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See detailThe phycologist Pierre Compère: his contribution to cyanobacterial studies
Golubic, Stjepko; Wilmotte, Annick ULg

in Plant Ecology and Evolution (2014), 147(3), 307-310

At the occasion of the 80th birthday of Pierre Compère, his rich career as a phycologist and cyanobacteriologist is placed in the context of the advances of the scientific theories, the evolution of the ... [more ▼]

At the occasion of the 80th birthday of Pierre Compère, his rich career as a phycologist and cyanobacteriologist is placed in the context of the advances of the scientific theories, the evolution of the cyanobacterial taxonomy and the nomenclatural discussions linked to the utilization of two different Codes of nomenclature. [less ▲]

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See detailPhylloblastia inexpectata (Verrucariaceae), a new species of foliicolous lichen from Western Europe and Madeira
Sérusiaux, Emmanuel ULg; Coppins, B. J.; Lucking, R.

in Lichenologist (2007), 39(Part 2), 103-108

Phylloblastia inexpectata Serus., Coppins

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See detailPhylogenetic analyses of mitochondrial and nuclear data in haematophagous flies support the paraphyly of the genus Stomoxys (Diptera: Muscidae)
Dsouli, N.; Delsuc, F.; Michaux, Johan ULg et al

in Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics of Infectious Diseases (2011), 11(3), 663-670

The genus Stomoxys Geoffroy (Diptera; Muscidae) contains species of parasitic flies that are of medical and economic importance. We conducted a phylogenetic analysis including 10 representative species of ... [more ▼]

The genus Stomoxys Geoffroy (Diptera; Muscidae) contains species of parasitic flies that are of medical and economic importance. We conducted a phylogenetic analysis including 10 representative species of the genus including multiple exemplars, together with the closely related genera Prostomoxys Zumpt, Haematobosca Bezzi, and Haematobia Lepeletier & Serville. Phylogenetic relationships were inferred using maximum likelihood and Bayesian methods from DNA fragments from the cytochrome c oxidase subunit I (COI, 753. bp) and cytochrome b (CytB, 587. bp) mitochondrial genes, and the nuclear ribosomal internal transcribed spacer 2 (ITS2, 426. bp). The combination of mitochondrial and nuclear data strongly supports the paraphyly of the genus Stomoxys because of the inclusion of Prostomoxys saegerae Zumpt. This unexpected result suggests that Prostomoxys should be renamed into Stomoxys. Also, the deep molecular divergence observed between the subspecies Stomoxys niger niger Macquart and S. niger bilineatus Grünbreg led us to propose that they should rather be considered as distinct species, in agreement with ecological data. Bayesian phylogenetic analyses support three distinct lineages within the genus Stomoxys with a strong biogeographical component. The first lineage consists solely of the divergent Asian species S. indicus Picard which appears as the sister-group to all remaining Stomoxys species. The second clade groups the strictly African species Stomoxys inornatus Grünbreg, Stomoxys transvittatus Villeneuve, Stomoxys omega Newstead, and Stomoxys pallidus Roubaud. Finally, the third clade includes both African occurring and more widespread species such as the livestock pest Stomoxys calcitrans Linnaeus. Divergence time estimates indicate that the genus Stomoxys originated in the late Oligocene around 30 million years ago, with the major lineages diversifying in the Early Miocene between 20 and 15 million years ago at a time when temperate forests developed in the Northern Hemisphere. © 2011 Elsevier B.V. [less ▲]

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See detailPhylogenetic analysis of the pearlfish Carapini (Ophidiiformes, Carapidae)
Parmentier, Eric ULg; Castillo Cabello, Gabriel ULg; Chardon, Michel ULg et al

in Acta Zoologica (2000), 81

Fishes of the tribe Carapini (Encheliophis and Carapus) share a noteworthy peculiarity: they shelter in holothurian echinoderms or bivalve hosts. Some species are considered parasitic, others commensal ... [more ▼]

Fishes of the tribe Carapini (Encheliophis and Carapus) share a noteworthy peculiarity: they shelter in holothurian echinoderms or bivalve hosts. Some species are considered parasitic, others commensal. This study focuses on the phylogeny of the tribe, using two other Carapidae species as an outgroup (Snyderidia canina and Onuxodon fowleri). Insofar as possible, the selected anatomical and behavioural characters where chosen in an ecomorphological perspective, as features that could be responses to various lifestyle-related constraints. Our character selection also took into account the fact that some features are (presumably) linked. Such features were grouped together as a single trait to avoid their overvaluation. This methodology enabled us to separate commensals from parasites, the former belonging to Carapus and the latter to Encheliophis. Carapus species reflect in their morphology the constraints imposed by a diet of hard, mobile, elusive prey, showing predator-type features: a strong dentition, a wide mouth opening, a robust food intake apparatus. On the other hand, the endoparasitic Encheliophis species show a generally weaker buccal apparatus and narrow mouth opening, in relation to the different constraints of their lifestyle where the diet constraints are less pronounced: they eat body parts of their host. We propose changes in both generic diagnoses and transfer three species from Encheliophis to Carapus. [less ▲]

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See detailPhylogenetic classification of the mitochondrial carrier family of Saccharomyces cerevisiae.
Elmoualij, Benaïssa ULg; Duyckaerts, Claire ULg; Brasseur, Josette ULg et al

in Yeast (Chichester, England) (1997), 13(6), 573-581

The screening of the open reading frames identified in the whole yeast genome has allowed us to discover 34 proteins belonging to the mitochondrial carrier family. By phylogenetic study, they can be ... [more ▼]

The screening of the open reading frames identified in the whole yeast genome has allowed us to discover 34 proteins belonging to the mitochondrial carrier family. By phylogenetic study, they can be divided into 27 subfamilies including ADP/ATP, phosphate and citrate carriers, putative oxoglutarate and GDC carriers and 22 new subfamilies. Topology predictions using the 'positive inside rule' approach have shown that the yeast carriers are similarly oriented with both extremities exposed to the cytosol. In each subfamily, a strict conservation of the charged residues in the six transmembrane alpha-helices is observed, suggesting a functional role for these residues and the existence of 27 functionally distinct carriers. [less ▲]

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See detailPhylogenetic placement, species delimitation, and cyanobiont identity of endangered aquatic Peltigera species (lichen-forming Ascomycota, Lecanoromycetes)
Miadlikowska, Jolanta; Richardson, David; Magain, Nicolas ULg et al

in American Journal of Botany (2014)

Premise of this study: Aquatic cyanolichens from the genus Peltigera section Hydrothyriae are subject to anthropogenic threats and, therefore, are considered endangered. In this study we addressed the ... [more ▼]

Premise of this study: Aquatic cyanolichens from the genus Peltigera section Hydrothyriae are subject to anthropogenic threats and, therefore, are considered endangered. In this study we addressed the phylogenetic placement of section Hydrothyriae within Peltigera. We delimited species within the section and identified their symbiotic cyanobacteria. • Methods: Species delimitation and population structure were explored using monophyly as a grouping criterion (RAxML) and Structurama based on three protein-coding genes in combination with two nuclear ribosomal loci. The 16S and rbcLX sequences for the cyanobionts were analyzed in the broad phylogenetic context of free-living and symbiotic cyanobacteria. • Key results: We confirm with high confidence the placement of section Hydrothyriae within the monophyletic genus Peltigera; however, its phylogenetic position within the genus remains unsettled. We recovered three distinct monophyletic groups corresponding to three species: P. hydrothyria, P. gowardii s.s., and P. aquatica Miadl. & Lendemer, the latter being formally introduced here. Each species was associated with an exclusive set of Nostoc haplotypes. • Conclusions: The ITS region alone provides sufficient genetic information to distinguish the three morphologically cryptic species within section Hydrothyriae. Section Hydrothyriae seems to be associated with a monophyletic lineage of Nostoc, that has not been found in symbiotic association with other members of Peltigera. Capsosira lowei should be transferred to the genus Nostoc. Potential threats to P. aquatica should be re-examined based on the recognition of two aquatic species in western North America. [less ▲]

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See detailPhylogenetic position of the Ohiya rat (Srilankamys ohiensis) based on mitochondrial and nuclear gene sequence analysis
Buzan, Elena; Pagès, Marie ULg; Michaux, Johan ULg et al

in Zoologica Scripta (2011), 40(6), 545-553

We investigated the phylogenetic position the Ohiya rat, endemic to Sri Lanka, Srilankamys (Rodentia, Murinae), within the tribe Rattini based on the combined analysis of three independent genes (a ... [more ▼]

We investigated the phylogenetic position the Ohiya rat, endemic to Sri Lanka, Srilankamys (Rodentia, Murinae), within the tribe Rattini based on the combined analysis of three independent genes (a mitochondrial one and two nuclear exons). Three major lineages (the Maxomys, the Dacnomys and the Rattus divisions) were retrieved as monophyletic groups within the tribe Rattini. Srilankamys was not affiliated to any of the representatives of the Dacnomys division as it was supposed based on morphological characters, but clearly appeared as the first genus to diverge among the Rattus division. The Mindanao Shrew Mouse, Crunomys melanius, emerged as a part of the Maxomys division raising questions about the validity of the Crunomys and the Maxomys divisions as currently defined. Molecular date of divergence between Srilankamys and the other representatives of the Rattus division falls within the interval 6.7 ± 0.74 Mya, coinciding with the time of the isolation of Sri Lanka from the Deccan peninsula and the aridification period owing to the climate change at the end of the Miocene epoch. We suggest that the isolation of Sri Lanka from the continent, reinforced by the action of a seasonal monsoon-dominated climate, would have led to the isolation of some ancestral rodents of the Rattus division, which would have differentiated later into the Ohiya rat by a vicariant process. In a more general point of view, our study supports the previous results obtained on other organisms and evidence that Sri Lanka appears to be characterized by a particular fauna as compared to the Indian mainland. This island would therefore be considered as a specific distinct hotspot of biodiversity. [less ▲]

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See detailPhylogenetic relationships among filamentous helical cyanobacteria investigated on the basis of 16S ribosomal RNA gene sequence analysis
Nelissen, Bart; Wilmotte, Annick ULg; Neefs, Jean-Marc et al

in Systematic & Applied Microbiology (1994), 17

The cyanobacterial genera Spirulina and Arthrospira are both characterized by helical trichomes but their taxonomy is controversial and a phylogenetic study is necessary. The sequence of the 16S rRNA gene ... [more ▼]

The cyanobacterial genera Spirulina and Arthrospira are both characterized by helical trichomes but their taxonomy is controversial and a phylogenetic study is necessary. The sequence of the 16S rRNA gene and the spacer between the 16S and 23S rRNA genes (ITS) was determined for three filamentous coiled cyanobacteria: Spirulina PCC 6313, Arthrospira PCC 7345 and Arthrospira PCC 8005. A distance tree based on the 16S rRNA sequences was constructed using the neighbor-joining method. This tree shows that the two Arthrospira strains are not closely related to the Spirulina strain but belong to a cluster of strains assigned to the genera Oscillatoria, Lyngbya, and Microcoleus. The strain Spirulina PCC 6313 belongs to a branching containing unicellular cyanobacteria. For the two Arthrospira strains, the sequenced ITS region contains the tRNA(Ile) and tRNA(Ala) genes, whereas the spacer region of strain Spirulina PCC 6313 contains only the tRNA(Ile) gene. [less ▲]

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See detailPhylogenetic relationships among the cyanobacteria based on 16S rRNA sequences
Wilmotte, Annick ULg; Herdman, Michael

in Garrity, George M; Castenholz, Richard W (Eds.) Bergey's Manual of Systematic Bacteriology. Volume One : The Archaea and the Deeply Branching and Phototrophic Bacteria (2001)

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See detailPhylogenetic Relationships of Nonaxenic Filamentous Cyanobacterial Strains Based on 16S rRNA Sequence Analysis
Nelissen, Bart; De Baere, Raymond; Wilmotte, Annick ULg et al

in Journal of Molecular Evolution (1996), 42

In order to determine the nearly complete 16S rRNA gene sequences of cyanobacteria originating from nonaxenic cultures, a cyanobacterium-specific oligonucleotide probe was developed to distinguish ... [more ▼]

In order to determine the nearly complete 16S rRNA gene sequences of cyanobacteria originating from nonaxenic cultures, a cyanobacterium-specific oligonucleotide probe was developed to distinguish polymerase chain reaction (PCR) products of the cyanobacterial rRNA operons from those resulting from amplification of contaminating bacteria. Using this screening method the 16S rRNA genes of four nonaxenic filamentous cyanobacterial strains belonging to the genera Leptolyngbya and OscitIatoria were cloned and sequenced. For the genus Leptolyngbya, the 16S rRNA sequence of the axenic strain PCC 73110 was also determined. Phylogenetic trees were constructed based on complete and partial sequences. The results show that the strains Leptolyngbya Jbveolarum Kom~rek 1964/112, Leptolyngbya sp. VRUC 135 Albertano t985/1, and LeptoIyngbya boryanum PCC 73110 belong to the same cluster. Strain Oscillatoria cf. corallinae SAG 8.92, which contains the rare photosynthetic pigment CUphycoerythrin, is not closely related to other CUphycoerythrin- containing cyanobacteria. Oscillatoria agardhii CYA 18, which is a representative of planktonic Oscillatoria species that form toxic blooms in Norwegian inland waters, has no close relatives in the tree. [less ▲]

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See detailPhylogenetic study of Aedes albopictus and Aedes koreicus (Diptera, Culicidae) origin, two invasive mosquito species in Belgium
Raharimalala, Fara Nantenaina ULg; Boukraa, Slimane ULg; Bawin, Thomas ULg et al

Poster (2014, April 10)

The main ways of the introduction of invasive mosquito species in Europe were greatly facilitated by the importation of used tires and plants from the South of China (Dracaena sanderiana, called "Lucky ... [more ▼]

The main ways of the introduction of invasive mosquito species in Europe were greatly facilitated by the importation of used tires and plants from the South of China (Dracaena sanderiana, called "Lucky bamboo"), which are a very good breeding sites of these mosquitoes (www.eidatlantique.eu). For Belgium, several species of exotic mosquitoes have already been listed such as Ochlerotatus japonicus japonicus, Aedes albopictus and A. koreicus. We have captured one male of A. albopictus in Belgium in July 2013 (Boukraa et al, 2013), and teams from other entomologist have been able to find several individuals in the months that have followed our discovery (personal communication). However, his presence was reported first in 2000 (Schaffner et al. 2004) but until 2012, no individuals have been found (Versteirt et al., 2013). We also could find larvae of A. koreicus in abundance. These discovery suggest that these two invasive species are being established in Belgium. Methods: Adult mosquitoes were collected by CO2-baited traps Mosquito Magnet Liberty Plus (MMLP) and immature stages by the dipping method from 8 sites of Belgium. Each individual was then determined morphologically. For A. albopictus and A. koreicus, reconfirmation by molecular method was performed with COI and ND5 mitochondrial primers and sequences were then aligned with those of mosquitoes available in databases by using BioEdit and Multialn softwares. The two gene sequences were concatenated to improve the reliability of the phylogenetic analysis and were carried out by using the Seaview software based on maximum likelihood (ML) methods. Trees were then constructed with the general time reversible (GTR) model, and branch supports were estimated by bootstrapping with 1000 replicates. Result: The aim of this work will focus on the study of the probable origin of these two species of Aedes, which are for the moment safe yet, but that might become dangerous in the event of massive outbreak. The knowledge of the probably origin of the two invasive mosquitoes allow take more protection against their way to enter in the country. [less ▲]

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See detailPHYLOGENETIC STUDY OF CYANOBACTERIA ON THE BASIS OF 16S RIBOSOMAL-RNA SEQUENCES
Nelissen, Bart; Wilmotte, Annick ULg; De Baere, Raymond et al

in Belgian Journal of Botany (1992), 125

In this study, the 16S rRNA sequences of five filamentous cyanobacteria (Cyanophyceae) have been determined. These sequences were used to construct, by a distance matrix method, a tree topology to depict ... [more ▼]

In this study, the 16S rRNA sequences of five filamentous cyanobacteria (Cyanophyceae) have been determined. These sequences were used to construct, by a distance matrix method, a tree topology to depict the phylogenetic relationships among cyanobacteria. [less ▲]

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See detailA Phylogenomic analysis of the origin of plastids
Cornet, Luc ULg; Javaux, Emmanuelle ULg; Wilmotte, Annick ULg et al

Conference (2014, June 24)

Cyanobacteria are a morphologically diverse phylum, with their first occurrence dating from the Precambrian. Oxygenic photosynthesis appeared in this group during the same geological period. Several ... [more ▼]

Cyanobacteria are a morphologically diverse phylum, with their first occurrence dating from the Precambrian. Oxygenic photosynthesis appeared in this group during the same geological period. Several publications have established, without any doubt, that plastids (both primary and complex) form a monophyletic ensemble emerging from Cyanobacteria. However, the exact position of plastids within Cyanobacteria is still uncertain, with several recent papers leading to very different hypotheses. Here we present a phylogenomic analysis of the origin of plastids. Our study takes advantage of all the available genomes and thus represents the best taxonomic sampling seen so far: 140 genomes of Cyanobacteria, 101 genomes of plastids and 27 outgroups taken in Melainabacteria and Chloroflexi. It results in an analysis using state-of-the-art methods (e.g., orthology assessment using USEARCH and OrthoMCL, phylogenetic inference using CAT and CAT-GTR models) based on more than 160 protein alignments totalizing over 20,000 unambiguously aligned amino acids. To confirm our results, we performed gene jackknife inferences and gene reconciliation analyses on the same dataset. We expect that out approach accounts for potential phylogenetic artefacts due to changes in the evolutionary process having occurred when the guest cyanobacterium became an endosymbiont and eventually a plastid. Meanwhile, we improve the phylogeny of Cyanobacteria per se, notably because of the presence of Melainabacteria in our dataset. [less ▲]

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See detailPhylogenomic evidence for separate acquisition of plastids in cryptophytes, haptophytes, and stramenopiles
Baurain, Denis ULg; Brinkmann, Henner; Petersen, Jorn et al

in Molecular Biology and Evolution (2010), 27(7), 1698-709

According to the chromalveolate hypothesis (Cavalier-Smith T. 1999. Principles of protein and lipid targeting in secondary symbiogenesis: euglenoid, dinoflagellate, and sporozoan plastid origins and the ... [more ▼]

According to the chromalveolate hypothesis (Cavalier-Smith T. 1999. Principles of protein and lipid targeting in secondary symbiogenesis: euglenoid, dinoflagellate, and sporozoan plastid origins and the eukaryote family tree. J Eukaryot Microbiol 46:347-366), the four eukaryotic groups with chlorophyll c-containing plastids originate from a single photosynthetic ancestor, which acquired its plastids by secondary endosymbiosis with a red alga. So far, molecular phylogenies have failed to either support or disprove this view. Here, we devise a phylogenomic falsification of the chromalveolate hypothesis that estimates signal strength across the three genomic compartments: If the four chlorophyll c-containing lineages indeed derive from a single photosynthetic ancestor, then similar amounts of plastid, mitochondrial, and nuclear sequences should allow to recover their monophyly. Our results refute this prediction, with statistical support levels too different to be explained by evolutionary rate variation, phylogenetic artifacts, or endosymbiotic gene transfer. Therefore, we reject the chromalveolate hypothesis as falsified in favor of more complex evolutionary scenarios involving multiple higher order eukaryote-eukaryote endosymbioses. [less ▲]

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See detailA phylogenomic falsification of the chromalveolate hypothesis
Baurain, Denis ULg; Brinkmann, Henner; Petersen, Jorn et al

Poster (2010, July)

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See detailPhylogenomics: how far back in the past can we go?
Brinkmann, Henner; Baurain, Denis ULg; Philippe, Hervé

in Pudritz, Ralph; Higgs, Paul; Stone, Jonathan (Eds.) Planetary Systems and the Origins of Life (2007)

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See detailPhylogénomique des lignées photosynthétiques
Baurain, Denis ULg; Brinkmann, Henner; Philippe, Hervé

Scientific conference (2006, December 22)

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See detailPhylogeny
Baudoin, Jean-Pierre ULg; Maquet, A.

in Plant and Soil (2003), 252(1), 55-128

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