Differences in water dynamics between deciduous aspen (Populus tremuloides) and co-occurring evergreen conifer species in the Northern Rocky Mountains result from complex physical and biological interactions. A comprehensive evaluation of individual water transfer mechanisms was used to elucidate the relative importance of several components of the hydro logic cycles of aspen and conifer, and determine which water transfer mechanisms have potential to cause differences in net water yield. Adjacent aspen and conifer stands were monitored to determine snow accumulation and ablation (snow survey), soil moisture recharge (capacitance probes), snowpack sublimation (sublimation pan), transpiration period (thermal dissipation probes), and evapotranspiration (soil water content). Snow accumulation was 34 and 44% higher in aspen during springs of 2005 and 2006, respectively. Ablation rates in aspen (9.58 mm day-1 ) were nearly double that of conifer (4.9 mm day-1). When changes in soil moisture (due to over winter snowmelt) were combined with snow accumulation in 2006, aspen had greater potential (42-83%) for runoff and groundwater recharge. Snowpack sublimation during the ablation period was not different between open, aspen, and conifer sites and comprised -1). Summertime ET rate was higher in an aspen stand (3.6 mm day-1) than in an adjacent conifer stand (2.7 mm day-1) amounting to ~126 mm more water lost over the growing season, but largely reflected post-ablation differences in stored soil water. The net effects of these water transfer processes could result in more watershed water yield from aspen than conifer forests. However, the difference in water yield between these two forests will largely depend on the fate of snow lost from the conifer canopy. Snow intercepted by conifer branches can be removed by the processes of sublimation (reduces water yield) and redistribution (does not affect water yield). Future studies should focus on partitioning the ratio of sublimation to redistribution to predict hydro logic response of vegetation conversions for water yield augmentation in snow-dominated watersheds.

Laboratory and field feeding tests with Leptoglossus occidentalis Heidemann proved that both immature and mature seed bugs can use cones and foliage of whitebark pine, Pinus albicaulis Engelmann, as a food source for 1- to 2-week periods. Damage to unprotected whitebark pine cones by seed bugs ranged from 0.3 to 2.1 % of seeds per cone, and for bagged cones averaged 0.7% of seeds per cone. Total insect damage ranged from 0.4 to 7.2% of seeds per cone. A seed chalcid, Megastigmus sp., was documented for the first time on whitebark pine and damaged 4.7% of examined seeds at one site. Four out of five upper elevation subsites had an average of 24.9% fewer filled seeds per cone than lower elevation subsites. Within-site elevation differences had no significant effect on cone length, number of seeds per cone, percentage of potential seeds per cone, or percentages of seed bug and insect-damaged seeds per cone. The larch cone fly Strobilomyia macalpinei Michelsen was found in cones of alpine larch, Larix lyallii Parl., in the Bitterroot Range of Montana. This is the first record of this species in the United States and the first since its description in 1988. Ninety-four percent of a sample of alpine larch cones were damaged by cone fly larvae, and 64% contained larvae or puparia. Colored traps did not succeed in trapping adult cone flies in an alpine larch stand with no cone crop.

A structure and a function of a monoculture woodland is diferent from the natural woodland condition. This is an influence of a herb layer diversity. The change of the herb layer are mainly distinguishable in the case of tree coniferous monoculture. They are the poorest at all of them viewpoint diverzity. The diversity of the woodland was analysed with an insuffiently consequence. This study get the knowledge about the species composition and the diversity of these monoculture. At the same time get the knowlege about next factores, which change diversity and species composition of stand. As a confirmation of this, coniferous monoculture are numerously and species-compositionally diferent from broadleave monoculture. And more, coniferous trees change the enviroment's condition and the whole biotopes. There are not depend any species of the herb layer at the coniferous monoculture on this studied site of Křivoklátsko.

Cette étude propose une analyse intégrée de biomarqueurs moléculaires de sols, depuis leur site de production jusqu'à leur archivage sédimentaire lacustre. Un inventaire des lipides neutres est d'abord réalisé sur des sols d'usages contrastés : prairies/pâtures et forêts. Globalement, cette approche permet de distinguer (1) des composés linéaires ubiquistes, et (2) des composés (poly-)cycliques, généralement spécifiques. Parmi ces derniers figurent les acétates de triterpényle et les méthoxyserratènes, respectivement biomarqueurs d'Astéracées et de Pinacées. La persistance de l'empreinte moléculaire d'un ancien usage des sols est aussi démontrée. Ensuite, l'analyse multi-proxy d'une carotte sédimentaire couvrant les 6700 dernières années révèle l'impact prépondérant des activités humaines sur le fonctionnement hydrologique du lac, depuis l'époque gallo-romaine. Les assemblages moléculaires précédemment définis dans les sols sont globalement retrouvés, associés à un nouveau biomarqueur spécifique du chanvre, d'intérêt paléoenvironnemental. Une tentative de reconstitution des anciennes occupations des sols apparaît conforme aux données historiques et paléoenvironnementales antérieures. / This study proposes an integrated analysis of molecular biomarkers of landuse, from their genesis in soils to their archiving in the lacustrine sediment. An inventory of neutral lipids is realized on soils of two contrasted landuses: grassland/pasture and forest. This approach globally allows to distinguish (1) ubiquist linear compounds and (2) (poly-)cyclic compounds, generally specific. Among these ones, triterpenyl acetates and methoxyserratenes are detected and are respectively biomarkers of Asteraceae and Pinaceae. The persistence of a molecular imprint of an ancient landuse is also demonstrated. Then, the multi-proxy analysis of a sedimentary core, covering the last 6700 years, shows the prominent impact of human activities on the hydrologic functioning of the lake since the gallo-roman period. Molecular assemblages previously defined in soils are globally detected in sediments, associated with a new specific biomarker of hemp, of palaeoenvironmental interest. Hypotheses for the reconstitution of past landuses appear to be consistent with previous historical and palaeoenvironmental data.

MADS-box genes are important regulators of reproductive development in seed plants, including both flowering plants and conifers. In this thesis the evolution of the AGAMOUS subfamily of MADS-box genes, and what the ancestral function of this group of genes might have been in the early seed plants about 300 million years ago, was addressed by the discovery of two novel conifer genes, both basal to all previously known AGAMOUS subfamily genes. DAL20, the most basal of these genes, was exclusively expressed in roots, unlike all previously known AGAMOUS subfamily genes. I also studied the evolutionary mechanisms leading to functional diversification of duplicated genes in two different subfamilies of MADS-box genes; the AGAMOUS and AGL6 subfamilies. Focus was on studying changes in gene expression pattern, representing changes in the transcriptional regulation between the genes, and on comparing the functional properties of the gene products, representing changes in the protein-coding sequence between the genes. Duplicated genes in the AGL6 subfamily were found to have evolved by both mechanisms. In the AGAMOUS subfamily I found duplicated spruce genes; DAL2 and DAL20, that appear to have functionally diversified mainly by changes in the transcriptional regulation. Conifer AGAMOUS subfamily genes were also used in a comparative developmental-genetics approach to evaluate hypotheses, based on the morphology of fossil and extant conifer seed cones, on the identity of the female reproductive organ, the ovuliferous scale, and the evolution of seed cone morphology in the conifer families Pinaceae, Taxodiaceae and Cupressaceae. Seed cones in these families have been hypothesized to have homologous ovule-bearing organs, but I found substantial differences in the expression patterns of orthologous AGAMOUS subfamily genes in seed cones of these families that are not compatible with this hypothesis, indicating that the evolutionary history of conifer seed cones is more diverse than previously thought.

Biological processes in living organisms consist of a vast number of different molecular networks and interactions, which are complex and often hidden from our understanding. This work is focused on recovery of such details for two quite distant examples: acclimation to extreme freezing tolerance in Siberian spruce (Picea obovata) and detection of proteins associated with prostate cancer. The first biological system in the study, upon P. obovata, is interesting by this species ability to adapt and sustain extremely low temperatures, such as -60⁰C or below. Despite decades of investigations, the essential features and mechanisms of the amazing ability of this species still remains unclear. To enhance knowledge about extreme freezing tolerance, the metabolome and proteome of P. obovata’s needles were collected during the tree’s acclimation period, ranging from mid August to January, and have been analyzed. The second system within this study is the plasma proteome analysis of high risk prostate cancer (PCa) patients, with and without bone metastases. PCa is one of the most common cancers among Swedish men, which can abruptly develop into an aggressive, lethal disease. The diagnostic tools, including PSA-tests, are insufficient in predicting the disease’s aggressiveness and novel prognostic markers are urgently required. Both biological systems have been analyzed following similar steps: by two-dimensional difference gel electrophoresis (2D-DIGE) techniques, followed by protein identification using mass spectrometry (MS) analysis and multivariate methods. Data processing has been utilized for searching for proteins that serve as unique indicators for characterizing the status of the systems. In addition, the gas chromatography-mass spectrometry (GC-MS) study of the metabolic content of P.obovata’s needles, from the extended observation period, has been performed. The studies of both systems, combined with thorough statistical analysis of experimental outcomes, have resulted in novel insights and features for both P. obovata and prostate cancer. In particular, it has been shown that dehydrins, Hsp70s, AAA+ ATPases, lipocalin and several proteins involved in cellular metabolism etc., can be uniquely associated with acclimation to extreme freezing in conifers. Metabolomic analysis of P. obovata needles has revealed systematic metabolic changes in carbohydrate and lipid metabolism. Substantial increase of raffinose, accumulation of desaturated fatty acids, sugar acids, sugar alcohols, amino acids and polyamines that may act as compatible solutes or cryoprotectants have all been observed during the acclimation process. Relevant proteins for prostate cancer progression and aggressiveness have been identified in the plasma proteome study, for patients with and without bone metastasis. Proteins associated with lipid transport, coagulation, inflammation and immune response have been found among them.

Face à la toxicité des éléments traces métalliques (ET) dans l’environnement, les plantes ont développé différentes stratégies aujourd’hui exploitées en phytoremédiation. Les arbres paraissent plus efficaces que les herbacées pour la phytoextraction de par leur importante biomasse et leur système racinaire plus profond. Ces travaux ont donc été menés sur des espèces ligneuses largement répandues dans la région Limousin, plus particulièrement des conifères: le Douglas, le mélèze hybride et ses deux parents, le mélèze d’Europe et le mélèze du Japon. Plusieurs modèles de culture ont été utilisés pour permettre, par des approches complémentaires, une meilleure appréhension des réponses de ces conifères aux ET : des plantules cultivées in vitro et des germinations ou des arbres âgés de 2 ans cultivés sous serre. Les conifères ont été exposés soit à un seul ET, le Cadmium (Cd), soit à plusieurs ET (As, Pb, Sb) présents dans des sols collectés sur deux anciens sites miniers. Les résultats ont montré que, parmi les espèces étudiées, le Douglas présentait le taux d’accumulation le plus élevé en Cd. Cependant, la quantité stockée dans la biomasse aérienne est restée faible par rapport à d’autres espèces d’arbres déjà utilisées en phytoextraction. Par ailleurs, la caractérisation chimique des pectines de la paroi a mis en évidence des modifications quantitatives et qualitatives suggérant un processus d’exclusion du Cd. Au niveau intracellulaire, les résultats ont montré que les polyamines et les oligopeptides riches en thiols ne semblaient pas impliqués dans la compartimentation du Cd. En revanche, une accumulation de proline a été observée en réponse au Cd et à d’autres ET, suggérant une implication de la proline comme molécule antioxydante et / ou chélatrice d’ET. L’ensemble des résultats a mis en évidence la nécessité d’optimiser la croissance des conifères et la phytodisponibilité des ET du sol avant de pouvoir proposer ces conifères, et notamment le Douglas, pour la phytoextraction d’ET. / Given the toxicity of trace elements (TE) in the environment, plants developed varions strategies used currently for phytoremediation. Trees appear more efficient than herbaceous species for phytoextraction as they have a larger biomass and a deeper root system. The work was thus performed on woody species widespread in Limousin region, particularly conifers: Douglas fir, hybrid larch and its two parents, European larch and Japanese larch. Several culture models were used to allow, through complementary approaches, a better understanding of the response of these conifers to TE: in vitro grown plantlets and seedlings or 2-year-old trees grown in greenhouse. Conifers were exposed to a single TE, cadmium (Cd), or to several TE (As, Pb, Sb) present in soils collected from two former mining sites. Among investigated species, results showed that Douglas exhibited the highest rate of Cd accumulation. However, the amount stored in aboveground biomass remained low compared to other tree species already used in phytoextraction. Furthermore, the chemical characterization of cell wall pectins highlighted quantitative and qualitative modifications suggesting a Cd exclusion process. At the intracellular level, results showed that polyamines and thiol-rich oligopeptides did not appear to be involved in Cd compartmentation. However, a proline accumulation was observed in response to Cd and other TE, suggesting an involvement of proline as antioxidant molecule and / or TE scavenger. Overall, results highlighted the need to optimize conifer growth and soil TE phytoavailability before to propose these conifers, particularly Douglas, for the phytoextraction of TE.

Abstract Both demographic histories and natural selection complicate the speciation process. There is a need to jointly study the effects of natural selection on so called magic traits that can cause reproductive isolation such as climatic adaptation, and its interaction with neutral demographic histories. Closely related incipient coniferous species offer us a great system for this effort. I used genetic variation at one set of climate-related candidate genes and another set of reference loci and cytoplasmic genomic fragments of two closely related parapatric pine species: Pinus massoniana Lamb. and Pinus hwangshanensis Hisa. Population genetic analyses were used to measure genetic variation and detect signals of ancient and recent selection. Speciation parameters including migration rates and divergence times at candidate genes and reference loci were compared under the Isolation with migration model. Hierarchical Approximate Bayesian Computation (ABC) was used to define demographic and speciation models. Intra- and interspecific genetic variation at cytoplasmic and nuclear intronic sequences were compared between parapatric populations and allopatric populations to distinguish the effects of introgression and incomplete lineage sorting in generating shared genetic variation between the species. The results showed that ancient selection were shared by the lineages leading to the species while recent selection has been species-specific. Candidate genes had significant lower migration rates compared to reference loci. Recent differential climatic selection might counteract against gene flow at underlying genes, which therefore favors divergence between the two pines through ecological speciation. Shared mitotypes were randomly distributed across species’ ranges, which therefore supported the incomplete lineage sorting hypothesis, but the shared nuclear intronic variation distributed more frequently in parapatric populations than in allopatric populations, supported the introgression hypothesis. ABC and species’ distribution modeling also supported the secondary gene flow model. The three genomes had different rates of mutation and gene flow might mirror different phases of the speciation continuum. The results in this thesis are valuable for understanding evolution in general and for other applied purposes such as tree breeding and climate change adaptation. / Tiivistelmä Luonnonvalinta ja populaatioiden historian demografia tekevät lajiutumisesta monimutkaisen tapahtumaketjun. Luonnonvalinnan ja demografisten tekijöiden vuorovaikutusta on paras tutkia samanaikaisesti, kun tarkastellaan lajiutumiseen vaikuttavia ominaisuuksia. Tällaisia ovat esimerkiksi ilmastoon sopeutumiseen liittyvät ominaisuudet. Lähisukuiset havupuulajit tarjoavat erinomaiset mahdollisuudet tähän työhön. Tutkin geneettistä muuntelua yhtäältä ilmastosopeutumiseen liittyvissä ns. ehdokasgeeneissä ja toisaalta neutraaleiksi oletetuissa verrokkigeeneissä sekä sytoplasman genomeissa kahdessa lähisukuisessa mäntylajissa Pinus massoniana Lamb. ja Pinus hwangshanensis Hisa, joiden populaatiot esiintyvät joskus erillään toisistaan (allopatrisesti), toisinaan vierekkäin (parapatrisesti). Mittasin muuntelun määrää ja etsin merkkejä valinnan vaikutuksesta. Vertasin erilaisia lajiutumismallien parametrejä verrokki- ja ehdokasgeeneissä. Käytin simulaatioita etsiäkseni parhaat demografiset ja lajiutumiseen liittyvät mallit. Vertasin kloroplastien ja mitokondrioiden genomien sekvenssien lajinsisäistä ja lajien välistä muuntelua allopatrisissa ja parapatrisissa populaatioissa tutkiakseni onko lajien yhteinen muuntelu seurausta siitä että lajien eriytymisestä on kulunut vain vähän aikaa vai siitä että sen jälkeen on tapahtunut geenivirtaa. Kauan sitten tapahtunut valinta on vaikuttanut samalla tavalla kumpaankin lajiin, osin koska tutkimus kohdistui myös niiden yhteiseen edeltäjälinjaan. Äskettäinen valinta taas oli suuremmassa määrin kummallekin lajille ominaista. Viime aikojen ilmastoon liittyvä valinta on voinut vähentää geenivirtaa ehdokasgeeneissä, mikä voisi edistää ekologista lajiutumista. Tuman DNA:n muuntelu jakautuminen tuki sitä mahdollisuutta että lajien yhteinen geneettinen muuntelu johtuu äskettäisestä geenivirrasta, ei vain siitä että lajiutuminen on niin varhaisessa vaiheessa. Mitokondrioiden geeneissä lajeilla yhtä paljon yhteistä muuntelua sekä allopatrisissa että parapatrisissa populaatioissa, mikä tukee sen sijaan eriytymisen jälkeistä epätäydellistä muuntelun erilaistumista. Eri genomit heijastavat lajiutumisprosessin eri vaiheita. Väitöskirjan tulokset ovat osaltaan tuottaneet uutta tietoa lajiutumisesta ja valinnasta. Lisäksi niillä on merkitystä ilmastomuutoksen vaikutusten ymmärtämisessä ja metsänjalostuksessa.

Almost all conifer ovules produce a liquid secretion as part of reproduction. This secretion, termed an ovular secretion, is produced during ovule receptivity and is involved in pollen capture and transport. Historically, examinations of the ovular secretion have focused on how they are part of pollination mechanisms. As a result, the chemical composition of the ovular secretion has not been examined systematically. Investigations into the constituents of the ovular secretion were limited to analyses for simple water soluble compounds such as sugars, minerals, amino acids and organic acids. More recently, the protein component of the secretion has been investigated using mass spectrometry-based proteomics. Proteins involved in processes such as carbohydrate modification, proteolysis, and defence have been identified in conifer ovular secretions. This biochemical complexity suggests a broader view of the function of the ovular secretion is warranted. However, protein identifications only provide putative information on function. Functional characterization of these proteins is needed in order to fully understand how they contribute to ovular secretion function. The research outlined in this dissertation describes the first functional characterizations of proteins found in conifer ovular secretions. Three proteins - invertase, chitinase, and thaumatin-like protein - were characterized in the ovular secretions of Douglas-fir (Pseudotsuga menziesii) and hybrid yew (Taxus × media). The Douglas-fir ovular secretion is capable of converting sucrose to glucose and fructose, confirming that invertases present in the secretion are functional. The invertase activity was maximal at pH 4.0. Activity was 77% of maximal at pH 4.5, the physiological pH. This indicates that post-secretory hydrolysis of sucrose occurs in situ in the Douglas-fir ovular secretion. Invertases in the ovular secretion are likely involved in controlling the movement of carbohydrates to developing pollen and could facilitate pollen selection. Chitinases present in the Douglas-fir ovular secretion are functional at physiological conditions. All three modes of chitinolytic activity, i.e. endochitinase, chitobiosidase and β-N-acetylglucosaminidase, were detected at physiological pH. β-N-acetylglucosaminidase activity was 80 % of maximal at physiological pH. Chitinases are pathogenesis-related proteins capable of hydrolysing chitin in fungal cell walls. These results suggest the ovular secretion is capable of defending the ovule against infection by phytopathogens. Thaumatin-like protein was immunolocalized to the cell wall and amyloplasts in Douglas-fir and yew nucellar tissue in a pattern consistent with a defensive role. It was also localized to the cell wall of fungal spores and germinating hyphae that were present in the micropyle of a yew ovule. These results provide additional evidence for an antifungal role for the ovular secretion. Functioning enzymes involved in pollen-ovule interactions and ovule defence are present in the conifer ovular secretion. The ovular secretion has functions beyond pollen capture. A revised functional model for the conifer ovular secretion is proposed. / Graduate / 2021-08-17

Eastern hemlock (Tsuga canadensis) is in decline because of infestation by the invasive hemlock woolly adelgid (Adelges tsugae; ‘HWA’) and, to a lesser extent, the elongate hemlock scale (Fiorinia externa; ‘EHS’). Many conifers respond to insect herbivory by inducing oleoresin-based defenses, however it is unknown whether eastern hemlock is capable of this inducible response. We conducted a plantation setting study of artificially infested saplings to determine if feeding by HWA or EHS induces changes in the tree’s volatile chemistry. The induced changes in volatiles we found were unlike the terpenoid-based defenses of related conifers. Only HWA feeding elevated methyl salicylate, a plant signal for systemic acquired resistance, and benzyl alcohol, a known antimicrobial and aphid deterrent. The influence of environmental conditions and tree life-stage on hemlock volatile chemistry, potentially important factors for wild hemlock populations, is unknown. We investigated whether mature and immature forest trees respond to HWA infestation with the same patterns of volatile production as plantation saplings in full sun and amended soils. HWA induced volatile changes comparable to those of plantation saplings, with many-fold benzenoid increases and no terpenoid-based resinosis. Nearly all volatiles were substantially more abundant in forest than plantation trees, suggesting the effect of site conditions should be addressed in investigations of mechanisms operative in HWA-resistant biotypes of eastern hemlock. Our findings represent the first important step toward understanding the influence of inducible phytochemical responses on hemlock susceptibility to exotic pests, and highlight the possibility of salicylic acid-dependent biosynthetic activity in this gymnosperm system.