Visualization of the interactome: What are we looking at?

Network visualization of the interactome has been become routine in systems biology research. Not only does it serve as an illustration on the cellular organization of protein-protein interactions, it also serves as a biological context for gaining insights from high-throughput data. However, the challenges to produce an effective visualization have been great owing to the fact that the scale, biological context and dynamics of any given interactome are too large and complex to be captured by a single visualization. Visualization design therefore requires a pragmatic trade-off between capturing biological concept and being comprehensible. In this review, we focus on the biological interpretation of different network visualizations. We will draw on examples predominantly from our experiences but elaborate them in the context of the broader field. A rich variety of networks will be introduced including interactomes and the complexome in 2D, interactomes in 2.5D and 3D and dynamic networks.     

Does fitness erode in the absence of selection? An experimental test with Tribolium

In the absence of natural selection, average fitness in the population is expected to decline due to the accumulation of deleterious mutations. Replicate populations of flour beetles (Tribolium confusum) were maintained for 22 generations in the virtual absence of selection (random mating, favorable environment, excess of food, and mortality of only 3%). Larva-to-adult survivorship rates were similar in the stock population and selection-free populations. In contrast, starvation resistance of adult beetles from selection-free populations was significantly reduced (by more than 2% per generation). When tested in the favorable environment, beetles in one selection-free population had significantly slower development and smaller sizes of females than beetles from the stock population. Since such changes in these fitness components are usually maladaptive, they indicate possible erosion of fitness under relaxed selection at the rate of 0.1-0.2% per generation. No fitness erosion was detectable in the second selection-free population.     

Reproductive isolation in Drosophila: how close are we to untangling the genetics of speciation?

Our understanding of the genetic basis of reproductive isolation in Drosophila has progressed rapidly over the past decade. Details of the genetic structure of hybrid sterility have been revealed and a general consensus has been reached concerning the genetic bases of Haldane's rule. Genetic analyses now reach beyond hybrid sterility and inviability, allowing us to make important comparisons across different traits involved in reproductive isolation. Expansion of genetic studies to include rescue of hybrid incompatibilities has opened the door for more detailed molecular and developmental analyses of reproductive isolation than has ever before been possible.     

What are the closest relatives of the hot-spring snakes (Colubridae, Thermophis), the relict species endemic to the Tibetan Plateau?

We conducted phylogenetic analyses to identify the closest related living relatives of the Xizang and Sichuan hot-spring snakes (T. baileyi and T. zhaoermii) endemic to the Tibetan Plateau, using mitochondrial DNA sequences (cyt b, ND4) from eight specimens, together with sequences from 95 additional caenophidian and five henophidian genera that were downloaded from GenBank. Phylogenetic trees were obtained using Bayesian Inference and Maximum likelihood methods. Results suggest that hot-spring snakes, which are adapted to high and cold environments, were clustered in the monophyletic Xenodontinae. Xenodontinae is one of the largest subfamilies of colubrid snakes, with about 90 genera and more than 500 species known, and are primarily tropical snakes previously thought to be restricted to the New World. Our data failed to provide any evidence that the New World xenodontines diverged from Thermophis and dispersed into the New World, also failed to suggest a colonization of Asia by New World xenodontines by dispersal from the New World. An alternative plausible scenario may be that Thermophis and the New World xenodontines evolved independently in Asia and America, respectively, after the divergence of their common ancestor. The divergence of the two species in Thermophis was caused by the barrier of the Hengduan Mountains, and the speciation had almost occurred when Tibetan Plateau attained present elevation.     

How independent are the appearances of n-mers in different genomes?

MOTIVATION: Analysis of statistical properties of DNA sequences is important for evolutional biology as well as for DNA probe and PCR technologies. These technologies, in turn, can be used for organism identification, which implies applications in the diagnosis of infectious diseases, environmental studies, etc. RESULTS: We present results of the correlation analysis of distributions of the presence/absence of short nucleotide subsequences of different length ('n-mers', n = 5-20) in more than 1500 microbial and virus genomes, together with five genomes of multicellular organisms (including human). We calculate whether a given n-mer is present or absent (frequency of presence) in a given genome, which is not the usually calculated number of appearances of n-mers in one or more genomes (frequency of appearance). For organisms that are not close relatives of each other, the presence/absence of different 7-20mers in their genomes are not correlated. For close biological relatives, some correlation of the presence of n-mers in this range appears, but is not as strong as expected. Suppressed correlations among the n-mers present in different genomes leads to the possibility of using random sets of n-mers (with appropriately chosen n) to discriminate genomes of different organisms and possibly individual genomes of the same species including human with a low probability of error.     

On the use of climate covariates in aquatic species distribution models: are we at risk of throwing out the baby with the bath water?

Species distribution models (SDMs) in river ecosystems can incorporate climate information by using air temperature and precipitation as surrogate measures of instream conditions or by using independent models of water temperature and hydrology to link climate to instream habitat. The latter approach is preferable but constrained by the logistical burden of developing water temperature and hydrology models. We therefore assessed whether regional scale, freshwater SDM predictions are fundamentally different when climate data versus instream temperature and hydrology are used as covariates. Maximum entropy (MaxEnt) SDMs were built for 15 freshwater fishes using one of two covariate sets: 1) air temperature and precipitation (climate variables) in combination with physical habitat variables; or 2) water temperature, hydrology (instream variables) and physical habitat. Three procedures were then used to compare results from climate vs instream models. First, equivalence tests assessed average pairwise differences (site‐specific comparisons throughout each species’ range) among climate and instream models. Second, ‘congruence’ tests determined how often the same stream segments were assigned high habitat suitability by climate and instream models. Third, Schoener's D and Warren's I niche overlap statistics quantified range‐wide similarity in predicted habitat suitability from climate vs instream models. Equivalence tests revealed small, pairwise differences in habitat suitability between climate and instream models (mean pairwise differences in MaxEnt raw scores for all species < 3 × 10^–4). Congruence tests showed a strong tendency for climate and instream models to predict high habitat suitability at the same stream segments (median congruence = 68%). D and I statistics reflected a high margin of overlap among climate and instream models (median D = 0.78, median I = 0.96). Overall, we found little support for the hypothesis that SDM predictions are fundamentally different when climate versus instream covariates are used to model fish species’ distributions at the scale of the Columbia Basin.     

Allozymes and nDNA markers show different levels of population differentiation in the mussel Mytilus?edulis on British coasts

In order to test the hypothesis that natural selection can be operating on allozymes, six nuclear DNA markers were used to study population structure in six Mytilus edulis (Linnaeus, 1758) populations around the British Isles and the results compared with previous allozyme data from the same (two sites) or very close localities (the other four sites). Allozymes and nDNA markers show significant differentiation between populations at the P < 0.01 level, with the exception of the nDNA marker PLIIa. The results also indicate significant differences (modified version of the Lewontin–Krakauer test) between the two sets of markers which are about one order of magnitude higher for nDNA than for the allozyme loci. The bootstrap analysis was carried out to correct for the possibility that this difference is a sample size artefact. These results are consistent with the operation of balancing selection on allozymes or on loci in linkage disequilibrium with them. Handling editor: C. Sturmbauer     

What are the determinants of explicit and implicit motor imagery ability in stroke patients?: a controlled study

Abstract

Purpose: The purposes of the study were to (a) investigate both explicit and implicit motor imagery ability (MIA) impairment after stroke, (b) examine predictive effects of clinical characteristics for MIA after stroke.

Materials and Methods: Forty one patients with stroke (PwS) (mean age 59.41?±?10.19?years; %41 female) and 36 healthy participants (mean age 62.47?±?9.29?years; %47 female) completed Chaotic Motor Imagery Assessment-Hand Rotation for implicit MIA and Movement Imagery Questionnaire-3 (MIQ-3) and Box and Block Test (BBT) for explicit MIA. The severity of motor and sensory impairments were determined by the Fugl-Meyer Assessment-Upper Extremity (FMAUE) scores. The Turkish version of Motor Activity Log-28 was used to assess amount of use (AUS) and quality of movement in daily life.

Results: Our results indicated that both implicit and explicit MIA (except kinaesthetic imagery of MIQ-3) in PwS were statistically impaired compared to controls (p?<?0.05). The sensorimotor impairment level, amount of use and movement quality of the affected upper limb were found to be correlated with MIA in various degrees. Total motor scores in FMAUE and AUS were significant predictors of explicit MIA (p?<?0.01). Additionally, explicit MIA scores of stroke subgroups were statistically different between severely and mildly impaired patients, in favour of mildly impaired group (p?<?0.05).

Conclusion: In conclusion, both motor impairment level and amount of daily use of upper extremity were found to be predictive factors for explicit MIA. Further investigation with brain imaging techniques is needed to explore the validity of these findings in establishing MIA.     

Adjustment of incubation according to the threat posed: a further signal of enemy recognition in the Blackcap Sylvia atricapilla?

Nest predation and brood parasitism are costly for nest owners, and natural selection should therefore favour the evolution of parental counterdefences. We addressed the question of whether Blackcaps Sylvia atricapilla change their incubation behaviour in response to various nest intruders and whether this adjustment matches the intensity of mobbing exhibited towards these intruders. Near focal nests, we successively exposed a dummy of a brood parasite, nest predator and an innocuous species. After the parents had responded, we removed the dummy and filmed their incubation. The most aggressive response towards the Common Cuckoo Cuculus canorus and high nest attendance after its disappearance indicated recognition of the brood parasite. Low-intensity response to the Jay Garrulus glandarius, together with reduced subsequent parental care, suggested that Blackcaps perceived it either as less deleterious at the egg stage than the Cuckoo or as a danger to themselves. Almost no aggression towards the Turtle Dove Streptopelia turtur, along with the resumption of incubation after its removal, implied that Blackcaps recognised it as harmless. In addition, we found that the level of aggression positively correlated with nest attendance, suggesting a link between the intensity of mobbing and subsequent parental care. Altogether, our results demonstrate that the issue of enemy recognition may be viewed as a complex of both aggressive and post-presentation behaviours.     

Do levels of income explain differences in game abundance? An empirical test in two Honduran villages

Although researchers have documented the role of anthropogenic huntingpressure on the abundance of game, few have measured the direct effects ofincome or economic development on game abundance. Economic theory tends topredict an ambiguous causal relation between income and the abundance of game.Here we test whether income (a standard proxy of economic development) erodesthe abundance of game in two Tawahka Amerindian villages in the rain forest ofHonduras. The two villages have similar ecologies and weather and lie 17km apart but differ in income, population size, wealth, thepresence of outside institutions, and hunting pressure. A census of animals doneover 2 continuous years suggests that the richer village had less game andrelatively fewer large-bodied animals. At the level of animal groups (e.g.,mammals) or individual species, or when we include controls for the simultaneouseffect of vegetation type, distance from the start of the hunting trail, andtime of the year through a random-effect probit model, the two villages displayno statistically significant differences in game abundance. A random-effect,multivariate tobit model, in fact, suggests that being in the more remotevillage correlated with 43.5% fewer animals seen in any one encounter; resultswere significant at the 99% confidence level. The conclusions contain adiscussion of why income might produce ambiguous effects on game abundance andthe tradeoffs of using bivariate and multivariate techniques to analyze thecovariates of game abundance in the tropical rain forests of the New World.     

Why are there about 5000 species of phytoplankton in the sea?

The relative abundances of phytoplankton taxa conform approximatelyto a finite geometric series in which there are 20–25species per decade of ranked abundance. Such series can contain160–400 species between the commonest (10²²–10²⁶cells) and the rarest (10¹⁰–10¹⁴ cells). Thus, between12 and 31 such series are needed to explain the observed diversity,5x10³ species, of marine phytoplankton. The number of seriesis similar to the number (20–25) of upper-ocean watermasses defined by dilution time scale of order 10¹–10²years. Interpretations of this coincidence are discussed.     

What works in the field? A comparison of different interviewing methods in ethnobotany with special reference to the use of photographs

Ethnobotanists use a variety of interview techniques to collect ethnobotanical data. Drawing upon the results from a quantitative ethnobotanical study in five Yuracaré and Trinitario communities in the Bolivian Amazon, the pros and cons of the following methods are evaluated: (1) interviews in situ during transects, walk-in-the-woods, and homegarden sampling; and (2) interviews ex situ with fresh plant material, voucher specimens, or plant photographs as reference tools. Although the systematic use of plant photographs for ethnobotanical interviews is poorly documented in literature, the results show that indigenoùs participants in our study recognize significantly more plant species from photographs than from voucher specimens. It is argued that, especially in remote and isolated study sites, photographs might be advantageous over voucher specimens.     

Are plant hybrid zones centers of vertebrate biodiversity? A test in the Quercus grisea × Quercus gambelii species complex

The plant-hybrid-zones-as-centers-of-biodiversity (hereafter, PHZCB) hypothesis posits that plant hybrid zones represent areas of elevated biodiversity, and supports the inclusion of plant hybrid zones in conservation efforts. Support for the PHZCB hypothesis is limited to a handful of cases involving insect and fungal species and to two studies involving higher trophic levels. The PHZCB hypothesis requires further testing before plant hybrid zones can be established with any certainty as centers of biodiversity. We test whether the PHZCB hypothesis holds for higher trophic levels by examining the community structure of birds and reptiles associated with the Quercus grisea × Quercus gambelii species complex. Specifically, we compare patterns of species richness and abundance of these taxa in 10 hybrid zones and 11 contact zones (i.e., zones where both parental species occur but hybrids do not). In contrast to predictions of the PHZCB hypothesis, contact zones supported significantly more species of birds and reptiles than did hybrid zones. Species abundances exhibited idiosyncratic responses to zone type, but were higher generally in the contact zones.     

Are most of the domoic acid-producing species of the diatom genus Pseudo-nitzschia cosmopolites?

Records from all oceans, most of them published during 1990–2000, and personal unpublished observations of nine Pseudo-nitzschia taxa known as potential domoic acid (DA) producers have been used to outline their geographical distribution. Pseudo-nitzschia seriata f. seriata as the only taxon was found in the North Atlantic Ocean exclusively. The records of P. multistriata were too few and the identification of P. turgidula from the North Atlantic too unreliable to provide an idea about their distribution. Pseudo-nitzschia pungens and the less frequently recorded P. fraudulenta, P. multiseries and P. australis appeared to be cosmopolites. The wide distribution of the apparently most efficient DA producers, P. australis and P. multiseries, is especially noteworthy. The records of P. delicatissima and P. pseudodelicatissima also indicate a cosmopolitan distribution although with the qualification of certain taxonomic and identification ambiguities. Hence, the question of whether most DA-producing Pseudo-nitzschia species are cosmopolites may be answered with a tentative “yes”.     

What are 60 warblers worth? Killing in the name of conservation

Ecological research sometimes entails animal suffering and even animal killing. The ethical appropriateness of animal suffering and killing in conservation research may entail considerations that differ from many other kinds of research. This is true, insomuch as conservation research is specifically motivated by an ethical premise: an appreciation for non-human life. In striking contrast with other academic fields (e.g. medicine), however, the ethical dimension of conservation research is only rarely discussed. When it is discussed, it tends to be characterized by logical errors. These errors are important because they are general (i.e. both common and with far-reaching implications), and they are easily made by intelligent people; especially those with no formal training in ethics or logic. Failure to recognize these errors could stymie efforts to increase the ethical quality of ecological research conducted in the name of conservation.
We take advantage of a recently published dialogue concerning the ethical appropriateness of a specific field experiment that entailed killing black-throated blue warblers, Dendroica caerulescens . Both sides of this debate exemplify the kinds of errors to which we refer. In this paper we briefly review the arguments presented on each side of this debate, highlight their mistakes, and indicate necessary corrections. We argue that: (1) compliance with animal research regulations, while important, inadequately accommodates the ethical aspects of animal research, and (2) individual ecologists ought to understand themselves what does and does not represent sound and valid arguments for ethical decisions. Finally, we discuss how any ecological researcher might begin to apply our analysis to his or her own research.     

An investigation of the inclusion complex of cyclomaltoheptaose (β-cyclodextrin) with N-methylanthranilic acid in the solid state

A 2:1 complex between cyclomaltoheptaose (β-cyclodextrin) and N-methylanthranilic acid has been studied in the solid state. The inclusion complex belongs to the triclinic system (space group P1) with unit cell dimensions a = 15.2773(15) Å, b = 15.4710(15) Å, c = 17.9627(18) Å, α = 99.632(5)°, β = 113.416(5)°, and γ = 102.818(5)°. The complex forms a head-to-head channel-type structure with the N-methylanthranilic acid lying between the β-cyclodextrin groups in a sandwich fashion, which is held in place by an extensive hydrogen-bonding network between the cyclodextrin molecules.     

Two species of the Rhodiola yunnanensis species complex distributed around the Sichuan Basin of China: Speciation in a ring?

A ring species consists of two reproductively isolated forms connected by a chain of intergrading populations encircling a geographic barrier. The mountains encircling the Sichuan Basin in southwestern China harbor great species diversity and endemism, and they are candidate regions for ring species. Here, we examined a potential ring species complex with a ring distribution surrounding the Sichuan Basinand the reproductive barrier between sibling species Rhodiola yunnanensis and R. henryi of the R. yunnanensis complex. In this study, we test the hypothesis that R. yunnanensis and R. henryi diverged by the ring-species model using an amplicon sequencing strategy targeting the introns of 27 single-copy nuclear genes and 14 chloroplast DNA sequences. Our studies indicated that the R. yunnanensis complex is monophyletic, originates at the late Miocene, and forms its current ring distribution pattern after the LIG. In addition, clear genetic intergradation was not found among R. henryi populations within the distribution ring. All these findings suggest that the divergence of two sibling species was not driven by the geographic isolation, and they were not originated from the ring-species model; however, the basin-surrounding distribution pattern and reproductive barrier between them meet some criteria for being a ring species.