Phylogenetic relationships within Ovulidae (Gastropoda: Cypraeoidea) based on molecular data from the 16S rRNA gene

Closely interacting groups, such as hosts and parasites, sometimes provide useful models to study evolution and adaptive processes. In Ovulidae, a widespread family of specialised browsing carnivorous molluscs that feed on polyps and tissues of Anthozoa, close association with the host has produced a plethora of adaptations affecting shell morphology, colour pattern and mantle shape. These morphological characters have been widely used in ovulid taxonomy, although putative differences are often based on trivial and inconsistent variations. In this work we used a molecular approach to generate the basal phylogeny of the family. Phylogenetic analyses of mitochondrial 16S rRNA gene sequences of 32 species from 23 genera reveal unexpected taxonomic groupings from the genus up to the family level, as well as unexpected phenomena of homoplasy in conchological features. Since molecular phylogenies also provide an evolutionary framework where character transformations are polarised, we used this basal ovulid phylogeny to explore the specificity of the association and the degree of morphological adaptation to the host.Electronic Supplementary Material Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00227-005-1566-0.Communicated by R. Cattaneo-Vietti, Genova     

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 data from the 16S rRNA gene for the phylogeny of Veneridae (Mollusca: Bivalvia)

Veneridae, a cosmopolitan and ubiquitous family in world-wide littoral environments, lists more than 500 species, many of which are often subject to intensive commercial exploitation due to their numerical dominance in benthic communities. Historically, the family has been divided into 12 subfamilies by M. Keen and, even though this taxonomical arrangement was adopted for convenience and does not necessarily reflect genetic relationships, as suggested by Keen herself, this classification is still accepted. To contribute to clarify the systematics and phylogeny of Veneridae, the portion of the nucleotide sequence corresponding to domains IV and V of the gene encoding the large subunit of mitochondrial ribosomal RNA was analysed in 14 species representative of 10 genera belonging to 6 different subfamilies. The results obtained using the maximum-parsimony and neighbour-joining methods indicate that the current placement of the genera into subfamilies does not always reflect a natural subdivision. In addition, the six species of Tapetinae studied, though confirmed to be a monophyletic clade, do not exhibit a correct attribution at the genus level.     

贵州浓香型白酒大曲中霉菌的18S rDNA系统发育分析

从贵州某名酒厂大曲中分离到104株丝状真菌(霉菌),通过形态特征和生理特性检测等传统鉴定方法,初步把形态和生理生化特征一致的霉菌归类为14个大类群;并采用18S rDNA序列分析,进一步把菌株归类为MJ-I至MJ-V五个类群,随后构建系统发育树.结果表明,样品中的霉菌以曲霉属(Aspergillus)为主,占总分离菌数...     

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.     

Clostridia dominate 16S rRNA gene libraries prepared from the hindgut of temperate marine herbivorous fishes

Bacterial diversity in the microbial communities of posterior gut sections of three temperate marine herbivorous fish species from New Zealand was characterised using Amplified Ribosomal DNA Restriction Analysis, and 16S rRNA gene amplification and sequencing methods. The fish were collected in 1999–2000 in the Hauraki Gulf, New Zealand (35°54’–36°24’S, 174°48’–175°25’E). The gastrointestinal bacterial communities of Kyphosus sydneyanus (Günther, 1886) (F. Kyphosidae), Odax pullus (Forster in Bloch and Schneider, 1801) (F. Labridae) and Aplodactylus arctidens Richardson, 1839 (F. Aplodactylidae) were dominated by five clades of bacteria, four of which belong to recognized clostridial clusters. The clone libraries of K. sydneyanus and O. pullus contained sequences from most of these clades, but were dominated by members of clostridial clusters XI and XIVa, respectively. The clone library of A. arctidens was dominated by members of clostridial cluster XIVb and an unassigned cluster containing Eubacterium desmolans and Papillibacter cinnaminovorans. The finding that strains of Firmicutes dominated the gastrointestinal microbial communities of all three fish species is consistent with the results of similar studies on terrestrial vertebrate herbivores. This work thus contributes to the view that gastrointestinal symbionts in some marine herbivorous fishes may play a similar role to those in terrestrial vertebrate herbivores studied to date.     

18S rRNA phylogeny of sea spiders with emphasis on the position of Rhynchothoracidae

The phylogenetic relationships among all living families of sea spiders (Arthropoda: Pycnogonida) are investigated using nearly complete 18S rRNA sequences from 57 ingroup species and five chelicerates under the Bayesian and maximum likelihood methods. Monophyly of Colossendeidae, Pycnogonidae, Phoxichilidiidae, Endeidae and Pallenopsidae is consistently supported. However, the genera formerly classified in the family Ammotheidae are split up into two distantly related groups. The genera Ascorhynchus and Eurycyde (here recognized as Ascorhynchidae) are possibly an early offshoot of sea spiders, whereas other ammotheids constitute a robust terminal clade with Pallenopsidae, Phoxichilidiidae and Endeidae. This topology also opposes the prevalent assumption of successive losses and simplification of three kinds of cephalic appendages like in a previous cladistic analysis. At least three independent losses are suggested for palps by the inferred topology, and both chelifores and female ovigers may have been lost twice. Our knowledge of early ontogeny and internal anatomy is more congruent with the present 18S rRNA data. The families Callipallenidae and Nymphonidae with unique “attaching larvae” are grouped together in present molecular trees, suggesting that extended paternal care of offspring evolved only once in Pycnogonida. Confident clustering of Pycnogonidae and Rhynchothoracidae indicates that the number of female genital pores is an evolutionary conservative character.     

Molecular phylogeny of Ostracoda (Crustacea) inferred from 18S ribosomal DNA sequences: implication for its origin and diversification

Nucleotide sequences for the 18S rDNA of 17 ostracod species, representing 4 extant orders and 12 superfamilies, were determined and compared with known sequences of other crustaceans. Resulting molecular phylogenetic trees based on maximum-likelihood, maximum-parsimony, and neighbor-joining methods consistently indicated that the Podocopida plus Platycopida forms a monophyletic group, but did not indicate monophyly of the Ostracoda consisting of the four orders, Podocopida, Platycopida, Kirkbyocopida, and Myodocopida. The tree topology and the crustacean fossil record suggest that the lineage of podocopidans and platycopidans, that of kirkbyocopidans, and that of myodocopidans should have separately been established already in the Cambrian, although there is no ostracod fossil record in that time period. Close relationships between the Bythocytheroidea and Cytheroidea and among the Macrocypridoidea, Pontocypridoidea, and Cypridoidea can safely be postulated, but other relationships among podocopidan and platycopidan superfamilies could not be resolved from the 18S rDNA data. The polychotomous relationship among five lineages of the podocopidan and platycopidan superfamilies, i.e. Cytherelloidea, Bairdioidea, Darwinuloidea, Bythocytheroidea plus Cytheroidea, and Macrocypridoidea plus Pontocypridoidea plus Cypridoidea, suggests that common ancestors of those lineages diverged from each other rapidly in short intervals in the early Paleozoic.     

Phylogenetic relationships of the intercellular fish pathogenIchthyophonus hoferi and fungi,choanoflagellates and the rosette agent

Ichthyophonus hoferi Plehn and Mulsow, 1911 is thought to be one of the few pathogenic fungal infections of marine fish. The result of an attack is severe epizootics in herring stocks with drastic reduction in the population as a consequence. The exact phylogenetic position of the genusIchthyophonus is not known. In the present study, a combination of molecular data, ultrastructure and biochemical characters were utilized to investigate the phylogeny ofI.hoferi. The genomic DNA encoding the small subunit ribosomal RNA (18S rRNA) was amplified and sequenced. Comparisons with other eukaryotic 18S rRNA sequences indicate thatI. hoferi is not a member of the Fungi. In both the parsimony and the neighborjoining trees,I. hoferi is the sister taxon to the rosette agent. The clade encompassingI.hoferi and the rosette organism is the sister group to the chanoflagellate clade in the neighbor-joining tree, while in the parsimony tree theI. hoferi/rosette clade is equally distant to both the choanoflagellate and animal clades. Transmission electron microscopy showed thatI. hoferi has a defined cell wall, an endoplasm that consists of a fine granulated matrix with numerous ribosomes, several nuclei, vacuoles of varying density distributed throughout the cell, and mitochondria with tubular cristae. The cell wall ofI. hoferi contains chitin.     

New insights on population genetic structure of <Emphasis Type="Italic">Delphinus delphis</Emphasis> from the northeast Atlantic and phylogenetic relationships within the genus inferred from two mitochondrial markers

The taxonomic status of common dolphins (Delphinus sp.) remains controversial despite the increased number of studies focusing on its populations. Two species are presently recognized, Delphinus delphis and D. capensis. Apart from a phylogeographic study of the genus Delphinus, genetic studies focusing specifically in the northeast (NE) Atlantic remain scarce. Following ecological and morphological evidence for the existence of different common dolphin morphotypes in the Portuguese coast, we examined the population structure of D. delphis from the NE Atlantic by comparing DNA sequences from two mitochondrial regions (control region and cytochrome b gene). Additionally, we compared the sequences obtained with existing sequences of D. delphis from the Azores, Black Sea, Canary Islands, Pacific Ocean, D. capensis and also two closely related delphinid species (Stenella coeruleoalba and Tursiops truncatus). In the analysis of the NE Atlantic populations, we found evidence for the existence of some level of genetic differentiation. In the broader phylogenetic analysis, D. delphis and D. capensis did not show reciprocal monophyly and we found a group of highly divergent individuals. We discuss the possibility for the existence of two divergent lineages that have evolved independently, a separate subspecies or events of introgressive hybridization. These findings could have important implications on a taxonomic level, although further investigation based on a larger geographical scale and on nuclear loci information will certainly elucidate the origin of these highly divergent individuals.     

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     

The utility of the 16S gene in investigating cryptic speciation within the Brachionus plicatilis species complex

Recent reports indicate an extensive amount of molecular evolution separating cryptic taxa as well as significant population structure at a microgeographical scale. Appropriate molecular markers are particularly suitable for distinguishing cryptic biological species. In this study, we examine the phylogenetic utility of 16S rRNA in elucidating the evolutionary relationships within the recently described euryhaline Brachionus plicatilis species complex. In addition, we assess the applicability of this marker in the genetic identification and monitoring of rotifer populations. We have sequenced a 378-bp fragment of the mitochondrial 16S rRNA gene in laboratory reference strains, hatchery clones as well as collections from a wild population of the subsaline Lake Koroneia (Northern Greece). Also, restriction fragment length polymorphism (RFLP) analysis was performed with eight restriction endonucleases. Rotifer samples are distinguished into six genetically divergent lineages. Average sequence divergence between lineages is 0.1038. The evolutionary relationships and divergence time-scales revealed with the 16S sequence data are in agreement with previous analyses using different mitochondrial and nuclear markers. The 16S region appears to have several advantages over other regions of the genome regarding use of species-specific primers, ease of amplification from single specimens and undiluted informational content over both recent and more ancient separations. It has also exhibited maximum discriminatory power (100% success) between lineages during RFLP analysis. The 16S assayed region has proven especially informative and consistent in detecting, supporting and establishing the lineage status within the B. plicatilis species complex both from a phylogenetic perspective and as an identification tool.     

Cytogenetic analysis of Epinephelus marginatus (Pisces: Serranidae), with the chromosome localization of the 18S and 5S rRNA genes and of the (TTAGGG)n telomeric sequence

 A cytogenetic analysis was carried out on specimens of Epinephelus marginatus (Lowe, 1834) from three localities in the Mediterranean Sea, to deepen knowledge of the chromosome complement of the species and identify any possible population-specific cytogenetic markers. All specimens had a 2n = 48 acrocentric karyotype with two Ag-, chromomycin A₃- and C-positive NORs (nucleolar organizer regions) in the subcentromeric region of the smallest chromosome pair. The constitutive heterochromatin was distributed centromerically. Except for NORs, neither eu- nor heterochromatin show fluorescence after fluorochrome staining, i.e. there is no localized increase of AT- or GC-rich DNA. In all populations, the (TTAGGG) _n telomeric sequences are restricted to the telomeres, and the 18S and the 5S rDNA clusters are located on different chromosome pairs. In specimens from Sardinia, additional signals after C-banding, Ag-staining and FISH (fluorescence in situ hybridization) with 18S rDNA can be observed in the telomeric region of one or two large-sized chromosomes, classified as No. 2. This suggests that additional and variable NORs could be detected in the species in addition to those on the genus-specific, NOR-bearing Chromosome Pair 24. Received: 20 October 1999 / Accepted: 14 April 2000     

Structure of and relationships within and between the littoral,rock-substrate fish communities off four islands in the Canarian Archipelago

A total of 577 visual surveys (each of 5 min in duration and 100 m² in area) were conducted throughout 1990 and 1991 at 32 locations off four Canary islands (i.e., Alegranza, Fuerteventura, Gran Canaria and Tenerife) with the objects of describing the coastal fish community, comparing the differences in the fish fauna within and between these islands, and determining the biotic and abiotic factors related to the structure of the fish communities. A total of 76 species were recorded; the most common were Abudefduf luridus, Canthigaster rostrata, Chromis limbatus, Sparisoma cretense and Thalassoma pavo (94.28, 86.48, 52.34, 73.31, and 94.10% frequency of occurrence, respectively). The abundance and average size of the commercially important species was greater in those locations where there was less fishing pressure. The stepwise linear regression models were capable of explaining only a low amount of variation in the dependent variables (i.e., number of species, number of individuals, average size and species diversity) of the fish community. The independent variables recorded were date, time of day, depth, slope of the substrate, substrate type, percentage of sand, percentage of algae, algal height, number of sea urchins (Diadema antillarum) and the individual islands. An ANOVA, using the islands only as independent variables, indicated that each island contributed significantly to the variation in the four dependent variables and there were significant differences among the islands. Detrended correspondence analysis (DCA) and a two-way indicator species analysis (TWINSPAN) determined associations between species and environmental attributes of the survey locations. The patterns in the TWINSPAN analysis indicated that localities had faunal resemblances based on the island off which where they were located.     

Differential reproductive success within the Krummhörn population (Germany, 18th and 19th centuries)

Summary On the basis of a family reconstitution study (Krummhörn, Germany, 18^th und 19^th centuries) it is shown how in one marriage cohort (1720–1750), family land ownership correlates with systematic fitness differentials. Farmers have a greater long-term fitness, on the average, than members of non-peasant population, and farmers possessing better than average wealth achieve a greater long-term fitness than farmers with medium-sized or small landholdings. The proximate causes herefore are to be found in both the varying patterns of marital fertility and in the differences in the marital and migration habits of the children from the various social groups. That is why the number of live births or even the number of surviving children is not the best estimate of a person's genetic contribution to the next generation of the local population. This can be shown by using a new algorithm for the assessment of long-term fitness differentials.     

Geographical variations in the trophic ecology of Japanese anchovy, Engraulis japonicus, inferred from carbon and nitrogen stable isotope ratios

Carbon and nitrogen stable isotope ratios of Japanese anchovy (Engraulis japonicus) and their stomach contents were examined and compared among various regions around Japan. Geographical variations in the isotope ratios were found between inshore and Pacific offshore regions. While most of the anchovy samples had isotope ratios around −17.6‰ for δ¹³C and 10.0‰ for δ¹⁵N as median values, higher (more enriched) isotope values were found in the anchovy sampled from inshore regions. On the contrary, lower (more depleted) values were found mostly in the anchovy from the Pacific offshore region including the Kuroshio Extension and Kuroshio-Oyashio transition zones. Higher carbon isotope ratios in the inshore regions may reflect a carbon source from benthic primary producers in addition to phytoplankton possibly through the consumption of the larvae of benthic organisms such as bivalves or decapods, which were found in the stomach contents of the inshore anchovy. Variations in the nitrogen isotope ratio may reflect not only differences in the trophic level of prey species, but also variations in the baseline level of food webs. Stable isotope ratios are potentially a useful tool for understanding the stock/population structure and migration of anchovy. The present findings indicate the potential importance of the “inshore–offshore” variations in the biology of Japanese anchovy populations in the northwestern Pacific waters.     

Population structure of yellowfin tuna (Thunnus albacares) in the western Pacific Ocean, inferred from microsatellite loci

Five polymorphic microsatellite loci were examined in 1391 yellowfin tuna (Thunnus albacares) from eight regions of the western (Coral Sea, eastern Australia, Fiji, Indonesia, Philippines and Solomon Islands) and eastern (California and Mexico ) Pacific Ocean. Across all samples, numbers of alleles per locus ranged from 7 to 30 (mean: 17.0), and observed heterozygosities per locus ranged from 0.223 to 0.955 (mean: 0.593). Temporal collections were available for three areas: no significant temporal heterogeneity was observed for the Coral Sea (1991/1992 and 1995/1996 collections) or eastern Australia (1994/1995, 1995/1996, 1996/1997 and 1997/1998), but there was slight but significant heterogeneity at one locus (cmrTa-161) between the two Philippines collections (1994/1995 and 1996/1997). Genotypes generally showed a good fit to Hardy-Weinberg expectations within populations; only cmrTa-208 in the pooled Coral Sea population gave a significant deviation after Bonferroni correction for 40 tests, with a small but significant excess of homozygotes. Four loci showed no evidence of population differentiation following contingency Chi-squared and F_ST analyses. The fifth locus, cmrTa-161, showed small but significant differentiation (F_ST=0.002, P<0.001). This heterogeneity was largely a result of the Philippines 1994/1995 and Fiji collections; there was no correlation with geographic distance. The average F_ST across all five loci was very low (F_ST=0.002), but it was significant (P<0.001). It is unclear whether this low but significant differentiation reflects noise in the dataset, perhaps arising from experimental error, or real population differentiation. The finding of very limited population heterogeneity accords with most of the earlier allozyme and mitochondrial DNA studies of yellowfin tuna in the Pacific Ocean.     

Karyotype, nucleolus organiser regions and constitutive heterochromatin in Ostrea angasi (Molluscae: Bivalvia): evidence of taxonomic relationships within the Ostreidae

Chromosome preparations from gill tissue of the Australian flat oyster Ostrea angasi Sowerby were studied with conventional Giemsa staining, C-banding and silver staining techniques. A diploid complement of 2n = 20 was observed, consisting of five metacentric, three submetacentric and two subtelocentric pairs. Constitutive heterochromatin was distributed as large centromeric blocks in Chromosome Pairs 3, 6, 8, 9 and 10. The nucleolus organizer regions (NORs) were located terminally on long arms of Chromosome Pairs 9 and 10. This allowed the identification of homologous chromosomes in submetacentric and subtelocentric pairs. Intraspecific variability in NOR pattern as revealed by differences in the number of silver-stained NORs (Ag-NORs) per cell was found to be very common. Comparison of the patterns of karyotype, C-band and Ag-NORs between species of the larviparous oysters for which data have been published demonstrate that the chromosomal structure of the endemic Australian and New Zealand species O. angasi shows little similarity to the Southern Hemisphere oysters O. (Eostrea)puelchana Orbigny and Tiostrea chilensis (Philippi) and the Indo-West Pacific oyster O. denselamellosa, but very high resemblance to the European species O. edulis. Received: 12 August 1996 / Accepted: 16 September 1996