Species richness in the African pike genus Hepsetus: a perfect match between genetics and morphology.

In this study, morphological differences were found that corroborate earlier results that showed the existence of six species within the previously monospecific African pike genus Hepsetus. Additional genetic data (coI, mtDNA and rag1, nDNA) confirm the morphology-based species delineations. Deep genetic divergences imply a relatively old age for diversification within the genus. An identification key for the six species is provided in the present study.

Water-level fluctuations and metapopulation dynamics as drivers of genetic diversity in populations of three Tanganyikan cichlid fish species.

Understanding how genetic variation is generated and maintained in natural populations, and how this process unfolds in a changing environment, remains a central issue in biological research. In this work, we analysed patterns of genetic diversity from several populations of three cichlid species from Lake Tanganyika in parallel, using the mitochondrial DNA control region. We sampled populations inhabiting the littoral rocky habitats in both very deep and very shallow areas of the lake. We hypothesized that the former would constitute relatively older, more stable and genetically more diverse populations, because they should have been less severely affected by the well-documented episodes of dramatic water-level fluctuations. In agreement with our predictions, populations of all three species sampled in very shallow shorelines showed traces of stronger population growth than populations of the same species inhabiting deep shorelines. However, contrary to our working hypothesis, we found a significant trend towards increased genetic diversity in the younger, demographically less stable populations inhabiting shallow areas, in comparison with the older and more stable populations inhabiting the deep shorelines. We interpret this finding as the result of the establishment of metapopulation dynamics in the former shorelines, by the frequent perturbation and reshuffling of individuals between populations due to the lake-level fluctuations. The repeated succession of periods of allopatric separation and secondary contact is likely to have further increased the rapid pace of speciation in lacustrine cichlids.

The evolutionary history of hepaciviruses.

In the search for natural reservoirs of hepatitis C virus (HCV), a broad diversity of non-human viruses within the Hepacivirus genus has been uncovered. However, the evolutionary dynamics that shaped the diversity and timescale of hepaciviruses evolution remain elusive. To gain further insights into the origins and evolution of this genus, we screened a large dataset of wild mammal samples (n = 1,672) from Africa and Asia, and generated 34 full-length hepacivirus genomes. Phylogenetic analysis of these data together with publicly available genomes emphasizes the importance of rodents as hepacivirus hosts and we identify 13 rodent species and 3 rodent genera (in Cricetidae and Muridae families) as novel hosts of hepaciviruses. Through co-phylogenetic analyses, we demonstrate that hepacivirus diversity has been affected by cross-species transmission events against the backdrop of detectable signal of virus-host co-divergence in the deep evolutionary history. Using a Bayesian phylogenetic multidimensional scaling approach, we explore the extent to which host relatedness and geographic distances have structured present-day hepacivirus diversity. Our results provide evidence for a substantial structuring of mammalian hepacivirus diversity by host as well as geography, with a somewhat more irregular diffusion process in geographic space. Finally, using a mechanistic model that accounts for substitution saturation, we provide the first formal estimates of the timescale of hepacivirus evolution and estimate the origin of the genus to be about 22 million years ago. Our results offer a comprehensive overview of the micro- and macroevolutionary processes that have shaped hepacivirus diversity and enhance our understanding of the long-term evolution of the Hepacivirus genus.

Complete mitochondrial DNA replacement in a Lake Tanganyika cichlid fish.

We used nuclear and mitochondrial DNA (mtDNA) sequences from specimens collected throughout Lake Tanganyika to clarify the evolutionary relationship between Lamprologus callipterus and Neolamprologus fasciatus. The nuclear data support the reciprocal monophyly of these two shell-breeding lamprologine cichlids. However, mtDNA sequences show that (i) L. callipterus includes two divergent and geographically disjunct (North-South) mtDNA lineages; and that (ii) N. fasciatus individuals cluster in a lineage sister group to the northern lineage of L. callipterus. The two mtDNA lineages of L. callipterus diverged c. 684 kya to 1.2 Ma, coinciding with a major water level low stand in Lake Tanganyika, which divided the lake into isolated sub-lakes. This suggests that the two mtDNA lineages originated as the result of the separation of L. callipterus populations in different sub-basins. The incongruent phylogenetic position of N. fasciatus can best be explained by an ancient unidirectional introgression from L. callipterus into N. fasciatus. Remarkably, our data indicate that this event resulted in the complete mtDNA replacement in N. fasciatus. Our data suggest that hybridization occurred soon after the divergence of the two L. callipterus mtDNA lineages, probably still during the water level low stand, and that subsequently the invading mtDNA lineage spread throughout the lake.

From conical to spatulate: intra- and interspecific changes in tooth shape in closely related cichlids (Teleostei; Cichlidae: Eretmodini).

The Eretmodini are closely related cichlids endemic to Lake Tanganyika with very divergent oral tooth shapes, ranging from spatulate in Eretmodus to conical in Tanganicodus. To study how closely related cichlids can generate such divergent tooth shapes, we investigated how the enamel organ directs the development of spatulate teeth in Eretmodus cf. cyanostictus (lineage A), both in ontogeny and in adults, and of conical teeth in adult Tanganicodus cf. irsacae, using 3D-reconstructions from serially sectioned tooth germs. The spatulate oral tooth shape that characterizes adult E. cf. cyanostictus (lineage A) is preceded early in ontogeny by a conical tooth shape. We propose two possible hypotheses to account for changes in the folding of the enamel organ (in particular its epithelio-mesenchymal boundary) capable of generating such distinct tooth shapes. Different arguments lead us to favor the hypothesis of an asymmetric growth and differentiation of the enamel organ, such that the tip of a conical tooth corresponds to one "corner" of a spatulate tooth. Applying current molecular models of tooth shape variation, this would imply the existence of asymmetric fields of inhibition. Whether such asymmetric growth reflects the reutilization of a simple mechanism operating in ontogeny has to be clarified.

[Evolutionary relationships among narrow-headed rats (genus Stenocephalemys, Muridae, Rodentia) inferred from complete cytochrome b gene sequences].

Using the data on complete sequences of cytochrome b gene, phylogenetic relationships were studied among the Stenocephalemys s. lat. (Stenocephalemys ssp. + Praomys albipes) murine rodents, inhabiting adjacent altitudinal belts of the isolated Ethiopian mountain massifs, and among the related Praomys s. lat. species. Extremely low resolution of the relationships among the main Praomys s. lat. lineages hampered identification of the nearest sister group for the Stenocephalemys s. lat. "Ethiopian" clade, monophyly of which was strongly supported. Sister relationships between P. albipes and S. griseicauda (implying "accelerated" morphological and chromosomal evolution upon the formation of the former species), as well as between S. albocaudata and the recently described novel chromosomal form of Stenocephalemus sp. A (2n = 50; NFa = 56) were demonstrated. Definite discordance between the rates of their molecular, chromosomal, and morphological evolution was revealed. Based on phylogenetic reconstructions and the estimates of the divergence time, obtained by use of molecular clock method, an attempt to draw a phylogenetic scenario for the group examined was made. The obtained data were compared to those for analogous Sigmodontinae species complexes, distributed across a marked altitudinal gradient on the Andean slopes. It was shown that molecular genetic data on the rodents from mountain tropics did not support the gradient model of diversification, based on the possibility of morphological diversification prior to their achievement of the species status (without interruption of the gene flow between the forms) due to differently directed selection across a strong environmental gradient.

Analysis of dominant enhancers and suppressors of activated Notch in Drosophila.

The Notch receptor controls cell fate decisions throughout Drosophila development. Truncated, ligand-independent forms of this protein delay or block differentiation. We have previously shown that expression of the intracellular domain of the receptor under the control of the sevenless enhancer/promoter induces a rough eye phenotype in the adult fly. Analysis of the resultant cellular transformations suggested that this form of Notch acts as a constitutively activated receptor. To identify gene products that interact with Notch, a second-site mutagenesis screen was performed to isolate enhancers and suppressors of the eye phenotype caused by expression of these activated Notch molecules. We screened 137,000 mutagenized flies and recovered 290 dominant modifiers. Many new alleles of previously identified genes were isolated, as were mutations defining novel loci that may function in the Notch signaling pathway. We discuss the data with respect to known features of Notch receptor signaling and Drosophila eye development.

The tissue polarity gene nemo carries out multiple roles in patterning during Drosophila development.

Drosophila nemo was first identified as a gene required for tissue polarity during ommatidial development. We have extended the analysis of nemo and found that it participates in multiple developmental processes. It is required during wing development for wing shape and vein patterning. We observe genetic interactions between nemo and mutations in the Notch, Wingless, Frizzled and Decapentaplegic pathways. Our data support the findings from other organisms that Nemo proteins act as negative regulators of Wingless signaling. nemo mutations cause polarity defects in the adult wing and overexpression of nemo leads to abdominal polarity defects. The expression of nemo during embryogenesis is dynamic and dsRNA inhibition and ectopic expression studies indicate that nemo is essential during embryogenesis.

Microsatellites reveal high levels of population substructuring in the species-poor Eretmodine cichlid lineage from Lake Tanganyika.

This study investigated fine-scale population substructuring in an apparently monogamous, biparental mouth-brooding cichlid. Microsatellite allele frequencies were determined at four polymorphic loci for nine populations of Eretmodus cyanostictus. We provide empirical support for the hypothesis that a species employing this breeding strategy should exhibit high levels of population substructuring. Stretches of sand represent considerable barriers to dispersal and, in contrast to the rock-dwelling cichlids of Lake Malawi, distance alone, along a continuous rocky shoreline, is sufficient to reduce gene flow significantly There was a significant pattern of isolation by distance both along the whole study area and over the stretch of continuous shoreline, suggesting that this species has poor dispersal capabilities and that juveniles establish territories close to their natal site. Despite limited dispersal, E. cyanostictus populations are not significantly more inbred than a more-widely dispersing rock-dwelling cichlid from Lake Malawi. This finding may cast doubt on the hypothesis that polyandry has evolved as a mechanism for maintaining genetic diversity in Lake Malawi cichlids. High levels of substructuring may not always promote high levels of speciation, and other factors, such as the intensity of sexual selection, may be more important in determining the speciation potential of a lineage.

Streptococcus suis type 2 infections in pigs in the Netherlands (Part two).

Since 1983 some pig breeding and fattening farms in the Netherlands have been faced with a considerable mortality in pigs due to Streptococcus suis type 2 infections. The most predominant clinical feature of S. suis type 2 infection is meningitis, although sudden deaths often occur. It was noted that some affected farms had imported breeding stock from the United Kingdom. Tonsils of slaughter pigs were collected from herds with and without a history of S. suis type 2 infections. Bacteriological examination was done by using an elective-selective medium. No significant difference was found in carrier rates of S. suis type 2 between clinically healthy and affected herds (38% vs. 45%). A cohort study was carried out by regular bacteriological examination of tonsil biopsies on a farm with a high incidence of streptococcal meningitis. Twenty-seven percent of the pigs were carriers of S. suis type 2 at nine weeks of age. Possible methods for disease control are discussed.

Molecular phylogeny of Myomys/Stenocephalemys complex and its relationships with related African genera.

Partial 16S rRNA mitochondrial gene sequences were used to infer the phylogenetic relationships among Stenocephalemys albocaudata, S. griseicauda and Myomys albipes, three closely related Ethiopian endemic murines and a selection of related species (Myomys daltoni, Praomys delectorum, Mastomys natalensis, Hylomyscus kaimosae, and Colomys goslingi) from other African regions. The obtained phylogeny confirms the close relationship between M. albipes and the two Stenocephalemys species, but it also suggests that both the genera Myomys and Stenocephalemys are paraphyletic, as M. albipes is closer to Stenocephalemys than to M. daltoni and S. griseicauda is more closely related to M. albipes than to S. albocaudata. These data, if confirmed, would argue that M. albipes should be renamed S. albipes. In conclusion, our study suggests that morphological similarity is not always a reliable measure for close genetic relationship in murines. Morphological similarity among species that evolved under similar ecological conditions can be the result of convergent evolution rather than a consequence of recent common ancestry.

Catalytic activation of OKO zeolite with intersecting pores of 10- and 12-membered rings using atomic layer deposition of aluminium.

Tetrahedral framework aluminium was introduced in all-silica zeolite -COK-14 using Atomic Layer Deposition (ALD) involving alternating exposure to trimethylaluminium and water vapour. The modification causes permanent conversion of the originally interrupted framework of -COK-14 to a fully connected OKO type framework, and generates catalytic activity in the acid catalysed hydrocarbon conversion reaction.

Cytochrome b sequence analysis reveals differential molecular evolution in African mole-rats of the chromosomally hyperdiverse genus Fukomys (Bathyergidae, Rodentia) from the Zambezian region.

African mole-rats (Bathyergidae, Rodentia) of the (eu)social genus Fukomys are one of the most speciose mammal genera endemic to Sub-Saharan Africa. Fukomys distributed in the Zambezian phytochorion is characterized by extreme chromosomal variation (2n=40-78). We inferred a molecular phylogeny of Zambezian Fukomys to resolve the interrelationships and the evolutionary history of the known chromosomal races. We sequenced the entire cytochrome b gene (1140bp) for a total of 66 specimens representing 18 karyotypical races from Zambia. An additional 31 sequences were retrieved from GenBank including data on all other chromosomal races. The haplotypes belonging to a small chromosomal race from Salujinga cluster with the Fukomys mechowii (Giant mole-rat) haplotypes. Differential degrees of chromosomal variation are observed among the major mole-rat clades, which is most pertinent when comparing the central Zambezian Fukomys micklemi and the northern Zambezian Fukomys whytei clades. The karyotypically hyper-diverse (12 known chromosomal races) Fukomys micklemi clade shows low levels of cytochrome b sequence divergence. Within the F. whytei clade we find a more conservative pattern of chromosomal diversification (three known chromosomal races) while the levels of sequence divergence are much higher then in the F. micklemi clade. Our results suggest that chromosomal changes may drive phyletic divergence and, eventually, speciation. The observed cladogenetic events during the Plio-Pleistocene within the F. mechowii, F. whytei, F. damarensis and F. micklemi clades appear to coincide with climatically mediated speciation bursts in other savannah dwelling mammals, including hominids. Based on the molecular data presented, combined with morphological and chromosomal data, the taxonomic implication seems to be that Fukomys may contain several (undescribed) cryptic species.

Mitochondrial phylogeny of African wood mice, genus Hylomyscus (Rodentia, Muridae): implications for their taxonomy and biogeography.

This paper investigates the usefulness of two mitochondrial genes (16S rRNA and cytochrome b) to solve taxonomical difficulties within the genus Hylomyscus and to infer its evolutionary history. Both genes proved to be suitable molecular markers for diagnosis of Hylomyscus species. Nevertheless the resolving powers of these two genes differ, and with both markers (either analyzed singly or in combination), some nodes remain unresolved. This is probably related to the fact that the species emerged during a rapid diversification event that occurred 2-6 Myr ago (4-5 Myr ago for most divergence events). Our molecular data support the recognition of an "aeta" group, while the "alleni" and "parvus" groups are not fully supported. Based on tree topology and genetic divergence, two taxa generally recognized as subspecies should be elevated at the species level (H. simus and H. cf kaimosae). H. stella populations exhibit ancient haplotype segregation that may represent currently unrecognized allopatric species. The existence of cryptic species within H. parvus is questioned. Finally, three potentially new species may occur in West Central Africa. The Congo and Oubangui Rivers, as well as the Volta and Niger Rivers and/or the Dahomey gap could have formed effective barriers to Hylomyscus species dispersal, favoring their speciation in allopatry. The pronounced shifts in African climate during the late Pliocene and Miocene, which resulted in major changes in the distribution and composition of the vegetation, could have promoted speciation within the genus (refuge theory). Future reports should focus on the geographic distribution of Hylomyscus species in order to get a better understanding of the evolutionary history of the genus.

Profilin mutations disrupt multiple actin-dependent processes during Drosophila development.

The chickadee gene of Drosophila encodes profilin, a small actin binding protein. We present the first analysis of the effects of profilin deletion in a multicellular organism. Genomic deletions of the chickadee locus result in a late embryonic lethal phenotype indicating that profilin is essential in flies. In addition, viable alleles of chickadee with defects in oogenesis, spermatogenesis and bristle formation provide insight into profilin function in a variety of cell types. Defects in oogenesis include the previously described failure to assemble nurse cell actin filament bundles in addition to abnormal regulation of mitosis, binucleate cells and stalled cell migration. Malformed bristles are a result of aberrant actin assembly. Monoclonal antibodies against Drosophila profilin were generated to study profilin's cellular and subcellular localization.

Mitochondrial phylogeny of the Lamprologini, the major substrate spawning lineage of cichild fishes from Lake Tanganyika in eastern Africa.

Lake Tanganyika harbors the oldest, morphologically and behaviorally most diverse flock of cichlid species. While the cichlids in Lakes Malawi and Victoria breed their eggs exclusively by buccal incubation (termed "mouthbrooding"), the Tanganyikan cichlid fauna comprise mouthbrooding and substrate-spawning lineages (fish spawn on rocks, and never orally incubate eggs or wrigglers). The substrate-spawning tribe Lamprologini appears to occupy a key position that might allow one to elucidate the origin of the Tanganyika flock, because five riverine (therefore nonendemic) species from the Zaire River system have been assigned to this tribe, in addition to the lake's endemic species, which make up almost 50% of all 171 species known from this lake (Poll 1986). From 16 species (18 individuals) of the tribe Lamprologini, a 402-bp segment of the mitochondrial cytochrome b gene was sequenced, and, from 25 lamprologine species (35 individuals), sequences from the mitochondrial control region were obtained. To place the Lamprologini into a larger phylogenetic framework, orthologous sequences were obtained from eight nonlamprologine Tanganyikan cichlid species (13 individuals). The Lamprologini are monophyletic, and a clade of six Tanganyikan lineages of mouthbrooders, representing five tribes (Poll 1986), appears to be their sister group. Comparisons of sequence divergences of the control region indicate that the Lamprologini may be older than the endemic Tanganyikan tribe Ectodini, and short basal branches might suggest a rapid formation of lineages at an early stage of the Tanganyika radiation. It is interesting that three analyzed riverine members of the tribe form a monophyletic group; however, they are not the most ancestral branch of the Lamprologini. This might indicate that they are derived from an endemic lamprologine ancestor that left Lake Tanganyika by entering the Zaire River system. These riverine species may not have seeded the Tanganyikan radiation, as currently thought, but may have recently recolonized the river after a long period of isolation, as soon as the lake was connected to the Zaire River again about 2 Mya. Neolamprologus moorii, endemic to Lake Tanganyika, appears to represent the most basal clade of the Lamprologini. Complex breeding behavior, involving the usage of gastropod shells and associated with dwarfism, is likely to have evolved in parallel in several lineages among the Lamprologini. The tribe Lamprologini may be in need of revision, since several genera appear to be polyphyletic.

chickadee encodes a profilin required for intercellular cytoplasm transport during Drosophila oogenesis.

The entire cytoplasmic contents of 15 highly polyploid nurse cells are transported rapidly to the oocyte near the end of Drosophila oogenesis. chickadee is one of a small group of genes whose mutant phenotype includes a disruption of this nurse cell cytoplasm transport. We have cloned the chickadee gene and found that cDNA clones encode a protein 40% identical to yeast and Acanthamoeba profilin. The nurse cells from chickadee egg chambers that lack ovary-specific profilin fail to synthesize cytoplasmic actin networks correctly. In addition, the nurse cell nuclei in chickadee egg chambers become displaced and often partially stretched through the channels leading into the oocyte, blocking the flow of cytoplasm. We suggest that the newly synthesized cytoplasmic actin networks are responsible for maintaining nuclear position in the nurse cells.

Replicated evolution of trophic specializations in an endemic cichlid fish lineage from Lake Tanganyika.

The current phylogenetic hypothesis for the endemic Lake Tanganyika cichlid fishes of the tribe Eretmodini is based solely on morphology and suggests that more complex trophic morphologies derived only once from a less specialized ancestral condition. A molecular phylogeny of eretmodine cichlids based on partial mitochondrial DNA cytochrome b and control-region sequences was used to reconstruct the evolutionary sequence of trophic adaptations and to test alternative models of morphological divergence. The six mitochondrial lineages found disagree with the current taxonomy and the morphology-based phylogeny. Mitochondrial lineages with similar trophic morphologies are not grouped monophyletically but are typically more closely related to lineages with different trophic phenotypes currently assigned to other genera. Our results indicate multiple independent origins of similar trophic specializations in these cichlids. A pattern of repeated divergent morphological evolution becomes apparent when the phylogeography of the mitochondrial haplotypes is analyzed in the context of the geological and paleoclimatological history of Lake Tanganyika. In more than one instance within Lake Tanganyika, similar morphological divergence of dentitional traits occurred in sympatric species pairs. Possibly, resource-based divergent selective regimes led to resource partitioning and brought about similar trophic morphologies independently and repeatedly.

The oxygen uptake of Sarotherodon niloticus L. and the oxygen binding properties of its blood and hemolysate (Pisces: Cichlidae).

The oxygen consumption of Sarotherodon niloticus L. was found to decline below a critical oxygen concentration of about 2 mg O2/l. An important influence of CO2 on the oxygen affinity of whole blood was observed at all temperatures between 20 and 35 degrees C for gas mixtures containing 5.6% CO2. Purified hemolysate showed extremely high oxygen affinities (p50 = 1.08 mmHg at pH 8.2 and 20 degrees C). Low cooperativity was observed at all temperatures from 20 to 35 degrees C, and pH values between 6.5 and 8.2. The Bohr effect proved to be important at pH values lower than pH 7.5 (phi = delta log P50/delta pH = -0.58 between pH 6.5 and 7.0 at 35 degrees C). The oxygen affinities show high thermal sensitivity without a marked pH influence (delta H value for overall oxygenation at pH was -71.7 kJ/mol). The obtained results are interpreted as adaptations to diurnal variations in ambient temperature and oxygen availability.

Tooth shape differences analyzed by biometric and morphometric approaches: a case study on two morphologically very similar lacustrine cichlid species.

Tooth shape is generally considered to be under strong genetic control, and highly species specific. It is therefore widely used for taxonomic studies. The tooth shape-based morphological classification of the Eretmodini (a tribe of closely related cichlids endemic to Lake Tanganyika), has, however, been shown to be in conflict with recent molecular data, which suggests the occurrence of parallel evolution. A detailed biometric and morphometric analysis of tooth shape has been undertaken for two genetic lineages of the taxon Eretmodus cyanostictus. The use of both landmark-based measurements and elliptic Fourier analysis reveals differences between both lineages and supports the molecular phylogeny. These differences further endorse the interpretation of parallel evolution. In addition, we here present a powerful tool for the analysis of tooth shape.