Oh brother,where art thou? A Bayes factor test for recombination with uncertain heritage

Current methods to identify recombination between subtypes of human immunodeficiency virus 1 (HIV-1) fall into a sequential testing trap, in which significance is assessed conditional on parental representative sequences and crossover points (COPs) that maximize the same test statistic. We overcame this shortfall by testing for recombination while inferring parental heritage and COPs using an extended Bayesian multiple change-point model. The model assumes that aligned molecular sequence data consist of an unknown number of contiguous segments that may support alternative topologies or varying evolutionary pressures. We allowed for heterogeneity in the substitution process and specifically tested for intersubtype recombination using Bayes factors. We also developed a new class of priors to assess significance across a wide range of support for recombination in the data. We applied our method to three putative gag gene recombinants. HIV-1 isolate RW024 decisively supported recombination with an inferred parental heritage of AD and a COP 95% Bayesian credible interval of (1,152, 1,178) using the HXB2 numbering scheme. HIV-1 isolate VI557 barely supported recombination. HIV-1 isolate RF decisively rejected recombination as expected, given that the sequence is commonly used as a reference sequence for subtype B. We employed scaled regeneration quantile plots to assess convergence and found this approach convenient to use even for our variable dimensional model parameter space.     

O anus,where art thou? An investigation of ctenostome bryozoans

Ctenostome bryozoans are a small group of approximately 350 currently described species that remain inadequately investigated anatomically. Recently, the importance of soft body morphology of zooids including the digestive tract has become more evident for addressing various biological aspects such as systematic, functional, or phylogenetic analyses. Particularly, the position of the anus shows considerable variation in ctenostomes and in its extreme form can either be at the lophophoral base or at the vestibular wall. However, it has never been analysed in a broader systematic, phylogenetic, or functional context. Hence, the purpose of this study is to assess the distribution of anus position among ctenostomes, analyse whether zooidal or colonial morphology affects anus position, and draw first conclusions on its functional effects. The survey shows that a vestibular anus is ubiquitously present in alcyonidioideans and several, probably closely related, walkerioideans. In other groups such as boring forms, it appears more patchily distributed, or in some currently unassignable genera, such as Monobryozoon, supports a closer relationship to alcyonidioideans. Other zooidal or colonial characters such as tentacle number or zooidal density in the colony do not show a distinct correlation to the position of the anus. It appears that the shift of the anus into a vestibular area occurred once or twice among ctenostomes; the reasons and functional effects remain unknown. Future important aspects of defecation research in bryozoans are discussed.     

O father where art thou? Paternity analyses in a natural population of the haploid–diploid seaweed Chondrus crispus

The link between life history traits and mating systems in diploid organisms has been extensively addressed in the literature, whereas the degree of selfing and/or inbreeding in natural populations of haploid–diploid organisms, in which haploid gametophytes alternate with diploid sporophytes, has been rarely measured. Dioecy has often been used as a proxy for the mating system in these organisms. Yet, dioecy does not prevent the fusion of gametes from male and female gametophytes originating from the same sporophyte. This is likely a common occurrence when spores from the same parent are dispersed in clumps and recruit together. This pattern of clumped spore dispersal has been hypothesized to explain significant heterozygote deficiency in the dioecious haploid–diploid seaweed Chondrus crispus. Fronds and cystocarps (structures in which zygotes are mitotically amplified) were sampled in two 25 m² plots located within a high and a low intertidal zone and genotyped at 5 polymorphic microsatellite loci in order to explore the mating system directly using paternity analyses. Multiple males sired cystocarps on each female, but only one of the 423 paternal genotypes corresponded to a field-sampled gametophyte. Nevertheless, larger kinship coefficients were detected between males siring cystocarps on the same female in comparison with males in the entire population, confirming restricted spermatial and clumped spore dispersal. Such dispersal mechanisms may be a mode of reproductive assurance due to nonmotile gametes associated with putatively reduced effects of inbreeding depression because of the free-living haploid stage in C. crispus.     

Hunter–Gatherer population structure and the evolution of contingent cooperation

Unlike other vertebrates, humans cooperate in large groups with unrelated individuals. Many authors have argued that the evolution of such cooperation has resulted from reciprocity and other forms of contingent cooperation. This argument is not well supported by existing theory. The theory of contingent cooperation in pairs is well developed: reciprocating strategies are stable when common, and can increase when rare as long as population structure leads to modest levels of relatedness. In larger groups, however, it is not clear whether contingent cooperation can increase when rare. Existing work suggests that contingent strategies cannot increase unless relatedness is high, but depends on unrealistic assumptions about the effects of population structure. Here we develop and analyze a model incorporating a two level population structure that captures important features of human hunter–gatherer societies. This model suggests that previous work underestimates the range of conditions under which contingent cooperation can evolve, but also predicts that cooperation will not evolve unless (1) social groups are small, and (2) the relatedness within ethnolinguistic groups is at the high end of the range of empirical estimates.     

Strong reciprocity or strong ferocity? A population genetic view of the evolution of altruistic punishment

Strong reciprocity, defined as a predisposition to help others and to punish those that are not helping, has been proposed as a potent force leading to the evolution of cooperation and altruism. However, the conditions under which strong reciprocity might be favored are not clear. Here we investigate the selective pressure on strong reciprocity by letting both limited dispersal (i.e., spatial structure) and recombination between helping and punishment jointly determine the evolutionary dynamics of strong reciprocity. Our analytical model suggests that when helping and punishment are perfectly linked traits (no recombination occurring between them), strong reciprocity can spread even when the initial frequency of strong reciprocators is close to 0 in the population (i.e., a rare mutant can invade). By contrast, our results indicate that when recombination can occur between helping and punishment (i.e., both traits coevolve) and is stronger than selection, punishment is likely to invade a population of defectors only when it gives a direct fitness benefit to the actor. Overall, our results delineate the conditions under which strong reciprocity is selected for in a spatially structured population and highlight that the forces behind its evolution involves kinship (be it genetic or cultural).     

Skeletons, noise and population growth: the end of an old debate?

Population dynamics models remain largely deterministic, although the presence of random fluctuations in nature is well recognized. This deterministic approach is based on the implicit assumption that systems can be separated into a deterministic part that captures the essential features of the system and a random part that can be neglected. But is it possible, in general, to understand population dynamics without the explicit consideration of random fluctuations? Here, we suggest perhaps not, and argue that the dynamics of many systems are a result of interactions between the deterministic nonlinear skeleton and noise.     

Activation of defence reactions in Solanaceae: where is the specificity?

When a potential pathogen attempts to infect a plant, biochemical and molecular communication takes place and leads to the induction of plant defence mechanisms. In the case of efficient defence, visible symptoms are restricted and the pathogen does not multiply (incompatible interaction); when defence is inefficient, the plant becomes rapidly infected (compatible interaction). During the last 30 years, a growing body of knowledge on plant-pathogen interactions has been gathered, and a large number of studies investigate the induction of various plant defence reactions by pathogens or by pathogen-derived compounds. However, as most papers focus on incompatible interactions, there is still a lack of understanding about the similarities and differences between compatible and incompatible situations. This review targets the question of specificity in Solanaceae-pathogen interactions, by comparing defence patterns in plants challenged with virulent or avirulent pathogens (or with pathogen-associated molecular patterns from these). A special emphasis is made on analysing whether defence reactions in Solanaceae depend primarily on the type of elicitor, on the plant genotype/species, or on the type of interaction (compatible or incompatible).     

Genetic structure of an isolated group of the indigenous population of northern Siberia, the Nganasans (Tavginians) of Ta?mir

Demographic data of genetic interest were studied in presently living population in comparison with preseding generations of Nganasans. Decrease of sex ratio in the whole population has been revealed along with the reduction of reproductive and, possibly, effective size. The number and variance of livebirths per female were 7.29 and 9.86 respectively. Crow' index of the opportunity for selection (I) and its components (Im and If) were estimated. I was found to be 1.17, whereas Im and If--1.56 and 0.18 respectively. Linear pattern of settling in the past as well as the type of migration between adjoining subpopulations depended on culture and economy of arctic reindeer hunters as well as landscape character.     

Oxidative damage, ageing, and life-history evolution: where now?

The idea that resources are limited and animals can maximise fitness by trading costly activities off against one another forms the basis of life-history theory. Although investment in reproduction or growth negatively affects survival, the mechanisms underlying such trade-offs remain obscure. One plausible mechanism is oxidative damage to proteins, lipids, and nucleic acids caused by reactive oxygen species (ROS). Here, we critically evaluate the premise that ROS-induced oxidative damage shapes life history, focussing on birds and mammals, and highlight the importance of ecological studies examining free-living animals within this experimental framework. We conclude by emphasising the value of using multiple assays to determine oxidative protection and damage. We also highlight the importance of using standardised and appropriate protocols, and discuss future research directions.     

Extensin,an underestimated key component of cell wall defence?

BackgroundExtensins are plant cell wall hydroxyproline-rich glycoproteins known to be involved in cell wall reinforcement in higher plants, and in defence against pathogen attacks. The ability of extensins to form intra- and intermolecular cross-links is directly related to their role in cell wall reinforcement. Formation of such cross-links requires appropriate glycosylation and structural conformation of the glycoprotein.ScopeAlthough the role of cell wall components in plant defence has drawn increasing interest over recent years, relatively little focus has been dedicated to extensins. Nevertheless, new insights were recently provided regarding the structure and the role of extensins and their glycosylation in plant–microbe interactions, stimulating an interesting debate from fellow cell wall community experts. We have previously revealed a distinct distribution of extensin epitopes in Arabidopsis thaliana wild-type roots and in mutants impaired in extensin arabinosylation, in response to elicitation with flagellin 22. That study was recently debated in a Commentary by Tan and Mort (Tan L, Mort A. 2020. Extensins at the front line of plant defence. A commentary on: ‘Extensin arabinosylation is involved in root response to elicitors and limits oomycete colonization’. Annals of Botany 125: vii–viii) and several points regarding our results were discussed. As a response, we herein clarify the points raised by Tan and Mort, and update the possible epitope structure recognized by the anti-extensin monoclonal antibodies. We also provide additional data showing differential distribution of LM1 extensin epitopes in roots between a mutant defective in PEROXIDASES 33 and 34 and the wild type, similarly to previous observations from the rra2 mutant defective in extensin arabinosylation. We propose these two peroxidases as potential candidates to specifically catalyse the cross-linking of extensins within the cell wall.ConclusionsExtensins play a major role within the cell wall to ensure root protection. The cross-linking of extensins, which requires correct glycosylation and specific peroxidases, is most likely to result in modulation of cell wall architecture that allows enhanced protection of root cells against invading pathogens. Study of the relationship between extensin glycosylation and their cross-linking is a very promising approach to further understand how the cell wall influences root immunity.     

Morphological variation and population structure on the island of Korčula,Yugoslavia

A comparison of head and body morphology on the ecologically uniform island of Korčula provides a good example of the balance that occurs in microevolution between selective pressures toward homogenization and selective inertia toward heterogeneity. thirty-eight measurements were made from a sample of 471 males and 526 females. Head variables, being more eco-stable than body variables, remain relatively more different between two distinct populations (eastern and western villages) than do the more eco-labile body variables, although both do vary significantly between east and west. The differences apply to both men and women. These east-west contrasts reflect the differential migration of Slavs to the island over the past three centuries, with a new wave of immigrants settling mainly in the east and introducing a new gene pool to the pre-existing Slavic hybrid population which had settled the island in the sixth to the eighth centuries. In addition to the predominant east-west differences in morphology, we also find significant variation between all villages in both head and body variables. We conclude that this is an indication of the considerable reproductive isolation that has persisted between all villages until the post-World War II period. This paper is a part of a study conducted with financial suport from the joint Yugoslav-United States Board for Bilateral Research, as a common Institute for Medical Research and Occupational Health (Zagreb) and Smithsonian Institution (Washington, DC) research, projects JFP-429 and JFP-674.     

Fusion of vacuoles--where are the membranes, and where are the holes?

In the February 8th issue of Cell, Wang et al. report the surprising finding that vacuolar fusion occurs at the periphery of the contact area of the vacuoles and not by the expansion of a central fusion pore. During fusion, a disk of boundary membrane is excised and left behind within the fused vacuoles.     

What changed the demography of an introduced population of an herbivorous lady beetle?

1. The population dynamics of an introduced population of Epilachna niponica (Lewis) (Coleoptera: Coccinellidae) was investigated for a 7-year period following its introduction to a site outside of its natural range. A population from Asiu Experimental Forest was introduced to Kyoto University Botanical Garden, 10 km south of its natural distribution.
2. Arthropod predation was much lower in the introduced than in the source population. As a result of the lower predation in the Botanical Garden, larvae reached densities five times higher than in the Asiu Forest and host plants were frequently defoliated. Food shortage caused larval deaths from starvation and increased dispersal.
3. The density of the introduced population was much more variable than that of the source population. The variation in population density in both the introduced and source populations is limited by density-dependent reduction in fecundity and female survival. However, variation in the introduced population's density was increased due to host plant defoliation that resulted in overcompensating density-dependent mortality. In years with high larval density plants were defoliated and this increased adult mortality during the prehibernation period. Besides, the density-dependent regulatory mechanisms that produce population stability were weaker in the introduced population than in the source population.     

Comparative population genetics of the immunity gene, Relish: is adaptive evolution idiosyncratic?

The frequency of adaptive evolution acting on common loci in distant lineages remains an outstanding question in evolutionary biology. We asked whether the immunity factor, Relish, a gene with a history of directional selection in Drosophila simulans, shows evidence of a similar selective history in other Drosophila species. We found only weak evidence of recurrent adaptive protein evolution at the Relish locus in three sister species pairs, suggesting that this key component of the insect immune system has an idiosyncratic evolutionary history in Drosophila.     

Refuge evolution and the population dynamics of coupled host—parasitoid associations

Summary We have investigated the theoretical consequences of character evolution for the population dynamics of a host—parasitoid interaction, assuming a monophagous parasitoid. In the purely ecological model it is assumed that hosts can escape parasitism by being in absolute refuges. A striking property of this model is a threshold effect in control of the host by the parasitoid, when host density dependence is weak. The approximate criteria for the parasitoid to regulate the host to low densities are (1) that the parasitoid's maximum population growth rate should exceed the host's and (2) that the maximum growth rate of the host in the refuge should be less than unity. We then use this ecological framework as a basis for a model which considers evolutionary changes in quantitative characters influencing the size of the absolute refuge. For each species, an increase in its refuge-determining character comes at a cost to maximum population growth rate. We show that refuge evolution can substantially alter the population dynamics of the purely ecological model, resulting in a number of emergent and sometimes counter-intuitive properties. In general, when the host has a high carrying capacity, systems are polarized either with low or minor refuge and top-down control of the host by the parasitoid or with a refuge and bottom-up control of the host by a combination of its own density dependence and the parasitoid. A particularly tantalizing result is that co-evolutionary dynamics can modify ecologically unstable systems into ones which are either stable or quasi-stable (with bouts of unstable dynamics, punctuating long-term periods of quasi-stable behaviour). We present five quantitative criteria which must all be met for the parasitoid to be the agent responsible for control of the host at a co-evolutionary equilibrium. The apparent stringency of this full set of requirements supports the empirically-based suggestion that monophagous parasitoid-driven systems should be less common in nature than those driven by multiple forms of density dependence. Further, we apply our theory to the question of whether exploiters may harvest their victims at maximum sustainable yields and to the evolutionary stability of biological control. Finally, we present a series of testable predictions of our theory and methods useful for testing them.     

A fluid–structure interaction-based numerical investigation on the evolution of stress,strength and rupture potential of an abdominal aortic aneurysm

An abdominal aortic aneurysm (AAA) is an irreversible dilation of the abdominal artery. Once an aneurysm is detected by doctors, clinical intervention is usually recommended. The interventions involve traditional open surgery repair and endovascular aneurysm repair with a stent graft. Both types of prophylactic procedures are expensive and not without any risk to the patient. It is very difficult to balance the risk of aneurysm repair and the chance of rupture. The reason lies in that the changing trend of characteristic physical quantities with the evolution of AAA and the mechanisms that give rise to it are still not completely clear. In this study, computational 3D patient-specific model for investigating AAA development was established based on computed tomography (CT) images. Results showed that as the aneurysm evolved, peak wall stress and time-averaged wall shear stress distribution patterns changed. The expansion of AAA wall resulted in the increment of peak stress. The AAA wall compliance not only showed different magnitudes at different cross-sections of the aneurismal body, but also changed with the development of the aneurysm. Furthermore, minimum wall strength and rupture potential index during the three stages of AAA evolution were also investigated in detail. This study might provide valuable information on how to further explore the mechanical basis and the rupture potential during AAA evolution, and that it may assist clinical diagnostic procedures and avoid the potential risk of unnecessary surgical intervention.     

Plague dynamics and population genetics of the desert locust: can turnover during recession maintain population genetic structure?

The desert locust (Schistocerca gregaria) undergoes crowding-induced phase transformation from solitary form to gregarious form. The transformations involves changes in behaviour, colour, development, morphometry, fecundity and endocrine physiology. Recession populations of the desert locust exist primarily in the solitary phase as small populations in patchy environments and are prone to extinction because of climatic events. Significant genetic differentiation among recession populations along the Red Sea coast of Eritrea was previously reported. It was hypothesized that despite the mixing effect of recurrent swarms, metapopulation dynamics could have produced genetic divergence among these highly scattered recession populations. A Monte Carlo simulation of the population dynamics of the desert locust in a metapopulation setting, with a realistic range of parameter values clearly demonstrated that this is possible. Population growth was represented by a discrete-time logistic equation. The duration of recessions and swarms was sampled from normal distributions whose means and standard deviations were varied based on reported estimates. An average recession duration of 10 +/- 3 generations and swarm periods half as long but almost twice as variable produced a partitioning of the total genetic variance most similar to that in the empirical study. In conventional metapopulation analysis, whether turnover leads to increased or reduced divergence is dependent on the number of colonists relative to the number of recurrent migrants, and on whether the colonists arise from a single patch or many patches. In the case of locusts, the stochastic boom and bust cycle is the overriding factor. Divergence between patches during recession due to founder effect and recurrent drift is balanced by the high rate of mixing during plagues.