La conservation des zones humides fortement modifiées par les pratiques anthropiques, nécessite l’acquisition de données scientifiques sur leur diversité et leur fonctionnement. Cette thèse vise à relier l’anthropisation des zones humides à la diversité génétique, niveau de base de la biodiversité lié à la capacité adaptative des populations et au maintien des espèces. L’effet de l’anthropisation sur la diversité génétique de végétaux aquatiques est étudié à plusieurs échelles d’espaces (zone humide et bassin versant) et de temps (études synchroniques et diachroniques). La diversité génétique de populations de deux espèces rudérales (Berula erecta et Apium nodiflorum) et une compétitive (Nuphar lutea) est comparée dans deux plaines alluviales contrastées (trophie, connectivité hydrologique et restauration), à l’aide de marqueurs microsatellites adaptés à l’étude d’espèces clonales. La diminution de la connectivité hydrologique augmente la différenciation génétique et diminue la diversité génétique pour les espèces rudérales étudiées alors qu’elle n’a pas d’effet sur l’espèce compétitive. L’impact de la connectivité est donc dépendant de la stratégie de reproduction. La diversité génétique des espèces rudérales diminue également dans les zones humides plus eutrophes. L’augmentation de la diversité génétique post-restauration chez B. erecta est corrélée à la fréquence des perturbations (assecs) qui créent des niches favorisant le recrutement des graines. Cette étude propose des préconisations de gestion pour les zones humides et apporte des connaissances sur la dynamique de la diversité génétique des plantes aquatiques en lien avec leur environnement / The conservation of wetlands which are strongly modified by human practices, requires the acquisition of knowledge about their diversity and functioning. This thesis aimed to link the human pressures and plant genetic diversity in wetlands, which is the basic level of biodiversity linked to the adaptive capacity of populations and species maintenance. The effect of anthropization on the genetic diversity of aquatic plants is studied at several spatial and temporal scales (wetland and watershed; synchronic vs. diachronic studies). The genetic diversity of populations of two ruderal (Berula erecta and Apium nodiflorum) and one competitive species (Nuphar lutea) in two contrasting floodplains (in terms of trophic status, hydrological connectivity and restoration) is compared using microsatellite markers suitable for the study of clonal species. A reduction in hydrological connectivity increases genetic differentiation and decreases genetic diversity for ruderal species studied, while it did not affect the competitive species. The impact of connectivity is related to plant reproductive strategy. The genetic diversity of ruderal species also decreases in most eutrophic wetlands. The increase of genetic diversity of B. erecta after restoration is correlated with the frequency of disturbances (dewatering) that create niches for seed recruitment. This study provides management recommendations for the impacted wetlands and provides knowledge about the dynamics of the genetic diversity of aquatic plants in relation to their environment

L'archipel des Mascareignes (Réunion, Maurice et Rodrigues) est, avec les Seychelles, les Comores et Madagascar, l'un des 34 « hotspots » de biodiversité reconnus à l'échelle mondiale. Dans un contexte de disparition des habitats par les activités humaines, l'objectif de la thèse a été de comprendre la dynamique évolutive à différentes échelles spatiales et temporelles d'une famille d'espèces indigènes des écosystèmes forestiers, les Sapotacées. Ces espèces arborées présentent une gamme diversifiée de niveaux d’endémisme, d'abondance, de modes de régénération et de caractéristiques biologiques. La famille des Sapotacées comprend 3 genres et 14 espèces indigènes des Mascareignes (Mimusops, Labourdonnaisia et Sideroxylon) dont certaines espèces, rares et protégées, sont endémiques d'une des trois îles de l'archipel des Mascareignes. À l'échelle de la famille, l'analyse des séquences chloroplastiques de la famille des Sapotacées a confirmé la forte différenciation entre genres avec deux clades. Le premier clade est constitué par toutes les espèces de Sideroxylon structurées en trois sous-clades distincts dont deux correspondent aux sections Eusideroxylon et Calvaria, montrant une diversité haplotypique importante. Le deuxième clade est constitué par deux sous-clades formés respectivement par les espèces de Labourdonnaisia et celles de Mimusops. Alors qu'il n'est pas possible de résoudre les relations de parenté des Mimusops, Labourdonnaisia présentent deux lignées évolutives soulevant une incongruence entre les données taxonomiques et phylogénétiques. À l'échelle des deux lignées du genre Sideroxylon (Sections Eusideroxylon et Calvaria), l'analyse des marqueurs microsatellites chloroplastiques a montré une forte diversité haplotypique à la fois chez des espèces communes comme S. borbonicum ou rares comme S. majus associé à différenciation marquée entre l'île Maurice et la Réunion au sein des deux lignées. De plus, il a été mis en évidence des patrons de structure de la diversité génétique différents selon l'île et l'espèce considérée : une structure spécifique dans le genre Sideroxylon de la section Calvaria à Maurice et une structure géographique chez S. cinereum de Maurice et les espèces réunionnaises. À l'échelle de la lignée des Sideroxylon de la section Calvaria, les marqueurs microsatellites nucléaires ont permis d'identifier clairement toutes les espèces avec une forte différenciation entre S. majus de la Réunion et l'ensemble des espèces mauriciennes. À Maurice, la différenciation est plus marquée entre S. grandiflorum et les deux autres espèces S. sessiliflorum et S. boutonianum avec des évènements d'hybridation entre ces deux dernières espèces possibles. À l'échelle de S. majus de la Réunion, une très forte diversité génétique structurée en trois groupes génétiques a été mise en évidence à l'aide de marqueurs microsatellites nucléaires. La comparaison de la diversité génétique des cohortes des adultes et des juvéniles ne présente pas d’érosion génétique. Des méthodes de conservation sont proposées en fonction de ces caractéristiques génétiques pour S. majus, espèce rare en danger. L'ensemble des résultats obtenus chez les Sapotacées endémiques des Mascareignes montre que la diversité génétique est structurée à différentes échelles spatiales, selon les espèces et les lignées évolutives considérées, soulignant la nécessité d'études complémentaires afin de déterminer les processus qui sont à l'origine des patrons détectés. / Madagascar is among the top five priorities "hotspots" for global biodiversity conservation. In Madagascar, melliferous flora is diverse and abundant; the endemic honey bee Apis melliferaunicolor inhabits all areas regardless of the climatic conditions and topography. As other islands, Madagascar is fragile and susceptible to invasions of alien species. In 2010, Varroa destructor has been reported parasitizing A. m. unicolor. The ectoparasite is not only a serious threat to beekeeping in Madagascar but it may also alter ecosystems balance.The objectives of this thesis were i) to study the genetic diversity and population structure of both A. m. unicolor and V. destructor in Madagascar, ii) to estimate the impact of V. destructor on honey bee colonies, and iii) to investigate the hygienic behaviour of honey beeOur results confirm that all honey bees collected in Madagascar belonged to the African evolutionary lineage and more than 99% were identified as A. m. unicolor. Despite its lownuclear genetic diversity, two genetic clusters have been detected, corresponding to geographic regions.In Madagascar, only one genetic strain of V. destructor was detected, the Korean haplotype (K1-1) which is the most widespread lineage in the world and the one present in Africa. Genetic studies showed a higher proportion of homozygous genotype (69.5%) and also a high number of MLG (Multi- Locus Genotypes) in the High Lands compared to the East coast. The presence of particular MLG on the High Land reinforces the assumption of its introduction into the capital. The spread of V. destructor in Madagascar is relatively slow in comparison with those observed in African countries. Its presence remains confined to the High Land and the East coast. The impact of the parasite on A. m. unicolor was severe; with about 60% of colony losses in a year reported in 2012. Nevertheless, this is less than observed in Europe, where many more colonies died at the early stage of infestation.Based on the percentage of cleaned cells observed 6 hour after pin killing the brood, the efficiency of A. m. unicolor colonies to detect and uncap cells was comparable to those of Africanised hygienic honey bees and was much higher than those of European honey bees. In Madagascar, the detection of highly hygienic colonies of A. m. unicolor is a great opportunity to develop a programme of selection of tolerant honey bee strains.

Doctor of Philosophy / Department of Biology / Carolyn J. Ferguson / Morus L. (Moraceae) is a temperate and subtropical genus of ten to 15 species distributed in Asia, Africa, Europe, North, Central and South America. Despite its broad distribution and economic importance, it has received little attention from systematic botanists. Two species of this genus, the native M. rubra and the exotic M. alba, co-occur in eastern North America including the Flint Hills region of the Central Plains. In my dissertation research, I have conducted both species level and population level studies to obtain insights into the diversification of Morus. At the species level, my objectives were to re-evaluate the taxonomy and reconstruct the phylogeny of Morus. Based on herbarium and literature study as well as some field study, I recognize 13 species: eight species occurring in Asia, one in Africa and four in the New World. I used sequence data from the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA and the trnL-trnF region of the chloroplast DNA to reconstruct the evolutionary history of Morus. The phylogenies were congruent and indicate a) a monophyletic core group of Morus with two well-supported geographical clades (one containing Asian taxa and one of New World taxa); and b) that Morus, as currently circumscribed, is non-monophyletic. At the population level, I studied sex expression pattern variation between the Morus native-exotic pair in the Flint Hills region, and assessed hybridization between these species at Konza Prairie Biological Station (KPBS). Both species are subdioecious, and Flint Hills populations exhibit significantly male-biased sex ratios, with sex expression being size independent. Approximately 10% of individuals of each species changed sex annually. In the population study at KPBS, I applied randomly amplified polymorphic DNA (RAPD) markers and microsatellites. The Morus species were moderately ([Theta]II = 0.079; RAPD data) to highly differentiated genetically (F[subscript]ST = 0.233; microsatellite data). Analysis of genetic structure suggested interspecific gene flow and indicated the presence of later generation hybrids. The presence of the exotic congener may affect the existence and genetic integrity of the native species. Overall, these studies contribute to our understanding of diversity in this interesting plant study system.

Doctor of Philosophy / Genetics Interdepartmental Program - Biology / Susan J. Brown / Understanding evolutionary processes that structure genetic variation associated with lineage diversification and speciation is a central problem. Shifts in host plant use by insect herbivores and subsequent divergence in mating signals can lead to sexual isolation, especially when selection for specialization on different hosts restricts gene flow among populations. The grasshopper Hesperotettix viridis (Thomas) is an oligophagous grasshopper feeding on plants primarily in the host plant genera Gutierrezia and Solidago in Kansas. I used mitochondrial and microsatellite genetic markers to evaluate the diversification pattern and underlying evolutionary mechanisms of two putative host races of H. viridis. I also quantified host preferences, the degree of sexual isolation among putative host races and divergence in cuticular attributes to identify the nature and origins of initial barriers that isolated populations in the formative stages of divergence. mtDNA data revealed a star-shaped phylogeny, suggesting isolation in a single refugium ~110,000 years ago based on a molecular clock, followed by rapid population expansion. Microsatellite data reveal significant host-based genetic differentiation and structuring in H. viridis populations in Kansas, including a microsatellite locus under strong divergent selection. Neutral microsatellite loci did not reveal a differentiation pattern specific to host plant use. Significant host-based preferences by individuals that fed on two host plant groups were detected in host paired-feeding preference studies. No-choice mate selection experiments revealed preferences for individuals collected from the same host species independent of location with little mating observed between individuals from different host species. Significant differentiation in color and cuticular composition among different host plant races within the study area was also detected. Correlations between host choice, mate choice and phenotypic divergence were observed and this host associated divergence appears to have a genetic basis. Based on the results of this study, I conclude that divergent selection for host plant use underlies observed sexual isolation among populations in this species. Hesperotettix viridis populations in Kansas that fed on Solidago and Gutierrezia species represent two incipient host races, early stages of diversification that could lead to speciation in insect herbivores.

Στην παρούσα εργασία αξιολογήθηκε η χρήση των μικροδορυφορικών δεικτών για τη μελέτη της γενετικής δομής και των φυλογενετικών σχέσεων των φυσικών πληθυσμών της Atherina boyeri που προέρχονταν τόσο από θαλάσσιες όσο και λιμναίες/λιμνοθαλάσσιες περιοχές της Ελλάδας. Προηγούμενες μελέτες βασιζόμενες κυρίως σε μιτοχονδριακούς και RAPD δείκτες έχουν υποδείξει την πιθανή παρουσία τριών ομάδων πληθυσμών στην Atherina boyeri με τόσο υψηλές γενετικές αποστάσεις μεταξύ τους που θα μπορούσαν να τις καθιστούν ακόμα και διαφορετικά είδη. Οι ομάδες αυτές είναι: οι θαλάσσιοι πληθυσμοί τύπου Ι (μη εστιγμένοι),οι θαλάσσιοι πληθυσμοί τύπου ΙΙ (εστιγμένοι) και οι λιμναίοι/λιμνοθαλάσσιοι πληθυσμοί. Η ανάλυση στην παρούσα εργασία πραγματοποιήθηκε με χρήση 11 μικροδορυφορικών δεικτών που σχεδιάστηκαν από τους Milana et al. (2009). Οι μικροδορυφορικοί δείκτες θεωρούνται εξαιρετικό εργαλείο μελέτης των φυλογενετικών σχέσεων μεταξύ πρόσφατα διαχωρισμένων ειδών δεδομένου ότι είναι άφθονοι, πυρηνικοί, διάσπαρτοι στο γονιδίωμα, υψηλά πολυμορφικοί και ταχέως εξελισσόμενοι. Τα αποτελέσματα έδειξαν πολύ υψηλό βαθμό πολυμορφισμού στους υπό ανάλυση πληθυσμούς και μεγάλη γενετική διαφοροποίηση μεταξύ των ελληνικών πληθυσμών του είδους όπως αυτή εκφράζεται από τις διαφορές στις συχνότητες των αλληλομόρφων των μικροδορυφορικών δεικτών. Φαίνεται επίσης να επιβεβαιώνεται η διάκριση μεταξύ των δυο θαλάσσιων τύπων της Atherina boyeri, ωστόσο οι λιμναίοι/λιμνοθαλάσσιοι πληθυσμοί παρουσιάζουν τόσο διαφορετικό γενετικό πρότυπο που θεωρείται εξαιρετικά δύσκολο να συνιστούν μια ενιαία ομάδα πληθυσμών. Οι δείκτες αυτοί δεν ήταν δυνατό να χρησιμοποιηθούν στην ανάλυση όλων των διαθέσιμων πληθυσμών, κυρίως λόγω της παρουσίας μη ενισχυόμενων (null) αλληλομόρφων, καθώς επίσης και πολλαπλών ή/και ασθενών ζωνών, γεγονός που επίσης υποδεικνύει την ύπαρξη μεγάλων γενετικών διαφοροποιήσεων, που πιθανώς ξεπερνούν τα όρια του είδους. Προκείμενου να ξεπεραστούν τα ανωτέρω προβλήματα απαιτείται η βελτιστοποίησή τους ανά ομάδα πληθυσμών, μέσω α) αλλαγών στις συνθήκες των PCR αντιδράσεων και β) κλωνοποίησης και αλληλούχισης των δεικτών αυτών από άτομα των πληθυσμών στα οποία ήταν λειτουργικοί, ώστε να επιτευχθεί ο σχεδιασμός νέων ζευγών εκκινητών, ειδικών για επιμέρους ομάδες πληθυσμών. / The present study aims at the measure of the genetic differentiation and the resolution of the phylogenetic relationships among A.boyeri populations originating from lakes/lagoons and marine sites of Greece. Previously studies based on RAPD and mitochondrial markers suggest the existence of three forms of populations of A.boyeri which could represent three different species. These three types are: marine type I, which includes almost all marine populations (non-punctuated), excluding specimens collected from Preveza, Evoia and Kos, which form the marine type II (punctuated) and the “lagoon” type which consists of all the lagoon/lake populations. In the present study, eleven microsatellite markers designed by Milana et al. (2009), were used. Microsatellite markers are supposed to be great tools in phylogenetic studies among recently separated species because they are abundant, nuclear, dispersed around the genome, highly polymorphic and rapidly evolving. Our results showed very high degree of polymorphism in the analyzed populations and extended genetic differentiation among Greek populations of the species as expressed by differences in allele frequencies of the microsatellite markers. They also seems to confirm the distinction between the two marine types of A.boyeri, but the lagoon/lake populations present different allele paterns, pointing to the possible existence of differentiated groups among them. Some of the markers could not be used in the analysis of all the available populations. This is mainly attributed to the presence of null alleles for some of the populations and to scoring difficulties raising from the presence of multiple and/or weak amplicons. This also indicates the existence of great genetic variations, which possibly exceed species limit. To overcome the above difficulties, optimization per marker is required, including a) optimization of PCR conditions and b) cloning and sequencing of these markers from individuals of the population that were functional to achieve the design of new prime pairs, specific for each group of populations .

Hieracium lepidulum is an invasive weed in New Zealand. It colonises a wide range of habitats including pine plantations, scrubland, native Nothofagus forest, and mid-altitude to alpine tussock grassland, where it is competing with indigenous species. Understanding the breeding systems and population genetic structure of H. lepidulum is important for biocontrol, and aids in the understanding of evolutionary colonisation processes. H. lepidulum is a triploid, diplosporous, obligate apomict. This type of reproduction through clonal seed does not involve meiosis or fertilisation, and theoretically populations should contain very low levels of genetic variation, the only source being somatic mutation. Common garden experiments and microsatellite markers were used to determine the population genetic structure of H. lepidulum populations in the Craigieburn Range, Canterbury. Both experiments revealed that populations, sampled from three replicate altitudes within three geographically-separated locations, contained no genetic variation; individuals all possessed the same microsatellite genotype. These results strongly suggest that the Craigieburn Range H. lepidulum individuals reproduce solely by apomixis and populations belong to the same clonal lineage. Populations were also examined for their response to two abiotic environmental ‘stresses’, drought and shade. H. lepidulum populations’ exhibited high drought tolerance, yet appeared to be shade-intolerant. Low levels of reproduction in light-limiting habitats will prevent the invasion of H. lepidulum into closed-canopy forest habitats. H. lepidulum appears to have overcome the reduction in fitness associated with apomictic reproduction by phenotypic plasticity, fixed heterozygosity and polyploidy – all associated with increased vigour, fitness, and the ability to occupy broader ecological niches. This study’s results are hopeful for the development of biocontrol programs involving genotype-specific pathogens but suggest that grazing management may not succeed. The data will be useful for future comparisons of genetic structure during the course of H. lepidulum invasions and will contribute to the management of this invasive weed.

The Leptonycteris yerbabuenae is found in southern Arizona, Mexico, Guatemala, and El Salvador. Some females are migratory, mating in southern Mexico, and migrating to maternity roosts in northern Mexico and southern Arizona to give birth. Twelve microsatellite loci markers and the Mitochondrial DNA Control Region (CR) were amplified to examine population structure and phylogenetic relationships among roosts. Twelve polymorphic microsatellite loci were isolated from L. yerbabuenae. A total of sixteen localities in AZ and Mexico were sampled. The mtDNA CR fragment resulted in 102 haplotypes. The phylogenetic analyses resulted in two clades, but no observable geographic structuring. The average FST value across all loci and all sampled localities was 0.022. Program STRUCTURE analyses indicate one population (K=1) throughout the sampling area. These results suggest movement between maternity colonies and transient roosts in Arizona, Sonora, and Chamela, Management recommendations based on these results would be to manage as a single population.

The American beaver, the largest rodent of North America, is distributed in ponds, lakes, and streams from Alaska to northern Mexico. This semi-aquatic mammal is considered an ecosystem engineer because beavers modify the landscape by cutting trees and by creating dams and ponds that have important effects on the aquatic community structure, providing habitat for aquatic invertebrates, fish, and birds. The American beaver has played an important socioeconomic role in the history of North America due to beavers' fur value, which caused the near extirpation of this mammal at the beginning of the 1900s due to overharvest by early Europeans. Because of the highly specific habitat requirements of beavers, this mammal also suffers the effects of habitat loss in some areas where riparian ecosystems are now scarce. My objectives in this study were to assess how climatic and geological events affected the current distribution of the American beaver in North America, and how the management actions to restore and control beaver populations have affected the genetic structure and conservation of beaver populations. Specifically, I addressed four aspects of the management and conservation genetics of the beaver: 1) a literature review of the management of beavers in the past 100 years; 2) the development of novel microsatellite DNA markers to address the population genetic structure aspects of the study; 3) the use of these microsatellite DNA markers to assess genetic diversity of current populations of beavers and to detect past population bottlenecks; and 4) the use of two mitochondrial DNA genes to resolve the current phylogeography of the American beaver in order to better understand how historical factors have affected the beaver's current distribution and genetic structure in North America. The results from this study provide information of the effects that management actions and climatic events can have on the genetic structure of beavers. This information can be used by wildlife biologists, and land managers, to develop future strategies for management and conservation of the American beaver.

Thesis (MMedSc)-University of KwaZulu-Natal, Durban, 2006.

Improving our understanding of the factors that shape the demography of populations now requires that we consider no event in isolation, and instead express current performance as a product of previous events and processes. Patterns of site choice and dispersal likely underpin a large proportion of the variation in reproductive success among individuals, but the consequences of dispersal decisions may only become apparent many months later at a separate stage of the annual cycle Only by studying the interactions among seasons can we determine how differences in annual routine translate into asymmetries in fitness, and subsequently apply this understanding to processes occurring at the population level. This thesis begins with a review of the phenomena known as carry-over effects (COEs; Chapter 2), where I find evidence to support their occurrence in a multitude of taxa and identify previously unconsidered drivers of carry-over effects that could potentially explain their widespread nature. The remainder of this thesis comprises empirical work using light-bellied Brent geese (Branta bernicla hrota) as a model system to study these processes. In Chapter 3 I show evidence of a COE in Brent geese mediated by body condition, but in addition demonstrate how the strength of this effect is moderated by downstream climatic conditions operating in a density-independent fashion. Chapter 4 describes the development of novel polymorphic microsatellite loci to be used in population genetic and parentage studies. In Chapter 5 I show that light-bellied Brent geese are highly site faithful and that this fidelity has a cultural basis. Finally in Chapter 6 I characterize patterns of mate choice, and investigate potential consequences of this pattern in light of the observed site fidelity, in terms of risk of inbreeding. Collectively my results demonstrate the utility of combining long-term datasets with genetic pedigrees to investigate patterns of dispersal in a migratory species. Moreover they highlight the necessity to study individual performance in the context of the entire annual cycle in order to fully characterize the nature and strength of fitness determinants operating at multiple stages in a migratory species.