Do ridge habitats contribute to pteridophyte diversity in tropical montane forests? A case study from southeastern Ecuador

We address the question to which degree ridge habitats in tropical montane forests contribute to overall plant diversity by analysing patterns of pteridophyte (i.e. lycophytes and ferns) assemblages on ridges and slopes in three montane forest sites near Podocarpus National Park, Ecuador. The analyses, which involved 158 pteridophyte species (110 terrestrial, 96 epiphytic, 48 both) from 28 plots of 20 m × 20 m (or an equivalent of 400 m²), showed that more species were typical of one of the three study sites than of one of the two habitats (ridge/slope). As found in previous studies, alpha diversity on ridges was lower than on slopes, accounted for by the absence of numerous species that are found on slopes. Pteridophyte assemblages on ridges were more similar across study sites than those on slopes. Thus, unlike the structurally comparable (i.e. stunted, open) Amazonian forests, the studied montane ridge forests harbour fairly homogenous pteridophytes assemblages with very few specialised species. Our study implies that slope forests are of higher conservation priority for pteridophytes in the study region than ridge habitats. However, comparative studies are needed because other geographical regions and other groups of organisms may not share this pattern. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Do lichens domesticate photobionts like farmers domesticate crops? Evidence from a previously unrecognized lineage of filamentous cyanobacteria

Phylogenetic diversity of lichen photobionts is low compared to that of fungal counterparts. Most lichen fungi are thought to be associated with just four photobiont genera, among them the cyanobacteria Nostoc and Scytonema, two of the most important nitrogen fixers in humid ecosystems. Although many Nostoc photobionts have been identified using isolated cultures and sequences, the identity of Scytonema photobionts has never been confirmed by culturing or sequencing. We investigated the phylogenetic placement of presumed Scytonema photobionts and unicellular morphotypes previously assigned to Chroococcus, from tropical Dictyonema, Acantholichen, Coccocarpia, and Stereocaulon lichens. While we confirm that filamentous and unicellular photobiont morphotypes belong to a single clade, this clade does not cluster with Scytonema but represents a novel, previously unrecognized, highly diverse, exclusively lichenized lineage, for which the name Rhizonema is available. The phylogenetic structure observed in this novel lineage suggests absence of coevolution with associated mycobionts at the species or clade level. Instead, highly efficient photobiont strains appear to have evolved through photobiont sharing between unrelated, but ecologically similar, coexisting lineages of lichenized fungi ("lichen guilds"), via the selection of particular photobiont strains through and subsequent horizontal transfer among unrelated mycobionts, a phenomenon not unlike crop domestication.     

Does diversity beget diversity? A case study of crops and weeds

Abstract. The ecological literature is ambiguous as to whether the initial diversity of a plant community facilitates or deters the diversity of colonizing species. We experimentally planted annual crop species in monoculture and polyculture, and examined the resulting weed communities. The species composition of weeds was similar among treatments, but the species richness of weeds was significantly higher in the polycultures than in the monocultures. This supports the ‘diversity begets diversity’ hypothesis. Environmental microheterogeneity, diversity promoters, and ecological equivalency do not seem able to explain the observed patterns.     

Is MHC diversity a better marker for conservation than neutral genetic diversity? A case study of two contrasting dolphin populations

Genetic diversity is essential for populations to adapt to changing environments. Measures of genetic diversity are often based on selectively neutral markers, such as microsatellites. Genetic diversity to guide conservation management, however, is better reflected by adaptive markers, including genes of the major histocompatibility complex (MHC). Our aim was to assess MHC and neutral genetic diversity in two contrasting bottlenose dolphin (Tursiops aduncus) populations in Western Australia—one apparently viable population with high reproductive output (Shark Bay) and one with lower reproductive output that was forecast to decline (Bunbury). We assessed genetic variation in the two populations by sequencing the MHC class II DQB, which encompasses the functionally important peptide binding regions (PBR). Neutral genetic diversity was assessed by genotyping twenty‐three microsatellite loci. We confirmed that MHC is an adaptive marker in both populations. Overall, the Shark Bay population exhibited greater MHC diversity than the Bunbury population—for example, it displayed greater MHC nucleotide diversity. In contrast, the difference in microsatellite diversity between the two populations was comparatively low. Our findings are consistent with the hypothesis that viable populations typically display greater genetic diversity than less viable populations. The results also suggest that MHC variation is more closely associated with population viability than neutral genetic variation. Although the inferences from our findings are limited, because we only compared two populations, our results add to a growing number of studies that highlight the usefulness of MHC as a potentially suitable genetic marker for animal conservation. The Shark Bay population, which carries greater adaptive genetic diversity than the Bunbury population, is thus likely more robust to natural or human‐induced changes to the coastal ecosystem it inhabits.     

Grassland restoration in practice: Do we achieve the targets? A case study from Saxony-Anhalt/Germany

Grassland restoration on arable land is the second most implemented compensation measure in Germany to counteract impacts of infrastructural projects on nature. Most grassland restoration has been carried out using standardized commercial seed mixtures with large amounts of perennial generalists, cultivars and seeds of non-local origin. To evaluate whether this current practice is appropriate for developing regional types of species-rich mesophile grasslands, we analyzed four widely used treatments in a real-world setting (48 plots): (1) sowing a non-site-specific herb-poor mixture; (2) sowing a non-site-specific herb-enriched mixture; (3) sowing a site-specific herb-enriched mixture; and (4) spontaneous regeneration. After up to nine years, restored sites differed from target grasslands in: (1) number of species; (2) abundance and dominance of target species; and (3) dominance structure. Sown fields were dominated by sown species from the beginning. Because most differences were due to increasing cover of a small number of sown species, we found little development toward regional types of species-rich mesophile grasslands. In contrast, species composition on spontaneously regenerated sites changed to a greater degree and showed gradual development toward target grasslands. The limiting factor for successful restoration on all sites was availability of propagules. On sown sites, dominance patterns - particularly of Festuca rubra cultivars - had a negative effect on immigration and development of target species. For future restoration practice, we strongly recommend avoiding standardized commercial non-local seed mixtures. In particular, highly competitive cultivars should never be used. Even spontaneous regeneration should be preferred over standardized mixtures. However, in species-poor environments enrichment with selected species is necessary to reach target state.     

Do species converge during adaptation? A case study in Drosophila

Adaptation to novel environments is a crucial theme in evolutionary biology, particularly because ex situ conservation forces populations to adapt to captivity. Here we analyze the evolution of life-history traits in two closely related species, Drosophila subobscura Collin and Drosophila madeirensis Monclus, during adaptation to the laboratory. Drosophila madeirensis, an endemic species from Madeira, is here shown to have less ability to adapt to the laboratory. Early fecundity was the only trait where this species showed a significant improvement with time. By comparison, D. subobscura improved in most traits, and its early fecundity increased faster than that of D. madeirensis. Our findings suggest that different species, even closely related ones, may adapt at different rates to the same environment.     

Does lake age affect zooplankton diversity in Mediterranean lakes and reservoirs? A case study from southern Italy

Zooplankton assemblages of 51 lacustrine environments located in the middle of the Mediterranean Region were analysed to evaluate the existence of an ‘age effect’ in determining their structure. The analysed datasets refer to two different geographic areas, one comprising 30 natural and artificial lakes in Sicily and the other an arrangement of 21 analogous aquatic ecosystems located at the bottom of the Italian Peninsula, a more pristine area called Southern Apennine region. Most of the natural lakes are of post-glacial origin. The artificial lakes in both datasets were built in the last century and offer the opportunity to evaluate the possible short-term effects of ageing on the structure of their zooplankton. A comparison of assemblages in the two regions by PERMANOVA and nMDS revealed that they are quite different; therefore they were analysed separately. An explorative analysis on the possible relationship between biological data and environmental data (including lake age) was performed on both datasets using DISTLM. The presence of an ‘age effect’ emerged only in the subset of artificial lakes of the Southern Apennine region; accordingly it was tested more in detail with an a posteriori PERMANOVA analysis in the subset of reservoirs that resulted positive in the first test. SIMPER allowed us to single out the main species responsible of changes in the zooplankton along the selected age groups. No age effect was evident in the Sicilian water bodies, where other variables, such as conductivity, trophic state, urbanisation and water level fluctuations proved to have a major role in shaping zooplankton assemblages. The results showed that the age effect is: (i) detectable only at a time scale of decades; (ii) masked by the human impact in the watershed.     

Are coffee agroforestry systems suitable for circa situm conservation of indigenous trees? A case study from Central Kenya

Coffee agroforestry systems (CAFS) are often considered to be species-rich, potentially contributing to the conservation of indigenous trees. To investigate the conservation capacity of a Kenyan CAFS, all tree species on 62 smallholder coffee farms (covering 39 ha in total) in the Aberdare Mountains of Central Kenya were recorded. In total, 6,642 trees of 59 species were enumerated, with a mean density of 256 trees per ha and a mean species richness of 11.2 species per farm. Indigenous species represented 63 % of the richness but only 31 % of the abundance. For individual farms, as expected, farm size had a positive correlation with tree species richness, but more interestingly there was a negative correlation with tree density. Cluster analysis based on densities of the 18 most important species (defined by an importance value index) revealed two groups of farms: one cluster represented small farms (mean size = 0.4 ha) with high tree species diversity and individual density, particularly of indigenous trees; the other cluster represented large (mean size = 1 ha) and less diverse farms with low tree densities, particularly regarding indigenous species. Tree individuals were unevenly distributed within farms, being more frequent in living fences (38 % of all individuals), the garden zone (20 %) and in coffee plots (18 %). The relative occurrence of indigenous species was also uneven, being greater in living fences and the garden zone. Most adult trees (83 %) were planted, but only 46 % of seedlings were, revealing the active removal of volunteer seedlings by farmers as trees mature. Surveyed coffee farms harboured 20 % of the 135 tree species of the potential natural vegetation for the region, but only 3.6 % of the on-farm tree individuals belonged to the most valuable types of dominant and forest vegetation. Thus, although a source of significant tree cover and heterogeneity at landscape level, the value of these CAFS as circa situm reservoirs of forest tree species is questionable.     

Is urbanization scrambling the genetic structure of human populations? A case study

Recent population expansion and increased migration linked to urbanization are assumed to be eroding the genetic structure of human populations. We investigated change in population structure over three generations by analysing both demographic and mitochondrial DNA (mtDNA) data from a random sample of 2351 men from 22 Iranian populations. Potential changes in genetic diversity (theta) and genetic distance (F(ST)) over the last three generations were analysed by assigning mtDNA sequences to populations based on the individual's place of birth or that of their mother or grandmother. Despite the fact that several areas included cities of over one million inhabitants, we detected no change in genetic diversity, and only a small decrease in population structure, except in the capital city (Tehran), which was characterized by massive immigration, increased theta and a large decrease in F(ST) over time. Our results suggest that recent erosion of human population structure might not be as important as previously thought, except in some large conurbations, and this clearly has important implications for future sampling strategies.     

Do eel parasites reflect the local crustacean community? A case study from the Rhine River system

In 2003, the parasite fauna of 197 European eels Anguilla anguilla, captured at three different locations (Laufenburg, Karlsruhe and Beneeden Leeuwen) in the River Rhine, was analysed. The eels harboured a total of 18 species, among them the protozoa (Myxidium giardi, Myxobolus kotlani and Trypanosoma granulosum), acanthocephalans (Acanthocephalus anguillae, Acanthocephalus lucii, Echinorhynchus truttae, Pomphorhynchus laevis), nematodes (Paraquimperia tenerrima, Pseudocapillaria tomentosa, Camallanus lacustris, Raphidascaris acus, Spinitectus inermis and Anguillicola crassus), cestodes (Bothriocephalus claviceps and Proteocephalus macrocephalus) and monogeneans (Pseudodactylogyrus sp.). The parasite fauna at the different locations is discussed with respect to the crustacean fauna present at these locations. The investigation shows that changes in the composition of the crustacean fauna, due to the anthropogenic breakdown of a biogeographic barrier, are reflected in the composition of the intestinal eel parasite fauna.     

Do brachiopods show substrate‐related phenotypic variation? A case study from the Burgess Shale

As sessile, benthic filter feeders, brachiopods share an intimate relationship with their chosen substrate. Individuals of Micromitra burgessensis in the Burgess Shale Formation are preserved in life position, attached to a range of hard substrates, including skeletal debris, conspecific brachiopods, sponges and enigmatic tubes. Here we investigate the phenotypic variability of M. burgessensis associated with differing substrate attachments. We apply geometric morphometrics to test for variation by plotting landmarks on the exterior of ventral and dorsal valves of M. burgessensis specimens that are preserved attached to different substrates. Using principal component, canonical variate analyses and anova , we determine that there is some variation in shape related to substrate. Canonical variate analyses, for ventral valves and dorsal valves, indicate that specimens attached to the same substrate are recognizable in shape from specimens attached to other substrate types. The strength of differentiation however, is not robust and combined with our discriminate analysis of separate populations suggests that there is the potential for substrates to exercise only weak control over the morphology of Brachiopoda.     

Are the adult odonate species found in a protected area different from those present in the surrounding zone? A case study from eastern Amazonia

We studied 30 streams in eastern Amazonia, 17 of which were located within a protected area (PA) and the other 13 in the surrounding zone, with the objective of evaluating the diversity of adult Odonata and if there was a difference between the physical habitat variables of the two environments. We hypothesized that a greater diversity of odonate species would be found in the PA due to a greater complexity of habitats. This hypothesis was rejected, however, due to the greater odonate diversity found in the surrounding zone in comparison with the PA. Differences were also found in the species composition of the two environments. Our results indicate that there are differences between the environmental variables in the areas, and the few alterations observed in the surrounding zone may have contributed to the formation of new conditions and habitats appropriate for species that may have been rare. The PA, despite having reduced species richness and abundance in comparison with the surrounding zone, was nevertheless characterized by a more heterogeneous species composition. A quarter of the species were common to both environments, while 34 % were exclusive to the surrounding zone. In this case, it appears that the combination of the protected area and the surrounding zone, which has a low level of disturbance, conserves a wider range of specialist species than either area on its own. The great challenge in the future is finding a way to identify the disturbance levels that would be acceptable, and to prevent over-exploitation of resources in such areas.     

Do flowers wave to attract pollinators? A case study with Silene maritima

To answer the question whether flowers wave to attract pollinators, we determine: (1) the heritability of floral mobility; (2) whether wavy flowers attract more insects; (3) does the duration of pollination affect seed set; and (4) the relationship between seed set and floral mobility. The pollination ecology of Silene maritima was investigated. Flowers on stalks of different waviness were used to investigate the effect of floral movement on pollinator visits. There is heritable variation in both direct and indirect estimates of floral mobility. The highest insect total visitation times were associated with medium length thin stalks that were visited more frequently and by more insect species. Although mean individual visit durations were less than those of less mobile flowers, this was compensated for by increased visits. Observations of controlled pollinations show that when the visit times are low, so is seed set and therefore low and high mobility flowers might suffer from reduced fitness. Combining these observations provides a mechanism that could be driving stabilizing selection for flower stalk traits, with a trade-off applying between waving to attract pollinators and not being too mobile as to prevent effective pollination. Further evidence for stabilizing selection is provided by the relationship observed in the field between seed set and floral mobility where the highest levels of fitness was associated with intermediate levels of floral waving.     

Reed die-back in southern Europe? A case study from Central Italy

Common reed die-back is a widely investigated phenomenon in Central Europe, not frequently recorded in S-European areas and almost unknown in the Mediterranean Basin. Symptoms of reed decline recently observed in the Italian Peninsula provided the starting point for a detailed investigation on a reed population in one of the largest freshwater ecosystems in Central Italy. The analyses were conducted over two vegetative seasons in 19 plots at seven locations. A set of 13 morphologic and phenologic reed traits were screened, monitored and statistically analysed. The data indicated the presence of the reed die-back syndrome in a wet Mediterranean ecosystem and enabled us to highlight a set of usable traits to detect the condition of decline. Among them, the stem height and diameter, the number of nodes, the relative growth rate and the lateral root diameter resulted the most significant factors highlighting the declining condition. Some environmental characteristics of the reed stands were also taken into account. The period of submersion and the presence of standing litter emerged as important features of the stands, strictly related to the degree of decline in the population. The results draw attention to the risk, in southern Europe too, of the loss of an ecosystem which plays an important role in biodiversity conservation.     

Do pathogens reduce genetic diversity of their hosts? Variable effects of sylvatic plague in black‐tailed prairie dogs

Introduced diseases can cause dramatic declines in—and even the loss of—natural populations. Extirpations may be followed by low recolonization rates, leading to inbreeding and a loss of genetic variation, with consequences on population viability. Conversely, extirpations may create vacant habitat patches that individuals from multiple source populations can colonize, potentially leading to an influx of variation. We tested these alternative hypotheses by sampling 15 colonies in a prairie dog metapopulation during 7 years that encompassed an outbreak of sylvatic plague, providing the opportunity to monitor genetic diversity before, during and after the outbreak. Analysis of nine microsatellite loci revealed that within the metapopulation, there was no change in diversity. However, within extirpated colonies, patterns varied: In half of the colonies, allelic richness after recovery was less than the preplague conditions, and in the other half, richness was greater than the preplague conditions. Finally, analysis of variation within individuals revealed that prairie dogs present in recolonized colonies had higher heterozygosity than those present before plague. We confirmed plague survivorship in six founders; these individuals had significantly higher heterozygosity than expected by chance. Collectively, our results suggest that high immigration rates can maintain genetic variation at a regional scale despite simultaneous extirpations in spatially proximate populations. Thus, virulent diseases may increase genetic diversity of host populations by creating vacant habitats that allow an influx of genetic diversity. Furthermore, even highly virulent diseases may not eliminate individuals randomly; rather, they may selectively remove the most inbred individuals.     

Exploitation of natural genetic diversity to study plant–virus interactions: what can we learn from Arabidopsis thaliana?

The development and use of cultivars that are genetically resistant to viruses is an efficient strategy to tackle the problems of virus diseases. Over the past two decades, the model plant Arabidopsis thaliana has been documented as a host for a broad range of viral species, providing access to a large panel of resources and tools for the study of viral infection processes and resistance mechanisms. Exploration of its natural genetic diversity has revealed a wide range of genes conferring virus resistance. The molecular characterization of some of these genes has unveiled resistance mechanisms distinct from those described in crops. In these respects, Arabidopsis represents a rich and largely untapped source of new genes and mechanisms involved in virus resistance. Here, we review the current status of our knowledge concerning natural virus resistance in Arabidopsis. We also address the impact of environmental conditions on Arabidopsis–virus interactions and resistance mechanisms, and discuss the potential of applying the knowledge gained from the study of Arabidopsis natural diversity for crop improvement.     

Epithelial oral mucosal cells: Do they behave differently when exposed to oral carcinogens?

Objective

To assess the level of maturation and proliferation of epithelial cells and the correlation with immunocytochemical expression of adhesion (E‐cadherin) and cell differentiation (involucrin) markers.

Methods

Cytopathological samples were obtained from four groups of patients: control (CG, n=30); alcohol/tobacco (ATG, n=31), leucoplakia (LG, n=31), and squamous cell carcinoma (SCCG, n=22). Cytopathological smears were collected from all groups for AgNOR, Papanicolaou and immunocytochemical staining.

Results

There was an increase in anucleated cells in ATG compared to CG and in LG compared to lesion‐free groups (P<.05). In addition, there was a higher rate of intermediate cells in lesion‐free groups than in LG (P=.001). When these findings were correlated with positive E‐cadherin expression, there was a smaller number of anucleated and intermediate cells (P<.05). The proliferation rate was higher in the SCCG than in the CG (P<.05) and in the ATG compared to LG (P<.05). Moreover, cell proliferation increased in the presence of positive E‐cadherin expression in the ATG and LG. No statistically significant results were obtained for involucrin analysis.

Conclusion

Cytopathology combined with quantitative techniques such as Papanicolaou, AgNOR, and immunocytochemical expression of E‐cadherin detects changes associated with oral carcinogenesis. The innovative approach used in this study allows assessing the expression of cell adhesion (E‐cadherin) and differentiation (involucrin) markers by means of oral mucosal cytopathology. The E‐cadherin imunocytochemical expression indicated changes associated with the oral carcinogenesis process. An increase in cell proliferation rate in oral squamous cell carcinoma group was associated with the lower immunoexpression of E‐cadherin. Cytopathology combined with quantitative techniques and immunocytochemical expression of E‐cadherin may detect early alterations associated with oral carcinogenesis.     

Landholding fragmentation: Are folk soil taxonomy and equity important? A case study from Mexico

Landholding fragmentation is a common feature of the agricultural systems of small farmers in the tropics. This paper presents a case study from an ejido in central Chiapas, Mexico, where this pattern is common. Farmers recognize soil types of different quality, embodied in a folk soil txonomy. They argue that fragmentation is the result of their desire to maintain an equitable distribution of all land types among them, independently of the amount of land each controls. ¯The evidence shows that while not all farmers have all soil types, farmers belonging to all ranges of socioeconomic strata control soils in all the soil classes. There is no marked concentration of any soil type by any specific group, types are distributed among farmers by their abundance. Farmers have rejected previous government proposals to consolidate their landholdings. Fragmentation is associated with a high degree of social control over the land and a participatory process present in this community.