A single European aspen (Populus tremula) tree individual may potentially harbour dozens of Cenococcum geophilum ITS genotypes and hundreds of species of ectomycorrhizal fungi

Ectomycorrhizal fungi (EcMF) form diverse communities and link different host plants into mycorrhizal networks, yet little is known about the magnitude of mycobiont diversity of a single tree individual. This study addresses species richness and spatial structure of EcMF in the root system of a single European aspen (Populus tremula) individual in an old-growth boreal mixed forest ecosystem in Estonia. Combining morphological and molecular identification methods for both plant and fungi, 122 species of EcMF were recovered from 103 root samples of the single tree. Richness estimators predicted the total EcMF richness to range from 182 to 207 species, reflecting the observation of 62.3% singletons and doubletons within the community. Fine-scale genetic diversity in Cenococcum geophilum indicates the presence of 23 internal transcribed spacer genotypes. EcMF community was significantly spatially autocorrelated only at the lineage level up to 3 m distance, but not at the species level. Proximity of other hosts had a significant effect on the spatial distribution of EcMF lineages. This study demonstrates that a single tree may host as many EcMF species and individuals as recovered on multiple hosts in diverse communities over larger areas.     

A note on the incidence of reverse complementary fungal ITS sequences in the public sequence databases and a software tool for their detection and reorientation

Reverse complementary DNA sequences––sequences that are inadvertently cast backward and in which all purines and pyrimidines are transposed––are not uncommon in sequence databases, where they may introduce noise into sequence-based research. We show that about 1% of the public fungal ITS sequences, the most commonly sequenced genetic marker in mycology, are reverse complementary, and we introduce an open source software solution to automate their detection and reorientation. The MacOSX/Linux/UNIX software operates on public or private datasets of any size, although some 50 base pairs of the 5.8S gene of the ITS region are needed for the analysis.     

Bucking the Trend in Wolf-Dog Hybridization: First Evidence from Europe of Hybridization between Female Dogs and Male Wolves

Studies on hybridization have proved critical for understanding key evolutionary processes such as speciation and adaptation. However, from the perspective of conservation, hybridization poses a concern, as it can threaten the integrity and fitness of many wild species, including canids. As a result of habitat fragmentation and extensive hunting pressure, gray wolf (Canis lupus) populations have declined dramatically in Europe and elsewhere during recent centuries. Small and fragmented populations have persisted, but often only in the presence of large numbers of dogs, which increase the potential for hybridization and introgression to deleteriously affect wolf populations. Here, we demonstrate hybridization between wolf and dog populations in Estonia and Latvia, and the role of both genders in the hybridization process, using combined analysis of maternal, paternal and biparental genetic markers. Eight animals exhibiting unusual external characteristics for wolves - six from Estonia and two from Latvia - proved to be wolf-dog hybrids. However, one of the hybridization events was extraordinary. Previous field observations and genetic studies have indicated that mating between wolves and dogs is sexually asymmetrical, occurring predominantly between female wolves and male dogs. While this was also the case among the Estonian hybrids, our data revealed the existence of dog mitochondrial genomes in the Latvian hybrids and, together with Y chromosome and autosomal microsatellite data, thus provided the first evidence from Europe of mating between male wolves and female dogs. We discuss patterns of sexual asymmetry in wolf-dog hybridization.     

Diversity and community composition of ectomycorrhizal fungi in a dry deciduous dipterocarp forest in Thailand

Large forest areas of South-East Asia, are dominated by the Dipterocarpaceae tree family, which contains many important timber species. Unlike many other tropical trees, Dipterocarpaceae rely on ectomycorrhizal (ECM) root symbiosis for their mineral nutrition. This study aims to document the richness and community composition of ECM fungi in a dry deciduous forest in Thailand. Combining morphological and molecular identification methods revealed 69 species of ECM fungi that belong to 17 phylogenetic lineages. The /russula-lactarius, /tomentella-thelephora, /sordariales, /sebacina and /cantharellus lineages were the most species-rich. The fungal richness is comparable to other tropical rain forest sites, but the phylogenetic community structure has elements of both tropical and temperate ecosystems. Unlike tropical rain forests, the Cenococcum geophilum complex was one of the most frequent fungal taxa that had a relatively high ITS genetic diversity over the small sampling area. This study provides the first snapshot insight into the fungal community of dry dipterocarp forests. However, it is necessary to broaden the spatial and temporal scales of sampling to improve our understanding of the below-ground relations of dry and humid tropical forests.     

Alu and LINE1 distributions in the human chromosomes: evidence of global genomic organization expressed in the form of power laws

Spatial distribution and clustering of repetitive elements are extensively studied during the last years, as well as their colocalization with other genomic components. Here we investigate the large-scale features of Alu and LINE1 spatial arrangement in the human genome by studying the size distribution of interrepeat distances. In most cases, we have found power-law size distributions extending in several orders of magnitude. We have also studied the correlations of the extent of the power law (linear region in double-logarithmic scale) and of the corresponding exponent (slope) with other genomic properties. A model has been formulated to explain the formation of the observed power laws. According to the model, 2 kinds of events occur repetitively in evolutionary time: random insertion of several types of intruding sequences and occasional loss of repeats belonging to the initial population due to "elimination" events. This simple mechanism is shown to reproduce the observed power-law size distributions and is compatible with our present knowledge on the dynamics of repeat proliferation in the genome.     

Identification of the coastal zone of the central and eastern Gulf of Finland by numerical modeling,measurements, and remote sensing of chlorophyll <Emphasis Type="Italic">a</Emphasis>

A combination of numerical modeling results with measurement and satellite imagery data was used during the biologically active period for the determination of the coastal zone extent in the central and eastern Gulf of Finland. Adopting the approach that the coastal zone can be identified by the spatial distribution of biotic parameters, spatial variations and gradients of chlorophyll a (chl-a) concentrations were analyzed. The results showed that chl-a concentrations vary in a wide range over the biologically active period. During heavy blooms, the coastal zone may appear occasionally and depend on the spatial distribution of the bloom. On average, clear limits of the coastal zone could be defined for the central and eastern Gulf of Finland. In the central Gulf of Finland, water and material exchange are rather intensive, and the coastal zone is narrower than in the eastern Gulf. In the easternmost part of the Gulf of Finland, chl-a concentrations were permanently high in an area of about 100 km width due to the discharge of the Neva River. The study has shown that gradients of chl-a spatial distribution can be applied for determining limits of the coastal zone extent. The standardized gradient of zero is shown to be a threshold separating the coastal zone (standardized gradients > 0) from the open sea (standardized gradients < 0). Guest editors: J. H. Andersen & D. J. Conley Eutrophication in Coastal Ecosystems: Selected papers from the Second International Symposium on Research and Management of Eutrophication in Coastal Ecosystems, 20–23 June 2006, Nyborg, Denmark     

Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes

Ciliates are unicellular eukaryotes with both a germline genome and a somatic genome in the same cytoplasm. The somatic macronucleus (MAC), responsible for gene expression, is not sexually transmitted but develops from a copy of the germline micronucleus (MIC) at each sexual generation. In the MIC genome of Paramecium tetraurelia, genes are interrupted by tens of thousands of unique intervening sequences called internal eliminated sequences (IESs), which have to be precisely excised during the development of the new MAC to restore functional genes. To understand the evolutionary origin of this peculiar genomic architecture, we sequenced the MIC genomes of 9 Paramecium species (from approximately 100 Mb in Paramecium aurelia species to >1.5 Gb in Paramecium caudatum). We detected several waves of IES gains, both in ancestral and in more recent lineages. While the vast majority of IESs are single copy in present-day genomes, we identified several families of mobile IESs, including nonautonomous elements acquired via horizontal transfer, which generated tens to thousands of new copies. These observations provide the first direct evidence that transposable elements can account for the massive proliferation of IESs in Paramecium. The comparison of IESs of different evolutionary ages indicates that, over time, IESs shorten and diverge rapidly in sequence while they acquire features that allow them to be more efficiently excised. We nevertheless identified rare cases of IESs that are under strong purifying selection across the aurelia clade. The cases examined contain or overlap cellular genes that are inactivated by excision during development, suggesting conserved regulatory mechanisms. Similar to the evolution of introns in eukaryotes, the evolution of Paramecium IESs highlights the major role played by selfish genetic elements in shaping the complexity of genome architecture and gene expression.

A comparative genomics study of nine Paramecium species reveals successful invasion of genes by transposable elements in their germline genomes, showing that the internal eliminated sequences (IESs) followed an evolutionary trajectory remarkably similar to that of spliceosomal introns.     

Power-laws in the genomic distribution of coding segments in several organisms:: An evolutionary trace of segmental duplications,possible paleopolyploidy and gene loss

Large-scale features of the spatial arrangement of protein-coding segments (PCS) are investigated by means of the inter-PCS spacers' size distributions, which have been found to follow power-laws. Linearity in double-logarithmic scale extends to several orders of magnitude in the genomes of organisms as disparate as mammals, insects and plants. This feature is also present in the most compact eukaryotic genomes and in half of the examined bacteria, despite their very limited non-coding space. We have tried to determine the sequence of events in the course of genomes' evolution which may account for the formation of the observed size distributions. The proposed mechanism essentially includes two types of events: (i) segmental duplications (and possibly paleopolyploidy), and (ii) the subsequent loss of most of the duplicated genes. It is shown by computer simulations that the formulated scenario generates power-law-like inter-PCS spacers' size distributions, which remain robust for a variety of parameter choices, even if insertion of external sequences, such as viruses or proliferating retroelements is included. Moreover, power-laws are preserved after most of the non-coding DNA has been removed, thus explaining the finding of this pattern in genomes as compact as that of Takifugu rubripes.