Population genetics of the wood-decay fungus Phlebia centrifuga P. Karst. in fragmented and continuous habitats

The basidiomycete Phlebia centrifuga is a wood-decay fungus characteristic for unmanaged old-growth forests of spruce, a habitat that has become increasingly fragmented due to forest management. The aim of this study was to investigate the genetic population structures of P. centrifuga in both continuous and fragmented habitats, and estimate the potential impact of fragmentation on the genetic diversity of the fungus. Three hundred fifteen single spore isolates (representing 47 spore families and 33 single isolates) from eight populations across northern Europe (Russia, Finland, and Sweden) were screened with seven microsatellite markers and arbitrary primed polymerase chain reaction with the M13 minisatellite. The two molecular methods generally gave the same pattern for the genetic population structure. There were no significant differences between the observed and the expected heterozygosities, and the inbreeding coefficient (FIS) did not indicate any inbreeding. The fixation index (FST) revealed a general pattern with little to moderate genetic differentiation for the majority of populations, while the southernmost Swedish population Norra Kvill was the only one showing high differentiation from about half of the other populations. Swedish population Fiby with the shortest distance to the continuous habitat was moderately differentiated from most of the others and to the largest extent differed from geographically closest population of Norra Kvill. The results indicate that the fragmentation of old-growth forest in Russia and Finland is more recent than the fragmentation in Sweden, and the genetic population structures of P. centrifuga in northern Europe might be related to differences in forest landscape dynamics between the two areas.     

Host pathogen protein interactions predicted by comparative modeling

Pathogens have evolved numerous strategies to infect their hosts, while hosts have evolved immune responses and other defenses to these foreign challenges. The vast majority of host-pathogen interactions involve protein-protein recognition, yet our current understanding of these interactions is limited. Here, we present and apply a computational whole-genome protocol that generates testable predictions of host-pathogen protein interactions. The protocol first scans the host and pathogen genomes for proteins with similarity to known protein complexes, then assesses these putative interactions, using structure if available, and, finally, filters the remaining interactions using biological context, such as the stage-specific expression of pathogen proteins and tissue expression of host proteins. The technique was applied to 10 pathogens, including species of Mycobacterium, apicomplexa, and kinetoplastida, responsible for "neglected" human diseases. The method was assessed by (1) comparison to a set of known host-pathogen interactions, (2) comparison to gene expression and essentiality data describing host and pathogen genes involved in infection, and (3) analysis of the functional properties of the human proteins predicted to interact with pathogen proteins, demonstrating an enrichment for functionally relevant host-pathogen interactions. We present several specific predictions that warrant experimental follow-up, including interactions from previously characterized mechanisms, such as cytoadhesion and protease inhibition, as well as suspected interactions in hypothesized networks, such as apoptotic pathways. Our computational method provides a means to mine whole-genome data and is complementary to experimental efforts in elucidating networks of host-pathogen protein interactions.     

Rates of change in tree communities of secondary Neotropical forests following major disturbances

Rates of change in tree communities following major disturbances are determined by a complex set of interactions between local site factors, landscape history and structure, regional species pools and species life histories. Our analysis focuses on vegetation change following abandonment of agricultural fields or pastures, as this is the most extensive form of major disturbance in Neotropical forests. We consider five tree community attributes: stem density, basal area, species density, species richness and species composition. We describe two case studies, in northeastern Costa Rica and Chiapas, Mexico, where both chronosequence and annual tree dynamics studies are being applied. These case studies show that the rates of change in tree communities often deviate from chronosequence trends. With respect to tree species composition, sites of different ages differ more than a single site followed over time through the same age range. Dynamic changes in basal area within stands, on the other hand, generally followed chronosequence trends. Basal area accumulation was more linked with tree growth rates than with net changes in tree density due to recruitment and mortality. Stem turnover rates were poor predictors of species turnover rates, particularly at longer time-intervals. Effects of the surrounding landscape on tree community dynamics within individual plots are poorly understood, but are likely to be important determinants of species accumulation rates and relative abundance patterns.     

Splenic lesions: FNA findings in 48 cases

OBJECTIVE: To study fine needle aspiration (FNA) cytological findings of splenic lesions and assess the role of FNA in the diagnosis of splenomegaly or splenic tumours. METHODS: This study consisted of 48 cases, 25 males and 23 females. The ages ranged between 3 and 71 years. Most of these cases were aspirated under ultrasonographic guidance and a small number were also aspirated directly by using a 22- to 23-gauge needles. The smears were stained with Wright-Giemsa and Papanicolaou methods. Special stains were used whenever necessary. RESULTS: In this study 14 cases were diagnosed as lymphoma-leukaemia, 7 cases as tuberculosis, 12 cases as kala-azar, 2 cases as hydatid cyst, 3 cases as storage diseases, 3 cases as simple cyst, 2 cases as myeloproliferative disorders, 2 cases as malignant tumours and 3 cases as hamartomas (these were wrongly diagnosed as malignant tumours). CONCLUSION: Splenic aspiration is a safe procedure and is very useful in the diagnosis of parasitic and infectious diseases, especially in endemic countries like Iran.     

The distribution pattern of centipedes in four primeval forests of central Slovakia

We investigated the distribution pattern of centipedes (Chilopoda) in four primeval forests of the western Carpathians, central Slovakia. The forests are located in two different mountain ranges (Kremnické vrchy and Pol’ana Mountains), which are exposed on either the southern (Boky, Rohy) or northern slopes (Pol’ana, Badín). In these forests, the influence of coarse woody debris (CWD) on centipede distribution was studied, by distinguishing sampling sites on the forest floor, close to CWD (c-CWD) and distant from CWD (d-CWD). In total, we collected 2,706 individuals from 20 species of centipedes. Average species richness and number of individuals per forest ranged from 8 to 12 species/m² and from 244 to 486 individuals/m². The oak forests on south facing slopes harboured several species, which did not occur in the more northern exposed fir-beech forests. Number of species as well as individuals, however, varied more within than between individual forests. Increase of species number and density was mainly caused by CWD and was more pronounced on the southern slopes (P<0.001), characterized by high temperatures and low precipitation, than on the northern slopes (n.s. to P<0.01), characterized by low temperatures and high precipitation. It was found that CWD did not generally increase (species) diversity.     

Biodiversity conservation in cocoa production landscapes: an overview

Cocoa agroforests that retain a floristically diverse and structurally complex shade canopy have the potential to harbour significant levels of biodiversity, yet few studies have documented the plant and animal species occurring within these systems or within landscapes dominated by cocoa production. In this special issue, we bring together nine studies from Latin America, Africa and Asia that document the contribution of cocoa agroforestry systems to biodiversity conservation, and explore how the design, management and location of these systems within the broader landscape influence their value as habitats, resources and biological corridors. Tree diversity within the cocoa production systems is variable, depending on management, cultural differences, location and farm history, among other factors. Animal diversity is typically highest in those cocoa agroforests that have high plant diversity, structurally complex canopies, and abundant surrounding forest cover. In general, both plant and animal diversity within cocoa agroforests is greater than those of other agricultural land uses, but lower than in the original forest habitat. There are several emerging threats to biodiversity conservation within cocoa production landscapes, including the loss of remaining forest cover, the simplification of cocoa shade canopies and the conversion of cocoa agroforestry systems to other agricultural land uses with lower biodiversity value. To counter these threats and conserve biodiversity over the long-term, land management should focus on conserving native forest habitat within cocoa production landscapes, maintaining or restoring floristically diverse and structurally complex shade canopies within cocoa agroforests, and retaining other types of on-farm tree cover to enhance landscape connectivity and habitat availability.     

Responses of plant and bird communities to prescribed burning in tallgrass prairies

Historic losses and fragmentation of tallgrass prairie habitat to agriculture and urban development have led to declines in diversity and abundance of plants and birds associated with such habitat. Prescribed burning is a management strategy that has potential for restoring and rejuvenating prairies in fragmented landscapes, and through such restoration, might create habitat for birds dependent upon prairies. To provide improved data for management decision-making regarding the use of prescribed fire in tallgrass prairies, we compared responses of plant and bird communities on five burned and five unburned tallgrass prairie fragments at the DeSoto National Wildlife Refuge, Iowa, USA, from 1995 to 1997. Overall species richness and diversity were unaffected by burning, but individual species of plants and birds were affected by year-treatment interactions, including northern bobwhite (Colinus virginianus) and ring-necked pheasant (Phasianus colchicus), which showed time-delayed increases in density on burned sites. Analyses of species/area relationships indicated that, collectively, many small sites did make significant contributions to plant biodiversity at landscape levels, supporting the overall conservation value of prairie fragments. In contrast, most birds species were present on larger sites. Thus, higher biodiversity in bird communities which contain area-sensitive species might require larger sites able to support larger, more stable populations, greater habitat heterogeneity, and greater opportunity for niche separation.     

How resilient are Andean montane forest bird communities to habitat degradation?

The threatened forest habitats of the tropical Andes are reportedly being modified and destroyed 30% faster than their lowland tropical counterparts, but impacts on the hyper-diverse resident avifauna have received little systematic study. We present a baseline analysis of the effects of habitat modification on birds in a lower montane forest landscape in Ecuador, comparing avian community composition in landscape elements subjected to different levels of human modification: primary forest, secondary forest, edge habitat and agricultural land. We use data from a point count survey of 300 counts at 150 sites to test whether community composition and density of birds with different reported habitat preferences and foraging strategies change among landscape elements. Species richness and diversity were lowest in agricultural land, but on some measures, equally low in primary forest. Richness and diversity peaked in secondary forest and edge habitat, but ordination and density analysis revealed clear differences in their species composition. While secondary forest contained mostly forest-preferring species, edge habitat harboured a mix of forest and open-land birds. There was a clearly structured gradient in species composition across landscape elements, with densities of habitat specialists, foraging guilds and families varying considerably from primary forest to agricultural land. Agricultural land was characterised by an assemblage of widespread, abundant species very different from that in core forest habitats. As such, while the majority of montane forest birds appear resilient to a certain level of habitat modification, they cannot persist, and are displaced, where forest has been cleared outright. We argue that, for Andean montane forests, preservation of mature secondary forest offers flexibility in supplementing preserved primary forest areas to provide sufficient habitat for the persistence of this incredibly diverse but severely threatened bird community.     

Traditional Ecological Knowledge of a Riverine Forest in Turkana, Kenya: Implications for Research and Management

The present study explores traditional ecological knowledge (TEK) of Turkana pastoralists and cultivators in the context of a riverine forest in northern Kenya. The Turkwel River and its floodplain sustain a thick forest, which is used for grazing and extraction of non-timber forest products. However, sedentarisation and agricultural expansion have resulted in localised clear-felling of trees, while river damming has altered the natural flow regime. A series of structured, semi-structured, and group interviews were combined with a botanical inventory in order to assess the relevance of TEK to ecological research and forest conservation. Turkana informants gave 102 vernacular names for the 113 woody species. Of these, 85% had a domestic or pastoral use among the 105 specific uses that were described. Ethnobotanical knowledge was relatively homogenous and not related to age, gender, or source of livelihood. The informants had in-depth knowledge of some key ecological processes. The conceived threats to forest survival were primarily cultivation and permanent settlements, while the effects of river damming and livestock grazing were disputed. A claimed decline in rainfall was confirmed by official data. There is strong evidence that TEK could be used to generate hypotheses for research and to design sustainable conservation strategies. A revised version of the indigenous system of tree management should be incorporated into the official forestry policy in order to resolve future conflicts between pastoralists and cultivators.     

Comparison of stream benthic invertebrate assemblages among forest types in the temperate region of Japan

We compared benthic invertebrate assemblages among headwater streams in several forest types in Japan. Forests were divided into three clusters based on vegetation composition: old-growth broad-leaved forest, planted coniferous forest, and mixed forest. The numbers of individuals and families and the diversity (Shannon-Wiener) of benthic invertebrate assemblages did not differ significantly among the three forest clusters. However, principal components analysis of family abundance showed differences in the benthic invertebrate assemblages among the three forest clusters. No environmental factors were correlated with these differences. Benthic invertebrate assemblages differed depending on forest composition. The abundances of Taeniopterygidae and Athericidae in old-growth broad-leaved forest were significantly greater than in planted coniferous forest. The abundances of Heptageniidae, Baetiidae, Stenopsychidae, Uenoidae, Chironomidae, and Potamidae in planted coniferous forest were significantly greater than in old-growth broad-leaved forest. If the remaining old-growth broad-leaved forest were to be converted to coniferous plantation, species that inhabit old-growth forest may become extinct.