Molecular Phylogeny of Coral-Reef Sea Cucumbers (Holothuriidae: Aspidochirotida) Based on 16S Mitochondrial Ribosomal DNA Sequence

Abstract

Members of the Holothuriidae, found globally at low to middle latitudes, are often a dominant component of Indo-West Pacific coral reefs. We present the first phylogeny of the group, using 8 species from the 5 currently recognized genera and based on approximately 540 nucleotides from a polymerase chain reaction-amplified and conserved 3' section of 16S mitochondrial ribosomal DNA. Parsimony and likelihood analyses returned identical topologies, permitting several robust inferences to be drawn. Several points corroborated the Linnean classification. Actinopyga and Bohadschia each appear monophyletic and Pearsonothuria is sister to Bohadschia. Other aspects of our phylogeny, however, were not in accord with the taxonomy of Holothuriidae or previous speculations about the group's evolutionary history. Most notably, the genus Holothuria appears paraphyletic. Actinopyga and Bohadschia, sometimes held to be closely related to one another because of certain morphologic similarities, are only distantly related. The morphologically distinct Labidodemas, even thought to warrant separation at the family level, is nested well within Holothuria. A maximum parsimony reconstruction of ancestral ossicle form on the phylogeny indicated that, in addition to a probable bout of elaboration in ossicle form (the modification of rods or rosettes to holothuriid-type buttons), at least 2 rounds of ossicle simplification also transpired in which buttons reverted to rods or rosettes. Cuvierian tubules, defensive organs unique to numerous members of Holothuriidae, were probably present before the initial radiation of the family, but the reconstruction is ambiguous as to their ancestral function.

Characterization of mitochondrial genome of sea cucumber Stichopus horrens: A novel gene arrangement in Holothuroidea

“…Because of its compact size, multiple copy status in a cell, rapid evolutionary rate and lack of recombination, mtDNA has been extensively used as a marker for evolutionary and genetic diversity studies and for the identification of species [2]. Studies into the phylogenetic relationship of metazoans based on mitochondrial genomic sequences have become increasingly popular [3,4]. In addition to mtDNA sequence data, the order of the mitoAbbreviations: atp6 and 8, ATPase subunits 6 and 8; cob, cytochrome b; cox1-3, cytochrome c oxidase subunits I-III; nad1-6 and 4L, NADH dehydrogenase subunits 1-6 and 4L; srRNA and lrRNA, small and large subunits ribosomal RNA; tRNA, transfer RNA (tRNA) genes; mtDNA: mitochondrial DNA; bp, base pair(s); L1, tRNA Leu(CUN) ; L2, tRNA Leu(UUR) ; S1, tRNA Ser(AGN) ; S2, tRNA Ser(UCN) .…”

Use of species-specific PCR for the identification of 10 sea cucumber species

“…As performed by Kerr et al (2005), the 16Sar/16Sbr primers were used to amplify a ca. 570 bp 16S rRNA mitochondrial region well conserved within sea cucumber species.…”

“…The reverse species-specifi c primers for each species were designed manually ( Table 2). The forward primer 16Sar (Palumbi et al, 1991;Kerr et al, 2005) was used for all species analyzed in this work.…”

“…About 570 bp 16S rRNA gene fragments of each sample were amplifi ed using the method of Kerr et al (2005). Amplifi ed products were purifi ed with the …”

Separation of a novel species from Actinopyga mauritiana (Holothuroidea: Holothuriidae) species complex, based on ecological, morphological and mitochondrial DNA evidence.

“…Actinopyga (Bronn, 1860) is one of the five genera in the family Holothuriidae (Rowe 1969;Rowe & Gates 1995;Massinet al, 2004;Kerr et al 2005;Samyn et al, 2005). Within the genus there are sixteen species generally recognized as valid :Actinopyga agassizii (Selenka, 1867); A. albonigra (Cherbonnier and Féral, 1984); A. bacilla (Cherbonnier, 1980); A. bannwarthi (Panning, 1944); A. caroliniana (Tan Tiu, 1981); A. crassa (Panning, 1944); A. echinites (Jaeger, 1833); A. flammea (Cherbonnier, 1979); A. fusca (Cherbonnier, 1980); A. lecanora (Jaeger, 1833); A. miliaris (Quoy & Gaimard, 1833); A. obese (Selenka, 1867); A. palauensis (Panning, 1944); A. serratidens (Pearson, 1903); A. spinea (Cherbonnier, 1980) and A. mauritiana (Quoy & Gaimard, 1833).…”