Horizontal gene transfer in plants

Horizontal gene transfer (HGT) describes the transmission of genetic material across species boundaries. HGT often occurs in microbic and eukaryotic genomes. However, the pathways by which HGTs occur in multicellular eukaryotes, especially in plants, are not well understood. We systematically summarized more than ten possible pathways for HGT. The intimate contact which frequently occurs in parasitism, symbiosis, pathogen, epiphyte, entophyte, and grafting interactions could promote HGTs between two species. Besides these direct transfer methods, genes can be exchanged with a vector as a bridge: possible vectors include pollen, fungi, bacteria, viruses, viroids, plasmids, transposons, and insects. HGT, especially when involving horizontal transfer of transposable elements, is recognized as a significant force propelling genomic variation and biological innovation, playing an important functional and evolutionary role in both eukaryotic and prokaryotic genomes. We proposed possible mechanisms by which HGTs can occur, which is useful in understanding the genetic information exchange among distant species or distant cellular components.     

Breaking down the Species Boundaries: Selective Pressures behind Interspecific Communication in Vertebrates

Studying heterospecific communication provides an opportunity to examine the dynamics of cross‐species social behaviour. It allows us to ask questions about the extent to which the transfer of information is adaptive or accidental and provides an empirically tractable context for manipulating relationships. To date, most studies of heterospecific communication have focussed on receivers. However, the selective pressures on signallers can be as important in determining the dynamics of interspecific communication. Here, we propose a simple framework for thinking about cross‐species information transfer, which (i) considers whether information exchange is either accidental or adaptive and (ii) whether it is unidirectional or bidirectional. To clearly classify interactions, it is necessary to quantify all of the payoffs of interspecific communication to both signallers and receivers. This requires accurate characterisation of the currency influenced by cross‐species communication (e.g. weight gain, foraging success, survival). However, quantifying the payoffs may be difficult, because each side may be benefiting via different currencies. To date, studies on heterospecific communication have focussed on only one dimension of a niche (usually antipredator or foraging signals). However, because niches are multidimensional, investigations should incorporate multiple aspects of a species’ niche, to get a better perspective on why we see certain patterns of information use between species.     

Interspecific social learning: novel preference can be acquired from a competing species

Nongenetic transmission of behavioral traits via social learning allows local traditions in humans, and, controversially, in other animals [1-4]. Social learning is usually studied as an intraspecific phenomenon (but see [5-7]). However, other species with some overlap in ecology can be more than merely potential competitors: prior settlement and longer residence can render them preferable sources of information [8]. Socially induced acquisition of choices or preferences capitalizes upon the knowledge of presumably better-informed individuals [9] and should be adaptive under many natural circumstances [10, 11]. Here we show with a field experiment that females of two migrant flycatcher species can acquire a novel, arbitrary preference of competing resident tits for a symbol attached to the nest sites. The experiment demonstrates that such blind acquisition of heterospecific traits can occur in the wild. Even though genetic variation for habitat preferences exists in many taxa [12] and overlap between bird species likely induces costs [13], this result shows that interspecific social learning can cause increased overlap in nest-site preferences. Conventional, negative species interactions push ecological niches of species apart, but the use of competing species as a source of information counters that force and may lead to convergence.     

Interspecific social networks promote information transmission in wild songbirds

Understanding the functional links between social structure and population processes is a central aim of evolutionary ecology. Multiple types of interactions can be represented by networks drawn for the same population, such as kinship, dominance or affiliative networks, but the relative importance of alternative networks in modulating population processes may not be clear. We illustrate this problem, and a solution, by developing a framework for testing the importance of different types of association in facilitating the transmission of information. We apply this framework to experimental data from wild songbirds that form mixed-species flocks, recording the arrival (patch discovery) of individuals to novel foraging sites. We tested whether intraspecific and interspecific social networks predicted the spread of information about novel food sites, and found that both contributed to transmission. The likelihood of acquiring information per unit of connection to knowledgeable individuals increased 22-fold for conspecifics, and 12-fold for heterospecifics. We also found that species varied in how much information they produced, suggesting that some species play a keystone role in winter foraging flocks. More generally, these analyses demonstrate that this method provides a powerful approach, using social networks to quantify the relative transmission rates across different social relationships.     

Lack of evidence for horizontal transfer of the lac operon into Escherichia coli

The idea that Escherichia coli gained the lac operon via horizontal transfer, allowing it to invade a new niche and form a new species, has become a paradigmatic example of bacterial nonpathogenic adaptation and speciation catalyzed by horizontal transfer. Surprisingly, empirical evidence for this event is essentially nonexistent. To see whether horizontal transfer occurred, I compared a phylogeny of 14 Enterobacteriaceae based on two housekeeping genes to a phylogeny of a part of their lac operon. Although several species in this clade appear to have acquired some or all of the operon via horizontal transfer, there is no evidence of horizontal transfer into E. coli. It is not clear whether the horizontal transfer events for which there is evidence were adaptive because those species which have acquired the operon are not thought to live in high lactose environments. I propose that vertical transmission from the common ancestor of the Enterobacteriaceae, with subsequent loss of these genes in many species can explain much of the patchy distribution of lactose use in this clade. Finally, I argue that we need new, well-supported examples of horizontal transfer spurring niche expansion and speciation, particularly in nonpathogenic cases, before we can accept claims that horizontal transfer is a hallmark of bacterial adaptation.     

Vultures acquire information on carcass location from scavenging eagles

Vultures are recognized as the scroungers of the natural world, owing to their ecological role as obligate scavengers. While it is well known that vultures use intraspecific social information as they forage, the possibility of inter-guild social information transfer and the resulting multi-species social dilemmas has not been explored. Here, we use data on arrival times at carcasses to show that such social information transfer occurs, with raptors acting as producers of information and vultures acting as scroungers of information. We develop a game-theoretic model to show that competitive asymmetry, whereby vultures dominate raptors at carcasses, predicts this evolutionary outcome. We support this theoretical prediction using empirical data from competitive interactions at carcasses. Finally, we use an individual-based model to show that these producer–scrounger dynamics lead to vultures being vulnerable to declines in raptor populations. Our results show that social information transfer can lead to important non-trophic interactions among species and highlight important potential links among social evolution, community ecology and conservation biology. With vulture populations suffering global declines, our study underscores the importance of ecosystem-based management for these endangered keystone species.     

Transmission,relatedness, and the evolution of cooperative symbionts

Cooperative interactions between species, termed mutualisms, play a key role in shaping natural ecosystems, economically important agricultural systems, and in influencing human health. Across different mutualisms, there is significant variation in the benefit that hosts receive from their symbionts. Empirical data suggest that transmission mode can help explain this variation: vertical transmission, where symbionts infect their host's offspring, leads to symbionts that provide greater benefits to their hosts than horizontal transmission, where symbionts leave their host and infect other hosts in the population. However, two different theoretical explanations have been given for this pattern: firstly, vertical transmission aligns the fitness interests of hosts and their symbionts; secondly, vertical transmission leads to increased relatedness between symbionts sharing a host, favouring cooperation between symbionts. We used a combination of analytical models and dynamic simulations to tease these factors apart, in order to compare their separate influences and see how they interact. We found that relatedness between symbionts sharing a host, rather than transmission mode per se, was the most important factor driving symbiont cooperation. Transmission mode mattered mainly because it determined relatedness. We also found evolutionary branching throughout much of our simulation, suggesting that a combination of transmission mode and multiplicity of infections could lead to the stable coexistence of different symbiont strategies.     

The architecture of weighted mutualistic networks

Several ecosystem services directly depend on mutualistic interactions. In species rich communities, these interactions can be studied using network theory. Current knowledge of mutualistic networks is based mainly on binary links; however, little is known about the role played by the weights of the interactions between species. What new information can be extracted by analyzing weighted mutualistic networks? In performing an exhaustive analysis of the topological properties of 29 weighted mutualistic networks, our results show that the generalist species, defined as those with a larger number of interactions in a network, also have the strongest interactions. Though most interactions of generalists are with specialists, the strongest interactions occur between generalists. As a result and by defining binary and weighted clustering coefficients for bipartite networks, we demonstrate that generalists form strongly‐interconnected groups of species. The existence of these strong clusters reinforces the idea that generalist species govern the coevolution of the whole community.     

Interactions Between Carnivores in Madagascar and the Risk of Disease Transmission

Introduced carnivores exert considerable pressure on native predators through predation, competition and disease transmission. Recent research shows that exotic carnivores negatively affect the distribution and abundance of the native and endangered carnivores of Madagascar. In this study, we provide information about the frequency and distribution of interactions between exotic (dogs and cats) and native carnivores (Eupleridae) in the Betampona Natural Reserve (BNR), Madagascar, using noninvasive camera trap surveys. Domestic dogs (Canis familiaris) were the most frequently detected carnivore species within the BNR, and we found that indirect interactions between exotic and native carnivores were frequent (n = 236). Indirect interactions were more likely to occur near the research station (incidence rate ratio = 0.91), which may constitute a disease transmission hot spot for carnivores at BNR. The intervals between capture of native and exotic carnivores suggest that there is potential for pathogen transmission between species in BNR. These capture intervals were significantly shorter near the edge of the reserve (P = 0.04). These data could be used to implement biosecurity measures to monitor interactions and prevent disease transmission between species at the domestic animal and wildlife interface.     

Zoonotic Disease Risk and Life-History Traits: Are Reservoirs Fast Life Species?

The relationship between humans, wildlife and disease transmission can be complex and context-dependent, and disease dynamics may be determined by idiosyncratic species. Therefore, an outstanding question is how general is the finding that species with faster life histories are more probable hosts of zoonoses. Ecological knowledge on species, jointly with public health data, can provide relevant information on species that should be targeted for epidemiological surveillance or management. We investigated whether mammal species traits can be good indicators of zoonotic reservoir status in an intensified agricultural region of Argentina. We find support for a relationship between reservoir status and the pace of life syndrome, confirming that fast life histories can be a factor of zoonotic risk. Nonetheless, we observed that for certain zoonosis, reservoirs may display a slow pace of life, suggesting that idiosyncratic interactions can occur. We conclude that applying knowledge from the life history-disease relationship can contribute significantly to disease risk assessment. Such an approach may be especially valuable in the current context of environmental change and agricultural intensification.

     

Potential effects of mixed infections in ticks on transmission dynamics of pathogens: comparative analysis of published records

Ticks are often infected with more than one pathogen, and several field surveys have documented nonrandom levels of coinfection. Levels of coinfection by pathogens in four tick species were analyzed using published infection data. Coinfection patterns of pathogens in field-collected ticks include numerous cases of higher or lower levels of coinfection than would be expected due to chance alone, but the vast majority of these cases can be explained on the basis of vertebrate host associations of the pathogens, without invoking interactions between pathogens within ticks. Nevertheless, some studies have demonstrated antagonistic interactions, and some have suggested potential mutualisms, between pathogens in ticks. Negative or positive interactions between pathogens within ticks can affect pathogen prevalence, and thus transmission patterns. Probabilistic projections suggest that the effect on transmission depends on initial conditions. When the number of tick bites is relatively low (e.g., for ticks biting humans) changes in prevalence in ticks are predicted to have a commensurate effects on pathogen transmission. In contrast, when the number of tick bites is high (e.g., for wild animal hosts) changes in pathogen prevalence in ticks have relatively little effect on levels of transmission to reservoir hosts, and thus on natural transmission cycles.     

What Evidence Is There for the Homology of Protein-Protein Interactions?

The notion that sequence homology implies functional similarity underlies much of computational biology. In the case of protein-protein interactions, an interaction can be inferred between two proteins on the basis that sequence-similar proteins have been observed to interact. The use of transferred interactions is common, but the legitimacy of such inferred interactions is not clear. Here we investigate transferred interactions and whether data incompleteness explains the lack of evidence found for them. Using definitions of homology associated with functional annotation transfer, we estimate that conservation rates of interactions are low even after taking interactome incompleteness into account. For example, at a blastp -value threshold of , we estimate the conservation rate to be about between S. cerevisiae and H. sapiens. Our method also produces estimates of interactome sizes (which are similar to those previously proposed). Using our estimates of interaction conservation we estimate the rate at which protein-protein interactions are lost across species. To our knowledge, this is the first such study based on large-scale data. Previous work has suggested that interactions transferred within species are more reliable than interactions transferred across species. By controlling for factors that are specific to within-species interaction prediction, we propose that the transfer of interactions within species might be less reliable than transfers between species. Protein-protein interactions appear to be very rarely conserved unless very high sequence similarity is observed. Consequently, inferred interactions should be used with care.     

Virus transfer between fingerpads and fomites

Aims: Virus transfer between individuals and fomites is an important route of transmission for both gastrointestinal and respiratory illness. The present study examines how direction of transfer, virus species, time since last handwashing, gender, and titre affect viral transfer between fingerpads and glass. Methods and Results: Six hundred fifty‐six total transfer events, performed by 20 volunteers using MS2, ?X174, and fr indicated 0·23 ± 0·22 (mean and standard deviation) of virus is readily transferred on contact. Virus transfer is significantly influenced by virus species and time since last handwashing. Transfer of fr bacteriophage is significantly higher than both MS2 and ?X174. Virus transfer between surfaces is reduced for recently washed hands. Conclusions: Viruses are readily transferred between skin and surfaces on contact. The fraction of virus transferred is dependent on multiple factors including virus species, recently washing hands, and direction of transfer likely because of surface physicochemical interactions. Significance and Impact of the Study: The study is the first to provide a large data set of virus transfer events describing the central tendency and distribution of fraction virus transferred between fingers and glass. The data set from the study, along with the quantified effect sizes of the factors explored, inform studies examining role of fomites in disease transmission.     

Fitness costs of phoretic nematodes in the burying beetle,Nicrophorus vespilloides

Nicrophorusvespilloides is a social beetle that rears its offspring on decomposing carrion. Wild beetles are frequently associated with two types of macrobial symbionts, mites, and nematodes. Although these organisms are believed to be phoretic commensals that harmlessly use beetles as a means of transfer between carcasses, the role of these symbionts on N. vespilloides fitness is poorly understood. Here, we show that nematodes have significant negative effects on beetle fitness across a range of worm densities and also quantify the density‐dependent transmission of worms between mating individuals and from parents to offspring. Using field‐caught beetles, we provide the first report of a new nematode symbiont in N. vespilloides, most closely related to Rhabditoides regina, and show that worm densities are highly variable across individuals isolated from nature but do not differ between males and females. Next, by inoculating mating females with increasing densities of nematodes, we show that worm infections significantly reduce brood size, larval survival, and larval mass, and also eliminate the trade‐off between brood size and larval mass. Finally, we show that nematodes are efficiently transmitted between mating individuals and from mothers to larvae, directly and indirectly via the carcass, and that worms persist through pupation. These results show that the phoretic nematode R. regina can be highly parasitic to burying beetles but can nevertheless persist because of efficient mechanisms of intersexual and intergenerational transmission. Phoretic species are exceptionally common and may cause significant harm to their hosts, even though they rely on these larger species for transmission to new resources. However, this harm may be inevitable and unavoidable if transmission of phoretic symbionts requires nematode proliferation. It will be important to determine the generality of our results for other phoretic associates of animals. It will equally be important to assess the fitness effects of phoretic species under changing resource conditions and in the field where diverse interspecific interactions may exacerbate or reduce the negative effects of phoresy.     

传粉网络的研究进展:网络的结构和动态

植物与传粉者之间相互作用,构成了复杂的传粉网络。近年来,社会网络分析技术的发展使得复杂生态网络的研究成为可能。从群落水平上研究植物与传粉者之间的互惠关系,为理解群落的结构和动态以及花部特征的演化提供了全新的视角。传粉网络的嵌套结构说明自然界的传粉服务存在冗余,而且是相对泛化的物种主导了传粉。在多年或者多季度的传粉网络中,虽然有很高的物种替换率,但是其网络结构仍然保持相对稳定,说明传粉网络对干扰有很强的抗性。尽管有关网络结构和动态的研究逐渐增多,但传粉网络维持的机制仍不清楚。网络结构可以部分由花部特征与传粉者的匹配来解释,也受到系统发生的制约,影响因素还包括群落构建的时间和物种多样性,以及物种在群落中的位置。开展大尺度群落动态的研究,为探索不同时间尺度、不同物种多样性水平上的传粉网络的生态学意义提供了条件。但已有的研究仍存在不足,比如基于访问观察的网络无法准确衡量传粉者的访问效率和植物间的花粉流动,以及结果受到调查精度区域研究不平衡的制约等。目前的研究只深入到传粉者携带花粉构成成分的水平,传粉者访问植物的网络不能代表植物的整个传粉过程。因此,研究应当更多地深入到物种之间关系对有性生殖的切实影响上。     

Exploring Spatial and Multitype Assemblages of Species Abundances

The ecological theory of the existence of multiple stable states between species, or the spatial heterogeneity of some unobserved environmental factor, supports the idea of multitype interactions between species. These multitype interactions can lead to different assemblages of species abundances. An exploratory tool for the detection of these species assemblages and for their spatial analysis is presented in this article. A two‐stage analysis is proposed. First, a classification into types of species assemblages using only the species abundances at each site, regardless of their spatial location, is performed. The clustering procedure is based on multivariate normal mixtures and provides a measure of the classification uncertainty. Second, some tools for the study of the spatial structure of these types of assemblages are presented. We transfer the classification uncertainty to the spatial analysis of the classes in order to draw more accurate conclusions. This classification and spatial analysis method is used to point out a spatial gradient of infection in a host–pathogen system in the Åland Islands in Finland. It can be a useful preliminary tool for ecological studies involving the spatial distributions of several species.     

Wild robust capuchin monkey interactions with sympatric primates

Primates - Examining interactions among sympatric primate species can provide interesting information about competition, cooperation, and avoidance between those species. Those interactions can be...     

Should models of disease dynamics in herbivorous insects include the effects of variability in host-plant foliage quality?

Interactions between insects and their baculovirus pathogens are often described using simple disease models. Baculoviruses, however, are transmitted when insects consume virus-contaminated foliage, and foliage variability, whether within or between host-plant species, can affect viral infectiousness. Insect-baculovirus interactions may thus be embedded in a tritrophic interaction with the insect's host plant, but disease models include only the host and the pathogen. We tested these models by measuring the transmission of a baculovirus of gypsy moths (Lymantria dispar) on red oak (Quercus rubra) and white oak (Quercus alba) in the field in six experiments over four years. In all experiments, there were only weak effects of host-tree species, and in only one did the best-fitting model include tree species effects. These weak effects of foliage variability on transmission were not due to a lack of foliage variability on viral infectiousness, because when larvae were force-fed virus-contaminated foliage, infection rates were higher on white oak. Our results suggest that feeding behavior plays an important role in baculovirus transmission and that models can usefully describe baculovirus dynamics even without including foliage variability. Our work provides a clear example of how two-species models are sometimes sufficient to describe what appear to be tritrophic interactions.     

Horizontal transfer of bacterial symbionts: heritability and fitness effects in a novel aphid host

Members of several bacterial lineages are known only as symbionts of insects and move among hosts through maternal transmission. Such vertical transfer promotes strong fidelity within these associations, favoring the evolution of microbially mediated effects that improve host fitness. However, phylogenetic evidence indicates occasional horizontal transfer among different insect species, suggesting that some microbial symbionts retain a generalized ability to infect multiple hosts. Here we examine the abilities of three vertically transmitted bacteria from the Gammaproteobacteria to infect and spread within a novel host species, the pea aphid, Acyrthosiphon pisum. Using microinjection, we transferred symbionts from three species of natural aphid hosts into a common host background, comparing transmission efficiencies between novel symbionts and those naturally infecting A. pisum. We also examined the fitness effects of two novel symbionts to determine whether they should persist under natural selection acting at the host level. Our results reveal that these heritable bacteria vary in their capacities to utilize A. pisum as a host. One of three novel symbionts failed to undergo efficient maternal transmission in A. pisum, and one of the two efficiently transmitted bacteria depressed aphid growth rates. Although these findings reveal that negative fitness effects and low transmission efficiency can prevent the establishment of a new infection following horizontal transmission, they also indicate that some symbionts can overcome these obstacles, accounting for their widespread distributions across aphids and related insects.     

Close encounters: contact-dependent interactions in bacteria

Bacterial cells interact extensively within and between species. These interactions can be divided into those that rely on diffusible factors and those that depend on direct cell-to-cell contacts. An example of a contact-dependent interaction is the transfer of lipoproteins between Myxococcus xanthus cells that leads to transient stimulation of motility in certain motility mutants. In this issue of Molecular Microbiology, Wei et al. (2011) provide mechanistic insights into this contact-dependent transfer of lipoproteins. Briefly, a heterologous protein fused to a type II (lipoprotein) signal sequence that targets the protein to the outer membrane is required and sufficient for transfer. Moreover, evidence is provided that transfer may depend on specific contacts between donor and recipient cells. The data demonstrate that lipoprotein transfer in M. xanthus is not restricted to a few odd motility proteins but could be a wide-spread phenomenon in M. xanthus and possibly other bacteria. Recent years have been fruitful in identifying contact-dependent interactions between bacterial cells. These interactions can be grouped into those that involve delivery of cargo to a recipient and those that seem to be involved in cell-to-cell signalling. Several contact-dependent interactions involve widely conserved proteins, suggesting that cell contact-dependent processes may be widespread among bacteria.