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Biology Direct  2006;1:22.
Ever since the discovery of 'genes in pieces' and mRNA splicing in eukaryotes, origin and evolution of spliceosomal introns have been considered within the conceptual framework of the 'introns early' versus 'introns late' debate. The 'introns early' hypothesis, which is closely linked to the so-called exon theory of gene evolution, posits that protein-coding genes were interrupted by numerous introns even at the earliest stages of life's evolution and that introns played a major role in the origin of proteins by facilitating recombination of sequences coding for small protein/peptide modules. Under this scenario, the absence of spliceosomal introns in prokaryotes is considered to be a result of "genome streamlining". The 'introns late' hypothesis counters that spliceosomal introns emerged only in eukaryotes, and moreover, have been inserted into protein-coding genes continuously throughout the evolution of eukaryotes. Beyond the formal dilemma, the more substantial side of this debate has to do with possible roles of introns in the evolution of eukaryotes.
I argue that several lines of evidence now suggest a coherent solution to the introns-early versus introns-late debate, and the emerging picture of intron evolution integrates aspects of both views although, formally, there seems to be no support for the original version of introns-early. Firstly, there is growing evidence that spliceosomal introns evolved from group II self-splicing introns which are present, usually, in small numbers, in many bacteria, and probably, moved into the evolving eukaryotic genome from the α-proteobacterial progenitor of the mitochondria. Secondly, the concept of a primordial pool of 'virus-like' genetic elements implies that self-splicing introns are among the most ancient genetic entities. Thirdly, reconstructions of the ancestral state of eukaryotic genes suggest that the last common ancestor of extant eukaryotes had an intron-rich genome. Thus, it appears that ancestors of spliceosomal introns, indeed, have existed since the earliest stages of life's evolution, in a formal agreement with the introns-early scenario. However, there is no evidence that these ancient introns ever became widespread before the emergence of eukaryotes, hence, the central tenet of introns-early, the role of introns in early evolution of proteins, has no support. However, the demonstration that numerous introns invaded eukaryotic genes at the outset of eukaryotic evolution and that subsequent intron gain has been limited in many eukaryotic lineages implicates introns as an ancestral feature of eukaryotic genomes and refutes radical versions of introns-late. Perhaps, most importantly, I argue that the intron invasion triggered other pivotal events of eukaryogenesis, including the emergence of the spliceosome, the nucleus, the linear chromosomes, the telomerase, and the ubiquitin signaling system. This concept of eukaryogenesis, in a sense, revives some tenets of the exon hypothesis, by assigning to introns crucial roles in eukaryotic evolutionary innovation.
The scenario of the origin and evolution of introns that is best compatible with the results of comparative genomics and theoretical considerations goes as follows: self-splicing introns since the earliest stages of life's evolution – numerous spliceosomal introns invading genes of the emerging eukaryote during eukaryogenesis – subsequent lineage-specific loss and gain of introns. The intron invasion, probably, spawned by the mitochondrial endosymbiont, might have critically contributed to the emergence of the principal features of the eukaryotic cell. This scenario combines aspects of the introns-early and introns-late views.
this article was reviewed by W. Ford Doolittle, James Darnell (nominated by W. Ford Doolittle), William Martin, and Anthony Poole.
PMCID: PMC1570339  PMID: 16907971
2.  New Maximum Likelihood Estimators for Eukaryotic Intron Evolution
PLoS Computational Biology  2005;1(7):e79.
The evolution of spliceosomal introns remains poorly understood. Although many approaches have been used to infer intron evolution from the patterns of intron position conservation, the results to date have been contradictory. In this paper, we address the problem using a novel maximum likelihood method, which allows estimation of the frequency of intron insertion target sites, together with the rates of intron gain and loss. We analyzed the pattern of 10,044 introns (7,221 intron positions) in the conserved regions of 684 sets of orthologs from seven eukaryotes. We determined that there is an average of one target site per 11.86 base pairs (bp) (95% confidence interval, 9.27 to 14.39 bp). In addition, our results showed that: (i) overall intron gains are ~25% greater than intron losses, although specific patterns vary with time and lineage; (ii) parallel gains account for ~18.5% of shared intron positions; and (iii) reacquisition following loss accounts for ~0.5% of all intron positions. Our results should assist in resolving the long-standing problem of inferring the evolution of spliceosomal introns.
When did spliceosomal introns originate, and what is their role? These questions are the central subject of the introns-early versus introns-late debate. Inference of intron evolution from the pattern of intron position conservation is vital for resolving this debate. So far, different methods of two approaches, maximum parsimony (MP) and maximum likelihood (ML), have been developed, but the results are contradictory. The differences between previous ML results are due predominantly to differing assumptions concerning the frequency of target sites for intron insertion. This paper describes a new ML method that treats this frequency as a parameter requiring optimization. Using the pattern of intron position in conserved regions of 684 clusters of gene orthologs from seven eukaryotes, the authors found that, on average, there is one target site per ~12 base pairs. The results of intron evolution inferred using this optimal frequency are more definitive than previous ML results. Since the ML method is preferred to the MP one for large datasets, the current results should be the most reliable ones to date. The results show that during the course of evolution there have been slightly more intron gains than losses, and thus they favor introns-late. These results should shed new light on our understanding of intron evolution.
PMCID: PMC1323467  PMID: 16389300
3.  Evolutionary Convergence on Highly-Conserved 3′ Intron Structures in Intron-Poor Eukaryotes and Insights into the Ancestral Eukaryotic Genome
PLoS Genetics  2008;4(8):e1000148.
The presence of spliceosomal introns in eukaryotes raises a range of questions about genomic evolution. Along with the fundamental mysteries of introns' initial proliferation and persistence, the evolutionary forces acting on intron sequences remain largely mysterious. Intron number varies across species from a few introns per genome to several introns per gene, and the elements of intron sequences directly implicated in splicing vary from degenerate to strict consensus motifs. We report a 50-species comparative genomic study of intron sequences across most eukaryotic groups. We find two broad and striking patterns. First, we find that some highly intron-poor lineages have undergone evolutionary convergence to strong 3′ consensus intron structures. This finding holds for both branch point sequence and distance between the branch point and the 3′ splice site. Interestingly, this difference appears to exist within the genomes of green alga of the genus Ostreococcus, which exhibit highly constrained intron sequences through most of the intron-poor genome, but not in one much more intron-dense genomic region. Second, we find evidence that ancestral genomes contained highly variable branch point sequences, similar to more complex modern intron-rich eukaryotic lineages. In addition, ancestral structures are likely to have included polyT tails similar to those in metazoans and plants, which we found in a variety of protist lineages. Intriguingly, intron structure evolution appears to be quite different across lineages experiencing different types of genome reduction: whereas lineages with very few introns tend towards highly regular intronic sequences, lineages with very short introns tend towards highly degenerate sequences. Together, these results attest to the complex nature of ancestral eukaryotic splicing, the qualitatively different evolutionary forces acting on intron structures across modern lineages, and the impressive evolutionary malleability of eukaryotic gene structures.
Author Summary
The spliceosomal introns that interrupt eukaryotic genes show great number and sequence variation across species, from the rare, highly uniform yeast introns to the ubiquitous and highly variable vertebrate intron sequences. The causes of these differences remain mysterious. We studied sequences of intron branch points and 3′ termini in 50 eukaryotic species. All intron-rich species exhibit variable 3′ sequences. However, intron-poor species range from variable sequences, to uniform branch point motifs, to uniform branch point motifs in uniform positions along the intronic sequence. This is a more complex pattern than the clear relationship between intron number and 5′ intron sequence uniformity found previously. The correspondence of sequence uniformity and intron number extends to species of the green algal genus Ostreococcus, in which the single intron-rich genomic region shows far more variable intron sequences than in the otherwise intron-poor genome. We suggest that different concentrations of spliceosomal complexes may explain these differences. In addition, we report the existence of 3′ polyT tails in diverse eukaryotic protists, suggesting that this structure is ancestral. Together, these results underscore the complexity of ancestral eukaryotic splicing, the qualitatively different evolutionary forces acting on intron sequences in modern eukaryotes, and the impressive evolutionary malleability of eukaryotic genes.
PMCID: PMC2483917  PMID: 18688272
4.  A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes
PLoS Computational Biology  2011;7(9):e1002150.
Protein-coding genes in eukaryotes are interrupted by introns, but intron densities widely differ between eukaryotic lineages. Vertebrates, some invertebrates and green plants have intron-rich genes, with 6–7 introns per kilobase of coding sequence, whereas most of the other eukaryotes have intron-poor genes. We reconstructed the history of intron gain and loss using a probabilistic Markov model (Markov Chain Monte Carlo, MCMC) on 245 orthologous genes from 99 genomes representing the three of the five supergroups of eukaryotes for which multiple genome sequences are available. Intron-rich ancestors are confidently reconstructed for each major group, with 53 to 74% of the human intron density inferred with 95% confidence for the Last Eukaryotic Common Ancestor (LECA). The results of the MCMC reconstruction are compared with the reconstructions obtained using Maximum Likelihood (ML) and Dollo parsimony methods. An excellent agreement between the MCMC and ML inferences is demonstrated whereas Dollo parsimony introduces a noticeable bias in the estimations, typically yielding lower ancestral intron densities than MCMC and ML. Evolution of eukaryotic genes was dominated by intron loss, with substantial gain only at the bases of several major branches including plants and animals. The highest intron density, 120 to 130% of the human value, is inferred for the last common ancestor of animals. The reconstruction shows that the entire line of descent from LECA to mammals was intron-rich, a state conducive to the evolution of alternative splicing.
Author Summary
In eukaryotes, protein-coding genes are interrupted by non-coding introns. The intron densities widely differ, from 6–7 introns per kilobase of coding sequence in vertebrates, some invertebrates and plants, to only a few introns across the entire genome in many unicellular forms. We applied a robust statistical methodology, Markov Chain Monte Carlo, to reconstruct the history of intron gain and loss throughout the evolution of eukaryotes using a set of 245 homologous genes from 99 genomes that represent the diversity of eukaryotes. Intron-rich ancestors were confidently inferred for each major eukaryotic group including 53% to 74% of the human intron density for the last eukaryotic common ancestor, and 120% to 130% of the human value for the last common ancestor of animals. Evolution of eukaryotic genes involved primarily intron loss, with substantial gain only at the bases of several major branches including plants and animals. Thus, the common ancestor of all extant eukaryotes was a complex organism with a gene architecture resembling those in multicellular organisms. The line of descent from the last common ancestor to mammals was an uninterrupted intron-rich state that, given the error-prone splicing in intron-rich organisms, was conducive to the elaboration of functional alternative splicing.
PMCID: PMC3174169  PMID: 21935348
5.  Origin and evolution of spliceosomal introns
Biology Direct  2012;7:11.
Evolution of exon-intron structure of eukaryotic genes has been a matter of long-standing, intensive debate. The introns-early concept, later rebranded ‘introns first’ held that protein-coding genes were interrupted by numerous introns even at the earliest stages of life's evolution and that introns played a major role in the origin of proteins by facilitating recombination of sequences coding for small protein/peptide modules. The introns-late concept held that introns emerged only in eukaryotes and new introns have been accumulating continuously throughout eukaryotic evolution. Analysis of orthologous genes from completely sequenced eukaryotic genomes revealed numerous shared intron positions in orthologous genes from animals and plants and even between animals, plants and protists, suggesting that many ancestral introns have persisted since the last eukaryotic common ancestor (LECA). Reconstructions of intron gain and loss using the growing collection of genomes of diverse eukaryotes and increasingly advanced probabilistic models convincingly show that the LECA and the ancestors of each eukaryotic supergroup had intron-rich genes, with intron densities comparable to those in the most intron-rich modern genomes such as those of vertebrates. The subsequent evolution in most lineages of eukaryotes involved primarily loss of introns, with only a few episodes of substantial intron gain that might have accompanied major evolutionary innovations such as the origin of metazoa. The original invasion of self-splicing Group II introns, presumably originating from the mitochondrial endosymbiont, into the genome of the emerging eukaryote might have been a key factor of eukaryogenesis that in particular triggered the origin of endomembranes and the nucleus. Conversely, splicing errors gave rise to alternative splicing, a major contribution to the biological complexity of multicellular eukaryotes. There is no indication that any prokaryote has ever possessed a spliceosome or introns in protein-coding genes, other than relatively rare mobile self-splicing introns. Thus, the introns-first scenario is not supported by any evidence but exon-intron structure of protein-coding genes appears to have evolved concomitantly with the eukaryotic cell, and introns were a major factor of evolution throughout the history of eukaryotes. This article was reviewed by I. King Jordan, Manuel Irimia (nominated by Anthony Poole), Tobias Mourier (nominated by Anthony Poole), and Fyodor Kondrashov. For the complete reports, see the Reviewers’ Reports section.
PMCID: PMC3488318  PMID: 22507701
Intron sliding; Intron gain; Intron loss; Spliceosome; Splicing signals; Evolution of exon/intron structure; Alternative splicing; Phylogenetic trees; Mobile domains; Eukaryotic ancestor
6.  Recurrent Loss of Specific Introns during Angiosperm Evolution
PLoS Genetics  2014;10(12):e1004843.
Numerous instances of presence/absence variations for introns have been documented in eukaryotes, and some cases of recurrent loss of the same intron have been suggested. However, there has been no comprehensive or phylogenetically deep analysis of recurrent intron loss. Of 883 cases of intron presence/absence variation that we detected in five sequenced grass genomes, 93 were confirmed as recurrent losses and the rest could be explained by single losses (652) or single gains (118). No case of recurrent intron gain was observed. Deep phylogenetic analysis often indicated that apparent intron gains were actually numerous independent losses of the same intron. Recurrent loss exhibited extreme non-randomness, in that some introns were removed independently in many lineages. The two larger genomes, maize and sorghum, were found to have a higher rate of both recurrent loss and overall loss and/or gain than foxtail millet, rice or Brachypodium. Adjacent introns and small introns were found to be preferentially lost. Intron loss genes exhibited a high frequency of germ line or early embryogenesis expression. In addition, flanking exon A+T-richness and intron TG/CG ratios were higher in retained introns. This last result suggests that epigenetic status, as evidenced by a loss of methylated CG dinucleotides, may play a role in the process of intron loss. This study provides the first comprehensive analysis of recurrent intron loss, makes a series of novel findings on the patterns of recurrent intron loss during the evolution of the grass family, and provides insight into the molecular mechanism(s) underlying intron loss.
Author Summary
The spliceosomal introns are nucleotide sequences that interrupt coding regions of eukaryotic genes and are removed by RNA splicing after transcription. Recent studies have reported several examples of possible recurrent intron loss or gain, i.e., introns that are independently removed from or inserted into the identical sites more than once in an investigated phylogeny. However, the frequency, evolutionary patterns or other characteristics of recurrent intron turnover remain unknown. We provide results for the first comprehensive analysis of recurrent intron turnover within a plant family and show that recurrent intron loss represents a considerable portion of all intron losses identified and intron loss events far outnumber intron gain events. We also demonstrate that recurrent intron loss is non-random, affecting only a small number of introns that are repeatedly lost, and that different lineages show significantly different rates of intron loss. Our results suggest a possible role of DNA methylation in the process of intron loss. Moreover, this study provides strong support for the model of intron loss by reverse transcriptase mediated conversion of genes by their processed mRNA transcripts.
PMCID: PMC4256211  PMID: 25474210
7.  Effects of Taxon Sampling in Reconstructions of Intron Evolution
Introns comprise a considerable portion of eukaryotic genomes; however, their evolution is understudied. Numerous works of the last years largely disagree on many aspects of intron evolution. Interpretation of these differences is hindered because different algorithms and taxon sampling strategies were used. Here, we present the first attempt of a systematic evaluation of the effects of taxon sampling on popular intron evolution estimation algorithms. Using the “taxon jackknife” method, we compared the effect of taxon sampling on the behavior of intron evolution inferring algorithms. We show that taxon sampling can dramatically affect the inferences and identify conditions where algorithms are prone to systematic errors. Presence or absence of some key species is often more important than the taxon sampling size alone. Criteria of representativeness of the taxonomic sampling for reliable reconstructions are outlined. Presence of the deep-branching species with relatively high intron density is more important than sheer number of species. According to these criteria, currently available genomic databases are representative enough to provide reliable inferences of the intron evolution in animals, land plants, and fungi, but they underrepresent many groups of unicellular eukaryotes, including the well-studied Alveolata.
PMCID: PMC3647540  PMID: 23671844
8.  Sm/Lsm Genes Provide a Glimpse into the Early Evolution of the Spliceosome
PLoS Computational Biology  2009;5(3):e1000315.
The spliceosome, a sophisticated molecular machine involved in the removal of intervening sequences from the coding sections of eukaryotic genes, appeared and subsequently evolved rapidly during the early stages of eukaryotic evolution. The last eukaryotic common ancestor (LECA) had both complex spliceosomal machinery and some spliceosomal introns, yet little is known about the early stages of evolution of the spliceosomal apparatus. The Sm/Lsm family of proteins has been suggested as one of the earliest components of the emerging spliceosome and hence provides a first in-depth glimpse into the evolving spliceosomal apparatus. An analysis of 335 Sm and Sm-like genes from 80 species across all three kingdoms of life reveals two significant observations. First, the eukaryotic Sm/Lsm family underwent two rapid waves of duplication with subsequent divergence resulting in 14 distinct genes. Each wave resulted in a more sophisticated spliceosome, reflecting a possible jump in the complexity of the evolving eukaryotic cell. Second, an unusually high degree of conservation in intron positions is observed within individual orthologous Sm/Lsm genes and between some of the Sm/Lsm paralogs. This suggests that functional spliceosomal introns existed before the emergence of the complete Sm/Lsm family of proteins; hence, spliceosomal machinery with considerably fewer components than today's spliceosome was already functional.
Author Summary
The spliceosome is a complex molecular machine that removes intervening sequences (introns) from mRNAs. It is unique to eukaryotes. Although prokaryotes have self-splicing introns, they completely lack spliceosomal introns and the spliceosome itself. Yet even the simplest eukaryotic organisms have introns and a rather complex spliceosomal apparatus. Little is known about how this amazing machine rapidly evolved in early eukaryotes. Here, we attempt to reconstruct a part of this evolutionary process using one of the most fundamental components of the spliceosome—the Sm and Lsm family of proteins. Using sequence and structure analysis as well as the analysis of the intron positions in Sm and Lsm genes in conjunction with a wealth of published data, we propose a plausible scenario for some aspects of spliceosomal evolution. In particular, we suggest that the Lsm family of genes could have been the first and the most essential component that allowed rudimentary splicing of early spliceosomal introns. Extensive duplications of Lsm genes and the later rise of the Sm gene family likely reflect a gradual increase in complexity of the spliceosome.
PMCID: PMC2650416  PMID: 19282982
9.  Nonsense-Mediated Decay Enables Intron Gain in Drosophila
PLoS Genetics  2010;6(1):e1000819.
Intron number varies considerably among genomes, but despite their fundamental importance, the mutational mechanisms and evolutionary processes underlying the expansion of intron number remain unknown. Here we show that Drosophila, in contrast to most eukaryotic lineages, is still undergoing a dramatic rate of intron gain. These novel introns carry significantly weaker splice sites that may impede their identification by the spliceosome. Novel introns are more likely to encode a premature termination codon (PTC), indicating that nonsense-mediated decay (NMD) functions as a backup for weak splicing of new introns. Our data suggest that new introns originate when genomic insertions with weak splice sites are hidden from selection by NMD. This mechanism reduces the sequence requirement imposed on novel introns and implies that the capacity of the spliceosome to recognize weak splice sites was a prerequisite for intron gain during eukaryotic evolution.
Author Summary
The surprising observation 30 years ago that genes are interrupted by non-coding introns changed our view of gene architecture. Intron number varies dramatically among species; ranging from nine introns/gene in humans to less than one in some simple eukyarotes. Here we ask where new introns come from and how they are maintained in a population. We find that novel introns do not arise from pre-existing introns, although the mechanisms that generate novel introns remain unclear. We also show that novel introns carry only weak signals for their identification and removal, and therefore depend on nonsense-mediated decay (NMD). NMD maintains RNA quality control by degrading transcripts that have not been spliced properly. We propose that NMD shelters novel introns from natural selection. This increases the likelihood that a novel intron will rise in frequency and be maintained within a population, thus increasing the rate of intron gain.
PMCID: PMC2809761  PMID: 20107520
10.  Phase distribution of spliceosomal introns: implications for intron origin
The origin of spliceosomal introns is the central subject of the introns-early versus introns-late debate. The distribution of intron phases is non-uniform, with an excess of phase-0 introns. Introns-early explains this by speculating that a fraction of present-day introns were present between minigenes in the progenote and therefore must lie in phase-0. In contrast, introns-late predicts that the nonuniformity of intron phase distribution reflects the nonrandomness of intron insertions.
In this paper, we tested the two theories using analyses of intron phase distribution. We inferred the evolution of intron phase distribution from a dataset of 684 gene orthologs from seven eukaryotes using a maximum likelihood method. We also tested whether the observed intron phase distributions from 10 eukaryotes can be explained by intron insertions on a genome-wide scale. In contrast to the prediction of introns-early, the inferred evolution of intron phase distribution showed that the proportion of phase-0 introns increased over evolution. Consistent with introns-late, the observed intron phase distributions matched those predicted by an intron insertion model quite well.
Our results strongly support the introns-late hypothesis of the origin of spliceosomal introns.
PMCID: PMC1574350  PMID: 16959043
11.  Comparative genomic analysis of fungal genomes reveals intron-rich ancestors
Genome Biology  2007;8(10):R223.
Analysis of intron gain and loss in fungal genomes provides support for an intron-rich fungus-animal ancestor.
Eukaryotic protein-coding genes are interrupted by spliceosomal introns, which are removed from transcripts before protein translation. Many facets of spliceosomal intron evolution, including age, mechanisms of origins, the role of natural selection, and the causes of the vast differences in intron number between eukaryotic species, remain debated. Genome sequencing and comparative analysis has made possible whole genome analysis of intron evolution to address these questions.
We analyzed intron positions in 1,161 sets of orthologous genes across 25 eukaryotic species. We find strong support for an intron-rich fungus-animal ancestor, with more than four introns per kilobase, comparable to the highest known modern intron densities. Indeed, the fungus-animal ancestor is estimated to have had more introns than any of the extant fungi in this study. Thus, subsequent fungal evolution has been characterized by widespread and recurrent intron loss occurring in all fungal clades. These results reconcile three previously proposed methods for estimation of ancestral intron number, which previously gave very different estimates of ancestral intron number for eight eukaryotic species, as well as a fourth more recent method. We do not find a clear inverse correspondence between rates of intron loss and gain, contrary to the predictions of selection-based proposals for interspecific differences in intron number.
Our results underscore the high intron density of eukaryotic ancestors and the widespread importance of intron loss through eukaryotic evolution.
PMCID: PMC2246297  PMID: 17949488
12.  Metabolic modeling of endosymbiont genome reduction on a temporal scale
This study explores the order in which individual metabolic genes are lost in an in silico evolutionary process leading from the metabolic network of Eschericia coli to that of the genome-reduced endosymbiont Buchnera aphidicola.
Simulating the reductive evolutionary process under several growth conditions, a remarkable correlation between in silico and phylogenetically reconstructed gene loss time is obtained.A gene's k-robustness (its depth of backups) is prime determinant of its loss time.In silico gene loss time is a better predictor of their actual loss times than genomic features and network properties.Simulating the reductive evolutionary process by the loss of large blocks followed by single-gene deletions, as known to occur in evolution, yields a remarkable correspondence with the phylogenetic reconstruction and the block loss reported in the literature.
An open fundamental challenge in Systems Biology is whether a genome-scale model can predict patterns of genome evolution by realistically accounting for the associated biochemical constraints. In this study, we explore the order in which individual genes are lost in an in silico evolutionary process, leading from the metabolic network of Eschericia coli to that of the endosymbiont Buchnera aphidicola.
To evaluate the in silico gene loss time, we repeated the reductive evolutionary process introduced by Pál et al (2006), denoting the in silico deletion time of a gene in a single run of the reductive evolutionary process as the number of genes deleted before its own deletion occurred. By comparing the in silico evaluations of the gene loss time to that obtained by a phylogenetic reconstruction (Figure 1), we could evaluate the ability of an in silico process to predict temporal patterns of genome reduction. Applying this procedure on a literature-based viable media, we obtained a mean Spearman's correlation of 0.46 (53% of the maximal correlation, empirical P-value <9.9e−4) between in silico and phylogenetically reconstructed loss times. In order to provide an upper bound on evolutionary necessity stemming from metabolic constraints, we searched the space of potential growth media and biomass functions via a simulated annealing search algorithm aimed at identifying an environment/biomass function that maximizes the target correlation between in silico and reconstructed loss times. Simulating the reductive evolutionary process under the growth conditions and biomass function obtained in this process, we managed to improve the correlation between in silico and reconstructed loss times to a mean Spearman's correlation of 0.54 (63% of the maximal correlation, empirical P-value <9.9e−4, Figure 3).
Examining the dependency of the predicted loss time of each gene on its intrinsic network-level properties we find a very strong inverse Spearman's correlation of −0.84 (empirical P-value <9.9e−4) between the order of gene loss predicted in silico and the k-robustness levels of the genes, the latter denoting the depth of their functional backups in the network (Deutscher et al, 2006). Moreover, in order to examine whether the relative loss time of a gene is influenced by its functional dependencies with other genes, we performed a flux-coupling analysis and identified pairs of reactions whose activities asymmetrically depend on each other, i.e., are directionally coupled (Burgard et al, 2004). We find that genes encoding reactions whose activity is needed for activating the other reaction (and not vice versa) have a tendency to be lost later, as one would expect (binomial P-value <1e−14).
To assess the scale of these results, we examined as a control how well genomic features and network properties predict the phylogenetically reconstructed gene loss times. We examined the dependency of the latter on several factors that are known be inversely correlated with the propensity of a gene to be lost (Brinza et al, 2009; Delmotte et al, 2006; Tamames et al, 2007), including the genes' mRNA levels, tAI values (Covert et al, 2004; Reis et al, 2004; Sharp and Li, 1987; Tuller et al, 2010a) and the number of partners the gene products have in a protein–protein interaction network. Remarkably, these genomic features yield considerably lower Spearman's correlation than that obtained by the in silico simulations. Moreover, multiply regressing the loss times from the phylogenetic reconstruction on the in silico gene loss time predictions and the genomic and network variables, we found that the (normalized) coefficient of the in silico predictions in the regression is much higher than those of the genomic features, further testifying to the considerable independent predictive power of the metabolic model.
Finally, simulating the evolutionary process as large block deletions at first followed by single-gene deletions as is thought to occur in evolution (Moran and Mira, 2001; van Ham et al, 2003), a remarkable correspondence with the phylogenetic reconstruction was found. Namely, we find that after a certain amount of genes are deleted from the genome, no further block deletions can occur due to the increasing density of essential genes. Notably, the maximum amount of genes that can be deleted in blocks (i.e., until no more blocks can be deleted) corresponds to the number of genes appearing in our phylogenetic reconstruction from the LCA (last common ancestor of Buchnera and E. coli) to the LCSA (last common symbiotic ancestor, nodes 1–3 in Figure 1A), as described in the literature.
A fundamental challenge in Systems Biology is whether a cell-scale metabolic model can predict patterns of genome evolution by realistically accounting for associated biochemical constraints. Here, we study the order in which genes are lost in an in silico evolutionary process, leading from the metabolic network of Eschericia coli to that of the endosymbiont Buchnera aphidicola. We examine how this order correlates with the order by which the genes were actually lost, as estimated from a phylogenetic reconstruction. By optimizing this correlation across the space of potential growth and biomass conditions, we compute an upper bound estimate on the model's prediction accuracy (R=0.54). The model's network-based predictive ability outperforms predictions obtained using genomic features of individual genes, reflecting the effect of selection imposed by metabolic stoichiometric constraints. Thus, while the timing of gene loss might be expected to be a completely stochastic evolutionary process, remarkably, we find that metabolic considerations, on their own, make a marked 40% contribution to determining when such losses occur.
PMCID: PMC3094061  PMID: 21451589
constraint-based modeling; endosymbiont; evolution; metabolism
13.  EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution
Advances in Bioinformatics  2010;2010:167408.
Evolutionary binary characters are features of species or genes, indicating the absence (value zero) or presence (value one) of some property. Examples include eukaryotic gene architecture (the presence or absence of an intron in a particular locus), gene content, and morphological characters. In many studies, the acquisition of such binary characters is assumed to represent a rare evolutionary event, and consequently, their evolution is analyzed using various flavors of parsimony. However, when gain and loss of the character are not rare enough, a probabilistic analysis becomes essential. Here, we present a comprehensive probabilistic model to describe the evolution of binary characters on a bifurcating phylogenetic tree. A fast software tool, EREM, is provided, using maximum likelihood to estimate the parameters of the model and to reconstruct ancestral states (presence and absence in internal nodes) and events (gain and loss events along branches).
PMCID: PMC2866244  PMID: 20467467
14.  Patterns of intron gain and conservation in eukaryotic genes
PMCID: PMC2151770  PMID: 17935625
15.  Analysis of Ribosomal Protein Gene Structures: Implications for Intron Evolution
PLoS Genetics  2006;2(3):e25.
Many spliceosomal introns exist in the eukaryotic nuclear genome. Despite much research, the evolution of spliceosomal introns remains poorly understood. In this paper, we tried to gain insights into intron evolution from a novel perspective by comparing the gene structures of cytoplasmic ribosomal proteins (CRPs) and mitochondrial ribosomal proteins (MRPs), which are held to be of archaeal and bacterial origin, respectively. We analyzed 25 homologous pairs of CRP and MRP genes that together had a total of 527 intron positions. We found that all 12 of the intron positions shared by CRP and MRP genes resulted from parallel intron gains and none could be considered to be “conserved,” i.e., descendants of the same ancestor. This was supported further by the high frequency of proto-splice sites at these shared positions; proto-splice sites are proposed to be sites for intron insertion. Although we could not definitively disprove that spliceosomal introns were already present in the last universal common ancestor, our results lend more support to the idea that introns were gained late. At least, our results show that MRP genes were intronless at the time of endosymbiosis. The parallel intron gains between CRP and MRP genes accounted for 2.3% of total intron positions, which should provide a reliable estimate for future inferences of intron evolution.
Genes in eukaryotes are usually intervened by extra bits of DNA sequence, called introns, that have to be removed after the genes are transcribed into RNA. Why do introns exist in eukaryotic genes? What is the reason for the increased intron density in higher eukaryotes? There is much that is not known about introns. This research tries to clarify the evolutionary process by which introns arose by comparing the gene structures of two types of ribosomal proteins; one in cytoplasm and the other in mitochondria of the cell. Since cytoplasm and mitochondria are of archaeal and bacterial origin, respectively, cytoplasmic ribosomal proteins (CRPs) and mitochondrial ribosomal proteins (MRPs) are believed to diverge at the same time with the divergence of archaea and bacteria. Thus, a comparative analysis of CRP and MRP genes may reveal whether introns already existed at the last common ancestor of archaea and bacteria (introns-early) or whether they emerged late (introns-late). The results make it clear, at least, that all of the introns in MRP genes were gained during the course of eukaryotic evolution and therefore lend more support to the introns-late theory.
PMCID: PMC1386722  PMID: 16518464
16.  Modeling the evolution dynamics of exon-intron structure with a general random fragmentation process
Most eukaryotic genes are interrupted by spliceosomal introns. The evolution of exon-intron structure remains mysterious despite rapid advance in genome sequencing technique. In this work, a novel approach is taken based on the assumptions that the evolution of exon-intron structure is a stochastic process, and that the characteristics of this process can be understood by examining its historical outcome, the present-day size distribution of internal translated exons (exon). Through the combination of simulation and modeling the size distribution of exons in different species, we propose a general random fragmentation process (GRFP) to characterize the evolution dynamics of exon-intron structure. This model accurately predicts the probability that an exon will be split by a new intron and the distribution of novel insertions along the length of the exon.
As the first observation from this model, we show that the chance for an exon to obtain an intron is proportional to its size to the 3rd power. We also show that such size dependence is nearly constant across gene, with the exception of the exons adjacent to the 5′ UTR. As the second conclusion from the model, we show that intron insertion loci follow a normal distribution with a mean of 0.5 (center of the exon) and a standard deviation of 0.11. Finally, we show that intron insertions within a gene are independent of each other for vertebrates, but are more negatively correlated for non-vertebrate. We use simulation to demonstrate that the negative correlation might result from significant intron loss during evolution, which could be explained by selection against multi-intron genes in these organisms.
The GRFP model suggests that intron gain is dynamic with a higher chance for longer exons; introns are inserted into exons randomly with the highest probability at the center of the exon. GRFP estimates that there are 78 introns in every 10 kb coding sequences for vertebrate genomes, agreeing with empirical observations. GRFP also estimates that there are significant intron losses in the evolution of non-vertebrate genomes, with extreme cases of around 57% intron loss in Drosophila melanogaster, 28% in Caenorhabditis elegans, and 24% in Oryza sativa.
PMCID: PMC3732091  PMID: 23448166
Evolution of exon-intron structure; General random fragmentation process; Simulation
17.  Computational identification of functional introns: high positional conservation of introns that harbor RNA genes
Nucleic Acids Research  2013;41(11):5604-5613.
An appreciable fraction of introns is thought to have some function, but there is no obvious way to predict which specific intron is likely to be functional. We hypothesize that functional introns experience a different selection regime than non-functional ones and will therefore show distinct evolutionary histories. In particular, we expect functional introns to be more resistant to loss, and that this would be reflected in high conservation of their position with respect to the coding sequence. To test this hypothesis, we focused on introns whose function comes about from microRNAs and snoRNAs that are embedded within their sequence. We built a data set of orthologous genes across 28 eukaryotic species, reconstructed the evolutionary histories of their introns and compared functional introns with the rest of the introns. We found that, indeed, the position of microRNA- and snoRNA-bearing introns is significantly more conserved. In addition, we found that both families of RNA genes settled within introns early during metazoan evolution. We identified several easily computable intronic properties that can be used to detect functional introns in general, thereby suggesting a new strategy to pinpoint non-coding cellular functions.
PMCID: PMC3675471  PMID: 23605046
18.  Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism
A comprehensive genome-scale metabolic network of Chlamydomonas reinhardtii, including a detailed account of light-driven metabolism, is reconstructed and validated. The model provides a new resource for research of C. reinhardtii metabolism and in algal biotechnology.
The genome-scale metabolic network of Chlamydomonas reinhardtii (iRC1080) was reconstructed, accounting for >32% of the estimated metabolic genes encoded in the genome, and including extensive details of lipid metabolic pathways.This is the first metabolic network to explicitly account for stoichiometry and wavelengths of metabolic photon usage, providing a new resource for research of C. reinhardtii metabolism and developments in algal biotechnology.Metabolic functional annotation and the largest transcript verification of a metabolic network to date was performed, at least partially verifying >90% of the transcripts accounted for in iRC1080. Analysis of the network supports hypotheses concerning the evolution of latent lipid pathways in C. reinhardtii, including very long-chain polyunsaturated fatty acid and ceramide synthesis pathways.A novel approach for modeling light-driven metabolism was developed that accounts for both light source intensity and spectral quality of emitted light. The constructs resulting from this approach, termed prism reactions, were shown to significantly improve the accuracy of model predictions, and their use was demonstrated for evaluation of light source efficiency and design.
Algae have garnered significant interest in recent years, especially for their potential application in biofuel production. The hallmark, model eukaryotic microalgae Chlamydomonas reinhardtii has been widely used to study photosynthesis, cell motility and phototaxis, cell wall biogenesis, and other fundamental cellular processes (Harris, 2001). Characterizing algal metabolism is key to engineering production strains and understanding photobiological phenomena. Based on extensive literature on C. reinhardtii metabolism, its genome sequence (Merchant et al, 2007), and gene functional annotation, we have reconstructed and experimentally validated the genome-scale metabolic network for this alga, iRC1080, the first network to account for detailed photon absorption permitting growth simulations under different light sources. iRC1080 accounts for 1080 genes, associated with 2190 reactions and 1068 unique metabolites and encompasses 83 subsystems distributed across 10 cellular compartments (Figure 1A). Its >32% coverage of estimated metabolic genes is a tremendous expansion over previous algal reconstructions (Boyle and Morgan, 2009; Manichaikul et al, 2009). The lipid metabolic pathways of iRC1080 are considerably expanded relative to existing networks, and chemical properties of all metabolites in these pathways are accounted for explicitly, providing sufficient detail to completely specify all individual molecular species: backbone molecule and stereochemical numbering of acyl-chain positions; acyl-chain length; and number, position, and cis–trans stereoisomerism of carbon–carbon double bonds. Such detail in lipid metabolism will be critical for model-driven metabolic engineering efforts.
We experimentally verified transcripts accounted for in the network under permissive growth conditions, detecting >90% of tested transcript models (Figure 1B) and providing validating evidence for the contents of iRC1080. We also analyzed the extent of transcript verification by specific metabolic subsystems. Some subsystems stood out as more poorly verified, including chloroplast and mitochondrial transport systems and sphingolipid metabolism, all of which exhibited <80% of transcripts detected, reflecting incomplete characterization of compartmental transporters and supporting a hypothesis of latent pathway evolution for ceramide synthesis in C. reinhardtii. Additional lines of evidence from the reconstruction effort similarly support this hypothesis including lack of ceramide synthetase and other annotation gaps downstream in sphingolipid metabolism. A similar hypothesis of latent pathway evolution was established for very long-chain fatty acids (VLCFAs) and their polyunsaturated analogs (VLCPUFAs) (Figure 1C), owing to the absence of this class of lipids in previous experimental measurements, lack of a candidate VLCFA elongase in the functional annotation, and additional downstream annotation gaps in arachidonic acid metabolism.
The network provides a detailed account of metabolic photon absorption by light-driven reactions, including photosystems I and II, light-dependent protochlorophyllide oxidoreductase, provitamin D3 photoconversion to vitamin D3, and rhodopsin photoisomerase; this network accounting permits the precise modeling of light-dependent metabolism. iRC1080 accounts for effective light spectral ranges through analysis of biochemical activity spectra (Figure 3A), either reaction activity or absorbance at varying light wavelengths. Defining effective spectral ranges associated with each photon-utilizing reaction enabled our network to model growth under different light sources via stoichiometric representation of the spectral composition of emitted light, termed prism reactions. Coefficients for different photon wavelengths in a prism reaction correspond to the ratios of photon flux in the defined effective spectral ranges to the total emitted photon flux from a given light source (Figure 3B). This approach distinguishes the amount of emitted photons that drive different metabolic reactions. We created prism reactions for most light sources that have been used in published studies for algal and plant growth including solar light, various light bulbs, and LEDs. We also included regulatory effects, resulting from lighting conditions insofar as published studies enabled. Light and dark conditions have been shown to affect metabolic enzyme activity in C. reinhardtii on multiple levels: transcriptional regulation, chloroplast RNA degradation, translational regulation, and thioredoxin-mediated enzyme regulation. Through application of our light model and prism reactions, we were able to closely recapitulate experimental growth measurements under solar, incandescent, and red LED lights. Through unbiased sampling, we were able to establish the tremendous statistical significance of the accuracy of growth predictions achievable through implementation of prism reactions. Finally, application of the photosynthetic model was demonstrated prospectively to evaluate light utilization efficiency under different light sources. The results suggest that, of the existing light sources, red LEDs provide the greatest efficiency, about three times as efficient as sunlight. Extending this analysis, the model was applied to design a maximally efficient LED spectrum for algal growth. The result was a 677-nm peak LED spectrum with a total incident photon flux of 360 μE/m2/s, suggesting that for the simple objective of maximizing growth efficiency, LED technology has already reached an effective theoretical optimum.
In summary, the C. reinhardtii metabolic network iRC1080 that we have reconstructed offers insight into the basic biology of this species and may be employed prospectively for genetic engineering design and light source design relevant to algal biotechnology. iRC1080 was used to analyze lipid metabolism and generate novel hypotheses about the evolution of latent pathways. The predictive capacity of metabolic models developed from iRC1080 was demonstrated in simulating mutant phenotypes and in evaluation of light source efficiency. Our network provides a broad knowledgebase of the biochemistry and genomics underlying global metabolism of a photoautotroph, and our modeling approach for light-driven metabolism exemplifies how integration of largely unvisited data types, such as physicochemical environmental parameters, can expand the diversity of applications of metabolic networks.
Metabolic network reconstruction encompasses existing knowledge about an organism's metabolism and genome annotation, providing a platform for omics data analysis and phenotype prediction. The model alga Chlamydomonas reinhardtii is employed to study diverse biological processes from photosynthesis to phototaxis. Recent heightened interest in this species results from an international movement to develop algal biofuels. Integrating biological and optical data, we reconstructed a genome-scale metabolic network for this alga and devised a novel light-modeling approach that enables quantitative growth prediction for a given light source, resolving wavelength and photon flux. We experimentally verified transcripts accounted for in the network and physiologically validated model function through simulation and generation of new experimental growth data, providing high confidence in network contents and predictive applications. The network offers insight into algal metabolism and potential for genetic engineering and efficient light source design, a pioneering resource for studying light-driven metabolism and quantitative systems biology.
PMCID: PMC3202792  PMID: 21811229
Chlamydomonas reinhardtii; lipid metabolism; metabolic engineering; photobioreactor
19.  Exon definition as a potential negative force against intron losses in evolution
Biology Direct  2008;3:46.
Previous studies have indicated that the wide variation in intron density (the number of introns per gene) among different eukaryotes largely reflects varying degrees of intron loss during evolution. The most popular model, which suggests that organisms lose introns through a mechanism in which reverse-transcribed cDNA recombines with the genomic DNA, concerns only one mutational force.
Using exons as the units of splicing-site recognition, exon definition constrains the length of exons. An intron-loss event results in fusion of flanking exons and thus a larger exon. The large size of the newborn exon may cause splicing errors, i.e., exon skipping, if the splicing of pre-mRNAs is initiated by exon definition. By contrast, if the splicing of pre-mRNAs is initiated by intron definition, intron loss does not matter. Exon definition may thus be a selective force against intron loss. An organism with a high frequency of exon definition is expected to experience a low rate of intron loss throughout evolution and have a high density of spliceosomal introns.
The majority of spliceosomal introns in vertebrates may be maintained during evolution not because of potential functions, but because of their splicing mechanism (i.e., exon definition). Further research is required to determine whether exon definition is a negative force in maintaining the high intron density of vertebrates.
This article was reviewed by Dr. Scott W. Roy (nominated by Dr. John Logsdon), Dr. Eugene V. Koonin, and Dr. Igor B. Rogozin (nominated by Dr. Mikhail Gelfand). For the full reviews, please go to the Reviewers' comments section.
PMCID: PMC2614967  PMID: 19014515
20.  Mechanisms Used for Genomic Proliferation by Thermophilic Group II Introns
PLoS Biology  2010;8(6):e1000391.
Studies of mobile group II introns from a thermophilic cyanobacterium reveal how these introns proliferate within genomes and might explain the origin of introns and retroelements in higher organisms.
Mobile group II introns, which are found in bacterial and organellar genomes, are site-specific retroelments hypothesized to be evolutionary ancestors of spliceosomal introns and retrotransposons in higher organisms. Most bacteria, however, contain no more than one or a few group II introns, making it unclear how introns could have proliferated to higher copy numbers in eukaryotic genomes. An exception is the thermophilic cyanobacterium Thermosynechococcus elongatus, which contains 28 closely related copies of a group II intron, constituting ∼1.3% of the genome. Here, by using a combination of bioinformatics and mobility assays at different temperatures, we identified mechanisms that contribute to the proliferation of T. elongatus group II introns. These mechanisms include divergence of DNA target specificity to avoid target site saturation; adaptation of some intron-encoded reverse transcriptases to splice and mobilize multiple degenerate introns that do not encode reverse transcriptases, leading to a common splicing apparatus; and preferential insertion within other mobile introns or insertion elements, which provide new unoccupied sites in expanding non-essential DNA regions. Additionally, unlike mesophilic group II introns, the thermophilic T. elongatus introns rely on elevated temperatures to help promote DNA strand separation, enabling access to a larger number of DNA target sites by base pairing of the intron RNA, with minimal constraint from the reverse transcriptase. Our results provide insight into group II intron proliferation mechanisms and show that higher temperatures, which are thought to have prevailed on Earth during the emergence of eukaryotes, favor intron proliferation by increasing the accessibility of DNA target sites. We also identify actively mobile thermophilic introns, which may be useful for structural studies, gene targeting in thermophiles, and as a source of thermostable reverse transcriptases.
Author Summary
Group II introns are bacterial mobile elements thought to be ancestors of introns and retroelements in higher organisms. They comprise a catalytically active intron RNA and an intron-encoded reverse transcriptase, which promotes splicing of the intron from precursor RNA and integration of the excised intron into new genomic sites. While most bacteria have small numbers of group II introns, in the thermophilic cyanobacterium Thermosynechococcus elongatus, a single intron has proliferated and constitutes 1.3% of the genome. Here, we investigated how the T. elongatus introns proliferated to such high copy numbers. We found divergence of DNA target specificity, evolution of reverse transcriptases that splice and mobilize multiple degenerate introns, and preferential insertion into other mobile introns or insertion elements, which provide new integration sites in non-essential regions of the genome. Further, unlike mesophilic group II introns, the thermophilic T. elongatus introns rely on higher temperatures to help promote DNA strand separation, facilitating access to DNA target sites. We speculate how these mechanisms, including elevated temperature, might have contributed to intron proliferation in early eukaryotes. We also identify actively mobile thermophilic introns, which may be useful for structural studies and biotechnological applications.
PMCID: PMC2882425  PMID: 20543989
21.  Evolutionary dynamics of U12-type spliceosomal introns
Many multicellular eukaryotes have two types of spliceosomes for the removal of introns from messenger RNA precursors. The major (U2) spliceosome processes the vast majority of introns, referred to as U2-type introns, while the minor (U12) spliceosome removes a small fraction (less than 0.5%) of introns, referred to as U12-type introns. U12-type introns have distinct sequence elements and usually occur together in genes with U2-type introns. A phylogenetic distribution of U12-type introns shows that the minor splicing pathway appeared very early in eukaryotic evolution and has been lost repeatedly.
We have investigated the evolution of U12-type introns among eighteen metazoan genomes by analyzing orthologous U12-type intron clusters. Examination of gain, loss, and type switching shows that intron type is remarkably conserved among vertebrates. Among 180 intron clusters, only eight show intron loss in any vertebrate species and only five show conversion between the U12 and the U2-type. Although there are only nineteen U12-type introns in Drosophila melanogaster, we found one case of U2 to U12-type conversion, apparently mediated by the activation of cryptic U12 splice sites early in the dipteran lineage. Overall, loss of U12-type introns is more common than conversion to U2-type and the U12 to U2 conversion occurs more frequently among introns of the GT-AG subtype than among introns of the AT-AC subtype. We also found support for natural U12-type introns with non-canonical terminal dinucleotides (CT-AC, GG-AG, and GA-AG) that have not been previously reported.
Although complete loss of the U12-type spliceosome has occurred repeatedly, U12 introns are extremely stable in some taxa, including eutheria. Loss of U12 introns or the genes containing them is more common than conversion to the U2-type. The degeneracy of U12-type terminal dinucleotides among natural U12-type introns is higher than previously thought.
PMCID: PMC2831892  PMID: 20163699
22.  Comparative analysis of information contents relevant to recognition of introns in many species
BMC Genomics  2011;12:45.
The basic process of RNA splicing is conserved among eukaryotic species. Three signals (5' and 3' splice sites and branch site) are commonly used to directly conduct splicing, while other features are also related to the recognition of an intron. Although there is experimental evidence pointing to the significant species specificities in the features of intron recognition, a quantitative evaluation of the divergence of these features among a wide variety of eukaryotes has yet to be conducted.
To better understand the splicing process from the viewpoints of evolution and information theory, we collected introns from 61 diverse species of eukaryotes and analyzed the properties of the nucleotide sequences relevant to splicing. We found that trees individually constructed from the five features (the three signals, intron length, and nucleotide composition within an intron) roughly reflect the phylogenetic relationships among the species but sometimes extensively deviate from the species classification. The degree of topological deviation of each feature tree from the reference trees indicates the lowest discordance for the 5' splicing signal, followed by that for the 3' splicing signal, and a considerably greater discordance for the other three features. We also estimated the relative contributions of the five features to short intron recognition in each species. Again, moderate correlation was observed between the similarities in pattern of short intron recognition and the genealogical relationships among the species. When mammalian introns were categorized into three subtypes according to their terminal dinucleotide sequences, each subtype segregated into a nearly monophyletic group, regardless of the host species, with respect to the 5' and 3' splicing signals. It was also found that GC-AG introns are extraordinarily abundant in some species with high genomic G + C contents, and that the U12-type spliceosome might make a greater contribution than currently estimated in most species.
Overall, the present study indicates that both splicing signals themselves and their relative contributions to short intron recognition are rather susceptible to evolutionary changes, while some poorly characterized properties seem to be preserved within the mammalian intron subtypes. Our findings may afford additional clues to understanding of evolution of splicing mechanisms.
PMCID: PMC3033335  PMID: 21247441
23.  Explaining evolution via constrained persistent perfect phylogeny
BMC Genomics  2014;15(Suppl 6):S10.
The perfect phylogeny is an often used model in phylogenetics since it provides an efficient basic procedure for representing the evolution of genomic binary characters in several frameworks, such as for example in haplotype inference. The model, which is conceptually the simplest, is based on the infinite sites assumption, that is no character can mutate more than once in the whole tree. A main open problem regarding the model is finding generalizations that retain the computational tractability of the original model but are more flexible in modeling biological data when the infinite site assumption is violated because of e.g. back mutations. A special case of back mutations that has been considered in the study of the evolution of protein domains (where a domain is acquired and then lost) is persistency, that is the fact that a character is allowed to return back to the ancestral state. In this model characters can be gained and lost at most once. In this paper we consider the computational problem of explaining binary data by the Persistent Perfect Phylogeny model (referred as PPP) and for this purpose we investigate the problem of reconstructing an evolution where some constraints are imposed on the paths of the tree.
We define a natural generalization of the PPP problem obtained by requiring that for some pairs (character, species), neither the species nor any of its ancestors can have the character. In other words, some characters cannot be persistent for some species. This new problem is called Constrained PPP (CPPP). Based on a graph formulation of the CPPP problem, we are able to provide a polynomial time solution for the CPPP problem for matrices whose conflict graph has no edges. Using this result, we develop a parameterized algorithm for solving the CPPP problem where the parameter is the number of characters.
A preliminary experimental analysis shows that the constrained persistent perfect phylogeny model allows to explain efficiently data that do not conform with the classical perfect phylogeny model.
PMCID: PMC4240218  PMID: 25572381
perfect phylogeny; persistent perfect phylogeny; fixed-parameter complexity
24.  Using Likelihood-Free Inference to Compare Evolutionary Dynamics of the Protein Networks of H. pylori and P. falciparum
PLoS Computational Biology  2007;3(11):e230.
Gene duplication with subsequent interaction divergence is one of the primary driving forces in the evolution of genetic systems. Yet little is known about the precise mechanisms and the role of duplication divergence in the evolution of protein networks from the prokaryote and eukaryote domains. We developed a novel, model-based approach for Bayesian inference on biological network data that centres on approximate Bayesian computation, or likelihood-free inference. Instead of computing the intractable likelihood of the protein network topology, our method summarizes key features of the network and, based on these, uses a MCMC algorithm to approximate the posterior distribution of the model parameters. This allowed us to reliably fit a flexible mixture model that captures hallmarks of evolution by gene duplication and subfunctionalization to protein interaction network data of Helicobacter pylori and Plasmodium falciparum. The 80% credible intervals for the duplication–divergence component are [0.64, 0.98] for H. pylori and [0.87, 0.99] for P. falciparum. The remaining parameter estimates are not inconsistent with sequence data. An extensive sensitivity analysis showed that incompleteness of PIN data does not largely affect the analysis of models of protein network evolution, and that the degree sequence alone barely captures the evolutionary footprints of protein networks relative to other statistics. Our likelihood-free inference approach enables a fully Bayesian analysis of a complex and highly stochastic system that is otherwise intractable at present. Modelling the evolutionary history of PIN data, it transpires that only the simultaneous analysis of several global aspects of protein networks enables credible and consistent inference to be made from available datasets. Our results indicate that gene duplication has played a larger part in the network evolution of the eukaryote than in the prokaryote, and suggests that single gene duplications with immediate divergence alone may explain more than 60% of biological network data in both domains.
Author Summary
The importance of gene duplication to biological evolution has been recognized since the 1930s. For more than a decade, substantial evidence has been collected from genomic sequence data in order to elucidate the importance and the mechanisms of gene duplication; however, most biological characteristics arise from complex interactions between the cell's numerous constituents. Recently, preliminary descriptions of the protein interaction networks have become available for species of different domains. Adapting novel techniques in stochastic simulation, the authors demonstrate that evolutionary inferences can be drawn from large-scale, incomplete network data by fitting a stochastic model of network growth that captures hallmarks of evolution by duplication and divergence. They have also analyzed the effect of summarizing protein networks in different ways, and show that a reliable and consistent analysis requires many aspects of network data to be considered jointly; in contrast to what is commonly done in practice. Their results indicate that duplication and divergence has played a larger role in the network evolution of the eukaryote P. falciparum than in the prokaryote H. pylori, and emphasize at least for the eukaryote the potential importance of subfunctionalization in network evolution.
PMCID: PMC2098858  PMID: 18052538
25.  Rapid Pathway Evolution Facilitated by Horizontal Gene Transfers across Prokaryotic Lineages
PLoS Genetics  2009;5(3):e1000402.
The evolutionary history of biological pathways is of general interest, especially in this post-genomic era, because it may provide clues for understanding how complex systems encoded on genomes have been organized. To explain how pathways can evolve de novo, some noteworthy models have been proposed. However, direct reconstruction of pathway evolutionary history both on a genomic scale and at the depth of the tree of life has suffered from artificial effects in estimating the gene content of ancestral species. Recently, we developed an algorithm that effectively reconstructs gene-content evolution without these artificial effects, and we applied it to this problem. The carefully reconstructed history, which was based on the metabolic pathways of 160 prokaryotic species, confirmed that pathways have grown beyond the random acquisition of individual genes. Pathway acquisition took place quickly, probably eliminating the difficulty in holding genes during the course of the pathway evolution. This rapid evolution was due to massive horizontal gene transfers as gene groups, some of which were possibly operon transfers, which would convey existing pathways but not be able to generate novel pathways. To this end, we analyzed how these pathways originally appeared and found that the original acquisition of pathways occurred more contemporaneously than expected across different phylogenetic clades. As a possible model to explain this observation, we propose that novel pathway evolution may be facilitated by bidirectional horizontal gene transfers in prokaryotic communities. Such a model would complement existing pathway evolution models.
Author Summary
Many biological functions, from energy metabolism to antibiotic resistance, are carried out by biological pathways that require a number of cooperatively functioning genes. Hence, underlying mechanisms in the evolution of biological pathways are of particular interest. However, compared to the evolution of individual genes, which has been well studied, the evolution of biological pathways is far less understood. In this study, we used the abundant genome sequences available today and a novel algorithm we recently developed to trace the evolutionary history of prokaryotic metabolic pathways and to analyze how these pathways emerged. We found that the pathways have experienced significantly rapid acquisition, which would play a key role in eliminating the difficulty in holding genes during the course of pathway evolution. In addition, the emergence of novel pathways was suggested to have occurred more contemporaneously than expected across different phylogenetic clades. Based on these observations, we propose that novel pathway evolution can be facilitated by bidirectional horizontal gene transfers in prokaryotic communities. This simple model may approach the question of how biological pathways requiring a number of cooperatively functioning genes can be obtained and are the core event within the evolution of biological pathways in prokaryotes.
PMCID: PMC2644373  PMID: 19266023

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Generalized Functions

The Wolfram Language's symbolic character allows it to handle generalized functions or "distributions" as a direct extension of classical mathematical functions, and to represent integrals and integral transforms that cannot be expressed in terms of continuous functions.

DiracDelta one-dimensional or multidimensional delta function

HeavisideTheta Heaviside step function, for and for

DiracComb  ▪  HeavisidePi  ▪  HeavisideLambda

Integrate, D integrals and derivatives of generalized functions

LaplaceTransform, FourierTransform integral transforms

Convolve convolve generalized functions

FunctionExpand expand out generalized functions

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Diets in Review - Find the Right Diet for You

Swim for an Effective Total Body Workout

woman swimmingSwimming is one of the best total body workouts for your body. Swimming, unlike running (for most people), is easy on the joints and can be fun depending on the type of swimming you are doing. Swimming with friends is a great way to enjoy yourself as well as enhance your physical and mental strength and endurance. This is also a great way to change up your workouts from time-to-time.

Research has shown that swimming workouts burn approximately three calories a mile per pound of body weight. One mile is 1,609 meters. So for a 150 pound person, at a 30-minute/mile pace, they would burn around 900 calories. Nine hundred calories in a half hour; it takes an hour on the treadmill at a fast pace to burn 900 calories! Below are a few different swimming workouts that you may want to give a shot!

Swim Workout 1:

Try each stroke for 25 meters: Front Crawl, Breast Stroke, Butterfly, Elementary Back Stroke, Back Crawl, and Side Stroke.

Swim Workout 2:

Try each of the previous strokes for 50 meters.

Swim Workout 3:

Try each previous stroke for 25 meters then tread water for 10 minutes and repeat.

Swim Workout 4:

Tread water for three minutes before performing each stroke for 50 meters. Example: Tread then breast stroke for 50 meters, then tread again before going into the front crawl and so on.

Swim Workout 5: Swim for as long as you can without stopping any stroke, plus the dog paddle. If you can only swim for a few minutes at a time, it is alright, just try and increase your swim time next time.

Here are a few stretches you should try before swimming:

March 8th, 2009


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yarns > Fiddle Knits > Etude Lace

Etude Lace
Fiddle Knits
Lace / 2 ply ?
875 yards (800 meters)
100 grams (3.53 ounces)
80% Merino
20% Silk

Etude Lace is an 80/20 blend of merino wool and silk. It’s soft and has a subtle sheen to it from the silk content.

TECHNICAL INFO: This yarn is dyed using acid dyes. Yarn was washed using unscented wool wash after dying. Please be aware that hand dyed yarns might bleed color slightly during their first washing.

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Top 10 Tallest Active NBA Players

It’s not news that basketball players tend to be on the tall side. But did you know that the average height of an NBA player is 6 feet 7 inches? When your career depends on your ability to take lengthy strides and reach 10-foot-high baskets, it’s not very surprising that the taller a basketball player, the better suited they are for the game.

Although there have been some short players in the NBA over the years, the vast majority of players tend to be giants (at least by non-NBA standards). Being tall is an advantage to both offensive as well as defensive players. From delivering the perfect slam dunk or 3-pointer, to preventing someone else from doing so, a player’s height plays a crucial role at every stage in the game. Since the goal of basketball is to deliver the ball to such a high basket, the advantages of being tall are pretty obvious. So, players who reach staggering heights (pun intended) in the sport are usually those who are taller than their opponents.

However, height is not the only factor that determines a player’s success in the game. The tallest players may not necessarily be the most speedy or agile. Many tall players may be clumsy because of the added coordination it requires for them to move around the court. Generally speaking, the highest-paid players are those who have a perfect combo of height and agility. Of course, being associated with a successful team helps as well. Here we list out the 10 tallest active NBA superstars and see how their salaries measure up.

10. Andrea Bargnani – 7’0″ – $10.75 million in 2013-14

Currently wearing jersey number 7 in the New York Knicks, Andrea Bargnani is originally from Italy. Standing 7’0″ tall and weighing in at 256 pounds, Bragnani began his basketball career in 2006. Before joining the Knicks squad, he played for the Toronto Raptors from 2006 to 2013. Nicknamed “Il Mago”, or “The Magician”, he helped the Raptors reach the Playoffs in his first two seasons with the team. Bargnani played in the Italian Serie A and the Euroleague prior to joining the NBA. As a forward for the Knicks, the 27-year-old athlete is making $10.75 million this season.


Here's a new entry into the continuing discussion on the Black and Latino experience.

NEGRITA, a forthcoming documentary from director/producer Magdalena Albizu, will look deeper into the experience of Afro Latinas in the United States. Consider this akin to the Black and Latino mini-doc that emerged back in January. But unlike that 10-minute piece, this project looks to be a feature-length doc with a scholarly focus on women.

The summary:

"NEGRITA will expose the dynamics of being 'Black,' the current tone of race relations between African-Americans and Hispanics in the United States, and how the Latino perception of being ‘Black’ affects Afro Latinas in the country, regardless of culture and nationality.

Why are Afro Latinas encouraged to 'marry lighter' in order to adelantar la raza (advance the race)? Why do Latinos tend to define and favor their Spanish and Indigenous heritage and often choose to identify as anything but Black?"

The production team includes producer Ingrid Matias, director of photography Donavan Lambert, and videograper Eddie Bailey.

The filmmakers are seeking $20,000 to cover the costs of research, equipment, transportation and crew, and have 15 days left to do so. Find their pitch below, and if  you like what you see, click HERE to contribute.


ingredient information
Glycerol Monooleate
Friction modifiers are added to lubricants to reduce the surface friction of the lubricated parts. Typically these are polar chemical compounds having high affinity for metal surfaces and possessing long alkyl chains. Glycerol mono-oleate is a common example of a friction modifier. This additive is needed in limited slip differentials. Glycerol is an organic compound, also commonly called glycerin or glycerine. It is a colorless, odorless, viscous liquid that is widely used in pharmaceutical formulations. Glycerol has three hydrophilic hydroxyl groups that are responsible for its solubility in water and its hygroscopic nature. The glycerol substructure is a central component of many lipids. Glycerol is sweet-tasting and of low toxicity. In foods and beverages, glycerol serves as a humectant, solvent and sweetener, and may help preserve foods. It is also used as filler in commercially prepared low-fat foods (e.g., cookies), and as a thickening agent in liqueurs. Glycerol and water are used to preserve certain types of leaves. As a sugar substitute, it has approximately 27 calories per teaspoon and is 60 percent as sweet as sucrose. Although it has about the same food energy as table sugar, it does not raise blood sugar levels, nor does it feed the bacteria that form plaques and cause dental cavities. As a food additive, glycerol is labeled as E number E422. Glycerol is also used to manufacture mono- and di-glycerides for use as emulsifiers, as well as polyglycerol esters going into shortenings and margarine. It is also used as a humectant (along with propylene glycol labelled as E1520 and/or E422) in the production of snus, a Swedish style snuff that the Swedish government subjects to the same regulations as "food" because it is used orally.


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They Wait

Review by:
Release Date:
Aspect Ratio:
Directed by:
Ernie Barbarash
Jaime King
Terry Chen
Pei-pei Cheng
Michael Biehn
Bottom Line:
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Sarah and Jason are a happy couple, living in Shanghai and raising their son Sammy.  Jason is a hard worker, dedicated to the opening of his company’s newest office. Sarah (King) is a loving mother.  Sammy is a typical kid with a rampant imagination and trouble sleeping in his own bed.
Jason receives a phone call in the middle of the night, informing him of his uncle’s death.  Soon, the trio travel to the funeral during the festival known as Ghost Month.  Sammy (Chen) almost stumbles into the forbidden part of the house, but he is stopped by Jason’s last living uncle. That scare is enough for him, and Sarah takes Sammy out of the house for some fresh air.
After running into an old photographer friend, Blake (Terminator and Aliens’ Michael Biehn), Sarah finds a pharmacist, and Sammy finds more information on the demons he sees.  Soon, Sammy comes face to face with his first demon, and a possible mentor in the strange pharmacist (Henry O). Sammy has a gift no one wants – the ability to see the dead as they come to accept the sacrifices offered them during the festival. Sammy gets his gift from his mother and she soon begins seeing her own troubled visions.
Sammy soon encounters an inviting ghost who leads him back to the forbidden area. This lab houses the processing facility where the deceased uncles employed their workers. The Chinese Humanitarian Society would often process corpses and return the bones back to their homeland. In this place, under frightening conditions, Sammy undergoes a change, setting forth the moments that will define his life, his mother and the relationship they share.
King has developed into a well-rounded actress, showing more acting chops than legs in this creepy flick. Chen is great as the focal point of the film’s first act, shifting from careful curiosity to outright panic as the script demands.
They Wait will inevitably be compared to other Asian horror films and while there are similarities, any connection should be limited to genre alone.  Ghosts and children have been at the heart of horror for decades, and while They Wait bears similarities to films like The Eye, it can just as easily be compared to Poltergeist. King’s need to track down the truth between worlds mirrors films like The Ring and The Grudge, but the film’s creativity arms it with a solid chance to overcome the retread of popular premises. Sarah’s willingness to sacrifice for her son’s life provides the payoff pitch.  Justice for those who deserve it is the key to whether or not viewers rank They Wait as its own film and not a re-tread hinges on this climax.
Hal Beckett’s original music accentuates the jumps and jolts of the film. The music is beautifully supportive of the film’s peace, making shocks stand out even more.

Your rating: None


Organized Labour, Govt Agree To Meet On Jan 26 Over Utility Hikes

The government and organised labour have made some progress towards reaching a common ground in their negotiations on workers’ demands over the upward adjustments in petroleum prices and utility tariffs.

The Minister of Employment and Labour Relations, Mr Haruna Idrissu, explained that that was after the government had agreed to provide a lifeline for the vulnerable, while organised labour also adjusted its earlier positions.

At a crunch meeting at the Flagstaff House yesterday, both parties agreed to meet on January 26 to bring finality to the negotiations to ensure industrial peace and harmony.

“I am happy to announce that we have made some progress and I am hopeful that in the early part of next week we will be able to reach a consensus with organised labour,” Mr Idrissu said.

The Secretary-General of the Trades Union Congress (TUC), Mr Kofi Asamoah, said the leadership would carry out further consultations with their members on the proposals put forward by the government.

Earlier in his opening remarks, the Employment Minister had said he had forwarded the demands made by organised labour to the President.

However, he made it clear that current economic conditions made it difficult for the government to meet those demands.

Finance Minister
The Finance Minister, Mr Seth Terkper, who was at the meeting, took the labour leaders through the prevailing economic position of the country.

He explained to them the need for the introduction of the tariffs to instill sanity in the economy and also address the power crisis.

Thousands of Ghanaian workers across the country last Wednesday poured onto the streets to demonstrate against the recent hikes in fuel and utility prices.

They wanted the government to withdraw the recently introduced Energy Sector Levies Act, which has led to a 28 per cent increase in the prices of petroleum products.

Besides, the workers wanted water and electricity tariffs, which have witnessed over 50 per cent increases, to be reduced drastically.

Two earlier meetings held between the government negotiating team and organised labour ended in deadlock, leading to the demonstration.

Labour threatened to follow a road map that would lead to a strike.

However, after yesterday’s meeting, Mr Asamoah said they would hold their fire until next week when they hoped to put an end to the disagreement.

However, he told journalists: “We will cross the bridge when nothing positive comes out of the final meeting.”

Source: Daily Graphic


12x12 frame

LeNae Gerig

12x12 frame
By LeNae Gerig

Click to Enlarge

Designer's Tip: Use wood, paper and metal elements on this collaged 3-D frame. Add some color and bring out the pattern in the paper leaves by blotting with the surface of an inkpad.

  1. Fold the bottom corner of the tan handwriting paper forward by 2". Glue a square of red dot paper behind the folded piece and glue to the center of the black frame.
  2. Mat a 5"x7" photo with textured red paper, leaving a 1/8" border, and brown cardstock, leaving a 1/2" border. Glue to the left side of the frame with the bottom corner under the fold. Glue the fold in place.
  3. Write on the journaling note card and tuck under the right side of the brown mat. Glue the postcard in place. Glue another journaling note under the top right corner of the photo.
  4. Adhere the swirl to the left side of the photo and glue tiny paper flowers and wood heart buttons threaded with red twine to the swirl.
  5. Blot the paper leaves with the brown inkpad to color. Glue under the flowers on the fold at the journaling note. Thread flower buttons with yellow twine and glue to the red dot paper under the fold. Glue 2 large buttons the post cards.
  6. Cover a chipboard door with red textured paper and trim around the door using the penknife. Lightly sand the edges and glue to the bottom right corner of the frame.
  7. Foam tape a wood tag to the top left side of the photo mat and the wood flags on the right corner of the mat. Foam tape a black blank ticket to overlap the chipboard door. Glue a twine threaded heart button to the blank ticket.
  8. Glue password notes below the photo and inside the chipboard door.


Rappaccini’s Daughter Summary Part 2

Rappaccini’s Daughter Summary Part 2

Table of Contents
Summary Part 2
Summary Part 3

Baglioni also tells him that Doctor Rappaccini is fascinated with vegetable and natural poisons and although the narrator states that there is a professional rivalry between Baglioni and Rappaccini, Giovanni wonders that at least Rappaccini must feel for his own daughter. Baglioni says he does not and that she herself (Beatrice) is an object of curiosity, both because of her beauty and high state of education from her father. Giovanni, still taking this in, leaves and with Beatrice in his mind, buys a bouquet of flowers to take back to his lodgings.

He returns with is flowers and sits, admiring the garden at his window before suddenly seeing Beatrice come out, looking radiant and he thinks again of the “analogy between the beautiful girl and the gorgeous shrub” that is in the middle of the strange garden. He watches as she approaches the strange purple flower bush and hears as she calls it “sister” as she tends to it. He also spots a small lizard that approaches Beatrice and a bit of moisture from the flower falls upon it and the lizard convulses and dies. He wonders if his imagination is betraying him and as he does so, he sees an insect that comes toward Beatrice as if attracted to her but upon coming near her, it too suddenly dies. Without knowing what he is doing, Giovanni suddenly throws the bouquet of flowers down to her in a greeting, asking her to wear one of the flowers but as she leaves and the bouquet remains, it begins to wilt and die almost immediately.

For the next several days, Giovanni tries to avoid the window and realizes that if he were wise, he would leave the lodgings, especially since his toss of the flowers opened a line of communication between the two. He is nonetheless unable to think of anything but Beatrice and one afternoon encounters Baglioni again on the streets and as Giovanni tries to avoid a conversation, the infamous dark Doctor Rappaccini comes along the sidewalk toward them and he gives Giovanni a strange cold glance. Baglioni insists that he must have scientific plans for him but Giovanni leaves him there, wondering what to do next and somehow understands that Rappaccini’s daughter is the cause for Giovanni’s distracted state.

As Giovanni returns home, his servant, Dame Lisabetta, shows him a secret entrance to the garden. He wanders in, not caring if Beatrice is an “angel or a demon” and admires the strange plants before happening upon Beatrice. He is completely taken with her and although he hints at what odd sights he saw, he does not address them directly and instead the two engage in flirtation. As they talk, Beatrice suddenly remembers to tend to the purple flower. They move near it but as Giovanni goes to touch it, she stops him, telling him it is fatal. He backs away and suddenly notices that Doctor Rappaccini is watching them but he doesn’t know for how long it had been. He returns to his chambers and is unable to think of anything but Rappaccini’s daughter.


Writer’s Block: Thoughts from a coaching seminar

Two weeks ago I wrote about the Minnesota State High School League’s “Why We Play” program and a coaches seminar at Coon Rapids High School.

Jason Olson
Jason Olson

I’ve never coached an organized team from the start of a season, so I haven’t had the chance to experience the roller coaster of emotions that make up a full season. I have helped run soccer practices here and there in my free time away from my newspaper duties. The practices were mostly fun, side games or introducing a new idea like how to defend a corner kick or more technical stuff, but it revolved around youth soccer programs in their infancy.

I have more experience with watching coaches from afar at games or practices. The variety of approaches is massive, but all seemed to have the students interests ahead of their own.

I learned several things from the condensed seminar at Coon Rapids, but what I’ve learned the most during my time working with more than a few of these educators is how much they genuinely care about the kids.

Of course we all would like to see a state title from every team, every season. That might be a goal but beyond that, what is the purpose of sport?

Teams are always going to prepare and perform to win each time they compete. That isn’t a purpose. Like Minnesota State High School League Associate Director Jody Redman described:“It’s two things. Human growth and development of the kids and connecting them to their school [and greater community].”

Separation of that goal (winning) from purpose (learn lifelong skills like teamwork, accountability and the other positive traits we look for in society) was one of the more poignant takeaways for me.

Looking back, common sense should say that in an educational-based athletic program (schools versus club-level team) the purpose should be more thoughtful than the famous Vince Lombardi quote of “Winning isn’t everything. It is the only thing.”

It sounds good in a quip or something to motivate a group of football players in a locker room before kickoff on a crisp fall night to get the emotions going. But we need to dig deeper than that.

The program looked at Joe Ehrmann’s book, “Inside Out Coaching” where he helps coaches develop a coaches statement and in turn develop that purpose using four questions: Why I coach? Why I coach the way I do? How does it feel to be coached by me? How do I define and measure success?

I received an email from a frustrated parent who appreciated the original piece but offered another angle. Paraphrasing their question: what happens when the coach puts winning as a purpose instead of a goal?

I think feelings are always going to be strong when a student is cut from a program or isn’t used in what they believe to be the best way to win.

I know the horrible feeling of being cut, but it helped form what I guess would be considered a purpose looking back as motivation to try a new sport.

Those that don’t make a team might have strong thoughts about winning at all costs, no matter age or experience level.

This begs the larger question to be answered about a play-up policy where upperclassmen are given priority on a varsity-level team over an underclassman.

I’ve seen compelling arguments on both sides of the issue from the senior that played on the JV team for three years and missed out on the varsity team for a younger student with more talent to the eighth-grader that excels on a national stage not be able to possibly bring a state title to the local school because of their age.

I’m not sure I have the perfect answer for this but I’m going to try and give my thoughts.

I understand the argument for high school varsity teams being reserved for juniors and seniors only. It is a scholastic-first idea and therefore, should be reserved as a reward for those that played at the younger levels in the program.

On the other side, if a goal is to win, shouldn’t coaches be able to start or dress those students they believe give the team the best chance to win regardless of age?

As long as the goals and purpose are clear and shared with administrators, parents and students, I believe the current state standard in place of seventh grade or older is a fitting guideline and should remain in place.

While the experience of playing a varsity sport is a unique life experience, that shouldn’t stand in the way of a capable younger student taking a spot simply based on age. That seems discriminatory on the basis of age and in all reality entitlement. Whomever performs better on the field, rink, mat or pool should earn that spot to help the team instead of giving one student a few more high school memories.

I know this might be harsh, but it seems like the only logical solution, coming from a senior captain who was a last-man cut as a freshman.

Jason Olson can be reached at  [email protected]