Divergence with gene flow and fine-scale phylogeographical structure in the wedge-billed woodcreeper, Glyphorynchus spirurus, a Neotropical rainforest bird.

Determining the relative roles of vicariance and selection in restricting gene flow between populations is of central importance to the evolutionary process of population divergence and speciation. Here we use molecular and morphological data to contrast the effect of isolation (by mountains and geographical distance) with that of ecological factors (altitudinal gradients) in promoting differentiation in the wedge-billed woodcreeper, Glyphorynchus spirurus, a tropical forest bird, in Ecuador. Tarsus length and beak size increased relative to body size with altitude on both sides of the Andes, and were correlated with the amount of moss on tree trunks, suggesting the role of selection in driving adaptive divergence. In contrast, molecular data revealed a considerable degree of admixture along these altitudinal gradients, suggesting that adaptive divergence in morphological traits has occurred in the presence of gene flow. As suggested by mitochondrial DNA sequence data, the Andes act as a barrier to gene flow between ancient subspecific lineages. Genome-wide amplified fragment length polymorphism markers reflected more recent patterns of gene flow and revealed fine-scale patterns of population differentiation that were not detectable with mitochondrial DNA, including the differentiation of isolated coastal populations west of the Andes. Our results support the predominant role of geographical isolation in driving genetic differentiation in G. spirurus, yet suggest the role of selection in driving parallel morphological divergence along ecological gradients.

Distribution and population genetic variation of cryptic species of the Alpine mayfly Baetis alpinus (Ephemeroptera: Baetidae) in the Central Alps.

BACKGROUND: Many species contain evolutionarily distinct groups that are genetically highly differentiated but morphologically difficult to distinguish (i.e., cryptic species). The presence of cryptic species poses significant challenges for the accurate assessment of biodiversity and, if unrecognized, may lead to erroneous inferences in many fields of biological research and conservation. RESULTS: We tested for cryptic genetic variation within the broadly distributed alpine mayfly Baetis alpinus across several major European drainages in the central Alps. Bayesian clustering and multivariate analyses of nuclear microsatellite loci, combined with phylogenetic analyses of mitochondrial DNA, were used to assess population genetic structure and diversity. We identified two genetically highly differentiated lineages (A and B) that had no obvious differences in regional distribution patterns, and occurred in local sympatry. Furthermore, the two lineages differed in relative abundance, overall levels of genetic diversity as well as patterns of population structure: lineage A was abundant, widely distributed and had a higher level of genetic variation, whereas lineage B was less abundant, more prevalent in spring-fed tributaries than glacier-fed streams and restricted to high elevations. Subsequent morphological analyses revealed that traits previously acknowledged as intraspecific variation of B. alpinus in fact segregated these two lineages. CONCLUSIONS: Taken together, our findings indicate that even common and apparently ecologically well-studied species may consist of reproductively isolated units, with distinct evolutionary histories and likely different ecology and evolutionary potential. 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.

Population connectivity buffers genetic diversity loss in a seabird

Background Ancient DNA has revolutionized conservation genetic studies as it allows monitoring of the genetic variability of species through time and predicting the impact of ecosystems" threats on future population dynamics and viability. Meanwhile, the consequences of anthropogenic activities and climate change to island faunas, particularly seabirds, remain largely unknown. In this study, we examined temporal changes in the genetic diversity of a threatened seabird, the Cory"s shearwater (Calonectris borealis). Findings We analysed the mitochondrial DNA control region of ancient bone samples from the late-Holocene retrieved from the Canary archipelago (NE Atlantic) together with modern DNA sequences representative of the entire breeding range of the species. Our results show high levels of ancient genetic diversity in the Canaries comparable to that of the extant population. The temporal haplotype network further revealed rare but recurrent long-distance dispersal between ocean basins. The Bayesian demographic analyses reveal both regional and local population size expansion events, and this is in spite of the demographic decline experienced by the species over the last millennia. Conclusions Our findings suggest that population connectivity of the species has acted as a buffer of genetic losses and illustrate the use of ancient DNA to uncover such cryptic genetic events.

Identification and conservation of remnant genetic resources of brown trout in relict populations from Western Mediterranean streams

Brown trout is a cold-adapted freshwater species with restricted distribution to headwater streams in rivers of the South European peninsulas, where populations are highly vulnerable because Mediterranean regions are highly sensitive to the global climatic warming. Moreover, these populations are endangered due to the introgressive hybridization with cultured stocks. Individuals from six remnant populations in Western Mediterranean rivers were sequenced for the complete mitochondrial DNA control region and genotyped for 11 nuclear markers. Three different brown trout lineages were present in the studied region. Significant genetic divergence was observed among locations and a strong effect of genetic drift was suggested. An important stocking impact (close to 25%) was detected in the zone. Significant correlations between mitochondrial-based rates of hatchery introgression and water flow variation suggested a higher impact of stocked females in unstable habitats. In spite of hatchery introgression, all populations remained highly differentiated, suggesting that native genetic resources are still abundant. However, climatic predictions indicated that suitable habitats for the species in these rivers will be reduced and hence trout populations are highly endangered and vulnerable. Thus, management policies should take into account these predictions to design upstream refuge areas to protect remnant native trout in the region

Evolutionary analysis of mitogenomes from parasitic and free-living flatworms

Mitochondrial genomes (mitogenomes) are useful and relatively accessible sources of molecular data to explore and understand the evolutionary history and relationships of eukaryotic organisms across diverse taxonomic levels. The availability of complete mitogenomes from Platyhelminthes is limited; of the 40 or so published most are from parasitic flatworms (Neodermata). Here, we present the mitogenomes of two free-living flatworms (Tricladida): the complete genome of the freshwater species Crenobia alpina (Planariidae) and a nearly complete genome of the land planarian Obama sp. (Geoplanidae). Moreover, we have reanotated the published mitogenome of the species Dugesia japonica (Dugesiidae). This contribution almost doubles the total number of mtDNAs published for Tricladida, a species-rich group including model organisms and economically important invasive species. We took the opportunity to conduct comparative mitogenomic analyses between available free-living and selected parasitic flatworms in order to gain insights into the putative effect of life cycle on nucleotide composition through mutation and natural selection. Unexpectedly, we did not find any molecular hallmark of a selective relaxation in mitogenomes of parasitic flatworms; on the contrary, three out of the four studied free-living triclad mitogenomes exhibit higher A+T content and selective relaxation levels. Additionally, we provide new and valuable molecular data to develop markers for future phylogenetic studies on planariids and geoplanids.

On Glucose Metabolism in Patients with the m.3243A>G Mutation

Background: The m.3243A>G mutation in mitochondrial DNA is the most common cause for mitochondrial diabetes. In addition, unexpected deaths related to the m.3243A>G associate with encephalopathy and cardiomyopathy. Failing mitochondrial respiratory chain in neurons, myocytes and beta cells is considered to underlie the multiorgan manifestations of the m.3243A>G. Aims: The primary aim of the study was to characterize the organ-specific glucose metabolism in patients with m.3243A>G and secondly, to study patients with or without signs of diabetes, cardiomyopathy or encephalopathy. The insulin-stimulated glucose metabolism in brain, heart, skeletal muscle, adipose tissue and liver were measured with 2-deoxy-2-[18F]fluoro-α-D-glucose in 15 patients and 14 controls. Brain oxygen metabolism was assessed with [15O]oxygen and insulin secretion was modelled based on oral glucose tolerance test. Results: The glucose oxidation in brain was globally decreased in patients with or without clinical encephalopathy. The insulin-stimulated glucose influx to skeletal muscle and adipose tissue was decreased in patients with or without diabetes as the hepatic glucose metabolism was normal. Impaired beta cell function and myocardial glucose uptake were associated with the high m.3243A>G heteroplasmy. Conclusions: This cross-sectional study suggests that: 1) The ability of insulin to stimulate glucose metabolism in skeletal muscle and adipose tissue is weakened before the beta cell failure results in mitochondrial diabetes. 2) Glucose oxidation defect is detected in otherwise unaffected cerebral regions in patients with the m.3243A>G, thus it likely precedes the clinical encephalopathy. 3) Uneconomical glucose hypometabolism during hyperinsulinemia contributes to the cardiac vulnerability in patients with high m.3243A>G heteroplasmy

High doses of riboflavin and the elimination of dietary red meat promote the recovery of some motor functions in Parkinson's disease patients

Abnormal riboflavin status in the absence of a dietary deficiency was detected in 31 consecutive outpatients with Parkinson's disease (PD), while the classical determinants of homocysteine levels (B6, folic acid, and B12) were usually within normal limits. In contrast, only 3 of 10 consecutive outpatients with dementia without previous stroke had abnormal riboflavin status. The data for 12 patients who did not complete 6 months of therapy or did not comply with the proposed treatment paradigm were excluded from analysis. Nineteen PD patients (8 males and 11 females, mean age ± SD = 66.2 ± 8.6 years; 3, 3, 2, 5, and 6 patients in Hoehn and Yahr stages I to V) received riboflavin orally (30 mg every 8 h) plus their usual symptomatic medications and all red meat was eliminated from their diet. After 1 month the riboflavin status of the patients was normalized from 106.4 ± 34.9 to 179.2 ± 23 ng/ml (N = 9). Motor capacity was measured by a modification of the scoring system of Hoehn and Yahr, which reports motor capacity as percent. All 19 patients who completed 6 months of treatment showed improved motor capacity during the first three months and most reached a plateau while 5/19 continued to improve in the 3- to 6-month interval. Their average motor capacity increased from 44 to 71% after 6 months, increasing significantly every month compared with their own pretreatment status (P < 0.001, Wilcoxon signed rank test). Discontinuation of riboflavin for several days did not impair motor capacity and yellowish urine was the only side effect observed. The data show that the proposed treatment improves the clinical condition of PD patients. Riboflavin-sensitive mechanisms involved in PD may include glutathione depletion, cumulative mitochondrial DNA mutations, disturbed mitochondrial protein complexes, and abnormal iron metabolism. More studies are required to identify the mechanisms involved.

Reduced folate carrier 1 (RFC1) is associated with cleft of the lip only

In this report, we have reanalyzed genotyping data in a collection of families from South America based on maternal origin. Genotyping analysis was performed at the Craniofacial Anomalies Research Center at the University of Iowa. These genotypes were derived from genomic DNA samples obtained from blood spots from children born with isolated orofacial clefts in 45 hospitals located in eight countries (Argentina, Bolivia, Brazil, Chile, Ecuador, Paraguay, Uruguay, and Venezuela) collaborating with ECLAMC (Latin American Collaborative Studies of Congenital Malformations) between January 1998 and December 1999. Dried blood samples were sent by regular mail to the Laboratory of Congenital Malformations, Federal University of Rio de Janeiro. Previous findings suggested that mitochondrial haplotype D is more commonly found among cleft cases born in South America. We hypothesized that association of certain genes may depend upon the ethnic origin, as defined by population-specific markers. Therefore, we tested if markers in MTHFR (5,10-methylenetetrahydrofolate reductase) and RFC1 (reduced folate carrier 1) were associated with oral clefts, depending on the maternal origin defined by the mitochondrial haplotype. Transmission distortion of alleles in MTHFR C677T and RFC1 G80A polymorphic variants was tested in 200 mother/affected child pairs taking into consideration maternal origin. RFC1 variation was over-transmitted to children born with cleft lip only (P = 0.017) carrying mitochondrial DNA haplotypes other than haplotype D. Our results provide a new indication that variation in RFC1 may contribute to cleft lip only. Future studies should investigate the association between oral clefts and RFC1 based on more discrete phenotypes.

The genetics of glucosamine in yeast : cytoplasmic determinants conferring resistance

Two cytoplasmic, glucosamine resistant mutants of Saccharomyces cerevisiae, GR6 and GR10, were examined to determine whether or not the lesions involved were located on mitochondrial DNA. Detailed investigation of crosses of GR6 and GR10 or their derivatives to strains bearing known mitochondrial markers demonstrated that: 1. the frequency of glucos~~ine resistance in diploids was independent of factors influencing mitochondrial marker output. 2. upon tetrad analysis a variety of tetrad ratios was observed for glucosamine resistance whereas mitochondrial markers segregated 4:0 or 0:4 (resistant:sensitive). 3. glucosamine resistance and mitochondrial markers segregated differentially with time. 4. glucosamine resistance persisted following treatment of a GRIO derivative with ethidium bromide at concentrations high enough to eliminate all mitochondrial DNA. 5. haploid spore clones displayed two degrees of glucosamine resistance, weak and strong, while growth due to mitochondrial mutations was generally thick and confluent. 6. a number of glucosamine resistant diploids and haploids, which also possessed a mithchondrial resistance mutation, were unable to grow on medium containing both glucosamine and the particular drug involved. 3 These observations 1~ 6 provided strong evidence that the cytoplasmic glucosamine resistant mutations present in GR6 and GRiO were not situated on mitochondrial DNA. Comparison of the glucosamine resistance mutations to some other known cytoplasmic determinants revealed that: 7. glucosamine resistance and the expression of the killer phenotype were separate phenomena. 8. unlike yeast carrying resistance conferring episomes GR6 and GR10 were not resistant to venturicidin or oligomycin and the GR factor exhibited genetic behaviour different from that of the episomal determinants. These results 7--+8 suggested that glucosamine resistance was not associated with the killer determinant nor with alleged yeast episomes. It is therefore proposed that a yeast plasmid(s), previously undescribed, is responsible for glucosamine resistance. The evidence to date is compatible with the hypothesis that GR6 and GR10 carry allelic mutations of the same plasmid which is tentatively designated (GGM).

Le meilleur intérêt de l'enfant, les tests de paternité et le droit civil québécois

"Mémoire présenté à la Faculté des études supérieures en vue de l'obtention du grade de maîtrise en Droit option Droit, Biotechnologies et Société"

La dignité humaine: limite à la brevetabilité du corps humain

Le thème de ce mémoire de Maîtrise en droit est « La dignité humaine: limite à la brevetabilité du corps humain». Dans ce travail, nous avons tenté d'apporter une contribution à un débat des plus importants de ce début du 21 e siècle. Deux parties composent ce mémoire. La première partie vise à présenter la thématique de la brevetabilité du corps humain. Elle fait l'analyse non seulement des normes juridiques interdisant la brevetabilité du corps humain, mais aussi elle se penche sur le corps humain comme source d'inventions brevetables. Dans la première sous-section, notre analyse porte sur l'étude des documents normatifs d'intérêt international, régional et national. Le modèle et les normes de la Communauté européenne ont largement retenu notre attention alors que le cas des États-Unis, du Canada et surtout de la France nous servait de guide de réflexion pour mieux comprendre l'état du droit au Canada. Par une argumentation serrée nous avons conclu cette partie en affirmant que le corps humain n'est pas brevetable. La prohibition de la brevetabilité du corps humain s'impose comme universelle. La dignité humaine a constitué un élément déterminant de cette prohibition. Ce qui nous a permis, dans la deuxième sous-section de considérer le brevetage de l'ADN. Après avoir présenté les trois critères juridiques de la brevetabilité, à savoir la nouveauté, l'utilité et l'inventivité, nous avons appliqué ces critères à l'ADN. Il s'est avéré que c'est à bon droit que la plupart des pays accordent le brevet sur l'ADN. Mais cet état de droit pose des problèmes sur le plan des valeurs éthiques. Il a notamment comme conséquence de relativiser la dignité humaine. Ces dernières considérations éthiques nous ont conduits à étendre à l'ADN les critères juridiques de la brevetabilité vus dans la première partie. Pour nous prononcer adéquatement sur ce sujet combien délicat, il a fallu considérer la question de la brevetabilité de l'ADN chez les vivants, depuis l'affaire Chakrabarty en 1980, aux États-Unis, en passant par la Directive européenne de 1998, l'affaire Harvard College au Canada jusqu'à Myriad Genetics Inc. En droit, la brevetabilité de l'ADN ne fait plus de doute. Mais elle continue de soulever des « gènes» sur le plan éthique. L'inquiétude que suscite la pente glissante nous a amenés, dans la deuxième partie, à nous pencher sur la brevetabilité dans son rapport avec la dignité humaine. La première sous-section se voulait une analyse permettant de montrer que la dignité humaine est une valeur absolue et inconditionnelle. Si nous considérons cette valeur comme absolue, il devient impossible de breveter le corps humain dans son ensemble. Par contre, en brevetant l'ADN humain, nos institutions se trouvent à relativiser la dignité humaine. C'est ce que la deuxième sous-section tendait à montrer. Soulignons que cette deuxième sous-section a été conçue également comme une conclusion. Elle s'articule autour notamment de la dignité humaine comme principe de précaution.

Identification et caractérisation de facteurs impliqués dans la réplication et la stabilité des génomes des organelles de plantes

Comparativement au génome contenu dans le noyau de la cellule de plante, nos connaissances des génomes des deux organelles de cette cellule, soit le plastide et la mitochondrie, sont encore très limitées. En effet, un nombre très restreint de facteurs impliqués dans la réplication et la réparation de l’ADN de ces compartiments ont été identifiés à ce jour. Au cours de notre étude, nous avons démontré l’implication de la famille de protéines Whirly dans le maintien de la stabilité des génomes des organelles. Des plantes mutantes pour des gènes Whirly chez Arabidopsis thaliana et Zea mays montrent en effet une augmentation du nombre de molécules d’ADN réarrangées dans les plastides. Ces nouvelles molécules sont le résultat d’une forme de recombinaison illégitime nommée microhomology-mediated break-induced replication qui, en temps normal, se produit rarement dans le plastide. Chez un mutant d’Arabidopsis ne possédant plus de protéines Whirly dans les plastides, ces molécules d’ADN peuvent même être amplifiées jusqu’à cinquante fois par rapport au niveau de l’ADN sauvage et causer un phénotype de variégation. L’étude des mutants des gènes Whirly a mené à la mise au point d’un test de sensibilité à un antibiotique, la ciprofloxacine, qui cause des bris double brin spécifiquement au niveau de l’ADN des organelles. Le mutant d’Arabidopsis ne contenant plus de protéines Whirly dans les plastides est plus sensible à ce stress que la plante sauvage. L’agent chimique induit en effet une augmentation du nombre de réarrangements dans le génome du plastide. Bien qu’un autre mutant ne possédant plus de protéines Whirly dans les mitochondries ne soit pas plus sensible à la ciprofloxacine, on retrouve néanmoins plus de réarrangements dans son ADN mitochondrial que dans celui de la plante sauvage. Ces résultats suggèrent donc une implication pour les protéines Whirly dans la réparation des bris double brin de l’ADN des organelles de plantes. Notre étude de la stabilité des génomes des organelles a ensuite conduit à la famille des protéines homologues des polymérases de l’ADN de type I bactérienne. Plusieurs groupes ont en effet suggéré que ces enzymes étaient responsables de la synthèse de l’ADN dans les plastides et les mitochondries. Nous avons apporté la preuve génétique de ce lien grâce à des mutants des deux gènes PolI d’Arabidopsis, qui encodent des protéines hautement similaires. La mutation simultanée des deux gènes est létale et les simples mutants possèdent moins d’ADN dans les organelles des plantes en bas âge, confirmant leur implication dans la réplication de l’ADN. De plus, les mutants du gène PolIB, mais non ceux de PolIA, sont hypersensibles à la ciprofloxacine, suggérant une fonction dans la réparation des bris de l’ADN. En accord avec ce résultat, la mutation combinée du gène PolIB et des gènes des protéines Whirly du plastide produit des plantes avec un phénotype très sévère. En définitive, l’identification de deux nouveaux facteurs impliqués dans le métabolisme de l’ADN des organelles nous permet de proposer un modèle simple pour le maintien de ces deux génomes.

Influence des routes sur la variance du succès reproducteur des populations de tortues peintes (Chrysemys Picta)

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

Phylogéographie comparée de la souris à pattes blanches et de la souris sylvestre, deux vecteurs de la maladie de Lyme au Québec

Mon étude vise à évaluer la propagation d’une zoonose en émergence au Québec, la maladie de Lyme, en conséquence du réchauffement climatique. Le pathogène responsable de cette infection, Borrelia burgdorferi, est transmis par l’intermédiaire d’une tique parasite, Ixodes scapularis, de plus en plus commune au Québec en raison de l’augmentation de la température moyenne du climat depuis les dernières décennies. Puisque la tique a une capacité de déplacement très restreinte, on s'attend à ce que sa dispersion soit liée à celle de son hôte primaire, soit la souris à pattes blanches (Peromyscus leucopus). Je décrirai donc d’abord les espèces impliquées, leur écologie et leur rôle dans ce système à trois niveaux (hôte/pathogène/vecteur). Puis, à l’aide de séquences d’ADN mitochondrial, je comparerai la phylogéographie des deux principales espèces de souris au Québec, la souris à pattes blanches et la souris sylvestre (P. maniculatus). Des analyses d’arbres et de réseaux d’haplotypes ont révélé des différences significatives dans la structure génétique et ainsi montré que les populations de P. leucopus seraient en expansion dans le sud du Québec. Cette étude nous a finalement permis d’émettre des hypothèses sur le patron d’établissement de la maladie de Lyme au Québec.