Characterization of <Emphasis Type="Italic">target</Emphasis> nuclear DNA from faeces reduces technical issues associated with the assumptions of low-quality and quantity template

Faecal material has increasingly become an important non-invasive source of DNA for wildlife population genetics. However, DNA from faecal sources can have issues associated with quantity (low-template and/or low target-to-total DNA ratio) and quality (degradation and/or low DNA-to-inhibitor ratio). A number of studies utilizing faecal material assume and compensate for the above properties with minimal characterization of quantity or quality of target DNA, which can unnecessarily increase the risk of downstream technical problems. Here, we present a protocol which quantifies faecal DNA using a two step approach: (1) estimating total DNA concentration using a Picogreen^TM fluorescence assay and (2) estimating target nuclear DNA concentration by comparing amplification products of field samples at suspected concentrations to those of control DNA at known concentrations. We applied this protocol to faecal material collected in the field from two species: woodland caribou (Rangifer tarandus) and swift fox (Vulpes velox). Total DNA estimates ranged from 6.5 ng/μl to 28.6 ng/μl (X = 16.2 ng/μl) for the caribou extracts and 1.0–26.1 ng/μl (X = 7.5 ng/μl) for the swift fox extracts. Our results showed high concordance between total and target DNA estimates from woodland caribou faecal extracts, with only 10% of the samples showing relatively lower target-to-total DNA ratios. In contrast, DNA extracts from swift fox scat exhibited low target DNA yields, with only 38% (19 of 50) of the samples showing comparative target DNA amplification of at least 0.1 ng. With this information, we were able to estimate the amount of target DNA entered into PCR amplifications, and identify samples having target DNA below a lower threshold of 0.2 ng and requiring modification to genotyping protocols such as multiple tube amplification. Our results here also show that this approach can easily be adapted to other species where faeces are the primary source of DNA template.     

Linking woodland key habitat inventory and forest inventory data to prioritize districts needing conservation efforts

Woodland key habitat (WKH) inventories have been conducted in northern European countries, with the aim to create networks of minimally disturbed forest stands for protection. The goal of national forest inventory is to provide information relevant to forest management, such as on forest types, trees species composition, age structure and wood volume. The aim of this study was to link these two inventory databases to identify districts of Latvia most deficient in connectivity and habitat quality, in order to prioritize districts needing conservation effort. As an example, the area of deciduous forest with nemoral tree species (oak, ash, lime, maple and elm) and aspen was chosen. These forests provide habitat for a specific community of epiphytes. Using information in the WKH database, habitat quality in different districts of Latvia was estimated by the frequencies of occurrence of structural elements and selected indicator epiphyte species in nemoral tree species and aspen WKHs. Using digital data in the national forest inventory database, fragmentation metrics were determined for forests that, according to age and tree species composition, could potentially be nemoral tree and aspen WKHs. On a regional level, the lowest habitat quality in WKH occurred in districts that had the least fragmentation of potential WKH forest. In the less fragmented areas, the habitat quality of the existing WKH will likely increase in the future, and could be promoted by management to create structural elements typical of natural forests. The districts with the most fragmented nemoral and aspen forests, contained WKHs with the best habitat quality. A focus on protection should be given to these stands as they are the most likely to support source populations, and there is a need to improve spatial continuity of suitable tree substrate in these areas.     

The relationships between Ixodes ricinus and small mammal species at the woodland–pasture interface

Ixodes ricinus, as vector, and small mammals, as reservoirs, are implicated in pathogen transmission between wild fauna, domestic animals and humans at the woodland–pasture interface. The ecological relationship between ticks and small mammals was monitored in 2005 on four bocage (enclosed pastureland) sites in central France, where questing ticks were collected by dragging and small mammals were trapped. Questing I. ricinus tick and small mammal locations in the environment were assessed through correspondence analysis. I. ricinus larval burden on small mammals was modeled using a negative binomial law. The correspondence analyses underlined three landscape features: grassland, hedgerow, and woodland. Seven small mammal species were trapped, while questing ticks were all I. ricinus, with the highest abundance in woodland and the lowest in pasture. The small mammals were overall more abundant in hedgerow, less present in woodland and sparse in grassland. They carried mainly I. ricinus, and secondarily I. acuminatus and I. trianguliceps. The most likely profile for a tick-infested small mammal corresponded to a male wood mouse (Apodemus sylvaticus) in woodland or hedgerow during a dry day. A. sylvaticus, which was the only species captured in grassland, but was also present in hedgerow and woodland, may be a primary means of transfer of I. ricinus larvae from woodland to pasture.     

The late Holocene palaeoecological sequence of Serranía de las Villuercas (southern Meseta,western Spain)

New pollen results and radiocarbon dating from a valley mire in south-western Spain are presented. This is a region where few palaeoecological records have been preserved and the sequence yields important new palaeobotanical evidence for the late Holocene. The landscape is shown as having been largely open woodland, but more wooded than at present. The vegetation history of the last four millennia in these montane territories of south-western Iberia is discussed in the light of anthropogenic indicators, archaeological and documentary archives; fire incidence and climate change. Alnus is the predominant pollen type, although a decline is noted during the last couple of centuries. Its presence is connected with local topography behaving as a phreatophyte, that is, a plant which obtains a significant amount of water from the zone of saturated soil. A framework is also provided for the age and ecological dynamics of some major woodland taxa—Betula, Corylus, Ilex, evergreen and deciduous oaks, Ericaceae and Pinus. In addition, the natural status of several pollen taxa and local trends in biodiversity are discussed. We consider that the results of our work will have important implications for the understanding of the vegetation history in a floristically very rich area, with a noticeable diversity of woody taxa, and a relatively well preserved ecosystem structure.     

Oak woodland restoration: testing the effects on biodiversity of mycetophilids in southern Sweden

The effect of harvesting biofuel and woodland restoration on biodiversity is debated. To evaluate the effects of partial cutting on more organism groups, we used pairwise experimental and undisturbed control stands in a large landscape. On average 26% of the basal area including 50–95% of the understorey was harvested at each of 15 oak-rich forest sites. Our earlier results of partial cutting suggested a positive short-term effect for vascular plants and beetles and no or minor negative effects for fungi. Here we analyse the response of mycetophilids (Diptera: Sciaroidea excl. Sciaridae), a neglected but species-rich insect group that was strongly disfavoured by clear-cutting in previous studies. Increased deadwood (slash) caused increase in the number of individuals of mycetophilids associated with wood or wood fungi. The rarefaction species numbers of mycetophilids declined after the treatment, but the absolute number of species was not affected. Our results indicate that a 25% harvest can be compatible with conservation of vascular plants, fungi, saproxylic and herbivorous beetles and mycetophilids in temperate hardwood stands of the type studied. However, more studies are needed to determine what level(s) of stand thinning can be tolerated by different taxa in landscapes with small fragmented conservation stands.     

Rock-eating mycorrhizas: their role in plant nutrition and biogeochemical cycles

Rates of water uptake by individual trees in a native Australian forest were measured on the Liverpool Plains, New South Wales, Australia, using sapflow sensors. These rates were up-scaled to stand transpiration rate (expressed per unit ground area) using sapwood area as the scalar, and these estimates were compared with modelled stand transpiration. A modified Jarvis-Stewart modelling approach (Jarvis 1976), previously used to calculate canopy conductance, was used to calculate stand transpiration rate. Three environmental variables, namely solar radiation, vapour pressure deficit and soil moisture content, plus leaf area index, were used to calculate stand transpiration, using measured rates of tree water use to parameterise the model. Functional forms for the model were derived by use of a weighted non-linear least squares fitting procedure. The model was able to give comparable estimates of stand transpiration to those derived from a second set of sapflow measurements. It is suggested that short-term, intensive field campaigns where sapflow, weather and soil water content variables are measured could be used to estimate annual patterns of stand transpiration using daily variation in these three environmental variables. Such a methodology will find application in the forestry, mining and water resource management industries where long-term intensive data sets are frequently unavailable.     

Taphonomy of the early Miocene flora, Hiwegi Formation, Rusinga Island, Kenya

A fossil flora was collected in situ from early Miocene deposits at site R117 in the Hiwegi Formation of Rusinga Island contemporaneous with and in close proximity to the sites from where the anthropoid primates were recovered. The flora exhibits a spatially and temporally patchy distribution of fruits and seeds, mixed with twigs of various sizes, fragments of wood, bark, and leaves, all with random orientations and very low depositional dips. There has been minimal transport and the flora evidently accumulated as in situ litter beneath local vegetation. Based on Nearest Living Relatives (NLR) of fruits and seeds, the vegetation represented is a deciduous broad-leaved woodland with continuous canopy, with trees, shrubs, lianas, and climbers, reminiscent of the structure of the modern vegetation in the steep-sided protected valleys in the Laetoli-Endulen area. The interpretation of the vegetation is supported by the presence of twigs, wood, and bark fragments from larger diameter axes. Climbers are represented by twining stem fragments as well as by a wide variety of distinctive fruits and seeds. The proportion of fossilised thorny twigs represents only 3% of the twig collections, and there are no unequivocal forest trees amongst the NLR. No grasses were present; monocotyledons are only represented by a single date palm stone. No conifer seeds or cones have been recovered, and there are no coniferous leafy shoots.