Seasonal occurrence and food habits of larvae and juveniles of two temperate basses in the Shimanto estuary,Japan

Larvae and juveniles ofLateolabrax japonicus andL. latus occurred from January to May 1986 in the shallow waters of the Shimanto estuary.L. japonicus markedly outnumberedL. latus. Distinct ecological differences were recognized in habitats and food habits between the two species:L. japonicus mainly inhabited eelgrass beds composed ofZostera nana, whileL. latus appeared evenly in both eelgrass beds and non-eelgrass habitats; the former fed on copepods and cladocerans, while the latter fed on copepods and fish larvae. From these habitat and food habit analyses, estuaries were considered to be important as a main habitat forL. japonicus, but not forL. latus. The fact that ecological differences have occurred during the early life stages was inferred to be one of the possible keys to speculate on the speciation of the two species.     

The phylogeny ofPapaver s. l. (Papaveraceae): Polyphyly or monophyly?

An RFLP analysis of the chloroplast genetrnK of 32 species of the generaPapaver, Roemeria, Stylomecon, andMeconopsis leads to the following conclusions: (1) AsianMeconopsis consists of two distinct clades and is paraphyletic in relation toPapaver, Roemeria, Stylomecon, and the W EuropeanMeconopsis cambrica. (2) Sister group relationships ofRoemeria toPapaver sect.Argemonidium and ofStylomecon toPapaver californicum are well-supported. (3)Meconopsis cambrica is nested withinPapaver (incl.Roemeria andStylomecon). The consideration of morphology, geographical distribution and ecology leads to the conclusion thatM. cambrica is best regarded as a member ofMeconopsis, and thatPapaver arose polyphyletically from within a paraphyleticMeconopsis in response to Tertiary climatic aridification. — The removal ofM. cambrica from the taxon matrix is discussed. It is concluded that this experiment illuminates the importance of critical taxon sampling, and shows that at least potentially the assessment of taxa as mono-, para-, or polyphyletic may characterize their present status only and need not reflect their phylogenetic history.     

On the presence of the genus Branchinecta Verrill, 1869 (Crustacea,Anostraca) in Yugoslavia

The genus Branchinecta Verrill, 1869 is represented in Yugoslavia by two species: Branchinecta ferox (Milne-Edwards, 1840) and Branchinecta orientalis G.O. Sars, 1901. The first species was collected in the steppe-like province of Banat, Pannonian Lowland, and in the lowland around the Skadar Lake, Montenegro, the second only in the province of Banat.On the basis of rich material of both species, a detailed study of the most essential morphological characters has been carried out and comparisons have been made with data in the literature. In B. ferox, significant morphological deviations are not found, whereas, in B. orientalis, essential features are clearly ascertained which were previously unknown or were not stated with sufficient precision. B. ferox is known to appear in small, temporary, natronsoda water rainpools, while B. orientalis has been found in a large temporary inundation pool with a high content of natronsoda and salt in the water.     

Branchinecta oterosanvicentei n. sp. (Branchiopoda: Anostraca), a new fairy shrimp from the Chihuahuan desert, with a proposal for the conservation of the Branchinectidae of Mexico

Branchinecta oterosanvicentei, new species, a fairy shrimp endemic to the south of Coahuila, Mexico is described and figured. Differential features between the new species and the related B. lindahli are discussed on the basis of a SEM micrographs. The main diagnostic characters of Branchinecta oterosanvicentei are: (1) a pulvinus covered by scales localized on the middle of the median side of the proximal article of antenna, and (2) a network of prominent cortical crests on the cyst surface. Of seven Branchinecta species occurring in Mexico, four (B. belki, B. mexicana, B. oterosanvicentei, and B. sandiegonensis) have a restricted geographic range. Because, in addition, extreme fluctuations in the number of mature individuals per population occur, the survival of all of these species is threatened, and measures should be taken to protect them. Branchinecta mackini has a wide distribution in North America, but even this form is rare in Mexico.     

Differential zooplankton feeding behaviors,selectivities, and community impacts of two planktivorous fishes

Synopsis We examined the feeding behaviors and selectives of two common planktivorous fishes, pumpkinseeds Lepomis gibbosa and fathead minnows Pimephales promelas in the laboratory. Ingestion rates for both pumpkinseeds and fathead minnows feeding on zooplankton increased as a function of fish length. Pumpkinseeds fed on zooplankton strictly as particulate feeders, with preferences increasing as a function of zooplankton body size regardless of taxonomic identity. Preferences were highest for large Daphnia, intermediate for intermediate-sized copepods, and lowest for small Ceriodaphnia. Fathead minnows displayed the ability to use both particulate-feeding and filter-feeding behaviors. Differential preferences tended to reflect both zooplankton size and taxon, being highest for large, slow-swimming Daphnia, intermediate for small Ceriodaphnia, and lowest for faster-swimming copepods. These differences in prey capture behaviors and preferences of the two fishes are reflected in the zooplankton taxonomic composition of small ponds containing each fish type. The crustacean zooplankton assemblages in ponds containing both pumpkinseeds and fathead minnows were dominated by copepods. Cladocerans were rare. In ponds containing pumpkinseeds, but no fathead minnows, cladocerans were abundant, generally accounting for up to 80% of total crustacean zooplankton biomass. These results suggest that the type of planktivore, and not simply the presence or abundance of planktivores in a system, can determine zooplankton community structure.     

Does the nutrient stoichiometry of primary producers affect the secondary consumer Pleurobrachia pileus?

We investigated whether phosphorus limitations of primary producers propagate upwards through the food web, not only to the primary consumer level but also onto the secondary consumers’ level. A tri-trophic food chain was used to assess the effects of phosphorus-limited phytoplankton (the cryptophyte Rhodomonas salina) on herbivorous zooplankters (the copepod Acartia tonsa) and finally on zooplanktivores (the ctenophore Pleurobrachia pileus). The algae were cultured in phosphorus-replete and phosphorus-limited media before being fed to two groups of copepods. The copepods in turn were fed to the top predator, P. pileus, in a mixture resulting in a phosphorus-gradient, ranging from copepods having received only phosphorus-replete algae to copepods reared solely on phosphorus-limited algae. The C:P ratio of the algae varied significantly between the two treatments, resulting in higher C:P ratios for those copepods feeding on phosphorus-limited algae, albeit with a significance of 0.07. The differences in the feeding environment of the copepods could be followed to Pleurobrachia pileus. Contrary to our expectations, we found that phosphorus-limited copepods represented a higher quality food source for P. pileus, as shown by the better condition (expressed as nucleic acid content) of the ctenophore. This could possibly be explained by the rather high C:P ratios of ctenophores, their resulting low phosphorus demand and relative insensitivity to P deficiency. This might potentially be an additional explanation for the observed increasing abundances of gelatinous zooplankton in our increasingly phosphorus-limited coastal seas.     

PACT: an efficient and powerful algorithm for generating area cladograms

Aim To introduce and describe the functioning of a new algorithm, phylogenetic analysis for comparing trees (PACT), for generating area cladograms that provide accurate representation of information contained in taxon–area cladograms. Methods PACT operates in the following steps. Convert all phylogenies to taxon–area cladograms. Convert all taxon–area cladograms to Venn diagrams. Choose any taxon–area cladogram from the set of taxon–area cladograms to be analysed and determine its elements. This will be the template area cladogram. Select a second taxon–area cladogram. Determine its elements. Document which elements in the second tree occur in the template tree (denoted by ‘Y’) and which do not (denoted by ‘N’). Each ‘Y’ indicates a match with previous pattern and these are combined. Each ‘N’ is a new element and is attached to the template area cladogram at the node where it is linked with a Y. This requires two rules: (1) ‘Y + Y = Y’ (combine common elements) as long as they are connected at the same node; and (2) ‘Y + N = YN’ (add novel elements to the template area cladogram at the node where they first appear). Once the novel elements in the second taxon–area cladogram have been added to the template area cladogram, see if any of them can be further combined. This requires three additional rules: (1) ‘Y(Y? = Y(Y?’ (do not combine Y's if they are attached at different nodes on the template area cladogram); (2) ‘Y + YN = YN’ (Y is part of group YN); and (3) ‘YN + YN = YNN’ (Y is the same for each, but each N is different). Repeat for all available taxon–area cladograms. Results Three exemplars demonstrate that PACT provides the most accurate area cladograms for vicariance‐driven biotic diversification, dispersal‐driven biotic diversification and taxon pulse‐driven biotic diversification. PACT can also be used as an a priori method of biogeographical analysis. Main conclusions PACT embodies all the strong points and none of the weaknesses of previously proposed methods of historical biogeography. It is most useful as an a posteriori method, but it is also superior to all previous a priori methods because it does not specify costs, or weights or probabilities, or likelihoods of particular biogeographical processes a priori and is thus sensitive to clade‐specific historical contingencies.     

The ultrastructure of the cuticle of Nematoda

 The ultrastructure of the body cuticle in species of six of seven representative genera of Stilbonematinae (Eubostrichus, Catanema, Laxus, Robbea, Leptonemella, and Stilbonema) was investigated using SEM and TEM techniques. Additionally, one species of Spirinia (Spiriniinae) and one of Desmodora (Desmodorinae) were studied for outgroup comparison. The body cuticle of all investigated stilbonematids shows a consistent pattern composed of specific elements in a characteristic arrangement to each other. This pattern does not occur in Stilbonematinae alone, but also in Desmodorinae and Spiriniinae. Furthermore, a comparison within the Desmodorida reveals that this cuticular pattern apparently is present in the cuticle of representatives of Monoposthiidae, Epsilonematidae, and Draconematidae. The present results lead to the following conclusions: (1) the cuticle of Stilbonematinae contains no autapomorphic characters for this taxon, (2) there is a common cuticular pattern within the Desmodorida, and (3) this pattern is an autapomorphic character for the order Desmodorida. Accepted: 4 February 1996     

Phylogenetic systematics and historical biogeography of the Neotropical electric fish Sternopygus (Teleostei: Gymnotiformes)

Interrelationships among 10 extant species of the Neotropical electric fish Sternopygus are inferred from phylogenetic analysis of 66 morphological characters, including features of pigmentation, body proportions, meristics and osteology. A total of 287 lots containing 677 specimens were examined. The important findings of this study are: (1) S. branco is the most basal species unique among congeners in being restricted to whitewater rivers in the Central Amazon Basin, (2) S. sp. ‘cau’ from the Rio Caura of Venezuela is the sister taxon to (S. obtusirostris + S. astrabes), (3) S. castroi is a junior synonym of S. astrabes, (4) S. macrurus is the sister taxon to (S. arenatus + S. xingu + S. aequilabiatus species group) and (5) S. arenatus is the sister taxon to (S. xingu + S. aequilabiatus species group). A key to the adults of Sternopygus species is provided. Several features of S. astrabes previously thought to be plesiomorphic are now considered derived, including: short body cavity, paedomorphic cranial osteology, and the habitat restriction to terra firme streams. Sternopygus species assemblages in the Pacific (trans‐Andean) and Atlantic (cis‐Andean) slopes of northwestern South America are not monophyletic and do not result exclusively from local or regional radiations. The clade composed of S. macrurus, S. arenatus, S. xingu and the S. aequilabiatus species group is inferred to predate the Middle Miocene uplift of the Eastern Cordillera (c. 11.8–12.2 Ma). As currently recognized S. macrurus is the most widely distributed and most eurytopic gymnotiform species, inhabiting all hydrogeographical regions of tropical South America and most lowland aquatic habitats. Other Sternopygus species have much more restricted geographic and ecological distributions. Perceptions of phylogenetic patterns in Sternopygus are shown to be highly sensitive to taxon sampling.     

Distribution and abundance of soft-sediment meiofauna and a predatory goby in a coral reef lagoon

Spatial patterns in the abundance of the softsediment meiofauna and a predatory goby, Valenciennia longipinnis, were examined in the lagoon of One Tree Reef (Great Barrier Reef). The study provided a quantitative framework to assess the importance of physical factors on and predator prey interactions between the meiofauna and V.longipinnis. Patterns of abundance were examined at two spatial scales: among four habitats (100's of m apart) and among sites (10's of m apart) within habitats. Of the four major constituents of the meiofauna (harpacticoid copepods, nematodes, polychaetes and oligochaetes), gut analyses showed that harpacticoid copepods were the primary prey of V.longipinnis. Spatial patterns of meiofaunal abundance in the lagoon were taxon specific. Polychaetes and harpacticoid copepods exhibited significant differences among habitats. Within habitats, however, polychaetes exhibited significant differences between sites whereas copepods were uniformly distributed. Abundances of nematodes and oligochaetes did not differ between habitats. Densities of nematodes differed significantly between sites while the number of oligochaetes were similar at both spatial scales. V.longipinnis was more abundant in shallow habitats than in deep ones. This study suggests that sediment type may be an important factor influencing the distribution of both the goby and the meiofauna. V.longipinnis and two of the four meiofaunal taxa (harpacticoid copepods and polychaetes) were more abundant in the shallow habitat with fine-grained sediments. There was no significant difference between abundances of meiofaunal taxa in sites where V.longipinnis was present or absent. Overall, more fish occurred in the habitat which had the highest densities of harpacticoid copepods.     

Skeletal morphology and the phylogeny of skuas (Aves: Charadriiformes,Stercorariidae)

The skuas (Aves: Charadriiformes, Stercorariidae) consist of two assemblages. On the basis of size, plumage, and distributional similarities, each of the two assemblages has long been considered monophyletic, and this traditional hypothesis has commonly been manifested in the recognition of two genera, Stercorarius and Catharacta; conversely, more recently collected molecular and ectoparasite evidence yields an alternative hypothesis, in which one member of Stercorarius, Stercorarius pomarinus, is more closely related to the forms in Catharacta than to the other Stercorarius sp. In this study we used skeletal morphology to test the competing hypotheses of skua phylogeny. Cladistic analysis of 141 osteological characters provided strong support for the molecular/ectoparasite hypothesis. However, those skeletal data did not support a sister‐taxon relationship between S. pomarinus and Catharacta skua, as inferred from mitochondrial DNA sequence data; instead, they resolved pomarinus as the sister of a monophyletic Catharacta. Additionally, our skeletal evidence did not support a sister‐group relationship between skuas and auks, as constraining skua/auk monophyly increased the tree length by nearly 5%. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 157 , 612–621.     

Shotgun metagenomics and microscopy indicate diverse cyanophytes,other bacteria,and microeukaryotes in the epimicrobiota of a northern Chilean wetland Nostoc (Cyanobacteria)

Prokaryotic Nostoc, one of the world's most conspicuous and widespread algal genera (similar to eukaryotic algae, plants, and animals) is known to support a microbiome that influences host ecological roles. Past taxonomic characterizations of surface microbiota (epimicrobiota) of free‐living Nostoc sampled from freshwater systems employed 16S rRNA genes, typically amplicons. We compared taxa identified from 16S, 18S, 23S, and 28S rRNA gene sequences filtered from shotgun metagenomic sequence and used microscopy to illuminate epimicrobiota diversity for Nostoc sampled from a wetland in the northern Chilean Altiplano. Phylogenetic analysis and rRNA gene sequence abundance estimates indicated that the host was related to Nostoc punctiforme PCC 73102. Epimicrobiota were inferred to include 18 epicyanobacterial genera or uncultured taxa, six epieukaryotic algal genera, and 66 anoxygenic bacterial genera, all having average genomic coverage ≥90X. The epicyanobacteria Geitlerinemia, Oscillatoria, Phormidium, and an uncultured taxon were detected only by 16S rRNA gene; Gloeobacter and Pseudanabaena were detected using 16S and 23S; and Phormididesmis, Neosynechococcus, Symphothece, Aphanizomenon, Nodularia, Spirulina, Nodosilinea, Synechococcus, Cyanobium, and Anabaena (the latter corroborated by microscopy), plus two uncultured cyanobacterial taxa (JSC12, O77) were detected only by 23S rRNA gene sequences. Three chlamydomonad and two heterotrophic stramenopiles genera were inferred from 18S; the streptophyte green alga Chaetosphaeridium globosum was detected by microscopy and 28S rRNA genes, but not 18S rRNA genes. Overall, >60% of epimicrobial taxa were detected by markers other than 16S rRNA genes. Some algal taxa observed microscopically were not detected from sequence data. Results indicate that multiple taxonomic markers derived from metagenomic sequence data and microscopy increase epimicrobiota detection.     

Early evolutionary relationships among known life forms inferred from elongation factor EF-2/EF-G sequences: Phylogenetic coherence and structure of the archaeal domain

Summary Phylogenies were inferred from both the gene and the protein sequences of the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria). All treeing methods used (distance-matrix, maximum likelihood, and parsimony), including evolutionary parsimony, support the archaeal tree and disprove the eocyte tree (i.e., the polyphyly and paraphyly of the Archaea). Distance-matrix trees derived from both the amino acid and the DNA sequence alignments (first and second codon positions) showed the Archaea to be a monophyletia-holophyletic grouping whose deepest bifurcation divides a Sulfolobus branch from a branch comprising Methanococcus, Halobacterium, and Thermoplasma. Bootstrapped distance-matrix treeing confirmed the monophyly-holophyly of Archaea in 100% of the samples and supported the bifurcation of Archaea into a Sulfolobus branch and a methanogen-halophile branch in 97% of the samples. Similar phylogenies were inferred by maximum likelihood and by maximum (protein and DNA) parsimony. DNA parsimony trees essentially identical to those inferred from first and second codon positions were derived from alternative DNA data sets comprising either the first or the second position of each codon. Bootstrapped DNA parsimony supported the monophyly-holophyly of Archaea in 100% of the bootstrap samples and confirmed the division of Archaea into a Sulfolobus branch and a methanogen-halophile branch in 93% of the bootstrap samples. Distance-matrix and maximum likelihood treeing under the constraint that branch lengths must be consistent with a molecular clock placed the root of the universal tree between the Bacteria and the bifurcation of Archaea and Eukarya. The results support the division of Archaea into the kingdoms Crenarchaeota (corresponding to the Sulfolobus branch and Euryarchaeota). This division was not confirmed by evolutionary parsimony, which identified Halobacterium rather than Sulfolobus as the deepest offspring within the Archaea.Offprint requests to: P. Cammarano     

Cross-breeding experiments among different populations of the ‘cosmopolitan’ species Phyllognathopus viguieri (Copepoda: Harpacticoida)

Populations of harpacticoid copepods belonging to the family Phyllognathopodidae found on most continents are usually assignable to the taxon of Phyllognathopus viguieri, as it is presently diagnosed, on the basis of their morphological characters. This taxon has been considered as cosmopolitan since the unifying revision of Lang in 1948. Here we reveal that Phyllognathopus viguieri is not a single biological species. Cross-breeding experiments with individuals from five different populations of Phyllognathopus viguieri obtained from Germany, Maryland and Florida in the USA, Jamaica, and Brazil indicated that two of these mutually distant populations were reproductively isolated from each other but crossed easily with others, whereas the other populations did not interbreed, with the exception of the two populations from the USA. From these results we conclude that Phyllognathopus viguieri is not a single cosmopolitan biological species. The high proportion of mutually non-reproducing populations identified in the five populations examined in this study indicate that further analysis of the micromorphology and genetic composition of populations over the entire putative range of Phyllognathopus viguieri will be necessary to clarify their interrelationships.     

INCORPORATION OF FRESHWATER RHODOPHYTA INTO THE CASES OF CHIRONOMID LARVAE (CHIRONOMIDAE,DIPTERA) FROM NORTH AMERICA1

Chironomid larvae incorporate pieces of freshwater red algae into their cases from a wide geographic range in North America, extending from southern Canada to central Mexico. The Rhodophyta used in this process represent two orders (Acrochaetiales and Batrachospermales), five genera (Audouinella, Batrachospermum, Lemanea, Paralemanea, and Sirodotia), and 14 species from 21 locations. Three genera from the chironomid subfamily Orthocladiinae make these cases: Cardiocladius, Eukiefferiella, and Orthocladius. The Eukiefferiella claripennis group was the most frequently observed infrageneric taxon using red algae in its cases. The cases were tubular in shape with longitudinally oriented strips of algae held together by silken threads. Some of the cases constructed with Batrachospermum and Sirodotia also had several lateral branches of the alga radiating from the tube.     

Molecular phylogeny of the superfamily Tephritoidea (Insecta: Diptera) reanalysed based on expanded taxon sampling and sequence data

Phylogenenetic relationships of the superfamily Tephritoidea (Diptera: Tephritidae) were reanalysed based upon four mitochondrial gene fragments (12S, 16S, cytochrome c oxidase I and cytochrome c oxidase II) from 53 tephritoid (10 families) and 30 outgroup (14 families) species. The data set of Han and Ro (Mol Phylogenet Evol, 39, 2005, 416) was expanded in terms of the number of taxa as well as molecular characters. We were able to sample the enigmatic families Ctenostylidae and Eurygnathomyiidae for the first time. Based on increased taxon sampling (from 49 to 83 species) and additional sequences (combined length of DNA fragments increased from 2451 to 4490 bp), the inferred phylogenetic trees suggest a number of interesting phylogenetic relationships, some of which were not recovered from the previous study. Some of the important findings are as follows: (1) monophyly of the superfamily Tephritoidea; (2) all the included tephritoid families except for Tephritidae were recovered as monophyletic groups; (3) Tephritoidea can be divided into two monophyletic groups – the Piophilidae Family Group (Pallopteridae, Circumphallidae?, Lonchaeidae, Piophilidae and Eurygnathomyiidae) and the Tephritidae Family Group (Richardiidae, Ulidiidae, Platystomatidae, Tephritidae, Ctenostylidae and Pyrgotidae); (4) Eurygnathomyiidae is recognized as an independent monophyletic family apart from Pallopteridae; (5) the enigmatic family Ctenostylidae is a member of the superfamily Tephritoidea; (6) parasitic Pyrgotidae + Ctenostylidae + Tachiniscinae and mostly phytophagous Tephritidae are recovered within a monophyletic group; and (7) according to an inferred chronogram, the first Tephritoidea might have evolved around the middle of Paleocene Epoch [~59 Million years ago (mya)] and the family Tephritidae around the late Eocene (~36 mya).     

Kallymenia crouaniorum (Kallymeniaceae,Rhodophyta), a new red algal species from the Laminaria hyperborea understorey community

In this paper we describe Kallymenia crouaniorum Vergés & Le Gall, sp. nov. (Kallymeniaceae), a new marine red alga from the north-eastern Atlantic Ocean. rbcL and LSU sequences of this species, previously misidentified in the field as Kallymenia reniformis, diverged from those of other Kallymenia species by at least 7.5% and 5.2%, respectively. Kallymenia crouaniorum also has a set of distinctive vegetative and reproductive characteristics, including a deeply lacerate frond, a short stipe, dentate margins, large cortical cells up to 110 μm in diameter, highly refractive stellate medullary cells with arms up to 1000 μm in length, and a monocarpogonial branch system. Molecular phylogenies inferred from rbcL and LSU data indicated, albeit with weak support, that this new species is a sister taxon of a lineage encompassing the generitype K. reniformis, as well as most species of Kallymenia included in the phylogenetic analysis. The main morphological characters that delineate monocarpogonial Kallymenia species are presented. Moreover, after reviewing the literature and several herbarium specimens, we found in the Weber-van Bosse Herbarium a specimen collected at Roscoff in August 1894 with the anatomical characters of the species described here, confirming that this newly described species has in fact been overlooked and is not a recent introduction.     

Relationships among the major lineages of Dictyoptera: the effect of outgroup selection on dictyopteran tree topology

Abstract Dictyoptera, comprising Blattaria, Isoptera, and Mantodea, are diverse in appearance and life history, and are strongly supported as monophyletic. We downloaded COII, 16S, 18S, and 28S sequences of 39 dictyopteran species from GenBank. Ribosomal RNA sequences were aligned manually with reference to secondary structure. We included morphological data (maximum of 175 characters) for 12 of these taxa and for an additional 15 dictyopteran taxa (for which we had only morphological data). We had two datasets, a 59‐taxon dataset with five outgroup taxa, from Phasmatodea (2 taxa), Mantophasmatodea (1 taxon), Embioptera (1 taxon), and Grylloblattodea (1 taxon), and a 62‐taxon dataset with three additional outgroup taxa from Plecoptera (1 taxon), Dermaptera (1 taxon) and Orthoptera (1 taxon). We analysed the combined molecular?morphological dataset using the doublet and MK models in Mr Bayes , and using a parsimony heuristic search in paup . Within the monophyletic Mantodea, Mantoida is recovered as sister to the rest of Mantodea, followed by Chaeteessa; the monophyly of most of the more derived families as defined currently is not supported. We recovered novel phylogenetic hypotheses about the taxa within Blattodea (following Hennig, containing Isoptera). Unique to our study, one Bayesian analysis places Polyphagoidea as sister to all other Dictyoptera; other analyses and/or the addition of certain orthopteran sequences, however, place Polyphagoidea more deeply within Dictyoptera. Isoptera falls within the cockroaches, sister to the genus Cryptocercus. Separate parsimony analyses of independent gene fragments suggest that gene selection is an important factor in tree reconstruction. When we varied the ingroup taxa and/or outgroup taxa, the internal dictyopteran relationships differed in the position of several taxa of interest, including Cryptocercus, Polyphaga, Periplaneta and Supella. This provides further evidence that the choice of both outgroup and ingroup taxa greatly affects tree topology.     

Phylogenetic incongruence between dinoflagellate endosymbionts (Symbiodinium) and their host foraminifera (Sorites): small-subunit ribosomal RNA gene sequence evidence

Phototrophic dinoflagellate zooxanthellae commonly occur as endosymbionts in many planktic and certain benthic foraminifera (soritids). Many taxonomic issues and specific identities of foraminiferal dinoflagellates are not yet resolved. To assess taxonomic affinities among other dinoflagellates, we have determined the complete nucleotide sequence of the small-subunit rRNA coding region from Symbiodinium sp., an endosymbiotic dinoflagellate of the larger foraminifer Sorites orbiculus. The poly merase chain reaction was adopted for the in vitro amplification of ribosomal DNA, utilizing primers complementary to conserved regions. PCR-amplified DNA was directly sequenced and the sequence was aligned to all complete 18S-rDNA dinoflagellate sequences currently available through GenBank. Apicomplexan, ciliate, chromistacean, and rhodophycean sequences were added to infer across-kingdom phylogenetic relationships. Phylogenetic analysis of aligned nucleotide sequences produced a single most parsimonious tree (generated by the branch and bound method of PAUP). The inferred phylogeny indicates that the dinoflagellate extracted from the foraminifer Sorites orbiculus is a sister taxon to the symbiont present in the larger foraminifera Marginopora kudakajimaensis, but only distantly related to the dinoflagellate isolated from the soritid Amphisorus hemprichii. The sequence heterogeneity demonstrates a high degree of genetic diversity among Symbiodinium-like zooxanthellae and re-emphasizes that they are a variety of distinct entities.The inferred molecular phylogenetic relationships among symbiotic dinoflagellates are not congruent with the foraminiferal phylogeny based on cladistic methodology. The lack of correlation between the evolutionary history of dinoflagellate symbionts and their foraminiferal hosts argues against co-evolution. This lack of co-evolution implies that flexible recombinations among hosts and symbionts are evolutionarily favorable over permanently associated lineages, at least in these benthic foraminifera.