Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes

The origin of eukaryotes represents an enigmatic puzzle, which is still lacking a number of essential pieces. Whereas it is currently accepted that the process of eukaryogenesis involved an interplay between a host cell and an alphaproteobacterial endosymbiont, we currently lack detailed information regarding the identity and nature of these players. A number of studies have provided increasing support for the emergence of the eukaryotic host cell from within the archaeal domain of life, displaying a specific affiliation with the archaeal TACK superphylum. Recent studies have shown that genomic exploration of yet-uncultivated archaea, the so-called archaeal ‘dark matter’, is able to provide unprecedented insights into the process of eukaryogenesis. Here, we provide an overview of state-of-the-art cultivation-independent approaches, and demonstrate how these methods were used to obtain draft genome sequences of several novel members of the TACK superphylum, including Lokiarchaeum, two representatives of the Miscellaneous Crenarchaeotal Group (Bathyarchaeota), and a Korarchaeum-related lineage. The maturation of cultivation-independent genomics approaches, as well as future developments in next-generation sequencing technologies, will revolutionize our current view of microbial evolution and diversity, and provide profound new insights into the early evolution of life, including the enigmatic origin of the eukaryotic cell.     

Variation between strains of the flour beetle Tribolium castaneum in relative performance on five flours

When populations are exposed to different environments, evolutionary processes can lead either to genetically differentiated strains or to the appearance of increased generalism at the individual level. For evolution to occur, genetic variability in performance in different environments is required. Here, intraspecific genetic variation across environments was estimated in the flour beetle Tribolium castaneum (Herbst) by comparing the responses of two strains of T. castaneum to different flour types. Replicated groups from each strain were allowed to develop on either the standard whole wheat medium or on one of four novel flours (wheat, rice, corn and oat). In several of the novel flours, clear differences in mean development time or population size of one or both strains were seen relative to performance in the standard medium. Moreover, the strains differed significantly in their phenotypic responses to the flours. One strain did particularly poorly on oat flour. Reduced oviposition, reduced larval survivorship and increased larval cannibalism were examined as possible causes of the low productivity on oat flour. These three factors accounted for about 70% of the reduction in population size when this strain oviposited and developed in oat flour. The difference between these two outbred strains in response to these five flours suggests that genetic variation in resource use is present within T. castaneum and may also be present within strains and natural populations in grain storage facilities. Such variation would permit an evolutionary response to selection in multiple environments (flours). This process has agricultural implications when several types of grain are stored in a single location because it could eventually lead to the evolution of highly generalized populations of T. castaneum, an important pest of stored products.     

New(t)s and views from hybridizing MHC genes: introgression rather than trans-species polymorphism may shape allelic repertoires

One of the key features of major histocompatibility complex (MHC) genes is the frequent occurrence of trans-species polymorphism, that is 'the passage of allelic lineages from ancestral to descendant species' (Klein et al. 2007). Selectively maintained ancestral polymorphism may, however, be hard to distinguish from introgression of MHC alleles between hybridizing species (Fig. 1). In this issue of Molecular Ecology, Nadachowska-Brzyska et al. (2012) present data that suggest that the latter can be observed in two closely related species of newts, Lissotriton vulgaris (Lv) and L. montandoni (Lm) from south-east Europe. Strikingly, allelic MHC variation displayed more structure between geographically separated populations of L. vulgaris than across species in the hybrid zone. This suggests that high MHC variation in L. montadoni may result from mainly unidirectional gene flow between species, while differentiation between northern and southern populations of L. vulgaris might reflect local adaptation.     

多寄主型寄生性天敌昆虫的寄主适应性及其影响因素

寄生性天敌昆虫对不同寄主资源的适应能力是其存活和繁殖的必要条件,它们的寄主选择行为则是其重要的适应结果。多寄主型寄生性天敌昆虫虽然对某种特定寄主资源的利用效率可能不如单寄主型寄生蜂,但却有利于拓展更宽的寄主范围,因此对环境的适应能力更强,更容易在自然界维持其种群的生存。统计结果也表明多寄主型天敌的生物防治效果往往比专食性天敌更高。有时生物防治成功的关键可能并不在于所利用的天敌种类的不同,而在于天敌的不同生物型或地理宗。总结了多寄主型寄生性天敌昆虫的寄主适应能力及其影响因素。寄生性天敌昆虫不仅因地理隔离产生种群分化,也可能因寄生不同的寄主产生种群内的分化,从而更加适应寄主的生活特性和栖境条件。寄主种类、寄主发育阶段、寄主大小、寄主营养、寄主免疫反应、寄主逃避反应、其它天敌的竞争、寄主共生或共栖生物的存在、寄主植物、天敌自身的学习能力及其共生微生物等多种因素对寄生性天敌昆虫的寄主适应性可产生影响。展望了多寄主型寄生性天敌昆虫对新寄主资源的拓展利用能力和适应性在生产上的可能应用前景和途径,以期为明确天敌与寄主间的互作关系,人工驯化寄生性天敌昆虫增强对靶标害虫的控制作用,合理利用天敌提高生物防治效率提供新的思路和理论支持。     

Relatively simple methodology for the determination of configuration of unsaturation of bacterial monounsaturated fatty acids: application to the unsaturates of Legionella spp.

Unsaturated fatty acids of known degree, position, and configuration of unsturation were esterified, and stereospecifically dihydroxylated at the double bond(s). cis-Hydroxylation was effected using Woodward's reagent (silver acetate/iodine/acetic acid), while trans-hydroxylation was effected using Fenton's reagent (hydrogen peroxide/ferrous sulfate/acetic acid). Diols derived from monounsaturated esters were recovered quantitatively, while tetraols derived from diunsaturates were lost, presumably during extensive washing. The stereospecifically dihydroxylated esters were analyzed by thin-layer chromatography on borate-impregnated silica gel plates, and by gas-liquid chromatography, on a nonpolar capillary column, as the trimethylsilyl, acetyl, n-butylboronyl, isopropylidene, and trifluoroacetyl derivatives. For each derivative, the erythro and threo diols were readily separable, and some resolution of positional isomers was observed. Thus, the cis/trans configuration, and in some instances, the position of unsaturation of the original monounsaturated fatty acid may be deduced. However, gas chromatography-mass spectrometry of appropriately derivatized diol esters is required for unambiguous determination of position of unsaturation in most cases. These reactions are simple, use readily available reagents, and require relatively little operator attention. Further, they do not require specialized apparatus, as do hydrogenation and ozonolysis, or potentially toxic chemicals, such as osmium tetroxide. This series of analyses was applied to the unsaturated non-hydroxylated fatty acids of Legionella species, which were shown to be monounsaturated and of the cis Δ9 family. Position of unsaturation was confirmed by gas chromatography-mass spectrometry.     

Multi‐locus sequence typing of Salmonella enterica serovar Typhimurium isolates from wild birds in northern England suggests host‐adapted strain

Aims: Recent studies have suggested that Salmonella Typhimurium strains associated with mortality in UK garden birds are significantly different from strains that cause disease in humans and livestock and that wild bird strains may be host adapted. However, without further genomic characterization of these strains, it is not possible to determine whether they are host adapted. The aim of this study was to characterize a representative sample of Salm. Typhimurium strains detected in wild garden birds using multi‐locus sequence typing (MLST) to investigate evolutionary relationships between them. Methods and Results: Multi‐locus sequence typing was performed on nine Salm. Typhimurium strains isolated from wild garden birds. Two sequence types were identified, the most common of which was ST568. Examination of the public Salmonella enterica MLST database revealed that only three other ST568 isolates had been cultured from a human in Scotland. Two further isolates of Salm. Typhimurium were determined to be ST19. Conclusions: Results of MLST analysis suggest that there is a predominant strain of Salm. Typhimurium circulating among garden bird populations in the United Kingdom, which is rarely detected in other species, supporting the hypothesis that this strain is host adapted. Significance and Impact of the Study: Host–pathogen evolution is often assumed to lead to pathogens becoming less virulent to avoid the death of their host; however, infection with ST568 led to high mortality rates among the wild birds examined, which were all found dead at wild bird‐feeding stations. We hypothesize that by attracting unnaturally high densities of birds, wild bird‐feeding stations may facilitate the transmission of ST568 between wild birds, therefore reducing the evolutionary cost of this pathogen killing its host, resulting in a host‐adapted strain with increased virulence.     

Divergence of ovipositor length and egg shape in a brood parasitic bitterling fish through the use of different mussel hosts

Bitterling fishes deposit their eggs on the gills of living mussels using a long ovipositor. We examined whether ovipositor length (OL) and egg shape correlated with differences in host mussel species in the family Unionidae among populations of the tabira bitterling (Acheilognathus tabira) in Japan. Bitterling populations that use mussels in the sub-family Anodontinae possessed longer ovipositors and more elongated eggs than those using mussels of Unioninae, as expected from the difference in host size between the sub-families (anodontine mussels are larger than unionine mussels). Based on a robust phylogeny of A. tabira populations, we demonstrated that the evolution of both OL and egg shape were correlated with host differences, but not with each other, suggesting that these traits have been selected for independently. Our study demonstrates how adaptive traits for brood parasitism may diverge with host shift due to different host availability and/or interspecific competition for hosts.     

The Role of Adaptation to Host Plants in the Evolution of Reproductive Isolation: Negative Evidence from Tetranychus Urticae Koch

Reproductive isolation between demes of a phytophagous arthropod population that use different host plant species could evolve in two different ways. First, adaptation to different host species might result in reproductive isolation as a pleiotropic by-product. Second, if adaptation to one host species strongly reduces fitness on others, selection could favour mechanisms, such as host fidelity and assortative mating, that restrict gene flow between host-adapted demes. A laboratory selection experiment on the broadly polyphagous spider mite Tetranychus urticae gave information on these possibilities. A population allowed to adapt to tomato plants showed increased survival, development rate and fecundity on tomato relative to the base population from which it was derived. In spite of the large difference between the tomato-adapted and base populations in performance on tomato plants, the two populations showed no evidence of reproductive isolation, as measured by the hatching rate of eggs laid by F1 hybrids between the lines. Furthermore, a genetically variable population formed by hybridizing the tomato-adapted and base populations did not show evidence for a decline in ability to survive on tomato after more than ten generations of mass rearing on lima bean, indicating that tomato-adapted genotypes suffered little or no selective disadvantage on bean. These results give no support for the role of host plants in the evolution of reproductive isolation in T. urticae.     

Field estimation of variation in host plant use between local populations of pea aphids from two crops

Abstract. 1. In a reciprocal transplant experiment on pea aphids (Acyrthosiphon pisum (Harris)), the relative performance of clones collected from nearby alfalfa and red clover fields was tested by allowing clonal replicates to develop on both crops under field conditions.
2. Populations from alfalfa and red clover differed in relative survivorship and probabilities of reproduction on the two crops. Clones had significantly higher performance on the crop from which they were collected (the 'home' crop) than they did on the other crop.
3. Evidence is presented that previous experience on these host plants cannot account for the increased probability of reproduction observed on the 'home' crop. Thus, the differences between these two populations in their relative performance on alfalfa and clover are likely to be genetically based.
4. These results illustrate that local adaptation to different host plants can occur within small geographical areas, despite the high probability that migrants are exchanged between nearby fields of the two crops.
5. Experimental designs of the type described here permit estimation of patterns of genetic variation within and between insect populations. When applied to pest species, such designs will facilitate the study of evolution in agricultural systems.     

Sympatric host races of the European corn borer: adaptation to host plants and hybrid performance

The European corn borer (ECB), Ostrinia nubilalis, is a major pest of maize crops. In Europe, two sympatric host races are found: one feeds on maize (Zea mays) and the other mainly on mugwort (Artemisia vulgaris). The two host races are genetically differentiated, seldom crossing in the laboratory or in the field, and females preferentially lay eggs on their native host species. We conducted two independent experiments, in field and greenhouse conditions, to determine whether the two host races are locally adapted to their host species. The effect of larval density and the performance of hybrids were also investigated. Despite some differences in overall larval feeding performance, both experiments revealed consistent patterns of local adaptation for survival and for larval weight in males. In females the same trend was observed but with weaker statistical support. F1 hybrids did not seem to be disadvantaged compared with the two parental races. Overall, our results showed that both host races are physiologically adapted to their native host. The fitness trade-off between the two host plants provides a potential driving force for ecological speciation in this species.