In the first part of the present study, samples of 13 native Turkish sheep breeds (n=628) were examined, individually and comparatively, with respect to their 19 microsatellite loci to characterize them by employing various statistical analyses. Low FST values, high mean number of alleles and allelic richness as well as results of Factorial Correspondence Analysis and Structure analyses showed the degree of admixture between native sheep breeds of Turkey, IVE and SAK were observed as the most distincts of the breeds and possible introgressions were detected in other breeds. The 2- BAD, a software to examine the admixtures, was employed to estimate the time of the admixtures and the MSVAR software was employed to detect past demographic histories. In the second part, evaluations based on their genetic characteristics were made in relation to their prioritization in conservation studies. By employing four different approaches, it has been concluded that IVE, SAK, KRY, KIV, HEM and breed from Central Anatolia should be included in a conservation program for the preservation of optimum genetic diversity. In the last part of the thesis breeds were also characterized with respect to their relative risk of extinctions and their merits, which were used to estimate the utilities of the breeds. Non-genetic factors, collected based on the existing literature and surveys throughthe questionnaires filled by the field specialists, were incorporated into genetic factors to estimate the utilities of the breeds under different scenarios. In this approach, it is concluded that NOR, AKK, SAK, IVE and HEM should be included in the conserved set of breeds. By the present study, it is believed that specific genetic features of the native Turkish sheep breeds were documented, effects of sampling on the population genetic studies was discussed, the need for a reliable data (genetic and nongenetic, for characterizing the risks and merits of the breeds) for the prioritization of the breeds in the long term sustainable conservation ofthem was emphasized.

The population genetic structure of Atlantic yellowfin tuna (Thunnus albacares) has received little attention despite the substantial fishing mortality of juveniles caused by purse seining around fish aggregating devices in the Gulf of Guinea targeting multi-species schools that also include similarly sized skipjack tuna (Katsuwonus pelamis) and bigeye tuna (T. obesus). We used sequence data from 355 bp of the mitochondrial control region I as well as six microsatellite loci to examine: (1) population structure, and (2) to look for evidence of reproductive variance. We analyzed two samples of adults from the Gulf of Mexico (GOM) and one sample of early juveniles (20-50 mm) from the Gulf of Guinea (GOG). We found no evidence of geographic or temporal differentiation among the samples. Accordingly, the null hypothesis of panmixia for yellowfin tuna in the Atlantic Ocean could not be rejected. A sudden expansion analysis based on mtDNA control region I sequence data of yellowfin tuna was highly significant. Time estimates for expansion were between 40,000 and 80,000 years before present. The associated high levels of homoplasy could be masking any existing population structure. Additional sampling from additional locations and across several years will be needed to test the hypothesis of panmixia. We also provide preliminary evidence of the Allendorf-Phelps effect, which may contribute to reproductive variance. This is the first evidence of this effect in any other tuna or pelagic species. Data indicates that early juveniles sharing the same mtDNA control region I haplotype were caught in the same tow and had a significant probability of halfsibship status as calculated from their haplotype and genotype at one microsatellite locus through kinship analysis. Sampling throughout the spawning season and across several years, as well as analysis with additional microsatellite loci that have a more even distribution of alleles, will be needed to more fully identify the sibling status of larvae and early juveniles caught in the same tow as well as the extent of this reproductive variance.

Au sein de la Sibérie Orientale, l'origine des Yakoutes reste une énigme qui demeure non résolue par les études classiques. Les Yakoutes représentent en effet le seul peuple d'éleveurs de bétail et de chevaux au sein d'un ensemble de populations composé de chasseurs et d'éleveurs de rennes. Leur langue, mélange de mots d'origine turque et mongole, ainsi que leurs pratiques culturelles accentuent encore ce contraste avec les populations alentour. <br />L'analyse moléculaire de spécimens yakoutes anciens apparaissait comme bien adaptée à l'étude de la formation de ce peuple. En effet, l'évolution récente des techniques de biologie moléculaire rend aujourd'hui possible l'analyse génétique des populations du passé et les conditions environnementales rencontrées en Sibérie Orientale sont particulièrement propices à la conservation des acides nucléiques. <br />L'étude de plus de 60 sujets anciens provenant de Yakoutie Centrale, a permis d'obtenir des résultats originaux concernant, d'une part, l'aspect moléculaire de ce travail et d'autre part, l'ethnogenèse yakoute. Ces résultats ont notamment permis de souligner la très grande qualité des échantillons provenant de Sibérie Orientale. Il a ainsi été possible d'étudier des marqueurs génétiques rarement analysables dans les études d'anthropologie moléculaire, comme les STR autosomaux et du chromosome Y, et d'obtenir des résultats uniques sur des substrats difficiles. Cet ensemble de facteurs a conduit à l'obtention de données dont l'authenticité est manifeste. En outre, le nombre important de sujets étudiés ainsi que la mise en parallèle de nouveaux protocoles sur plusieurs types de prélèvements ont permis d'apporter des informations sur les propriétés de ces différents substrats. <br />La comparaison des résultats collectés pour le chromosome Y et l'ADN mitochondrial des sujets anciens avec les populations voisines mais également du sud de la Sibérie, ont permis de dégager de nouvelles hypothèses concernant les origines des lignées paternelles et maternelles des Yakoutes. L'influence méridionale semble confirmée par notre étude, mais nos résultats mettent également en avant que des contacts anciens, précédant les migrations déjà proposées, ont du se produire entre les peuples nomades des steppes et les populations de Sibérie Orientale. De plus, la population yakoute apparaît extrêmement stable au cours des siècles malgré des changements notables dans les influences culturelles et l'arrivée des colons russes au XVIIIième siècle. Ainsi, certaines lignées masculines, spécifiques à la population yakoute, montrent une pérennité exceptionnelle puisqu'elles se sont maintenues depuis le XVième siècle jusqu'à nos jours, avec des fréquences très importantes.<br />La qualité des données obtenues ainsi que les conclusions qui ont pu être proposées suite à ce travail de recherche confirment à nouveau la pertinence de la mise en œuvre d'un approche moléculaire dans la compréhension de la formation et de l'organisation des populations du passé.

The three South African crane species, namely, the Wattled Crane (Bugeranus carunculatus), the Blue Crane (Anthropoides paradisea) and the Grey Crowned Crane (Balearica regulorum regulorum) are all threatened. South African legislation protects the cranes, however eggs and/or fledglings are sometimes illegally collected from the wild. These are then sold, often by registered breeders, who falsely claim them as the offspring of their captive breeding pair. DNA fingerprinting is one method to detect this crime. Fifteen RAPD primers were screened for polymorphism in the three species. Seven primers produced polymorphic profiles in the Blue Crane and eight each in the Grey Crowned Crane and Wattled Crane, with an average of 14.57, 12.38 and 5.88 scorable loci per primer, respectively. The Band Sharing Coefficient for unrelated individuals was found to be 0.665, 0.745 and 0.736 for the Blue, Grey Crowned and Wattled Crane respectively. Five microsatellite primers, originally developed for use in Whooping Cranes (Grus american), had previously been shown to be polymorphic in the Wattled Crane. This was also the case in this study with an average of 3.6 alleles per primer. Although all primers cross amplified, only a single primer each showed polymorphism in the Blue Crane (showing 6 alleles) and the Grey Crowned Crane (showing 5 alleles). The RAPDs were found to be irreproducible, show high numbers of novel bands and had parent: offspring BSC values that were not significantly higher than those of unrelated individuals. Statistics showed that, in the Blue Crane, the probability that misassigned parents would be detected was low whilst there was an almost certainty that true parents would be incorrectly excluded. The five microsatellite primers examined gave exclusionary powers of 0.869 and 0.641 where one or two parents were unknown in the Wattled Crane. The exclusionary powers for the Blue Crane and Grey Crowned Crane calculated at only one locus were much lower. It was concluded that RAPDs were totally inappropriate for parentage analyses, however, microsatellites are a suitable technique and recommendations are made that other microsatellites, developed for other species of crane, should be examined for their potential in this respect. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2004.

Migration acts as a selective force on the ecology and evolutionary trajectory of species, as well as presenting fundamental challenges for conservation. My thesis examines the impact of migration by exploring patterns of differentiation among and within migratory and non-migratory populations of the Loggerhead Shrike (Lanius ludovicianus). First, I use morphological, genotypic, stable isotope and leg band recovery data to quantify migratory connectivity in the species. Comparison across markers reveals a generally concordant pattern of moderate connectivity to the Gulf Coast, but overall mixing among populations on the wintering grounds. Combining data from multiple markers in a Bayesian framework improves the resolution of assignment of wintering birds to a breeding ground origin. Information on the species’ migratory patterns provides an explicit framework for interpreting patterns of genetic and ecological variation. I test two hypotheses regarding the interaction of gene flow and migratory habit: (1) migration facilitates gene flow; and (2) gene flow will occur most often along the axis of migration. Genetic population structure in migratory populations is weaker than in non-migratory populations, with gene flow facilitated by dispersal movements of females and first year breeders. As predicted, gene flow occurs most often along the north-south axis of migration, likely due either to opportunistic settling of dispersers or potentially, pairing on the wintering grounds. I investigate variation in the extent and scheduling of moult in relation to underlying genetic differences among populations, age, sex, body size, food availability and migratory habit. I find a pattern of interrupted moult across migratory populations, which may represent a trade-off between time allocated to breeding versus molt and migration. Loggerhead Shrikes in eastern and more southerly migratory populations undergo a greater extent of their moult on the breeding grounds and non-migratory individuals undergo a more extensive pre-formative moult than migratory individuals. I interpret this as suggesting a trade-off between resources allocated to molt versus those required for reproduction. / Thesis (Ph.D, Biology) -- Queen's University, 2011-01-25 15:54:36.593

The blue crane (Grus paradisea) is endemic to southern Africa and has the smallest geographical range of the 15 crane species occurring world-wide. Although this species is still found throughout most of its historic range, it has experienced a significant and rapid decline in numbers over the last 20 years. One factor causing this decline is the illegal removal of chicks from the wild. Permits are required to keep, trade in and breed cranes in captivity. However, birds must be captive bred in order to obtain a permit. Therefore, chicks taken illegally from the wild are fraudulently incorporated into an existing captive population under the pretence that they offspring of a legal captive pair. This study describes the development of a set of microsatellite markers to assist the identification of illegal trade in the blue crane. These markers can ultimately be used to verify the relationship between the offspring and its claimed parents by performing parentage analyses. Forty microsatellite loci were obtained from genomic libraries previously developed in two other crane species and tested for cross-species utility in the blue crane. In addition, 42 loci were developed for this study from a blue crane species-specific genomic microsatellite library, of which 19 were tested for polymorphism in this species. The microsatellite markers characterised here were also tested for their utility in two other crane species: wattled crane (G. carunculatus) and grey-crowned crane (Balearica regulorum). One locus, Gamu007, was found to be sex-linked and therefore excluded from the set of markers. A total of 28 polymorphic loci were tested for the suitability in parentage analysis in the blue crane. Of these, a set of 16 loci were determined to be as suitable for this purpose. These loci were shown to be inherited in a Mendelian fashion in a single blue crane family. In addition, statistical analysis of the loci were identified as exhibiting linkage equilibrium, this was supported by their distant association on a predicted Grus microsatellite map based on the chicken genome. The selected loci were also identified as having a low frequency of null alleles as well as a total first and second parent exclusion power of 0.9999 and 1.0000, respectively. These loci provide a valuable tool for parentage testing in blue crane, and may also be valuable in population genetic studies to assist conservation strategies. In addition, this set may be used to assist legal cases involving the illegal trade in blue cranes upon completion of additional microsatellite marker validation procedures. Twenty-seven loci were polymorphic in the wattled and grey-crowned crane. These could provide a valuable source of micro satellite loci in these species, and could potentially eliminate the need for the development of a species-specific microsatellite library. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2007.

The use of microsatellite markers has matured and become commonplace for plant genome analyses and is now poised for widespread practical application in sugarcane. Sequence Tagged Microsatellite Site (STMS) amplification is the most prevalent microsatellite-based approach and involves the amplification of a microsatellite by designing primers that flank and hence define the microsatellite site, revealing variation in the length of repeat motifs between individuals. Twenty-six microsatellite primer pairs received from the International Sugarcane Microsatellite Consortium (ISMC) were evaluated and the STMS protocol was optimised to ensure robust and reproducible results. The objectives of this study were to use STMS for sugarcane parentage analysis and fingerprinting. Previously, Restriction Fragment Length Polymorphism (RFLP) marker data had suggested that the parentage of a genetic mapping population, sugarcane cross AA40 (N18 x CP57/614), was incorrect. Based on the assertion that the incorrect parentage was as a result of either mislabelling at planting or at seed collection, microsatellite parentage analysis was carried out on eight potential parent pairs (13 cultivars). A total of 75 markers were scored with non-parental bands (12 on average) being observed for all of the potential parent pairs and none could be identified as the true AA40 parents. It has been suggested in other plant species that PCR artefacts could give rise to non-parental bands and to investigate this the marker data of single parent DNA reactions and pooled parent pair DNA reactions or 'synthetic offspring' were compared. The results suggested that either a certain percentage of non-parental bands, perhaps 10% (maximum value observed), should be tolerated in microsatellite parentage analysis or a marker should only be considered to be discriminating for parentage if it is absent in both the parents and the pooled parent pair amplifications. Fingerprinting of 20 cultivars using 14 microsatellite primer pairs was conducted to evaluate the potential of the STMS approach for sugarcane varietal identification. It was found that only two microsatellite primer pairs were required to discriminate between all 20 cultivars with a theoretical number of non-differentiated pairs of cultivars (XK) of only 0.03. This estimator was used to determine the approximate number of microsatellites necessary for large-scale sugarcane fingerprinting. / Thesis (M.Sc.)-University of Natal, Durban, 2002.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal

Le lagopède alpin (Lagopus muta) et la perdrix grise (Perdix perdix) atteignent dans les Pyrénées les limites méridionales de leurs aires de répartition mondiale. Les populations pyrénéennes de ces deux sous-espèces (Lagopus muta pyrenaica et Perdix perdix hispaniensis) sont donc en situation d'isolat biogéographique. Les deux espèces sont d'excellents bio-indicateurs de l'évolution des milieux ouverts d'altitude. Sous la pression conjuguée des contraintes environnementales et anthropiques, ces milieux connaissent actuellement une évolution sensible caractérisée par un relèvement altitudinal des étages de végétation et donc un rétrécissement de l'habitat disponible pour les espèces d'altitude. La régression des activités agro-pastorales accentue ce phénomène généralisé de reforestation des milieux. Une conséquence attendue de ces bouleversements est l'augmentation du degré de fragmentation des habitats notamment pour les populations d'altitude. Au-delà de l'influence du paysage sur la structuration des populations, un autre facteur pourrait structurer les populations de perdrix grise : les lâchers d'individus d'élevage dans des populations sauvages. Dans cette thèse, nous nous intéressons à la structuration génétique du lagopède alpin des Pyrénées et de la perdrix grise en France afin d'aider à la décision des plans de conservation.

The population structure of a lichen, Thamnolia subuliformis and a moss, Dicranum elongatum, was examined in northeastern regions of Wapusk National Park. With the use of microsatellite molecular markers, it was reported that the sterile lichen had a level of variation similar to that of a sexually reproducing species. The variation reported for the moss, where sporophytes were not encountered, supported subdivided populations. It was concluded that these species have the genetic resources necessary to adapt to changing environmental conditions.