Males make poor meals: a comparison of nutrient extraction during sexual cannibalism and predation

Cannibalism is hypothesized to have evolved as a way to obtain a high-quality meal. We examined the extraction of lipid and protein by female wolf spiders, Hogna helluo, during sexual cannibalism of males and predation of crickets. Most food-limited females did not cannibalize males but immediately consumed a size-matched cricket. When consuming male H. helluo and crickets, female H. helluo only consumed 51% of the male body while they consumed 72% of the cricket body. While males had higher protein content in their bodies than crickets and other insects, female H. helluo ingested similar amounts of protein from male H. helluo and crickets. Female H. helluo extracted 47% of the protein present in male H. helluo and 67% of the protein present in crickets. Females were able to extract nearly all of the lipid present in male H. helluo and crickets. However, crickets and other insects had almost 4 times higher lipid content than male H. helluo. The ratio of lipid to protein consumed from crickets appeared more similar to the nutritional requirements of egg production than that of males. Taken together, female hesitancy to engage in cannibalism, low extraction of nutrients from males and a low ratio of lipid to protein in the food extracted from males suggest that males may be poor-quality prey items compared to common insects such as crickets.     

啮总目昆虫的线粒体基因组多样性及系统发育研究进展

啮总目包括啮虫目（皮虱和书虱）和虱目（羽虱和吸虱）,是农业和医学等领域具有重要经济意义和研究价值的类群,目前已鉴定和描述的物种超过10 000个。啮总目昆虫线粒体基因组的变异性在昆虫各类群中最为剧烈,这些变异包括基因组的结构、基因排序、基因含量和链上分布等诸多方面。本文全面分析和总结了啮总目昆虫裂化线粒体基因组的进化属性,并结合两侧对称动物线粒体基因组的裂化特征重构了线粒体基因组环裂化的过程。引入“线粒体基因组核型”的概念来描述动物线粒体基因组丰富的变异程度。动物线粒体的染色体有减小的趋势,而线粒体基因组的裂化正是体现这种趋势的一种重要策略。同时,总结和探讨了目前具有争议的啮总目主要类群间的系统发育关系。本综述为啮总目昆虫线粒体基因组学、啮总目系统发生关系以及两侧对称动物线粒体基因组进化模式的研究提供一个新的视角。     

Extreme rates and heterogeneity in insect DNA evolution

Summary DNA-DNA hybridization studies of insects, more specificallyDrosophila and cave crickets, have revealed interesting patterns of genome evolution that contrast markedly with what has been seen in other taxa, especially mammals and birds. Insect genomes are composed of sections of single-copy DNA with extreme variation in rates of evolutionary change. This variation is more extreme than between introns and exons; introns fall into the relatively conserved fraction of the genome. Attempts to calculate absolute rates of change inDrosophila DNA have all led to estimates some 5–10 times faster than those found in most vertebrates; this is true even for the more conservative part of the nuclear genome. Finally we point out that morphological similarity, chromosomal similarity, and/or ability to form interspecific hybrids is often associated with quite high levels of single-copy DNA divergence in insects as compared to mammals and birds.     

突变在基因组进化中的意义

在漫长的进化历史中,各物种间和物种内基因组的差异是如何形成、积累乃至保留下来的,不仅是进化生物学中需要解决的核心问题,也是整个生命科学面临的基本问题之一。对该问题的探求必然要通过对突变的深入了解,因为突变不仅是基因组进化的重要驱动力,还是基因 组进化研究的基础。文章围绕突变的性质及其在基因组进化中的深远意义,系统介绍了国际上相关研究的发展历程,所获得的成果和最新动向。     

Visual and nutritional food cues fine-tune timing of reproduction in a neotropical rainforest bird

Food may act as a proximate factor in the regulation of avian seasonal breeding. Food cues could provide particularly important seasonal information to birds living in variable tropical environments, but this has not yet been tested. Spotted antbirds (Hylophylax n. naevioides) inhabiting a humid forest in central Panama (9 degrees N) likely use changes in the tropical photoperiod to time reproduction on a long-term, seasonal basis. We predicted that these insectivorous birds also adjust reproduction to short-term cues such as food availability because the onset of the rainy season and the resulting increase in insect abundance varies considerably between years. To test this prediction, prior to their breeding season (when they had half-maximal gonads), we either exposed captive male spotted antbirds to an ad libitum standard diet only or added live crickets to this diet. Males that received live crickets significantly increased gonad sizes within 3 weeks over controls on the standard diet. Moreover, in six additional experiments cricket availability always increased song rate, usually within a few days. The stimulatory effect of live crickets on song activity may function independent of nutritional aspects: Freshly killed crickets, providing similar nutritional content as live crickets, did not stimulate the birds' song activity. However, song activity increased to intermediate levels when live crickets were shown under a clear plastic wrap, i.e., when birds could see but not eat crickets. We hypothesize that the opportunity to see and handle live insects stimulates song and reproductive activity in these birds. Our data indicate for the first time that a tropical rainforest bird can use food cues to evaluate the suitability of local environmental conditions for breeding. J. Exp. Zool. 286:494-504, 2000.     

Complete nucleotide sequence of the <Emphasis Type="Italic">Cryptomeria japonica</Emphasis>D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species

Background  

The recent determination of complete chloroplast (cp) genomic sequences of various plant species has enabled numerous comparative analyses as well as advances in plant and genome evolutionary studies. In angiosperms, the complete cp genome sequences of about 70 species have been determined, whereas those of only three gymnosperm species, Cycas taitungensis, Pinus thunbergii, and Pinus koraiensis have been established. The lack of information regarding the gene content and genomic structure of gymnosperm cp genomes may severely hamper further progress of plant and cp genome evolutionary studies. To address this need, we report here the complete nucleotide sequence of the cp genome of Cryptomeria japonica, the first in the Cupressaceae sensu lato of gymnosperms, and provide a comparative analysis of their gene content and genomic structure that illustrates the unique genomic features of gymnosperms.     

基因组时代的昆虫学研究

昆虫种类繁多,它与生态系统中的生物多样性,以及人类的日常生活和生产密切相关。自2000年黑腹果蝇Drosophila melanogaster全基因组测序完成以来,至今已先后开展了88种昆虫全基因组测序工作,这标志着昆虫学研究进入了基因组时代。本文综述了近年来昆虫基因组测序进展,以及基于基因组的昆虫学研究方法及应用等两方面的研究成果。同时,着重介绍了昆虫全基因组测序进程,昆虫基因组在个体生物学、多物种间及种群,及系统生物学研究中的应用等方面的内容。最后,还探讨了基因组时代昆虫学研究所面临的挑战。     

The evolution of the flagellar assembly pathway in endosymbiotic bacterial genomes

Genome shrinkage is a common feature of most intracellular pathogens and symbionts. Reduction of genome sizes is among the best-characterized evolutionary ways of intracellular organisms to save and avoid maintaining expensive redundant biological processes. Endosymbiotic bacteria of insects are examples of biological economy taken to completion because their genomes are dramatically reduced. These bacteria are nonmotile, and their biochemical processes are intimately related to those of their host. Because of this relationship, many of the processes in these bacteria have been either lost or have suffered massive remodeling to adapt to the intracellular symbiotic lifestyle. An example of such changes is the flagellum structure that is essential for bacterial motility and infectivity. Our analysis indicates that genes responsible for flagellar assembly have been partially or totally lost in most intracellular symbionts of gamma-Proteobacteria. Comparative genomic analyses show that flagellar genes have been differentially lost in endosymbiotic bacteria of insects. Only proteins involved in protein export within the flagella assembly pathway (type III secretion system and the basal body) have been kept in most of the endosymbionts, whereas those involved in building the filament and hook of flagella have only in few instances been kept, indicating a change in the functional purpose of this pathway. In some endosymbionts, genes controlling protein-export switch and hook length have undergone functional divergence as shown through an analysis of their evolutionary dynamics. Based on our results, we suggest that genes of flagellum have diverged functionally as to specialize in the export of proteins from the bacterium to the host.     

Lessons from the genomes of extremely acidophilic bacteria and archaea with special emphasis on bioleaching microorganisms

This mini-review describes the current status of recent genome sequencing projects of extremely acidophilic microorganisms and highlights the most current scientific advances emerging from their analysis. There are now at least 56 draft or completely sequenced genomes of acidophiles including 30 bacteria and 26 archaea. There are also complete sequences for 38 plasmids, 29 viruses, and additional DNA sequence information of acidic environments is available from eight metagenomic projects. A special focus is provided on the genomics of acidophiles from industrial bioleaching operations. It is shown how this initial information provides a rich intellectual resource for microbiologists that has potential to open innovative and efficient research avenues. Examples presented illustrate the use of genomic information to construct preliminary models of metabolism of individual microorganisms. Most importantly, access to multiple genomes allows the prediction of metabolic and genetic interactions between members of the bioleaching microbial community (ecophysiology) and the investigation of major evolutionary trends that shape genome architecture and evolution. Despite these promising beginnings, a major conclusion is that the genome projects help focus attention on the tremendous effort still required to understand the biological principles that support life in extremely acidic environments, including those that might allow engineers to take appropriate action designed to improve the efficiency and rate of bioleaching and to protect the environment.     

The Genome Strikes Back: The Evolutionary Importance of Defence Against Mobile Elements

Increasingly, we regard the genome as a site and source of genetic conflict. This fascinating ‘bottom-up’ view brings up appealing connections between genome biology and whole-organism ecology, in which populations of elements compete with one another in their genomic habitat. Unlike other habitats, though, a host genome has its own evolutionary interests and is often able to defend itself against molecular parasites. Most well-studied organisms employ strategies to protect their genomes against the harmful effects of genomic parasites, including methylation, various pathways of RNA interference, and more unusual tricks such as repeat induced point-mutation (RIP). These genome defence systems are not obscure biological curiosities, but fundamentally important to the integrity and cohesion of the genome, and exert a powerful influence on genome evolution.     

The frontier between cell and organelle: genome analysis of <Emphasis Type="Italic">Candidatus</Emphasis> Carsonella ruddii

Background  

Bacterial symbioses are widespread among insects. The early establishment of such symbiotic associations has probably been one of the key factors for the evolutionary success of insects, since it may have allowed access to novel ecological niches and to new imbalanced food resources, such as plant sap or blood. Several genomes of bacterial endosymbionts of different insect species have been recently sequenced, and their biology has been extensively studied. Recently, the complete genome sequence of Candidatus Carsonella ruddii, considered the primary endosymbiont of the psyllid Pachpsylla venusta, has been published. This genome consists of a circular chromosome of 159,662 bp and has been proposed as the smallest bacterial endosymbiont genome known to date.     

Unraveling the effect of genomic structural changes in the rhesus macaque - implications for the adaptive role of inversions

Background

By reshuffling genomes, structural genomic reorganizations provide genetic variation on which natural selection can work. Understanding the mechanisms underlying this process has been a long-standing question in evolutionary biology. In this context, our purpose in this study is to characterize the genomic regions involved in structural rearrangements between human and macaque genomes and determine their influence on meiotic recombination as a way to explore the adaptive role of genome shuffling in mammalian evolution.

Results

We first constructed a highly refined map of the structural rearrangements and evolutionary breakpoint regions in the human and rhesus macaque genomes based on orthologous genes and whole-genome sequence alignments. Using two different algorithms, we refined the genomic position of known rearrangements previously reported by cytogenetic approaches and described new putative micro-rearrangements (inversions and indels) in both genomes. A detailed analysis of the rhesus macaque genome showed that evolutionary breakpoints are in gene-rich regions, being enriched in GO terms related to immune system. We also identified defense-response genes within a chromosome inversion fixed in the macaque lineage, underlying the relevance of structural genomic changes in evolutionary and/or adaptation processes. Moreover, by combining in silico and experimental approaches, we studied the recombination pattern of specific chromosomes that have suffered rearrangements between human and macaque lineages.

Conclusions

Our data suggest that adaptive alleles – in this case, genes involved in the immune response – might have been favored by genome rearrangements in the macaque lineage.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-530) contains supplementary material, which is available to authorized users.     

A Phylogenetic Analysis of the Evolution of the Stridulatory Apparatus in True Crickets (Orthoptera, Grylloidea)

The stridulatory apparatus (or stridulum) is currently assumed ancestral in crickets. Models of its subsequent evolution consider only one modality of evolutionary change: the stridulum would have been progressively lost in multiple cricket lineages. A phylogenetic test of this hypothesis is presented here. The morpho-functional types of stridulum have been optimized on the cladistic phylogenies of two monophyletic cricket clades, and parsimonious evolutionary scenarios of the evolution of the stridulum in these clades have been derived. The phylogenetic patterns thus obtained support the hypothesis that the stridulum has been lost several times convergently in crickets. They indicate, however, that the loss of the stridulum could be reversible, and that several modalities of evolutionary change exist for the stridulum. Phylogenetic analysis thus reveals an unsuspected complexity in the evolution of acoustic communication in crickets.     

Genomic gigantism: DNA loss is slow in mountain grasshoppers

Several studies have shown DNA loss to be inversely correlated with genome size in animals. These studies include a comparison between Drosophila and the cricket, Laupala, but there has been no assessment of DNA loss in insects with very large genomes. Podisma pedestris, the brown mountain grasshopper, has a genome over 100 times as large as that of Drosophila and 10 times as large as that of Laupala. We used 58 paralogous nuclear pseudogenes of mitochondrial origin to study the characteristics of insertion, deletion, and point substitution in P. pedestris and Italopodisma. In animals, these pseudogenes are "dead on arrival"; they are abundant in many different eukaryotes, and their mitochondrial origin simplifies the identification of point substitutions accumulated in nuclear pseudogene lineages. There appears to be a mononucleotide repeat within the 643-bp pseudogene sequence studied that acts as a strong hot spot for insertions or deletions (indels). Because the data for other insect species did not contain such an unusual region, hot spots were excluded from species comparisons. The rate of DNA loss relative to point substitution appears to be considerably and significantly lower in the grasshoppers studied than in Drosophila or Laupala. This suggests that the inverse correlation between genome size and the rate of DNA loss can be extended to comparisons between insects with large or gigantic genomes (i.e., Laupala and Podisma). The low rate of DNA loss implies that in grasshoppers, the accumulation of point mutations is a more potent force for obscuring ancient pseudogenes than their loss through indel accumulation, whereas the reverse is true for Drosophila. The main factor contributing to the difference in the rates of DNA loss estimated for grasshoppers, crickets, and Drosophila appears to be deletion size. Large deletions are relatively rare in Podisma and Italopodisma.     

The Visayan Warty Pig (Sus cebifrons) Genome Provides Insight Into Chromosome Evolution and Sensory Adaptation in Pigs

It is largely unknown how mammalian genomes evolve under rapid speciation and environmental adaptation. An excellent model for understanding fast evolution is provided by the genus Sus, which diverged relatively recently and lacks postzygotic isolation. Here, we present a high-quality reference genome of the Visayan warty pig, which is specialized to a tropical island environment. Comparing the genome sequences and chromatin contact maps of the Visayan warty pig (Sus cebifrons) and domestic pig (Sus scrofa), we characterized the dynamics of chromosomal structure evolution during Sus speciation, revealing the similar chromosome conformation as the potential biological mechanism of frequent postdivergence hybridization among Suidae. We further investigated the different signatures of adaptive selection and domestication in Visayan warty pig and domestic pig with specific emphasize on the evolution of olfactory and gustatory genes, elucidating higher olfactory diversity in Visayan warty pig and positive and relaxed evolution of bitter and fat taste receptors, respectively, in domestic pig. Our comprehensive evolutionary and comparative genome analyses provide insight into the dynamics of genomes and how these change over relative short evolutionary times, as well as how these genomic differences encode for differences in the phenotypes.