Experts and Doctors on phylogeny in Lausanne, Vaud, Switzerland


Locale: Lausanne, Vaud, Switzerland
Topic: phylogeny

Top Publications

  1. Thomas V, Herrera Rimann K, Blanc D, Greub G. Biodiversity of amoebae and amoeba-resisting bacteria in a hospital water network. Appl Environ Microbiol. 2006;72:2428-38 pubmed
    ..001) and mycobacteria (P = 0.009) further suggests that FLA are a reservoir for these ARB and underlines the importance of considering amoebae when water control measures are designed. ..
  2. Sentchilo V, Mayer A, Guy L, Miyazaki R, Green Tringe S, Barry K, et al. Community-wide plasmid gene mobilization and selection. ISME J. 2013;7:1173-86 pubmed publisher
    ..This suggests that plasmids not only contribute to the adaptation of single individual prokaryotic species, but of the prokaryotic community as a whole under local selective conditions. ..
  3. Romiguier J, Cameron S, Woodard S, Fischman B, Keller L, Praz C. Phylogenomics Controlling for Base Compositional Bias Reveals a Single Origin of Eusociality in Corbiculate Bees. Mol Biol Evol. 2016;33:670-8 pubmed publisher
    ..Interpreted as a consequence of genome-wide variations in recombination rates, this GC effect can affect all taxa featuring GC-biased gene conversion, which is common in eukaryotes. ..
  4. Ventura M, Canchaya C, Meylan V, Klaenhammer T, Zink R. Analysis, characterization, and loci of the tuf genes in lactobacillus and bifidobacterium species and their direct application for species identification. Appl Environ Microbiol. 2003;69:6908-22 pubmed
    ..In contrast, bioinformatic and transcriptional analyses of the DNA region flanking the tuf gene in four Lactobacillus species indicated the same four-gene unit and suggested a novel tuf operon specific for the genus Lactobacillus. ..
  5. Zhang X, Kupiec M, Gophna U, Tuller T. Analysis of coevolving gene families using mutually exclusive orthologous modules. Genome Biol Evol. 2011;3:413-23 pubmed publisher
    ..5) CO dehydrogenase and thymidylate synthase and the glycine cleavage genes mutually exclude each other in archaea; this may represent an alternative route for generation of methyl donors for thymidine synthesis. ..
  6. Junier P, Kim O, Junier T, Ahn T, Imhoff J, Witzel K. Community analysis of betaproteobacterial ammonia-oxidizing bacteria using the amoCAB operon. Appl Microbiol Biotechnol. 2009;83:175-88 pubmed publisher
  7. Hijri M, Niculita H, Sanders I. Molecular characterization of chromosome termini of the arbuscular mycorrhizal fungus Glomus intraradices (Glomeromycota). Fungal Genet Biol. 2007;44:1380-6 pubmed
    ..intradicies will be essential for making a physical map of the G. intraradices genome and could provide molecular markers for future studies of genetic variation among nuclei in these multigenomic fungi. ..
  8. Liechti R, Gleizes A, Kuznetsov D, Bougueleret L, le Mercier P, Bairoch A, et al. OpenFluDB, a database for human and animal influenza virus. Database (Oxford). 2010;2010:baq004 pubmed publisher
    ..Database URL: ..
  9. Ventura M, Zink R. Comparative sequence analysis of the tuf and recA genes and restriction fragment length polymorphism of the internal transcribed spacer region sequences supply additional tools for discriminating Bifidobacterium lactis from Bifidobacterium animalis. Appl Environ Microbiol. 2003;69:7517-22 pubmed
    ..Therefore, all strains of B. lactis and B. animalis could be unified as the species B. animalis and divided into two subspecies, Bifidobacterium animalis subsp. lactis and Bifidobacterium animalis subsp. animalis. ..

More Information


  1. Witsenburg F, Salamin N, Christe P. The evolutionary host switches of Polychromophilus: a multi-gene phylogeny of the bat malaria genus suggests a second invasion of mammals by a haemosporidian parasite. Malar J. 2012;11:53 pubmed publisher
    ..The invasion of mammals as hosts has, therefore, not been a unique event in the evolutionary history of Haemosporida, despite the suspected costs of adapting to a new host. This was, moreover, accompanied by a switch in dipteran host. ..
  2. Leemann C, Gambillara E, Prod hom G, Jaton K, Panizzon R, Bille J, et al. First case of bacteremia and multifocal cellulitis due to Helicobacter canis in an immunocompetent patient. J Clin Microbiol. 2006;44:4598-600 pubmed
    ..Here we report on the first human case of H. canis bacteremia in an immunocompetent host. Identification of the organism was made by genetic and phylogenetic analyses of the complete 16S rRNA sequence. ..
  3. Jousson O, Léchenne B, Bontems O, Mignon B, Reichard U, Barblan J, et al. Secreted subtilisin gene family in Trichophyton rubrum. Gene. 2004;339:79-88 pubmed
    ..The set of deduced amino acid sequences of T. rubrum SUB ORFs allowed the identification of orthologous Subs secreted by other dermatophyte species using proteolysis and mass spectrometry. ..
  4. Vivien R, Ferrari B, Pawlowski J. DNA barcoding of formalin-fixed aquatic oligochaetes for biomonitoring. BMC Res Notes. 2016;9:342 pubmed publisher
  5. Christin P, Salamin N, Kellogg E, Vicentini A, Besnard G. Integrating phylogeny into studies of C4 variation in the grasses. Plant Physiol. 2009;149:82-7 pubmed publisher
  6. Pellissier L, Oppliger A, Hirzel A, Savova Bianchi D, Mbayo G, Mascher F, et al. Airborne and Grain Dust Fungal Community Compositions Are Shaped Regionally by Plant Genotypes and Farming Practices. Appl Environ Microbiol. 2016;82:2121-2131 pubmed publisher
    ..In addition, elevation and soil CaCO3 concentrations shaped the alpha diversity, whereas wheat cultivar, cropping history, and the number of freezing days per year shaped the taxonomic beta diversity of these communities. ..
  7. Studer R, Person E, Robinson Rechavi M, Rossier B. Evolution of the epithelial sodium channel and the sodium pump as limiting factors of aldosterone action on sodium transport. Physiol Genomics. 2011;43:844-54 pubmed publisher
    ..The establishment of multicellularity and the associated extracellular compartment ("internal milieu") precedes the emergence of other key elements of the aldosterone signaling pathway. ..
  8. Dubey S, Cosson J, Magnanou E, Vohralík V, Benda P, Frynta D, et al. Mediterranean populations of the lesser white-toothed shrew (Crocidura suaveolens group): an unexpected puzzle of Pleistocene survivors and prehistoric introductions. Mol Ecol. 2007;16:3438-52 pubmed
    ..Four deeply divergent clades of the C. suaveolens group occur in the area, meaning that a hypothetical contact zone remains to be located in central western Iran. ..
  9. Dubey S, Cosson J, Vohralík V, Krystufek B, Diker E, Vogel P. Molecular evidence of Pleistocene bidirectional faunal exchange between Europe and the Near East: the case of the bicoloured shrew (Crocidura leucodon, Soricidae). J Evol Biol. 2007;20:1799-808 pubmed
    ..We hypothesize that the western population was confined to a small Italo-Balkanic refugium, whereas the eastern population subsisted in several refugia along the southern coast of the Black Sea. ..
  10. Vuataz L, Sartori M, Gattolliat J, Monaghan M. Endemism and diversification in freshwater insects of Madagascar revealed by coalescent and phylogenetic analysis of museum and field collections. Mol Phylogenet Evol. 2013;66:979-91 pubmed publisher
    ..Our results underline the important role that museum collections can play in molecular studies, especially in critically endangered biodiversity hotspots like Madagascar where entire species or populations may go extinct very quickly. ..
  11. Jousson O, Léchenne B, Bontems O, Capoccia S, Mignon B, Barblan J, et al. Multiplication of an ancestral gene encoding secreted fungalysin preceded species differentiation in the dermatophytes Trichophyton and Microsporum. Microbiology. 2004;150:301-10 pubmed
  12. Thomas V, Bertelli C, Collyn F, Casson N, Telenti A, Goesmann A, et al. Lausannevirus, a giant amoebal virus encoding histone doublets. Environ Microbiol. 2011;13:1454-66 pubmed publisher
    ..The discovery of Lausannevirus and the analysis of its genome provide some insight in the evolution of these large amoebae-infecting viruses. ..
  13. Corsaro D, Feroldi V, Saucedo G, Ribas F, Loret J, Greub G. Novel Chlamydiales strains isolated from a water treatment plant. Environ Microbiol. 2009;11:188-200 pubmed publisher
  14. Christin P, Salamin N, Muasya A, Roalson E, Russier F, Besnard G. Evolutionary switch and genetic convergence on rbcL following the evolution of C4 photosynthesis. Mol Biol Evol. 2008;25:2361-8 pubmed publisher
    ..The introgression of C4-like high-efficiency Rubisco would strongly enhance C3 crop yields in the future CO2-enriched atmosphere. ..
  15. Tingley R, Dubey S. Disparity in the timing of vertebrate diversification events between the northern and southern hemispheres. BMC Evol Biol. 2012;12:244 pubmed publisher
  16. Houtkooper R, Pirinen E, Auwerx J. Sirtuins as regulators of metabolism and healthspan. Nat Rev Mol Cell Biol. 2012;13:225-238 pubmed publisher
  17. Germond J, Lapierre L, Delley M, Mollet B, Felis G, Dellaglio F. Evolution of the bacterial species Lactobacillus delbrueckii: a partial genomic study with reflections on prokaryotic species concept. Mol Biol Evol. 2003;20:93-104 pubmed publisher
    ..This study has consequences on the prokaryotic species concept, since genomic flexibility of prokaryotes collides with a stable classification, necessary from a scientific and applied point of view...
  18. Santoni de Sio F, Barde I, Offner S, Kapopoulou A, Corsinotti A, Bojkowska K, et al. KAP1 regulates gene networks controlling T-cell development and responsiveness. FASEB J. 2012;26:4561-75 pubmed publisher
    ..These results reveal the so far unsuspected yet important role of KAP1-mediated epigenetic regulation in T-lymphocyte differentiation and activation. ..
  19. Rosso L, Marques A, Reichert A, Kaessmann H. Mitochondrial targeting adaptation of the hominoid-specific glutamate dehydrogenase driven by positive Darwinian selection. PLoS Genet. 2008;4:e1000150 pubmed publisher
    ..We suggest that rapid, selectively driven subcellular adaptation, as exemplified by GLUD2, represents a common route underlying the emergence of new gene functions...
  20. Parisod C, Besnard G. Glacial in situ survival in the Western Alps and polytopic autopolyploidy in Biscutella laevigata L. (Brassicaceae). Mol Ecol. 2007;16:2755-67 pubmed
  21. Léchenne B, Reichard U, Zaugg C, Fratti M, Kunert J, Boulat O, et al. Sulphite efflux pumps in Aspergillus fumigatus and dermatophytes. Microbiology. 2007;153:905-13 pubmed
    ..Sulphite transporters could be a new target for antifungal drugs in dermatology, since proteolytic digestion of hard keratin would not be possible without prior reduction of disulphide bridges. ..
  22. Dubey S, Salamin N, Ohdachi S, Barrière P, Vogel P. Molecular phylogenetics of shrews (Mammalia: Soricidae) reveal timing of transcontinental colonizations. Mol Phylogenet Evol. 2007;44:126-37 pubmed
    ..Using molecular dating, the first exchanges between Africa and Eurasia occurred during the middle Miocene. The last one took place in the Late Miocene, with the dispersion of the genus Crocidura through the old world...
  23. Croll D, Sanders I. Recombination in Glomus intraradices, a supposed ancient asexual arbuscular mycorrhizal fungus. BMC Evol Biol. 2009;9:13 pubmed publisher
    ..Finally, our results reconcile seemingly contradictory studies on whether AMF are clonal or form recombining populations. ..
  24. Mueller L, Bertelli C, Pillonel T, Salamin N, Greub G. One Year Genome Evolution of Lausannevirus in Allopatric versus Sympatric Conditions. Genome Biol Evol. 2017;9:1432-1449 pubmed publisher
    ..Moreover, in our conditions and with our analyses we detected no horizontal gene transfer during one year of co-culture. ..
  25. Croset V, Rytz R, Cummins S, Budd A, Brawand D, Kaessmann H, et al. Ancient protostome origin of chemosensory ionotropic glutamate receptors and the evolution of insect taste and olfaction. PLoS Genet. 2010;6:e1001064 pubmed publisher
    ..Furthermore, this work identifies novel targets for manipulating chemosensory-driven behaviours of agricultural pests and disease vectors. ..
  26. Casson N, Entenza J, Greub G. Serological cross-reactivity between different Chlamydia-like organisms. J Clin Microbiol. 2007;45:234-6 pubmed
    ..These results are important to better interpret serological studies and assess the pathogenic role of these obligate intracellular bacteria...
  27. Fumeaux J, Mock M, Ninet B, Jan I, Bontems O, Léchenne B, et al. First report of Arthroderma benhamiae in Switzerland. Dermatology. 2004;208:244-50 pubmed
    ..Identification of dermatophytes often remains difficult or uncertain because there are variations from one isolate to another and overlapping characteristics between species...
  28. Yurovsky A, Moret B. FluReF, an automated flu virus reassortment finder based on phylogenetic trees. BMC Genomics. 2011;12 Suppl 2:S3 pubmed publisher
    ..However, current methods are limited to pairwise segment comparisons...
  29. Gotzek D, Robertson H, Wurm Y, Shoemaker D. Odorant binding proteins of the red imported fire ant, Solenopsis invicta: an example of the problems facing the analysis of widely divergent proteins. PLoS ONE. 2011;6:e16289 pubmed publisher
    ..As previously suggested, our results underscore the importance for careful exploration of the sensitivity to the effects of alignment methods for data comprising widely divergent sequences...
  30. Greub G, Collyn F, Guy L, Roten C. A genomic island present along the bacterial chromosome of the Parachlamydiaceae UWE25, an obligate amoebal endosymbiont, encodes a potentially functional F-like conjugative DNA transfer system. BMC Microbiol. 2004;4:48 pubmed
    ..The genome of Protochlamydia amoebophila UWE25, a Parachlamydia-related endosymbiont of free-living amoebae, was recently published, providing the opportunity to search for genomic islands (GIs)...
  31. Cissé O, Pagni M, Hauser P. De novo assembly of the Pneumocystis jirovecii genome from a single bronchoalveolar lavage fluid specimen from a patient. MBio. 2012;4:e00428-12 pubmed publisher
    ..jirovecii is an obligate parasite specialized in the colonization of human lungs, which causes disease only in immune-deficient individuals. This genome sequence will boost research on this deadly pathogen...
  32. Stöck M, Horn A, Grossen C, Lindtke D, Sermier R, Betto Colliard C, et al. Ever-young sex chromosomes in European tree frogs. PLoS Biol. 2011;9:e1001062 pubmed publisher
    ..This raises intriguing perspectives regarding the evolutionary dynamics of sexually antagonistic genes and the mechanisms that control X-Y recombination...
  33. Junier P, Frutschi M, Wigginton N, Schofield E, Bargar J, Bernier Latmani R. Metal reduction by spores of Desulfotomaculum reducens. Environ Microbiol. 2009;11:3007-17 pubmed publisher
    ..This is the first report of a bacterium able to reduce metals while in a sporulated state and underscores the novel nature of the mechanism of metal reduction by strain MI-1...
  34. Brawand D, Soumillon M, Necsulea A, Julien P, Csárdi G, Harrigan P, et al. The evolution of gene expression levels in mammalian organs. Nature. 2011;478:343-8 pubmed publisher
  35. Corona M, Libbrecht R, Wurm Y, Riba Grognuz O, Studer R, Keller L. Vitellogenin underwent subfunctionalization to acquire caste and behavioral specific expression in the harvester ant Pogonomyrmex barbatus. PLoS Genet. 2013;9:e1003730 pubmed publisher
    ..barbatus the Vg gene underwent subfunctionalization after duplication to acquire caste- and behavior- specific expression associated with reproductive and non-reproductive functions, supporting the validity of the RGPH in ants. ..
  36. Germond J, Mamin O, Mollet B. Species specific identification of nine human Bifidobacterium spp. in feces. Syst Appl Microbiol. 2002;25:536-43 pubmed
    ..or directly from total bacteria recovered from human fecal samples. The technique was shown to be useful to detect dominant species and, when primers were used in separate reactions, underrepresented species could be identified as well...
  37. Lienard J, Croxatto A, Aeby S, Jaton K, Posfay Barbe K, Gervaix A, et al. Development of a new chlamydiales-specific real-time PCR and its application to respiratory clinical samples. J Clin Microbiol. 2011;49:2637-42 pubmed publisher
    ..4%) samples were determined to be positive, and 45 of these were successfully sequenced. The majority of the sequences corresponded to Chlamydia-related bacteria and especially to members of the Parachlamydiaceae family...
  38. Burki F, Kaessmann H. Birth and adaptive evolution of a hominoid gene that supports high neurotransmitter flux. Nat Genet. 2004;36:1061-3 pubmed publisher
    ..The amino acid changes responsible for the unique brain-specific properties of the enzyme derived from GLUD2 occurred during a period of positive selection after the duplication event...
  39. Christinat Y, Moret B. Inferring transcript phylogenies. BMC Bioinformatics. 2012;13 Suppl 9:S1 pubmed
  40. Senn L, Entenza J, Greub G, Jaton K, Wenger A, Bille J, et al. Bloodstream and endovascular infections due to Abiotrophia defectiva and Granulicatella species. BMC Infect Dis. 2006;6:9 pubmed
    ..In this study, we reviewed the clinical manifestations of infections due to A. defectiva and Granulicatella species that occurred at our institution between 1998 and 2004...
  41. Junier P, Junier T, Podell S, Sims D, Detter J, Lykidis A, et al. The genome of the Gram-positive metal- and sulfate-reducing bacterium Desulfotomaculum reducens strain MI-1. Environ Microbiol. 2010;12:2738-54 pubmed publisher
    ..In addition, both H(2) -evolving and H(2) -consuming cytoplasmic hydrogenases were identified in the genome, pointing to potential cytoplasmic H(2) cycling in the bacterium. The mechanism of metal reduction remains unknown...
  42. Privman E, Wurm Y, Keller L. Duplication and concerted evolution in a master sex determiner under balancing selection. Proc Biol Sci. 2013;280:20122968 pubmed publisher
    ..These results suggest that concerted evolution plays an adaptive role in the evolution of this gene family...
  43. Thomas V, Loret J, Jousset M, Greub G. Biodiversity of amoebae and amoebae-resisting bacteria in a drinking water treatment plant. Environ Microbiol. 2008;10:2728-45 pubmed publisher
    ..As amoebae mainly multiply in sand and GAC filters, optimization of filter backwash procedures probably offers a possibility to better control these protists and the risk associated with their intracellular hosts...
  44. Pellissier L, Ndiribe C, Dubuis A, Pradervand J, Salamin N, Guisan A, et al. Turnover of plant lineages shapes herbivore phylogenetic beta diversity along ecological gradients. Ecol Lett. 2013;16:600-8 pubmed publisher
    ..Along ecological gradients, the bottom up control of herbivore diversity is thus driven by phylogenetically structured turnover of plant traits as well as environmental variables. ..
  45. Halbert J, Ayong L, Equinet L, Le Roch K, Hardy M, Goldring D, et al. A Plasmodium falciparum transcriptional cyclin-dependent kinase-related kinase with a crucial role in parasite proliferation associates with histone deacetylase activity. Eukaryot Cell. 2010;9:952-9 pubmed publisher
    ..Taken together, our data strongly suggest that Pfcrk-3 fulfils a crucial role in the intraerythrocytic development of P. falciparum, presumably through chromatin modification-dependent regulation of gene expression. ..
  46. Besnard G, Rubio de Casas R, Christin P, Vargas P. Phylogenetics of Olea (Oleaceae) based on plastid and nuclear ribosomal DNA sequences: tertiary climatic shifts and lineage differentiation times. Ann Bot. 2009;104:143-60 pubmed publisher
    ..To clarify the biogeographical history of this group, a molecular analysis of Olea and related genera of Oleaceae is thus necessary...
  47. Johnson D, Czechowska K, Chèvre N, van der Meer J. Toxicity of triclosan, penconazole and metalaxyl on Caulobacter crescentus and a freshwater microbial community as assessed by flow cytometry. Environ Microbiol. 2009;11:1682-91 pubmed publisher
    ..Because 10 nM of triclosan is within the range of concentrations observed in freshwater systems, these results also raise concerns about the risk of introducing triclosan into the environment...
  48. Finka A, Saidi Y, Goloubinoff P, Neuhaus J, Zryd J, Schaefer D. The knock-out of ARP3a gene affects F-actin cytoskeleton organization altering cellular tip growth, morphology and development in moss Physcomitrella patens. Cell Motil Cytoskeleton. 2008;65:769-84 pubmed publisher
    ..patens Arp3a and its Arabidopsis thaliana orthologs efficiently complement the mutated phenotype indicating a high degree of evolutionary conservation of the Arp3 function in land plants...
  49. Gonzalez D, Kozdon J, McAdams H, Shapiro L, Collier J. The functions of DNA methylation by CcrM in Caulobacter crescentus: a global approach. Nucleic Acids Res. 2014;42:3720-35 pubmed publisher
    ..crescentus and, presumably, of many other Alphaproteobacteria...
  50. Saladin B, Leslie A, Wüest R, Litsios G, Conti E, Salamin N, et al. Fossils matter: improved estimates of divergence times in Pinus reveal older diversification. BMC Evol Biol. 2017;17:95 pubmed publisher
    ..The sets of dated phylogenetic trees of pines presented here provide a way to account for uncertainties in age estimations when applying comparative phylogenetic methods. ..
  51. Nair N, Hunter L, Shao M, Grnarova P, Lin Y, Bucher P, et al. A maximum-likelihood approach for building cell-type trees by lifting. BMC Genomics. 2016;17 Suppl 1:14 pubmed publisher
    ..We show that our ML-based approach outperforms previously proposed techniques such as distance-based and parsimony-based methods. We show our lifting-based approach works well on both simulated and real data. ..
  52. Meunier J, Lemoine F, Soumillon M, Liechti A, Weier M, Guschanski K, et al. Birth and expression evolution of mammalian microRNA genes. Genome Res. 2013;23:34-45 pubmed publisher
    ..Overall, our study thus provides detailed insights into the birth and evolution of mammalian miRNA genes and the associated selective forces. ..
  53. Burri R, Salamin N, Studer R, Roulin A, Fumagalli L. Adaptive divergence of ancient gene duplicates in the avian MHC class II beta. Mol Biol Evol. 2010;27:2360-74 pubmed publisher
    ..These results provide new insights into the long-term evolutionary relationships among avian MHC genes and open interesting perspectives for comparative and population genomic studies of avian MHC evolution. ..
  54. Wurm Y, Wang J, Riba Grognuz O, Corona M, Nygaard S, Hunt B, et al. The genome of the fire ant Solenopsis invicta. Proc Natl Acad Sci U S A. 2011;108:5679-84 pubmed publisher
    ..Some of these and other unique aspects of the fire ant genome are likely linked to the complex social behavior of this species. ..
  55. Gotzek D, Clarke J, Shoemaker D. Mitochondrial genome evolution in fire ants (Hymenoptera: Formicidae). BMC Evol Biol. 2010;10:300 pubmed publisher
    ..We also discuss ways that may help improve the use of mitogenomes in phylogenetic analyses by accounting for non-stationary and non-homogeneous evolution among branches. ..
  56. Lucchini S, Sidoti J, Br ssow H. Broad-range bacteriophage resistance in Streptococcus thermophilus by insertional mutagenesis. Virology. 2000;275:267-77 pubmed publisher
  57. Thomas V, Casson N, Greub G. Criblamydia sequanensis, a new intracellular Chlamydiales isolated from Seine river water using amoebal co-culture. Environ Microbiol. 2006;8:2125-35 pubmed
    ..This work confirmed that amoebal co-culture is a relevant method to isolate new chlamydiae, and that it can be successfully applied to ecosystems colonized with a complex microbial community...
  58. Fitze P, Gonzalez Jimena V, San Jose L, San Mauro D, Aragon P, Suarez T, et al. Integrative analyses of speciation and divergence in Psammodromus hispanicus (Squamata: Lacertidae). BMC Evol Biol. 2011;11:347 pubmed publisher
    ..It suggests that geographic isolation and vicariance played an important role in the early diversification of the group, and that lineage diversification was further amplified through ecological divergence. ..
  59. Megali A, Yannic G, Zahno M, Brugger D, Bertoni G, Christe P, et al. Surveillance for European bat lyssavirus in Swiss bats. Arch Virol. 2010;155:1655-62 pubmed publisher
    ..Three M. daubentoni bats were found to be seropositive by RFFIT. In conclusion, even though the prevalence is low in Switzerland, continuous management and surveillance are required to assess the potential risk to public health...
  60. Corsaro D, Michel R, Walochnik J, Müller K, Greub G. Saccamoeba lacustris, sp. nov. (Amoebozoa: Lobosea: Hartmannellidae), a new lobose amoeba, parasitized by the novel chlamydia 'Candidatus Metachlamydia lacustris' (Chlamydiae: Parachlamydiaceae). Eur J Protistol. 2010;46:86-95 pubmed publisher
    ..Phylogenetic analysis based on the 16S rDNA indicated that it is a new member of the family Parachlamydiaceae (order Chlamydiales), for which we proposed the name 'Candidatus Metachlamydia lacustris'...
  61. Zuercher E, Butticaz C, Wyniger J, Martinez R, Battegay M, Boffi El Amari E, et al. Genetic diversity of EBV-encoded LMP1 in the Swiss HIV Cohort Study and implication for NF-?b activation. PLoS ONE. 2012;7:e32168 pubmed publisher
  62. Besnard G, Muasya A, Russier F, Roalson E, Salamin N, Christin P. Phylogenomics of C(4) photosynthesis in sedges (Cyperaceae): multiple appearances and genetic convergence. Mol Biol Evol. 2009;26:1909-19 pubmed publisher
    ..These lines of evidence give new insights into the constraints that govern molecular evolution...
  63. Renaud M, Praz V, Vieu E, Florens L, Washburn M, l Hôte P, et al. Gene duplication and neofunctionalization: POLR3G and POLR3GL. Genome Res. 2014;24:37-51 pubmed publisher
  64. Lucas F, Broennimann O, Febbraro I, Heeb P. High diversity among feather-degrading bacteria from a dry meadow soil. Microb Ecol. 2003;45:282-90 pubmed
    ..5 U keratinase per mL. Keratinase activities across the 13 strains were positively correlated with the percentage of feather fragmentation and protein concentration. ..
  65. Ventura M, Canchaya C, van Sinderen D, Fitzgerald G, Zink R. Bifidobacterium lactis DSM 10140: identification of the atp (atpBEFHAGDC) operon and analysis of its genetic structure, characteristics, and phylogeny. Appl Environ Microbiol. 2004;70:3110-21 pubmed
    ..lactis DSM 10140. The rapid increase in the level of atp operon transcripts upon exposure to low pH suggested that the ATPase complex of B. lactis DSM 10140 was regulated at the level of transcription and not at the enzyme assembly step...
  66. Corradi N, Sanders I. Evolution of the P-type II ATPase gene family in the fungi and presence of structural genomic changes among isolates of Glomus intraradices. BMC Evol Biol. 2006;6:21 pubmed
  67. Imbeault M, Helleboid P, Trono D. KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks. Nature. 2017;543:550-554 pubmed publisher
    ..Together, our results demonstrate that KZFPs partner with transposable elements to build a largely species-restricted layer of epigenetic regulation. ..
  68. Marques A, Dupanloup I, Vinckenbosch N, Reymond A, Kaessmann H. Emergence of young human genes after a burst of retroposition in primates. PLoS Biol. 2005;3:e357 pubmed
  69. Blanquart F, Wymant C, Cornelissen M, Gall A, Bakker M, Bezemer D, et al. Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe. PLoS Biol. 2017;15:e2001855 pubmed publisher
    ..An overall heritability of 31% (CI 15%-43%) is consistent with other studies based on regression of viral load in donor-recipient pairs. Thus, about a third of variation in HIV-1 virulence is attributable to viral genetic variation. ..
  70. Leys M, Keller I, Räsänen K, Gattolliat J, Robinson C. Distribution and population genetic variation of cryptic species of the Alpine mayfly Baetis alpinus (Ephemeroptera: Baetidae) in the Central Alps. BMC Evol Biol. 2016;16:77 pubmed publisher
    ..These findings emphasize the need to investigate hidden diversity even in well-known species to allow for appropriate assessment of biological diversity and conservation measures. ..
  71. Besnard G, Henry P, Wille L, Cooke D, Chapuis E. On the origin of the invasive olives (Olea europaea L., Oleaceae). Heredity (Edinb). 2007;99:608-19 pubmed
    ..Furthermore, one hybrid (cuspidata x europaea) was identified in East Australia. The importance of hybridizations in the future evolution of the olive invasiveness remains to be investigated...
  72. Brawand D, Wahli W, Kaessmann H. Loss of egg yolk genes in mammals and the origin of lactation and placentation. PLoS Biol. 2008;6:e63 pubmed publisher
  73. Gharib W, Robinson Rechavi M. The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC. Mol Biol Evol. 2013;30:1675-86 pubmed publisher
    ..Moreover, neither shifts of GC content on a specific branch nor major shifts in GC along the gene sequence generate many false positives. Our results confirm that the branch-site is a very conservative test. ..