Conifers are evolutionarily more ancient than their angiosperm counterparts, and thus some adaptive mechanisms and features influenced by epigenetic mechanisms appear more highly displayed in these woody gymnosperms. Conifers such as Norway spruce have very long generation times and long life spans, as well as large genome sizes. This seemingly excessive amount of genomic DNA without apparent duplications could be a rich source of sites for epigenetic regulation and modifications. In Norway spruce, an important adaptive mechanism has been identified, called epigenetic memory. This affects the growth cycle of these trees living in environments with mild summers and cold winters, allowing them to adapt rapidly to new and/or changing environments. The temperature during post-meiotic megagametogenesis and seed maturation epigenetically shifts the growth cycle programme of the embryos. This results in significant and long-lasting phenotypic change in the progeny, such as advance or delay of vital phenological processes of high adaptive value, like bud break and bud set. This phenomenon is not only of important evolutionary significance but has clear practical implications for forest seed production and conservation of forest genetic resources. The underlying molecular mechanism that causes the ‘memory’ in long-lived woody species is currently under investigation. Here we summarize the information related to epigenetic memory regulation in gymnosperms, with special emphasis on conifers. The molecular mechanism behind this is still unknown but transcriptional changes are clearly involved. Epigenetic regulation may be realized through several mechanisms, including DNA methylation, histone modification, chromatin remodelling, small non-coding RNAs and transposable element regulation, of which non-coding RNAs might be one of the most important determinants.

Seed germination experiments are conducted in a wide variety of biological disciplines. Numerous methods of analysing the resulting data have been proposed, most of which fall into three classes: intuition-based germination indexes, classical non-linear regression analysis and time-to-event analysis (also known as survival analysis, failure-time analysis and reliability analysis). This paper briefly reviews all three of these classes, and argues that time-to-event analysis has important advantages over the other methods but has been underutilized to date. It also reviews in detail the types of time-to-event analysis that are most useful in analysing seed germination data with standard statistical software. These include non-parametric methods (life-table and Kaplan–Meier estimators, and various methods for comparing two or more groups of seeds) and semi-parametric methods (Cox proportional hazards model, which permits inclusion of categorical and quantitative covariates, and fixed and random effects). Each method is illustrated by applying it to a set of real germination data. Sample code for conducting these analyses with two standard statistical programs is also provided in the supplementary material available online (at http://journals.cambridge.org/). The methods of time-to-event analysis reviewed here can be applied to many other types of biological data, such as seedling emergence times, flowering times, development times for eggs or embryos, and organism lifetimes.

Assessments of seed storage physiology among Arecaceae (palm) species are often inconclusive because seeds exhibit diverse responses to low temperature and moisture conditions. Interrelationships between dry matter accumulation, cell structure and water relations during seed development of the endangered Hawaiian endemic palm, Pritchardia remota, suggest that damage from drying results from mechanical strain. Endosperm and fruits accumulate dry mass through most of the 400 d gestation period, but embryos reached maximum dry mass about 250 d post-anthesis (DPA). Mostly sucrose and some triacylglycerols accumulated in the cytoplasm and vacuoles of embryo cells, and organelles in mature embryo cells de-differentiated. Water content and water potential decreased as embryos matured and embryos contained about 0.45 g H2O (g dry mass)− 1 ( − 26 MPa) at shedding. Mature embryos survived drying to 0.16 g g− 1 ( − 49 MPa), but further drying was lethal. A model of allowable cell shrinkage is consistent with the substantial, but incomplete, desiccation tolerance acquired in P. remota embryos, and provides a new framework to explain variation in critical water contents as embryos develop. We suggest that desiccation tolerance, which distinguishes recalcitrant and orthodox physiologies among seeds, can be quantified by mechanical strain when embryo cells shrink during drying.

Tephroseris longifolia subsp. moravica (Asteraceae) is an endangered narrow endemic taxon recently recorded from nine sites in Slovakia and the Czech Republic. We provide the first consistent information on its reproductive biology – mating system, seed output, germination, seedling emergence and survival. Based on results from isolation, hybridization and emasculation experiments on different subspecies, T. longifolia s.l. should be treated as an allogamous taxon without apomictic reproduction. Five populations of T. l.moravica were studied in detail for seed output and germination characteristics. The output of well-developed seeds per flowering shoot was estimated to be 592 (1125 seeds per flowering plant). A granivorous butterfly, Phycitodes albatella (family Pyralidae), was identified as a pest, reducing seed output by 18–28%. Germination (reaching 30–62% after dry storage for 4 months) rapidly decreased with storage in room conditions. Deep freeze storage increased germination, although not significantly. Seeds obtained from natural populations had higher germination percentages and germinated faster than seeds from cultivated plants. Seedling emergence in situ was very low (0.9–2.06% of the sown seeds) without significant differences among sites.

This study investigates how methodological aspects of seed-bank sampling affect seed-bank records in temperate deciduous forests. We focused explicitly on seed-bank records of ancient forest species, which are assumed to lack a persistent seed bank; a hypothesis suspected to be partly due to methodological shortcomings. Through a quantitative review of 31 seed-bank studies in temperate deciduous forests of central and north-west Europe, we quantified the role of sampling methodology in constraining total seed-bank records and seed-bank records of ancient forest species (γ-diversity, average species' retrieval frequency and average seed density). A major methodological trade-off was established between sampled plot area and the number of plots: at an increased number of plots, the area sampled per plot decreased significantly. The total surface area sampled in a study was the primary determinant of γ-diversity, both for overall species richness and for ancient forest species richness. A high retrieval frequency of ancient forest species indicated that few plots were intensively sampled. The parallel increase in total species richness and ancient forest species richness and the non-significance of their ratio in relation to methodological variables suggests that ancient forest species are not particularly rare in the seed bank compared to other species. These results imply that sampling methodology has a far-reaching impact on seed-bank records such as γ-diversity, the detection of ancient forest species and ultimately seed-bank composition. We formulate a set of guidelines to improve the quality of seed-bank studies in temperate deciduous forests.

The naturally occurring fungal seed pathogen, Pyrenophora semeniperda, reduces the seed bank of Bromus tectorum but the role of plant litter in this seed–pathogen interaction is unexplored. To investigate the direct and indirect effects of litter on this interaction, we first collected field seed-bank samples from low and high Bromus litter patches. From these data, we explored the relationship between litter depth, seed-bank density and seed mortality from P. semeniperda. Second, we manipulated the fungal stages (conidial spores and mycelium) in/on the litter through sterilization techniques, to measure the direct effect of litter on seed death. Third, for indirect effects, we manipulated litter levels and held seed density and inoculum constant to determine whether Bromus litter could modify the seed zone microsites to favour disease. We found that seed-bank samples from high-litter patches contained higher field-killed seed densities compared with low-litter patches, although the percent difference of disease between litter patch types varied among sites and years (e.g. 80% to 46%). In testing the direct effects of litter on the seed–pathogen interaction, we found that litter can act as a direct inoculum source for the pathogen in the early summer but decreases in disease transmission by the following spring when the litter naturally is in contact with seeds. Investigating indirect effects, we found four times as many pathogen-killed seeds in high-litter treatments as compared with low-litter treatments when inoculum loads and seed densities were held constant. In addition, we found that litter influences the seed–pathogen interaction through density-dependent disease transmission. Our findings demonstrate the ecological importance of litter in semi-arid environments as it influences disease levels of a seed pathogen by direct and indirect means.