Gerard Oostermeijer

How do plant ecologists use matrix population models

Matrix projection models are among the most widely used tools in plant ecology. However, the way in which plant ecologists use and interpret these models differs from the way in which they are presented in the broader academic literature. In contrast to calls from earlier reviews, most studies of plant populations are based on < 5 matrices and present simple metrics such as deterministic population growth rates. However, plant ecologists also cautioned against literal interpretation of model predictions. Although academic studies have emphasized testing quantitative model predictions, such forecasts are not the way in which plant ecologists find matrix models to be most useful. Improving forecasting ability would necessitate increased model complexity and longer studies. Therefore, in addition to longer term studies with better links to environmental drivers, priorities for research include critically evaluating relative/comparative uses of matrix models and asking how we can use many short-term studies to understand long-term population dynamics.

Ability of matrix models to explain the past and predict the future of plant populations.

Uncertainty associated with ecological forecasts has long been recognized, but forecast accuracy is rarely quantified. We evaluated how well data on 82 populations of 20 species of plants spanning 3 continents explained and predicted plant population dynamics. We parameterized stage-based matrix models with demographic data from individually marked plants and determined how well these models forecast population sizes observed at least 5 years into the future. Simple demographic models forecasted population dynamics poorly; only 40% of observed population sizes fell within our forecasts 95% confidence limits. However, these models explained population dynamics during the years in which data were collected; observed changes in population size during the data-collection period were strongly positively correlated with population growth rate. Thus, these models are at least a sound way to quantify population status. Poor forecasts were not associated with the number of individual plants or years of data. We tested whether vital rates were density dependent and found both positive and negative density dependence. However, density dependence was not associated with forecast error. Forecast error was significantly associated with environmental differences between the data collection and forecast periods. To forecast population fates, more detailed models, such as those that project how environments are likely to change and how these changes will affect population dynamics, may be needed. Such detailed models are not always feasible. Thus, it may be wiser to make risk-averse decisions than to expect precise forecasts from models.

On the life cycle and germination of Hottonia Palustris L. in a wetland forest

Abstract In 1986 and 1987, years that differed considerably in climatological conditions, the seasonal variation in biomass of Hottonia palustris L. was studied in the understory of a wetland forest. Furthermore, observations on its regeneration were made in the field and in the laboratory. The Hottonia population studied is characterized by early flowering, a large seed production, early development of maximum biomass, a well-developed vegetative regeneration and the ability to tolerate emergence and frost. The absence of overlying water in the summer of 1986 coincided with a relatively high biomass of Hottonia , while in the summer of 1987, when high water levels were recorded, its biomass considerably decreased. The seeds are characterized by their lack of innate dormancy, by the ability to remain viable after desiccation and by the ability to germinate over a relatively wide range of temperatures in the light and in an aerobic environment. No germination was observed under dark anaerobic conditions, and germination percentages were higher on a moist substrate than when the seeds were submerged. In the presence of overlying water most of the young seedlings rise to the water surface and may float there for several weeks. For their further development, however, a more or less permanent contact with the substrate seems to be required. Because of these life cycle characteristics, Hottonia palustris is well adapted to grow in the understory of wetland forests and in shallow waters that regularly dry up.

High levels of effective long-distance dispersal may blur ecotypic divergence in a rare terrestrial orchid

BackgroundGene flow and adaptive divergence are key aspects of metapopulation dynamics and ecological speciation. Long-distance dispersal is hard to detect and few studies estimate dispersal in combination with adaptive divergence. The aim of this study was to investigate effective long-distance dispersal and adaptive divergence in the fen orchid (Liparis loeselii (L.) Rich.). We used amplified fragment length polymorphism (AFLP)-based assignment tests to quantify effective long-distance dispersal at two different regions in Northwest Europe. In addition, genomic divergence between fen orchid populations occupying two distinguishable habitats, wet dune slacks and alkaline fens, was investigated by a genome scan approach at different spatial scales (continental, landscape and regional) and based on 451 AFLP loci.ResultsWe expected that different habitats would contribute to strong divergence and restricted gene flow resulting in isolation-by-adaptation. Instead, we found remarkably high levels of effective long-distance seed dispersal and low levels of adaptive divergence. At least 15% of the assigned individuals likely originated from among-population dispersal events with dispersal distances up to 220xa0km. Six (1.3%) ‘outlier’ loci, potentially reflecting local adaptation to habitat-type, were identified with high statistical support. Of these, only one (0.22%) was a replicated outlier in multiple independent dune-fen population comparisons and thus possibly reflecting truly parallel divergence. Signals of adaptation in response to habitat type were most evident at the scale of individual populations.ConclusionsThe findings of this study suggest that the homogenizing effect of effective long-distance seed dispersal may overwhelm divergent selection associated to habitat type in fen orchids in Northwest Europe.

BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology

BackgroundMaking forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as “Web services”) and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust “in silico” science. However, use of this approach in biodiversity science and ecology has thus far been quite limited.ResultsBioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on-line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible ‘virtual laboratory’, free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity.ConclusionsOur work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.

Matrix population models from 20 studies of perennial plant populations

Demographic transition matrices are among the most commonly applied population models for both basic and applied ecological research. The relatively simple framework of these models and simple, easily interpretable summary statistics they produce have prompted the wide use of these models across an exceptionally broad range of taxa. Here, we provide annual transition matrices and observed stage structures/population sizes for 20 perennial plant species which have been the focal species for long-term demographic monitoring. These data were assembled as part of the “Testing Matrix Models” working group through the National Center for Ecological Analysis and Synthesis (NCEAS). The data represent 82 populations with >460 total population-years of observations. It is our hope that making these data available will help promote and improve our ability to monitor and understand plant population dynamics. The complete data sets corresponding to abstracts published in the Data Papers section of the journal are publ...

Does pollen limitation affect population growth of the endangered Dracocephalum austriacum L.

Reproductive strategies can have significant consequences for the viability of plant populations. Still, the effects of lower fruit set due to pollen limitation on plant demography and population persistence have rarely been explored. The objectives of this study were to assess the ecological factors determining female reproductive success and to study the impact of pollen limitation on population growth of Dracocephalum austriacum L. (Lamiaceae), a critically endangered species with a discontinuous distribution across Europe. Despite the significant background information gathered on the population dynamics and genetic diversity of D. austriacum, little is known about its reproductive strategy and the effect it has on population growth. Thus, the reproductive system, pollinator assemblage and pollen limitation were studied in natural populations and the impact of pollen-limited seed production on population growth was assessed using existing transition matrix models. The results revealed that D. austriacum is protandrous self-compatible species that produces very few seeds in the absence of pollinators. The flowers are visited by several insects, including legitimate pollinators (e.g., Bombus hortorum, Osmia spp.) and nectar robbers (other Bombus spp., O. aurulenta). Fruit and seed production was significantly pollen-limited in all populations studied. However, despite the positive effect of pollen supplementation on seed production, the resulting increase in seed number did not significantly increase population growth rates in any of the studied populations. Hence, we conclude that populations are demographically stable and current natural seed production is sufficient for the species’ persistence.

Commercial harvesting and regeneration of epiphytic macrolichen communities in the Western Ghats, India

SUMMARY Non-timber forest products form a substantial contribution to the livelihood of many rural communities worldwide. In the Western Ghats, India, epiphyticmacrolichensareharvestedbyPaliyantribes to generate supplementary income. Paliyan tribes employ two harvesting methods: shallow harvesting, with a minimum of attached bark substratum, and deep harvesting, which exposes the sapwood. To evaluate the regeneration of the lichen community in termsofspeciesdiversity,abundanceandcomposition, 320 bark samples of up to 50 cm 2 were collected from bark patches where lichens had been harvested previously, as shown by bark scars. Samples selected represented four host tree species, both harvesting methods and seven one-year intervals of time since harvesting. In each case, the field guide estimated sample age, and peer-testing proved these estimates to be reliable up to an age of seven years. Seven years after harvesting, the lichen community showed noteworthy regeneration capacity in terms of total lichencoverageandspeciesrichness.However,toassess the risk of local species loss in the long-term, any harvesting should include continuous monitoring of lichen species composition. Since shallow harvesting resulted in a swifter recovery of species abundance and richness compared with deep harvesting, harvesters should preferentially employ the shallow harvesting method.

Window of opportunity of Liparis loeselii populations during vegetation succession on the Wadden Sea islands

The present study aims at assessing the life span of populations of the orchid L. loeselii during successional in dune slacks on the Wadden Sea islands. An inventory of Liparis loeselii populations was carried out on 6 islands, while the population structure was assessed in more detail on the island of Texel. The occurrence of the orchid was related to soil factors and hydrological conditions. Groundwater levels were measured in a dune area with natural dune slack formation. The groundwater composition was analyses and the freshwater lenses were modelled. Various scenarios were investigated, including sea level rise and sand nourishment. The window of opportunity for L. loeselii to colonize a new slack is relatively narrow. Under favorable management, the population can survive c. 20xa0years. Soil pH was positively correlated with the occurrence of L. loeselii populations, while a high organic matter content was negatively correlated. Sites with large populations of L. loeselii, were situated in young dune slacks, that functioned as flow-through lakes and has top soilsinfluenced by anoxic calcareous groundwater. Modelling showed that the freshwater lens would decrease due to sea level rise, while artificial sand nourishment could counteract this effect. The populations of the Hors area on Texel, the Netherlands, can survive for several decades due to continuous formation of new slacks. Discharge of calcareous groundwater is essential to keep the pH on a high level. The hydrological systems that supply dune slack with groundwater are relatively small and are vulnerable for changes in sea level rise.

Outbreeding depression and breeding system evolution in small, remnant populations of Primula vulgaris: consequences for genetic rescue

Many species suffer from anthropogenic habitat fragmentation. The resulting small and isolated populations are more prone to extinction due to, amongst others, genetic erosion, inbreeding depression and Allee-effects. Genetic rescue can help mitigate such problems, but might result in outbreeding depression. We evaluated offspring fitness after selfing and outcrossing within and among three very small and isolated remnant populations of the heterostylous plant Primula vulgaris. We used greenhouse-grown offspring from these populations to test several fitness components. One population was fixed for the pin-morph, and was outcrossed with another population in the field to obtain seeds. Genetic diversity of parent and offspring populations was studied using microsatellites. Morph and population-specific heterosis, inbreeding and outbreeding depression were observed for fruit and seed set, seed weight and cumulative fitness. Highest fitness was observed in the field-outcrossed F1-population, which also showed outbreeding depression following subsequent between-population (back)crossing. Despite outbreeding depression, fitness was still relatively high. Inbreeding coefficients indicated that the offspring were more inbred than their parent populations. Offspring heterozygosity and inbreeding coefficients correlated with observed fitness. One population is evolving homostyly, showing a thrum morph with an elongated style and high autonomous fruit and seed set. This has important implications for conservation strategies such as genetic rescue, as the mating system will be altered by the introduction of homostyles.