In the Most Basin, there is a rich variety of plant macrofossils, whose findings are described for the first time already in the 19th century. The presented thesis is focused on conifer wood preserved as xylitic stumps in situ. The samples come from the so-called "stumpy horizont No. 31" situated in the roof of the main lignite seam in the Bílina Mine. A detailed xylotomical study with scanning electron microscopy allows their assignment to the Cupressaceae s.l., to the morphospecies Glyptostroboxylon rudolphii and Taxodioxylon gypsaceum.

Quacking aspen (Populus tremuloides Michx.) is an iconic species in western United States that offers multiple ecosystem services, including carbon sequestration. A shift in forest cover towards coniferous species due to natural succession, land management practices, or climate change may modify soil organic carbon (SOC) dynamics and CO2 emissions. The objectives of this study were to: (i) assess the effects of overstory composition on SOC storage and stability across the aspen-conifer ecotone, (ii) use Fourier transform infrared spectroscopy attenuated total reflectance (FTIR-ATR) to assess whether SOC storage is associated with preferential adsorption of certain organic molecules to the mineral surfaces, and (iii) develop models using near-infrared reflectance spectroscopy (NIRS) to predict aspen- and conifer-derived SOC concentration. Mineral soils (0 – 15 cm) were sampled in pure and mixed aspen and conifer stands in Utah and subjected to physical fractionation to characterize SOC stability (i.e., SOC protected against microbial decomposition), long term laboratory incubations (i.e., SOC decomposability), and hot water extractions (i.e., SOC solubility). Vegetation cover had no effect on SOC storage (47.0 ± 16.5 Mg C ha−1), SOC decomposability (cumulative released CO2-C of 93.2 ± 65.4 g C g−1 C), SOC solubility (9.8 ± 7.2 mg C g−1 C). Mineral-associated SOC (MoM) content was higher under aspen (31.2 ± 15.1 Mg C ha-1) than under mixed (25.7 ± 8.8 Mg C ha−1) and conifer cover (22.8 ± 9.0 Mg C ha−1), indicating that aspen favors long-term SOC storage. FTIR-ATR spectral analysis indicated that higher MoM content under aspen is not due to higher concentration of recalcitrant compounds (e.g., aliphatic and aromatic C), but rather to stabilization of simple molecules (e.g., polysaccharides) of plant or microbial origin. NIRS models performed well during calibration-validation stage (ratio of standard deviation of reference values to standard error of prediction (RPD) ≥ 2). However, model performance decreased during independent validation (RPD = 1.2 – 1.6), probably due to the influence of soil texture, mineralogy, understory vegetation, and land history on SOC spectra. Further improvement of NIRS models could provide insight on SOC dynamics under potential conifer encroachment in semiarid montane forests.

Many fire-prone forests in western North America suffer from hazardous fuel conditions. Mechanical mastication is an increasingly common method of fuels treatment, but little is known regarding long-term effectiveness. A randomized block design at two sites (northern Sierras and southern Cascades) compared ladder fuels and overstory growth among treatments including mastication alone and mastication followed with prescribed fire or herbicide 10 or 11 years post-treatment. Subsequent herbicide application reduced ladder fuels in comparison to mastication alone or with prescribed fire. Prescribed fire further reduced ladder fuels at the southern Cascades site, however, in the northern Sierras postire ladder fuels were positively related to overstory absence. Mastication alone effectively released ponderosa pine at the southern Cascades site, whereas neither herbicide nor prescribed fire affected pine radial growth. This study demonstrates the feasibility of prescribed fire and herbicide for increasing treatment longevity of mastication, but also highlights potential limitations and important considerations.

No description available.

The Sierra Madre Occidental and neighboring Madrean Sky Islands span a large and biologically diverse region of northwest Mexico and portions of the southwestern United States. Little is known about the abundance and habitat use of breeding birds in this region of Mexico, but such information is important for guiding conservation and management. We assessed densities and habitat relationships of breeding birds across Sky Island mountain ranges in Mexico and adjacent portions of the Sierra Madre from 2009 to 2012. We estimated densities at multiple spatial scales, assessed variation in densities among all major montane vegetation communities, and identified and estimated the effects of important habitat attributes on local densities. Regional density estimates of 65% of 72 focal species varied significantly among eight montane vegetation communities that ranged from oak savannah and woodland at low elevations to pine and mixed-conifer forest at high elevations. Greater proportions of species occurred at peak densities or were relatively restricted to mixed-conifer forest and montane riparian vegetation likely because of higher levels of structural or floristic diversity in those communities, but those species were typically rare or uncommon in the Sky Islands. Fewer species had peak densities in oak and pine-oak woodland, and species associated with those communities were often more abundant across the region. Habitat models often included the effects of broadleaf deciduous vegetation cover (30% of species), which, together with tree density and fire severity, had positive effects on densities and suggest ways for managers to augment and conserve populations. Such patterns combined with greater threats to high-elevation conifer forest and riparian areas underscore their value for conservation. Significant populations of many breeding bird species, including some that are of concern or were not known to occur regionally or in mountain ranges we surveyed, highlight the importance of conservation efforts in this area of Mexico.

Forest soils store as much carbon (C) as the vegetation that grows on them, and the carbon in soil is more stable than the C in biomass. Quaking aspen (Populus tremuloides Michx.) is the most widespread tree species in North America, and aspen forests in the Western US have been found to store more soil organic carbon (SOC) in the mineral soil than nearby conifers. Fire exclusion and grazing often promote the succession of aspen to conifer dominated forests due to their effect on aspen regeneration. So far the factors driving the differential SOC accumulation, and the effects of the vegetation shift on SOC pools, are not well understood. In this dissertation I aimed to evaluate how various forest vegetation characteristics – tree type, detritus fluxes, detritus chemistry – affect SOC pools and stability from a global to a molecular level using two contrasting forest types – aspen and conifer. A meta-analysis showed that, while conifer forests worldwide had higher C pools in the forest floor, this difference did not translate into the mineral soil, suggesting that the mechanisms that control SOC storage differ between both soil compartments. Above- and belowground detritus input fluxes were similar between aspen and conifer forests, and did not explain the higher SOC pools under aspen. A sorption study revealed that the more labile aspen foliage dissolved organic carbon (DOC) was more effectively retained in soil than aspen root, and conifer substrate DOC. Furthermore, soils that contained aspen SOC retained new DOC better than soils with conifer SOC, irrespective of the source of the DOC. Finally, foliage and root specific compounds that were identified for aspen and subalpine fir provide a base for future studies aiming to identify the source of SOC under both overstory types. Overall, the results of the dissertation suggest that substrate chemistry more than detritus fluxes drive the differences between SOC pools under aspen and conifer forests in Utah. This finding indicates that the link between C input amounts and SOC pools is not as direct as currently assumed in most SOC models. Furthermore, a tree species effect on SOC as distinct as aspen vs conifer is not common between all hardwood and conifer comparisons worldwide, thus suggesting that the effect of vegetation can be overridden by other factors.

Araucaria cunninghamii is an ancient tropical conifer with substantial value as a forestry species in Australia and Papua New Guinea, and has been subject to a genetic improvement program for more than 50 years. This study was undertaken to demonstrate the utility of quantitative genetic analysis in describing the genetic architecture of commercial traits in A. cunninghamii. Linkage maps were prepared using the pseudotestcross strategy in what was believed to be a wide interprovenance cross using microsatellites and AFLP. A very low rate of marker polymorphism and limited differentiation between the parental provenances was identified, resulting in low mapping efficiency. The population genetic structure of A. cunninghamii was assessed to establish the underlying causes for the limited differentiation and low marker heterozygosity and assess the implications for future analysis of quantitative traits. Despite the limited mapping efficiency, genetic maps were generated for both parents. The maternal map for individual H15 contained 14 linkage groups comprising of 51 AFLP and one microsatellite. The map covered 1290 cM, representing 89% of the estimated genome size. The paternal map for individual Gil24 was 633 cM, consisting of eight linkage groups. Genetic architecture of quantitative traits was examined with putative QTL identified for height, DBH and stem straightness; one was highly significant (p<0.01), three significant (0.01<p<0.05) and 13 suggestive (p<0.10). Significant QTL each accounted for 7-11% of the phenotypic variance with a high allele substitution effect (0.63-0.81). These QTL were likely to be associated with genes of moderate effect. The suggestive QTL each accounted for 3-6% of the phenotypic variance with an allele substitution effect of 0.40-0.63. Three genomic regions contributed to the expression of multiple traits at multiple ages. Stable QTL had decreasing phenotypic effects with increasing age. The population genetic survey characterised low levels of allelic diversity across the geographic range. Three broad regions were characterised; Papua New Guinea, Cape York and northern Queensland to NSW. There was limited differentiation between provenances within these regions, and high diversity within provenances. Limited genetic differentiation between provenances seems to be the result of genetic stability due to long overlapping generations, limited founder effects and a very low mutation rate. The latter may also contribute the low heterozygosity. Limited marker polymorphism and limited differentiation between provenances within broad regions are common features in A. cunninghamii. Therefore careful parental selection and alternative experimental approaches will be required before undertaking further analysis of quantitative traits.

Araucaria cunninghamii is an ancient tropical conifer with substantial value as a forestry species in Australia and Papua New Guinea, and has been subject to a genetic improvement program for more than 50 years. This study was undertaken to demonstrate the utility of quantitative genetic analysis in describing the genetic architecture of commercial traits in A. cunninghamii. Linkage maps were prepared using the pseudotestcross strategy in what was believed to be a wide interprovenance cross using microsatellites and AFLP. A very low rate of marker polymorphism and limited differentiation between the parental provenances was identified, resulting in low mapping efficiency. The population genetic structure of A. cunninghamii was assessed to establish the underlying causes for the limited differentiation and low marker heterozygosity and assess the implications for future analysis of quantitative traits. Despite the limited mapping efficiency, genetic maps were generated for both parents. The maternal map for individual H15 contained 14 linkage groups comprising of 51 AFLP and one microsatellite. The map covered 1290 cM, representing 89% of the estimated genome size. The paternal map for individual Gil24 was 633 cM, consisting of eight linkage groups. Genetic architecture of quantitative traits was examined with putative QTL identified for height, DBH and stem straightness; one was highly significant (p<0.01), three significant (0.01<p<0.05) and 13 suggestive (p<0.10). Significant QTL each accounted for 7-11% of the phenotypic variance with a high allele substitution effect (0.63-0.81). These QTL were likely to be associated with genes of moderate effect. The suggestive QTL each accounted for 3-6% of the phenotypic variance with an allele substitution effect of 0.40-0.63. Three genomic regions contributed to the expression of multiple traits at multiple ages. Stable QTL had decreasing phenotypic effects with increasing age. The population genetic survey characterised low levels of allelic diversity across the geographic range. Three broad regions were characterised; Papua New Guinea, Cape York and northern Queensland to NSW. There was limited differentiation between provenances within these regions, and high diversity within provenances. Limited genetic differentiation between provenances seems to be the result of genetic stability due to long overlapping generations, limited founder effects and a very low mutation rate. The latter may also contribute the low heterozygosity. Limited marker polymorphism and limited differentiation between provenances within broad regions are common features in A. cunninghamii. Therefore careful parental selection and alternative experimental approaches will be required before undertaking further analysis of quantitative traits.

La polyploïdie est un processus important et un moteur de la diversification et de l'évolution des plantes. Peu de polyploïdes naturels ont été décrits chez Juniperus, un genre de conifère représenté par 75 espèces d'arbres ou arbustes à feuilles persistantes, largement réparties dans l'hémisphère nord. Dans ce travail de recherche, l’implication de la polyploïdie dans l'évolution de Juniperus et l’élucidation des mécanismes sous-jacents à ces événements de polyploïdisation sont explorées. La taille du génome (TG) et le niveau de ploïdie ont été évalués chez 111/115 taxons en utilisant la cytométrie en flux et les comptages chromosomiques. Le taux de polyploïdie chez les genévriers s’est avéré être exceptionnellement élevé : 15 taxons sont des tétraploïdes et un seul taxon (J. foetidissima) est hexaploïde. Juniperus foetidissima représente le seul conifère hexaploïde découvert à ce jour à part Sequoia sempervirens. Nous avons également utilisé des approches de modélisation phylogénétique pour déterminer la TG ancestrale dans les trois clades de Juniperus et pour reconstruire le processus évolutif de la polyploïdisation chez ce genre. Au moins 10 événements de polyploïdisation ont eu lieu au cours de l'évolution et de la diversification de Juniperus. Nous avons ensuite exploré l’origine de la polyploïdie chez certaines espèces méditerranéennes. La variation de la TG et le niveau de ploïdie de deux variétés de J. sabina ont été estimés : Les populations échantillonnées de J. sabina var. sabina se sont avérées être diploïdes, tandis que les populations de J. sabina var. balkanensis étaient toutes tétraploïdes. Ces derniers auraient été issus d'une ancienne hybridation entre le tétraploïde J. thurifera et le diploïde J. sabina. Dans les Alpes françaises, où J. sabina var. sabina et J. thurifera sont en sympatrie, des individus présentant des morphologies intermédiaires entre ces deux espèces sont observés. Suite à des estimations des TG, de séquençage des ITS et de régions chloroplastiques, ces individus sont considérés comme des hybrides triploïdes. Enfin, l’utilisation des marqueurs AFLP pour déchiffrer les relations phylogénétiques entre des espèces méditerranéenne a montré que plusieurs pools génétiques contribuent à la diversité de Juniperus. Aussi ces marqueurs ont contribué à la découverte des contributions de ces pools génétiques aux taxons polyploïdes. Alors que les populations libanaises de l'hexaploïde J. foetidissima sont issues d'une lignée ancestrale unique, la population grecque semble résulter d'un mélange inégal de deux lignées anciennes. Ces deux lignées contribuent également au tétraploïde J. thurifera. Cette analyse a également montré que l’espèce méditerranéenne J. excelsa et l’espèce africaine J. procera partagent la même lignée ancestrale. Cependant, des analyses supplémentaires sont nécessaires pour une interprétation plus complète des données. L'importance de l'hybridation interspécifique et de la polyploïdie dans l'évolution des espèces de Juniperus nécessite d’amples recherches visant à comprendre le lien entre ces mécanismes et l'adaptation de ces espèces à un large spectre d'habitats extrêmes. Ces recherches futures devraient aussi contribuer à découvrir comment les espèces de conifères peuvent s’adapter aux changements climatiques. / Polyploidy is considered as an important phenomenon and a key driving force for plant diversification and evolution. Few natural polyploid species have been described in Juniperus, a coniferous genus represented by 75 species of evergreen trees or shrubs widely distributed in the North Hemisphere. The occurrence of polyploidy in the evolution of this genus as well as a more comprehensive view of pathways that were involved in these polyploidization events are explored in this research work. Genome size (GS) and ploidy level assessments were conducted on 111/115 taxa using flow-cytometry and chromosome counts. Juniperus holds an exceptionally high rate of polyploidy, 15 taxa being tetraploids and just one (J. foetidissima) being hexaploid. It represents the only hexaploid conifer discovered to date after Sequoia sempervirens. We also used phylogenetically-informed trait evolution modelling approaches to determine ancestral GS in the three clades of Juniperus and to reconstruct the evolutionary process of polyploidization in Juniperus. At least 10 polyploidization events have occurred during Juniperus evolution and diversification. We then explored the origin of polyploidy in selected Mediterranean species. The GS variation and the ploidy level of two J. sabina varieties were estimated: J. sabina var. sabina sampled populations were shown to be diploid, while J. sabina var. balkanensis populations were all tetraploid. The latter has been postulated to have arisen from an ancient hybridization between the tetraploid J. thurifera and the diploid J. sabina. In the French Alps, where J. sabina var. sabina and J. thurifera occur in sympatry, individuals with intermediate morphologies between these two species are observed. Evidences based on GS assessments, ITS and chloroplastic sequences demonstrated these individuals as triploid hybrids. Finally, the use of AFLP markers to decipher phylogenetic relationships between Mediterranean and Eastern Mediterranean species showed that multiple lineages contributes to Juniperus diversity and shed light on some polyploid taxa origins. While the Lebanese populations of the hexaploid J. foetidissima are issued from a unique ancestral lineage, the Greek population seems to be the result of an unequal admixture of two ancient lineages. These two lineages contribute also to the tetraploid J. thurifera. This analysis showed also that the Mediteranean J. excelsa and the African taxa J. procera shares the same ancestral lineage. However, further analyses are needed for a more complete interpretation of the data. The importance of interspecific hybridization and of polyploidization in the evolution of Juniperus species argues in favor of the development of researches aiming at understanding the link between these mechanisms and the adaptation of those species to a wide range of extreme habitats. Such future researches should contribute to predict how conifer species may adapt to dramatic changes in the Earth’s climate.

In the Intermountain West, aspen (Populus tremuloides) has declined mainly due to a combination of successional processes, fire suppression and long-term use of ungulates which has led to replacement by conifers, sagebrush or other shrub communities. Conifer encroachment is believed to cause critical changes in the ecosystem properties. In order to understand the impacts of conifer encroachment on soil properties such as soil organic carbon (SOC) storage, soil morphology, and soil chemical properties, and the implications of such changes, it is very important to assess the soil properties under the two vegetation types. The objectives of this study were to i) quantify SOC stocks and their variability in pure aspen forests; ii) evaluate the role of various biotic and abiotic site parameters as drivers of this SOC; iii) evaluate the effect of conifer encroachment on SOC storage, soil morphology, soil microclimate and soil chemical properties. The study was conducted in three catchments in Northern Utah in two phases: i) a transect study with 33 sampling points in a pure aspen community; ii) a paired plot study based on comparing six plots in to aspen and nearby conifer plots as representatives of end-member communities. Soils under aspen were mainly Mollisols, whereas the soils associated with conifers were classified as Alfisols, Inceptisols and Entisols. Even under pure aspen there was a significant SOC variability among sampling points and aspects, and SOC was negatively correlated with soil moisture index and average tree diameter and positively correlated with vegetation density. The paired plot comparison showed that SOC in the mineral soil (0-60 cm) was significantly higher under aspen, while O horizon thickness and C content was higher under conifers. The total SOC (O layer + mineral soil) was not significantly different among the vegetation types, suggesting an upward redistribution of SOC in conifer soils. The soil moisture in summer was also higher under aspen compared to conifers. Other chemical properties were not affected by vegetation types. Our study indicates that i) no differences in SOC can be detected in surface soil horizons (<20 >cm); ii) SOC is highly variable and greatly influenced by soil moisture and forest characteristics; iii) conifer encroachment is likely to alter soil microclimatic and SOC amount and distribution.