On Irish stickleback:Morphological diversification in a secondary contact zone

Question: How parallel is adaptive evolution when it occurs from different genetic backgrounds? Background: Divergent evolutionary lineages of several post-glacial fish species including the threespine stickleback are found together in Ireland. Goals: To investigate the morphological diversity of stickleback populations in Ireland and assess whether morphology evolved in parallel between evolutionary lineages. Methods: We sampled stickleback from lake, river, and coastal habitats across Ireland. Microsatellite and mitochondrial DNA data revealed evolutionary history. Geometric morphometrics and linear trait measurements characterized morphology. We used a multivariate approach to quantify parallel and non-parallel divergence within and between lineages. Results: Repeated evolution of similar morphologies in similar habitats occurred across Ireland, concordant with patterns observed elsewhere in the stickleback distribution. A strong pattern of habitat-specific morphology existed even among divergent lineages. Furthermore, a strong signal of shared morphological divergence occurred along a marine-freshwater axis. Evidently, deterministic natural selection played a more important role in driving freshwater adaptation than independent evolutionary history. © 2013 Mark Ravinet.

The co-occurrence of mtDNA mutations on different oxidative phosphorylation subunits, not detected by haplogroup analysis, affects human longevity and is population specific.

To re-examine the correlation between mtDNA variability and longevity, we examined mtDNAs from samples obtained from over 2200 ultranonagenarians (and an equal number of controls) collected within the framework of the GEHA EU project. The samples were categorized by high-resolution classification, while about 1300 mtDNA molecules (650 ultranonagenarians and an equal number of controls) were completely sequenced. Sequences, unlike standard haplogroup analysis, made possible to evaluate for the first time the cumulative effects of specific, concomitant mtDNA mutations, including those that per se have a low, or very low, impact. In particular, the analysis of the mutations occurring in different OXPHOS complex showed a complex scenario with a different mutation burden in 90+ subjects with respect to controls. These findings suggested that mutations in subunits of the OXPHOS complex I had a beneficial effect on longevity, while the simultaneous presence of mutations in complex I and III (which also occurs in J subhaplogroups involved in LHON) and in complex I and V seemed to be detrimental, likely explaining previous contradictory results. On the whole, our study, which goes beyond haplogroup analysis, suggests that mitochondrial DNA variation does affect human longevity, but its effect is heavily influenced by the interaction between mutations concomitantly occurring on different mtDNA genes

On Irish sticklebacks: morphological diversification in a secondary contact zone

Question: How parallel is adaptive evolution when it occurs from different genetic backgrounds?
Background: Divergent evolutionary lineages of several post-glacial fish species including the threespine stickleback are found together in Ireland.
Goals: To investigate the morphological diversity of stickleback populations in Ireland and assess whether morphology evolved in parallel between evolutionary lineages.
Methods: We sampled stickleback from lake, river, and coastal habitats across Ireland. Microsatellite and mitochondrial DNA data revealed evolutionary history. Geometric morphometrics and linear trait measurements characterized morphology. We used a multivariate approach to quantify parallel and non-parallel divergence within and between lineages.
Results: Repeated evolution of similar morphologies in similar habitats occurred across Ireland, concordant with patterns observed elsewhere in the stickleback distribution. A strong pattern of habitat-specific morphology existed even among divergent lineages. Furthermore, a strong signal of shared morphological divergence occurred along a marine–freshwater axis. Evidently, deterministic natural selection played a more important role in driving freshwater adaptation than independent evolutionary history.

A primer for use of genetic tools in selecting and testing the suitability of set-aside sites protected from deep-sea seafloor massive sulfide mining activities

Seafloor massive sulfide (SMS) mining will likely occur at hydrothermal systems in the near future. Alongside their mineral wealth, SMS deposits also have considerable biological value. Active SMS deposits host endemic hydrothermal vent communities, whilst inactive deposits support communities of deep water corals and other suspension feeders. Mining activities are expected to remove all large organisms and suitable habitat in the immediate area, making vent endemic organisms particularly at risk from habitat loss and localised extinction. As part of environmental management strategies designed to mitigate the effects of mining, areas of seabed need to be protected to preserve biodiversity that is lost at the mine site and to preserve communities that support connectivity among populations of vent animals in the surrounding region. These "set-aside" areas need to be biologically similar to the mine site and be suitably connected, mostly by transport of larvae, to neighbouring sites to ensure exchange of genetic material among remaining populations. Establishing suitable set-asides can be a formidable task for environmental managers, however the application of genetic approaches can aid set-aside identification, suitability assessment and monitoring. There are many genetic tools available, including analysis of mitochondrial DNA (mtDNA) sequences (e.g. COI or other suitable mtDNA genes) and appropriate nuclear DNA markers (e.g. microsatellites, single nucleotide polymorphisms), environmental DNA (eDNA) techniques and microbial metagenomics. When used in concert with traditional biological survey techniques, these tools can help to identify species, assess the genetic connectivity among populations and assess the diversity of communities. How these techniques can be applied to set-aside decision making is discussed and recommendations are made for the genetic characteristics of set-aside sites. A checklist for environmental regulators forms a guide to aid decision making on the suitability of set-aside design and assessment using genetic tools. This non-technical primer document represents the views of participants in the VentBase 2014 workshop.

Biogeography of the fire salamander (Salamandra salamandra, L.) in Portugal

Dissertação de mest., Biologia Marinha, Faculdade de Ciências do Mar e do Ambiente, Universidade do Algarve, 2008

Salamandra salamandra (Amphibia: Caudata: Salamandridae) in Portugal: not all black and yellow

The fire salamander complex is quite diverse in the Iberian Peninsula where nine subspecies of Salamandra salamandra are currently recognized. Here, we analysed the geographical distribution of the subspecies S. s. gallaica and S. s. crespoi using partial sequences of the mitochondrial cytochrome b gene of 168 individuals from 12 locations in Portugal. Our results support the existence of a deep lineage divergence between the two subspecies, with non-overlapping geographical distributions except in two contact zones: one in Sesimbra on the western coast, and another in Alcoutim on the southeastern border with Spain. Moreover, S. s. crespoi displays signs of gene flow among the sampled locations whereas S. s. gallaica shows evidence of some restriction to gene flow. Present-day genetic make-up of S. s. gallaica and S. s. crespoi is a result of past historical events, fine-tuned by contemporary Iberian geoclimate. Humid mountain areas were found to harbour increased genetic diversity possibly acting as past refugia during drier interglacial periods. To analyse wider geographical patterns and lineage splitting events within S. salamandra we performed a Bayesian dating analysis completing our data set with previously published sequences. The observed divergences were associated to successive biogeographic scenarios, and to other Iberian species showing similar trends.

Phylogeography and hybridisation in the european polecat : (mustela putorius)

Tese de doutoramento, Biologia (Biologia da Conservação), Universidade de Lisboa, Faculdade de Ciências, 2014

New Sorex araneus karyotypes from Germany and the postglacial recolonization of central Europe

New G-banded karyotypes from populations of the common shrew Sorex araneus Linnaeus, 1758 provide a clearer picture of the distribution of chromosome races in central Europe. As expected according to their occurrence in neighbouring countries, the Jutland (kq, no), Laska (k/o) and Drnholec (ko, nr) races are also found in Germany. A new chromosome race "Rugen" (kq) is described from this Baltic Island. Together with the previously recorded races Ulm and Mooswald (kr), six chromosome races are now known from Germany. The resulting distribution pattern is characterized by high frequencies of different race-specific metacentrics at the periphery of the country and clines with decreasing frequencies towards the centre which is occupied by the Ulm race. This race is acrocentric for all chromosome arms involved in the observed race-specific fusions and represents a buffer between the surrounding, more metacentric races. According to the present distribution of these metacentrics, a scenario for the postglacial recolonization of central Europe by S. araneus populations on three different routes is proposed: from the east along the northern slopes of the Carpathian Arc, from the south-east along the Danube Valley and from the south-west through the Upper Rhine Valley.

Microsatellites can be misleading: an empirical and simulation study.

It has been long recognized that highly polymorphic genetic markers can lead to underestimation of divergence between populations when migration is low. Microsatellite loci, which are characterized by extremely high mutation rates, are particularly likely to be affected. Here, we report genetic differentiation estimates in a contact zone between two chromosome races of the common shrew (Sorex araneus), based on 10 autosomal microsatellites, a newly developed Y-chromosome microsatellite, and mitochondrial DNA. These results are compared to previous data on proteins and karyotypes. Estimates of genetic differentiation based on F- and R-statistics are much lower for autosomal microsatellites than for all other genetic markers. We show by simulations that this discrepancy stems mainly from the high mutation rate of microsatellite markers for F-statistics and from deviations from a single-step mutation model for R-statistics. The sex-linked genetic markers show that all gene exchange between races is mediated by females. The absence of male-mediated gene flow most likely results from male hybrid sterility.

Methylation profile of TP53 regulatory pathway and mtDNA alterations in breast cancer patients lacking TP53 mutations.

The present study investigated promoter hypermethylation of TP53 regulatory pathways providing a potential link between epigenetic changes and mitochondrial DNA (mtDNA) alterations in breast cancer patients lacking a TP53 mutation. The possibility of using the cancer-specific alterations in serum samples as a blood-based test was also explored. Triple-matched samples (cancerous tissues, matched adjacent normal tissues and serum samples) from breast cancer patients were screened for TP53 mutations, and the promoter methylation profile of P14(ARF), MDM2, TP53 and PTEN genes was analyzed as well as mtDNA alterations, including D-loop mutations and mtDNA content. In the studied cohort, no mutation was found in TP53 (DNA-binding domain). Comparison of P14(ARF) and PTEN methylation patterns showed significant hypermethylation levels in tumor tissues (P < 0.05 and <0.01, respectively) whereas the TP53 tumor suppressor gene was not hypermethylated (P < 0.511). The proportion of PTEN methylation was significantly higher in serum than in the normal tissues and it has a significant correlation to tumor tissues (P < 0.05). mtDNA analysis revealed 36.36% somatic and 90.91% germline mutations in the D-loop region and also significant mtDNA depletion in tumor tissues (P < 0.01). In addition, the mtDNA content in matched serum was significantly lower than in the normal tissues (P < 0.05). These data can provide an insight into the management of a therapeutic approach based on the reversal of epigenetic silencing of the crucial genes involved in regulatory pathways of the tumor suppressor TP53. Additionally, release of significant aberrant methylated PTEN in matched serum samples might represent a promising biomarker for breast cancer.

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).

Liberté de la recherche et modification du génome humain : le cas du transfert d'ooplasme

"Mémoire présenté à la faculté des études supérieures en vue de l'obtention du grade de maîtrise en droit (LL.M.) option droit, biotechnologies et société"

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.