Do miRNAs have a deep evolutionary history?

The recent discovery of microRNAs (miRNAs) in unicellular eukaryotes, including miRNAs known previously only from animals or plants, implies that miRNAs have a deep evolutionary history among eukaryotes. This contrasts with the prevailing view that miRNAs evolved convergently in animals and plants. We re-evaluate the evidence and find that none of the 73 plant and animal miRNAs described from protists meet the required criteria for miRNA annotation and, by implication, animals and plants did not acquire any of their respective miRNA genes from the crown ancestor of eukaryotes. Furthermore, of the 159 novel miRNAs previously identified among the seven species of unicellular protists examined, only 28 from the algae Ectocarpus and Chlamydomonas, meet the criteria for miRNA annotation. Therefore, at present only five groups of eukaryotes are known to possess miRNAs, indicating that miRNAs have evolved independently within eukaryotes through exaptation of their shared inherited RNAi machinery.     

Do we have a right to an unmanipulated genome? The human genome as the common heritage of mankind

The human genome is commonly regarded as a ‘natural’ connection between all human beings, as it has been handed down to us by our predecessors. As such, it is believed to represent common heritage of humanity, e.g. a resource of outstanding value that should be the object of special protection and international concern. Some critics argue that germline manipulation would disrupt this natural heritage and that we have a duty to preserve the integrity of the human germline. However, a closer look reveals that the concept of common heritage of humanity does not necessarily imply the impermissibility of germline manipulation. If it is restricted to the prevention of severe diseases, germline manipulation does not represent a threat to the unity and identity of the human species, even though this would create a new form of relationship between human beings, namely that between a designer and a genetically designed person.     

Do vertebrate neural crest and cranial placodes have a common evolutionary origin?

Two embryonic tissues-the neural crest and the cranial placodes-give rise to most evolutionary novelties of the vertebrate head. These two tissues develop similarly in several respects: they originate from ectoderm at the neural plate border, give rise to migratory cells and develop into multiple cell fates including sensory neurons. These similarities, and the joint appearance of both tissues in the vertebrate lineage, may point to a common evolutionary origin of neural crest and placodes from a specialized population of neural plate border cells. However, a review of the developmental mechanisms underlying the induction, specification, migration and cytodifferentiation of neural crest and placodes reveals fundamental differences between the tissues. Taken together with insights from recent studies in tunicates and amphioxus, this suggests that neural crest and placodes have an independent evolutionary origin and that they evolved from the neural and non-neural side of the neural plate border, respectively.     

Do more complex organisms have a greater proportion of membrane proteins in their genomes?

One may speculate that higher organisms require a proportionately greater abundance of membrane proteins within their genomes in order to furnish the requirements of differentiated cell types, compartmentalization, and intercellular signalling. With the recent availability of several complete prokaryotic genome sequences and sufficient progress in many eukaryotic genome sequencing projects, we seek to test this hypothesis. Using optimized hydropathy analysis of proteins in several, diverse proteomes, we show that organisms of the three domains of life-Eukarya, Eubacteria, and Archaea-have similar proportions of alpha-helical membrane proteins within their genomes and that these are matched by the complexity of the aqueous components.     

Do New Zealand invertebrates reflect the dominance of birds in their evolutionary history?

Pre-human New Zealand had some unusual feeding guilds of birds (e.g. the herbivorous moa fauna), thought to have developed as a result of the absence of a ?normal? mammal fauna. Insectivorous birds, on the other hand, are an integral part of all the world?s ecosystems, regardless of the presence or absence of mammals. While it is acknowledged the overall predation impact from birds in New Zealand is unlikely to have differed greatly from elsewhere, the low impact of mammalian insectivores (apart from microbats), coupled with the presence of a specialised avian feeding guild that concentrated on ground-active prey, might have exerted certain unique selection pressures. Do New Zealand invertebrates reflect this? It would be necessary to compare the New Zealand invertebrate fauna with that of mammal-dominated lands in greater detail than is available today before we could assert whether any unique anti-predator characteristics have evolved. Knowledge of the insects that succumbed to extinction when mammals invaded New Zealand should provide clues to avian-adapted features that might have rendered them particularly vulnerable to introduced rodents. Predation by kiwi (Apteryx spp.), an extraordinarily mammal-like nocturnal bird, may to some extent have prepared the invertebrate fauna for the arrival of small mammals.     

Towards a framework for the evolutionary genomics of Kinetoplastids: what kind of data and how much?

The current status of kinetoplastids phylogeny and evolution is discussed in view of the recent progresses on genomics. Some ideas on a potential framework for the evolutionary genomics of kinetoplastids are presented.     

Do light intensity,temperature and photoperiod affect the entrapment of mites on glandular hairs of cultivated tomatoes?

The effects of plant growth conditions (light intensity, temperature and photoperiod) on the proportion of spider mites (Tetranychus urticae) and predatory mites (Phytoseiulus persimilis) entrapped by type VI trichomes were investigated in the cultivated tomato Lycopersicon esculentum. Trichomes released sticky substances showing rapid hardening when the trichome head was ruptured by contact with mites. Adult individuals of both species of mites were immobilized by exudates in a higher percentage on leaf stalks from plants grown in the light (160 einsteins cm^-2s^-1) than on leaf stalks from plants grown in the shade (50 einsteins cm^-2 s^-1). Leaf stalks from plants grown in the light showed bigger trichome heads. More predatory mites were also entrapped on the leaf stalks from plants grown at 18°C (65% RH) as compared to the ones grown at 24°C (60% RH), whereas trichome heads were bigger under the former conditions. Contrary to leaf stalks, leaflet areas, through differences in trichome density and size, showed no diffences in predator and spider mite entrapment. Trichome head size was probably related to mite entrapment. It is also hypothesised that temperature increase might influence predator entrapment through effects on trichome quality.     

Critical-like self-organization and natural selection: Two facets of a single evolutionary process?

We argue that critical-like dynamics self-organize relatively easily in non-equilibrium systems, and that in biological systems such dynamics serve as templates upon which natural selection builds further elaborations. These critical-like states can be modified by natural selection in two fundamental ways, reflecting the selective advantage (if any) of heritable variations either among avalanche participants or among whole systems. First, reproducing (avalanching) units can differentiate, as units adopt systematic behavioural variations. Second, whole systems that are exposed to natural selection can become increasingly or decreasingly critical. We suggest that these interactions between SOC-like dynamics and natural selection have profound consequences for biological systems because they could have facilitated the evolution of division of labour, compartmentalization and computation, key features of biological systems. The logical conclusion of these ideas is that the fractal geometry of nature is anything but coincidental, and that natural selection is itself a fractal process, occurring on many temporal and spatial scales.     

What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

Some notable exceptions aside, eukaryotic genomes are distinguished from those of Bacteria and Archaea in a number of ways, including chromosome structure and number, repetitive DNA content, and the presence of introns in protein-coding regions. One of the most notable differences between eukaryotic and prokaryotic genomes is in size. Unlike their prokaryotic counterparts, eukaryotes exhibit enormous (more than 60 000-fold) variability in genome size which is not explained by differences in gene number. Genome size is known to correlate with cell size and division rate, and by extension with numerous organism-level traits such as metabolism, developmental rate or body size. Less well described are the relationships between genome size and other properties of the genome, such as gene content, transposable element content, base pair composition and related features. The rapid expansion of ‘complete’ genome sequencing projects has, for the first time, made it possible to examine these relationships across a wide range of eukaryotes in order to shed new light on the causes and correlates of genome size diversity. This study presents the results of phylogenetically informed comparisons of genome data for more than 500 species of eukaryotes. Several relationships are described between genome size and other genomic parameters, and some recommendations are presented for how these insights can be extended even more broadly in the future.     

Do eosinophils have a role in the killing of helminth parasites?

Eosinophils have been shown to be potent effector cells for the killing of helminth parasites in in vitro cultures. However, an in vivo role for eosinophils has been more difficult to establish. Early data showed close associations between eosinophils and damaged or dead parasites in histological sections, and significant correlations between resistance to parasites and the capacity to induce eosinophilia after infection. However, more recent studies, using mice that have reduced or increased eosinophil levels through targeting of the eosinophil-specific cytokine interleukin 5, have not unanimously supported an in vivo role for eosinophils in resistance to parasites. Here, Els Meeusen and Adam Balic review these studies and suggest a major role for the innate immune response in unnatural mouse-parasite models to explain some of the findings. They conclude that the data so far are consistent with a role for eosinophils in the killing of infective larval stages, but not adults, of most helminth parasites.     

What's in the genome of a filamentous fungus? Analysis of the Neurospora genome sequence

The German Neurospora Genome Project has assembled sequences from ordered cosmid and BAC clones of linkage groups II and V of the genome of Neurospora crassa in 13 and 12 contigs, respectively. Including additional sequences located on other linkage groups a total of 12 Mb were subjected to a manual gene extraction and annotation process. The genome comprises a small number of repetitive elements, a low degree of segmental duplications and very few paralogous genes. The analysis of the 3218 identified open reading frames provides a first overview of the protein equipment of a filamentous fungus. Significantly, N.crassa possesses a large variety of metabolic enzymes including a substantial number of enzymes involved in the degradation of complex substrates as well as secondary metabolism. While several of these enzymes are specific for filamentous fungi many are shared exclusively with prokaryotes.     

Classification and evolutionary history of the single-strand annealing proteins,RecT, Redβ, ERF and RAD52

Background  

The DNA single-strand annealing proteins (SSAPs), such as RecT, Redβ, ERF and Rad52, function in RecA-dependent and RecA-independent DNA recombination pathways. Recently, they have been shown to form similar helical quaternary superstructures. However, despite the functional similarities between these diverse SSAPs, their actual evolutionary affinities are poorly understood.     

Do different disparity proxies converge on a common signal? Insights from the cranial morphometrics and evolutionary history of Pterosauria (Diapsida: Archosauria)

Disparity, or morphological diversity, is often quantified by evolutionary biologists investigating the macroevolutionary history of clades over geological timescales. Disparity is typically quantified using proxies for morphology, such as measurements, discrete anatomical characters, or geometric morphometrics. If different proxies produce differing results, then the accurate quantification of disparity in deep time may be problematic. However, despite this, few studies have attempted to examine disparity of a single clade using multiple morphological proxies. Here, as a case study for this question, we examine the disparity of the volant Mesozoic fossil reptile clade Pterosauria, an intensively studied group that achieved substantial morphological, ecological and taxonomic diversity during their 145+ million-year evolutionary history. We characterize broadscale patterns of cranial morphological disparity for pterosaurs for the first time using landmark-based geometric morphometrics and make comparisons to calculations of pterosaur disparity based on alternative metrics. Landmark-based disparity calculations suggest that monofenestratan pterosaurs were more diverse cranially than basal non-monofenestratan pterosaurs (at least when the aberrant anurognathids are excluded), and that peak cranial disparity may have occurred in the Early Cretaceous, relatively late in pterosaur evolution. Significantly, our cranial disparity results are broadly congruent with those based on whole skeleton discrete character and limb proportion data sets, indicating that these divergent approaches document a consistent pattern of pterosaur morphological evolution. Therefore, pterosaurs provide an exemplar case demonstrating that different proxies for morphological form can converge on the same disparity signal, which is encouraging because often only one such proxy is available for extinct clades represented by fossils. Furthermore, mapping phylogeny into cranial morphospace demonstrates that pterosaur cranial morphology is significantly correlated with, and potentially constrained by, phylogenetic relationships.     

Does the evolutionary history of aminoacyl-tRNA synthetases explain the loss of mitochondrial tRNA genes?

The importation of cytosolic tRNAs is required for protein synthesis in the mitochondria of the wide variety of eukaryotes that lack a complete set of mitochondrial tRNA genes. The evolutionary history of the process, however, is still enigmatic. The analysis presented here suggests that the loss of distinct mitochondrial tRNA genes was not random and that it might be explained by the differential capabilities of mitochondrial aminoacyl-tRNA synthetases to charge imported eukaryotic-type tRNAs with amino acid.     

Insights into the metabolism,lifestyle and putative evolutionary history of the novel archaeal phylum ‘Diapherotrites'

The archaeal phylum ‘Diapherotrites'' was recently proposed based on phylogenomic analysis of genomes recovered from an underground water seep in an abandoned gold mine (Homestake mine in Lead, SD, USA). Here we present a detailed analysis of the metabolic capabilities and genomic features of three single amplified genomes (SAGs) belonging to the ‘Diapherotrites''. The most complete of the SAGs, Candidatus ‘Iainarchaeum andersonii'' (Cand. IA), had a small genome (∼1.24 Mb), short average gene length (822 bp), one ribosomal RNA operon, high coding density (∼90.4%), high percentage of overlapping genes (27.6%) and low incidence of gene duplication (2.16%). Cand. IA genome possesses limited catabolic capacities that, nevertheless, could theoretically support a free-living lifestyle by channeling a narrow range of substrates such as ribose, polyhydroxybutyrate and several amino acids to acetyl-coenzyme A. On the other hand, Cand. IA possesses relatively well-developed anabolic capabilities, although it remains auxotrophic for several amino acids and cofactors. Phylogenetic analysis suggests that the majority of Cand. IA anabolic genes were acquired from bacterial donors via horizontal gene transfer. We thus propose that members of the ‘Diapherotrites'' have evolved from an obligate symbiotic ancestor by acquiring anabolic genes from bacteria that enabled independent biosynthesis of biological molecules previously acquired from symbiotic hosts. ‘Diapherotrites'' 16S rRNA genes exhibit multiple mismatches with the majority of archaeal 16S rRNA primers, a fact that could be responsible for their observed rarity in amplicon-generated data sets. The limited substrate range, complex growth requirements and slow growth rate predicted could be responsible for its refraction to isolation.     

With the finished human genome in hand,what next?

A report on the eighth annual meeting of the Human Genome Organization (HGM2003), Cancun, Mexico, 27-30 April 2003.