Chloroplast microsatellites: new tools for studies in plant ecology and systematics

The nonrecombinant, uniparentally inherited nature of organelle genomes
makes them useful tools for evolutionary studies. However, in plants, detecting
useful polymorphism at the population level is often difficult because of the
low level of substitutions in the chloroplast genome, and because of the slow
substitution rates and intramolecular recombination of mtDNA. Chloroplast
microsatellites represent potentially useful markers to circumvent this problem
and, to date, studies have demonstrated high levels of intraspecific variability.
Here,we discuss the use of these markers in ecological and evolutionary
studies of plants, as well as highlighting some of the potential problems
associated with such use.

Woodland decline in upland Scotland

The recent article by Fenton (Fenton JH. 2008. A postulated natural origin for the open landscape of upland Scotland. Plant Ecology & Diversity 1:115–127) has argued that the landscapes of upland Scotland are treeless because of long-term deterioration of soil conditions. There are reasons for thinking that this might be the case in the absence of human activity. However, there have been considerable anthropogenic pressures on these landscapes for several millenia, documented archaeologically and palaeoecologically. Attempting to exclude these pressures from the discussion can only lead to an incomplete and misleading account of a complex series of changes involving an interaction which includes natural vegetational and environmental processes, climatic changes and human pressures.

Long-term ecology of native pinewood communities in East Glen Affric, Scotland

Fossil pollen, stomata and charcoal were examined from a lake sedimentary sequence in the Glen Affric National Nature Reserve, one of the largest areas of remnant native pine woodland in Scotland, in order to assess ecosystem dynamics over the last 11 000 years. Results reveal that pinewood communities have been continuously present in East Glen Affric for the last 8300 years. Pinus sylvestris fi rst arrived in the area around 9900 cal. BP, but occurred in only low abundance for the subsequent 1600 years. Pine populations expanded around 8300 cal. BP and remained in relatively constant abundance throughout the remainder of the Holocene. There is no evidence of a hypothesized regional mid-Holocene ‘ pine decline ’ at the site. Charcoal results reveal that pinewood communities in East Glen Affric do not appear to have been dependent on fire for either their establishment or their maintenance as has previously been suggested.

A set of primers for plastid indels and nuclear microsatellites in the invasive plant Heracleum mantegazzianum (Apiaceae) and their transferability to Heracleum sphondylium

This study reports the isolation and polymorphism characterization of four plastid indels and six nuclear microsatellite loci in the invasive plant Heracleum mantegazzianum. These markers were tested in 27 individuals from two distant H. mantegazzianum populations. Plastid indels revealed the presence of five chlorotypes while five nuclear microsatellite loci rendered polymorphism. Applications of these markers include population genetics and phylogeography of H. mantegazzianum. A very good transferability of markers to Heracleum sphondylium was demonstrated.

Development of microsatellites for the invasive riparian plant Impatiens glandulifera (Himalayan balsam) using intersimple sequence repeat cloning

Impatiens glandulifera (Himalayan balsam) is an invasive riparian plant species that can outcompete native perennials. Population genetic data on dispersal may aid in the management of invasive species, so we have developed microsatellite markers for this significant invader using an intersimple sequence repeat (ISSR)-based cloning method. Eight polymorphic markers displayed between two and five alleles, with overall levels of observed and expected heterozygosities ranging from 0.0500 to 0.7500 and from 0.1449 to 0.7692, respectively.

Variability in thermal and UV-B energy fluxes through time and their influence on plant diversity and speciation

Throughout Earth's history there have been temporal and spatial variations in the amount of visible and ultraviolet radiation received by ecosystems. This paper examines if temporal changes in these forms of energy receipt could have influenced the tempo and mode of plant diversity and speciation, focusing in particular upon Cenozoic time-scales. Evidence for changing patterns of plant diversity and speciation apparent in various fossil records and molecular phylogenies are considered alongside calculated changes in thermal and solar ultraviolet energy (specifically UV-B) over the past 50 Myr. We suggest that changes in thermal energy influx (amount and variability) affected the tempo of evolution through its influence upon community dynamics (e.g. population size, diversity, turnover, extinctions). It was not only the amount of thermal energy but also variability in its flux that may have influenced these processes, and ultimately the rate of diversification. We suggest that variations in UV-B would have influenced the mode and tempo of speciation through changes to genome stability during intervals of elevated UV-B. We argue, therefore, that although variability in thermal energy and UV-B fluxes through time may lead to the same end-point (changing the rate of diversification), the processes responsible are very different and both need to be considered when linking evolutionary processes to energy flux.

Refugial persistence and postglacial recolonization of North America by the cold-tolerant herbaceous plant Orthilia secunda

Previous phylogeographical and palaeontological studies on the biota of northern North America have revealed a complex scenario of glacial survival in multiple refugia and differing patterns of postglacial recolonization. Many putative refugial regions have been proposed both north and south of the ice sheets for species during the Last Glacial Maximum, but the locations of many of these refugia remain a topic of great debate. In this study, we used a phylogeographical approach to elucidate the refugial and recolonization history of the herbaceous plant species Orthilia secunda in North America, which is found in disjunct areas in the west and east of the continent, most of which were either glaciated or lay close to the limits of the ice sheets. Analysis of 596-bp of the chloroplast trnS-trnG intergenic spacer and five microsatellite loci in 84 populations spanning the species' range in North America suggests that O.secunda persisted through the Last Glacial Maximum (LGM) in western refugia, even though palaeodistribution modelling indicated a suitable climate envelope across the entire south of the continent. The present distribution of the species has resulted from recolonization from refugia north and south of the ice sheets, most likely in Beringia or coastal regions of Alaska and British Columbia, the Washington/Oregon region in the northwest USA, and possibly from the region associated with the putative 'ice-free corridor' between the Laurentide and Cordilleran ice sheets. Our findings also highlight the importance of the Pacific Northwest as an important centre of intraspecific genetic diversity, owing to a combination of refugial persistence in the area and recolonization from other refugia.

Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus.

Bursaphelenchus xylophilus is the nematode responsible for a devastating epidemic of pine wilt disease in Asia and Europe, and represents a recent, independent origin of plant parasitism in nematodes, ecologically and taxonomically distinct from other nematodes for which genomic data is available. As well as being an important pathogen, the B. xylophilus genome thus provides a unique opportunity to study the evolution and mechanism of plant parasitism. Here, we present a high-quality draft genome sequence from an inbred line of B. xylophilus, and use this to investigate the biological basis of its complex ecology which combines fungal feeding, plant parasitic and insect-associated stages. We focus particularly on putative parasitism genes as well as those linked to other key biological processes and demonstrate that B. xylophilus is well endowed with RNA interference effectors, peptidergic neurotransmitters (including the first description of ins genes in a parasite) stress response and developmental genes and has a contracted set of chemosensory receptors. B. xylophilus has the largest number of digestive proteases known for any nematode and displays expanded families of lysosome pathway genes, ABC transporters and cytochrome P450 pathway genes. This expansion in digestive and detoxification proteins may reflect the unusual diversity in foods it exploits and environments it encounters during its life cycle. In addition, B. xylophilus possesses a unique complement of plant cell wall modifying proteins acquired by horizontal gene transfer, underscoring the impact of this process on the evolution of plant parasitism by nematodes. Together with the lack of proteins homologous to effectors from other plant parasitic nematodes, this confirms the distinctive molecular basis of plant parasitism in the Bursaphelenchus lineage. The genome sequence of B. xylophilus adds to the diversity of genomic data for nematodes, and will be an important resource in understanding the biology of this unusual parasite.

Testate amoebae as indicators of hydroseral change: an 8,500 year record from Mer Bleue Bog, eastern Ontario, Canada.

Testate amoebae have been used widely as a proxy of hydrological change in ombrotrophic peatlands, although their response to abiotic controls in other types of mire and fenland palaeo-environments is less well understood. This paper examines the response of testate amoebae to hydroseral and other environmental changes at Mer Bleue Bog, Ontario, Canada, a large ombrotrophic peatland, which evolved from a brackish-water embayment in the early Holocene. Sediments, plant macrofossils and diatoms examined from a 5.99 m core collected from the dome of the bog record six stages of development: i) a quiet, brackish-water riverine phase (prior to ca. 8500 cal BP); ii) a shallow lake (ca. 8500–8200 cal BP); iii) fen (8200–7600 cal BP); iv) transitional mire (7600–6900 cal BP); v) pioneer raised mire (6900–4450 cal BP); and vi) ombrotrophic bog (4450 cal BP-present).

Testate amoebae, notably small (<25 µm diameter) specimens of Centropyxis aculeata type, first appear in low abundances in sediments ascribed to the lacustrine phase. Diatoms from the same horizons record a shallowing in water depth, a decline in salinity and the development of emergent macrophytic vegetation, which may have provided favourable conditions for testate amoeba colonization. The testate amoeba communities of the inferred fen phase are more diverse and include centropyxids, cyclopyxids, Arcellidae and Hyalospheniidae, although the assemblages show some differences to those recently reported in modern European fen environments. The Fen–Bog Transition (FBT) is also dominated by C. aculeata type. The change in testate amoeba communities around this key transition is apparent in the results of Detrended Correspondence Analysis (DCA), and appears to reflect a latent nutrient gradient and a secondary moisture gradient. DCA analyses of plant macrofossil remains around the FBT show a similar trend, although the sensitivity of the two proxies to the inferred environmental changes differs. Comparisons with other regional mid-Holocene peatland records confirm the important influence of reduced effective precipitation on the testate amoeba communities during the initiation and development of Sphagnum-dominated, raised bog communities.

Novel bioassays to examine the host-finding ability of plant-parasitic nematodes

We present two novel bioassays to be used in the examination of plant-parasitic nematode host-finding ability. The host-finding 'pipette-bulb assay' was constructed from modelled Pasteur pipette bulbs and connecting barrels using parafilm fastenings. This assay examines the direction of second-stage juvenile (J2) migration in response to a host seedling, through a moistened sand substrate, which underlies terminal upward-facing 'seedling bulbs', one containing a host seedling in potting compost, the other with only potting compost. An equal watering regime through both upward-facing seedling bulbs creates a directional concentration gradient of host diffusate chemotactic factors. Positive chemotactic stimuli cause the J2 to orientate and migrate towards the host plant. We present validation data collected from assays of the root-knot nematode, Meloidogyne incognita, and the potato cyst nematode, Globodera pallida, which indicate a highly significant positive attraction of J2 of both species to respective host plants. This represents a simple, quick and inexpensive method of assessing host-finding behaviour in the laboratory. We consider that the pipette-bulb assay improves on previous host-finding/chemo-attraction assays through creating a more biologically relevant environment for experimental J2; analysis is quick and easy, allowing the straightforward interpretation of results. In addition, we have developed an 'agar trough' sensory assay variant which we believe can be used rapidly to ratify nematode responses to chemical gustatory or olfactory cues. This was constructed from a water agar substrate such that two counting wells were connected by a raised central trough, all flooded with water. Two small water agar plugs were dehydrated briefly in an oven and then hydrated in either an attractant, repellent or water control; these plugs were then placed in the terminal counting wells and subsequently leached the attractant or repellent to form a concentration gradient along the central trough, which contained the initial J2 innoculum. Our data show that both M. incognita and G. pallida J2 are positively attracted to host diffusates. In addition, they displayed a strong repulsion in response to 1 M NaCl2. J2 of M. incognita displayed a mild aversion to a non-host oak root diffusate, whereas G. pallida J2 displayed a strong aversion to the same non-host diffusate; neither species responded to a compost leachate. We believe that the agar trough assay improves on previous methods by facilitating rapid diffusion of attractant or repellents. Both of the aforementioned assays were designed as tools to assess the impact of RNAi-based reverse genetics screens for gene targets involved in chemosensory orientation.

Hierarchical Bayesian models in ecology: Reconstructing species interaction networks from non-homogeneous species abundance data

The relationships among organisms and their surroundings can be of immense complexity. To describe and understand an ecosystem as a tangled bank, multiple ways of interaction and their effects have to be considered, such as predation, competition, mutualism and facilitation. Understanding the resulting interaction networks is a challenge in changing environments, e.g. to predict knock-on effects of invasive species and to understand how climate change impacts biodiversity. The elucidation of complex ecological systems with their interactions will benefit enormously from the development of new machine learning tools that aim to infer the structure of interaction networks from field data. In the present study, we propose a novel Bayesian regression and multiple changepoint model (BRAM) for reconstructing species interaction networks from observed species distributions. The model has been devised to allow robust inference in the presence of spatial autocorrelation and distributional heterogeneity. We have evaluated the model on simulated data that combines a trophic niche model with a stochastic population model on a 2-dimensional lattice, and we have compared the performance of our model with L1-penalized sparse regression (LASSO) and non-linear Bayesian networks with the BDe scoring scheme. In addition, we have applied our method to plant ground coverage data from the western shore of the Outer Hebrides with the objective to infer the ecological interactions. (C) 2012 Elsevier B.V. All rights reserved.

Trait assembly in plant assemblages and its modulation by productivity and disturbance

Understanding how communities assemble is a key challenge in ecology. Conflicting hypotheses suggest that plant traits within communities should show divergence to reflect strategies to reduce competition or convergence to reflect strong selection for the environmental conditions operating. Further hypotheses suggest that plant traits related to productivity show convergence within communities, but those related to disturbance show divergence. Data on functional diversity (FD ) of 12 traits from 30 communities ranging from arable fields, mown and grazed grasslands to moorland and woodland were employed to test this using randomisations tests and correlation and regression analysis. No traits showed consistent significant convergence or divergence in functional diversity. When correlated to measures of the environment, the most common pattern was for functional diversity to decline (7 out of 12 traits) and the degree of convergence (7 out of 12 traits) to increase as the levels of productivity (measured as primary productivity, soil nitrogen release and vegetation C:N) and disturbance increased. Convergence or a relationship between functional diversity and the environment was not seen for a number of important traits, such as LDMC and SLA, which are considered as key predictors of ecosystem function. The analysis indicates that taking into account functional diversity within a system may be a necessary part of predicting the relationship between plant traits and ecosystem function, and that this may be of particular importance within less productive and less disturbed systems. © 2011 Springer-Verlag.