Phylogenetic relationships ofPolemoniaceae inferred from 18S ribosomal DNA sequences

Cladistic analyses of chloroplast DNA disagree with current classifications by placingPolemoniaceae near sympetalous families with two staminal whorls, includingFouquieriaceae andDiapensiaceae, rather than near sympetalous families with a single staminal whorl, such asHydrophyllaceae andConvolvulaceae. To explore further the affinities ofPolemoniaceae, we sequenced 18S ribosomal DNA for eight genera ofPolemoniaceae and 31 families representing a broadly definedAsteridae. The distribution of variation in these sequences suggest some sites are hypervariable and multiple hits at these sites have obscured much of the hierarchical structure present in the data. Nevertheless, parsimony, least-squares minimum evolution, and maximum likelihood methods all support a monophyleticPolemoniaceae that is placed nearFouquieriaceae, Diapensiaceae and related ericalean families.     

Phylogenetic relationships of the Acanthocephala inferred from 18S ribosomal DNA sequences

Phylogenetic relationships within the Acanthocephala have remained unresolved. Past systematic efforts have focused on creating classifications with little consideration of phylogenetic methods. The Acanthocephala are currently divided into three major taxonomic groups: Archiacanthocephala, Palaeacanthocephala, and Eoacanthocephala. These groups are characterized by structural features in addition to the taxonomy and habitat of hosts parasitized. In this study the phylogenetic relationships of 11 acanthocephalan species are examined with 18S rDNA sequences. Maximum parsimony, minimum evolution, and maximum likelihood methods are used to estimate phylogenetic relationships. Within the context of sampled taxa, all phylogenetic analyses are consistent with monophyly of the major taxonomic groups of the Acanthocephala, suggesting that the current higher order classification is natural. The molecular phylogeny is used to examine patterns of character evolution for various structural and ecological characteristics of the Acanthocephala. Arthropod intermediate host distributions, when mapped on the phylogeny, are consistent with monophyletic groups of acanthocephalans. Vertebrate definitive host distributions among the Acanthocephala display independent radiations into similar hosts. Levels of uncorrected sequence divergence among acanthocephalans are high; however, relative-rate tests indicate significant departure from rate uniformity among acanthocephalans, arthropods, and vertebrates. This precludes comparison of 18S divergence levels to assess the relative age of the Acanthocephala. However, other evidence suggests an ancient origin of the acanthocephalan-arthropod parasitic association.     

Filling a gap in the phylogeny of flatworms: relationships within the Rhabdocoela (Platyhelminthes), inferred from 18S ribosomal DNA sequences

The phylogeny of the Rhabdocoela, a species-rich taxon of free-living flatworms, is reconstructed based on complete 18S rDNA sequences. The analysis includes 62 rhabdocoels and 102 representatives of all major flatworm taxa. In total, 46 new sequences are used, 41 of them from rhabdocoel species, five from proseriates. Phylogenetic analysis was performed using maximum parsimony and Bayesian inference. Clade support was evaluated with parsimony jackknifing, Bremer support indices and Bayesian posterior probabilities. The resulting cladogram corroborates that the Rhabdocoela is monophyletic, but its sister group remains uncertain. The 'Dalyellioida' and the 'Typhloplanoida', both former rhabdocoel subtaxa, are polyphyletic. Within the Rhabdocoela the monophyletic Kalyptorhynchia, characterized by a muscular proboscis, forms the sister group of all other rhabdocoels. The Schizorhynchia is a monophyletic subtaxon of the Kalyptorhynchia, with the split proboscis as a synapomorphy. Except for the Dalyelliidae and the Typhloplanidae, both freshwater taxa, none of the 'families' previously included in the 'Typhloplanoida' and the 'Dalyellioida' appears to be monophyletic. As a result of this analysis, three existing and four new taxon names are formally defined following the rules of the Phylocode.     

基于部分18S rDNA, 28S rDNA和COI基因序列的索科线虫亲缘关系

通过PCR扩增获得我国常见昆虫病原索科线虫6属10种18S rDNA、28S rDNA(D3区)和COI基因序列,结合来自GenBank中6属10种索科线虫的18S rDNA同源序列,用邻接法和最大简约法构建系统进化树。结果显示:12属索科线虫分为三大类群,第一大类群是三种罗索属线虫(Romanomermis)先聚在一起,再与两索属(Amphimermis)和蛛索属(Aranimermis)线虫聚为一支;在第二大类群中,六索属(Hexamermis)、卵索属线虫(Ovomermis)和多索属(Agamermis)亲缘关系最近,先聚在一起,再与八腱索属(Octomyomermis)和Thaumamermis线虫聚为一支。第三大类群由索属(Mermis)和异索属(Allomermis)线虫以显著水平的置信度先聚在一起,再与蠓索属(Heleidomermis)和施特克尔霍夫索属(Strelkovimermis)线虫聚为一支。从遗传距离看,基于3个基因的数据集均显示索科线虫属内种间差异明显小于属间差异,武昌罗索线虫(R.wuchangensis)和食蚊罗索线虫(R.culicivorax)同属蚊幼寄生罗索属线虫,其种间的遗传距离最小。     

18S rDNA sequences and the holometabolous insects

The Holometabola (insects with complete metamorphosis: beetles, wasps, flies, fleas, butterflies, lacewings, and others) is a monophyletic group that includes the majority of the world's animal species. Holometabolous orders are well defined by morphological characters, but relationships among orders are unclear. In a search for a region of DNA that will clarify the interordinal relationships we sequenced approximately 1080 nucleotides of the 5' end of the 18S ribosomal RNA gene from representatives of 14 families of insects in the orders Hymenoptera (sawflies and wasps), Neuroptera (lacewing and antlion), Siphonaptera (flea), and Mecoptera (scorpionfly). We aligned the sequences with the published sequences of insects from the orders Coleoptera (beetle) and Diptera (mosquito and Drosophila), and the outgroups aphid, shrimp, and spider. Unlike the other insects examined in this study, the neuropterans have A-T rich insertions or expansion regions: one in the antlion was approximately 260 bp long. The dipteran 18S rDNA evolved rapidly, with over 3 times as many substitutions among the aligned sequences, and 2-3 times more unalignable nucleotides than other Holometabola, in violation of an insect-wide molecular clock. When we excluded the long-branched taxa (Diptera, shrimp, and spider) from the analysis, the most parsimonious (minimum-length) trees placed the beetle basal to other holometabolous orders, and supported a morphologically monophyletic clade including the fleas+scorpionflies (96% bootstrap support). However, most interordinal relationships were not significantly supported when tested by maximum likelihood or bootstrapping and were sensitive to the taxa included in the analysis. The most parsimonious and maximum-likelihood trees both separated the Coleoptera and Neuroptera, but this separation was not statistically significant.(ABSTRACT TRUNCATED AT 250 WORDS)     

Angiosperm phylogeny inferred from 18S rDNA, vbcL, and atpB sequences

A phylogenetic analysis of a combined data set for 560 angiosperms and seven outgroups based on three genes, 18S rDNA (1855 bp), rbcL (1428 bp), and atpB (1450 bp) representing a total of 4733 bp is presented. Parsimony analysis was expedited by use of a new computer program, the RATCHET. Parsimony jackknifing was performed to assess the support of clades. The combination of three data sets for numerous species has resulted in the most highly resolved and strongly supported topology yet obtained for angiosperms. In contrast to previous analyses based on single genes, much of the spine of the tree and most of the larger clades receive jackknife support 250%. Some of the noneudicots form a grade followed by a strongly supported eudicot clade. The early‐branching angiosperms are Amborellaceae, Nymphaeaceae, and a clade of Austrobaileyaceae, Illiciaceae, and Schi‐sandraceae. The remaining noneudicots, except Ceratophyllaceae, form a weakly supported core eumagnoliid clade comprising six well‐supported subclades: Chloranthaceae, monocots, WinteraceaeICanellaceae, Piperales, Laurales, and Magnoliales. Ceratophyllaceae are sister to the eudicots. Within the well‐supported eudicot clade, the early‐diverging eudicots (e.g. Proteales, Ranunculales, Trochodendraceae, Sabiaceae) form a grade, followed by the core eudicots, the monophyly of which is also strongly supported. The core eudicots comprise six well‐supported subclades: (1) Berberidopsidaceae/Aextoxicaceae; (2) Myrothamnaceae/ Gunneraceae; (3) Saxifragales, which are the sister to Vitaceae (including Leea) plus a strongly supported eurosid clade; (4) Santalales; (5) Caryophyllales, to which Dilleniaceae are sister; and (6) an asterid clade. The relationships among these six subclades of core eudicots do not receive strong support. This large data set has also helped place a number of enigmatic angiosperm families, including Podostemaceae, Aphloiaceae, and Ixerbaceae. This analysis further illustrates the tractability of large data sets and supports a recent, phylogenetically based, ordinal‐level reclassification of the angiosperms based largely, but not exclusively, on molecular (DNA sequence) data.     

The phylogeny of Paralabrax (Perciformes: Serranidae) and allied taxa inferred from partial 16S and 12S mitochondrial ribosomal DNA sequences

Partial sequences of 16S and 12S mitochondrial ribosomal DNA were used to examine the phylogenetic relationships of the primarily eastern Pacific genus Paralabrax (Perciformes: Serranidae) and allied taxa. Paralabrax is considered a basal serranine, which is itself considered the basal subfamily in the Serranidae. Multiple serranines reported closely related to Paralabrax from the genera Serranus, Hypoplectrus, Cratinus, and Centropristis were used as outgroups. Species from the remaining two subfamilies, Epinephilinae and Anthiinae, of the Serranidae were also used in the analyses. The tree of the Serranidae was rooted with the families Polyprionidae and Priacanthidae. Paralabrax, the Serranidae, and the Serraninae were monophyletic in this study. Serranus was found to be paraphyletic. Centropristis, formerly considered the sister taxon to Paralabrax, was not closely related in these analyses. Cratinus agassizii, a monotypic genus from the eastern Pacific, was found to be the sister taxon to Paralabrax. There is greater resolution for intergeneric and subfamily relations than interspecific relationships. A single most parsimonious tree for the interspecific relationships of Paralabrax and allied taxa is proposed. This proposed molecular phylogeny is consistent with known biogeographic processes in the eastern Pacific.     

The syndermatan phylogeny and the evolution of acanthocephalan endoparasitism as inferred from 18S rDNA sequences

The phylogeny of the Syndermata (Rotifera: Monogononta, Bdelloidea, Seisonidea; Acanthocephala: Palaeacanthocephala, Eoacanthocephala, Archiacanthocephala) is key to understanding the evolution of acanthocephalan endoparasitism from free-living ancestors. In the present study, maximum likelihood, distance/neighbor-joining, and maximum parsimony analyses have been carried out based on 18S rDNA data of 22 species (four new sequences). The results suggest a monophyletic origin of the Eurotatoria (Monogononta+Bdelloidea). Seison appears as the acanthocephalan sistergroup. Palaeacanthocephala split into an "Echinorhynchus"-and a "Leptorhynchoides"-group, the latter sharing a monophyletic origin with the Eoacanthocephala and Archiacanthocephala. As inferred from the phylogeny obtained acanthocephalan endoparasitism evolved from a common ancestor of Seison and Acanthocephala that lived epizoically on an early mandibulate. Probably, an acanthocephalan stem species invaded the mandibulate host, thus establishing an endoparasitic lifestyle. Subsequently, vertebrates (or gnathostomes) became part of the parasite's life cycle. In the stem line of the Archiacanthocephala, a terrestrial life cycle has evolved, with an ancestor of the Tracheata (Insecta, Myriapoda) acting as intermediate host.     

Marine-freshwater colonizations of haptophytes inferred from phylogeny of environmental 18S rDNA sequences

The Haptophyta is a common algal group in many marine environments, but only a few species have been observed in freshwaters, with DNA sequences available from just a single species, Crysochromulina parva Lackey, 1939. Here we investigate the haptophyte diversity in a high mountain lake, Lake Finsevatn, Norway, targeting the variable V4 region of the 18S rDNA gene with PCR and 454 pyrosequencing. In addition, the freshwater diversity of Pavlovophyceae was investigated by lineage-specific PCR-primers and clone library sequencing from another Norwegian lake, Lake Svaersvann. We present new freshwater phylotypes belonging to the classes Prymnesiophyceae and Pavlovophyceae, as well as a distinct group here named HAP-1. This is the first molecular evidence of a freshwater species belonging to the class Pavlovophyceae. The HAP-1 and another recently detected marine group (i.e. HAP-2) are separated from both Pavlovophyceae and Prymnesiophyceae and may constitute new higher order taxonomic lineages. As all obtained freshwater sequences of haptophytes are distantly related to the freshwater species C. parva, the phylogeny demonstrates that haptophytes colonized freshwater on multiple independent occasions. One of these colonizations, which gave rise to HAP-1, took place very early in the history of haptophytes, before the radiation of the Prymnesiophyceae.     

Molecular phylogeny of Alnus (Betulaceae), inferred from nuclear ribosomal DNA ITS sequences

The nuclear ITS region of 19 species of Alnus was amplified and sequenced. The inferred molecular phylogeny shows that all species of the genus Alnus form a monophyletic group close to Betula and that the fundamental dichotomy within the genus lies between the subgenera Alnaster and Gymnothyrsus, sensu Murai (1964). The subgenus Alnaster appears to be basal in the genus, based on archaism of morphological features, and branching close to the root of the trees due to low ITS divergence from genus Betula. The monophyly of the section Clethropsis is not supported by the present data: Alnus nepalensis is positioned in the subgenus Gymnothyrsus, away from A. nitida and A. maritima. Surprisingly, A. formosana sect. Japonicae is closely tied to A. maritima sect. Clethropsis, with which it shares few morphological traits, and is separate from A. japonica sect. Japonicae with which it shares many traits. An increase in substitution rate is noted in the group comprising A. formosana, A. maritima and A. nitida relative to the rest of the genus, which appears to have had, on the average, a very slow mutation rate. Alnus glutinosa, the designated type for the genus, appears to be representative of the genus both for morphological characters and evolutionary rate. North-East Asia is comforted in its position of origin of the genus since not only does it have the highest number of species and representatives in all deep branching lineages, there are also fewer transcontinental migrations when a North-East Asian ancestor is postulated than when a North American ancestor is postulated.     

New insights into polychaete phylogeny (Annelida) inferred from 18S rDNA sequences

Annelid systematics and the ingroup relationships of polychaete annelids are matter of ongoing debates in recent analyses. For the investigation of sedentary polychaete relationships a molecular phylogenetic analysis was conducted based on 94 sequences of 18S rDNA, including unpublished sequences of 13 polychaete species. The data set was analyzed with maximum parsimony and maximum likelihood methods, as wells as Bayesian inference. As in previous molecular analyses the monophyly of many traditional polychaete families is confirmed. No evidence has been found for a possible monophyly of Canalipalpata or Scolecida. In all analyses a placement of the Echiura as a derived polychaete ingroup with a close relationship to the Capitellidae is confirmed. The orbiniids appear paraphyletic with regard to Questa. Travisia is transferred from Opheliidae to Scalibregmatidae. The remaining opheliids include a yet undescribed ctenodrilid species from Elba, whereas the other investigated ctenodrilid Ctenodrilus serratus groups with the Cirratulidae and shows a close affinity to the cirratulid genus Dodecaceria. A common ancestry of Branchiomaldane and Arenicola, which has been predicted on morphological data, is confirmed by the analysis and a sistergroup relationship between Arenicolidae and Maldanidae is also recovered. These results support our assumption that on the basis of a broader taxon sampling the phylogenetic position of controversially discussed taxa can be inferred by using 18S rDNA sequence data.     

Human 18 S ribosomal RNA sequence inferred from DNA sequence. Variations in 18 S sequences and secondary modification patterns between vertebrates.

We have determined the DNA sequences encoding 18 S ribosomal RNA in man and in the frog, Xenopus borealis. We have also corrected the Xenopus laevis 18 S sequence: an A residue follows G-684 in the sequence. These and other available data provide a number of representative examples of variation in primary structure and secondary modification of 18 S ribosomal RNA between different groups of vertebrates. First, Xenopus laevis and Xenopus borealis 18 S ribosomal genes differ from each other by only two base substitutions, and we have found no evidence of intraspecies heterogeneity within the 18 S ribosomal DNA of Xenopus (in contrast to the Xenopus transcribed spacers). Second, the human 18 S sequence differs from that of Xenopus by approx. 6.5%. About 4% of the differences are single base changes; the remainder comprise insertions in the human sequence and other changes affecting several nucleotides. Most of these more extensive changes are clustered in a relatively short region between nucleotides 190 and 280 in the human sequence. Third, the human 18 S sequence differs from non-primate mammalian sequences by only about 1%. Fourth, nearly all of the 47 methyl groups in mammalian 18 S ribosomal RNA can be located in the sequence. The methyl group distribution corresponds closely to that in Xenopus, but there are several extra methyl groups in mammalian 18 S ribosomal RNA. Finally, minor revisions are made to the estimated numbers of pseudouridines in human and Xenopus 18 S ribosomal RNA.     

18S ribosomal DNA sequences provide insight into the phylogeny of patellogastropod limpets (Mollusca: Gastropoda)

To investigate the phylogeny of Patellogastropoda, the complete 18S rDNA sequences of nine patellogastropod limpets Cymbula canescens (Gmelin, 1791), Helcion dunkeri (Krauss, 1848), Patella rustica Linnaeus, 1758, Cellana toreuma (Reeve, 1855), Cellana nigrolineata (Reeve, 1854), Nacella magellanica Gmelin, 1791, Nipponacmea concinna (Lischke, 1870), Niveotectura pallida (Gould, 1859), and Lottia dorsuosa Gould, 1859 were determined. These sequences were then analyzed along with the published 18S rDNA sequences of 35 gastropods, one bivalve, and one chiton species. Phylogenetic trees were constructed by maximum parsimony, maximum likelihood, and Bayesian inference. The results of our 18S rDNA sequence analysis strongly support the monophyly of Patellogastropoda and the existence of three subgroups. Of these, two subgroups, the Patelloidea and Acmaeoidea, are closely related, with branching patterns that can be summarized as [(Cymbula + Helcion) + Patella] and [(Nipponacmea + Lottia) + Niveotectura]. The remaining subgroup, Nacelloidea, emerges as basal and paraphyletic, while its genus Cellana is monophyletic. Our analysis also indicates that the Patellogastropoda have a sister relationship with the order Cocculiniformia within the Gastropoda.     

Animal phylogeny and the ancestry of bilaterians: inferences from morphology and 18S rDNA gene sequences

SUMMARY Insight into the origin and early evolution of the animal phyla requires an understanding of how animal groups are related to one another. Thus, we set out to explore animal phylogeny by analyzing with maximum parsimony 138 morphological characters from 40 metazoan groups, and 304 18S rDNA sequences, both separately and together. Both types of data agree that arthropods are not closely related to annelids: the former group with nematodes and other molting animals (Ecdysozoa), and the latter group with molluscs and other taxa with spiral cleavage. Furthermore, neither brachiopods nor chaetognaths group with deuterostomes; brachiopods are allied with the molluscs and annelids (Lophotrochozoa), whereas chaetognaths are allied with the ecdysozoans. The major discordance between the two types of data concerns the rooting of the bilaterians, and the bilaterian sister-taxon. Morphology suggests that the root is between deuterostomes and protostomes, with ctenophores the bilaterian sister-group, whereas 18S rDNA suggests that the root is within the Lophotrochozoa with acoel flatworms and gnathostomulids as basal bilaterians, and with cnidarians the bilaterian sister-group. We suggest that this basal position of acoels and gnathostomulids is artifactal because for 1000 replicate phylogenetic analyses with one random sequence as outgroup, the majority root with an acoel flatworm or gnathostomulid as the basal ingroup lineage. When these problematic taxa are eliminated from the matrix, the combined analysis suggests that the root lies between the deuterostomes and protostomes, and Ctenophora is the bilaterian sister-group. We suggest that because chaetognaths and lophophorates, taxa traditionally allied with deuterostomes, occupy basal positions within their respective protostomian clades, deuterostomy most likely represents a suite of characters plesiomorphic for bilaterians.     

A molecular phylogeny of eurytomid wasps inferred from DNA sequence data of 28S, 18S, 16S, and COI genes

Using partial DNA sequence data from nuclear 28S and 18S genes and mitochondrial 16S and COI genes, we reconstructed a phylogeny of the family Eurytomidae. Both maximum parsimony and Bayesian methods were employed. The analysis revealed a significant incongruence between the mitochondrial genes and the nuclear genes, and we chose the results from the nuclear genes as our preferred hypothesis. Our phylogeny suggested that the family Eurytomidae is not a monophyletic group; neither are the genera Eurytoma and Bruchophagus. The monophyly of genera Sycophila and Plutarchia was well supported, as was the close association of the genera Aiolomorphus, Tenuipetiolus, Bephratelloides, and Phylloxeroxenus. Our phylogeny also revealed an anticipated pattern, in which species groups from the genera Eurytoma and Bruchophagus are often more closely related to other small genera than to other species groups of the same genus. Subsequent taxonomic revisions include elevating the subfamily Rileyinae to a family status and the divisions of the genera Eurytoma and Bruchophagus.     

Higher-level snake phylogeny inferred from mitochondrial DNA sequences of 12S rRNA and 16S rRNA genes

Portions of two mitochondrial genes (12S and 16S ribosomal RNA) were sequenced to determine the phylogenetic relationships among the major clades of snakes. Thirty-six species, representing nearly all extant families, were examined and compared with sequences of a tuatara and three families of lizards. Snakes were found to constitute a monophyletic group (confidence probability [CP] = 96%), with the scolecophidians (blind snakes) as the most basal lineages (CP = 99%). This finding supports the hypothesis that snakes underwent a subterranean period early in their evolution. Caenophidians (advanced snakes), excluding Acrochordus, were found to be monophyletic (CP = 99%). Among the caenophidians, viperids were monophyletic (CP = 98%) and formed the sister group to the elapids plus colubrids (CP = 94%). Within the viperids, two monophyletic groups were identified: true vipers (CP = 98%) and pit vipers plus Azemiops (CP = 99%). The elapids plus Atractaspis formed a monophyletic clade (CP = 99%). Within the paraphyletic Colubridae, the largely Holarctic Colubrinae was found to be a monophyletic assemblage (CP = 98%), and the Xenodontinae was found to be polyphyletic (CP = 91%). Monophyly of the henophidians (primitive snakes) was neither supported nor rejected because of the weak resolution of relationships among those taxa, except for the clustering of Calabaria with a uropeltid, Rhinophis (CP = 94%).      

Systematic relationships of hymenolepidid cestodes of rodents and shrews inferred from sequences of 28S ribosomal RNA

Haukisalmi, V., Hardman, L. M., Foronda, P., Feliu, C., Laakkonen, J., Niemimaa, J., Lehtonen, J. T. & Henttonen, H. (2010). Systematic relationships of hymenolepidid cestodes of rodents and shrews inferred from sequences of 28S ribosomal RNA. —Zoologica Scripta, 39, 631–641. This study attempts to elucidate systematic relationships of hymenolepidid cestodes of rodents (18 species), shrews (13 species) and bats (one species) using sequences of partial 28S ribosomal RNA, with special reference to the genus Rodentolepis. The main finding is the presence of four multispecies clades of hymenolepidid cestodes showing pronounced morphological variation and frequent colonizations between unrelated hosts. Neither the hymenolepidid cestodes of shrews nor rodents were monophyletic. Also, the genus Rodentolepis sensu Vaucher in Czaplinski & Vaucher (1994, Keys to the Cestode Parasites of Vertebrates. Commonwealth Agricultural Bureaux International, Cambridge) is clearly non‐monophyletic. Although rostellar morphology is obviously a key feature on specific and generic levels, on higher systematic levels it seems to be a rather poor indicator of phylogenetic affinity in hymenolepidid cestodes. The presence of clades with more than one rostellar type (armed rostellum present, rudimentary unarmed rostellum present and rostellum absent) also conflicts with the proposed subfamilial and tribal classifications of hymenolepidid cestodes. The overall evidence suggests that the recent trend of splitting hymenolepidid cestodes into multiple genera will produce a more stable and practical classification than the earlier practice of favouring a few, morphologically variable genera. New classifications of hymenolepidid cestodes should, however, consider both morphological and molecular evidence.     

Dinoflagellate phylogeny as inferred from heat shock protein 90 and ribosomal gene sequences

Background

Interrelationships among dinoflagellates in molecular phylogenies are largely unresolved, especially in the deepest branches. Ribosomal DNA (rDNA) sequences provide phylogenetic signals only at the tips of the dinoflagellate tree. Two reasons for the poor resolution of deep dinoflagellate relationships using rDNA sequences are (1) most sites are relatively conserved and (2) there are different evolutionary rates among sites in different lineages. Therefore, alternative molecular markers are required to address the deeper phylogenetic relationships among dinoflagellates. Preliminary evidence indicates that the heat shock protein 90 gene (Hsp90) will provide an informative marker, mainly because this gene is relatively long and appears to have relatively uniform rates of evolution in different lineages.

Methodology/Principal Findings

We more than doubled the previous dataset of Hsp90 sequences from dinoflagellates by generating additional sequences from 17 different species, representing seven different orders. In order to concatenate the Hsp90 data with rDNA sequences, we supplemented the Hsp90 sequences with three new SSU rDNA sequences and five new LSU rDNA sequences. The new Hsp90 sequences were generated, in part, from four additional heterotrophic dinoflagellates and the type species for six different genera. Molecular phylogenetic analyses resulted in a paraphyletic assemblage near the base of the dinoflagellate tree consisting of only athecate species. However, Noctiluca was never part of this assemblage and branched in a position that was nested within other lineages of dinokaryotes. The phylogenetic trees inferred from Hsp90 sequences were consistent with trees inferred from rDNA sequences in that the backbone of the dinoflagellate clade was largely unresolved.

Conclusions/Significance

The sequence conservation in both Hsp90 and rDNA sequences and the poor resolution of the deepest nodes suggests that dinoflagellates reflect an explosive radiation in morphological diversity in their recent evolutionary past. Nonetheless, the more comprehensive analysis of Hsp90 sequences enabled us to infer phylogenetic interrelationships of dinoflagellates more rigorously. For instance, the phylogenetic position of Noctiluca, which possesses several unusual features, was incongruent with previous phylogenetic studies. Therefore, the generation of additional dinoflagellate Hsp90 sequences is expected to refine the stem group of athecate species observed here and contribute to future multi-gene analyses of dinoflagellate interrelationships.     

Molecular phylogeny of gibbons inferred from mitochondrial DNA sequences: Preliminary report

We analyzed the 896 base-pair (bp) mitochondrial DNA (mtDNA) sequences for seven gibbons, representative of three out of four subgenera. The result from our molecular analysis is consistent with previous studies as to the monophyly of subgenus Hylobates species, yet the relationship among subgenera remains slightly ambiguous. A striking result of the analysis is the phylogenetic location of Kloss's gibbon (H. klossii). Kloss's gibbon has been considered to be an initial off-shoot of the subgenus Hylobates because of its morphological primitiveness. However, our molecular data strongly suggest that Kloss's gibbon speciated most recently within the subgenus Hylobates. Correspondence to: S. Horai