Effect of habitat quality and phenotypic variation on abundance- and trait-based early warning signals of population collapses

Loss of resilience in population numbers in response to environmental perturbations may be predicted with statistical metrics called early warning signals (EWS) that are derived from abundance time series. These signals, however, have been shown to have limited success, leading to the development of trait-based EWS that are based on information collected from phenotypic traits such as body size. Experimental work assessing the efficacy of EWS under varying ecological and environmental factors are rare. In addition, disentangling how such warning signals are affected under varying ecological and environmental factors is key to their application in biological conservation. Here, we experimentally test how different rates of environmental forcing (i.e. warming) and varying ecological factors (i.e. habitat quality and phenotypic diversity) affected population stability and predictive power of early warning signals of population collapse. We analyzed population density and body size time series data from three phenotypically different populations of a protozoan ciliate Askenasia volvox in two levels of habitat quality subjected to three different treatments of warming (i.e. no warming, fast warming and slow warming). We then evaluated how well abundance- and trait-based EWS predicted population collapses under different levels of phenotypic diversity, habitat quality and warming treatments. Our results suggest that habitat quality and warming treatments had more profound effects than phenotypic diversity had on both population stability and on the performance of abundance-based signals of population collapse. In addition, trait-based EWS generally performed well, were reliable and more robust in forecasting population collapse than abundance-based EWS, regardless of variation in environmental and ecological factors. Our study points towards the development of a predictive framework that includes information from phenotypic traits such as body size as an indicator of loss of resilience of ecological systems in response to environmental perturbations.     

Lineage-Specific Differences in the Amino Acid Substitution Process

In Darwinian evolution, mutations occur approximately at random in a gene, turned into amino acid mutations by the genetic code. Some mutations are fixed to become substitutions and some are eliminated from the population. Partitioning pairs of closely related species with complete genome sequences by average population size of each pair, we looked at the substitution matrices generated for these partitions and compared the substitution patterns between species. We estimated a population genetic model that relates the relative fixation probabilities of different types of mutations to the selective pressure and population size. Parameterizations of the average and distribution of selective pressures for different amino acid substitution types in different population size comparisons were generated with a Bayesian framework. We found that partitions in population size as well as in substitution type are required to explain the substitution data. Selection coefficients were found to decrease with increasingly radical amino acid substitution and with increasing effective population size.To further explore the role of underlying processes in amino acid substitution, we analyzed embryophyte (plant) gene families from TAED (The Adaptive Evolution Database), where solved structures for at least one member exist in the Protein Data Bank. Using PAML, we assigned branches to three categories: strong negative selection, moderate negative selection/neutrality, and positive diversifying selection. Focusing on the first and third categories, we identified sites changing along gene family lineages and observed the spatial patterns of substitution. Selective sweeps were expected to create primary sequence clustering under positive diversifying selection. Co-evolution through direct physical interaction was expected to cause tertiary structural clustering. Under both positive and negative selection, the substitution patterns were found to be nonrandom. Under positive diversifying selection, significant independent signals were found for primary and tertiary sequence clustering, suggesting roles for both selective sweeps and direct physical interaction. Under strong negative selection, the signals were not found to be independent. All together, a complex interplay of population genetic and protein thermodynamics forces is suggested.     

Correlative coherence analysis: variation from intrinsic and extrinsic sources in competing populations

The concept of the correlation between two signals is generalized to the correlative coherence of a set of n signals by introducing a Shannon-Weaver-type measure of the entropy of the normalized eigenvalues of the n-dimensional correlation matrix associated with the set of signals. Properties of this measure are stated for canonical cases. The measure is then used to evaluate which subsets of a particular set of n signals are more or less coherent. This set of signals comprises extrinsic, stochastic resource inputs and the population trajectories obtained from simulations of a discrete time model of competing biological populations driven by these resource inputs. The analysis reveals that, at low levels of competition, the correlative coherence of the combined system of intrinsic population and extrinsic resource variables is relatively low, but increases with increasing variation in the resources. Further, at intermediate and high competition levels, the correlative coherence depends more strongly on competition than entrainment of stochasticity in the extrinsic resource variables. Density dependence has the effect of amplifying variation in noise only when this variation is relatively large. Also, chaotic systems appear to be entrained by sufficiently noisy environmental inputs.     

Intraspecific variability in the “vowel”‐like sounds of beluga whales (Delphinapterus leucas): Intra‐ and interpopulation comparisons

The beluga whale (Delphinapterus leucas) has a rich and complicated vocal repertoire. However, different populations use similar and common types of signals. We studied physical features of one of these types, “vowels,” in three Russian populations: the White Sea population (European North), the Chukotka population (the Bering Sea, Chukotka), and the Okhotsk Sea population (Russian Far East) as well as in four summer aggregations of the White Sea belugas over several years in duration. The pulse repetition rate (PRR) at half of the duration of the signal was measured. We found that the PRR of “vowels” collected in the same summer aggregation during different years is stable in time but varies between locations. The degree of variation corresponds with the geographic distance between different locations. Significant differences were discovered between populations separated by thousands of kilometers, and to a lesser extent, between summer aggregations inhabiting different bays of the White Sea. The variation in PRR between the locations can be caused by the divergence of signals owing to the accumulation of random errors during transmission of these signals from generation to generation, which progressed independently in different summer aggregations and populations.     

A map of recent positive selection in the human genome

The identification of signals of very recent positive selection provides information about the adaptation of modern humans to local conditions. We report here on a genome-wide scan for signals of very recent positive selection in favor of variants that have not yet reached fixation. We describe a new analytical method for scanning single nucleotide polymorphism (SNP) data for signals of recent selection, and apply this to data from the International HapMap Project. In all three continental groups we find widespread signals of recent positive selection. Most signals are region-specific, though a significant excess are shared across groups. Contrary to some earlier low resolution studies that suggested a paucity of recent selection in sub-Saharan Africans, we find that by some measures our strongest signals of selection are from the Yoruba population. Finally, since these signals indicate the existence of genetic variants that have substantially different fitnesses, they must indicate loci that are the source of significant phenotypic variation. Though the relevant phenotypes are generally not known, such loci should be of particular interest in mapping studies of complex traits. For this purpose we have developed a set of SNPs that can be used to tag the strongest ∼250 signals of recent selection in each population.     

Threshold behavior in the initiation of hippocampal population bursts

Hippocampal population discharges such as sharp waves, epileptiform firing, and GDPs recur at long and variable intervals. The mechanisms for their precise timing are not well understood. Here, we show that population bursts in the disinhibited CA3 region are initiated at a threshold level of population firing after recovery from a previous event. Each population discharge follows an active buildup period when synaptic traffic and cell firing increase to threshold levels. Single-cell firing can advance burst onset by increasing population firing to suprathreshold values. Population synchrony is suppressed when threshold frequencies cannot be reached due to reduced cellular excitability or synaptic efficacy. Reducing synaptic strength reveals partially synchronous population bursts that are curtailed by GABA(B)-mediated conductances. Excitatory glutamatergic transmission and delayed GABA(B)-mediated signals have opposing feedback effects on CA3 cell firing and so determine threshold behavior for population synchrony.     

A model for the pulsatile secretion of gonadotropin-releasing hormone from synchronized hypothalamic neurons

Cultured gonadotropin-releasing hormone (GnRH) neurons have been shown to express GnRH receptors. GnRH binding to its receptors activates three types of G-proteins at increasing doses. These G-proteins selectively activate or inhibit GnRH secretion by regulating the intracellular levels of Ca2+ and cAMP. Based on these recent observations, we build a model in which GnRH plays the roles of a feedback regulator and a diffusible synchronizing agent. We show that this GnRH-regulated GnRH-release mechanism is sufficient for generating pulsatile GnRH release. The model reproduces the observed effects of some key drugs that disturb the GnRH pulse generator in specific ways. Simulations of 100 heterogeneous neurons revealed that the synchronization mediated by a common pool of diffusible GnRH is robust. The population can generate synchronized pulsatile signals even when all the individual GnRH neurons oscillate at different amplitudes and peak at different times. These results suggest that the positive and negative effects of the autocrine regulation by GnRH on GnRH neurons are sufficient and robust in generating GnRH pulses.     

Song diversity predicts the viability of fragmented bird populations

In the global scenario of increasing habitat fragmentation, finding appropriate indicators of population viability is a priority for conservation. We explored the potential of learned behaviours, specifically acoustic signals, to predict the persistence over time of fragmented bird populations. We found an association between male song diversity and the annual rate of population change, population productivity and population size, resulting in birds singing poor repertoires in populations more prone to extinction. This is the first demonstration that population viability can be predicted by a cultural trait (acquired via social learning). Our results emphasise that cultural attributes can reflect not only individual-level characteristics, but also the emergent population-level properties. This opens the way to the study of animal cultural diversity in the increasingly common human-altered landscapes.     

密度对不同类型玉米源库关系及产量的调控

通过对不同类型玉米品种在4个不同生态条件下的密度定额试验发现,随着密度的增加,群体库源也随着增加,但两者增加幅度不同,群体库的增加幅度超过群体源的增加幅度。高密度下群体源不足是产量提高的主要限制因素。保证一定总粒数,增加吐丝后干物质积累量,提高成粒率,强源促库是玉米高产的关键。     

QTL Mapping of Wood FT-IR Chemotypes Shows Promise for Improving Biofuel Potential in Short Rotation Coppice Willow (<Emphasis Type="Italic">Salix</Emphasis> spp.)

An increasing interest to convert lignocellulosic biomass into biofuels has highlighted the potential of using willows for this purpose, due to its fast growth in short rotation coppice systems. Here, we use a mapping population of 463 individuals of a cross between Salix viminalis and S. viminalis × S. schwerinii to investigate the genetic background of different wood chemical traits, information of importance for breeding towards different uses of wood. Furthermore, using a subset of the mapping population, the correlation between biogas production and chemical traits was investigated. The phenotyping of wood was carried by Furrier-transformed-Infrared spectrometry (FT-IR) and water content analysis. Quantitative trait loci (QTLs) analysis was used to identify regions in the genome of importance for the phenotypic variation of these chemical traits. We found 27 QTLs for various traits. On linkage group (LG) VI-1, QTLs for signals assigned to G-lignin, lignin, and the S/G ratio were collocated and on LG XIV we found a cluster of QTLs representing signals assigned to lignin, cellulose, hemicellulose, and water. The QTLs explained from 3.4 to 6.9% of the phenotypic variation indicating a quantitative genetic background where many genes influence the traits. For the biogas production, a positive and negative correlation was seen with the signals assigned to acetyl and lignin, respectively. This study represents a first step in the understanding of the genetic background of wood chemical traits for willows, information needed for complementary studies, mapping of important genes, and for breeding of varieties for biofuel production purposes.     

A game theoretical approach to the evolution of structured communication codes

Structured meaning-signal mappings, i.e., mappings that preserve neighborhood relationships by associating similar signals with similar meanings, are advantageous in an environment where signals are corrupted by noise and sub-optimal meaning inferences are rewarded as well. The evolution of these mappings, however, cannot be explained within a traditional language evolutionary game scenario in which individuals meet randomly because the evolutionary dynamics is trapped in local maxima that do not reflect the structure of the meaning and signal spaces. Here we use a simple game theoretical model to show analytically that when individuals adopting the same communication code meet more frequently than individuals using different codes—a result of the spatial organization of the population—then advantageous linguistic innovations can spread and take over the population. In addition, we report results of simulations in which an individual can communicate only with its K nearest neighbors and show that the probability that the lineage of a mutant that uses a more efficient communication code becomes fixed decreases exponentially with increasing K. These findings support the mother tongue hypothesis that human language evolved as a communication system used among kin, especially between mothers and offspring.     

How can automimicry persist when predators can preferentially consume undefended mimics?

It is common for species that possess toxins or other defences to advertise these defences to potential predators using aposematic ("warning") signals. There is increasing evidence that within such species, there are individuals that have reduced or non-existent levels of defence but still signal. This phenomenon (generally called automimicry) has been a challenge to evolutionary biologists because of the need to explain why undefended automimics do not gain such as a fitness advantage by saving the physiological costs of defence that they increase in prevalence within the population, hence making the aposematic signal unreliable. The leading theory is that aposematic signals do not stop all predatory attacks but rather encourage predators to attack cautiously until they have identified the defence level of a specific individual. They can then reject defended individuals and consume the undefended. This theory has recently received strong empirical support, demonstrating that high-accuracy discrimination appears possible. However, this raises a new evolutionary problem: if predators can perfectly discriminate the defended from the undefended and preferentially consume the latter, then how can automimicry persist? Here, we present four different mechanisms that can allow non-trivial levels of automimics to be retained within a population, even in the extreme case where predators can differentiate defended from undefended individuals with 100% accuracy. These involve opportunity costs to the predator of sampling carefully, temporal fluctuation in predation pressure, predation pressure being correlated with the prevalence of automimicry, or developmental or evolutionary constraints on the availability of defence. These mechanisms generate predictions as to the conditions where we would expect aposematically signalling populations to feature automimicry and those where we would not.     

SEXUALLY MONOMORPHIC MATING PREFERENCES CONTRIBUTE TO PREMATING ISOLATION BASED ON SONG IN EUROPEAN GREEN LACEWINGS

When species are in intermediate stages of divergence, complicated patterns of reproductive isolation can arise among males and females of the incipient species. The Chrysoperla carnea group of green lacewings (Neuroptera: Chrysopidae) has recently experienced rapid speciation. They possess sexually monomorphic mating signals that were assumed to be important in mate recognition. Our objective was to compare patterns of reproductive isolation among five European species within the species complex as well as sex differences in mating strategies that contribute to those patterns. The species were in fact reproductively isolated based on mating signals. In addition, different species showed different degrees of responsiveness to conspecific signals, and those species that responded more frequently to conspecific signals were less discriminating against heterospecific signals. This suggests differences in mating strategies among species that may be related to population densities and heterospecific encounter rates. Sexual dimorphism in mating preference was apparent only in C. agilis , whose males were more responsive to all signals and less discriminating against heterospecific signals compared to females. Thus high variance in male quality may be characteristic of C. agilis , but not the remaining four species, whose male versus female mating strategies were similar.     

Fragmentation genetics of rainforest animals: insights from recent studies

Habitat fragmentation is one of the most prominent effects of anthropogenic ecosystem degradation. However, despite the accumulating evidence that anthropogenic habitat fragmentation acts negatively on the dynamics and viability of many species, rainforest fragmentation can occur naturally. The need to disentangle ‘natural’ fragmentation processes from (often) very recent anthropogenic effects poses a methodological challenge in the field of conservation genetics. Additional challenges include sampling schemes that can generate false signals of population size changes or population genetic structure. Finally, limited analytical power often results from restricted sample sizes, numbers of markers, or their informativeness. We reviewed the available literature on the effects of habitat fragmentation in non-aquatic tropical animal species over the last 10 years to ask what has been learned as a result of the increasing attention paid to these methodological issues. Fifty-four studies contained relevant datasets on the question of fragmentation effects in 74 animal species. Primates (n = 18) and passerine birds (n = 17) contributed most species to the survey. Unambiguous signals of fragmentation effects were reported in 33.8 % of species, whereas the remaining species showed either equivocal (36.5 %) or no evidence (29.7 %) of fragmentation effects. Our review further reveals that uneven sampling cannot be ruled out as possible explanation for many of the reported genetic bottleneck signals and genetic structure effects. Based on the reviewed evidence, methodological (e.g. improving sampling schemes, multiple analytical approaches, added value of different markers) and conceptual recommendations offering a better understanding of general and species-specific evolutionary responses to fragmentation are formulated for future studies.     

Evolution of stress response in the face of unreliable environmental signals

Most organisms live in ever-changing environments, and have to cope with a range of different conditions. Often, the set of biological traits that are needed to grow, reproduce, and survive varies between conditions. As a consequence, organisms have evolved sensory systems to detect environmental signals, and to modify the expression of biological traits in response. However, there are limits to the ability of such plastic responses to cope with changing environments. Sometimes, environmental shifts might occur suddenly, and without preceding signals, so that organisms might not have time to react. Other times, signals might be unreliable, causing organisms to prepare themselves for changes that then do not occur. Here, we focus on such unreliable signals that indicate the onset of adverse conditions. We use analytical and individual-based models to investigate the evolution of simple rules that organisms use to decide whether or not to switch to a protective state. We find evolutionary transitions towards organisms that use a combination of random switching and switching in response to the signal. We also observe that, in spatially heterogeneous environments, selection on the switching strategy depends on the composition of the population, and on population size. These results are in line with recent experiments that showed that many unicellular organisms can attain different phenotypic states in a probabilistic manner, and lead to testable predictions about how this could help organisms cope with unreliable signals.     

Pressure-Temperature Analysis of the Stability of the CTL9 Domain Reveals Hidden Intermediates

The observation of two-state unfolding for many small single-domain proteins by denaturants has led to speculation that protein sequences may have evolved to limit the population of partially folded states that could be detrimental to fitness. How such strong cooperativity arises from a multitude of individual interactions is not well understood. Here, we investigate the stability and folding cooperativity of the C-terminal domain of the ribosomal protein L9 in the pressure-temperature plane using site-specific NMR. In contrast to apparent cooperative unfolding detected with denaturant-induced and thermal-induced unfolding experiments and stopped-flow refolding studies at ambient pressure, NMR-detected pressure unfolding revealed significant deviation from two-state behavior, with a core region that was selectively destabilized by increasing temperature. Comparison of pressure-dependent NMR signals from both the folded and unfolded states revealed the population of at least one invisible excited state at atmospheric pressure. The core destabilizing cavity-creating I98A mutation apparently increased the cooperativity of the loss of folded-state peak intensity while also increasing the population of this invisible excited state present at atmospheric pressure. These observations highlight how local stability is subtly modulated by sequence to tune protein conformational landscapes and illustrate the ability of pressure- and temperature-dependent studies to reveal otherwise hidden states.     

A review on directional information in neural signals for brain-machine interfaces

Brain-machine interfaces (BMIs) can be characterized by the technique used to measure brain activity and by the way different brain signals are translated into commands that control an effector. We give an overview of different approaches and focus on a particular BMI approach: the movement of an artificial effector (e.g. arm prosthesis to the right) by those motor cortical signals that control the equivalent movement of a corresponding body part (e.g. arm movement to the right). This approach has been successfully applied in monkeys and humans by accurately extracting parameters of movements from the spiking activity of multiple single-units. Here, we review recent findings showing that analog neuronal population signals, ranging from intracortical local field potentials over epicortical ECoG to non-invasive EEG and MEG, can also be used to decode movement direction and continuous movement trajectories. Therefore, these signals might provide additional or alternative control for this BMI approach, with possible advantages due to reduced invasiveness.     

Your attention please: increasing ambient noise levels elicits a change in communication behaviour in humpback whales (Megaptera novaeangliae)

High background noise is an important obstacle in successful signal detection and perception of an intended acoustic signal. To overcome this problem, many animals modify their acoustic signal by increasing the repetition rate, duration, amplitude or frequency range of the signal. An alternative method to ensure successful signal reception, yet to be tested in animals, involves the use of two different types of signal, where one signal type may enhance the other in periods of high background noise. Humpback whale communication signals comprise two different types: vocal signals, and surface-generated signals such as ‘breaching’ or ‘pectoral slapping’. We found that humpback whales gradually switched from primarily vocal to primarily surface-generated communication in increasing wind speeds and background noise levels, though kept both signal types in their repertoire. Vocal signals have the advantage of having higher information content but may have the disadvantage of loosing this information in a noisy environment. Surface-generated sounds have energy distributed over a greater frequency range and may be less likely to become confused in periods of high wind-generated noise but have less information content when compared with vocal sounds. Therefore, surface-generated sounds may improve detection or enhance the perception of vocal signals in a noisy environment.     

Interpopulational Variations in Sexual Chemical Signals of Iberian Wall Lizards May Allow Maximizing Signal Efficiency under Different Climatic Conditions

Sexual signals used in intraspecific communication are expected to evolve to maximize efficacy under a given climatic condition. Thus, chemical secretions of lizards might evolve in the evolutionary time to ensure that signals are perfectly tuned to local humidity and temperature conditions affecting their volatility and therefore their persistence and transmission through the environment. We tested experimentally whether interpopulational altitudinal differences in chemical composition of femoral gland secretions of male Iberian wall lizards (Podarcis hispanicus) have evolved to maximize efficacy of chemical signals in different environmental conditions. Chemical analyses first showed that the characteristics of chemical signals of male lizards differed between two populations inhabiting environments with different climatic conditions in spite of the fact that these two populations are closely related genetically. We also examined experimentally whether the temporal attenuation of the chemical stimuli depended on simulated climatic conditions. Thus, we used tongue-flick essays to test whether female lizards were able to detect male scent marks maintained under different conditions of temperature and humidity by chemosensory cues alone. Chemosensory tests showed that chemical signals of males had a lower efficacy (i.e. detectability and persistence) when temperature and dryness increase, but that these effects were more detrimental for signals of the highest elevation population, which occupies naturally colder and more humid environments. We suggest that the abiotic environment may cause a selective pressure on the form and expression of sexual chemical signals. Therefore, interpopulational differences in chemical profiles of femoral secretions of male P. hispanicus lizards may reflect adaptation to maximize the efficacy of the chemical signal in different climates.