How mankind has shaped European nature

A monographic book volume on the history of the rural landscape of Europe is presented (Emanuelsson, The rural landscape of Europe. How man has shaped European nature, 383, 2009). The focus is on various land-use phases, their history from the Neolithic period to modern time and the survival of traditional farming today in Europe. This is described and illustrated by examples from marginal farming areas, particularly in mountainous regions of southern and northern Europe. Some of these are important as modern analogues when interpreting past cultural landscapes.     

Feeding ecology has shaped the evolution of modern sharks

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担子菌类食用菌交配型位点结构的研究进展

大多数可栽培的食用菌是属于担子菌的大型真菌,具有复杂的交配型系统,通常涉及到两类交配型基因,即编码同源域转录因子的A交配型基因以及编码脂肽信息素和信息素受体的B交配型基因。对担子菌交配型系统的研究已经有上百年的历史,近年来随着高通量测序技术的发展,很多常见食用菌的基因组获得测序,使得我们对不同类型交配型位点的分子遗传学结构能够进行更加细致的解析。本文在概述了担子菌有性生殖系统和交配型基因分子特点的基础上,对常见食用菌中的香菇、金针菇、灵芝、糙皮侧耳、刺芹侧耳、白灵侧耳、裂褶菌、双孢蘑菇、草菇和虎皮香菇以及模式生物灰盖鬼伞等物种的交配型位点的结构进行了总结和分析。从已有的研究结果来看,常见食用菌的交配型位点的分子遗传学结构存在多样性,不同物种的交配型位点具有不同的结构特点。从物种内不同菌株之间的交配型结构比较来看,交配型基因的位置和数量也具有丰富的多样性。在分子遗传学层面对常见食用菌交配型位点结构的认识将有助于深入阐明交配型基因对子实体发育的调控以及解决食用菌生产实际中的科学问题,但是目前对食用菌交配型位点和基因的研究仍旧存在很多空白,有待于进一步深入和拓展。     

How predation shaped fish: the impact of fin spines on body form evolution across teleosts

It is well known that predators can induce morphological changes in some fish: individuals exposed to predation cues increase body depth and the length of spines. We hypothesize that these structures may evolve synergistically, as together, these traits will further enlarge the body dimensions of the fish that gape-limited predators must overcome. We therefore expect that the orientation of the spines will predict which body dimension increases in the presence of predators. Using phylogenetic comparative methods, we tested this prediction on the macroevolutionary scale across 347 teleost families, which display considerable variation in fin spines, body depth and width. Consistent with our predictions, we demonstrate that fin spines on the vertical plane (dorsal and anal fins) are associated with a deeper-bodied optimum. Lineages with spines on the horizontal plane (pectoral fins) are associated with a wider-bodied optimum. Optimal body dimensions across lineages without spines paralleling the body dimension match the allometric expectation. Additionally, lineages with longer spines have deeper and wider body dimensions. This evolutionary relationship between fin spines and body dimensions across teleosts reveals functional synergy between these two traits and a potential macroevolutionary signature of predation on the evolutionary dynamics of body shape.     

Dikaryons of the basidiomycete fungus Schizophyllum commune: evolution in long-term culture

The impact of ploidy on adaptation is a central issue in evolutionary biology. While many eukaryotic organisms exist as diploids, with two sets of gametic genomes residing in the same nucleus, most basidiomycete fungi exist as dikaryons in which the two genomes exist in separate nuclei that are physically paired and that divide in a coordinated manner during hyphal extension. To determine if haploid monokaryotic and dikaryotic mycelia adapt to novel environments under natural selection, we serially transferred replicate populations of each ploidy state on minimal medium for 18 months (approximately 13,000 generations). Dikaryotic mycelia responded to selection with increases in growth rate, while haploid monokaryotic mycelia did not. To determine if the haploid components of the dikaryon adapt reciprocally to one another's presence over time, we recovered the intact haploid components of dikaryotic mycelia at different time points (without meiosis) and mated them with nuclei of different evolutionary histories. We found evidence for coadaptation between nuclei in one dikaryotic line, in which a dominant deleterious mutation in one nucleus was followed by a compensatory mutation in the other nucleus; the mutant nuclei that evolved together had the best overall fitness. In other lines, nuclei had equal or higher fitness when paired with nuclei of other histories, indicating a heterozygote advantage. To determine if genetic exchange occurs between the two nuclei of a dikaryon, we developed a 24-locus genotyping system based on single nucleotide polymorphisms to monitor somatic exchange. We observed genetic exchange and recombination between the nuclei of several different dikaryons, resulting in genotypic variation in these mitotic cell lineages.     

How we are shaped: the biomechanics of gastrulation

Although it is rarely considered so in modern developmental biology, morphogenesis is fundamentally a biomechanical process, and this is especially true of one of the first major morphogenic transformations in development, gastrulation. Cells bring about changes in embryonic form by generating patterned forces and by differentiating the tissue mechanical properties that harness these forces in specific ways. Therefore, biomechanics lies at the core of connecting the genetic and molecular basis of cell activities to the macroscopic tissue deformations that shape the embryo. Here we discuss what is known of the biomechanics of gastrulation, primarily in amphibians but also comparing similar morphogenic processes in teleost fish and amniotes, and selected events in several species invertebrates. Our goal is to review what is known and identify problems for further research.     

Bacterial communities associated with mushrooms in the Qinghai-Tibet Plateau are shaped by soil parameters

International Microbiology - Fungi capable of producing fruit bodies are essential food and medicine resources. Despite recent advances in the study of microbial communities in mycorrhizospheres,...     

Reaction norms with bifurcations shaped by evolution

Two versions of a model for the evolution of seasonal polyphenism investigate the evolution of reaction norm bifurcation and branching. The first version is without a specific submodel for morphological development and the second has an explicit developmental map. Version 1 is evolutionarily relatively unconstrained: (i) reaction norms are specified by matrices containing the probabilities of occurrence of environment-phenotype combinations, (ii) all conceivable reaction norm matrices are reachable through a sequence of mutations, and (iii) small as well as large mutational effects occur. This version is used to find the evolutionarily stable strategy favoured by the population ecology that is characterized by stabilizing viability selection with a cyclically fluctuating selection optimum. When the strength of selection is large and when the lag between initiation of development and selection on mature phenotype is not a multiple of half the period of the environmental cycle, a branching reaction norm evolves. In the second model version, branching reaction norms occur for certain parameter combinations of the developmental submodel, but the evolution of this pattern is often constrained. The evolutionary trajectory becomes trapped in a local selective optimum for the parameters of the developmental system. Substantial developmental noise evolves, but mutations that produce a selectively advantageous branching pattern do not occur from there.     

The brown-rot basidiomycete Fomitopsis palustris has the endo-glucanases capable of degrading microcrystalline cellulose

Two endoglucanases with processive cellulase activities, produced from Fomitopsis palustris grown on 2% microcrystalline cellulose (Avicel), were purified to homogeneity by anion-exchange and gel filtration column chromatography systems. SDS-PAGE analysis indicated that the molecular masses of the purified enzymes were 47 kDa and 35 kDa, respectively. The amino acid sequence analysis of the 47-kDa protein (EG47) showed a sequence similarity with fungal glycoside hydrolase family 5 endoglucanase from the white-rot fungus Phanerochaete chrysosporium. N-terminal and internal amino acid sequences of the 35-kDa protein (EG35), however, had no homology with any other glycosylhydrolases, although the enzyme had high specific activity against carboxymethyl cellulose, which is a typical substrate for endoglucanases. The initial rate of Avicel hydrolysis by EG35 was relatively fast for 48 h, and the amount of soluble reducing sugar released after 96 h was 100 microg/ml. Although EG47 also hydrolyzed Avicel, the hydrolysis rate was lower than that of EG35. Thin layer chromatography analysis of the hydrolysis products released from Avicel indicated that the main product was cellobiose, suggesting that the brown-rot fungus possesses processive EGs capable of degrading crystalline cellulose.     

Biometric evidence that sexual selection has shaped the hominin face

We consider sex differences in human facial morphology in the context of developmental change. We show that at puberty, the height of the upper face, between the lip and the brow, develops differently in males and females, and that these differences are not explicable in terms of sex differences in body size. We find the same dimorphism in the faces of human ancestors. We propose that the relative shortening in men and lengthening in women of the anterior upper face at puberty is the mechanistic consequence of extreme maxillary rotation during ontogeny. A link between this developmental model and sexual dimorphism is made for the first time, and provides a new set of morphological criteria to sex human crania. This finding has important implications for the role of sexual selection in the evolution of anthropoid faces and for theories of human facial attractiveness.     

Siboglinid evolution shaped by habitat preference and sulfide tolerance

Siboglinids are tube-dwelling annelids that inhabit marine reducing habitats such as anoxic mud bottoms, seeps and hydrothermal vents. As adults, they lack a functional digestive system and rely on chemoautotrophic microbial endosymbionts. Based on morphological analyses, Siboglinidae form a clade with the Sabellariidae, Serpulidae and Sabellidae within the Annelida. The sister group to this clade is the Oweniidae. Three subgroups constitute the Siboglinidae: Frenulata typically inhabit anoxic sediments, Sclerolinium (a.k.a., Monilifera) live on decaying organic matter or reduced sediments and Vestimentifera are mostly found at hydrocarbon seeps and hydrothermal vents. Recent studies suggest that Sclerolinum is the sister group to the Vestimentifera. Within the Vestimentifera, the species inhabiting bare-rock hydrothermal vents represent a derived clade. The seep-inhabiting genus Lamellibrachia forms a basal branch within the Vestimentifera. Trends in siboglinid evolution are most notable with regard to the level of sulfide tolerance and type of substrate. Basal groups inhabit soft substrate with only slightly elevated sulfide levels, whereas more derived species colonize hard substrate and tolerate elevated temperatures and high levels of sulfide. The type of substrate correlates with tube morphology and the function of the opisthosome. The role of the symbionts in habitat selection needs further investigation.     

The evolution of spore size in Agarics: do big mushrooms have big spores?

As a first attempt to investigate evolutionary patterns of spore size in Agarics, I tested whether this trait was correlated to the size of the fruit-body (basidiocarp). Based on phylogenetically independent contrasts, it was shown that big mushroom species had on average 9% longer, 9% wider and 33% more voluminous spores (all with P < 0.05, one-tailed tests) than small congeneric species (a three-fold difference in cap diameter was used to discriminate big and small mushrooms). It is argued that larger spore size does not consistently confer higher fitness in fungi, owing to aerodynamic constraints. Surprisingly, the cap–spore correlation was strongly lineage-specific. Thus, spore volume correlated significantly with cap diameter in five of 16 large genera (four positive and one negative correlation). Positive cap–spore correlations are interpreted in terms of developmental constraints, mediated by hyphal swelling during cap expansion. The possible mechanisms which can account for the breakdown of this constraint in the majority of genera investigated are discussed.     

Inter-phylum HGT has shaped the metabolism of many mesophilic and anaerobic bacteria

Genome sequencing has revealed that horizontal gene transfer (HGT) is a major evolutionary process in bacteria. Although it is generally assumed that closely related organisms engage in genetic exchange more frequently than distantly related ones, the frequency of HGT among distantly related organisms and the effect of ecological relatedness on the frequency has not been rigorously assessed. Here, we devised a novel bioinformatic pipeline, which minimized the effect of over-representation of specific taxa in the available databases and other limitations of homology-based approaches by analyzing genomes in standardized triplets, to quantify gene exchange between bacterial genomes representing different phyla. Our analysis revealed the existence of networks of genetic exchange between organisms with overlapping ecological niches, with mesophilic anaerobic organisms showing the highest frequency of exchange and engaging in HGT twice as frequently as their aerobic counterparts. Examination of individual cases suggested that inter-phylum HGT is more pronounced than previously thought, affecting up to ∼16% of the total genes and ∼35% of the metabolic genes in some genomes (conservative estimation). In contrast, ribosomal and other universal protein-coding genes were subjected to HGT at least 150 times less frequently than genes encoding the most promiscuous metabolic functions (for example, various dehydrogenases and ABC transport systems), suggesting that the species tree based on the former genes may be reliable. These results indicated that the metabolic diversity of microbial communities within most habitats has been largely assembled from preexisting genetic diversity through HGT and that HGT accounts for the functional redundancy among phyla.