Analysis of intragenomic variation of the rDNA internal transcribed spacers (ITS) in Halichondrida (Porifera: Demospongiae)

Abstract

Three species of sponges, Axinella aruensis, Phakellia sp. and Acanthella cavernosa, were selected to investigate the extent of intragenomic variation (IGV) in the internal transcribed spacers (ITS-1 and ITS-2) of the ribosomal DNA within the order Halichondrida. The IGV was detected in both the spacers and in the three species. At least three non-identical sequences were found in any single individual with the number of polymorphic sites within species ranging from 6 to 77. Uncorrected distance values up to 29% were observed in the ITS-2 of Axinella aruensis. The levels of polymorphism found in this species are the highest reported for Porifera and comparable to those observed in hybrid species of scleractinean corals. Analyses of ITS sequences from multiple clones from individuals of Halichondrida are strongly recommended if these genetic markers are to be used to depict phylogenetic and/or phylogeographic relationships of closely related species and their populations. Data from other nuclear and mitochondrial markers should be used to complement conclusions derived from studies based on ITS sequences.

Analysis of ITS1 and ITS2 sequences in Ensis razor shells: suitability as molecular markers at the population and species levels, and evolution of these ribosomal DNA spacers

“…Even though concerted evolution functions extremely well on all nrDNA genes and spacers in the vast majority of organisms (Eickbush and Eickbush 2007), some authors have recommended analysing the intragenomic divergence levels before using the internal transcribed spacers of the major ribosomal genes (ITS1 and ITS2) as molecular markers (Leo and Barker 2002;Wörheide et al 2004;Alvarez et al 2007;Sword et al 2007). Interestingly, according to Harris and Crandall (2000), in all cases reported so far where intragenomic divergence was looked for within ITS1 and ITS2, it was found to some degree.…”

A skeleton‐less sponge ofCaribbean mangroves: invasive or undescribed?

“…Unfortunately, the slow rate of change of most mitochondrial genes in Porifera, relative to other metazoans, has made it impossible to obtain a reliable molecular clock for this phylum (Huang et al 2008 . However, this level of variability was ten times lower than the greatest intraspecific variation estimated for this marker in sponges, 29% in Acanthella cavernosa DENDY 1922 ( Alvarez et al 2007).…”

“…However, this level of variability was ten times lower than the greatest intraspecific variation estimated for this marker in sponges, 29% in Acanthella cavernosa Dendy 1922 (Álvarez et al. ).…”

“…; Álvarez et al. ; Redmond & McCormack ). The internal transcribed spacer (ITS) regions located between nuclear ribosomal genes also present levels of genetic variation that have allowed detection of species boundaries and patterns of population differentiation among geographic samples in sponges (e.g., Wörheide et al.…”

“…Molecular markers (based on DNA sequences) are required to define species boundaries in sponges when morphological, histological, and biochemical characters do not provide sufficient discriminatory power, as in the genus Halisarca (Borchiellini et al 2000;Boury-Esnault & Sol e-Cava 2004;Heim et al 2007). The genetic marker most used in sponge taxonomy and systematics is the mitochondrial gene COI, which, in most cases, shows levels of variation that can be correlated with species boundaries (e.g., Lopez et al 2002;W€ orheide et al 2002b;Duran et al 2004a;Alvarez et al 2007;Redmond & McCormack 2009). The internal transcribed spacer (ITS) regions located between nuclear ribosomal genes also present levels of genetic variation that have allowed detection of species boundaries and patterns of population differentiation among geographic samples in sponges (e.g., W€ orheide et al 2002b).…”