Nest area exploration and recognition in leafcutter ants (Atta cephalotes)

Workers of Atta cephalotes deposit “nest exit pheromones” in the vicinity of their nest entrances. Lasting for a period of at least 24 h, these substances orient the workers to the nest openings and increase the rate of trail laying, leaf cutting, and leaf retrieval. Their perception by the workers forms part of a cognitive map by which the ants adjust the form and level of their activity during foraging.The structure and behavioural roles of the known abdominal exocrine glands have been evaluated. An arrestant is produced by the hind gut. The pygidial gland is vestigial, and a cylindrical epithelium on the 7th abdominal sternite might function as a sternal gland. Both the Dufour's gland and valves gland are well developed and produce alarm pheromones. The valves gland is not the source of a territorial pheromone, as reported by previous authors, and in fact we could find no evidence of the existence of a special substance of this nature from any source. However, colony-specific substances, possibly one or more of the nest-exit pheromones, are deposited around the nest openings. When workers encounter deposits by alien colonies at this site, they increase the rate of abdominal dipping, thus seemingly adding colony-specific chemicals of their own.     

Self-restraint and sterility in workers of Acromyrmex and Atta leafcutter ants

Summary. Queens of leafcutter ants (Acromyrmex and Atta) are highly multiply mated, resulting in a potential queenworker and worker-worker conflict over who should produce the males in the colony. We studied whether this conflict is expressed, by determining the amount of reproductive egg-laying by workers in queenright colonies of Acromyrmex echinatior, Acromyrmex octospinosus, Atta cephalotes, and Atta sexdens through ovary dissections. Worker sons are absent or rare in queenright Acromyrmex colonies, but can be produced in orphaned colonies. In Atta, most workers have rudimentary ovaries that never produce eggs, but a few (mostly small and medium workers that form a retinue around the queen) lay many trophic eggs for consumption by the queen. These eggs are large, flaccid, and lacking in yolk compared to queen-laid eggs, and appear to be always inviable. In Acromyrmex, many workers (especially young large workers) lay eggs that are similar in size to queen-laid eggs, but mostly with a reduced amount of yolk. Trophic eggs appear to be an important source of food for larvae in Acromyrmex (especially in Ac. echinatior), but not in Atta. Five (0.8) of 616 dissected Ac. echinatior workers but no Ac. octospinosus workers (n = 552), had ready-to-lay reproductive eggs. Old workers in all four species are incapable of laying eggs due to ovary resorption. We conclude that Atta workers are sterile, while Acromyrmex workers display reproductive self-restraint, possibly representing an earlier stage in the evolution towards worker sterility. Worker selfrestraint in Acromyrmex may be maintained by a queen or worker policing mechanism, but individual cost-benefit explanations may also apply.Received 1 March 2004; revised 28 June 2004; accepted 1 July 2004.     

Worldwide mitochondrial DNA diversity and phylogeography of pilot whales (Globicephala spp.)

Pilot whales (Globicephala spp.) provide an interesting example of recently diverged oceanic species with a complex evolutionary history. The two species have wide but largely non‐overlapping ranges. Globicephala melas (long‐finned pilot whale; LFPW) has an antitropical distribution and is found in the cold‐temperate waters of the North Atlantic and Southern Hemisphere, whereas Globicephala macrorhynchus (short‐finned pilot whale; SFPW) has a circumglobal distribution and is found mainly in the tropics and subtropics. To investigate pilot whale evolution and biogeography, we analysed worldwide population structure using mitochondrial DNA (mtDNA) control region sequences (up to 620 bp) from a variety of sources (LFPW = 643; SFPW = 150), including strandings in New Zealand and Tasmania, and whale‐meat products purchased on the markets of Japan and Korea. Phylogenetic reconstructions failed to support a reciprocal monophyly of the two species, despite six diagnostic substitutions, possibly because of incomplete lineage sorting or inadequate phylogenetic information. Both species had low haplotype and nucleotide diversity compared to other abundant widespread cetaceans (LFPW, π = 0.35%; SFPW, π = 0.87%) but showed strong mtDNA differentiation between oceanic basins. Strong levels of structuring were also found at the regional level. In LFPW, phylogeographic patterns were suggestive either of a recent demographic expansion or selective sweep acting on the mtDNA. For SFPW, the waters around Japan appear to represent a centre of diversity, with two genetically‐distinct forms, as well as a third population of unknown origin. The presence of multiple unique haplotypes among SFPW from South Japan, together with previously documented morphological and ecological differences, suggests that the southern form represents a distinct subspecies and/or evolutionary significant unit. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98 , 729–744.     

Pitx genes in Tunicates provide new molecular insight into the evolutionary origin of pituitary

We have initiated a project aimed at documenting molecular and cellular changes underlying the emergence of the hypothalamo-hypophyseal axis in Chordates. Considering the phylogenetic position of Tunicates and the 'pan-hypophyseal' expression pattern of Pitx genes in Vertebrate pituitary, we searched for a Pitx-related homeobox gene in the ascidian Ciona intestinalis, and identified Ci-Pitx (ona intestinalis uitary homeobo gene). We also isolated Cs-Pitx and Bs-Pitx, the Ci-Pitx respective counterparts of Ciona savignyi and Botryllus schlosseri, two other Tunicate species. Ci-Pitx mRNA encodes a putative protein exhibiting the diagnostic K50-Paired-class homeodomain and a conserved C-terminal Aristaless domain. Embryonic expression pattern of Ci-Pitx revealed a conserved expression domain in the anterior neural ridge and subsequently in the pharyngeal primordium, defined in Vertebrates as the stomodeal ectomere, which encompasses the presumptive pituitary territory. This shows that expression at early steps of pituitary development is a feature of Pitx-related genes that was already present in the last common ancestor of Chordates.     

Sponge genes provide new insight into the evolutionary origin of the neurogenic circuit

The nerve cell is a eumetazoan (cnidarians and bilaterians) synapomorphy [1]; this cell type is absent in sponges, a more ancient phyletic lineage. Here, we demonstrate that despite lacking neurons, the sponge Amphimedon queenslandica expresses the Notch-Delta signaling system and a proneural basic helix loop helix (bHLH) gene in a manner that resembles the conserved molecular mechanisms of primary neurogenesis in bilaterians. During Amphimedon development, a field of subepithelial cells expresses the Notch receptor, its ligand Delta, and a sponge bHLH gene, AmqbHLH1. Cells that migrate out of this field express AmqDelta1 and give rise to putative sensory cells that populate the larval epithelium. Phylogenetic analysis suggests that AmqbHLH1 is descendent from a single ancestral bHLH gene that later duplicated to produce the atonal/neurogenin-related bHLH gene families, which include most bilaterian proneural genes [2]. By way of functional studies in Xenopus and Drosophila, we demonstrate that AmqbHLH1 has a strong proneural activity in both species with properties displayed by both neurogenin and atonal genes. From these results, we infer that the bilaterian neurogenic circuit, comprising proneural atonal-related bHLH genes coupled with Notch-Delta signaling, was functional in the very first metazoans and was used to generate an ancient sensory cell type.     

Phylogenetic origins of local-scale diversity patterns and the causes of Amazonian megadiversity

What explains the striking variation in local species richness across the globe and the remarkable diversity of rainforest sites in Amazonia? Here, we apply a novel phylogenetic approach to these questions, using treefrogs (Hylidae) as a model system. Hylids show dramatic variation in local richness globally and incredible local diversity in Amazonia. We find that variation in local richness is not explained primarily by climatic factors, rates of diversification (speciation and extinction) nor morphological variation. Instead, local richness patterns are explained predominantly by the timing of colonization of each region, and Amazonian megadiversity is linked to the long-term sympatry of multiple clades in that region. Our results also suggest intriguing interactions between clade diversification, trait evolution and the accumulation of local richness. Specifically, sympatry between clades seems to slow diversification and trait evolution, but prevents neither the accumulation of local richness over time nor the co-occurrence of similar species.     

Agonists for 13 trace amine-associated receptors provide insight into the molecular basis of odor selectivity

Trace amine-associated receptors (TAARs) are vertebrate olfactory receptors. However, ligand recognition properties of TAARs remain poorly understood, as most are "orphan receptors" without known agonists. Here, we identify the first ligands for many rodent TAARs and classify these receptors into two subfamilies based on the phylogeny and binding preference for primary or tertiary amines. Some mouse and rat orthologs have similar response profiles, although independent Taar7 gene expansions led to highly related receptors with altered ligand specificities. Using chimeric TAAR7 receptors, we identified an odor contact site in transmembrane helix III that functions as a selectivity filter. Homology models based on the β(2) adrenergic receptor structure indicate spatial proximity of this site to the ligand. Gain-of-function mutations at this site created olfactory receptors with radically altered odor recognition properties. These studies provide new TAAR ligands, valuable tools for studying receptor function, and general insights into the molecular pharmacology of G protein-coupled receptors.     

Pleistocene phylogeography and phylogenetic concordance in cold-adapted spring snails (Bythinella spp.)

Previous studies on Pleistocene phylogeography of European taxa are biased towards (i) vertebrates, (ii) terrestrial taxa, (iii) single species, and (iv) taxa that survived the Pleistocene in southern refugia. Relatively little is known about whether evolutionary patterns of vertebrate and terrestrial taxa are also applicable to freshwater invertebrates, whether cold-adapted freshwater species could survive in extensive permafrost areas without retreating into refugia, and whether Pleistocene phylogeographical patterns are influenced by phylogeny. Here, the widespread and species-rich European spring snail genus Bythinella Moquin-Tandon, 1856 is utilized in an attempt to mitigate this bias. These strongly cold-adapted freshwater animals mostly occur in springs — highly isolated habitats that are relatively unaffected by anthropogenic influences. Phylogenetic and phylogeographical analyses based on mitochondrial DNA and nuclear DNA sequence data were conducted in 458 specimens from 142 populations occurring throughout Europe. The study provides evidence that most Bythinella spp. survived the Pleistocene in restricted northern glacial refugia that largely correspond to refugia previously recognized for other European biota. However, survival of Bythinella spp. in extensive permafrost areas outside of refugia can likely be rejected. Low dispersal ability and the isolation and fragmentation of spring habitats, as well as the distribution of perennial springs within permafrost regions, may account for this result. Tests involving a total of 29 nominal species showed that phylogenetically closely related Bythinella species did not occupy similar refugia. This lack of phylogenetic concordance could possibly be explained by the stochasticity of survival and dispersal in spring snails.     

Global and local molecular dynamics of a bacterial carboxylesterase provide insight into its catalytic mechanism

Carboxylesterases (CEs) are ubiquitous enzymes responsible for the detoxification of xenobiotics. In humans, substrates for these enzymes are far-ranging, and include the street drug heroin and the anticancer agent irinotecan. Hence, their ability to bind and metabolize substrates is of broad interest to biomedical science. In this study, we focused our attention on dynamic motions of a CE from B. subtilis (pnbCE), with emphasis on the question of what individual domains of the enzyme might contribute to its catalytic activity. We used a 10 ns all-atom molecular dynamics simulation, normal mode calculations, and enzyme kinetics to understand catalytic consequences of structural changes within this enzyme. Our results shed light on how molecular motions are coupled with catalysis. During molecular dynamics, we observed a distinct C-C bond rotation between two conformations of Glu310. Such a bond rotation would alternately facilitate and impede protonation of the active site His399 and act as a mechanism by which the enzyme alternates between its active and inactive conformation. Our normal mode results demonstrate that the distinct low-frequency motions of two loops in pnbCE, coil_5 and coil_21, are important in substrate conversion and seal the active site. Mutant CEs lacking these external loops show significantly reduced rates of substrate conversion, suggesting this sealing motion prevents escape of substrate. Overall, the results of our studies give new insight into the structure-function relationship of CEs and have implications for the entire family of α/β fold family of hydrolases, of which this CE is a member.     

A comparative assessment of phenotypic and molecular diversity in Doum (Hyphaene thebaica L.)

Doum palm (Hyphaene thebaica L.) has been reported as one of the most beneficial species worldwide. Its fruits are a good source of fibers, antioxidants, B-complex vitamins, essential minerals, monosaccharides, essential oil and flavonoids. Fruit extract shows anti-inflammatory, antioxidant, antimicrobial, anticancer and pharmacological potential. However, there is a lack of investigations dealing with its genetic diversity. Therefore, a collection of twelve mature female palm landraces grown in the botanical garden of Aswan, “Egypt” were used for genetic diversity assessment based on phenotypic and molecular levels. 18 vegetal and chemical traits were evaluated. Fifteen of them showed highly significant variation among the tested landraces. Euclidian-based-dendrogram discriminated the tested landraces based on their phenotypic similarities to three main clusters showing a high level of variability. Molecular analysis using inter simple sequence repeats (ISSR) vis-à-vis start codon targeted (SCoT) polymorphism markers displayed the relationships among the tested landraces molecularly. Both markers showed a reasonable degree of polymorphism, however SCoT was more effective than the ISSR by showing a higher percentage of polymorphism, polymorphism information content, resolving power and diversity index. Cluster analysis based on molecular data showed a clear relationship among the doum landraces. However, ISSR- and SCoT-based dendrograms were slightly different, and completely unlike that based on phenotypic data. Nevertheless, phenotypic and molecular evaluations might complement each other, and by data of both an excellent overview was obtained from principle coordinate analysis. The information herein is valuable and considered as a keystone for further proximate studies on doum genetic diversity to help in improvement and breeding approaches.

     

CR1 retroposons provide a new insight into the phylogeny of Phasianidae species (Aves: Galliformes)

Chicken repeat 1 (CR1) elements, a class of retroposons belonging to non-long-terminal repeats, have been recognized as powerful tools for phylogenetic studies. Here we examine the phylogenetic relationships of 11 Phasianidae species based on CR1 retroposons. Together with 19 loci reported previously, a total of 99 CR1 loci were identified from chicken genome and turkey BAC clone sequences. 75 insertion events were used to address the branching order of 11 species in Phasianidae. The topology of our tree suggests that: 1) Gallus gallus possessed a basal phylogenetic position within Phasianidae and was related to Bambusicola thoracica (BSP=100%); 2) After the split of G. gallus and B. thoracica, Arborophila rufipectus diverged from Phasianidae (BSP=100%). Nine unambiguous insertion events supported a phylogenetic position of A. rufipectus different to previous mitochondrial data suggesting a hybrid origin or an ancient introgression of A. rufipectus; and 3) 22 CR1 insertion events strongly supported the eight phasianids under investigation sharing a common ancestor. Our study has revisited the phylogenetic position of G. gallus and A. rufipectus and provided a new insight into the phylogeny of Phasianidae birds. It showed that a CR1-based methodology has a great potential to be informative within Phasianidae in resolving relationships of closely related species whose radiation and speciation have occurred very recently.     

Ecology and diversity of waxcap (Hygrocybe spp.) Fungi

Summary

Members of the genus Hygrocybe are ubiquitous and colourful components of many undisturbed and nutrient-poor grasslands in the UK. Through a number of detailed surveys of the distribution of Hygrocybe spp. and of genera showing similar patterns of occurrence (e.g. Clavaria spp., Entoloma spp., Geoglossum spp.) a picture is gradually emerging of the more important ‘waxcap grassland’ sites, and of those species in greatest need of protection. Waxcap fungi are far from ideal experimental organisms which explains why so little has been published about their biology and ecology. They cannot be cultured on laboratory media and the correct conditions for inducing spores of most species to germinate have yet to be established. Nevertheless approaches such as isotope ratio mass spectrometry and the use of molecular biology techniques are beginning to provide an insight into the role played by these organisms in grassland ecosystems, and why they are so adversely affected by many agricultural practices. Current field experiments at various sites including Sourhope near Kelso will also permit investigations into waxcap ecology to be correlated with parallel studies of other members of the soil biota.     

Omics technologies provide new insights into the molecular physiopathology of equine osteochondrosis

Background

Osteochondrosis (OC(D)) is a juvenile osteo-articular disorder affecting several mammalian species. In horses, OC(D) is considered as a multifactorial disease and has been described as a focal disruption of endochondral ossification leading to the development of osteoarticular lesions. Nevertheless, OC(D) physiopathology is poorly understood. Affected horses may present joint swelling, stiffness and lameness. Thus, OC(D) is a major concern for the equine industry. Our study was designed as an integrative approach using omics technologies for the identification of constitutive defects in epiphyseal cartilage and/or subchondral bone associated with the development of primary lesions to further understand OC(D) pathology. This study compared samples from non-affected joints (hence lesion-free) from OC(D)-affected foals (n = 5, considered predisposed samples) with samples from OC-free foals (n = 5) considered as control samples. Consequently, results are not confounded by changes associated with the evolution of the lesion, but focus on altered constitutive molecular mechanisms. Comparative proteomics and micro computed tomography analyses were performed on predisposed and OC-free bone and cartilage samples. Metabolomics was also performed on synovial fluid from OC-free, OC(D)-affected and predisposed joints.

Results

Two lesion subtypes were identified: OCD (lesion with fragment) and OC (osteochondral defects). Modulated proteins were identified using omics technologies (2-DE proteomics) in cartilage and bone from affected foals compare to OC-free foals. These were associated with cellular processes including cell cycle, energy production, cell signaling and adhesion as well as tissue-specific processes such as chondrocyte maturation, extracellular matrix and mineral metabolism. Of these, five had already been identified in synovial fluid of OC-affected foals: ACTG1 (actin, gamma 1), albumin, haptoglobin, FBG (fibrinogen beta chain) and C4BPA (complement component 4 binding protein, alpha).

Conclusion

This study suggests that OCD lesions may result from a cartilage defect whereas OC lesions may be triggered by both bone and cartilage defects, suggesting that different molecular mechanisms responsible for the equine osteochondrosis lesion subtypes and predisposition could be due to a defect in both bone and cartilage. This study will contribute to refining the definition of OC(D) lesions and may improve diagnosis and development of therapies for horses and other species, including humans.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-947) contains supplementary material, which is available to authorized users.     

Crystallographic insight into the evolutionary origins of xyloglucan endotransglycosylases and endohydrolases

The xyloglucan endotransglycosylase/hydrolase (XTH) gene family encodes enzymes of central importance to plant cell wall remodeling. The evolutionary history of plant XTH gene products is incompletely understood vis‐à‐vis the larger body of bacterial endoglycanases in Glycoside Hydrolase Family 16 (GH16). To provide molecular insight into this issue, high‐resolution X‐ray crystal structures and detailed enzyme kinetics of an extant transitional plant endoglucanase (EG) were determined. Functionally intermediate between plant XTH gene products and bacterial licheninases of GH16, Vitis vinifera EG16 (VvEG16) effectively catalyzes the hydrolysis of the backbones of two dominant plant cell wall matrix glycans, xyloglucan (XyG) and β(1,3)/β(1,4)‐mixed‐linkage glucan (MLG). Crystallographic complexes with extended oligosaccharide substrates reveal the structural basis for the accommodation of both unbranched, mixed‐linked (MLG) and highly decorated, linear (XyG) polysaccharide chains in a broad, extended active‐site cleft. Structural comparison with representative bacterial licheninases, a xyloglucan endotranglycosylase (XET), and a xyloglucan endohydrolase (XEH) outline the functional ramifications of key sequence deletions and insertions across the phylogenetic landscape of GH16. Although the biological role(s) of EG16 orthologs remains to be fully resolved, the present biochemical and tertiary structural characterization provides key insight into plant cell wall enzyme evolution, which will continue to inform genomic analyses and functional studies across species.     

The relationship between soil variables and leafcutter ant (Atta sexdens) nest distribution in the Colombian Amazon

We determined the relationships between several soil variables and the distribution of leafcutter ant (Atta sexdens) nests on the Colombian shore of the Amazon River. Seven habitats were identified in which nests were consistently present or absent. Soil samples for physiochemical analysis were taken near nest sites in three habitats where nests were present and from randomly selected sites in four other habitats where nests were absent. Percent canopy cover and soil resistance were also measured for each site. Almost all of the 20 identified soil variables were significantly different between habitats with and without A. sexdens nests, and the values of all variables were heterogeneous between the seven habitats. The most important variables correlated with leafcutter ant nest presence were percent canopy cover (positively), percent silt, soil resistance at 0–20 cm, and pH (all negatively). We deduced a binomial and a multinomial logistic regression which showed how each of these variables was related to nest presence and habitat, respectively. We describe how each variable may affect leafcutter ant nest development, especially in its earliest stages, and therefore influences nest distribution. We propose a suitable-soil hypothesis which, complementary to the palatable forage hypothesis, aims to explain patterns in leafcutter ant nest demography based on soil conditions.     

Genetic diversity and phylogeography of broomcorn millet (Panicum miliaceum L.) across Eurasia

Broomcorn millet (Panicum miliaceum L.) is one of the world's oldest cultivated cereals, with several lines of recent evidence indicating that it was grown in northern China from at least 10,000 cal bp. Additionally, a cluster of archaeobotanical records of P. miliaceum dated to at least 7000 cal bp exists in eastern Europe. These two centres of early records could either represent independent domestications or cross-continental movement of this cereal that would predate that of any other crop by some 2 millennia. Here, we analysed genetic diversity among 98 landrace accessions from across Eurasia using 16 microsatellite loci, to explore phylogeographic structure in the Old World range of this historically important crop. The major genetic split in the data divided the accessions into an eastern and a western grouping with an approximate boundary in northwestern China. A substantial number of accessions belonging to the 'western' genetic group were also found in northeastern China. Further resolution subdivided the western and eastern genepools into 2 and 4 clusters respectively, each showing clear geographic patterning. The genetic data are consistent with both the single and multiple domestication centre hypotheses and add specific detail to what these hypotheses would entail regarding the spread of broomcorn millet. Discrepancies exist between the predictions from the genetic data and the current archaeobotanical record, highlighting priorities for investigation into early farming in Central Asia.