Molecular phylogeny of Collembola inferred from ribosomal RNA genes
Introduction
Collembolans are small, wingless arthropods. More specifically, they are hexapods related to insects. More than 7850 species are known in the world (Janssens, 2007), and in some environments they are the most abundant group of animals (Palacios-Vargas and González, 1995, Hopkin, 1998). They live almost everywhere, with great variation in color and body shape. Börner (1904) used morphological characters to divide Collembola into two suborders: Arthropleona and Symphypleona. Two years later, he produced a detailed evolutionary tree of 30 Collembolan taxa (Börner, 1906a), which is very close to the modern concept of the relations within this class, and which remained unsurpassed until recently. Salmon (1964) set up a taxonomical hierarchy of Collembola of four suborders (Arthropleona, Neoarthropleona, Metaxypleona, and Symphypleona) and 17 families. He united Poduridae and Actaletidae into a new suborder Metaxypleona based on shared features of the oral organs and body segments, and he also divided the traditional Arthropleona into two groups: a redefined Arthropleona (with biting mouthparts) and Neoarthropleona (with sucking mouthparts). Later, two important taxonomic works (Yosii, 1977, Christiansen and Bellinger, 1980–1981) used a system that put Collembola into just two suborders Arthropleona and Symphypleona, in which Arthropleona comprises two sections Poduromorpha and Entomobryomorpha, and Symphypleona consists of Neelidae and Sminthuridae. All three of these taxonomic hierarchies (Salmon, 1964, Yosii, 1977, and Christiansen and Bellinger, 1980–1981), have been widely used over the past decades.
The traditional taxonomic system based on morphology continued to be improved with the development of cladistic analyses. With Protura as the outgroup, Lee and Thibaud (1998) analyzed the relationships among seven families of Arthropleona based on 28 morphological characters, together with ecobiological analysis and 18S rDNA data. Their results supported the division of Arthropleona into Poduroidea and Entomobryoidea, but provided no deep insight into the relationships between the common families within Arthropleona. D’Haese (2003a) performed a cladistic analysis of 131 morphological characters from 67 species of Collembola, and constructed the phylogenetic relationships of Collembola as, Poduromorpha versus (Entomobryomorpha + (Neelipleona + Symphypleona)). This scheme did not have a monophyletic Arthropleona.
Following the quick development of molecular systematics, mitochondrial DNA, ribosomal DNA, and other nuclear gene sequences have been used to study collembolan relationships (Frati et al., 1997, Frati and Dell’Ampio, 2000, Fanciulli et al., 2000). D’Haese (2002) analyzed the phylogenetic relationships among Symphypleona, Entomobryomorpha, and Poduromorpha based on the 28S rDNA (D1–D2 regions) sequences for 55 collembolans. In his study, Poduromorpha was monophyletic with two subclades: (Triacanthella + Odontellidae + Onychiuridae) and (Poduridae + Brachystomellidae + Neanuridae + Hypogastruridae); Entomobryomorpha was paraphyletic, and the (Tomoceridae + Oncopoduridae) group of “entomobryomorphs” was the sister group of Poduromorpha; Symphypleona was paraphyletic, with its Katiannidae being the sister of (Entomobryomorpha + Poduromorpha). By analyzing complete 18S rDNA and 28S rDNA (D3–D5 regions) sequences of 10 collembolans, Luan et al. (2005) got results similar to those of D’Haese (2002). The monophyly of Poduromorpha was also well-supported, Podura aquatica was the sister group of Neanuridae, and there was some evidence of paraphyly of the Symphypleona. Furthermore, these studies indicated that 18S + partial 28S rDNA is a good marker for constructing the phylogeny of Collembola.
None of these molecular phylogenetic studies included the important order, Neelipleona, and most of these studies were limited to the relationships of just one group of Collembola (Frati et al., 1997, Frati and Dell’Ampio, 2000, Fanciulli et al., 2000, Dell’Ampio et al., 2002) or to the phylogenetic position of Collembola in Arthropoda (Luan et al., 2005, Nardi et al., 2003).
Traditional concepts of the phylogeny of Collembola have been challenged in recent years. Arthropleona was replaced by two orders Poduromorpha and Entomobryomorpha (Cassagnau, 1971) and Neelidae was separated from Symphypleona as Order Neelipleona (Massoud, 1976, Christian, 1987). The four modern orders of Collembola (Poduromorpha, Entomobryomorpha, Symphypleona and Neelipleona) were summarized by Deharveng (2004), and are listed in Table 1. Janssens (2007) reviewed the recent opinions, and concluded that Neelipleona is not close to Symphypleona, but is a derived member of Entomobryomorpha instead.
Therefore, many important questions are still debated, such as the validity and the phylogenetic inter-relationships of the four orders (Table 1), the relationships among the groups within each order, the monophyly of Entomobryomorpha and Symphypleona, as well as the position of Neelipleona in Collembola. To address these questions here, we analyzed the complete 18S and partial 28S rRNA sequences (D7–D10 regions) of 30 species from 29 genera from 14 families, representing all the major subgroups of collembolans, including Neelipleona. To the best of our knowledge, no other laboratory has included Neelipleona for molecular phylogenetic analysis.
Section snippets
Specimens and outgroup selection
Collembolan specimens were collected in 75% ethanol by the Tullgren funnel method, from Shanghai, Zhejiang, Jiangsu and Hainan Provinces in China. All were stored in 100% ethanol at −20 °C after identification based on their morphological characters. Species details are given in Table 2.
Choosing an outgroup for collembolan species is difficult because there is no clear idea about the sister group of Collembola. From the traditional point of view, Collembola is close to Protura and Diplura in
Sequence variation and nucleotide composition
For 30 collembolan sequences, about 6% of the sites were ambiguously aligned and thus were excluded; such sites were mainly located in the V2, V4, and V7–9 variable regions of the 18S, and in the D8 and D10 divergent domains of the 28S rDNA sequences. The remaining alignment contained 2505 sites (including indels) for the phylogenetic analysis without the outgroups. Then, in the alignment that included the two outgroups, another 2% of the sites were found to be ambiguously aligned and excluded.
Unrooted trees versus rooted trees
Very similar topological structures of 30 Collembolans were obtained for the unrooted and rooted trees based on the ML/Bayesian analyses (Fig. 2, Fig. 3). Most of the bootstrap values are higher in the rooted tree than in the unrooted tree, which suggested that the insect outgroups were appropriate, and confirmed the monophyly of Poduromorpha and of Symphypleona. It also may mean that the less-conserved sites that were included in the unrooted analysis but had to be excluded from the rooted
Acknowledgments
Thanks to Dr. Feng Zhang from Nanjing University for identifying the specimens of genus Homidia. The authors are especially indebted to Dr. Yong-gang Yao from Kunming Institute of Zoology, Chinese Academy of Sciences, and Dr. Jon M. Mallatt from Washington State University, USA for their thoughtful suggestions, critical comments and linguistic improvement on the article. We thank Professor José G. Palacios-Vargas from National Autonomous University of Mexico, Professor Louis Deharveng from
References (50)
Recent advances in Collembola systematics
Pedobiologia
(2004)- et al.
Secondary structure and sequence variation of the 28S rRNA gene in the Neanuridae and its utility as a phylogenetic marker
Pedobiologia
(2002) - et al.
Molecular phylogeny of three subfamilies of the Neanuridae (Insecta, Collembola) and the position of the Antarctic species Friesea grisea Schäffer
Pedobiologia
(2000) - et al.
Is Ellipura monophyletic? A combined analysis of basal hexapod relationships with emphasis on the origin of insects
Org. Divers. Evol.
(2004) - et al.
Analysis of 18S rRNA gene of Octostigma sinensis (Projapygoidea: Octostigmatidae) supports the monophyly of Diplura
Pedobiologia
(2004) - et al.
Ecdysozoan phylogeny and Bayesian inference: first use of nearly complete 28S and 18S rRNA gene sequences to classify the arthropods and their kin
Mol. Phylogenet. Evol.
(2004) - et al.
Further use of nearly complete 28S and 18S rRNA genes to classify Ecdysozoa: 37 more arthropods and a kinorhynch
Mol. Phylogenet. Evol.
(2006) - et al.
Comprehensive comparison of structural characteristics in eukaryotic cytoplasmic large subunit (23S-like) ribosomal RNA
J. Mol. Evol.
(1996) - et al.
Phylogenetic relationships of basal hexapods among the mandibulate arthropods: a cladistic analysis based on comparative morphological characters
Zool. Scr.
(2004) Zur Systematik der Hexapoden
Zool. Anz.
(1904)
Das system der collembolen, nebst beschreibung neuer collembolen des hamburger naturhistorischen museums
Mitt. Naturh. Mus. Hamburg
Sobre la clasificación de los Oncopoduridae (Collembola), con descripción de species nuevas
Sobretiro de Los Anales De La Escuela Nacional De Ciencias Biologicas
The Collembola of North America North of the Rio Grand
The Collembola of North America North of the Rio Grande, A Taxonomic Analysis
Were the first springtails semi-aquatic? A phylogenetic approach by means of 28S rDNA and optimization alignment
Proc. R. Soc. Lond. B
Morphological appraisal of Collembola phylogeny with special emphasis on Poduromorpha and a test of the aquatic origin hypothesis
Zoo. Scr.
Homology and morphology in Poduromorpha (Hexapoda, Collembola)
Eur. J. Entomol.
Evolution of the mitochondrial cytochrome oxidase II gene in Collembola
J. Mol. Evol.
Population structure, gene flow and evolutionary relationships in four species of genera Tomocerus and Pogonognathellus (Collembola, Tomoceridae)
Biol. J. Linn. Soc. Lond.
Arthropod phylogeny based on eight molecular loci and morphology
Nature
Type I repressors of P element mobility
Genetics
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