Low genetic diversity in tepui summit vertebrates

The Pantepui region of South America, located in southern Venezuela, northern Brazil, and western Guyana, is characterized by table mountains (tepuis) made of Proterozoic (> 1.5 billion years old) sandstone - the highest reaching nearly 3 km - that are isolated from their surroundings by up to 1000 m high vertical cliffs (Figure 1A). Tepuis are among the most inaccessible places on earth (Supplemental information), and the majority of their summits have been visited less than the moon. Due to its age and topography [1,2], this region has been assumed to be an ideal nursery of speciation and a potential inland counterpart to oceanic islands [3,4]. High endemism has been reported for the flora (25% in vascular plants) and fauna (68.5% in amphibians and reptiles) of single tepuis [5,6], and an ancient origin has been postulated for some of these organisms. But, it has also been suggested that a few taxa living in habitats extending from lowlands to summits (e.g., savannah) invaded some of the more accessible tepuis only recently [6-8]. Taken at face value, the overall timing and extent of biotic interchange between tepui summits has remained unstudied. Here, we show that recent faunal interchange among currently isolated tepui summits has been extensive, and affected even taxa living in some of the most tepui-specific habitats and on the most inaccessible summits.     

Importance of grazing and soil acidity for plant community composition and trait characterisation in coastal dune grasslands

Question: Does grazing by large herbivores affect species composition or community‐wide variation in plant functional traits? Location: Dune grasslands at the Belgian coast. Methods: Plant cover and soil data were collected in 146 plots that were randomly selected at 26 grazed and ungrazed grassland sites. Plant community composition was assessed by Detrended Correspondence Analysis and mean values of plant trait categories were calculated across the plots. Results: Differentiation of plant composition and community‐wide plant trait characteristics was largely determined by grazing, soil acidity and their interaction. In ungrazed situations, a clear floristic distinction appears between acidic (non‐calcareous) and alkaline (calcareous) grasslands. In grazed situations, these floristic differences largely disappeared, indicating that grazing results in a decrease of natural variation in species composition. At higher soil pH, a larger difference in plant community composition and community‐wide plant traits was observed between grazed and ungrazed plots. In ungrazed situations, shifts in plant functional traits along the acidity gradient were observed. Conclusions: Grazing is responsible for shifts in plant community composition, and hence a decrease in plant diversity among grasslands at opposing acidity conditions in coastal dune grasslands. Therefore, care should be taken when introducing grazing as a system approach for nature conservation in dune grasslands as it may eliminate part of the natural variation in plant diversity along existing abiotic gradients.     

Can a seed bank maintain the genetic variation in the above ground plant population?

There are indications that a persistent seed bank can protect small and isolated plant populations from local extinction. Genetic mechanisms contributing to this phenomenon are the increase of local effective population size – and hence the decrease of genetic drift – through a reservoir of persistent seeds, and the accumulation of intergenerational genetic diversity in the seed bank. To find evidence for these mechanisms, we conducted two formal meta-analyses. First, we analyzed 42 published habitat fragmentation studies and investigated whether the degree of genetic differentiation between fragmented plant populations was mediated by seed longevity. Second, we reviewed 13 published studies reporting the genetic diversity of both the seed bank and the above ground plants, aiming at comparing genetic diversity contained in the seed bank with the above ground vegetation. We conclude that a persistent seed bank may indeed mitigate the consequences of habitat fragmentation and protect a species from genetic drift and population genetic differentiation. We found no evidence, however, of high levels of genetic diversity accumulating in the soil seed bank. If genetic differences are present between the standing crop and the seed bank, they are very likely the result of local selection acting either directly or indirectly as a filter on the alleles present in the seed bank. We finally suggest that 1) the role of the seed bank should not be neglected in habitat fragmentation studies and 2) it is not very fruitful to continue comparing seed bank genetic diversity with above ground plant genetic diversity, unless this is performed under different selection regimes.     

Toad radiation reveals into-India dispersal as a source of endemism in the Western Ghats-Sri Lanka biodiversity hotspot

Background  

High taxonomic level endemism in the Western Ghats-Sri Lanka biodiversity hotspot has been typically attributed to the subcontinent's geological history of long-term isolation. Subsequent out of – and into India dispersal of species after accretion to the Eurasian mainland is therefore often seen as a biogeographic factor that 'diluted' the composition of previously isolated Indian biota. However, few molecular studies have focussed on into-India dispersal as a possible source of endemism on the subcontinent. Using c. 6000 base pairs of mitochondrial and nuclear DNA, we investigated the evolutionary history and biogeography of true toads (Bufonidae), a group that colonized the Indian Subcontinent after the Indo-Asia collision.     

Towards complete and accurate reporting of studies of diagnostic accuracy: the STARD initiative

ObjectiveTo improve the accuracy and completeness of reporting of studies of diagnostic accuracy, to allow readers to assess the potential for bias in a study, and to evaluate a study''s generalisability.MethodsThe Standards for Reporting of Diagnostic Accuracy (STARD) steering committee searched the literature to identify publications on the appropriate conduct and reporting of diagnostic studies and extracted potential items into an extensive list. Researchers, editors, and members of professional organisations shortened this list during a two day consensus meeting, with the goal of developing a checklist and a generic flow diagram for studies of diagnostic accuracy.ResultsThe search for published guidelines about diagnostic research yielded 33 previously published checklists, from which we extracted a list of 75 potential items. At the consensus meeting, participants shortened the list to a 25 item checklist, by using evidence, whenever available. A prototype of a flow diagram provides information about the method of patient recruitment, the order of test execution, and the numbers of patients undergoing the test under evaluation and the reference standard, or both.ConclusionsEvaluation of research depends on complete and accurate reporting. If medical journals adopt the STARD checklist and flow diagram, the quality of reporting of studies of diagnostic accuracy should improve to the advantage of clinicians, researchers, reviewers, journals, and the public.The Standards for Reporting of Diagnostic Accuracy (STARD) steering group aims to improve the accuracy and completeness of reporting of studies of diagnostic accuracy. The group describes and explains the development of a checklist and flow diagram for authors of reports     

Assignment of the fucosidase pseudogene FUCA1P to chromosome region 2q31----q32

FUCA1P is a pseudogene of the structural fucosidase gene FUCA1. The former has been mapped to human chromosome 2, whereas the latter has been localized to chromosome 1p34----p36. We have further localized FUCA1P to chromosomal band 2q31----q32 by fluorescent in situ hybridization and digital imaging microscopy. This localization was confirmed by linkage analysis between FUCA1P and the COL3A1 gene in 2q24----q32 which gave maximal lod scores of 4.03 at 3% recombination.     

Seed bank and vegetation composition of forest stands of varying age in central Belgium: consequences for regeneration of ancient forest vegetation

Vegetation composition differs significantly between ancientand recent forest, due to slow colonization capacity of typical forest speciesand the higher abundance of early successional species in recent forest.However, little is known about differences in persistent seed bank compositionbetween ancient and recent forest and about the interaction between seed bankand vegetation in relation with forest age. We surveyed the seed bank and theunderstorey vegetationcomposition in transects from ancient to recent forest. Seed bank and fieldlayer vegetation characteristics and similarity between seed bank andvegetationwere analysed in relation to recent forest age and distance to the ancientforest. A total of 39 species and 14,911 seedlings germinated, whichcorresponds with a seed density of 12,426 seeds/m².Total seed density is significantly higher in the youngest recent forest parcel(55 years). Also the seed bank composition in the youngest forest parceldifferssignificantly from the other parcels. After a longer period of reforestation,the seed bank approaches that of the ancient forest, suggesting seed bankdepletion, although the seed bank is permanently replenished to some extent byseed bank forming species from local disturbances. Seed bank composition doesnot change significantly with distance to the ancient forest. Similaritybetween seed bank and vegetation composition, nomatter the forest age, is very low, but decreases with increasing forest age.The most frequent species in the vegetation are absent in the seed bank andvice versa. The contribution of forest species is highin the vegetation and they almost not occur in the seed bank, while species offorest edges and clearings, and species of disturbed environments are morefrequent in the seed bank. The seed bank is mainly composed of earlysuccessional species of former forest stages or species which temporary occurinsmall-scale disturbances. The seed bank may enhance the negative effects ofearlysuccessional, mainly competitive species to the forest species richness in therecent forest. In this respect, forest management should minimise forestdisturbances, to prevent germination of competitive species form buriedseeds.     

The role of soil seed banks in the restoration of dry acidic dune grassland after burning of Ulex europaeus scrub

Question: Can the seed bank play a significant role in the restoration of plant communities of dry acidic dune grassland where fire has destroyed Ulex europaeus scrub? Location: Northern French Atlantic coast. Methods: One year after the fire, the seed bank and vegetation were sampled in 1 m × 1 m plots along three transects from the oldest scrub vegetation towards the grassland. Differences in species richness, seed density and contribution of ecological groups in the seed bank and vegetation along the transects were analysed. Results: Seed density and species richness in the seed bank decreased significantly from the grassland towards the centre of the scrub vegetation; 50% of the seed bank consisted of core species of the target plant community, such as Carex arenaria, Aira praecox, Rumex acetosella and Agrostis capillaris. Seeds of these species were also found in the deeper soil layers beneath the oldest scrub vegetation, indicating that they can be considered to be long‐term persistent. Beneath the youngest scrub vegetation, seeds of rare satellite target species also occurred. However, no target species were established on the burned site after one year, resulting in a large discrepancy between seed bank and vegetation. Conclusions: Although the seeds present in the soil indicate that restoration of the acidic grassland based on the seed bank is possible, additional management actions such as mowing and soil disturbance may be necessary to restrict resprouting of Ulex and to stimulate the germination of seeds of target species in the deeper soil layers.     

Seedling establishment after endozoochory in disturbed and undisturbed grasslands

Local plant community composition and structure may be largely influenced by germination and seedling establishment from seeds dispersed in animal dung, through seed input, gap creation and nutrient enrichment. With an experimental approach we assessed (1) what the effect is of dung deposition on the number of seedlings in the plant community 3 months and 1 year after dung deposition, (2) what the effect is of this seedling establishment on the local plant community characteristics such as species richness and (3) if this effect interacts with large-scale soil disturbance which removes the close canopy, such as sod-cutting. Viable seeds of monocotylous species were abundantly present in the dung, and dung deposition led to a higher number of monocotylous seedlings after 3 months. However, this effect was no longer significant after 1 year. Moreover, the proportion of viable monocotylous seeds that effectively established in the field after 3 months was less than 5%. A lower number of viable seeds of the less-dominant dicotylous species was dispersed in the dung but they had a higher cover and species richness after 1 year. This resulted in an increased total small-scale species richness and diversity after dung deposition through a decreasing dominance of monocotylous species. Sod-cutting had a pronounced effect on seedling emergence: viable seeds dispersed by dung had a higher probability of successful establishment when the dung was deposited in large gaps. This indicates that an increase of safe sites associated with disturbance strengthens the effects of seed dispersal and gap creation by dung deposition.