Genetic diversity at the Dhn3 locus in Turkish Hordeum spontaneum populations with comparative structural analyses

We analysed Hordeum spontaneum accessions from 21 different locations to understand the genetic diversity of HsDhn3 alleles and effects of single base mutations on the intrinsically disordered structure of the resulting polypeptide (HsDHN3). HsDHN3 was found to be YSK2-type with a low-frequency 6-aa deletion in the beginning of Exon 1. There is relatively high diversity in the intron region of HsDhn3 compared to the two exon regions. We have found subtle differences in K segments led to changes in amino acids chemical properties. Predictions for protein interaction profiles suggest the presence of a protein-binding site in HsDHN3 that coincides with the K1 segment. Comparison of DHN3 to closely related cereals showed that all of them contain a nuclear localization signal sequence flanking to the K1 segment and a novel conserved region located between the S and K1 segments [E(D/T)DGMGGR]. We found that H. vulgare, H. spontaneum, and Triticum urartu DHN3s have a greater number of phosphorylation sites for protein kinase C than other cereal species, which may be related to stress adaptation. Our results show that the nature and extent of mutations in the conserved segments of K1 and K2 are likely to be key factors in protection of cells.

Environmental controls on the distribution and diversity of lentic Chironomidae (Insecta: Diptera) across an altitudinal gradient in tropical South America

To predict the response of aquatic ecosystems to future global climate change, data on the ecology and distribution of keystone groups in freshwater ecosystems are needed. In contrast to mid- and high-latitude zones, such data are scarce across tropical South America (Neotropics). We present the distribution and diversity of chironomid species using surface sediments of 59 lakes from the Andes to the Amazon (0.1–17°S and 64–78°W) within the Neotropics. We assess the spatial variation in community assemblages and identify the key variables influencing the distributional patterns. The relationships between environmental variables (pH, conductivity, depth, and sediment organic content), climatic data, and chironomid assemblages were assessed using multivariate statistics (detrended correspondence analysis and canonical correspondence analysis). Climatic parameters (temperature and precipitation) were most significant in describing the variance in chironomid assemblages. Temperature and precipitation are both predicted to change under future climate change scenarios in the tropical Andes. Our findings suggest taxa of Orthocladiinae, which show a preference to cold high-elevation oligotrophic lakes, will likely see range contraction under future anthropogenic-induced climate change. Taxa abundant in areas of high precipitation, such as Micropsectra and Phaenopsectra, will likely become restricted to the inner tropical Andes, as the outer tropical Andes become drier. The sensitivity of chironomids to climate parameters makes them important bio-indicators of regional climate change in the Neotropics. Furthermore, the distribution of chironomid taxa presented here is a vital first step toward providing urgently needed autecological data for interpreting fossil chironomid records of past ecological and climate change from the tropical Andes.

Explaining patterns of avian diversity and endemicity: climate and biomes of southern Africa over the last 140,000 years

Aim Test hypotheses that present biodiversity and endemic species richness are related to climatic stability and/or biome persistence.Location Africa south of 15° S. Methods Seventy eight HadCM3 general circulation model palaeoclimate experiments spanning the last 140,000 years, plus a pre-industrial experiment,were used to calculate measures of climatic variability for 0.5° grid cells. Models were fitted relating distributions of the nine biomes of South Africa,Lesotho and Swaziland to present climate. These models were used to simulate potential past biome distribution and extent for the 78 palaeoclimate experiments, and three measures of biome persistence. Climatic response surfaces were fitted for 690 bird species regularly breeding in the region and used to simulate present species richness for cells of the 0.5° grid. Species richness was evaluated for residents, mobile species (nomadic or partially/altitudinally migrant within the region), and intra-African migrants, and also separately for endemic/near-endemic (hereafter ‘endemic’) species as a whole and those associated with each biome. Our hypotheses were tested by analysing correlations between species richness and climatic variability or biome persistence. Results The magnitude of climatic variability showed clear spatial patterns. Marked changes in biome distributions and extents were projected, although limited areas of persistence were projected for some biomes. Overall species richness was not correlated with climatic variability, although richness of mobile species showed a weak negative correlation. Endemic species richness was significantly negatively correlated with climatic variability. Strongest correlations, however, were positive correlations between biome persistence and richness of endemics associated with individual biomes. Main conclusions Low climatic variability, and especially a degree of stability enabling biome persistence, is strongly correlated with species richness of birds endemic to southern Africa. This probably principally reflects reduced extinction risk for these species where the biome to which they are adapted persisted

How to be a fig wasp down under: the diversity and structure of an Australian fig wasp community

Endophytic insects and their parasitoids provide valuable models for community ecology. The wasp communities in inflorescences of fig trees have great potential for comparative studies, but we must first describe individual communities. Here, we add to the few detailed studies of such communities by describing the one associated with Ficus rubiginosa in Australia. First, we describe community composition, using two different sampling procedures. Overall, we identified 14 species of non-pollinating fig wasp (NPFW) that fall into two size classes. Small wasps, including pollinators, gallers and their parasitoids, were more abundant than large wasps (both galler and parasitoid species). We show that in figs where wasps emerge naturally, the presence of large wasps may partly explain the low emergence of small wasps. During fig development, large gallers oviposit first, before and around the time of pollination, while parasitoids lay eggs after pollination. We further show that parasitoids in the subfamily Sycoryctinae, which comprise the majority of all individual NPFWs, segregate temporally by laying eggs at different stages of fig development. We discuss our results in terms of species co-existence and community structure and compare our findings to those from fig wasp communities on other continents.

Patterns of hominin occupation and cultural diversity across the Gebel Akhdar of Northern Libya over the last ~200 kyr

Excavations at Haua Fteah cave in Cyrenaica, Libya, have revealed a cultural sequence that may span the last glacial–interglacial-glacial cycle. The TRANS-NAP project has been re-excavating Haua Fteah and conducting geoarchaeological survey of an ecologically diverse landscape that includes the fertile Gebel Akhdar and littoral, pre-desert, and desert biomes. A major aim of this project is to characterize cultural and environmental changes across the region and correlate the surface archaeology with that from Haua Fteah. To date, 181 sites have been recorded, ranging from the Middle Stone Age (MSA) to Late Stone Age (LSA). Their geographic distribution suggests temporal variation in patterns of hominin habitat preference, with significantly more LSA than MSA sites at higher elevations. The surface archaeology also points to substantial spatiotemporal technological variation within the MSA. These patterns may be explained by both paleoenvironmental change and paleodemographic shifts in the region, resulting in a variety of hominin adaptive responses.

Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level

Abstract Background: The amount and structure of genetic diversity in dessert apple germplasm conserved at a European level is mostly unknown, since all diversity studies conducted in Europe until now have been performed on regional or national collections. Here, we applied a common set of 16 SSR markers to genotype more than 2,400 accessions across 14 collections representing three broad European geographic regions (North+East, West and South) with the aim to analyze the extent, distribution and structure of variation in the apple genetic resources in Europe. Results: A Bayesian model-based clustering approach showed that diversity was organized in three groups, although these were only moderately differentiated (FST=0.031). A nested Bayesian clustering approach allowed identification of subgroups which revealed internal patterns of substructure within the groups, allowing a finer delineation of the variation into eight subgroups (FST=0.044). The first level of stratification revealed an asymmetric division of the germplasm among the three groups, and a clear association was found with the geographical regions of origin of the cultivars. The substructure revealed clear partitioning of genetic groups among countries, but also interesting associations between subgroups and breeding purposes of recent cultivars or particular usage such as cider production. Additional parentage analyses allowed us to identify both putative parents of more than 40 old and/or local cultivars giving interesting insights in the pedigree of some emblematic cultivars. Conclusions: The variation found at group and sub-group levels may reflect a combination of historical processes of migration/selection and adaptive factors to diverse agricultural environments that, together with genetic drift, have resulted in extensive genetic variation but limited population structure. The European dessert apple germplasm represents an important source of genetic diversity with a strong historical and patrimonial value. The present work thus constitutes a decisive step in the field of conservation genetics. Moreover, the obtained data can be used for defining a European apple core collection useful for further identification of genomic regions associated with commercially important horticultural traits in apple through genome-wide association studies.

Mosquito (Diptera: Culicidae) Diversity of a Forest-Fragment Mosaic in the Amazon Rain Forest

To study the impact of Amazonian forest fragmentation on the mosquito fauna, an inventory of Culicidae was conducted in the upland forest research areas of the Biological Dynamics of Forest Fragments Project located 60 km north of Manaus, Amazonas, Brazil. The culicid community was sampled monthly between February 2002 and May 2003. CDC light traps, flight interception traps, manual aspiration, and net sweeping were used to capture adult specimens along the edges and within forest fragments of different sizes (1, 10, and 100 ha), in second-growth areas surrounding the fragments and around camps. We collected 5,204 specimens, distributed in 18 genera and 160 species level taxa. A list of mosquito taxa is presented with 145 species found in the survey, including seven new records for Brazil, 16 new records for the state of Amazonas, along with the 15 morphotypes that probably represent undescribed species. No exotic species [Aedes aegypti (L.) and Aedes albopictus (Skuse)] were found within the sampled areas. Several species collected are potential vectors of Plasmodium causing human malaria and of various arboviruses. The epidemiological and ecological implications of mosquito species found are discussed, and the results are compared with other mosquito inventories from the Amazon region.

Temporal Diversity Patterns and Phenology in Fruit-feeding Butterflies in the Atlantic Forest

The Atlantic Forest deserves special attention due to its high level of species endemism and degree of threat. As in other tropical biomes, there is little information about the ecology of the organisms that occur there. The objectives of this study were to verify how fruit-feeding butterflies are distributed through time, and the relation with meteorological conditions. Species richness and Shannon index were partitioned additively at the monthly level, and beta diversity, used as a hierarchical measure of temporal species turnover, was calculated among months, trimesters, and semesters. Circular analysis was used to verify how butterflies are distributed along seasons and its relation with meteorological conditions. We sampled 6488 individuals of 73 species. Temporal diversity of butterflies was more grouped than expected by chance among the months of each trimester. Circular analyses revealed that diversity is concentrated in hot months (September-March), with the subfamily Brassolinae strongly concentrated in February-March. Average temperature was correlated with total abundance of butterflies, abundance of Biblidinae, Brassolinae and Morphinae, and richness of Satyrinae. The present results show that 3mo of sampling between September and March is enough to produce a nonbiased sample of the local assemblage of butterflies, containing at least 70 percent of the richness and 25 percent of abundance. The influence of temperature on sampling is probably related to butterfly physiology. Moreover, temperature affects resource availability for larvae and adults, which is higher in hot months. The difference in seasonality patterns among subfamilies is probably a consequence of different evolutionary pressures through time.

Consequences of Simulated Loss of Open Cerrado Areas to Bird Functional Diversity

Over the past 35 years, more than two thirds of the Cerrado`s original expanse has been taken by agriculture. Even if some attempts have been made to conserve closed cerrado physiognomies, open cerrado physiognomies, richer in species and more fragile, have been systematically ignored. These open physiognomies are used by almost half of the Cerrado bird species, many of which being endemics. Using data from 11 surveys carried out in Cerrado landscapes, we asked what would happen to bird functional diversity if open cerrado species became extinct. Open cerrado birds would be able to keep on average 59% of the functional diversity. If they became extinct, on average 27% of the functional diversity would be lost. In this case, the remaining functional diversity would be lower than what would be expected by chance in five sites. Although many functions were shared by both open cerrado and forest species, there was some degree of complementarity between them, highlighted by the decrease in functional diversity when the former became extinct. Destruction of open cerrado physiognomies would lead to a habitat simplification, decrease in bird functional diversity, and, ultimately, to a considerable impact on community functioning. Thus, open cerrado physiognomies must receive much more conservation attention than they are currently receiving, because they maintain a high bird functional diversity that would otherwise be considerably diminished Were open cerrado species to become extinct.

Habitat fragmentation reduces genetic diversity and connectivity among toad populations in the Brazilian Atlantic Coastal Forest

Tropical rainforests are becoming increasingly fragmented and understanding the genetic consequences of fragmentation is crucial for conservation of their flora and fauna. We examined populations of the toad Rhinella ornata, a species endemic to Atlantic Coastal Forest in Brazil, and compared genetic diversity among small and medium forest fragments that were either isolated or connected to large forest areas by corridors. Genetic differentiation, as measured by F(ST), was not related to geographic distance among study sites and the size of the fragments did not significantly alter patterns of genetic connectivity. However, population genetic diversity was positively related to fragment size, thus haplotype diversity was lowest in the smallest fragments, likely due to decreases in population sizes. Spatial analyses of genetic discontinuities among groups of populations showed a higher proportion of barriers to gene flow among small and medium fragments than between populations in continuous forest. Our results underscore that even species with relatively high dispersal capacities may, over time, suffer the negative genetic effects of fragmentation, possibly leading to reduced fitness of population and cases of localized extinction. (C) 2008 Elsevier Ltd. All rights reserved.

Relation of pretreatment sequence diversity in NS5A region of HCV genotype 1 with immune response between pegylated-INF/ribavirin therapy outcomes

Hepatitis C virus (HCV) infection frequently persists despite substantial virus-specific immune responses and the combination of pegylated interferon (INF)-alpha and ribavirin therapy. Major histocompatibility complex class I restricted CD8+ T cells are responsible for the control of viraemia in HCV infection, and several studies suggest protection against viral infection associated with specific HLAs. The reason for low rates of sustained viral response (SVR) in HCV patients remains unknown. Escape mutations in response to cytotoxic T lymphocyte are widely described; however, its influence in the treatment outcome is ill understood. Here, we investigate the differences in CD8 epitopes frequencies from the Los Alamos database between groups of patients that showed distinct response to pegylated alpha-INF with ribavirin therapy and test evidence of natural selection on the virus in those who failed treatment, using five maximum likelihood evolutionary models from PAML package. The group of sustained virological responders showed three epitopes with frequencies higher than Non-responders group, all had statistical support, and we observed evidence of selection pressure in the last group. No escape mutation was observed. Interestingly, the epitope VLSDFKTWL was 100% conserved in SVR group. These results suggest that the response to treatment can be explained by the increase in immune pressure, induced by interferon therapy, and the presence of those epitopes may represent an important factor in determining the outcome of therapy.