Two eucalypt clines were examined using morphological, ecophysiological and molecular analyses. The species complexes examined were an ironbark complex (Eucalyptus melanophloia x E. whitei) and a box complex (E. brownii x E. populnea). Both of these complexes demonstrate continuous morphological variation across their clines. The origin of these morphological clines has previously been interpreted as the product of secondary contact between allopatric species. In this study, an analysis of morphological variation across the clines did not identify an increase in trait variance in the intermediate populations, which suggests that previous theories concerning the origin of these clines may not be valid. Genetic structuring in nuclear and chloroplast DNA was examined across the clines to investigate whether the morphological clines were the product of secondary contact between two independent evolutionary lineages, or whether the clines represent a single evolutionary lineage that has undergone primary differentiation. The microsatellite analyses indicated that there was little genetic structuring across either cline, and that there were only low levels of population differentiation. The lack of hierarchical structuring in the distribution of nuclear genetic variation suggests that these clines are unlikely to be the product of recent gene flow between two formerly allopatric species/populations. A nested clade analysis of the JLA+ region of the cpDNA provides additional evidence to reject the null hypothesis that the morphospecies classifications represent distinct evolutionary lineages. Instead the analyses indicate that each cline represents a single cohesion species and a single evolutionary lineage. The phylogeographic distribution of cpDNA haplotypes is likely to have resulted from restricted seed mediated gene flow with isolation by distance. A more cogent explanation for the clines, based on the genetic data, is that they have arisen through the process of continuous morphological diversification that has been promoted by a directional selection gradient. Drought experiments were conducted in the glasshouse to investigate whether differences in physiological performance under water stress helps to explain the maintenance of the ironbark cline. Under increasing water stress, the morphotypes showed differences in their ability to maintain water status and photosynthetic rates, yet there was no obvious pattern to these differences across the cline. Physiological differences are therefore inadequate to explain the maintenance of the ironbark cline and highlight the compensatory role that morphological variation may play in alleviating water stress. The value of adopting the cohesion species concept and a hypothesis-testing framework to assess species status is demonstrated in this study. This framework provided a statistical approach to distinguish independent evolutionary lineages from interspecific populations and provides evidence to refute the current species status of the species complexes studied. Eucalypt classification is predominantly based on morphology, which results in taxonomic classification that may not reflect genealogical relationships. This is due to the disparity between morphological and phylogenetic relationships. I therefore suggest that current presumptions regarding the prevalence and importance of hybridisation within the genus may reflect taxonomic classification. An accurate assessment of the prevalence and importance of hybridisation requires species classification to be based on genealogical relationships.

Orientador: Louis Bernard Klaczko / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-08T02:56:34Z (GMT). No. of bitstreams: 1 Silva_LauraHelenaHafnerda_M.pdf: 2141945 bytes, checksum: 17c00d0d744de62b04cc274305caedb5 (MD5) Previous issue date: 2006 / Resumo: O presente trabalho tem como objetivo caracterizar a variação do tamanho e forma das asas de populações de Drosophila melanogaster em três pontos ao longo de uma grande amplitude latitudinal na costa brasileira. O trabalho foi feito a partir de coletas realizadas no Recife, Rio de Janeiro e Porto Alegre, e os seguintes aspectos foram abordados: 1) variação geográfica; 2) variação temporal; 3) herdabilidade; e 4) a influência de inversões cromossômicas. Para este fim, o método da elipse foi aplicado a imagens digitalizadas das asas, e foram analisados: o tamanho das asas, sua forma e as posições dos pontos de junção e das extremidades das veias (caracterizadas por suas coordenadas angulares é radiais, essas padronizadas pelo tamanho da asa). Os resultados obtidos mostraram que a variação de tamanho em D. melanogaster no Brasil segue a tendência mundial de formação de clines latitudinais, com indiv.íduos maiores sendo encontrados a latitudes também maiores. No entanto, a herdabilidade e a variação temporal entre múltiplas coletas realizadas no Recife e no Rio de Janeiro não apresentou um padrão regular nítido. O único efeito consistente e significativo de inversões cromossômicas que pudemos observar foi o de In(3R)Payne sobre o tamanho corporal, sendo também consistente com achados prévios descritos na literatura. Entretanto, não detectamos efeito significativo de interação genótipo-ambiente, quer entre coletas, quer entre localidades / Abstract: The present work aims to characterize the variation of wing size and shape in Drosophila melanogaster populations from three localities distributed along a wide latitudinal range of the Brazilian coast. The work was performed based on collections made in the cities of Recife, Rio de Janeiro and Porto Alegre. The aspects studied were: 1) geographic variation; 2) temporal variation; 3) heritability; and 4) the influence of chromosomal inversions. To this end, the ellipse method was applied to digitized images of the wings. We analyzed wing size, wing shape and the position of vein junctions and extremities (characterized by their angular and radial coordinates, the latter being standardized by wing size). The results obtained showed that size variatiorn in Brazilian D. melanogaster follows the worldwide tendency toward the formation of latitudinal clines, with larger individuaJs being found at higher latitudes. However, the heritability and temporal variation among multiple collections performed in Recife and Rio de Janeiro did not show a clear regular pattern. The only consistent and significant effect of chromosomal inversions that we could observe was that of In(3R)Payne on body size, which is also consistent with previous findings reported in the literature. However, we did not detect a significant effect of genotype-environment interactions, neither among collections, nor among localities / Mestrado / Genetica Animal e Evolução / Mestre em Genética e Biologia Molecular

Investigating secondary contact of historically isolated lineages can provide insight into how selection and drift influence genomic divergence and admixture. Here, we studied the genomic landscape of divergence and introgression following secondary contact between lineages of the Western Diamondback Rattlesnake (Crotalus atrox) to determine whether genomic regions under selection in allopatry also contribute to reproductive isolation during introgression. We used thousands of nuclear loci to study genomic differentiation between two lineages that have experienced recent secondary contact following isolation, and incorporated sampling from a zone of secondary contact to identify loci that are resistant to gene flow in hybrids. Comparisons of patterns of divergence and introgression revealed a positive relationship between allelic differentiation and resistance to introgression across the genome, and greater-than-expected overlap between genes linked to lineage-specific divergence and loci that resist introgression. Genes linked to putatively selected markers were related to prominent aspects of rattlesnake biology that differ between populations of Western Diamondback rattlesnakes (i.e., venom and reproductive phenotypes). We also found evidence for selection against introgression of genes that may contribute to cytonuclear incompatibility, consistent with previously observed biased patterns of nuclear and mitochondrial alleles suggestive of partial reproductive isolation due to cytonuclear incompatibilities. Our results provide a genome-scale perspective on the relationships between divergence and introgression in secondary contact that is relevant for understanding the roles of selection in maintaining partial isolation of lineages, causing admixing lineages to not completely homogenize.

La dispersion est un processus clef dans la dynamique et l'évolution des populations naturelles. En plus de son rôle primordial dans les processus de colonisation, la dispersion influence également les processus d'adaptation des organismes. Chez les pathogènes, une meilleure compréhension des processus de dispersion apparaît de ce fait être un enjeu majeur pour mieux les contrôler. Durant cette thèse, nous avons étudié les processus de dispersion et quantifié les flux de gènes qui en découlent chez le champignon parasite du bananier Mycosphaerella fijiensis. Cette étude a été réalisée à l'échelle locale d'un bassin de production du Cameroun (la région dite du Moungo) et nous avons combiné plusieurs approches complémentaires considérant différentes échelles spatio-temporelles. Dans un premier temps, nous avons décrit, à l'aide de marqueurs génétiques neutres, la structuration spatiale des populations de M. fijiensis dans la région du Moungo qui présente différentes barrières potentielles à la dispersion. Nous n'avons décelé aucun effet du paysage ni de la distance géographique sur la structuration génétique. Cependant, une rupture spatiale dans les fréquences alléliques, vraisemblablement de nature historique a été mise en évidence. Ces résultats suggèrent l'existence de grandes populations de M. fijiensis s'écartant de l'équilibre mutation-dérive. Dans un second temps, nous avons utilisé la théorie des clines génétiques pour étudier les forces à l'origine de la mise en en place et de l'évolution de gradients spatiaux de fréquences alléliques. En particulier, l'analyse de la variation spatio-temporelle de la discontinuité génétique précédemment détectée par un modèle de clines neutres nous a permis d'estimer l'intensité des flux géniques ( =1175 m/génération). Finalement, nous avons mesuré la distribution des distances de dispersion des deux types de spores produites par M. fijiensis à partir d'une source d'inoculum primaire. Cette expérimentation nous a permis de confirmer que les ascospores participent à une dispersion à grande distance alors que les conidies sont impliquées dans une dispersion à très courte distance. Nous avons estimé une distance moyenne de dispersion de 3,12 et de 283 mètres/génération respectivement pour les conidies et les ascospores et montré que le noyau de dispersion des ascospores est caractérisé par une queue lourde. Cette thèse a permis de préciser comment M. fijiensis se disperse et les estimations réalisées pourront être intégrées dans des modèles théoriques afin de mieux comprendre l'évolution des résistances aux fongicides et de définir des stratégies durables d'utilisation raisonnée des traitements chimiques. / Dispersal is a key process for both the dynamics and evolution of natural populations. In addition to being crucial for colonization, dispersal also influences the processes occurring during adaptation. For pathogens, a better understanding of dispersal processes may improve our capacity to control the diseases that they cause. In this thesis, we studied dispersal processes and quantified gene flow in the banana plant pathogen Mycosphaerella fijiensis at the local scale of a production area in South-West Cameroon (named Moungo). For this purpose, several approaches differing in the spatio-temporal scale to which they refer were combined. First, neutral markers were used to describe the spatial genetic structure of this pathogen in the Moungo area, which includes several potential ecological barriers to dispersal. No effects on genetic structure of landscape elements or geographical distance were found. However, we detected a spatial break in allelic frequencies that appeared to be explained by an historical event. This result suggests the existence of large M. fijiensis populations out of the mutation-migration-drift genetic equilibrium. Second, genetic cline theory was applied to study the evolutionary forces implicated in the installation and evolution of spatial gradients in allelic frequencies. More specifically, we analysed the spatio-temporal variation of the genetic discontinuity previously detected through a neutral cline model to estimate the intensity of gene flow in this area ( =1175 m/generation). Lastly, we measured the distribution of dispersal distances of M. fijiensis spores from a primary source of inoculum was. Such an experiment allowed us to confirm that conidia are implicated in short-distance dispersal whereas ascospores are responsible for spread of the disease over longer distances. The estimated mean dispersal distance travelled by spores was 3.12 and 283 metres/generation for conidia and ascospores, respectively, and the ascospore dispersal kernel was shown to be fat-tailed. This thesis adds to global knowledge of M. fijiensis dispersal and the measures of dispersal estimated in this work will be useful in parameterizing models aimed at a better understanding of the spatial patterns of fungicide resistance evolution under different management strategies.

<p>For ectotherms living in seasonal environments, time available for development and growth is often constrained by the length of the growth season. Declining season length towards higher latitudes often select for latitudinal clines in development and growth rates, exhibiting increasing growth and developmental rates towards the north. However, the physiological and ecological factors enabling these clines are poorly understood.</p><p>Our study system included eight populations of <i>Rana temporaria</i> along a 1500 km latitudinal gradient. We found increased growth rates in populations at higher latitudes to be the result of higher growth efficiency, partly due to increased relative gut length. Populations with higher growth rates also exhibited lower standard metabolic rates, implying that fast-growing individuals are able to achieve high growth rates by spending less energy on maintenance metabolism under low activity conditions.</p><p>Predator densities, and antipredatory defenses in prey, are assumed to decrease towards higher latitudes. While all study populations responded to predator presence by decreasing activity and foraging, high latitude populations maintained higher activity levels in the presence of the predator. In trials with a free-ranging predator, high latitude tadpoles experienced higher mortality than those from the low latitudes. The higher activity level in the northern populations increases mortality under predation risk, but is probably needed to maintain high growth and development rates.</p><p>When competing over resources, tadpoles from the low latitude population were inferior competitors, as indicated by their longer development time when raised together with high latitude tadpoles. We found no effect of latitude on size-corrected burst speed. The general effect of predator presence on burst speed depended on food availability, with well fed tadpoles being faster in the absence, and food restricted being faster in the presence of a predator.</p>

For ectotherms living in seasonal environments, time available for development and growth is often constrained by the length of the growth season. Declining season length towards higher latitudes often select for latitudinal clines in development and growth rates, exhibiting increasing growth and developmental rates towards the north. However, the physiological and ecological factors enabling these clines are poorly understood. Our study system included eight populations of Rana temporaria along a 1500 km latitudinal gradient. We found increased growth rates in populations at higher latitudes to be the result of higher growth efficiency, partly due to increased relative gut length. Populations with higher growth rates also exhibited lower standard metabolic rates, implying that fast-growing individuals are able to achieve high growth rates by spending less energy on maintenance metabolism under low activity conditions. Predator densities, and antipredatory defenses in prey, are assumed to decrease towards higher latitudes. While all study populations responded to predator presence by decreasing activity and foraging, high latitude populations maintained higher activity levels in the presence of the predator. In trials with a free-ranging predator, high latitude tadpoles experienced higher mortality than those from the low latitudes. The higher activity level in the northern populations increases mortality under predation risk, but is probably needed to maintain high growth and development rates. When competing over resources, tadpoles from the low latitude population were inferior competitors, as indicated by their longer development time when raised together with high latitude tadpoles. We found no effect of latitude on size-corrected burst speed. The general effect of predator presence on burst speed depended on food availability, with well fed tadpoles being faster in the absence, and food restricted being faster in the presence of a predator.

Cette thèse s’inscrit dans le contexte de la biologie de l’invasion de la chrysomèle des racines du maïs, Diabrotica virgifera virgifera (Dvv), en Europe. Les introductions multiples de cette peste sur le vieux continent à partir des années 1990 et en provenance des États-Unis ont conduit à la formation de plusieurs foyers envahissants dont deux principaux, différenciés génétiquement et situés en Italie du Nord-Ouest (Italie NO) et en Europe Centrale et du Sud-Est (Europe CSE). Ces deux foyers sont entrés en contact en 2008, en Italie du Nord, dans la région de la Vénétie. L’objectif principal de ces trois années de recherche était de détecter, d’étudier et de documenter un cas précis d’hybridation au cours d’une invasion biologique. Dans un premier temps, j'ai montré que la zone de contact détectée en Vénétie résultait bien en une zone hybride. Pour cela plusieurs types d’analyses de génétique des populations ont été réalisés à l’aide de marqueurs micro-satellites. Dans un second temps, j'ai exploité cette zone hybride et utilisé la théorie des clines neutres et le déséquilibre de liaison pour estimer la dispersion (σ) de Dvv en Italie du Nord aux alentours de 20 km.génération−1/2. Enfin j'ai montré l’absence d'impact de l’hybridation au cours de l’invasion européenne de Dvv in natura, en mesurant sur des génotypes hybrides et parentaux, de nombreux traits phénotypiques positivement liés à la fitness des individus. Ainsi, une sélection ou contre sélection des hybrides est à exclure dans ce cas précis d’hybridation et la dynamique de l’invasion de cette peste en Europe ne devrait être affectée en aucune façon. / This thesis deals with the invasion biology of the western corn rootworm, (WCR) in Europe. Multiple introductions of this pest in Europe from the United States and the 90’s, led to the formation of two main invasive outbreaks, genetically differentiated and located in Northwest Italy (NW Italy) and in Central and South-Eastern Europe (CSE Europe). Both outbreaks converged towards each other and came into contact in 2008, in the region of Veneto (Northern Italy). The main objective of these three years of research was to detect study and document a precise case of hybridization during a biological invasion. First of all, I showed that the contact zone detected in Veneto results in a hybrid zone. For that, several types of population genetics analyses were performed using microsatellite markers. In a second time, I exploited this hybrid zone and used the theory of neutral clines and the linkage disequilibrium to estimate dispersal (σ) of WCR in Northern Italy around 20 km.generation-1/2. Finally I showed the absence of impact of hybridization in the european invasion of WCR in natura, by measuring on hybrid and parental genotypes, numerous phenotypic traits positively associated to the fitness of individuals. Thus, a selection or a selection against hybrids is excluded in this particular case of hybridization and the invasion dynamics of WCR in Europe should not be affected in any way.

Plants have spread to almost everywhere in the world. As they disperse, they meet many different environments to which they may be able to adapt. For a plant species to adapt to a new environment, genetic variation is needed. The individuals differ from each other in their genetic composition, which often means differences in phenotypes. Those individuals that manage to reproduce will form the next generation. With different conditions in different environments, it will not be the same phenotypes that reproduce everywhere. In that way, plant species will form into a mosaic of locally adapted populations varying genetically as the species disperses. After the last ice age plants have started to disperse away from the equators. With increasing latitudes come increasing challenges to migrating plants. As plant species disperse northwards along this gradient of varying conditions individuals are selected for cold adaptive traits like flowering time and freezing tolerance, acquired by cold acclimation. In this way, genetic variation from the original populations for these traits becomes sorted out along a latitudinal cline. The aim of this thesis was to understand how selection along a latitudinal gradient has shaped natural variation in cold adaptive traits in plants dispersing northwards, and specifically, to investigate what variation can be observed in phenotypes for these traits and how these traits correlate with genetic variation in genes known to be involved in cold acclimation. In this study significant variation was found in a sample of the model plan Arabidopsis thaliana accessions in cold adaptive traits flowering time and freezing tolerance. A clear latitudinal cline in the cold adaptive traits freezing tolerance for A. thaliana was observed. Analysis of nucleotide polymorphism for the cold responsive ICE1 (inducer of CBF expression 1) transcription factor revealed a haplotype structure with two allelic clades as well as unusually high levels of synonymous polymorphism. Nucleotide polymorphism analysis for the transcription factors CBF1, CBF2 and CBF3 (C-repeat binding factors) that play a key role in regulating the expression of a group of target genes known as the “CBF regulon” showed a distinct geographical haplotype structure. One haplotype was dominant in southern accessions while in the other northern accessions overrepresented. There was a significant effect of CBF haplotype on both freezing tolerance and flowering time even after correcting for latitude. Significant differences in CBF expression levels were found between the different CBF genes as well as between different accessions. Sequence variation at CBF was shown to have a significant effect on expression levels of CBF2. No clear correlations were found between CBF gene expression and freezing tolerance or temperature sensitivity for any of the accessions used in the study. This highlights the complex relationship between sequence variation in candidate genes and gene expression, and the problems associated with unraveling the genetic basis of ecologically important traits.

Western redcedar (Thuja plicata Donn ex D. Don; redcedar), an indeterminate conifer in the Cupressaceae family, is vulnerable to maladaptation in the face of climate change. Assisted gene flow is one mitigation strategy and involves human-mediated migration of populations, where the projected climate of the area of deployment matches the source climate of the population. Despite the overall projections of warmer temperatures globally, in British Columbia (B.C.), the risk of seasonal frost events will remain and therefore the potential for cold damage and mortality of redcedar exists if the newly migrated populations cannot withstand these freezing events. Knowledge of redcedar's ability to withstand freezing temperatures (cold hardiness) is therefore crucial. Redcedar, like many Cupressaceae species, produces and accumulates the purple-coloured carotenoid rhodoxanthin during the winter. This was hypothesized to be correlated with cold hardiness. Assessment of variation in overall, fall and spring cold hardiness and associated rhodoxanthin concentrations were done through repeated, seasonal freeze testing of clonal grafts originating from across the range of redcedar, and seedling progeny from a subset of these clones. Cold damage was quantified using electrolyte leakage and rhodoxanthin concentrations were quantified using high performance liquid chromatography. Cold hardiness and rhodoxanthin were individually modelled using univariate and bivariate mixed effect models with clone/family as a random effect. Model outputs were compared to climatic variables associated with clonal origin to test for climatic relationships. This study found genetic variation in cold hardiness of redcedar with weak climatic clines. This indicates that assisted gene flow of redcedar should be done on a case-by-case basis, with no need for a climatic threshold. Overall heritability of cold hardiness was 0.17 ± 0.03. Novel findings included the positive genetic correlation between fall and spring cold hardiness (0.55 ± 0.33); lack of reciprocal or parental effect for overall cold hardiness; and weak climatic relationships between cold hardiness and predominantly temperature, with the strongest correlation between number of frost-free days in January (0.38, p < 0.01) in the location of origin and cold hardiness. All findings related to rhodoxanthin were novel. Rhodoxanthin varied with family/provenance and season with heritabilities of 0.30 ± 0.09 in fall, 0.42 ± 0.09 in winter and 0.28 ± 0.09 in spring. Winter and spring rhodoxanthin concentrations were phenotypically correlated (0.50, p < 0.01) and genetically correlated (0.76 ± 0.14). Surprisingly, rhodoxanthin was not detected in clonal grafts of redcedar in any season. Results also indicate that rhodoxanthin cannot be used to estimate cold hardiness. The absence of rhodoxanthin in the clonal grafts compared to the seedlings suggests that plant age impacts rhodoxanthin accumulation. / Graduate / 2021-12-14

<p>The main aim of this work was to identify local adaptation processes in amphibian populations, thereby improving the general understanding of genetics and mechanisms behind the evolution and maintenance of biological diversity. Phenotypic and genetic variation in life-history traits was studied within and between populations common frog (<i>Rana temporaria</i>) populations along a 1600 km transect from southern Sweden to northern Finland.</p><p>Embryonic and larval development and growth was investigated both under field and laboratory conditions. The results suggest ample genetic diversity in larval life-history traits among Fennoscandian common frog populations. Larval developmental rate along the gradient has evolved a countergradient variation pattern of genotypes and phenotypes as indicated by the positive relationship between developmental rate and latitude under laboratory conditions and the lack of such a relationship in the field. The data suggest that this pattern has evolved because of time constraints due to decreasing length of growth season with latitude. Neither field-caught adults nor laboratory raised larvae displayed a linear latitudinal size cline as expected from the so called Bergmanns rule. Rather, size increased towards the mid-latitude populations and decreased thereafter, indicating that body size is a product of direct environmental induction or a trade-off with other life-history characters. Age and size at hatching showed no consistent latitudinal pattern, indicating that the embryonic stage is not as time constrained as the larval stage.</p><p>A large part of the variation in age and size at metamorphosis among populations was due to additive genetic effects. However, small, but significant maternal effects, mostly due to variation in egg size and non-additive genetic effects also contributed to among population variation. A comparison of divergence in presumably neutral molecular genetic markers (F_ST) and quantitative characters (Q_ST) revealed that although both estimates of divergence were relatively high, estimates of Q_ST was generally higher than those of F_ST, indicating that the genetic variation observed in larval traits is primarily a result of natural selection rather than genetic drift. Hence, our results reinforce the conclusion that intraspecific genetic heterogeneity in the young northern European ecosystems may be more widespread than previously anticipated</p>