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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 and systematics of the lichen family Gomphillaceae (Ostropales) inferred from cladistic analysis of phenotype data
Lücking, Robert; Sérusiaux, Emmanuël ULg; Vezda, Antonin

in Lichenologist (2005), 37

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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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See detailPhylogeographic history of north European mammals : implication on their genetic diversity and their conservation
Michaux, Johan ULg

in Abstract book of the 7th Baltic Theriological conference (2008)

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See detailPhylogeographic history of the yellow-necked fieldmouse (Apodemus flavicollis) in Europe and in the Near and Middle East.
Michaux, Johan ULg; Libois, Roland ULg; Paradis, E. et al

in Molecular Phylogenetics & Evolution (2004), 32(3), 788-98

The exact location of glacial refugia and the patterns of postglacial range expansion of European mammals are not yet completely elucidated. Therefore, further detailed studies covering a large part of ... [more ▼]

The exact location of glacial refugia and the patterns of postglacial range expansion of European mammals are not yet completely elucidated. Therefore, further detailed studies covering a large part of the Western Palearctic region are still needed. In this order, we sequenced 972 bp of the mitochondrial DNA cytochrome b (mtDNA cyt b) from 124 yellow-necked fieldmice (Apodemus flavicollis) collected from 53 European localities. The aims of the study were to answer the following questions: Did the Mediterranean peninsulas act as the main refuge for yellow-necked fieldmouse or did the species also survive in more easterly refugia (the Caucasus or the southern Ural) and in Central Europe? What is the role of Turkey and Near East regions as Quaternary glacial refuges for this species and as a source for postglacial recolonisers of the Western Palearctic region? The results provide a clear picture of the impact of the quaternary glaciations on the genetic and geographic structure of the fieldmouse. This species survived the ice ages in two main refuges, the first one in the Italo-Balkan region; the second one in Turkey and the Near East regions. It is from the Balkan refuge that it recolonised all European regions at the end of the last glaciation. The Turkish and Near East populations are distinct from the European ones and they did not recolonise the Palearctic region probably because: (i) they were blocked by the Black Sea and the Caucasus, (ii) the long term presence of fieldmice populations in the Balkans prevented their expansion. These are genetically differentiated from the European and Russian ones and could be described as a particular subspecies. This result emphasises the importance of Turkey and the Near and Middle East regions as a refuge for Palearctic mammals. [less ▲]

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See detailPhylogeographical analysis of bovine herpesvirus 4: demonstration that inter strain recombination events took place after acquisition of the bo17 gene from an ancestor of the african buffalo
Dewals, Benjamin G ULg; Markine-Goriaynoff, Nicolas; de Fays, Kataline et al

Poster (2005, March)

Recently, our phylogenetic study revealed that the Bovine herpesvirus 4 (BoHV 4) Bo17 gene has been acquired from an ancestor of the African buffalo around 1.5 million years ago, implying that cattle ... [more ▼]

Recently, our phylogenetic study revealed that the Bovine herpesvirus 4 (BoHV 4) Bo17 gene has been acquired from an ancestor of the African buffalo around 1.5 million years ago, implying that cattle subsequently acquired BoHV 4 by cross species transmission (Markine-Goriaynoff et al., 2003, 77:1784-1792). In the present study, we pursued our investigation on the origin and the evolution of BoHV 4. Firstly, with the goal in mind to further precise the origin of the Bo17 gene, the C2GnT M gene sequence was determined for each subspecies of African buffalo and for three types of Asian buffalo. Phylogenetic analyses of these new sequences further supported our conclusion that the Bo17 gene has been acquired from an ancestor of the African buffalo, possibly of the Syncerus caffer caffer subspecies from East-Africa origin. Secondly, to investigate the phylogeographical relationships among BoHV-4 strains isolated from four different continents, phylogenetic analyses were performed based on six different regions distributed throughout the genome. Analyses of these regions revealed a clear correlation between the phylogenetic relationships among BoHV-4 strains and their geographical origin, leading to the concept of BoHV-4 geographical clades. These analyses also demonstrated that since the acquisition of the Bo17 gene, recombination events occurred at different time in the past between ancestors of actual geographical clades. These recombinations provided an opportunity to learn how after acquisition of the Bo17 gene in Africa around 1.5 million years ago, BoHV-4 has spread to the world to form phylogenetically related geographical clades. [less ▲]

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See detailPhylogéographie du complexe d'espèces Brassica oleracea
Aigoin, Delphine ULg

Master of advanced studies dissertation (2005)

The aim of this work is to clarify the genetic relationship between the species of the complex Brassica sect. oleracea and to suggest a historical scenario of cabbage domestication. We collected 79 ... [more ▼]

The aim of this work is to clarify the genetic relationship between the species of the complex Brassica sect. oleracea and to suggest a historical scenario of cabbage domestication. We collected 79 accessions, corresponding to 2 to 5 individus for each of the 11 taxons of this complex. Three types of molecular markers were studied on these individuals : two nuclear genes (sequencing of Adh and G3pdh genes), for microsatellite loci, and AFLP markers. Only the first two types of markers were used for phylogenetic reconstructions. Overall there is little consistency among markers and among studies. However a few solid results can be outlined, such as 1/ the grouping of endemic species from Sicilia (B. rupestris, B. villosa, B. macrocarpa), 2/ the grouping of cultivated accesions with the taxon B. oleracea, suggesting a unique domestication event. Considerations from the various phylogenetic reconstructions, from morphological data, and from historical records, suggest that such domestication event first occured in the mediterranean islands, and that the presently «wild» populations of the atlantic coast were in fact probably produced from these domesticated populations. [less ▲]

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See detailPhylogéographie mitochondriale du mulot sylvestre (Apodemus sylvaticus) dans la région paléarctique occidentale
Michaux, Johan ULg; Magnanou, Elodie; Nieberding, Caroline et al

in Biosystema, Systématique et biogéographie (2002), 20

We have sequenced 965 base pairs of the mitochondrial DNA cytochrome b from 102 woodmice (Apodemus sylvaticus) samples collected from 40 European localities. The aims of the study were to answer the ... [more ▼]

We have sequenced 965 base pairs of the mitochondrial DNA cytochrome b from 102 woodmice (Apodemus sylvaticus) samples collected from 40 European localities. The aims of the study were to answer the following questions: i) Did the Mediterranean peninsulas play a role as a refuge for small mammals? ii) Is the genetic variability of a small mammal like A. sylvaticus higher in the Mediterranean regions as compared with northern Europe? iii)Is it possible to find patterns of postglacial colonisation of Europe other than those presently recognised ? Sequence data were analysed using Distance and Maximum Parsimony phylogenetic reconstruction methods. A minimum spanning network was also calculated. Population genetic structure was determined by analysis of molecular variance (AMOVA). A "mismatch distribution" analysis was also performed to estimate the patterns of expansion. The results provide a clear picture of the impact of Quaternary glaciations on the genetic and geographic structure of the woodmouse. Analyses indicate a higher genetic variability for the woodmouse in the Mediterranean peninsulas as compared to northern Europe and the role of these peninsulas as refuge regions for small mammals. A new pattern of postglacial colonisation is also proposed where the Iberian and southern France refuge populations colonised almost all the European regions. The Sicilian population appears to be highly differentiated and highly variable. This result emphasises the importance of this island as a "hot spot" for the intraspecific genetic diversity of the woodmouse. Finally, populations of this species in North Africa originated from south-western Europe and are probably the result of a recent anthropogenic introduction. [less ▲]

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See detailPhylogeography and evolutionary history of Leopoldamys neilli, a Murinae rodent endemic to limestone karsts, in Thailand
Latinne, Alice ULg; Waengsothorn, Surachit; Herbreteau, Vincent et al

Conference (2012, May 15)

Limestone karsts are highly threatened biodiversity hotspots supporting high levels of endemic species. Karsts are patchy distributed within Southeast Asia and their isolation from one another give them ... [more ▼]

Limestone karsts are highly threatened biodiversity hotspots supporting high levels of endemic species. Karsts are patchy distributed within Southeast Asia and their isolation from one another give them the features of “islands on the continent” and has important consequences for the genetic structure of endemic taxa. In present study, we have studied the phylogeography of Neill’s Rat Leopoldamys neilli, a threatened Murinae rodent species endemic to limestone karsts of Thailand, on the basis of two mitochondrial markers, two nuclear fragments, as well as twelve microsatellite loci. Our study gave evidence of a complex and strong geographic structure of the genetic diversity for L. neilli. Several highly differentiated genetic lineages were observed throughout Thailand. These results suggest a severe fragmentation of L. neilli’s populations, correlated to the fragmented distribution of its habitat and highlight its high endemicity to limestone karsts. The evolutionary history of L. neilli was investigated using Approximate Bayesian computation (ABC) and our results suggest that the current phylogeographic pattern of this species result from several deep vicariant events during Plio-Pleistocene. To conclude, this study revealed an unexpected high level of intraspecific diversity within L. neilli. These results consolidate the importance to strengthen the protection of limestone habitats and to preserve not only their high interspecific but also intraspecific diversity. [less ▲]

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See detailPhylogeography and taxonomy of woodmice (Apodemus sylvaticus) populations from Western Palearctic: RFLP of the mtDNA variability
Michaux, JR; Libois, Roland ULg; Ramalhinho, Maria da Graça et al

in Ylönen, Hannu; Hentonnen, Heikki; Laajalahti, Päivi (Eds.) et al 3rd European congress of mammalogy (1999, May)

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See detailPhylogeography of a nematode (Heligmosomoides polygyrus) in the western Palearctic region: persistence of northern cryptic populations during ice ages?
Nieberding, Caroline M. ULg; Libois, Roland ULg; Douady, C. J. et al

in Molecular Ecology (2005), 14(3), 765-79

This study establishes the continental phylogeographical pattern of a European nematode, Heligmosomoides polygyrus (Dujardin, 1845; Heligmosomoidea). We sequenced 687 base pairs of the mitochondrial DNA ... [more ▼]

This study establishes the continental phylogeographical pattern of a European nematode, Heligmosomoides polygyrus (Dujardin, 1845; Heligmosomoidea). We sequenced 687 base pairs of the mitochondrial DNA (mtDNA) cyt b gene for 136 individuals collected in 22 localities. The results revealed that H. polygyrus populations are separated into five major units corresponding to the Italian, northern European (Denmark and Ireland), Iberian, western European, and Balkan populations. Different subclades were also observed within the first two groups. Based on the rate of molecular evolution of H. polygyrus cyt b gene-estimated to 3.5%-3.7% divergence per million years (Myr) in a previous study--the isolation time of the five clades was estimated between 2.5 +/- 0.24 and 1.5 +/- 0.23 million years ago. Moreover, H. polygyrus presents a higher genetic variability in the Mediterranean peninsulas as compared to northwestern Europe, highlighting the role of these regions as refuge areas. Like its specific host, the wood mouse Apodemus sylvaticus, H. polygyrus' pattern of postglacial recolonization of northwestern Europe was initiated from Iberian populations, while Italian and Balkan populations did not expand to the north. The results also suggest the existence of forested and temperate refuges in the southern British Isles during the Quaternary. Finally, the genetic diversity as well as the level of genetic divergence between the lineages of H. polygyrus are compared to those observed in other vertebrate and invertebrate phylogeographical studies: the existence of highly differentiated lineages in H. polygyrus (5%-10% of genetic divergence) highlights that the effects of Pleistocene climate changes on free-living organisms are also reflected in their obligate parasites. [less ▲]

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