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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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See detailPhylogeny and Morphological Evolution of the Amblystegiaceae (Bryopsida)
Vanderpoorten, Alain ULg; Hedenäs, L.; Cox, C. J. et al

in Molecular Phylogenetics & Evolution (2002), 23

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See detailPhylogeny of the genus Apodemus with a special emphasis on the subgenus Sylvaemus using the nuclear IRBP gene and two mitochondrial markers: cytochrome b and 12S rRNA.
Michaux, Johan ULg; Chevret, P.; Filippucci, M*-G et al

in Molecular Phylogenetics & Evolution (2002), 23(2), 123-36

Phylogenetic relationships among 17 extant species of Murinae, with special reference to the genus Apodemus, were investigated using sequence data from the nuclear protein-coding gene IRBP (15 species ... [more ▼]

Phylogenetic relationships among 17 extant species of Murinae, with special reference to the genus Apodemus, were investigated using sequence data from the nuclear protein-coding gene IRBP (15 species) and the two mitochondrial genes cytochrome b and 12S rRNA (17 species). The analysis of the three genes does not resolve the relationships between Mus, Apodemus, and Rattus but separates Micromys from these three genera. The analysis of the two mitochondrial regions supported an association between Apodemus and Tokudaia and indicated that these two genera are more closely related to Mus than to Rattus or Micromys. Within Apodemus, the mitochondrial data sets indicated that 8 of the 9 species analyzed can be sorted into two main groups: an Apodemus group, with A. agrarius, semotus, and peninsulae, and a Sylvaemus group, with uralensis, flavicollis, alpicola, sylvaticus, and hermonensis. The position of Apodemus mystacinus is ambiguous and might be either included in Sylvaemus or considered a distinct subgenus, Karstomys, more closely related to Sylvaemus than to Apodemus. Estimation of the divergence time for these taxa suggests a separation between 7 and 8 My ago for the three groups (mystacinus and the two subgenera Apodemus and Sylvaemus). Within each subgenus, divergence times are between 5.4 and 6 My for Apodemus and between 2.2 and 3.5 My for Sylvaemus and mystacinus. [less ▲]

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See detailPhylogeny, biogeography, and the evolution of life-history traits in Leucadendron (Proteaceae)
Barker, N. P.; Vanderpoorten, Alain ULg; Morton, C. M. et al

in Molecular Phylogenetics and Evolution (2004), 33(3), 845-860

Leucadendron is a moderately large genus of Proteaccae almost entirely restricted to the Cape Floristic Region of southern Africa. The genus is unusual in being dioecious and sexually dimorphic. ITS ... [more ▼]

Leucadendron is a moderately large genus of Proteaccae almost entirely restricted to the Cape Floristic Region of southern Africa. The genus is unusual in being dioecious and sexually dimorphic. ITS sequence data were obtained from 62 of the 96 currently recognized taxa (85 species and 11 subspecies). Phylogenetic analyses were conducted under Maximum Likelihood and parsimony and resolved nine groups of species with varying degrees of bootstrap support, but relationships between these groups are largely unsupported. The phylogeny conflicts with the current taxonomic arrangement, which is based mainly on fruit morphology. The two sections of the genus, Alatosperma and Leucadendron, and several subsections within these sections, are resolved as non-monophyletic. This means that taxonomically important characters (such as fruit shape) have evolved multiple times, as the species with nutlike fruit (resolved into two of the nine groups) appear to have evolved independently from ancestors with winged fruit. Based on the topology obtained, the life history traits of anemophily, myrmechochory, and re-sprouting have also originated multiple times. Dispersal-Vicariance (DIVA) analysis suggests that the genus had an ancestral area in the Karoo Mountain and Southeastern phytogeographic centres of endemism in the southwestern Cape. (C) 2004 Elsevier Inc. All rights reserved. [less ▲]

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See detailPhylogeny, classification and species delimitation in the liverwort genus Odontoschisma (Cephaloziaceae)
Aranda, S.C.; Gradstein, S.R.; Patino, J. et al

in Taxon (in press)

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See detailPhylogeographic footprints of the Strait of Gibraltar and Quaternary climatic fluctuations in the western Mediterranean: a case study with the greater white-toothed shrew Crocidura russula (Mammalia: Soricidae)
Cosson, Jean François; Hutterer, Rainer; Libois, Roland ULg et al

in Molecular Ecology (2005), 14

We used mitochondrial cyt b sequences to investigate the phylogenetic relationships of Crocidura russula (sensu lato) populations across the Strait of Gibraltar, western Europe, Maghreb, and the ... [more ▼]

We used mitochondrial cyt b sequences to investigate the phylogenetic relationships of Crocidura russula (sensu lato) populations across the Strait of Gibraltar, western Europe, Maghreb, and the Mediterranean and Atlantic islands. This revealed very low genetic divergence between European and Moroccan populations. The application of a molecular clock previously calibrated for shrews suggested that the separation of European from Moroccan lineages occurred less than 60000 BP, which is at least 5 million years (Myr) after the reopening of the Strait of Gibraltar. This means that an overwater dispersal event was responsible for the observed phylogeographical structure. In contrast, genetic analyses revealed that Moroccan populations were highly distinct from Tunisian ones. According to the molecular clock, these populations separated about 2.2 million years ago (Ma), a time marked by sharp alternations of dry and humid climates in the Maghreb. The populations of the Mediterranean islands Ibiza, Pantellaria, and Sardinian were founded from Tunisian populations by overwater dispersal. In conclusion, overwater dispersal across the Strait of Gibraltar, probably assisted by humans, is possible for small terrestrial vertebrates. Moreover, as in Europe, Quaternary climatic fluctuations had a major effect on the phylogeographical structure of the Maghreb biota. [less ▲]

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