Exploring the environmental diversity of kinetoplastid flagellates in the high-throughput DNA sequencing era

The class Kinetoplastea encompasses both free-living and parasitic species from awide range of hosts. Several representatives of this group are responsible for severehuman diseases and for economic losses in agriculture and livestock. While this groupencompasses over 30 genera, most of the available information has been derived fromthe vertebrate pathogenic genera LeishmaniaandTrypanosoma. Recent studies of the previously neglected groups ofKinetoplastea indicated that the actual diversity is much higher than previouslythought. This article discusses the known segment of kinetoplastid diversity and howgene-directed Sanger sequencing and next-generation sequencing methods can help todeepen our knowledge of these interesting protists.     

The evolution of kinetoplastid glycosomes

The available data on carbohydrate metabolism in Kinetoplastida have been reviewed. Based on the metabolic pattern of different kinetoplastid organisms, on the subcellular distribution of their glycolytic enzymes, and on the structural and regulatory properties of these proteins, we propose that the glycosome developed from an endosymbiont, as a specific manner to control carbohydrate and energy metabolism. It is discussed how the enzymes were subcellularly recompartmentalized during evolution as adaptation to the environment encountered by the organisms.     

Elucidating the evolution and diversity of Uroglena-like colonial flagellates (Chrysophyceae): polyphyletic origin of the morphotype

ABSTRACT

The Uroglena-like morphotype represents a prototype of a colonial naked chrysophyte, comprising plastid-bearing cells that are arranged as the surface monolayer of the spherical colony. So far, insufficient molecular characterization appears to be the most significant brake on the modern taxonomic revision of this ecologically and morphologically coherent group of organisms. The general aim of this work was to conduct a modern taxonomic revision of Uroglena-like flagellates by using combined molecular, morphological and ultrastructural methodology, complemented by exploring type localities of Uroglena volvox and Uroglenopsis americana in Europe and North America, respectively. On the basis of phylogenetic analysis of concatenated nuclear SSU rDNA and plastid rbcL sequences we show that Uroglena-like colonial flagellates form three genetically and morphologically distinct lineages within the Ochromonadales (Chrysophyceae), distinguished here as Uroglena, Uroglenopsis and Urostipulosphaera gen. nov. The taxonomic status of the other chrysophyte genera with spherical colonies is discussed in light of our findings.     

On the evolution of hexose transporters in kinetoplastid potozoans

Glucose, an almost universally used energy and carbon source, is processed through several well-known metabolic pathways, primarily glycolysis. Glucose uptake is considered to be the first step in glycolysis. In kinetoplastids, a protozoan group that includes relevant human pathogens, the importance of glucose uptake in different phases of the life cycles is well established, and hexose transporters have been proposed as targets for therapeutic drugs. However, little is known about the evolutionary history of these hexose transporters. Hexose transporters contain an intracellular N- and C- termini, and 12 transmembrane spans connected by alternate intracellular and extracellular loops. In the present work we tested the hypothesis that the evolutionary rate of the transmembrane span is different from that of the whole sequence and that it is possible to define evolutionary units inside the sequence. The phylogeny of whole molecules was compared to that of their transmembrane spans and the loops connecting the transmembrane spans. We show that the evolutionary units in these proteins primarily consist of clustered rather than individual transmembrane spans. These analyses demonstrate that there are evolutionary constraints on the organization of these proteins; more specifically, the order of the transmembrane spans along the protein is highly conserved. Finally, we defined a signature sequence for the identification of kinetoplastid hexose transporters.     

The chaperonin genes of jakobid and jakobid-like flagellates: implications for eukaryotic evolution

The jakobids are free-living mitochondriate protists that share ultrastructural features with certain amitochondriate groups and possess the most bacterial-like mitochondrial genomes described thus far. Jakobids belong to a diverse group of mitochondriate and amitochondriate eukaryotes, the excavate taxa. The relationships among the various excavate taxa and their relationships to other putative deep-branching protist groups are largely unknown. With the hope of clarifying these issues, we have isolated the cytosolic chaperonin CCTalpha gene from the jakobid Reclinomonas americana (strains 50394 and 50283), the jakobid-like malawimonad Malawimonas jakobiformis, two heteroloboseans (Acrasis rosea and Naegleria gruberi), a euglenozoan (Trypanosoma brucei), and a parabasalid (Monocercomonas sp.). We also amplified the CCTdelta gene from M. jakobiformis. The Reclinomonas and Malawimonas sequences presented here are among the first nuclear protein-coding genes to be described from these organisms. Unlike other putative early diverging protist lineages, a high density of spliceosomal introns was found in the jakobid and malawimonad CCTs-similar to that observed in vertebrate protein-coding genes. An analysis of intron positions in CCT genes from protists, plants, animals, and fungi suggests that many of the intron-sparse or intron-lacking protist lineages may not be primitively so but have lost spliceosomal introns during their evolutionary history. In phylogenetic trees constructed from CCTalpha protein sequences, R. americana (but not M. jakobiformis) shows a weak but consistent affinity for the Heterolobosea and Euglenozoa.     

The evolution of pheromone diversity

Pheromones are chemical signals whose composition varies enormously between species. Despite pheromones being a nearly ubiquitous form of communication, particularly among insects, our understanding of how this diversity has arisen, and the processes driving the evolution of pheromones, is less developed than that for visual and auditory signals. Studies of phylogeny, genetics and ecological processes are providing new insights into the patterns, mechanisms and drivers of pheromone evolution, and there is a wealth of information now available for analysis. Future research could profitably use these data by employing phylogenetic comparative techniques to identify ecological correlates of pheromone composition. Genetic analyses are also needed to gain a clearer picture of how changes in receivers are associated with changes in the signal.     

Species diversity of heterotrophic flagellates in White Sea littoral sites

The species diversity and distribution of benthic heterotrophic flagellates in sediment samples from along the salinity gradient in the Chernaya River Estuary and from Velikaya Salma Strait (Kandalaksha Bay, the White Sea) were investigated during August 2004. One hundred and six taxa have been identified by means of phase and interference contrast light microscopy and transmission electron microscopy. The majority of observed flagellates were bacterivores. The species diversity of the following groups: choanoflagellates, euglenids, kinetoplastids, bicosoecids, chrysomonads, thaumatomonads and flagellates Incertae sedis was the highest. Ancyromonas sigmoides and Petalomonas pusilla were the most common species. The species richness was lowest in the brackish water estuarine part with salinity levels between 5 per thousand and 8 per thousand. The distribution of heterotrophic flagellates conforms to the so-called "rule of critical salinity", possessing, apparently, the same universal character for organisms of different size levels. Heterotrophic flagellate communities in these littoral sites were highly heterogeneous. The curve of "cumulative species number vs. sampling effort" is well fitted by equation S=21.17N(0.50) and unsaturated, which indicates that more intensive investigations of the heterotrophic flagellates in the White Sea should be expected to reveal more species.     

Evolution of the haem synthetic pathway in kinetoplastid flagellates: An essential pathway that is not essential after all?

For a vast majority of living organisms, haem is an essential compound that is synthesised through a conserved biosynthetic pathway. However, certain organisms are haem auxotrophs and need to obtain this molecule from exogenous sources. Kinetoplastid flagellates represent an interesting group of species, as some of them lost the complete pathway while others possess only the last three biosynthetic steps. We decided to supplement a current view on the phylogeny of these important pathogens with the expected state of haem synthesis in representative species. We propose a scenario in which the ancestor of all trypanosomatids was completely deficient of the synthesis of haem. In trypanosomatids other than members of the genus Trypanosoma, the pathway was partially rescued by genes encoding enzymes for the last three steps, supposedly obtained by horizontal transfer from a γ-proteobacterium. This event preceded the diversification of the non-Trypanosoma trypanosomatids. Later, some flagellates acquired a β-proteobacterial endosymbiont which supplied them with haem precursors. On the other hand, the medically important trypanosomes have remained fully deficient of haem synthesis and obtain this compound from the host.     

The evolution of plant sexual diversity

Charles Darwin recognized that flowering plants have an unrivalled diversity of sexual systems. Determining the ecological and genetic factors that govern sexual diversification in plants is today a central problem in evolutionary biology. The integration of phylogenetic, ecological and population-genetic studies have provided new insights into the selective mechanisms that are responsible for major evolutionary transitions between reproductive modes.     

The evolution of genetic diversity.

The existence within natural populations of large amounts of genetic variation in molecules and morphology presents an evolutionary problem. The 'neutralist' solution to this problem, that the variation is usually unimportant to the organism displaying it, has now lost much of its strength. Interpretations that assume widespread heterozygous advantage also face serious difficulties. A resolution is possible in terms of frequency-dependent selection by predators, parasites and competitors. The evidence for pervasive frequency-dependent selection is now very strong. It appears to follow naturally from the behaviour of predators, from the evolutionary lability of parasites, from the ecology of competition and, at the molecular level, from the phenomena of enzyme kinetics. Such selection can explain the maintenance not only of conventional polymorphism but also of continuous variation in both molecular and morphological characters. It can account for the occurrence of diversity within groups of haploid and self-fertilizing organisms, and for the evolution of differences between individuals in their systems of genetic control.     

Ribosomal RNA phylogeny of bodonid and diplonemid flagellates and the evolution of euglenozoa

Euglenozoa is a major phylum of excavate protozoa (comprising euglenoids, kinetoplastids, and diplonemids) with highly unusual nuclear, mitochondrial, and chloroplast genomes. To improve understanding of euglenozoan evolution, we sequenced nuclear small-subunit rRNA genes from 34 bodonids (Bodo, Neobodo, Parabodo, Dimastigella-like, Rhynchobodo, Rhynchomonas, and unidentified strains), nine diplonemids (Diplonema, Rhynchopus), and a euglenoid (Entosiphon). Phylogenetic analysis reveals that diplonemids and bodonids are more diverse than previously recognised, but does not clearly establish the branching order of kinetoplastids, euglenoids, and diplonemids. Rhynchopus is holophyletic; parasitic species arose from within free-living species. Kinetoplastea (bodonids and trypanosomatids) are robustly holophyletic and comprise a major clade including all trypanosomatids and most bodonids ('core bodonids') and a very divergent minor one including Ichthyobodo. The root of the major kinetoplastid clade is probably between trypanosomatids and core bodonids. Core bodonids have three distinct subclades. Clade 1 has two distinct Rhynchobodo-like lineages; a lineage comprising Dimastigella and Rhynchomonas; and another including Cruzella and Neobodo. Clade 2 comprises Cryptobia/ Trypanoplasma, Procryptobia, and Parabodo. Clade 3 is an extensive Bodo saltans species complex. Neobodo designis is a vast genetically divergent species complex with mutually exclusive marine and freshwater subclades. Our analysis supports three phagotrophic euglenoid orders: Petalomonadida (holophyletic), Ploeotiida (probably holophyletic), Peranemida (paraphyletic).     

The evolution of the diversity of cultures

The abundant evidence that Homo sapiens evolved in Africa within the past 200,000 years, and dispersed across the world only within the past 100,000 years, provides us with a strong framework in which to consider the evolution of human diversity. While there is evidence that the human capacity for culture has a deeper history, going beyond the origin of the hominin clade, the tendency for humans to form cultures as part of being distinct communities and populations changed markedly with the evolution of H. sapiens. In this paper, we investigate 'cultures' as opposed to 'culture', and the question of how and why, compared to biological diversity, human communities and populations are so culturally diverse. We consider the way in which the diversity of human cultures has developed since 100,000 years ago, and how its rate was subject to environmental factors. We argue that the causes of this diversity lie in the distribution of resources and the way in which human communities reproduce over several generations, leading to fissioning of kin groups. We discuss the consequences of boundary formation through culture in their broader ecological and evolutionary contexts.     

Peroxisome diversity and evolution

Peroxisomes are organelles bounded by a single membrane that can be found in all major groups of eukaryotes. A single evolutionary origin of this cellular compartment is supported by the presence, in diverse organisms, of a common set of proteins implicated in peroxisome biogenesis and maintenance. Their enzymatic content, however, can vary substantially across species, indicating a high level of evolutionary plasticity. Proteomic analyses have greatly expanded our knowledge on peroxisomes in some model organisms, including plants, mammals and yeasts. However, we still have a limited knowledge about the distribution and functionalities of peroxisomes in the vast majority of groups of microbial eukaryotes. Here, I review recent advances in our understanding of peroxisome diversity and evolution, with a special emphasis on peroxisomes in microbial eukaryotes.     

The role of ontogeny in wood diversity and evolution

Evolutionary developmental biology (evo-devo) explores the link between developmental patterning and phenotypic change through evolutionary time. In this review, we highlight the scientific advancements in understanding xylem evolution afforded by the evo-devo approach, opportunities for further engagement, and future research directions for the field. We review evidence that (1) heterochrony—the change in rate and timing of developmental events, (2) homeosis—the ontogenetic replacement of features, (3) heterometry—the change in quantity of a feature, (4) exaptation—the co-opting and repurposing of an ancestral feature, (5) the interplay between developmental and capacity constraints, and (6) novelty—the emergence of a novel feature, have all contributed to generating the diversity of woods. We present opportunities for future research engagement, which combine wood ontogeny within the context of robust phylogenetic hypotheses, and molecular biology.     

The evolution of foliar terpene diversity in Myrtaceae

Plant terpenes play many roles in natural systems, from altering plant–animal interactions, to altering the local abiotic environment. Additionally, many industries depend on terpenes. For example, commercially used essential oils, including tea tree oil and lavender oil, are a mixture of terpenes. Many species of the family Myrtaceae form a key resource for these industries due to the high concentration of terpenes found predominately in their leaves. The frequency of chemotypic differences within many species and populations can lead to costly errors in industry. Terpene diversity in Myrtaceae is driven by variation in the terpene synthase enzymes, which catalyse the conversion a few common substrates into thousands of terpene structures. We review terpene diversity within and between species of Myrtaceae and relate this to variation in the terpene synthase enzymes to reconstruct the evolution of foliar terpene diversity in Myrtaceae. We found that (1) high inter- and intra-species variation exists in terpene profile and that α-pinene the most likely ancestral foliar terpene, and (2) that high concentration of 1,8-cineole (a compound which is regarded as the signature compound of Myrtaceae) is limited to just four Myrtaceae sub-families. We suggest that the terpene synthase enzymes do not limit terpene diversity in this family and variation in these enzymes suggests a mode of enzymatic evolution that could lead to high 1,8-cineole production. Our analysis highlights the need to standardise methods for collecting and reporting foliar terpene data, and we discuss some methods and issues here. Although there are many gaps in the published data, our large scale analysis using the results of many studies, shows the value of a family wide analysis for understanding both the evolution and industrial potential of terpene-producing plants.     

The global impact of Wolbachia on mitochondrial diversity and evolution

The spread of maternally inherited microorganisms, such as Wolbachia bacteria, can induce indirect selective sweeps on host mitochondria, to which they are linked within the cytoplasm. The resulting reduction in effective population size might lead to smaller mitochondrial diversity and reduced efficiency of natural selection. While documented in several host species, it is currently unclear if such a scenario is common enough to globally impact the diversity and evolution of mitochondria in Wolbachia‐infected lineages. Here, we address this question using a mapping of Wolbachia acquisition/extinction events on a large mitochondrial DNA tree, including over 1000 species. Our analyses indicate that on a large phylogenetic scale, other sources of variation, such as mutation rates, tend to hide the effects of Wolbachia. However, paired comparisons between closely related infected and uninfected taxa reveal that Wolbachia is associated with a twofold reduction in silent mitochondrial polymorphism, and a 13% increase in nonsynonymous substitution rates. These findings validate the conjecture that the widespread distribution of Wolbachia infections throughout arthropods impacts the effective population size of mitochondria. These effects might in part explain the disconnection between genetic diversity and demographic population size in mitochondria, and also fuel red‐queen‐like cytonuclear co‐evolution through the fixation of deleterious mitochondrial alleles.