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Muller's ratchet in random graphs and scale free networks
Get PDFMuller's ratchet is an evolutionary process that has been implicated in the extinction of asexual species, the evolution of mitochondria, the degeneration of the Y chromosome, the evolution of sex and recombination and the evolution of microbes. Here we study the speed of Muller's ratchet in a population subdivided into many small subpopulations connected by migration, and distributed on a network. We compare the speed of the ratchet in two distinct types of topologies: scale free networks and random graphs. The difference between the topologies is noticeable when the average connectivity of the network and the migration rate is large. In this situation we observe that the ratchet clicks faster in scale free networks than in random graphs. So contrary to intuition, scale free networks are more prone to loss of genetic information than random graphs. On the other hand, we show that scale free networks are more robust to the random extinction than random graphs. Since these complex networks have been shown to describe well real-life systems, our results open a framework for studying the evolution of microbes and disease epidemics
BOLITA, an Arabidopsis AP2/ERF-like transcription factor that affects cell expansion and proliferation/differentiation pathways
Get PDFThe BOLITA (BOL) gene, an AP2/ERF transcription factor, was characterized with the help of an activation tag mutant and overexpression lines in Arabidopsis and tobacco. The leaf size of plants overexpressing BOL was smaller than wild type plants due to a reduction in both cell size and cell number. Moreover, severe overexpressors showed ectopic callus formation in roots. Accordingly, global gene expression analysis using the overexpression mutant reflected the alterations in cell proliferation, differentiation and growth through expression changes in RBR, CYCD, and TCP genes, as well as genes involved in cell expansion (i.e. expansins and the actin remodeling factor ADF5). Furthermore, the expression of hormone signaling (i.e. auxin and cytokinin), biosynthesis (i.e. ethylene and jasmonic acid) and regulatory genes was found to be perturbed in bol-D mutant leave
Did Germinal Centers evolve under differential effects of diversity vs affinity?
Get PDFThe classical view on the process of mutation and affinity
maturation that occurs in GCs assumes that their major role is to generate
high affinity levels of serum Abs, as well as a dominant pool of high
affinity memory B cells, through a very efficient selection process. Here
we present a model that considers different types of structures where a
mutation selection process occurs, with the aim at discussing the evolution
of Germinal Center reactions. Based on the results of this model, we
suggest that in addition to affinity maturation, the diversity generated
during the GC reaction may have also been important in the evolution towards
the presently observed highly organized structure of GC in higher
vertebrates
3D complex: a structural classification of protein complexes
No full textMost of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexe
The tragedy of the commons, the public goods dilemma, and the meaning of rivalry and excludability in evolutionary biology
Get PDFProblem: In the study of conflicts, both economists and evolutionary biologists use the
concepts ‘tragedy of the commons’ and ‘public goods dilemma’. What is the relationship
between the economist and evolutionist views of these concepts?
Model features: The economics literature defines the tragedy of the commons and the public
goods dilemma in terms of rivalry and excludability of the good. In contrast, evolutionists
define these conflicts based on fitness functions with two components: individual and group
components of fitness.
Mathematical method: Evolutionary game theory and the calculation of evolutionarily stable
strategy trait values by standard optimization techniques and by replacing slopes of group
phenotype on individual genotype by coefficients of relatedness.
Conclusion: There is a direct relationship between rivalry and the individual component of
fitness and between excludability and the group component of fitness. Moreover, although the
prisoner’s dilemma constitutes a suitable metaphor to analyse both the public goods dilemma
and the tragedy of the commons, it gives the false idea that the two conflicts are symmetric since
they refer to situations in which individuals consume a common resource – tragedy of the
commons – or contribute to a collective action or common good – public goods dilemma.
However, the two situations are clearly not symmetric: from the economical point of view they
differ by rivalry, and from the evolutionary biology point of view the two conflicts differ by the
significance of the within-group competition in the fitness function
Gametophyte interaction and sexual reproduction: how plants make a zygote
Get PDFThe evolutionary success of higher plants relies on a very short gametophytic phase, which underlies the sexual reproduction cycle. Sexual plant reproduction takes place in special organs of the flower: pollen, the male gametophyte, is released from the anthers and then adheres, grows and interacts along various tissues of the female organs, collectively known as the pistil. Finally, it fertilizes the female gametophyte, the embryo sac. Pollen is released as bi or tricellular, highly de-hydrated and presumably containing all the biochemical components and transcripts to germinate. Upon hydration on the female tissues, it develops a cytoplasmic extension, the pollen tube, which is one of the fastest growing cells in nature. Pollen is completely "ready-to-go", but despite this seemingly simple reaction, very complex interactions take place with the female tissues. In higher animals, genetic mechanisms for sex determination establish striking developmental differences between males and females. In contrast, most higher plant species develop both male and female structures within the same flower, allowing self-fertilization. Outcrossing is ensured by self-incompatibility mechanisms, which evolved under precise genetic control, controlling self-recognition and cell-to-cell interaction. Equally important is pollen selection along the female tissues, where interactions between different cell types with inherent signalling properties correspond to check-points to ensure fertilization. Last but not least, pollen-pistil interaction occurs in a way that enables the correct targeting of the pollen tubes to the receptive ovules. In this review, we cover the basic mechanisms underlying sexual plant reproduction, from the structural and cellular determinants, to the most recent genetic advances
Scaling, genetic drift and clonal interference in the extinction pattern of asexual populations
Get PDFWe investigate the dynamics of loss of favorable mutations in an asexual haploid population. In the current work, we consider homogeneous as well as spatially structured population models. We focus our analysis on statistical measurements of the probability distribution of the maximum population size N(sb) achieved by those mutations that have not reached fixation. Our results show a crossover behavior which demonstrates the occurrence of two evolutionary regimes. In the first regime, which takes place for small N(sb) , the probability distribution is described by a power law with characteristic exponent theta(d) =1.8 +/- 0.01. This power law is not influenced by the rate of beneficial mutations. The second regime, which occurs for intermediate to large values of N(sb), has a characteristic exponent theta(c) which increases as the rate of beneficial mutations grows. These results establish where genetic drift and clonal interference become the main underlying mechanism in the extinction of advantageous mutations
Gene family analysis of the Arabidopsis pollen transcriptome reveals biological implications for cell growth, division control and gene expression regulation
Get PDFUpon germination, pollen forms a tube that elongates dramatically through female tissues to reach and fertilize ovules. While
essential for the life cycle of higher plants, the genetic basis underlying most of the process is not well understood. We
previously used a combination of flow cytometry sorting of viable hydrated pollen grains and GeneChip array analysis of onethird
of the Arabidopsis (Arabidopsis thaliana) genome to define a first overview of the pollen transcriptome. We now extend
that study to approximately 80% of the genome of Arabidopsis by using Affymetrix Arabidopsis ATH1 arrays and perform
comparative analysis of gene family and gene ontology representation in the transcriptome of pollen and vegetative tissues.
Pollen grains have a smaller and overall unique transcriptome (6,587 genes expressed) with greater proportions of selectively
expressed (11%) and enriched (26%) genes than any vegetative tissue. Relative gene ontology category representations in
pollen and vegetative tissues reveal a functional skew of the pollen transcriptome toward signaling, vesicle transport, and the
cytoskeleton, suggestive of a commitment to germination and tube growth. Cell cycle analysis reveals an accumulation of G2/Massociated
factors that may play a role in the first mitotic division of the zygote. Despite the relative underrepresentation of
transcription-associated transcripts, nonclassical MADS box genes emerge as a class with putative unique roles in pollen. The
singularity of gene expression control in mature pollen grains is further highlighted by the apparent absence of small RNA
pathway components
The evolution of a conjugative plasmid and its ability to increase bacterial fitness.
Get PDFConjugative plasmids are extra-chromosomal DNA elements that are capable of horizontal transmission and are found in many natural isolated bacteria. Although plasmids may carry beneficial genes to their bacterial host, they may also cause a fitness cost. In this work, we studied the evolution of the R1 plasmid and we found that, in spite of the R1 plasmid conferring an initial cost to its host, after 420 generations the cost disappeared in all five independent evolution experiments. In fact, in two of these five experiments evolved conjugative plasmids actually conferred a fitness advantage to their hosts. Furthermore, the relative fitness of the ancestral clone bearing one of the evolved plasmids is significantly higher than both the plasmid-free ancestral cells and the evolved cells carrying the evolved plasmid. Given that the R1 plasmid may spread among different species of enterobacteria, we wondered what the effect of the evolved plasmid would be inside Salmonella enterica cells. We found that the evolved plasmid is also able to dramatically increase the relative fitness of these cells. Our results suggest that even if general usage of antibiotics is halted, conjugative plasmids that have been selected with antibiotics in previous years can still persist among bacterial populations or even invade new strains