Comparative analysis of complete genomes reveals gene loss, acquisition and acceleration of evolutionary rates in Metazoa, suggests a prevalence of evolution via gene acquisition and indicates that the evolutionary rates in animals tend to be conserved

In this study we systematically examined the differences between the proteomes of Metazoa and other eukaryotes. Metazoans (Homo sapiens, Ceanorhabditis elegans and Drosophila melanogaster) were compared with a plant (Arabidopsis thaliana), fungi (Saccharomyces cerevisiae and Schizosaccaromyces pombe) and Encephalitozoan cuniculi. We identified 159 gene families that were probably lost in the Metazoan branch and 1263 orthologous families that were specific to Metazoa and were likely to have originated in their last common ancestor (LCA). We analyzed the evolutionary rates of pan-eukaryotic protein families and identified those with higher rates in animals. The acceleration was shown to occur in: (i) the LCA of Metazoa or (ii) independently in the Metazoan phyla. A high proportion of the accelerated Metazoan protein families was found to participate in translation and ribosome biogenesis, particularly mitochondrial. By functional analysis we show that no metabolic pathway in animals evolved faster than in other organisms. We conclude that evolution in the LCA of Metazoa was extensive and proceeded largely by gene duplication and/or invention rather than by modification of extant proteins. Finally, we show that the rate of evolution of a gene family in animals has a clear, but not absolute, tendency to be conserved.     

Evolutionary origins of germline segregation in Metazoa: evidence for a germ stem cell lineage in the coral Orbicella faveolata (Cnidaria,Anthozoa)

The ability to segregate a committed germ stem cell (GSC) lineage distinct from somatic cell lineages is a characteristic of bilaterian Metazoans. However, the occurrence of GSC lineage specification in basally branching Metazoan phyla, such as Cnidaria, is uncertain. Without an independently segregated GSC lineage, germ cells and their precursors must be specified throughout adulthood from continuously dividing somatic stem cells, generating the risk of propagating somatic mutations within the individual and its gametes. To address the potential for existence of a GSC lineage in Anthozoa, the sister-group to all remaining Cnidaria, we identified moderate- to high-frequency somatic mutations and their potential for gametic transfer in the long-lived coral Orbicella faveolata (Anthozoa, Cnidaria) using a 2b-RAD sequencing approach. Our results demonstrate that somatic mutations can drift to high frequencies (up to 50%) and can also generate substantial intracolonial genetic diversity. However, these somatic mutations are not transferable to gametes, signifying the potential for an independently segregated GSC lineage in O. faveolata. In conjunction with previous research on germ cell development in other basally branching Metazoan species, our results suggest that the GSC system may be a Eumetazoan characteristic that evolved in association with the emergence of greater complexity in animal body plan organization and greater specificity of stem cell functions.     

Adaptive radiation in extremophilic Dorvilleidae (Annelida): diversification of a single colonizer or multiple independent lineages?

Metazoan inhabitants of extreme environments typically evolved from forms found in less extreme habitats. Understanding the prevalence with which animals move into and ultimately thrive in extreme environments is critical to elucidating how complex life adapts to extreme conditions. Methane seep sediments along the Oregon and California margins have low oxygen and very high hydrogen sulfide levels, rendering them inhospitable to many life forms. Nonetheless, several closely related lineages of dorvilleid annelids, including members of Ophryotrocha, Parougia, and Exallopus, thrive at these sites in association with bacterial mats and vesicomyid clam beds. These organisms are ideal for examining adaptive radiations in extreme environments. Did dorvilleid annelids invade these extreme environments once and then diversify? Alternatively, did multiple independent lineages adapt to seep conditions? To address these questions, we examined the evolutionary history of methane-seep dorvilleids using 16S and Cyt b genes in an ecological context. Our results indicate that dorvilleids invaded these extreme habitats at least four times, implying preadaptation to life at seeps. Additionally, we recovered considerably more dorvilleid diversity than is currently recognized. A total of 3 major clades (designated “Ophryotrocha,” “Mixed Genera” and “Parougia”) and 12 terminal lineages or species were encountered. Two of these lineages represented a known species, Parougia oregonensis, whereas the remaining 10 lineages were newly discovered species. Certain lineages exhibited affinity to geography, habitat, sediment depth, and/or diet, suggesting that dorvilleids at methane seeps radiated via specialization and resource partitioning.     

Rod1, an arrestin-related protein, is phosphorylated by Snf1-kinase in Saccharomyces cerevisiae

Metazoan arrestin proteins bind to seven-transmembrane proteins, mediate their internalization and play central roles in the subsequent signal transduction pathway. In Saccharomyces cerevisiae, there are several arrestin-related proteins. One of those proteins, Rod1, has been identified to have the ability to confer resistance to o-dinitrobenzene. We found that Rod1 interacted with Snf4, a subunit of Snf1-kinase complex. Both snf4 and snf1 mutants were also sensitive to the drug and the kinase activity of Snf1 was required for the drug tolerance. In immunoblotting analysis, the Rod1 protein was phosphorylated in an Snf1-dependent manner in vivo, and the phosphorylation of the serine residue 447 of Rod1 was responsible for the band-shift. Furthermore, the Rod1 protein was directly phosphorylated by Snf1-kinase in vitro. The substitution of the serine residue 447 to alanine slightly enhanced the resistance to the drug. We discuss possible functions of Rod1.     

A Novel Predicted Calcium-Regulated Kinase Family Implicated in Neurological Disorders

The catalogues of protein kinases, the essential effectors of cellular signaling, have been charted in Metazoan genomes for a decade now. Yet, surprisingly, using bioinformatics tools, we predicted protein kinase structure for proteins coded by five related human genes and their Metazoan homologues, the FAM69 family. Analysis of three-dimensional structure models and conservation of the classic catalytic motifs of protein kinases present in four out of five human FAM69 proteins suggests they might have retained catalytic phosphotransferase activity. An EF-hand Ca²⁺-binding domain in FAM69A and FAM69B proteins, inserted within the structure of the kinase domain, suggests they may function as Ca²⁺-dependent kinases. The FAM69 genes, FAM69A, FAM69B, FAM69C, C3ORF58 (DIA1) and CXORF36 (DIA1R), are by large uncharacterised molecularly, yet linked to several neurological disorders in genetics studies. The C3ORF58 gene is found deleted in autism, and resides in the Golgi. Unusually high cysteine content and presence of signal peptides in some of the family members suggest that FAM69 proteins may be involved in phosphorylation of proteins in the secretory pathway and/or of extracellular proteins.     

Introduction to ‘Origin and evolution of the nervous system’

In 1665, Robert Hooke demonstrated in Micrographia the power of the microscope and comparative observations, one of which revealed similarities between the arthropod and vertebrate eyes. Utilizing comparative observations, Saint-Hilaire in 1822 was the first to propose that the ventral nervous system of arthropods corresponds to the dorsal nervous system of vertebrates. Since then, studies on the origin and evolution of the nervous system have become inseparable from studies about Metazoan origins and the origins of organ systems. The advent of genome sequence data and, in turn, phylogenomics and phylogenetics have refined cladistics and expanded our understanding of Metazoan phylogeny. However, the origin and evolution of the nervous system is still obscure and many questions and problems remain. A recurrent problem is whether and to what extent sequence data provide reliable guidance for comparisons across phyla. Are genetic data congruent with the geological fossil records? How can we reconcile evolved character loss with phylogenomic records? And how informative are genetic data in relation to the specification of nervous system morphologies? These provide some of the background and context for a Royal Society meeting to discuss new data and concepts that might achieve insights into the origin and evolution of brains and nervous systems.     

Threats and opportunities of plant pathogenic bacteria

Plant pathogenic bacteria can have devastating effects on plant productivity and yield. Nevertheless, because these often soil-dwelling bacteria have evolved to interact with eukaryotes, they generally exhibit a strong adaptivity, a versatile metabolism, and ingenious mechanisms tailored to modify the development of their hosts. Consequently, besides being a threat for agricultural practices, phytopathogens may also represent opportunities for plant production or be useful for specific biotechnological applications. Here, we illustrate this idea by reviewing the pathogenic strategies and the (potential) uses of five very different (hemi)biotrophic plant pathogenic bacteria: Agrobacterium tumefaciens, A. rhizogenes, Rhodococcus fascians, scab-inducing Streptomyces spp., and Pseudomonas syringae.     

Metabolomic Analysis of Cooperative Adaptation between Co-Cultured Bacillus cereus and Ketogulonicigenium vulgare

The cooperative adaptation of subcultivated Bacillus cereus and Ketogulonicigenium vulgare significantly increased the productivity of 2-keto-L-gulonic acid, the precursor of vitamin C. The mechanism of cooperative adaptation of the serial subcultivated B. cereus and K. vulgare was investigated in this study by culturing the two strains orthogonally on agar plates. It was found that the swarming distance of B. cereus along the trace of K. vulgare on the plate decreased after 150 days'' subcultivation. Metabolomic analysis on these co-cultured B. cereus and K. vulgare strains showed that their cooperative adaptation was accomplished by three key events: (i) the ability of nutrients (e.g., amino acids and purines) searching and intaking, and proteins biosynthesis is increased in the evolved B. cereus; (ii) the capability of protein degradation and amino acids transportation is enhanced in evolved K. vulgare; (iii) the evolved B. cereus was found to provide more nutrients (mostly amino acids and purines) to K. vulgare, thus strengthening the oxidation and energy generation of K. vulgare. Our results provided novel insights into the systems-level understanding of the cooperative adaptation between strains in synergistic consortium.     

Systematic revision of Siwalik Rhizomyidae (Rodentia)

Larges samples of fossil rhizomyids from the Siwalikmolasse deposits of the Potwar Plateau, Pakistan, enable reevaluation of fossil taxa and their evolutionary relationships. Siwalik Rhizomyidae constitute a basis for analysis of poorly represented rhizomyids from other areas in Asia and contribute to biochronological correlation. The extant Tachyoryctinae and Rhizomyinae diverged during the early history of the family and diagnoses of the subfamilies are amended to include extinct genera. Siwalik tachyoryctines include Kanisamys, Protachyoryctes, Rhizomyides, and Eicooryctes nov. gen.; rhizomyines are Brachyrhizomys and Anepsirhizomys nov. gen. Kanisamys, the earliest Siwalik rhizomyid, appeared by about 13 Ma and evolved slowly, displaying stasis in K. sivalensis. Brachyrhizomys evolved from Kanisamys by 9.5 Ma and radiated rapidly. B. nagrii displays rapid increase in size through time. About 7 Ma, Kanisamys and Brachyrhizomys became extinct locally and Protachyoryctes, Eicooryctes, and Rhizomyides appeared, perhaps in response to increasing aridity. After 5.5 Ma, rhizomyids became uncommon in the Potwar and Anepsirhizomys (3.0 Ma) constitutes the latest record of Rhizomyidae in Pakistan.     

Some Possible Cases of Escape Mimicry in Neotropical Butterflies

The possibility that escape or evasive mimicry evolved in butterflies and other prey insects in a similar fashion to classical Batesian and Müllerian mimicry has long been advanced in the literature. However, there is a general disagreement among lepidopterists and evolutionary biologists on whether or not escape mimicry exists, as well as in which mimicry rings this form of mimicry has evolved. Here, we review some purported cases of escape mimicry in Neotropical butterflies and suggest new mimicry rings involving several species of Archaeoprepona, Prepona, and Doxocopa (the “bright blue bands” ring) and species of Colobura and Hypna (the “creamy bands” ring) where the palatability of butterflies, their ability to escape predator attacks, geographic distribution, relative abundance, and co-occurrence in the same habitats strongly suggest that escape mimicry is involved. In addition, we also indicate other butterfly taxa whose similarities of coloration patterns could be due to escape mimicry and would constitute important case studies for future investigation.     

Pollination,biogeography and phylogeny of oceanic island bellflowers (Campanulaceae)

We studied the pollination biology of nine island Campanulaceae species: Azorina vidalii, Musschia aurea, M. wollastonii, Canarina canariensis, Campanula jacobaea, Nesocodon mauritianus, and three species of Heterochaenia. In addition, we compared C. canariensis to its two African mainland relatives C. eminii and C. abyssinica. We asked to what extent related species converge in their floral biology and pollination in related habitats, i.e. oceanic islands. Study islands were the Azores, Madeira, Canary Islands, Cape Verde, Mauritius, and Réunion. Information about phylogenetic relationships of these species and their relatives were gathered from atpB, matK, rbcL and trnL-F regions, building the most complete phylogeny of Campanulaceae to date. Six of the island bellflower species were bird-pollinated and two (A. vidalii and M. aurea) were lizard-pollinated. Insects also visited some of the species, and at least C. jacobaea had both insect- and self-pollination. Several morphological traits were interpreted as adaptations to bird and lizard pollination, e.g. all had a robust flower morphology and, in addition, bird-pollinated species were scentless, whereas lizard-pollinated species had a weak scent. These examples of vertebrate pollination evolved independently on each island or archipelago. We discuss if these pollination systems have an island or mainland origin and when they may have evolved, and finally, we attempt to reconstruct the pollinator-interaction history of each species.     

Photodynamic antimicrobial activity of avian eggshell pigments

Pigmentation in avian eggshells appears to be associated with shell strength, temperature regulation, and camouflage. The pigments found in eggshells are mainly porphyrins, which have been utilized therapeutically as photosensitizers. Here, we examined the photoinactivation of gram-positive (Staphylococcus aureus, Bacillus cereus) and gram-negative bacteria (Escherichia coli, Salmonella enteritidis) by hen eggshells and their pigments. The results indicated that eggshells have a light-dependent antimicrobial activity against gram-positive, but not gram-negative, bacteria. Our results indicate the possibility that the natural pigments used therapeutically have evolved in nature as a defence system.     

Molecular signatures of cell migration in C. elegans Q neuroblasts

Metazoan cell movement has been studied extensively in vitro, but cell migration in living animals is much less well understood. In this report, we have studied the Caenorhabditis elegans Q neuroblast lineage during larval development, developing live animal imaging methods for following neuroblast migration with single cell resolution. We find that each of the Q descendants migrates at different speeds and for distinct distances. By quantitative green fluorescent protein imaging, we find that Q descendants that migrate faster and longer than their sisters up-regulate protein levels of MIG-2, a Rho family guanosine triphosphatase, and/or down-regulate INA-1, an integrin α subunit, during migration. We also show that Q neuroblasts bearing mutations in either MIG-2 or INA-1 migrate at reduced speeds. The migration defect of the mig-2 mutants, but not ina-1, appears to result from a lack of persistent polarization in the direction of cell migration. Thus, MIG-2 and INA-1 function distinctly to control Q neuroblast migration in living C. elegans.     

Did Drosera evolve long scapes to stop their pollinators from being eaten?

Background and Aims

Insectivorous plants frequently display their flowers on the ends of long racemes. Conventional wisdom is that long racemes in insectivorous plants have evolved to provide spatial separation between flowers and traps, which consequently prevents pollinators from being captured. However, it is also possible that long racemes evolved for better seed dispersal or to make flowers more visible to pollinators.

Methods

Two sympatric insectivorous plants with identical pollinators were studied: Drosera cistiflora, with an upright growth form but a short raceme; and Drosera pauciflora, with a basal rosette of traps and a very long raceme. If long racemes evolved to protect their pollinators then D. cistiflora should capture more pollinators than D. pauciflora. However, if long racemes evolved to attract pollinators then taller flowers should receive more pollination visits than shorter flowers.

Key Results

Examination of D. pauciflora and D. cistiflora traps revealed that no pollinators were captured by either species, suggesting that long racemes did not evolve to protect pollinators from being captured. Experimental manipulations of flower height in D. cistiflora showed that experimentally shortened plants received significantly fewer pollination visits than plants which were taller in stature.

Conclusions

Long scapes in Drosera and non-insectivorous plants probably evolved due to similar selective pressures such as pollinator attraction.     

Diversity,evolution, and function of stomata bearing structures in Cuscuta (dodders,Convolvulaceae): From extrafloral nectar secretion to transpiration in arid conditions

Cuscuta includes ca. 200 species of functionally holoparasitic plants grouped in four subgenera: Monogynella, Cuscuta, Pachystigma, and Grammica. Multicellular structures with stomata in Cuscuta are represented by extrafloral nectaries (ENs), reported from the stems of one Monogynella species, and stomatiferous protuberances (SPs), which are non-secretory. These latter structures had been noted on the stems of three Grammica species more than a century ago but entirely forgotten until recently when similar, non-secretory SPs were reported on the flowers of several new Grammica species. Here we study for the first time: (1) the extent of occurrence, diversity and evolution of secretory (ENs) and non-secretory (SPs) multicellular structures in Cuscuta, and (2) the function of SPs. We undertook a character evolution study of ENs and SPs on the stems and flowers of 136 Cuscuta taxa, and examined the structure/ultrastructure of SPs. ENs are inferred as primitive and characterize subg. Monogynella. SPs are derived in the remaining subgenera; they are ubiquitous on the flowers of Cuscuta and Pachystigma, but absent on their stems. Subgenus Grammica species develop two functional types of stems during their life cycle: vegetative, exploratory stems with very low stomatal densities (and no SPs), and reproductive, haustorial stems with numerous SPs. Moreover, 24 species from nine clades of subg. Grammica have evolved morphologically diverse floral SPs with systematic significance. To preliminarily ascertain SP function, we determined in the field the water uptake of Tithonia tubiformis plants parasitized or not by Cuscuta costaricensis, a species with both stem and floral SPs, and the stomatal conductance of dodder stems and flowers, as well as host leaves. Water uptake of parasitized hosts was significantly higher compared to non-parasitized plants, even after host leaves were removed, both during the day and night. The increased water uptake of parasitized hosts and stomatal conductance values suggest a transpiration role for the SPs, which is also confirmed by their lacunar structure. Grammica species with floral SPs grow in arid areas or characterized by a pronounced dry season during flowering/fruiting, which suggests that SPs may have evolved to stimulate the host water uptake during these phenophases.     

Enzymatic Relationships and Evolution in the Genus Meloidogyne (Nematoda: Tylenchida)

Thirty populations of Meloidogyne of diverse geographic origin representing 10 nominal species and various reproductive, cytological, and physiological forms known to exist in the genus were examined to determine their enzymatic relationships. The 184 bands resolved in the study of 27 enzymes were considered as independent characters. Pair-wise comparisons of populations were performed in all possible combinations to estimate the enzymatic distances (ED) and coefficients of similarity (S). A phylogenetic tree was constructed. The apomictic species M. arenaria, M. microcephala, M. javanica, and M. incognita shared a common lineage. M. arenaria was highly polytypic, whereas conspecific populations of M. javanica and M. incognita were largely monomorphic. The mitotic and meiotic forms of M. hapla were very similar (S = 0.93), suggesting that the apomictic race B evolved only recently from the meiotic race A. The five remaining meiotic species (M. chitwoodi, M. graminicola, M. graminis, M. microtyla, and M. naasi - each represented by a single population) were not closely related to each other or to the mitotic species.     

Comparative analysis of 18 sex pheromone plasmids fromEnterococcus faecalis: detection of a new insertion element on pPD1 and implications for the evolution of this plasmid family

A new IS element, IS1062, related to the enterococcal IS elements IS6770 and IS1252, was detected in the 3′-terminus of the surface exclusion gene,sep1, of sex pheromone plasmid pPD1 inEnterococcus faecalis. pPD1-bearing cells lack the surface exclusion function, probably as a consequence of this insertion. Analysis of pAD1 and pPD1 sequences (7.5 kb and 2.7 kb, respectively) downstream of their aggregation substance genes revealed no similarity in these DNA regions. Detailed DNA/DNA hybridization studies using DNA probes specific for various pAD1-encoded genes needed for plasmid transfer indicated that the sex pheromone plasmids have evolved by repeated recombination and insertion of diverse transposable elements which presumably account for recent acquisition of antibiotic resistances.     

Floral structure and development in Nartheciaceae (Dioscoreales), with special reference to ovary position and septal nectaries

We present a comparative study of the floral structure and development of Nartheciaceae, a small dioscorealean family consisting of five genera (Aletris, Lophiola, Metanarthecium, Narthecium, and Nietneria). A noticeable diversity existed in nine floral characters. Analyses of their respective character states in the light of a phylogenetic context revealed that the flowers of Nartheciaceae, whose plesiomorphies occur in Aletris and Metanarthecium, have evolved toward in all or part of Lophiola, Narthecium, and Nietneria: (1) loss of a perianth tube; (2) stamen insertion at the perianth base; (3) congenital carpel fusion; (4) loss of the septal nectaries; (5) unilocular style; (6) unfused lateral carpellary margins in the style; (7) flower with the median outer tepal on the abaxial side; (8) flower with moniliform hairs; and (9) flower with weak monosymmetry. We further found that, as the flowers developed, the ovary shifted its position from inferior to superior. As a whole, their structure changes suggest that the Nartheciaceae flowers have evolved in close association with pollination and seed dispersal. By considering inferior ovaries and the presence of septal nectaries as plesiomorphies of Nartheciaceae, we discussed evolution of the ovary position and septal nectaries in all the monocots.