Running with the Red Queen: the role of biotic conflicts in evolution

What are the causes of natural selection? Over 40 years ago, Van Valen proposed the Red Queen hypothesis, which emphasized the primacy of biotic conflict over abiotic forces in driving selection. Species must continually evolve to survive in the face of their evolving enemies, yet on average their fitness remains unchanged. We define three modes of Red Queen coevolution to unify both fluctuating and directional selection within the Red Queen framework. Empirical evidence from natural interspecific antagonisms provides support for each of these modes of coevolution and suggests that they often operate simultaneously. We argue that understanding the evolutionary forces associated with interspecific interactions requires incorporation of a community framework, in which new interactions occur frequently. During their early phases, these newly established interactions are likely to drive fast evolution of both parties. We further argue that a more complete synthesis of Red Queen forces requires incorporation of the evolutionary conflicts within species that arise from sexual reproduction. Reciprocally, taking the Red Queen''s perspective advances our understanding of the evolution of these intraspecific conflicts.     

The impact of environmental change on host-parasite coevolutionary dynamics

Environmental factors are known to affect the strength and the specificity of interactions between hosts and parasites. However, how this shapes patterns of coevolutionary dynamics is not clear. Here, we construct a simple mathematical model to study the effect of environmental change on host-parasite coevolutionary outcome when interactions are of the matching-alleles or the gene-for-gene type. Environmental changes may effectively alter the selective pressure and the level of specialism in the population. Our results suggest that environmental change altering the specificity of selection in antagonistic interactions can produce alternating time windows of cyclical allele-frequency dynamics and cessation thereof. This type of environmental impact can also explain the maintenance of polymorphism in gene-for-gene interactions without costs. Overall, our study points to the potential consequences of environmental variation in coevolution, and thus the importance of characterizing genotype-by-genotype-by-environment interactions in natural host-parasite systems, especially those that change the direction of selection acting between the two species.     

Three-dimensional structure of echistatin and dynamics of the active site

Summary The snake venom protein echistatin contains the cell recognition sequence Arg-Gly-Asp and is a potent inhibitor of platelet aggregation. The three-dimensional structure of echistatin and the dynamics of the active RGD site are presented. A set of structures was determined using the Distance Geometry method and subsequently refined by Molecular Dynamics and energy minimization. Disulfide pairings are suggested, based on violations of experimental constraints. The structures satisfy 230 interresidue distance constraints, derived from nuclear Overhauser effect measurements, five hydrogen-bonding constraints, and 21 torsional constraints from vicinal spin-spin coupling constants. The segment from Gly⁵ to Cys²⁰ and from Asp³⁰ to Asn⁴² has a well-defined conformation and the Arg-Gly-Asp sequence, which adopts a turn-like structure, is located at the apex of a nine-residue loop connecting the two strands of a distorted -sheet. The mobility of the Arg-Gly-Asp site has been quantitatively characterized by ¹⁵N relaxation measurements. The overall correlation time of echistatin was determined from fluorescence measurements, and was used in a model-free analysis to determine internal motional parameters. The active site has order parameters of 0.3–0.5, i.e., among the smallest values ever observed at the active site of a protein. Correlation of the flexible region of the protein as characterized by relaxation experiments and the NMR solution structures was made by calculating generalized order parameters from the ensemble of three-dimensional structures. The motion of the RGD site detected experimentally is more extensive than a simple RGD loop wagging motional model, suggested by an examination of superposed solution structures.     

Membrane localization and dynamics of Nile Red: Effect of cholesterol

The organization and dynamics of the hydrophobic fluorescent probe Nile Red incorporated in DOPC vesicles containing varying amounts of cholesterol has been monitored utilizing fluorescence-based approaches which include the red edge excitation shift (REES) approach and the parallax method for depth determination. Our results show that the fluorescence emission maximum, intensity, polarization, and lifetime of Nile Red vary with the cholesterol content of the membrane. Interestingly, Nile Red exhibits significant REES independent of the presence of cholesterol. This indicates that Nile Red is localized in a motionally restricted environment in the membrane. This is supported by analysis of membrane penetration depth of Nile Red using the parallax method which points out to a membrane interfacial localization of Nile Red. These results could be useful in analyzing membrane organization and heterogeneity in natural membranes using Nile Red.     

The Red Tooth Hypothesis: A computational model of predator-prey relations, protean escape behavior and sexual reproduction

This paper presents an extension of the Red Queen Hypothesis (hereafter, RQH) that we call the Red Tooth Hypothesis (RTH). This hypothesis suggests that predator-prey relations may play a role in the maintenance of sexual reproduction in many higher animals. RTH is based on an interaction between learning on the part of predators and evolution on the part of prey. We present a simple predator-prey computer simulation that illustrates the effects of this interaction. This simulation suggests that the optimal escape strategy from the prey's standpoint would be to have a small number of highly reflexive, largely innate (and, therefore, very fast) escape patterns, but that would also be unlearnable by the predator. One way to achieve this would be for each individual in the prey population to have a small set of hard-wired escape patterns, but which were different for each individual.We argue that polymorphic escape patterns at the population level could be produced via sexual reproduction at little or no evolutionary cost and would be as, or potentially more, efficient than individual-level protean (i.e., random) escape behavior. We further argue that, especially under high predation pressure, sexual recombination would be a more rapid, and therefore more effective, means of producing highly variable escape behaviors at the population level than asexual reproduction.     

An epidemiological model of host–parasite coevolution and sex

The Red Queen hypothesis posits a promising way to explain the widespread existence of sexual reproduction despite the cost of producing males. The essence of the hypothesis is that coevolutionary interactions between hosts and parasites select for the genetic diversification of offspring via cross‐fertilization. Here, I relax a common assumption of many Red Queen models that each host is exposed to one parasite. Instead, I assume that the number of propagules encountered by each host depends on the number of infected hosts in the previous generation, which leads to additional complexities. The results suggest that epidemiological feedbacks, combined with frequency‐dependent selection, could lead to the long‐term persistence of sex under biologically reasonable conditions.     

Coevolution of slow-fast populations: evolutionary sliding, evolutionary pseudo-equilibria and complex Red Queen dynamics

We study the interplay of ecological and evolutionary dynamics in communities composed of populations with contrasting time-scales. In such communities, genetic variation of individual traits can cause population transitions between stationary and cyclic ecological regimes, hence abrupt variations in fitness. Such abrupt variations raise ridges in the adaptive landscape, where the populations are poised between equilibrium and cyclic coexistence and along which evolutionary trajectories can remain sliding for long times or halt at special points called evolutionary pseudo-equilibria. These novel phenomena should be generic to all systems in which ecological interactions cause fitness to vary discontinuously. They are demonstrated by the analysis of a predator-prey community, with one adaptive trait for each population. The eco-evolutionary dynamics of the system show a number of other distinctive features, including evolutionary extinction and two forms of Red Queen dynamics. One of them is characterized by intermittent bouts of cyclic oscillations of the two populations.     

The Red Queen theory of recombination hotspots

Recombination hotspots are small chromosomal regions, where meiotic crossover events happen with high frequency. Recombination is initiated by a double‐strand break (DSB) that requires the intervention of the molecular repair mechanism. The DSB repair mechanism may result in the exchange of homologous chromosomes (crossover) and the conversion of the allelic sequence that breaks into the one that does not break (biased gene conversion). Biased gene conversion results in a transmission advantage for the allele that does not break, thus preventing recombination and rendering recombination hotspots transient. How is it possible that recombination hotspots persist over evolutionary time (maintaining the average chromosomal crossover rate) when they are self‐destructive? This fundamental question is known as the recombination hotspot paradox and has attracted much attention in recent years. Yet, that attention has not translated into a fully satisfactory answer. No existing model adequately explains all aspects of the recombination hotspot paradox. Here, we formulate an intragenomic conflict model resulting in Red Queen dynamics that fully accounts for all empirical observations regarding the molecular mechanisms of recombination hotspots, the nonrandom targeting of the recombination machinery to hotspots and the evolutionary dynamics of hotspot turnover.     

The potential role of chromosome telomere resetting consequent upon sex in the population dynamics of aphids: an hypothesis

Models of population structure have emphasized the importance of sex in maintaining lineages. This is because, despite the well known ‘two‐fold cost of sex’ compared with asex, it is considered that recombination rids the genome of accumulated mutations and increases its potential for adaptive variation. However, asexual lineages of eukaryotic organisms can also rapidly gain genetic variance directly by various mutational processes, thereby proving that so‐called ‘clones’ do not have strict genetic fidelity ( Lushai & Loxdale, 2002 ; Loxdale & Lushai, 2003a ), whereas the variation so produced may well have adaptive advantage during the evolutionary process. This being so, obligated asexuals or cyclical parthenogens that occasionally indulge in sexual recombination (‘rare sex’) cannot be deemed as ‘evolutionary dead‐ends’( Lushai, Loxdale & Allen, 2003a ). In addition, the persistence of asexual lineages (i.e. lineage longevity) may also involve the integrity of the telomere region, the physical end of the chromosomes ( Loxdale & Lushai, 2003b ). In this earlier study on this topic, we argued that the persistence and ultimate senescence of eukaryotic cell lineages (based upon the frequency of ‘capped’ and ‘uncapped’ chromosomes related to telomere functionality; Blackburn, 2000 ) may directly relate to the survival and persistence of lineages of whole asexual organisms. Aphids are a good model system to test this hypothesis because they show a variety of sexual/asexual reproductive strategies, whereas their mode of asexual reproduction is of the mitotic (= apomictic) type. We also suggested that many aphid lineages require occasional or even rare sexual recombination to re‐set telomere length to allow lineages to persist. Ample empirical evidence from diverse taxa, lineages, and different developmental stages now reveals that the telomere states are indeed re‐set by recombination (homologous or meiotic), thereby rejuvenating the lineage in question. The generational clock element of telomeric functionality has also been successfully described in artificially‐induced mammalian clonal systems. It thus appears that telomere function is a central molecular mechanism instigating and promoting lineage continuity per se. By contrast, we hypothesized that other long‐lived asexuals, or the rare category of ancient asexuals such as bdelloid rotifers, have compensatory mechanisms for maintaining chromosome functional integrity, which are somewhat different from conventional telomeric repeats. In the present study, we carry the analogy between eukaryotic cell functionality and aphid lineages a stage further. Here, we hypothesize that the changing frequency of capped and uncapped telomeres, progressing to senescence in a stochastic manner, may be an underlying factor that significantly contributes to population dynamics in asexual lineage evolution. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 90 , 719–728.     

Analyzing the dynamics of emotional scene sequence using recurrent neuro-fuzzy network

In this paper, we propose a new framework to analyze the temporal dynamics of the emotional stimuli. For this framework, both electroencephalography signal and visual information are of great importance. The fusion of visual information with brain signals allows us to capture the users’ emotional state. Thus we adopt previously proposed fuzzy-GIST as emotional feature to summarize the emotional feedback. In order to model the dynamics of the emotional stimuli sequence, we develop a recurrent neuro-fuzzy network for modeling the dynamic events of emotional dimensions including valence and arousal. It can incorporate human expertise by IF-THEN fuzzy rule while recurrent connections allow the fuzzy rules of network to see its own previous output. The results show that such a framework can interact with human subjects and generate arbitrary emotional sequences after learning the dynamics of an emotional sequence with enough number of samples.     

Queen pheromones affecting the production of queen-like secretion in workers

The honeybee queen pheromones promote both worker sterility and worker-like pheromone composition; in their absence workers become fertile and express the queen pheromones. Which of the queen pheromones regulate worker pheromone expression and how, is still elusive. Here we investigated how two queen pheromones, the mandibular and Dufour’s, singly or combined, affect worker ovarian activation and occurrence of queen-like Dufour’s esters. Although queen mandibular pheromone (QMP) alone, or combined with Dufour’s secretion, inhibited to some extent worker reproduction, neither was as effective as the queen. The effect of the queen pheromones on worker pheromone expression was limited to workers with developed ovaries. Here too, QMP and Dufour’s combined had the greatest inhibitory effect. In contrast, treatment with Dufour’s alone resulted in augmentation of esters in the workers. This is another demonstration that a pheromone emitted by one individual affects the rates of its production in another individual. Ester production was tightly coupled to ovarian development. However fertile workers from queenright or QMP-treated colonies had significantly higher amounts of esters in their Dufour’s gland than untreated queenless colonies. The fact that the queen or QMP exert greater suppression on signal production than on ovary activation, suggests disparate regulatory pathways, and presents a challenging ultimate as well as proximate questions.     

Seasonal dynamics of phytoplankton in the Gulf of Aqaba,Red Sea

Seawater samples were collected biweekly from the northern Gulf of Aqaba, Red Sea, for Phytoplankton analysis during the period May 1998 to October 1999. Microscopic counts and HPLC methods were employed. Procaryotic and eucaryotic ultraplankton dominated throughout most of the year, with larger nano- and microplankton making up only 5% of the photosynthetic biomass. Moderate seasonal variations in the 0–125 m integrated Chl a contrasted with a pronounced seasonal succession of the major taxonomic groups, reflecting the changes in the density stratification of the water column: Prochlorococcus dominated during the stratified summer period and were almost absent in winter. Chlorophyceae and Cryptophyceae were dominant during winter mixing but scarce or absent during summer. Diatoms and Synechococcus showed sharp and moderate biomass peaks in late winter and spring respectively, but remained at only low Chl a levels for the rest of the year. Chrysophyceae, Prymnesiophyceae and the scarce Dinophyceae showed no clear seasonal distribution pattern. The implications of alternating procaryotic and eucaryote dominated algal communities for the Red Sea pelagic food web are discussed. Electronic Supplementary Material Electronic supplementary material is available for this article at and accessible for authorised users.     

Bacterial origin of the Red Pigmentation in the devonian Slivenec Limestone, Czech Republic

Summary The deep-red lenses of the Pragian Slivenec Limestone have been extensively quarried for ornamental purposes since the XII^th century. Petrographic microscope observations indicate that the hematite stainings of the limestone follow ten different patterns. They range from massive non-directional filling of cavities to mineralized films and microstromatolites. Numerous ironrich endolithes are observed. Some could be derived from bacterial or lichen perforations and some related to ferric bacteria. Infiltration along welded calcite crystals, regular mineralized films and microstromatolites suggest a ferric bacterial origin for the pigment. This is confirmed by scanning microscope examinations of polished sections, that show hematite concentrations along micrometric filamentous sheaths.     

<Emphasis Type="Italic">Agrobacterium</Emphasis>-mediated genetic transformation of pineapple var. Queen using a novel encapsulation-based antibiotic selection technique

A protocol for Agrobacterium-mediated transformation of a local ‘elite’ Indian variety (Queen) of pineapple [Ananus comosus (L.) Merr, family Bromeliaceae] has been established using a standard transformation vector (pCAMBIA 1304). High transformation efficiency, expressed as the mean percentage of transgenic micro-shoots regenerated from initial callus explants (20.6%) was achieved using a novel encapsulation-based, antibiotic selection procedure. The Agrobacterium-infected micro-shoots derived from callus explants survived selection in high concentration of hygromycin (60 mg l⁻¹ and beyond) in encapsulated alginate beads. The integration of transgene in hygromycin-resistant shoots and plants was confirmed by histochemical GUS assay, PCR amplification and Southern hybridization. It is possible to eliminate false antibiotic positives in pineapple transformation program to a large extent following this procedure.     

Uptake of L-leucine by Trout Red Blood Cells and Peripheral Lymphocytes

The uptake of l-leucine by trout red blood cells and peripheral lymphocytes has been analyzed. The present study shows two functionally different Na⁺-independent systems for apolar branched-chain amino acids. They are designated as L systems because they share some properties with the mammalian L system. The carrier present in red blood cells has low K _m values, is trans-stimulable and not stereospecific for leucine uptake; on the other hand, the system present in lymphocytes is stereospecific for leucine uptake and trans-inhibitable. Both carriers are pH sensitive in a similar fashion at low pHs, but there are important differences at higher pH values (above neutrality). These properties are compared with these of the asc systems previously reported in these cells. Received: 2 June 1995/Revised: 7 March 1996     

笼养红斑羚生态生物学的初步观察

This study presents the results of a demographic analysis of 20 years of birth and death records of red gorals kept at the Shanghai Zoo.The age of the first successful breeding,sex ratio at birth,seasonality of reproduction and mortality rate are presented.The females or males of red goral born in captivity can give their first birth at the age of 2 or 3 separately.The births mainly occurred from May to July and peaked in June.Ratio of females to males at birth was 2.36:1.1 The mortality rate for infants and adults were 23.1% and 11.8%,respectively while there was no sub-adult death recorded during the 20 years period.There was a definite relation between mortality rate and seasons and mainly in July.     

小熊猫妊娠期粪便中孕酮、雌二醇的水平变化

2000年3—8月在成都动物园和成都大熊猫繁育研究基地,用放射免疫分析法测定了6只雌性小熊猫粪样中孕酮（P）和雌二醇（E2）的水平变化,同时对其繁殖行为进行了观察。研究结果表明,交配后的雌体粪样中E2浓度下降至基础水平,P浓度在30d后上升至150ng／g以上;怀孕雌体在妊娠期粪样中P水平在200ng／g以上,P峰值可以达500ng／g以上;假妊娠者粪样中P水平一般不超过150ng／g,P峰值在200ng／g以下;雌体产前半个月孕酮迅速下降,E2缓慢上升,产后P保持在基础水平。这意味着可通过测定粪便中P水平进行早孕诊断、产期预测和真假妊娠判断。根据行为观察和粪样激素分析可知,雌兽妊娠期为123—128d（X=124,N=5）,产仔率为1．8／胎（N=5）。