Duets in Yellow-Naped Amazons: Variation in Syntax, Note Composition and Phonology at Different Levels of Social Organization

Complex vocal signals composed of multiple notes are used by many species. Such signals may vary in a number of features such as the rules that govern note order and timing (syntax), the relative number and types of different notes (note composition), and the acoustic structure of notes (phonology). Previous research examining male song in songbirds typically has shown greater conservation of syntax than phonology. Here we investigated whether these patterns of variation are also found in the duets of parrots. We examined geographic variation in the pair duets of yellow-naped amazons, Amazona auropalliata , at five sites within one vocal dialect. We also examined variation at several levels of social organization, including within pairs, among pairs and among sites, to assess where variability was greatest. Variation was highest at the within-pair level, although variation was also present at all other levels and for all of the duet factors. We hypothesize that variation at the among-site level allows duets to indicate site membership, while variation at the within-pair level allows pairs to change their duet to match their current social or physical environment. Syntax and phonology are also more conserved than note composition for all levels of social organization. This pattern may result because note composition is less important in duet function than syntax or phonology, or because development of syntax and phonology is more heavily influenced by genetic templates.     

Contact pairs of RNA with magnesium ions-electrostatics beyond the Poisson-Boltzmann equation

The electrostatic interaction of RNA with its aqueous environment is most relevant for defining macromolecular structure and biological function. The attractive interaction of phosphate groups in the RNA backbone with ions in the water environment leads to the accumulation of positively charged ions in the first few hydration layers around RNA. Electrostatics of this ion atmosphere and the resulting ion concentration profiles have been described by solutions of the nonlinear Poisson-Boltzmann equation and atomistic molecular dynamics (MD) simulations. Much less is known on contact pairs of RNA phosphate groups with ions at the RNA surface, regarding their abundance, molecular geometry, and role in defining RNA structure. Here, we present a combined theoretical and experimental study of interactions of a short RNA duplex with magnesium (Mg²⁺) ions. MD simulations covering a microsecond time range give detailed hydration geometries as well as electrostatics and spatial arrangements of phosphate-Mg²⁺ pairs, including both pairs in direct contact and separated by a single water layer. The theoretical predictions are benchmarked by linear infrared absorption and nonlinear two-dimensional infrared spectra of the asymmetric phosphate stretch vibration which probes both local interaction geometries and electric fields. Contact pairs of phosphate groups and Mg²⁺ ions are identified via their impact on the vibrational frequency position and line shape. A quantitative analysis of infrared spectra for a range of Mg²⁺-excess concentrations and comparison with fluorescence titration measurements shows that on average 20–30% of the Mg²⁺ ions interacting with the RNA duplex form contact pairs. The experimental and MD results are in good agreement. In contrast, calculations based on the nonlinear Poisson-Boltzmann equation fail in describing the ion arrangement, molecular electrostatic potential, and local electric field strengths correctly. Our results underline the importance of local electric field mapping and molecular-level simulations to correctly account for the electrostatics at the RNA-water interface.     

Chromosome ends in Chironomus pallidivittatus contain different subfamilies of telomere-associated repeats

Tandemly repeated 340 bp sequences, TA repeats, are present in seven of the eight pairs of chromosome ends in Chironomus pallidivittatus, being absent from the telocentric left end of chromosome four. We have previously shown that the family of TA repeats consists of four main subfamilies. One subfamily is composed of a master unit and the other three contain derived units, each of which has a small region where the master sequence is highly mutated. Here we find that there are considerable variations in numbers of TA repeats between animals and for the same telomere in different animals. We also show that the seven telomere pairs containing TA repeats differ with regard to the content of derived subfamilies. The master unit is probably present in all seven pairs. Two of the derived units are exclusively present in two telomere pairs. The third derived unit shows a more irregular distribution. Some of the telomeres have highly variable contents of such units among animals. Subfamilies thus have different behaviour as reflected in their stable and variable patterns of distribution between individual telomeres.W. Hennig     

Hydration of RNA base pairs

The hydration patterns around the RNA Watson-Crick and non-Watson-Crick base pairs in crystals are analyzed and described. The results indicate that (i) the base pair hydration is mostly "in-plane"; (ii) eight hydration sites surround the Watson-Crick G-C and A-U base pairs, with five in the deep and three in the shallow groove, an observation which extends the characteristic isostericity of Watson-Crick pairs; (iii) while the hydration around G-C base pairs is well defined, the hydration around A-U base pairs is more diffuse; (iv) the hydration sites close to the phosphate groups are the best defined and the most recurrent ones; (v) a string of water molecules links the two shallow groove 2'-hydroxyl groups, and (vi) the water molecules fit into notches, the size and accessibility of which are almost as important as the number and strength of the hydrophilic groups lining the cavity. Residence times of water molecules at specific hydration sites, inferred from molecular dynamics simulations, are discussed in the light of present data.     

Confidence Limits on the Ratio of the Mean Failure Times Based on Paired Exponential Observations

This paper discusses interval estimation for the ratio of the mean failure times on the basis of paired exponential observations. This paper considers five interval estimators: the confidence interval using an idea similar to Fieller's theorem (CIFT), the confidence interval using an exact parametric test (CIEP), the confidence interval using the marginal likelihood ratio test (CILR), the confidence interval assuming no matching effect (CINM), and the confidence interval using a locally most powerful test (CIMP). To evaluate and compare the performance of these five interval estimators, this paper applies Monte Carlo simulation. This paper notes that with respect to the coverage probability, use of the CIFT, CILR, or CIMP, although which are all derived based on large sample theory, can perform well even when the number of pairs n is as small as 10. As compared with use of the CILR, this paper finds that use of the CIEP with equal tail probabilities is likely to lose efficiency. However, this loss can be reduced by using the optimal tail probabilities to minimize the average length when n is small (<20). This paper further notes that use of the CIMP is preferable to the CIEP in a variety of situations considered here. In fact, the average length of the CIMP with use of the optimal tail probabilities can even be shorter than that of the CILR. When the intraclass correlation between failure times within pairs is 0 (i.e., the failure times within the same pair are independent), the CINM, which is derived for two independent samples, is certainly the best one among the five interval estimators considered here. When there is an intraclass correlation but which is small (<0.10), the CIFT is recommended for obtaining a relatively short interval estimate without sacrificing the loss of the coverage probability. When the intraclass correlation is moderate or large, either the CILR or the CIMP with the optimal tail probabilities is preferable to the others. This paper also notes that if the intraclass correlation between failure times within pairs is large, use of the CINM can be misleading, especially when the number of pairs is large.     

Evolution of a climbing habit promotes diversification in flowering plants

Key innovations are traits that are associated with the particular evolutionary 'success' of some taxonomic groups. Climbing plants depend on the availability of physical support to reach the canopy and thereby prevent shading by neighbouring plants. The present article shows that the evolution of a climbing habit in flowering plants constitutes a key innovation. A literature survey identified 48 pairs of sister groups from 45 families of flowering plants for which information on phylogenetic relationships, growth habit and species richness was available. In 38 cases, the climbing taxa were more diverse than their non-climbing sister groups. This pattern was highly significant. The same result was found when separate analyses were carried out for herbaceous and woody climbing plants, which differ in their constraints for successfully reaching a support.     

A Note on Interval Estimation of the Simple Difference in Data with Correlated Matched Pairs

When we employ cluster sampling to collect data with matched pairs, the assumption of independence between all matched pairs is not likely true. This paper notes that applying interval estimators, that do not account for the intraclass correlation between matched pairs, to estimate the simple difference between two proportions of response can be quite misleading, especially when both the number of matched pairs per cluster and the intraclass correlation between matched pairs within clusters are large. This paper develops two asymptotic interval estimators of the simple difference, that accommodate the data of cluster sampling with correlated matched pairs. This paper further applies Monte Carlo simulation to compare the finite sample performance of these estimators and demonstrates that the interval estimator, derived from a quadratic equation proposed here, can actually perform quite well in a variety of situations.     

A new ant species of the genus Tapinoma (Hymenoptera, Formicidae) from Saudi Arabia with a key to the Arabian species

Tapinoma wilsonisp. n. is described and illustrated from Saudi Arabia based on the worker caste collected from Al Baha, Saudi Arabia. It closely resembles Tapinoma lugubre Santschi 1917, from Zimbabwe in body measurements but can be distinguished from the latter species by the yellowish brown color; the yellowish pubescence, the two pairs of hairs present on the anterior part of the head; and the distinctly concave anterior clypeal margin. Biological and ecological notes of the new species are presented. An identification key to the workers of the Arabian species of the genus Tapinoma is given.     

The Abantis species (Lepidoptera: Hesperiidae) of western West Africa

Abstract. The genus Abantis Hopffer contains eight species in western West Africa. One species, Abantis pseudonigeriana sp.n., is described as new. Distributional notes and a key are given for all species. In general the species of this genus are rare and poorly represented in collections, but there are interesting examples of pairs of very similar species (nigeriana and pseudonigeriana; elegantula and maesseni).     

Independent evolution of song structure and note structure in American wood warblers

This study addresses the issue of how evolutionary convergence within shared environments shapes some features of bird song while leaving others unaffected, using as an example the songs of 51 North American wood warblers (Parulinae). I combined published information on breeding habitats and evolutionary relationships to show that the structure of warbler songs is correlated with habitat, whereas the structure of the notes that comprise the songs is relatively unaffected by habitat and more closely related to phylogenetic history. The results confirm known relationships between bird song and habitat, including correlations between song frequency and the type and density of canopy foliage, and between the number and arrangement of notes in the song and foliage density and moisture. More importantly, the results suggest that individual notes and whole songs are to some extent functionally independent, because the configuration of notes shows more evidence of evolutionary constraint than does the way notes are assembled into songs.     

We still fail to account for Mendel's observations

Background  

The present article corrects common textbook accounts of Mendel's experiments by re-establishing what he wrote and how he accounted for his observations. It notes the long-established tests for the validity of any explanations that purport to explain observations obtained by experiment. Application of these tests to Mendel's paper shows that the arguments he used to explain his observations were internally consistent but were, on one crucial issue, implausible. The same tests are applied to the currently accepted explanation for Mendel's observations.     

Sex Differences in the Song of <Emphasis Type="Italic">Indri indri</Emphasis>

In some primate species, males and females within a social group emit loud calls in a coordinated manner or chorus. Indri indri emits a very conspicuous loud call that elicits the loud calls of neighboring groups. Previous investigations have hypothesized that the main functions of the indri chorus are related to territorial announcement, intergroup avoidance, and group cohesion. We investigated sex differences in indri song. We recorded and analysed songs given by 10 different groups over 160 d. Overall singing duration did not vary between the sexes. However, males emitted significantly fewer but longer notes. Adult males and females of each group participated in the song with sex-specific repertoires. Females had a song repertoire of 8 note types; males shared all of their 6 notes with females. Apart from the initial roars, in all note types shared by both sexes, male notes were significantly longer than female ones, whereas variations in frequency parameters differed according to the note type. These findings suggest that indri song may provide cues to conspecifics, such as group size and sex composition, which could influence interactions between groups.     

Sound Spectrum Characteristics of Songs of Hainan Gibbon (Nomascus hainanus)

Gibbons are characterized by their species-specific calls, or songs. There are few studies of songs of Hainan gibbon (Nomascus hainanus). To study the sound spectrum characteristics and test for intergroup differences in Hainan gibbon song, we studied the singing behavior of Hainan gibbons in Bawangling National Nature Reserve, Hainan Province, China, intermittently from August 2002 to February 2013, collecting 184 recordings. Our results show that: 1) Hainan gibbon song bouts occur mainly 0–4 h after dawn. 2) The songs of adult males living in groups are composed mainly of one to three short notes and one to five long notes, while solitary adult male songs consist only of long frequency modulated notes and no short or single notes. 3) The song chorus is dominated by adult males, while females add a great call. Males do not have a great call, unlike those in other gibbon species. There are no female solos. 4) The sound spectrum frequency is similar in adult males living in two different groups, but the duration of the first long note differed significantly between the groups. The sonic frequencies of male and female songs are lower than those of other gibbons: no more than 2 kHz. Hainan gibbon sound structure is simple, although females participate in the chorus, reflecting their primitive status among gibbon species.     

Crystal structure of a brominated RNA helix with four mismatched base pairs: An investigation into RNA conformational variability.

The X-ray crystal structure of a brominated RNA helix with four mismatched base pairs and sequence r(UG(Br)C(Br)CAGUUCGCUGGC)(2) was determined to 2.1 A using the methods of multiwavelength anomalous diffraction (MAD) applied to the bromine K-absorption edge. There are three molecules in the asymmetric unit with unique crystal-packing environments, revealing true conformational variability at high resolution for this sequence. The structure shows that the sequence itself does not define a consistent pattern of solvent molecules, with the exception of the mismatched base pairs, implying that specific RNA-protein interactions would occur only with the nucleotides. There are a number of significant tertiary interactions, some of which are a result of the brominated base pairs and others that are directly mediated by the RNA 2' hydroxyl groups. The mismatched base pairs exhibit a solvent network as well as a stacking pattern with their nearest neighbors that validate previous thermodynamic analysis.     

Comparative analysis of the circulatory system in Amphipoda (Malacostraca, Crustacea)

We present data on the haemolymph vascular system (HVS) in four representatives of the major amphipod lineages Gammaridea, Hyperiidea and Caprellidea based on corrosion casting and three‐dimensional reconstructions of histological semi‐thin sections. In all these species the HVS comprises a dorsal pulsatile heart, which is continued in the body axis by the anterior and posterior aortae. The heart is equipped with three pairs of incurrent ostia. The number of cardiac arteries that lead off the heart varies among species: in the studied Gammaridea four pairs occur, in Hyperia galba only the three posterior pairs of cardiac arteries occur, while in Caprella mutica cardiac arteries are absent. In all the studied species the posterior aorta leads as a simple tube into the pleon attached to the dorsal diaphragm. The anterior aorta runs from its origin in the anterior part of the second thoracic segment into the cephalothorax. Both pairs of antennae have an arterial supply off the anterior aorta. An overview of previously studied species including our present findings shows the amphipod HVS to be relatively uniform and the gammarid form is discussed as being closest to the ground pattern of Amphipoda.     

Phenotypic divergence and reproductive isolation between sympatric forms of Japanese threespine sticklebacks

The threespine stickleback ( Gasterosteus aculeatus ) species complex is well suited for identifying the types of phenotypic divergence and isolating barriers that contribute to reproductive isolation at early stages of speciation. In the present study, we characterize the patterns of genetic and phenotypic divergence as well as the types of isolating barriers that are present between two sympatric pairs of threespine sticklebacks in Hokkaido, Japan. One sympatric pair consists of an anadromous and a resident freshwater form and shows divergence in body size between the forms, despite the lack of genetic differentiation between them. The second sympatric pair consists of two anadromous forms, which originated before the last glacial period and are currently reproductively isolated. These two anadromous forms have diverged in many morphological traits as well as in their reproductive behaviours. Both sexual isolation and hybrid male sterility contribute to reproductive isolation between the anadromous species pair. We discuss the shared and unique aspects of phenotypic divergence and reproductive isolation in the Japanese sympatric pairs compared with postglacial stickleback species pairs. Further studies of these divergent species pairs will provide a deeper understanding of the mechanisms of speciation in sticklebacks.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 91 , 671–685.     

Contribution of histones H2A and H2B to the folding of nucleosomal DNA

We have studied the structural properties of nucleosomal particles deficient in histones H2A and H2B produced by modification of histone amino groups with dimethylmaleic anhydride [Jordano, J., Montero, F., & Palacián, E. (1984) Biochemistry (preceding paper in this issue)]. Digestion with DNase I of residual particles containing only 15% of the original H2A . H2B complement produces only discrete DNA fragments no longer than 70 nucleotides. As compared with the original nucleosomes, thermal denaturation of the residual particles shows a decrease from 140 to about 90 in the number of nucleotide base pairs per particle that melt at the highest temperature transition as well as a drop in the temperature of this transition. Circular dichroism spectra of the residual particles give ellipticity values around 275 nm, much higher than those corresponding to the control nucleosomes, which appears to indicate a loss in the compact DNA tertiary structure. When regeneration of the modified amino groups of the residual particles takes place in the presence of the complementary fraction containing histones H2A and H2B, but not in its absence, nucleosomal particles with the structural properties of the original nucleosomes are reconstituted. Therefore, the structural change observed in the residual particles can be assigned to the lack of histones H2A and H2B and not to the modified amino groups of the histones present in the residual particles. The results are consistent with the stabilization by histones H2A and H2B of a DNA length of 50-70 base pairs per nucleosome.     

Quantum Chemical Studies of Structures and Binding in Noncanonical RNA Base pairs: The Trans Watson-Crick:Watson-Crick Family

Abstract

The trans Watson-Crick/Watson-Crick family of base pairs represent a geometric class that play important structural and possible functional roles in the ribosome, tRNA, and other functional RNA molecules. They nucleate base triplets and quartets, participate as loop closing terminal base pairs in hair pin motifs and are also responsible for several tertiary interactions that enable sequentially distant regions to interact with each other in RNA molecules. Eleven representative examples spanning nine systems belonging to this geometric family of RNA base pairs, having widely different occurrence statistics in the PDB database, were studied at the HF/6–31G (d, p) level using Morokuma decomposition, Atoms in Molecules as well as Natural Bond Orbital methods in the optimized gas phase geometries and in their crystal structure geometries, respectively. The BSSE and deformation energy corrected interaction energy values for the optimized geometries are compared with the corresponding values in the crystal geometries of the base pairs. For non protonated base pairs in their optimized geometry, these values ranged from ?8.19 kcal/mol to ?21.84 kcal/mol and compared favorably with those of canonical base pairs. The interaction energies of these base pairs, in their respective crystal geometries, were, however, lesser to varying extents and in one case, that of A:A W:W trans, it was actually found to be positive. The variation in RMSD between the two geometries was also large and ranged from 0.32–2.19 Å. Our analysis shows that the hydrogen bonding characteristics and interaction energies obtained, correlated with the nature and type of hydrogen bonds between base pairs; but the occurrence frequencies, interaction energies, and geometric variabilities were conspicuous by the absence of any apparent correlation. Instead, the nature of local interaction energy hyperspace of different base pairs as inferred from the degree of their respective geometric variability could be correlated with the identities of free and bound hydrogen bond donor/acceptor groups present in interacting bases in conjunction with their tertiary and neighboring group interaction potentials in the global context. It also suggests that the concept of isostericity alone may not always determine covariation potentials for base pairs, particularly for those which may be important for RNA dynamics. These considerations are more important than the absolute values of the interaction energies in their respective optimized geometries in rationalizing their occurrences in functional RNAs. They highlight the importance of revising some of the existing DNA based structure analysis approaches and may have significant implications for RNA structure and dynamics, especially in the context of structure prediction algorithms.     

Historical Archeology in Missouri Basin Reservoir Areas: Current Investigations

Abstract

A review of the present status of research, field reconnaissance, excavatlon, and analysis of sites of the historic period in the Missouri Basin, of both native and white origin, which are located within reservoir areas and have been, or will be, inundated, with notes on plans for future investigations. Mention is also made of comparable undertakings outside reservoir areas by both public and private groups.     

Receivers respond differently to chick-a-dee calls varying in note composition in Carolina chickadees, Poecile carolinensis

The chick-a-dee call of the avian genus Poecile is a structurally complex vocal system because it possesses a set of simple rules that governs how the notes of the call are ordered, and variable numbers of each of the note types strung together can generate an extraordinary number of unique calls. Whereas it has been hypothesized that chick-a-dee calls with different notes may convey different information, no experimental evidence has been offered in support of the hypothesis. Previously published studies suggested that flock members use chick-a-dee calls in the context of moving to or from a feeding site. Here, we tested Carolina chickadees' responses to playbacks of chick-a-dee calls that differed in note composition. Playbacks were conducted in the field in the context of a novel food source. Our pilot data had indicated that chick-a-dee calls with relatively large numbers of ‘C’ notes were given by birds on their first contact with a novel seed stand. In the present study, we found that chickadees flew in close to the playback speaker and subsequently took seed from a seed stand more often during playbacks of chick-a-dee calls containing C notes than chick-a-dee calls not containing C notes or than control playbacks. Vocal responses of chickadees to the playbacks also differed in relation to the particular vocal signal being played back. These results indicate that receivers respond differently to chick-a-dee calls containing different compositions of note types and represent a first step to link variation in note composition and ordering in these calls to possible meanings.Copyright 2002 The Association for the Study of Animal Behaviour. Published by Elsevier Science Ltd. All rights reserved .