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Trends in Evolutionary Biology

Female-biased sex ratios occur in many insect species as a consequence of infection by maternally-inherited male-killing bacterial endosymbionts. In this paper, we revise the research conducted on the phenomenon of male-killing in African nymphalid butterflies, with special focus on the cases of Danaus chrysippus, Acraea encedon and Acraea encedana. The evolution of male-killing in each case was addressed, together with the phylogeny of male-killers that were identified from this group. Moreover, the potential impacts that male-killers might impose on the evolution of their butterfly hosts were thoroughly investigated. In the end of this review, we present a number of unanswered questions to be targeted by future research work on the male-killing in these butterflies. 2013/04/08 - 21:31

Alternative splicing, allowing multiple mRNAs to be generated from a single gene, is a major source of proteome diversity in eukaryotes. Intron retention (IR), one type of alternative splicing, is the complete retention of an intron in a mature transcript. IR is believed to be associated with failure of the recognition of weak splice sites flanking introns. Mutations in DNA sequences, including point mutations and sequence insertions or deletions, can be at the origin and evolution of IR. The strength of weaker splice sites is the main cause of IR, but some cis-regulatory elements and trans-regulatory factors can also play crucial roles in regulating IR. IR can result in the regulation of gene expression and may contribute to increase protein diversity. IR has been shown to occur in a variety of diseases, and it frequently leads to aberrant splicing. 2013/03/08 - 08:26

The unifying principle in almost all of bioinformatics is sequence analysis: no matter if you are predicting the structure of proteins, analyzing the genetic variation in a population, or deciphering the evolutionary history of your favorite gene, your analysis hinges on looking at biological sequences and how they change over time, between species, or from gene to gene. Biological sequence analysis is the cornerstone. 2012/11/19 - 18:50

CASS (coarse-grained artificial sequence simulator) is a software package for simulating protein sequences with an explicit genotype-to-phenotype mapping that takes protein structure and function into account. It is capable of reproducing many structure-specific properties of protein sequence evolution, most notably spatial and temporal variation in rates, and has been used to investigate several hypotheses about the influence of thermodynamics on molecular evolution. The software is implemented in object-oriented C++, is supported on Linux, and the source code is made freely available under the GPL v3 license at sGroup/CASS/. 2012/11/14 - 19:02

Repetitive DNA is among the fastest evolving types of genomic DNA, which includes simple sequence repeats (SSRs), short regions of tandemly repeated one to six nucleotides long motifs. SSRs are found most frequently in noncoding regions. Repeat number variation occurs rapidly and is presumably neutral such that polymorphic SSRs are frequently used as genetic markers to characterize and classify populations. Despite their rapid evolution, recent reports suggested that SSR loci can be retained over hundreds of millions of years. We here investigate the dynamics and genomic features of SSR evolution in syntenic regions conserved across twelve Drosophila species and within a D. melanogaster population dataset. We find that SSR loci decay exponentially with time, the percentage of retained SSRs mostly reflects species relationships and correlates well with the sequence similarity of neighboring genes. About 47% of repeat loci within syntenic regions may share common ancestry due to predicted conservation in at least two species from the Drosophila subgenera Sophophora and Drosophila respectively, i.e. after 80 million years of divergence time. Since loci which are highly polymorphic at the population level also decay faster across species, SSR evolution appears to be a gradual process in which conservation pressure may act at relatively constant rates across time scales. A higher proportion of SSR loci are retained among Drosophila subgenus species considering their evolutionary distance and the expected decay rate estimated across all Drosophila species. This prolonged SSR retention might be caused by a higher SSR mutation rate and a lower nucleotide substitution rate in the Drosophila subgenus compared to Sophophora species. SSRs in exons and on autosomes evolve more slowly than SSRs located outside of exons or on the sex chromosome, respectively, both within and across species. SSR variability and phylogenetic conservation thus varies depending on the genomic location. These findings provide new insights into the dynamics of SSRs at both micro- and macro-evolutionary scales. The development of robust models of SSR long-term evolution will facilitate more in-depth analyses in general and the prediction of neutrally evolving SSRs and SSRs evolving under purifying selection, extending our knowledge of the functional impact of SSRs in genome evolution. 2012/07/20 - 09:32

Douglas Theobald recently developed an interesting test putatively capable of quantifying the evidence for a Universal Common Ancestry uniting the three domains of life (Eukarya, Archaea and Bacteria) against hypotheses of Independent Origins for some of these domains. We review here his model, in particular in relation to the treatment of Horizontal Gene Transfer and to the quality of sequence alignment. 2012/05/10 - 06:46

Recent work in the field of plant epigenetics is adding to a growing understanding of how epigenetic variation can be an important source of phenotypic variation in natural populations. Therefore, it has the potential to play a major role in adaptation to environmental change. Most epigenetic variation is reset between generations, however, in some instances environmentally-induced epigenetic variation can result in heritable phenotypic plasticity that invokes Lamarkian-like inheritance. Epigenetic variation can also be the result of random epimutations that can have both higher mutation and reversal rates than DNA sequence mutations. We discuss several examples documenting epigenetic variation in wild populations. We also discuss laboratory studies that investigate the rate of epimutations and reversals, and how that has been incorporated into evolutionary theory. We suggest that modern evolutionary theory will benefit from the incorporation of epigenetics, but it is not in need of a complete revision, as has been suggested. 2012/05/01 - 10:35

Ferritins are ubiquitous, highly-conserved proteins that constitute one of the most important components of the cellular machinery devoted to the management of iron levels. Various ferritins have been described in vertebrates, though their exact functions and phylogenetic relationships remain to be established. Our attempts to properly annotate two ferritin subunits isolated from the Asian sea bass Lates calcarifer, prompted us to investigate the evolutionary relationships among vertebrate ferritins and their relationships with non-vertebrate homologs. We carried out a detailed screening of mined ferritin sequences by examining the regulatory elements and gene structures. Subsequently, we performed comprehensive phylogenetic analyses involving the various metazoan and vertebrate ferritin chain types, respectively. Our analyses suggest that a single ferritin chain duplicated in the early vertebrates and that the various ferritin chain types in vertebrate and non-vertebrate species evolved independently through lineage-specific duplications. Notably, this includes the mitochondrial ferritin found only in insects and mammals that we show to result from two parallel lineage-specific duplications followed by convergent events of mitochondrial targeting. Regarding the various cytosolic ferritin chains in vertebrates, our results suggest a scenario of a duplication at the base of vertebrates followed by more recent duplications in teleosts and amphibians. This scenario implies that the light chain in mammals is orthologous to the middle chain in teleosts, in contrast to previous claims of a paralogous relationship coupled with differential gene loss. We hypothesise that the extensive differences in sequence and function between these two orthologous chains may have been driven by the adaptation of tetrapods to terrestrial environments, which involved changes in the dynamics of iron uptake and storage. Altogether, our analyses clarify the evolutionary relationships among vertebrate ferritins and pave the way for the interpretation of functional adaptations within an evolutionary framework. 2012/03/14 - 19:09

Convergent Evolution: Limited Forms Most Beautiful by George McGhee attempts the first systematic examination of the timely topic of convergent evolution. The author’s expertise and passion really lie in studies of morphology and behavior and these trajectories are the strongest of the work. 2012/03/01 - 17:17

Sex refers to any biological process selected for genetic exchange but the reason for why sex is so common in Eukaryotes continues to resist understanding. Bacteria appear to adapt and proliferate despite the fact that they lack genes for sex. To understand why sex has evolved, we must answer two crucial questions: i) what are the key differences between eukaryotes and bacteria and ii) why do some eukaryotes use asexual reproduction. Recently, new ideas about the evolution of sex are being proposed which point out that sex and recombination could be the result of very primitive interactions. 2012/01/17 - 16:50

Species trees are an essential tool in conservation and evolutionary biology. In phylogenomics, not only is data choice (e.g. using unlinked orthologs rather than paralogs) an important systematic consideration, but the choice of phylogenetic algorithm is also important. Since individual gene phylogenies can differ from the true species phylogeny, new methods have been proposed for species tree estimation using multiple unlinked genes. Improvements in genome sequencing technologies have increased the amount of data available to researchers and this has increased the utility of multi-locus species tree inference methods. The Bayesian methods BEST and *BEAST that incorporate a coalescent model to account for gene tree and species tree conflict offer promising advances in species tree inference directly from DNA sequences. Methods that infer species trees from gene trees rather than directly from sequence data such as STAR, STEAC, NJst and the likelihood method STEM have been recently developed as computationally efficient alternatives. Bayesian concordance analysis, which has been shown to perform well when horizontal gene transfer is the cause of gene tree and species tree conflict, is also discussed. Furthermore, methods for species delimitation including a non-parametric species tree inference method that does not require a priori species assignments can remove subjectivity from species delimitation. Here, I review the assumptions, required inputs, and the performance of these methods under simulation and in recent empirical studies. Researchers in many disciplines should understand the methods available for phylogenomic species tree inference in order to enhance evolutionary and conservation studies. 2011/12/21 - 22:10

The uniting thread of the book is an attempt at an integrated view of the evolution of sensory systems, life, and its consciousness. To accomplish this, the book fuses opinions from different fields of science, and just like the greek mythical fire-breathing chimera, the result is strong, but also impossible. The book starts out with prototypes of life, and their complex beginnings and interactions. Viruses are introduced as harbingers of selves, as regulators of life and creators of novel genetic combinations. This is followed by an argument for the simultaneous nature of growth processes and early life, contrasting it to the galvanism of the primordial soup theory. Bacterial signaling and sensing is treated as the forerunner of community forming and interaction. 2011/11/25 - 18:16

Directed mutation is a controversial process that allows mutations to occur at higher frequencies when they are beneficial. Here we review evidence for transposon-mediated directed mutation. crp deletion mutants (Glp–) of Escherichia coli (E. coli) mutate specifically to glycerol utilization (Glp+) at rates that are enhanced by glycerol or the loss of the glycerol repressor (GlpR), and depressed by glucose or glpR overexpression. Of the four tandem GlpRbinding sites (O1-O4), O4 specifically controls glpFK expression while O1 controls mutation rate. Mutation is due to insertion of the IS5 transposon into a specific site upstream of the glpFK promoter. Mutational control by GlpR is independent of the selection and assay procedures, and IS5 insertion into other gene activation sites is unaffected by the presence of glycerol or the loss of GlpR. The results establish an example of transposon-mediated directed mutation, identify the protein responsible for its regulation, and define essential features of the mechanism involved. We discuss this phenomenon from an evolutionary standpoint and provide examples of analogous switch mechanisms that may or may not be directed. 2011/09/15 - 20:27

The RNA world hypothesis for the origin of life is widely accepted in spite of the complexity of RNA synthesis. An alternative hypothesis is advanced for the origin and evolution of protein and nucleic acid synthesis.  At an early stage synthesis of poly-(b-malic acid), the initial evolutionary predecessor of nucleic acids, and polypeptides was coupled.  This evolved into a singlet coding system in which glycine and alanine were specified by two derivatives of malic acid with different amide side chains.  In stages, the linear polyester backbone evolved into the phosphodiester backbone of RNA and the amide side chains evolved into the purine and pyrimidine bases.  The replication process for RNA used aminoacyl-NMP monomers (N= pyrimidine or purine) with a singlet coding system in which the four bases coded for glycine, alanine, valine and aspartic acid.  Ribosomal protein synthesis (RPS) evolved from coupled replication by using tRNAs and separating fidelity checking and peptide bond formation functions into small and large ribosomal subunits.  Continuity was maintained during the transition to the triplet process by using the same catalysts that aminoacylated NMPs to aminoacylate four different bases at the 3’ ends of the original tRNAs.  Four GNC codons used the central base to designate the same four amino acids that were coded in singlet replication.  Triplet-coded protein synthesis had the advantage of producing multiple copies of protein from a single copy of RNA, and eventually replaced protein synthesis via singlet-coded replication.  Evolution of the simple triplet-coded process into RPS is described. 2011/03/01 - 23:29