Comparative in silico analysis of SSRs in coding regions of high confidence predicted genes in Norway spruce (Picea abies) and Loblolly pine (Pinus taeda)

Background: Microsatellites or simple sequence repeats (SSRs) are DNA sequences consisting of 1-6 bp tandem repeat motifs present in the genome. SSRs are considered to be one of the most powerful tools in genetic studies. We carried out a comparative study of perfect SSR loci belonging to class I (>= 20) and class II (>= 12 and < 20 bp) types located in coding regions of high confidence genes in Picea abies and Pinus taeda. SSRLocator was used to retrieve SSRs from the full length CDS of predicted genes in both species. Results: Trimers were the most abundant motifs in class I followed by hexamers in Picea abies, while trimers and hexamers were equally abundant in Pinus taeda class I SSRs. Hexamers were most frequent within class II SSRs followed by trimers, in both species. Although the frequency of genes containing SSRs was slightly higher in Pinus taeda, SSR counts per Mbp for class I was similar in both species (P-value = 0.22); while for class II SSRs, it was significantly higher in Picea abies (P-value = 0.00009). AT-rich motifs were higher in abundance than the GC-rich motifs, within class II SSRs in both the species (P-values = 10(-9) and 0). With reference to class I SSRs, AT-rich and GC-rich motifs were detected with equal frequency in Pinus taeda (P-value = 0.24); while in Picea abies, GC-rich motifs were detected with higher frequency than the AT-rich motifs (P-value = 0.0005). Conclusions: Our study gives a comparative overview of the genome SSRs composition based on high confidence genes in the two recently sequenced and economically important conifers and, also provides information on functional molecular markers that can be applied in genetic studies in Pinus and Picea species

A phytosociological survey of the boreal forest (Vaccinio-Piceetea) in North America

A survey of syntaxa of vegetation of North American boreal forests (class Vaccinio-Piceetea) is presented. This phytosociological survey, carried out combining the Braun-Blanquet method with numerical syntaxonomical analyses (cluster and correspondence analysis), describes the associations of the North American boreal forests, which have several species, varieties or vicariant species in common with their Eurasian counterparts, and can be placed in the class Vaccinio-Piceetea. By means of tabular and multivariate analyses, 2084 North American relevés were compared with 3273 relevés from European, Japanese and Korean boreal forest, to describe and typify 4 orders, 10 alliances and 37 associations. Diagnostic tables, ordination, clustering, and climatic, edaphic and biogeographical data were used to show floristic affinities among these syntaxa and interpret their distribution areas. Syntaxa were briefly characterized by their floristic composition, physiognomy, succession, zonation, and biogeographical distribution

Frost and Forest Stand Effects on the Population Dynamics of Asplenium scolopendrium

Our objective was to analyze which factors are critical for the dynamics of terrestrial Asplenium scolopendrium populations at the northern edge of its distribution. Therefore, a long-term study (1978–1999) on the performance and demography of this fern species has been carried out in three different forest stands (Picea sitchensis with Fagus sylvatica, P. sitchensis with thinning, and Fraxinus excelsior) in the Netherlands. We used the recorded demographic data to parameterize 37 transition matrices. The number of frost days in severe winters correlated closely with frond damage and resulted in increased mortality and retrogression. Landslip on the trench banks and intraspecific competition were also found to increase mortality. In the F. excelsior plot, plants grew faster and bigger, produced more fronds and formed a more closed fern cover than in the P. sitchensis stands, likely due to higher light levels. Life-table response experiments revealed that reproduction contributed greatly to the differences in projected population growth rates: reproduction was importantly higher in the F. excelsior and in the thinned P. sitchensis plots than in the P. sitchensis–F. sylvatica plot. These differences can be attributed to an initial difference in light climate and to the accumulation of F. sylvatica litter which reduced recruitment. Recruitment occurred on bare soil but also in open moss carpets. We expect that the fern Asplenium scolopendrium will profit at its northern distribution edge when severe winters will occur less frequently, which is one of the expectations for global climate change

Possibilities and limitations of vegetative propagation in breeding and mass propagation of Norway spruce

The use of vegetative mass propagation in practical forestry with Norway spruce (Picea abies (L.) Karst.) is limited at present, although its potential to deliver high genetic gains is obvious. The objective of this thesis was to study possibilities and limitations of vegetative propagation when applied in different parts of a breeding/mass propagation system for Norway spruce. Two vegetative propagation methods were studied: somatic embryogenesis and cutting propagation. Somatic embryogenesis was accompanied by losses of genotypes during the propagation process. The embryogenic response at proliferation and maturation was under family control, while germination was obtained for all families. Parental effects on proliferation and maturation were found for male parents but not for female. However, no correlations between embryogenic characters and breeding goal traits could be detected on parental level. Shortening of treatment with abscisic acid (ABA) during somatic embryo development gave pronounced positive effects on height growth of regenerated plants. An improved protocol, including five weeks ABA treatment and root development in liquid medium significantly improved performance of the resulting plants. The number of plants with lateral roots at the time of ex vitro transfer increased substantially with this protocol. Lateral roots at ex vitro transfer were shown to be a marker for good height growth and clonal uniformity during the next two years. Selection for height of cutting propagated clones in the nursery resulted in low responses in height after six years in field. The likely reason for this was low correlations between nursery traits and field traits. Genotype x environment interactions in the studied clonal test series varied from close to zero to more than 50% of the clone component. A tendency towards increased interaction components with age was obtained in one of the series. In situations with large genotype x environment interactions, clonal stability over sites should be included in the selection criteria

Temporal variations in English Populations of a forest insect pest, the green spruce aphid (Elatobium abietinum), associated with the North Atlantic Oscillation and global warming

Based on an exceptionally long modern ecological dataset (41 years), it has been possible to show that warm weather in England associated with a positive North Atlantic Oscillation (NAO) index causes the spring migration of the green spruce aphid (Elatobium abietinum), a pest species of spruce trees (Picea) to start earlier, continue for longer and contain more aphids. An upward trend in the NAO index during the period 1966-2006 is associated with an increasing population size of E. abietinum. It is important to understand the mechanisms behind the population fluctuations, because this aphid causes considerable damage to Picea plantations. Present day weather associated fluctuations in forest insect pests may be useful analogues in understanding past pest outbreaks in forests

Occurrence, morphology and growth of understory saplings in Swedish forests

Growing demands for a multipurpose forestry leads to increased use of silvicultural systems that avoid clear-cutting. Regeneration in such systems is based on establishment and ingrowth of new seedlings under a more or less closed canopy. At long-term forestry planning reliable ingrowth models are needed to predict the future wood production. The objectives of this thesis were to review the field of ingrowth in established stands, to develop a model for prediction of ingrowth for the planning system Heureka and to deepen the insight in the ingrowth process by a case study. The ingrowth model consisted of four parts, describing: Probability for occurrence of saplings (1-39 mm diameter at breast height (DBH)) on plots with r = 5 m. Number of saplings on stocked plots (plots with saplings of target species). Probability for ingrowth of a sapling over 39 mm DBH during a 5-year period. Diameter of ingrown trees at the end of the 5-year period. The model was based on data from permanent plots at the National Forest Inventory. Separate functions were developed for seven species and species groups. Picea abies saplings had the widest distribution and occurred on 58 % of 12 469 representative plots in established forests. Betula spp. saplings occurred on 50 % of the plots, while the occurrence of saplings of other species was less than 20 %. Sapling density on stocked plots was highest for Betula spp, in average 10 per plot. Average ingrowth rate was 14.6 stems per ha and year, and P. abies made up more than half of this. The ingrowth varied according to the different functions with age, density and species composition of the stand and the moisture and fertility of the site. Growth and morphology of young conifers was examined in a species experiment on a clearcut and in shelterwoods of three different densities (41 – 124 stems per hectare). The largest intra-specific differences between clearcut and shelterwood were found for Pinus spp, while moderate differences were found for Picea spp. For Pinus spp, stem height and diameter decreased, while the stem slenderness increased with increasing shelterwood density. Moreover, the number of branches per whorl and the crown ratio decreased with increasing shelterwood density. The proportion of biomass in roots, stem, branches and needles was analysed as a function of estimated irradiance transmission for each individual. The proportion of stem decreased and the proportion of branches increased with increasing irradiance for Pinus spp. No significant trends were found for Picea spp

Ecology of the Cerambycidae (Coleoptera) of the Huron Mountains in Northern Michigan

Eighty-nine species of Cerambycidae were collected during a five-year survey of the woodboring beetle fauna of the Huron Mountains in Marquette County, Michigan. Host plants were determined for 51 species. Observations were made of species abundance and phenology, and the blossoms visited by anthophilous cerambycids

Geochemical analysis of Cenozoic fossil conifers at high latitudes: Implications for molecular preservation and environmental change

Fossil materials record ancient life and their adapted environment. Arctic plant fossils are critical for our understanding of the Earth’s paleoenvironment when high latitudes were under ice-free conditions. All Arctic plant fossils in this research are conifers, plants conducive for morphological and molecular study because of their incredible genetic stability. Miocene (15 million year old) and Pliocene (5 million year old) conifer leaves were collected from Banks Island, Canada (Williams et al., 2008). Samples were analyzed and compared with Paleocene (60 million year old) and Eocene (45 million year old) samples from Axel Heiberg Island, Canada and with modern equivalent species from Washington D.C., USA (William et al., 2008). This paper has three main sample analyses. First, Pyrolysis-Mass Spectrometry-Gas Chromatography technology was used to detect organic volatile compounds. The amounts and types of organic volatile compounds provide further insights into the molecular preservation of the Miocene and Pliocene fossilized samples. Molecular preservation from this research was compared to previous research that used Scanning Electron Microscope observations of Paleocene and Eocene transverse sections to indicate extraordinary morphological preservation (Yang et al., 2005; Yang et al., 2007). Second, Miocene and Pliocene bulk peat were cross-referenced with known species in the region to reconstruct Arctic environmental changes between 5 million and 15 million years ago. Third, the ratios of three stable compounds were analyzed as biomarkers, essentially benchmarks for plant fossil preservation. However, biomarkers were inconclusive because of complications including age, species type, and environmental conditions. Overall, our analyses provide the first assessments of molecular preservation for these rare Arctic fossils which offer unique material for further paleoclimate analysis

Analyzing tree distribution and abundance in Yukon-Charley Rivers National Preserve: developing geostatistical Bayesian models with count data

Master's Project (M.S.) University of Alaska Fairbanks, 2018Species distribution models (SDMs) describe the relationship between where a species occurs and underlying environmental conditions. For this project, I created SDMs for the five tree species that occur in Yukon-Charley Rivers National Preserve (YUCH) in order to gain insight into which environmental covariates are important for each species, and what effect each environmental condition has on that species' expected occurrence or abundance. I discuss some of the issues involved in creating SDMs, including whether or not to incorporate spatially explicit error terms, and if so, how to do so with generalized linear models (GLMs, which have discrete responses). I ran a total of 10 distinct geostatistical SDMs using Markov Chain Monte Carlo (Bayesian methods), and discuss the results here. I also compare these results from YUCH with results from a similar analysis conducted in Denali National Park and Preserve (DNPP)

Some aerophytic algae in the „Mokry Bór” reserve

The results of investigation on aerophytic algae grown on different tree species in the area of the „Mokry Bor” reserve carried in February 1995. Among the found green algae Apatococcus lobatus played important role. It occurred on the surface of nearly all examined trees creating dark green coatings on the tree barks (excluding Carpinus be lulus). On Abies and Picea apart from Apatococcus also other synantropic green alga occurred Gloeotila protogenita. They were accompanied by the following species: Chlorella vulgaris, Ch. ellipsoidea, Klebsormidium flaccidum, Stichococcus bacillaris, Pseudococcomyxa simplex and Heterothrix exilis, representing probably previous natural communities. Obtained ultrastructures of cells of Apatococcus showed inside some specimens presence of fungus haustorium, which however did not affect cellular structures of this algae. This form of symbiosis has not been observed so far in the case of this green alga. Characteristic ultrastructure observed in the green alga Gloeotila (in particular the thick layer of mucus surrounding the vegetative cells) proves presence on this area of a typical land form containing pyrenoid of a specific structure. Its land character is also proven by the reproduction ways.W tej pracy przedstawione zostały wyniki badań dotyczące glonów aerofitycznych, występujących na różnych drzewach na terenie rezerwatu ścisłego „Mokry Bór” (Świętokrzyski Park Narodowy). Materiał został zebrany w lutym 1995 r. Stwierdzono na prawie wszystkich badanych drzewach (z wyjątkiem Carpinus betulus) obecność Apatococcus lobatus.Zadanie pt. Digitalizacja i udostępnienie w Cyfrowym Repozytorium Uniwersytetu Łódzkiego kolekcji czasopism naukowych wydawanych przez Uniwersytet Łódzki nr 885/P-DUN/2014 zostało dofinansowane ze środków MNiSW w ramach działalności upowszechniającej naukę