sorgeloos P, Beardmore JA. 2002a. Genetic characterization of Artemia tibetiana (Crustacea: Anostraca). Biol J Linnean Soc 75: 333-344.

Agatsuma T, Arakawa Y, Iwagami M, HonzakoY, Cahyaningsih U, Kang Sh-Y, Hong SJ. 2000 Molecular evidence of natural hybridization between Fasciola hepatica and F. gigantica. Parasitol Int 49: 231-238.

Alfaro ME, Zoller S, Lutzoni F. 2003. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov Chain Monte Carlo sampling and boostrappinginassessingphylogeneticconfidence. Mol Biol Evol 20: 255-266.

Amat F, Cohen RG, Hontoria F, Navarro JC. 2004. Further evidence and characterization of Artemia franciscana (Kellogg, 1906) populations in Argentina. J Biogeogr 31: 1735-1749.

Amat F, Hontaria F, Navarro JC, Vieira N, Mura G. 2007. Biodiversity loss in the genus Artemia in the Western Mediterranean Region. Limnetica 26: 177-194.

Asem A, Eimanifar A, Sun SC. 2016. Genetic variation and evolutionary origins of parthenogenetic Artemia (Crustacea: Anostraca) with different ploidies. Zool Scr 45: 421-436.

Asem A, Rastegar-Pouyani N, De losRios P. 2010. The genus Artemia Leach, 1819 (Crustacea: Branchiopoda): true and false taxonomical descriptions. Lat Am J Aquat Res 38: 501-506.

Baxevanis AD, Kappas I, Abatzopoulos TJ. 2006. Molecular phylogenetics and asexuality in the brine shrimp Artemia. Mol Phylogenet Evol 40: 724-738.

Baxevanis AD, Triantaphyllidis GV, Kappas I, Triantafyllidis A, Triantaphyllidis CD, Abatzopoulos TJ. 2005. Evolutionary assessment of Artemia tibetiana (Crustacea, Anostraca) based on morphometry and 16S rRNA RFLP analysis. J Zool Sys Evol Res 43: 189-198.

Beardmore JA, Abreu-Grobois FA. 1983. Taxonomy and evolution in the brine shrimp Artemia. In: Oxford GS, Rollinson D (eds) Protein Polymorphism: Adaptive and Taxonomic Significance. Academic Press, London, pp. 153-164.

Campbell CS, Wright WA, Cox M, Vining TF, Major CS, Arsenault MP. 2005. Nuclear ribosomal DNA internal transcribed spacer 1 (ITS1) in Picea (Pinaceae): sequence divergence and structure. Mol Phylogenet Evol 35: 165-185.

Cohen RG. 2012. Review of the biogeography of Artemia Leach, 1819 (Crustacea: Anostraca). Int J Artemaia Biol 2: 9-23.

Coleman AW. 2013. Analysis of mammalian rDNA internal transcribed spacers. PLoS One 8(11): e79122.

Coyne JA, Orr HA. 1997. Patterns of speciation in Drosophila revisited. Evolution 51: 295-303.

Eimanifar A, Van Stappen G, Marden B, Wink M. 2014. Artemia biodiversity in Asia with the focus on the phylogeography of the introduced American species Artemia franciscana Kellogg, 1906. Mol Phylogenet Evol 79:392-403.

Gajardo G, Beardmore JA, Sorgeloos P. 2001a. International study on Artemia LXII. Genomic relationships between Artemia franciscana and A. persimilis, inferred from chromocentre numbers. Heredity 87:172-177.

Gajardo G, Conceicao DM, Weber L, Beardmore JA. 1995. Genetic variability and inter populational differentiation of Artemia strains from South America. Hydrobiologia 302:21-29.

Gajardo G, Crespo J, Triantafyllidis A, Tzika A, Baxevanis A, Kappas I, Abatzopoulos TJ. 2004. Species identification of Chilean Artemia populations based on mitochondrial DNA RFLP analysis. J Biogeogr 31:547-555.

Gajardo G, Parraguez M, Beardmore JA, Sorgeloos P. 2001b. Reproduction in the brine shrimp Artemia: evolutionary relevance of laboratory cross-fertility tests. J Zool 253:25-32.

Gottschling M, Plotner J. 2004. Secondary structure models of the nuclear internal transcribed spacer regions and 5.8S rRNA in Calciodinelloideae (Peridiniaceae) and other dinoagellates. Nucleic Acids Res 32: 307-315.

Hillis DM, Bull JJ. 1993. An empirical test of bootstrapping as a method for assessing confidence In phylogenetic analysis. Syst Boil 42: 182-192.

Hodac L, Scheben AP, Hojsgaard D, Paun O, Horandl E. 2014. ITS Polymorphisms shed light on hybrid evolution in apomictic plants: A case study on the ranunculusauricomuscomplex. PLoS One 9: e103003.

Hofacker IL, Fekete M, Stadler PF. 2002. Secondary structure prediction for aligned RNA sequences. J Mol Biol 319: 1059-1066.

Hosseinzadeh Colagar A, Yousefzadeh H, Shayanmehr F, Jalali SG, Zare H, Tippery NP. 2016. Molecular taxonomy of Hyrcanian Alnus using nuclear ribosomal ITS and chloroplast trnH-psbA DNA barcode markers. Syst Biodiver, 14(1): 88-101.

Hou L, Bi X, Zou X, He C, Yang L, Qu R, Liu Z. 2006. Molecular systematics of bisexual Artemia populations. Aquacult Res 37: 671-680.

Kappas I, Baxevanis AD, ManiatsiS, Abatzopoulos TJ. 2009. Porous genomes and species integrity in the branchiopod Artemia. Mol Phylogenet Evol 52: 192-204.

Kovalev SY, Golovljova IV, Mukhacheva TA. 2016. Natural hybridization between Ixodes ricinus and Ixodes persulcatus ticks evidenced by molecular genetics methods. Ticks Tick-borne Dis 7: 113-118.

Librado P, Rozas J. 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.

Maccari M, Amat F, Gómez A. 2013. Origin and genetic diversity of diploid parthenogenetic Artemia in Eurasia. PLoS One 8(12): e83348.

Mallet J, Beltrán M, Neukirchen W, Linares M. 2007. Natural hybridization in heliconiine butterflies: the species boundary as a continuum. BMC Evol Biol 7(28):1-16.

Mallet J. 2005. Hybridization as an invasion of the genome. Trends Ecolo Evol 20:229-237.

ManiatsiS, Baxevanis AD, Kappas I, Deligiannidis P, Triantafyllidis A, Papakostas S, Bougiouklis D, Abatzopoulos TJ. 2011. Is polyploidy a persevering accident or an adaptive evolutionary pattern? The case of the brine shrimp Artemia. Mol Phylogenet Evol 58: 353-364.

ManiatsiS, Kappas I, Baxevanis AD, Farmaki T, Abatzopoulos TJ. 2009. Sharp Phylogeographic Breaks and Patterns of Genealogical Concordance in the Brine Shrimp Artemia franciscana. Int J Mol Sci 10: 5455-5470.

Mathews DH, Sabina J, Zuker M, Turner DH. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288: 911-940.

Miller MA, Pfeiffer W, Schwartz T. 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees Gateway Computing Environments Workshop (GCE), IEEE 1-8.

Nylander JAA. 2004. MrModeltest v2.Programdistributedbythe author. Evolutionary Biology Centre, Uppsala University.

Papeschi AG, Cohen RG, Pastorino XI, Amat F. 2000. Cytogenetic proof that the brine shrimp Artemia franciscana (Crustacea, Branchiopoda) is found in Argentina Hereditas 133: 159-166.

Parraguez M, Gajardo G, Beardmore JA. 2009. The New World Artemia species A. franciscana and A. persimilis are highly differentiated for chromosome size and heterochromatin content. Hereditas 146: 93-103.

Pilla EJS, Beardmore JA. 1994. Genetic and morphometric differentiation in old world bisexual species of Artemia (the brine shrimp). Heredity 73: 47-56.

Price TD, Bouvier MM. 2002. The evolution of F1 postzygotic incompatibilities in birds. Evol 56: 2083-2089.

Rambaut A. 2012. FigTree (version 1.4.0). Available at

Reblova M, Untereiner WA, Reblova K. 2013. Novel evolutionary lineages revealed in the chaetothyriales(Fungi) based on multigene phylogenetic analyses and comparison of ITS secondary structure. PLoS ONE 8(5): e63547

Reuter JS, Mathews DH. 2010. RNA structure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics 11: 129.

Ruiz O, Amat F, Saavedra C, Papeschi A, Cohen RG, Baxevanis AD, Kappas I, Abatzopoulos TJ, Navarro JC. 2008. Genetic characterization of argentineanArtemia species with different fatty acid profiles. Hydrobiologia 610: 223-234.

Seehausen O. 2004. Hybridization and adaptive radiation. Trends Ecol Evol 19: 198-206.

Seibel P, Muller T, Dandekar T, Schultz J, Wolf M. 2006. 4SALE-a tool for synchronous RNA sequence and secondary structure alignment and editing. BMC Bioinformatics 7: 498.

Sun P, Clamp C, Xu D. 2010. Analysis of the secondary structure of ITS transcripts in peritrich ciliates (Ciliophora, Oligohymenophorea): Implications for structural evolution and phylogenetic reconstruction. Mol Phylogenet Evol 56: 242-251.

Sun Y, Zhong YC, Song WQ, Zhang RS, Chen RY. 1999. Detection of genetic relationships among four Artemia species using randomly amplified polymorphic DNA (RAPD). Int J Salt Lake Res 8: 139-147.

Tamura K, Stecher G, Peterson D, Filipski A, Kuma, S. 2013. MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30: 2725-2729.

Triantaphyllidis GV, Criel GRJ, Abatzopoulos TJ, Sorgeloos P. 1997. International study on Artemia. LIII. Morphological study of Artemia with emphasis to old world strains. I. Bisexual populations. Hydrobiologia 357: 139-153.

Vikas PA, SajeshkumarNK, Thomas PC, Chakraborty K, Vijayan KK. 2012. Aquaculture relatedinvasionoftheexoticArtemia franciscana and displacement of the autochthonous Artemia populations from the hypersaline habitats of India. Hydrobiologia 684: 129-142.

Wang P, Gaao F, Huang J, Strüder-Kypke M, Yi Z. 2015. A case study to estimate the applicability of secondary structures of SSU-rRNA gene in taxonomy and phylogenetic analyses of ciliates. Zool Scr 44: 574–585.

Wolf M, Ruderisch B, Dandekar T, Schultz J, Muller T. 2008. ProfDistS: (profile-) distance based phylogeny on sequence-structure alignments. Bioinformatics 24: 2401-2402.

Yosefzadeh H, Hosseinzadeh Colagar A, Tabari M, Sattarian A, Assadi M. 2012 Utility of ITS region sequence and structure for molecular identification of Tilia species from Hyrcanian forests, Iran. Plant Syst Evol 298: 947-961.

Zheng B, Sun SC. 2013. Review of the biogeography of Artemia Leach, 1819 (Crustacea: Anostraca) in China. Int J Artemia Biol 3: 20-50.

Zuker M. 1989. On finding all suboptimal foldings of an RNA molecule. Science 244: 48-52.

Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415.

Zuñiga O, Wilson R, Amat F, Hontoria F. 1999. Distribution and characterization of Chilean populations of the brine shrimp Artemia (Crustacea, Branchiopoda, Anostraca). Int J Salt Lake Res 8: 23-40.