Phylogenetic relationships of coral-associated gobies (Teleostei,Gobiidae) from the Red Sea based on mitochondrial DNA data

Bryaninops, Gobiodon, Paragobiodon and Pleurosicya are the most abundant genera of coral-associated gobies. These genera are adapted to live among coral, while other small reef gobies (e.g., the genus Eviota) show no obligate association with this living substrate. Thirteen coral-associated species and two Eviota species were sampled from different regions of the Red Sea, along with four populations/species of Gobiodon from the Indian and western Pacific Oceans. A molecular phylogenetic analysis was performed using partial sequences of 12S rRNA, 16S rRNA and cytochrome b mitochondrial genes, 1,199 base pairs in total. Several clades were consistently resolved in neighbor joining-, maximum parsimony-, maximum likelihood and Bayesian analyses. While each of the four genera Gobiodon, Paragobiodon, Bryaninops and Pleurosicya proved to be monophyletic, their relative position in the phylogeny did not support an emergence of coral-associated gobiids as a monophyletic assemblage. Instead, two separate monophyletic sub-groups were discovered, the first comprising Gobiodon and Paragobiodon, and the second Bryaninops and Pleurosicya. Our molecular phylogenetic examinations also revealed one unassigned species of Gobiodon from the Maldives as a distinct species and confirmed three putative and yet unassigned species from the Red Sea. Moreover, the uniformly black colored species of Gobiodon are not monophyletic but have evolved independently within two distinct species groups. Genetic distances were large in particular within Pleurosicya and Eviota. Estimated divergence times suggest that coral-associated gobies have diversified in parallel to their preferred host corals. In particular, divergence times of Gobiodon species closely match those estimated for their typical host coral genus Acropora.     

Phylogenetic relationships within the Octocorallia (Cnidaria: Anthozoa) based on nuclear 18S rRNA sequences

We determined the nuclear 18S rRNA sequences for 41 species of octocorals and used these to address the validity of the historical ordinal divisions and the current subordinal divisions within the subclass Octocorallia. We also explored the phylogenetic affinities of the species Dendrobrachia paucispina, which was originally classified in the order Antipatharia (subclass Ceriantipatharia) although polyp structure indicates it belongs in the subclass Octocorallia. Trees constructed using maximum likelihood techniques are incongruent with the current and historical taxonomy of the Octocorallia. There appeared to be three major clades of octocorals. The first clade included most, but not all, pennatulaceans as a monophyletic group. The second clade contained 21 species, representing all major octocoral groups other than pennatulaceans. The third clade contained members from three suborders of the Alcyonacea and one member of the Pennatulacea. These data could not be used to distinguish the branching order of the three major clades. The species D. paucispina had a close affinity with the genera Corallium and Paragorgia (Alcyonacea: Scleraxonia), although its morphology suggests it is more similar to the genus Chrysogorgia (Alcyonacea: Calcaxonia). The morphological character of dimorphism (the presence of both autozooids and siphonozooids within a single colony) corresponded loosely with the topology of the most likely trees, and a single origin of dimorphism could not be rejected. Despite sampling from the majority of families within the Octocorallia, many of the relationships within this group remain ambiguous. Received: 16 June 2000 / Accepted: 14 September 2000     

Molecular evidence for multiple lineages in the gorgonian family Plexauridae (Anthozoa: Octocorallia)

Octocorals are diverse and abundant on many marine hard substrates, and, within this group, members of the family Plexauridae are an important component of tropical reef assemblages, especially in the Caribbean. To understand historical relationships within this large and diverse assemblage, and to test the monophyly of the family and some of its genera, DNA sequences of two mitochondrial loci (msh1 and ND2, ~1,185 bp) were analyzed from 46 species in 21 genera from deep and shallow waters in the tropical western Atlantic and in the tropical western and eastern Pacific (plus 9 taxa in the closely related Gorgoniidae and 1 species of the more distantly related Alcyoniidae). Five strongly supported clades were recovered. Three large clades correspond roughly to the Plexauridae, Paramuriceidae, and Gorgoniidae, and two smaller clades were comprised of taxa previously assigned to several families. Astrogorgia sp. did not group with any of the clades. The mutual relationships among the five clades remain unclear. Several genera previously regarded as unrelated appear to be grouped among the three families; e.g. Hypnogorgia sp. (Paramuriceidae) falls within a clade consisting of both Pacific and Atlantic Muricea spp. (Plexauridae), while Swiftia sp., Scleracis sp., and an Atlantic Thesea sp. (all Paramuriceidae) group with the gorgoniids. In several instances, genera containing Atlantic and Pacific species were recovered as monophyletic (Muricea spp., Bebryce spp.). However, in at least three cases (Echinomuricea spp., Thesea spp., Villogorgia spp.), placement of Atlantic and Pacific species in the same genus may reflect convergence of sclerite morphology. The results indicate a strong need for reexamination of octocoral taxonomy using a combination of molecular, morphological, and chemical evidence.Electronic Supplementary Material Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00227-005-1592-y.Communicated by J.P. Grassle, New Brunswick     

Phylogeny and biogeography of Sicydiinae (Teleostei: Gobiidae) inferred from mitochondrial and nuclear genes

In the Indo-Pacific area, the Caribbean region and West Africa, insular systems are colonised by particular Gobiids of the Sicydiinae subfamily. These species spawn in freshwater, the free embryos drift downstream to the sea where they undergo a planktonic phase, before returning to rivers to grow and reproduce; an amphidromous lifestyle. These gobies are the biggest contributors to the diversity of fish communities in insular systems and have the highest levels of endemism, yet their phylogeny has not been explored before with molecular data. To understand the phylogeny and the biogeography of this subfamily, sequences from the mitochondrial 16S rDNA and cytochrome oxidase I and from the nuclear rhodopsin gene were obtained for 50 Sicydiinae specimens of seven genera. Our results support the monophyly of the subfamily and of all the genera except Sicyopus, which is polyphyletic. Five major clades were identified within this subfamily. One clade clusters Sicyopterus and Sicydium as sister genera, one contains the genus Stiphodon split into two different groups, two other clades include only Sicyopus (Smilosicyopus) and Cotylopus, respectively, and the last clade groups Akihito, Lentipes and Sicyopus (Sicyopus). As a result, the subgenus Smilosicyopus is elevated herein as a genus. A molecular dating approach helps the interpretation of these phylogenetic results in terms of amphidromy and biogeographical events that have allowed the Sicydiinae to colonise the Indo-Pacific, West African and Caribbean islands.     

Phylogenetic relationship among several genera of Dictyotaceae (Dictyotales, Phaeophyceae) based on 18S rRNA and partial rbcL gene sequences

The partial sequences of the 18S rRNA gene and the rbcL gene, RuBisCo spacer region of representatives of the Dictyotaceae were determined and compared to resolve their phylogenetic relationships. A total of 1,861 base pairs of 18S rDNA sequences were aligned and examined. There was a high similarity of nucleotide sequences within the tribe Dictyoteae (99.4-99.6%) and the tribe Zonarieae (92.8-99.8%). The largest intergeneric divergence within the Dictyotaceae was 7.31%, between Dilophus and Zonaria. The aligned 422 bases of partial rbcL gene sequences gave a similar phylogenetic relationship among taxa to those of the 18S rDNA sequences, although our alignment covered less than 30% of the whole gene. All genera of Dictyotales consisted of several clades forming a polychotomy in MP trees based on partial rbcL gene sequences and on 18S rDNA sequences. The genera within the tribe Dictyoteae formed a clade, a Dictyota-Phacydictyon-Dilophus clade, while genera of the tribe Zonarieae formed four clades: Padina; Distromium-Lobophora-Zonaria; Spatoglossum-Lobospira; and Dictyopteris-Spatoglossum. All genera of the Dictyotaceae included in these sequence analyses are classified into five groups, which have little phylogenetic resolution among them. The genera classified in the tribe Zonarieae according to Womersley's criteria do not appear to be monophyletic, based on our analyses. Although not all genera of Dictyotaceae were analysed, our data suggest that the status of the meristem cells should not be a criterion for separating tribes within the family Dictyotaceae and that other hierarchical systems should be adopted to properly reflect phylogenetic relationships.     

Molecular characterization of the zoanthid genus <Emphasis Type="Italic">Isaurus</Emphasis> (Anthozoa: Hexacorallia) and associated zooxanthellae (<Emphasis Type="Italic">Symbiodinium</Emphasis> spp.) from Japan

The zoanthid genus Isaurus (Anthozoa: Hexacorallia) is known from both the Indo-Pacific and Atlantic Oceans, but phylogenetic studies examining Isaurus using molecular markers have not yet been conducted. Here, two genes of markers [mitochondrial cytochrome oxidase subunit I (COI) and mitochondrial 16S ribosomal DNA (mt 16S rDNA)] from Isaurus specimens collected from southern Japan (n = 19) and western Australia (n = 3) were sequenced in order to investigate the molecular phylogenetic position of Isaurus within the order Zoantharia and the family Zoanthidae. Additionally, obtained sequences and morphological data (polyp size, mesentery numbers, mesogleal thickness) were utilized to examine Isaurus species diversity and morphological variation. By comparing our obtained sequences with the few previously acquired sequences of genera Isaurus as well as with Zoanthus, Acrozoanthus (both family Zoanthidae), and Palythoa spp. (family Spenophidae) sequences, the phylogenetic position of Isaurus as sister to Zoanthus within the Family Zoanthidae was suggested. Based on genetic data, Isaurus is most closely related to the genus Zoanthus. Despite considerable morphological variation (in particular, polyp length, mesentery numbers, external coloration) between collected Isaurus specimens, all specimens examined are apparently conspecific or very closely related based on molecular data and observed morphological variation within colonies. Additionally, obtained internal transcribed spacer of ribosomal DNA (ITS-rDNA) sequences from symbiotic zooxanthellae (Symbiodinium spp.) from all Isaurus specimens were shown to be subclade C1-related Symbiodinium. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Interrelationships of the two families constituting the Lophogastrida (Crustacea: Mysidacea) inferred from morphological and molecular data

The Lophogastrida are primitive Mysidacea and comprise only six genera. One of these, Eucopia is considered as highly specialized and constitutes the family Eucopiidae; the other genera constitute the Lophogastridae. Among the latter family, the genus Gnathophausia is closely related to Eucopia, with two species (G. gracilis and E. sculpticauda) sharing similar morphological characteristics [i.e. ornamentation (spines) of the uropods, and the gastric mill]. This indicates that these species are phylogenetically related. To test this hypothesis, the partial 16S mitochondrial ribosomal RNA gene from various representative species of Gnathophausia and Eucopia were compared. The resulting phylogenetic tree suggests that each genus is monophyletic, and that Gnathophausia, which is the deepest-branching genus, is the most primitive, with the Eucopiidae originating from the Lophogastridae. The molecular results support the morphological hypothesis, and suggest an early separation of the two genera or a rapid divergence of Eucopia due to morphological specialization. Received: 29 June 1997 / Accepted: 16 March 1998     

Molecular phylogeny of mud crabs (Brachyura: Panopeidae) from the northwestern Atlantic and the role of morphological stasis and convergence

 Mud crabs of the family Panopeidae are common organisms in coastal soft-bottom, vegetated, rubble, and oyster-bed communities along the temperate and tropical coastlines of the American continent. Similar morphology among many species renders their distinction and classification difficult. Here, we present phylogenies of western Atlantic Panopeidae based on DNA sequences of the mitochondrial large subunit rRNA (16S; 529 basepairs) and cytochrome oxidase I (COI; 640 basepairs) genes. Results suggest that the speciose genera Panopeus and Eurypanopeus are not monophyletic and that their taxonomy does not accurately reflect evolutionary partitions. In two cases (P. herbstii complex and E. depressus and allies), the molecular findings strongly support sister-species relationships that differ from previous morphology-based assumptions. We suggest that convergence or morphological stasis are responsible for the phenotypic similarities between divergent evolutionary lineages. Received: 23 July 1999 / Accepted: 5 April 2000     

Phylogeography of the Southwestern Atlantic menhaden genus <Emphasis Type="Italic">Brevoortia</Emphasis> (Clupeidae,Alosinae)

Among pelagic fish, the Southwestern Atlantic menhaden genus Brevoortia (Clupeidae, Alosinae) constitutes an important species model to investigate the patterns of genetic differentiation. It is abundant in the Río de la Plata estuary and in the Atlantic coastal lagoons system from Uruguay and Southern Brazil. To access in the taxa discrimination and population structure in Brevoortia we perform a phylogeographic approach based on mitochondrial cytochrome b (cyt-b) sequences including 240 individuals from 16 collecting sites. Among the 720 bp cyt-b sequenced, 199 correspond to variables and 88 to phylogenetically informative sites. High values of haplotype diversity (h = 1.000) and nucleotide diversity (π = 0.061), as well as an average of 0.084 polymorphic segregating sites and 46 different haplotypes were found. Maximum likelihood analysis based on the GTR + I + G model and Bayesian inference strongly support the idea that B. aurea is the only species of the genus inhabiting the Southwestern Atlantic region. Our analyses revealed a complex population pattern characterized by the existence of long-term highly structured genetic assemblages of mixed stocks. Each monophyletic entity included individuals from different collecting sites, different age groups and collected in different years. Our data also suggest that the recruitment of unrelated mtDNA haplotypes carried out by individuals within schools could be occurring in the same nursery areas revealing the existence of many different maternal lineages. A scenario where different simultaneously and successively mixed mtDNA lineages remain historically connected through basal haplotypes among different clades could explains more accurately the complex and ordered metapopulation dynamic found in this pelagic fish.     

Molecular population structure of the marine benthic copepod Microarthridion littorale along the southeastern and Gulf coasts of the USA

Relationships among populations (southeast Atlantic and northern Gulf coast, USA) of a ubiquitous, estuarine, harpacticoid copepod (Microarthridion littorale Poppe) were estimated using sequence data from two loci: one mitochondrial [cytochrome b (Cyt b)] and one nuclear [first internal transcribed spacer of ribosomal DNA (ITS-1)]. Copepods were collected from seven estuaries in 1997/98. Allelic phylogenies based on both genes were generally concordant, and suggested that M. littorale populations are structured over large geographic scales (hundreds of kilometers). Three well-supported groups were found in both gene trees comprising clades of alleles sampled from South Carolina, Florida, and Louisiana. Alleles from the Savannah, Georgia sample formed a monophyletic group using the Cyt b data, but this clade was not distinguishable with comparable ITS-1 data. A single specimen from Louisiana was classified in different clades depending on the locus assayed. Received: 11 June 1998 / Accepted: 29 April 1999     

Evolutionary relationships of deep-sea hydrothermal vent and cold-water seep clams (Bivalvia: Vesicomyidae): results from the mitochondrial cytochrome oxidase subunit I

Phylogenetic relationships among vesicomyid clams (Bivalvia: Vesicomyidae) and their placement within the order Heterodonta were examined using mitochondrial encoded cytochrome oxidase subunit I (COI) DNA sequences. The presently analyzed vesicomyids represent a recent monophyletic radiation that probably occurred within the Cenozoic. Nucleotide phylogenetic analyses resolved discrete clades that were consistent with currently recognized species: Calyptogena magnifica, C. ponderosa, Ectenagena extenta, C. phaseoliformis, Vesicomya cordata, Calyptogena n. sp. (Gulf of Mexico), C. kaikoi, C. nautilei, C. solidissima and C. soyoae (Type-A). However, specimens variously identified as: V. gigas, C. kilmeri, C. pacifica, and V. lepta comprised two “species complexes”, each composed of multiple evolutionary lineages. Most taxa are limited to hydrothermal-vent or cold-seep habitats, but the “vent” versus “seep” clams do not constitute separate monophyletic groups. Current applications of the generic names Calyptogena, Ectenagena, and Vesicomya are not consistent with phylogenetic inferences. Received: 24 July 1997 / Accepted: 22 August 1997     

High diversity of deep-sea Gromia from the Arabian Sea revealed by small subunit rDNA sequence analysis

Gromia is a large marine protist with filose pseudopodia and ovoid test, common in coastal intertidal and sublittoral waters. Although deep-water Gromia-like morphospecies were discovered in the 1990s, their relations to the shallow water species have never been established. Moreover, very little is known about the diversity within Gromia, reflecting the fact that these morphologically relatively simple protists have few characters useful for species identification. Consequently, we have analysed the SSU rDNA and ITS rDNA genes to examine gromiid diversity in two different areas located on the Oman and Pakistan margins of the Arabian Sea (water depths 1,000–2,000 m). In total, 27 deep-sea gromiid sequences of the SSU rDNA gene and six sequences of the ITS rDNA region were obtained. Our data confirm that Gromia-like protists from the bathyal deep sea are related to the shallow-water gromiids. Within Arabian Sea Gromia, we identified seven distinctive lineages, five of which form a monophyletic group branching as a sister group to shallow-water species. Six lineages of Arabian Sea Gromia can be defined morphologically, while one lineage includes specimens that look identical to specimens from two other lineages. This indicates that each Gromia lineage represents probably a separate species and suggests that deep-sea gromiid diversity is higher than indicated by their simple morphology.     

Geographic clines and stepping-stone patterns detected along the East Pacific Rise in the vetigastropod Lepetodrilus elevatus reflect species crypticism

Three different molecular markers (i.e. seven allozyme loci, two nuclear gene loci and, mtCOI DNA sequences) were used to assess the genetic structure of the vent gastropod Lepetodrilus elevatus collected from three vent fields along the East Pacific Rise (13°N, 9°50′N and 17°S). While allozymes and nuclear loci suggested a strong stepping-stone pattern, a multivariate analysis performed on allozymic frequencies showed the presence of two distinct evolutionary lineages: the first situated in the north from 13°N to 9°50′N and the second in the south from 9°50′N to 17°S. The analysis of mitochondrial DNA sequences confirmed the separation of L. elevatus into two distinct clades with a divergence of 6.5%, which is consistent with the interspecific level of sequence variation in other vent species. A divergence time of 6–14 Mya was estimated between the two clades from previous clock calibrations. Our results suggest that these taxa followed an allopatric speciation between the northern and southern parts of the EPR with a recent demographic expansion of the southern clade to the north and a subsequent secondary contact (clade hybridisation). This speciation was probably reinforced by a habitat specialisation of the two cryptic species because the southern clade was mainly found associated with mussel-dominated communities and the northern clade with tubeworm-dominated communities. However, the analysis of shell morphology failed to separate the two cryptic species based on this sole criterion although they differed from Lepetodrilus elevatus galriftensis (Galapagos population) by a higher shell elevation. Within each clade, genetic differentiation was not related to the distance across populations and could be within vent field as important as between fields. While both clades appear to be in expansion since their speciation, significant excesses in heterozygotes suggest a very recent and local bottleneck at 17°S, probably due to massive site extinction in this region.     

Evolutionary divergence among lineages of the ocean sunfish family,Molidae (Tetraodontiformes)

Ocean sunfish, family Molidae, are enigmatic members of the epipelagic fauna of all tropical and temperate oceans. A study, begun in 1998, initially focused on the population genetics of Mola mola Linnaeus 1758 immediately indicated high levels of genetic divergence in the d-loop and cytochrome b mitochondrial genes. This preliminary effort was expanded to include Masturus lanceolatus Liénard 1840, Ranzania laevis Pennant 1776, and representative sequences of other Tetraodontiformes. Analysis of the sequence data confirms that there are two species in the genus Mola, Mola mola and M. ramsayi Giglioli 1883, with the latter presumed to be limited to the southern hemisphere. There is an indication of inter-ocean subdivision within both species originating 0.05–0.32 and 1.55–4.10 million years ago, respectively. Given limited sample sizes, however, the divergence estimates are minimums and the isolating mechanisms remain speculative. The systematic analysis provided strong support for the sister taxa relationship between genera Masturus and Mola and the basal position of the genus Ranzania within the family, as well as the sister group relationship of the Tetraodontiform families Tetraodontidae + Diodontidae to the Molidae.     

Sympatric size variants of the microcopepod Oncaea venusta exhibit distinct lineages in DNA sequences

We investigated the phylogenetic relationships among different size groups of the pelagic microcopepod Oncaea venusta Philippi, 1843, by comparing the patterns of genetic variation of specimens collected at five locations of the Indo-West Pacific Ocean. Phylogenetic analyses were based on sequence data obtained from two DNA markers: A 310 bp fragment of the mitochondrial cytochrome b (cyt b) gene and a 480 bp fragment of the nuclear internal transcribed spacer 1 (ITS1). The cyt b sequences showed a much higher level of variation than those from ITS1, but the conclusion from both genes was concordant. Four genetic clades could be differentiated. A small- and a large-size group were unambiguously assigned to two distinct clades or lineages. Unexpectedly, the medium-sized individuals could be divided into another two different genetic clades. All four lineages were supported by high bootstrap values. The high levels of sequence divergence under sympatric conditions indicated that at least the two main groups, the large and the small one, may be assigned to different species. For the medium-size group additional morphological studies and more sensitive nuclear markers are required to clarify their taxonomic status.     

Species boundaries in the starfish genus Linckia

 The genetic basis for species boundaries in the starfish genus Linckia was examined using variation observed in 613 base pairs (bp) of sequence from the cytochrome oxidase I gene of mtDNA and 16 allozyme loci. Five groups within Linckia were clearly genetically differentiated; L. columbiae, L. bouvieri, two clades within L. guildingi, and one clade with two sub-clades consisting of both L. laevigata and L. multifora. Genetic divergence among these groups is consistent with interspecific variation. The two clades within L. guildingi suggest the presence of a cryptic, partially sympatric, species. Genetic divergence between these two clades implies that they have been genetically distinct from each other for at least one million years. In contrast, genetic data suggest that L. laevigata and L. multifora are a single species, despite the fact that live individuals can be distinguished by their colour and colour pattern, number of madreporites and ratio of arm length to breadth. There are probably three closely related groups within the L. laevigata/L. multifora clade –L. multifora, and two groups in L. laevigata defined by biogeographic province. It is difficult to determine boundaries for these three entities, since genetic and morphological differences are complicated by phenotypic differences arising from both environmental variation and population genetic structure. The difficulties encountered in defining species boundaries in Linckia, particularly with respect to variation arising from the overlap of Indian and Pacific biogeographic provinces, may be a general issue for many marine organisms from this region. Received: 24 May 1999 / Accepted: 6 October 1999     

Sympatry and allopatry in the deeply divergent mitochondrial DNA clades of the estuarine pulmonate gastropod genus <Emphasis Type="Italic">Phallomedusa</Emphasis> (Mollusca,Gastropoda)

DNA sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene were collected from estuarine snails in the genus Phallomedusa to examine the effects of estuarine isolation on population structure and gene flow. Three clades were recovered, one corresponding to Phallomedusa austrina and two others with the morphology of Phallomedusa solida. The haplotype diversity in all three clades indicated recent population expansion. Phallomedusa austrina was restricted to the west of a previous land bridge in the Bass Strait between mainland Australia and Tasmania, and P. solida to its east and to northern Tasmania. Phylogeographic analysis of P. austrina and P. solida shows strong geographic separation of species, but no local genetic structure indicative of regional or estuarine isolation. The clades of P. solida exhibit substantial genetic divergence and were sympatric across their entire distribution in eastern Tasmania and mainland Australia. Such a situation, which has not previously been observed in phylogeographic studies of southeast Australia, suggests that P. solida has had a complex refugial history during periods of environmental challenge.     

Phylogeography of the pipefish, <Emphasis Type="Italic">Urocampus carinirostris</Emphasis>, suggests secondary intergradation of ancient lineages

We assayed the pattern of mitochondrial DNA evolution in the live bearing, seagrass specialist pipefish, Urocampus carinirostris, in eastern Australia. These life history attributes were predicted to result in strong phylogeographic structure in U. carinirostris. Phylogenetic analysis of cytochrome b sequences detected two monophyletic mtDNA clades that differed by 8.69% sequence divergence - a large level of intraspecific divergence for a marine fish. The geographical distribution of clades was non-random and resembled clinal secondary intergradation over a 130-km stretch of coastline. Contrary to phylogeographic predictions, this large phylogeographic break does not occur across a traditionally recognised biogeographic boundary. Analyses of historical demography suggested that individuals belonging to the most widespread clade underwent a population expansion from a small refuge population during the Pleistocene.     

Using a combined approach to explain the morphological and ecological diversity in <Emphasis Type="Italic">Phanogenia gracilis</Emphasis> Hartlaub, 1893 (Echinodermata: Crinoidea) <Emphasis Type="Italic">sensu lato</Emphasis>: two species or intraspecific variation?

Phanogenia gracilis sensu lato is a shallow-water crinoid distributed throughout the Indo-western Pacific. The taxonomy of P. gracilis s.l. is clouded by the presence of two distinct morphotypes, each differing in morphology and ecology. The goal was to determine the taxonomic status of P. gracilis s.l. using partial gene sequences of two mitochondrial DNA genes, cytochrome oxidase c subunit I and NADH dehydrogenase subunit II, in conjunction with morphological and ecological data. The molecular phylogenies revealed three lineages separated by 5.0–6.6% corrected genetic distance, which is consistent with the genetic distances among other echinoderm species. Neither morphotype was monophyletic, nor was any examined morphological character exclusive to any one lineage. Discriminant function analysis (DFA) of the morphological and ecological data yielded significant results when grouping P. gracilis by morphotype and by clades recovered in the phylogenetic analyses, but grouping by sample locality was rejected. Although DFA results of grouping by clade were significant, jackknife support was weak, while only correctly grouping specimens by their respective clades 65% of the time. The results suggest the possibility of cryptic species, but additional molecular and morphological data are needed to confirm this. This study demonstrates the need to reevaluate the taxonomy of crinoid species and their respective diagnostic characters.