Multiple origins and nrDNA internal transcribed spacer homeologue evolution in the Glycine tomentella (Leguminosae) allopolyploid complex

Despite the importance of polyploidy in the evolution of plants, patterns of molecular evolution and genomic interactions following polyploidy are not well understood. Nuclear ribosomal DNA is particularly complex with respect to these genomic interactions. The composition of nrDNA tandem arrays is influenced by intra- and interlocus concerted evolution and their expression is characterized by patterns such as nucleolar dominance. To understand these complex interactions it is important to study them in diverse natural polyploid systems. In this study we use direct sequencing to isolate and characterize nrDNA internal transcribed spacer (ITS) homeologues from multiple accessions of six different races in the Glycine tomentella allopolyploid complex. The results indicate that in most allopolyploid accessions both homeologous nrDNA repeats are present, but that there are significant biases in copy number toward one homeologue, possibly resulting from interlocus concerted evolution. The predominant homeologue often differs between races and between accessions within a race. A phylogenetic analysis of ITS sequences provides evidence for multiple origins in several of the polyploid races. This evidence for diverse patterns of nrDNA molecular evolution and multiple origins of polyploid races will provide a useful system for future studies of natural variation in patterns of nrDNA expression.     

Teaching evolution using a card game: negative frequency-dependent selection

Teaching biological evolution can be difficult on a number of levels, be it student confusion arising from prior conceptions and the controversy surrounding evolution, or simply because the material is complex. Games and simulations can help to convey complex topics and also to increase variety in teaching methods. Here I describe a card game that can be used to teach the advanced topic of protected polymorphism in higher education settings. Protected polymorphism is allelic variation resulting from negative frequency-dependent selection; when the fitness of an allele increases when it becomes rare, the allele will be ‘protected’ from extinction. Negative frequency-dependent selection is proposed to maintain genetic variation in nature, which is required for evolution by natural selection. Protected polymorphisms primarily play a role in biological interactions, such as immune systems, plant-pathogen interactions, sexual selection and predator-prey interactions. The card game described here uses plant pollination alleles as an example. The game is played using eleven stocks of traditional playing cards per group of about six students. Specific topics addressed include negative frequency-dependent selection, polyploidy, dominance, selfing and inbreeding depression.     

A graph model for the evolution of specificity in humoral immunity

The immune system protects the body against health-threatening entities, known as antigens, through very complex interactions involving the antigens and the system's own entities. One remarkable feature resulting from such interactions is the immune system's ability to improve its capability to fight antigens commonly found in the individual's environment. This adaptation process is called the evolution of specificity. In this paper, we introduce a new mathematical model for the evolution of specificity in humoral immunity, based on Jerne's functional, or idiotypic, network. The evolution of specificity is modeled as the dynamic updating of connection weights in a dynamic graph whose nodes are related to the network's idiotypes. At the core of this weight-updating mechanism are the increase in specificity caused by clonal selection and the decrease in specificity due to the insertion of uncorrelated idiotypes by the bone marrow. As we demonstrate through numerous computer experiments, for appropriate choices of parameters the new model correctly reproduces, in qualitative terms, several immune functions.     

Evolution of acoustically vaporized microdroplets in gas embolotherapy

Acoustic vaporization dynamics of a superheated dodecafluoropentane (DDFP) microdroplet inside a microtube and the resulting bubble evolution is investigated in the present work. This work is motivated by a developmental gas embolotherapy technique that is intended to treat cancers by infarcting tumors using gas bubbles. A combined theoretical and computational approach is utilized and compared with the experiments to understand the evolution process and to estimate the resulting stress distribution associated with vaporization event. The transient bubble growth is first studied by ultra-high speed imaging and then theoretical and computational modeling is used to predict the entire bubble evolution process. The evolution process consists of three regimes: an initial linear rapid spherical growth followed by a linear compressed oval shaped growth and finally a slow asymptotic nonlinear spherical bubble growth. Although the droplets are small compared to the tube diameter, the bubble evolution is influenced by the tube wall. The final bubble radius is found to scale linearly with the initial droplet radius and is approximately five times the initial droplet radius. A short pressure pulse with amplitude almost twice as that of ambient conditions is observed. The width of this pressure pulse increases with increasing droplet size whereas the amplitude is weakly dependent. Although the rise in shear stress along the tube wall is found to be under peak physiological limits, the shear stress amplitude is found to be more prominently influenced by the initial droplet size. The role of viscous dissipation along the tube wall and ambient bulk fluid pressure is found to be significant in bubble evolution dynamics.     

Molecular evolution of growth hormone gene family in old world monkeys and hominoids

Growth hormone is a classic molecule in the study of the molecular clock hypothesis as it exhibits a relatively constant rate of evolution in most mammalian orders except primates and artiodactyls, where dramatically enhanced rate of evolution (25–50-fold) has been reported. The rapid evolution of primate growth hormone occurred after the divergence of tarsiers and simians, but before the separation of old world monkeys (OWM) from new world monkeys (NWM). Interestingly, this event of rapid sequence evolution coincided with multiple duplications of the growth hormone gene, suggesting gene duplication as a possible cause of the accelerated sequence evolution. Here we determined 21 different GH-like sequences from four species of OWM and hominoids. Combining with published sequences from OWM and hominoids, our analysis demonstrates that multiple gene duplications and several gene conversion events both occurred in the evolutionary history of this gene family in OWM/hominoids. The episode of recent duplications of CSH-like genes in gibbon is accompanied with rapid sequence evolution likely resulting from relaxation of purifying selection. GHN genes in both hominoids and OWM are under strong purifying selection. In contrast, CSH genes in both lineages are probably not. GHV genes in OWM and hominoids evolved at different evolutionary rates and underwent different selective constraints. Our results disclosed the complex history of the primate growth hormone gene family and raised intriguing questions on the consequences of these evolutionary events.     

Evolution of reduced dispersal mortality and 'fat-tailed' dispersal kernels in autocorrelated landscapes

Models describing the evolution of dispersal strategies have mostly focused on the evolution of dispersal rates. Taking trees as a model for organisms with undirected, passive dispersal, we have developed an individual-based, spatially explicit simulation tool to investigate the evolution of the dispersal kernel, P(r), and its resulting cumulative seed-density distribution, D(r). Simulations were run on a variety of fractal landscapes differing in the fraction of suitable habitat and the spatial autocorrelation. Starting from a uniform D(r), evolution led to an increase in the fraction of seeds staying in the home cell, a reduction of the dispersal mortality (arrival in unsuitable habitat), and the evolution of 'fat-tailed' D(r) in autocorrelated landscapes and approximately uniform D(r) in random landscapes. The evolutionary process was characterized by long periods of stasis with a few bouts of rapid change in the dispersal rate.     

The evolution of self-fertilization in density-regulated populations

The evolution of selfing in hermaphrodites has been studied to reveal the demographic conditions that lead to intermediate selfing rates. Using a demographic model based on Ricker-type density regulation, we assume first that, independent of population density, inbred individuals survive less well than outbred individuals and second, that inbred and outbred individuals differ in their competitive abilities in density-regulated populations. The evolution of selfing, driven by inbreeding depression and the cost of outcrossing, is then analysed for three fundamentally different demographic scenarios: stable population densities, deterministically varying population densities (resulting from cyclical or chaotic population dynamics) and stochastic fluctuations of carrying capacities (resulting from environmental noise). We show that even under stable demographic conditions evolutionary outcomes are not confined to either complete selfing or full outcrossing. Instead, intermediate selfing rates arise under a wide range of conditions, depending on the nature of competitive interactions between inbred and outbred individuals. We also explore the evolution of selfing under deterministic and stochastic density fluctuations to demonstrate that such environmental conditions can evolutionarily stabilize intermediate selfing rates. This is the first study, to our knowledge, to consider in detail the effect of density regulation on the evolution of selfing rates.     

Constraints on Viral Evolution during Chronic Hepatitis C Virus Infection Arising from a Common-Source Exposure

Extraordinary viral sequence diversity and rapid viral genetic evolution are hallmarks of hepatitis C virus (HCV) infection. Viral sequence evolution has previously been shown to mediate escape from cytotoxic T-lymphocyte (CTL) and neutralizing antibody responses in acute HCV infection. HCV evolution continues during chronic infection, but the pressures driving these changes are poorly defined. We analyzed plasma virus sequence evolution in 5.2-kb hemigenomes from multiple longitudinal time points isolated from individuals in the Irish anti-D cohort, who were infected with HCV from a common source in 1977 to 1978. We found phylogenetically distinct quasispecies populations at different plasma time points isolated late in chronic infection, suggesting ongoing viral evolution and quasispecies replacement over time. We saw evidence of early pressure driving net evolution away from a computationally reconstructed common ancestor, known as Bole1b, in predicted CTL epitopes and E1E2, with balanced evolution toward and away from the Bole1b amino acid sequence in the remainder of the genome. Late in chronic infection, the rate of evolution toward the Bole1b sequence increased, resulting in net neutral evolution relative to Bole1b across the entire 5.2-kb hemigenome. Surprisingly, even late in chronic infection, net amino acid evolution away from the infecting inoculum sequence still could be observed. These data suggest that, late in chronic infection, ongoing HCV evolution is not random genetic drift but rather the product of strong pressure toward a common ancestor and concurrent net ongoing evolution away from the inoculum virus sequence, likely balancing replicative fitness and ongoing immune escape.     

Finite volume and asymptotic methods for stochastic neuron models with correlated inputs

We consider a pair of stochastic integrate and fire neurons receiving correlated stochastic inputs. The evolution of this system can be described by the corresponding Fokker?CPlanck equation with non-trivial boundary conditions resulting from the refractory period and firing threshold. We propose a finite volume method that is orders of magnitude faster than the Monte Carlo methods traditionally used to model such systems. The resulting numerical approximations are proved to be accurate, nonnegative and integrate to 1. We also approximate the transient evolution of the system using an Ornstein?CUhlenbeck process, and use the result to examine the properties of the joint output of cell pairs. The results suggests that the joint output of a cell pair is most sensitive to changes in input variance, and less sensitive to changes in input mean and correlation.     

Ploidy of the eusocial beetle Austroplatypus incompertus (Schedl) (Coleoptera, Curculionidae) and implications for the evolution of eusociality

In the hymenopterans, haplodiploidy, leading to high-genetic relatedness amongst full sisters has been regarded as critical to kin selection and inclusive fitness hypotheses that explain the evolution of eusociality and altruistic behaviours. Recent evidence for independent origins of eusociality in phylogenetically diverse taxa has led to the controversy regarding the general importance of relatedness to eusociality and its evolution. Here, we developed a highly polymorphic microsatellite marker to test whether the eusocial ambrosia beetle Austroplatypus incompertus (Schedl) is haplodiploid or diplodiploid. We found that both males and females of A. incompertus are diploid, signifying that altruistic behaviour resulting from relatedness asymmetries did not play a role in the evolution of eusocialty in this species. This provides additional evidence against the haplodiploidy hypothesis and implicates alternative hypotheses for the evolution of eusociality.     

Early post-metamorphic,Carboniferous blastoid reveals the evolution and development of the digestive system in echinoderms

Inferring the development of the earliest echinoderms is critical to uncovering the evolutionary assembly of the phylum-level body plan but has long proven problematic because early ontogenetic stages are rarely preserved as fossils. Here, we use synchrotron tomography to describe a new early post-metamorphic blastoid echinoderm from the Carboniferous (approx. 323 Ma) of China. The resulting three-dimensional reconstruction reveals a U-shaped tubular structure in the fossil interior, which is interpreted as the digestive tract. Comparisons with the developing gut of modern crinoids demonstrate that crinoids are an imperfect analogue for many extinct groups. Furthermore, consideration of our findings in a phylogenetic context allows us to reconstruct the evolution and development of the digestive system in echinoderms more broadly; there was a transition from a straight to a simple curved gut early in the phylum''s evolution, but additional loops and coils of the digestive tract (as seen in crinoids) were not acquired until much later.     

Evolution of development type in benthic octopuses: holobenthic or pelago-benthic ancestor?

Octopuses of the family Octopodidae are singular among cephalopods in their reproductive behavior, showing two major reproductive strategies: the first is the production of few and large eggs resulting in well-developed benthic hatchlings (holobenthic life history); the second strategy is the production of numerous small eggs resulting in free-swimming planktonic hatchlings (pelago-benthic life history). Here, we utilize a Bayesian-based phylogenetic comparative method using a robust molecular phylogeny of 59 octopus species to reconstruct the ancestral states of development type in benthic octopuses, through the estimation of the most recent common ancestors and the rate of gain and loss in complexity (i.e., planktonic larvae) during the evolution. We found a high probability that a free-swimming hatchling was the ancestral state in benthic octopuses, and a similar rate of gain and loss of planktonic larvae through evolution. These results suggest that in benthic octopuses the holobenthic strategy has evolved from an ancestral pelago-benthic life history. During evolution, the paralarval stage was reduced to well-developed benthic hatchlings, which supports a “larva-first” hypothesis. We propose that the origin of the holobenthic life history in benthic octopuses is associated with colonization of cold and deep sea waters.     

The island rule in large mammals: paleontology meets ecology

The island rule is the phenomenon of the miniaturization of large animals and the gigantism of small animals on islands, with mammals providing the classic case studies. Several explanations for this pattern have been suggested, and departures from the predictions of this rule are common among mammals of differing body size, trophic habits, and phylogenetic affinities. Here we offer a new explanation for the evolution of body size of large insular mammals, using evidence from both living and fossil island faunal assemblages. We demonstrate that the extent of dwarfism in ungulates depends on the existence of competitors and, to a lesser extent, on the presence of predators. In contrast, competition and predation have little or no effect on insular carnivore body size, which is influenced by the nature of the resource base. We suggest dwarfism in large herbivores is an outcome of the fitness increase resulting from the acceleration of reproduction in low-mortality environments. Carnivore size is dependent on the abundance and size of their prey. Size evolution of large mammals in different trophic levels has different underlying mechanisms, resulting in different patterns. Absolute body size may be only an indirect predictor of size evolution, with ecological interactions playing a major role.     

Rapid proliferation of daughter cells lacking particular chromosomes due to multipolar mitosis promotes clonal evolution in colorectal cancer cells

Aneuploidy and chromosome instability (CIN) are hallmarks of the vast majority of solid tumors. However, the origins of aneuploid cells are unknown. The aim of this study is to improve our understanding of how aneuploidy and/or CIN arise and of karyotype evolution in cancer cells. By using fluorescence in situ hybridization (FISH) on cells after long-term live cell imaging, we demonstrated that most (> 90%) of the newly generated aneuploid cells resulted from multipolar divisions. Multipolar division occurred in mononucleated and binucleated parental cells, resulting in variation of chromosome compositions in daughter cells. These karyotypes can have the same chromosome number as their mother clone or lack a copy of certain chromosomes. Interestingly, daughter cells that lost a chromosome were observed to survive and form clones with shorter cell cycle duration. In our model of cancer cell evolution, the rapid proliferation of daughter cells from multipolar mitosis promotes colonal evolution in colorectal cancer cells.     

Developmental plasticity and disparity in early dipnoan (lungfish) dentitions

Although the lungfish (Dipnoi) belong within the Osteichthyes, their dentitions are radically different from other osteichthyans. Lungfish dentitions also show a uniquely high structural disparity during the early evolution of the group, partly owing to the independent variation of odontogenic and odontoclastic processes that are tightly and stereotypically coordinated in other osteichthyans. We present a phylogenetic analysis of early lungfishes incorporating a novel approach to coding these process characters in preference to the resultant adult dental morphology. The results only partially resolve the interrelationships of Devonian dipnoans, but show that the widely discussed hypothesis of separate tooth-plated, dentine-plated, and denticulated lineages is unlikely to be true. The dipnoan status of Diabolepis is corroborated. Lungfish dentitions seem to have undergone extensive and nonparsimonious evolution during the early history of the group, but much of the resulting disparity can be explained by a modest number of evolutionary steps in the underlying developmental processes, those for dental formation (odontogenic) and those for the remodeling of dentine tissue (odontoclastic). Later in lungfish evolution, this disparity was lost as the group settled to a pattern of dental development that is just as stereotypic as, but completely different from, that of other osteichthyans.     

ESSs with two types of players II (intra- and interspecific competition between haploid species)

The investigation of strategy evolution resulting from animal behavior is continued using a new approach to multispecies evolutionary games. A different interpretation of the known result that contestants in asymetrical games choose pure strategies is proven. This leads to a classification of all evolutionarily stable strategies (ESS) when there is no selection from interspecific competitions. In case the dimension of the strategy space is restricted as in a diallelic haploid model, the phase portrait of the evolutionary dynamics is illustrated. The results are then compared with the previous approach and to models of sex dependent selection in randomly mating diploid species.     

The evolutionary origin of Xanthomonadales genomes and the nature of the horizontal gene transfer process

Determining the influence of horizontal gene transfer (HGT) on phylogenomic analyses and the retrieval of a tree of life is relevant for our understanding of microbial genome evolution. It is particularly difficult to differentiate between phylogenetic incongruence due to noise and that resulting from HGT. We have performed a large-scale, detailed evolutionary analysis of the different phylogenetic signals present in the genomes of Xanthomonadales, a group of Proteobacteria. We show that the presence of phylogenetic noise is not an obstacle to infer past and present HGTs during their evolution. The scenario derived from this analysis and other recently published reports reflect the confounding effects on bacterial phylogenomics of past and present HGT. Although transfers between closely related species are difficult to detect in genome-scale phylogenetic analyses, past transfers to the ancestor of extant groups appear as conflicting signals that occasionally might make impossible to determine the evolutionary origin of the whole genome.     

Convergence, adaptation, and constraint

Convergent evolution of similar phenotypic features in similar environmental contexts has long been taken as evidence of adaptation. Nonetheless, recent conceptual and empirical developments in many fields have led to a proliferation of ideas about the relationship between convergence and adaptation. Despite criticism from some systematically minded biologists, I reaffirm that convergence in taxa occupying similar selective environments often is the result of natural selection. However, convergent evolution of a trait in a particular environment can occur for reasons other than selection on that trait in that environment, and species can respond to similar selective pressures by evolving nonconvergent adaptations. For these reasons, studies of convergence should be coupled with other methods-such as direct measurements of selection or investigations of the functional correlates of trait evolution-to test hypotheses of adaptation. The independent acquisition of similar phenotypes by the same genetic or developmental pathway has been suggested as evidence of constraints on adaptation, a view widely repeated as genomic studies have documented phenotypic convergence resulting from change in the same genes, sometimes even by the same mutation. Contrary to some claims, convergence by changes in the same genes is not necessarily evidence of constraint, but rather suggests hypotheses that can test the relative roles of constraint and selection in directing phenotypic evolution.     

The evolution of insect/vertebrate associations

The evolution of close vertebrate associations has occurred in seven orders of insects, resulting in a great diversity of interactions which range from commensalism to true parasitism. The evolution of each taxon of vertebrate associates is discussed in turn, some new ideas on the development of certain groups are presented and, on a broader scale, a general model for the evolution of ectoparasitic insects is proposed. It argues that all vertebrate associates have evolved along one of two macroevolutionary pathways which differ only in the sequencing of adaptations facilitating host association and host feeding. These pathways lead to parasite types which differ greatly in their life history and intimacy of host association.
Some microevolutionary processes influencing the diversification of ectoparasites are discussed, in particular the process of insect/vertebrate coevolution and the forms this may take. Host specificity, one consequence of coevolution, is recognised as an important factor influencing the structure of ectoparasite communities, and a hypothesis is presented that competition between ectoparasite species, mediated by host defensive responses, is also important in determining community structure.