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'Frozen' virus genome sequences are sampled from outbreaks and have unusually low sequence divergence when compared to genome sequences from historical strains. A growing number of 'frozen' virus genome sequences are being reported as virus genome sequencing becomes more common. Examples of 'frozen' sequences include the 1977 H1N1 'Russian' flu; Venezuelan Equine Encephalitis Virus from Venezuela and Colombia in 1995; E71 sequences from a Hand, Foot and Mouth outbreak in 2007-2009 in China; and a polio strain isolated in 2014 from Anhui, China. The origin of these 'frozen' sequences has been attributed to escapes from research facilities and often appears to be associated with vaccine work. Consequently, a new paradigm for pathogen emergence appears in operation, that involves laboratory research or vaccine production which utilizes 'live' virus isolates of historical strains. The accidental release and re-emergence of such strains are straightforward to detect from their genome sequences and should spur the routine sequencing and publication of all known pathogenic viral strains undergoing experimentation, or being used for vaccine manufacture, in order to facilitate tracing. However, it is noted that novel pathogenic viruses accidentally released into the population from research facilities are harder to detect if their sequence has first not been made public, which should prompt the routine sequencing and reporting of all novel pathogenic viruses before experimentation.

The eukaryotic lineage has enjoyed a long-term "stable" mutualism between nucleus and mitochondrion, since mitochondrial endosymbiosis began about 2 billion years ago. This mostly cooperative interaction has provided the basis for eukaryotic expansion and diversification, which has profoundly altered the forms of life on Earth. While we ignore the exact biochemical details of how the alpha-proteobacterial ancestor of mitochondria entered into endosymbiosis with a proto-eukaryote, in more general terms, we present a signaling games perspective of how the cooperative relationship became established, and has been maintained. While games are used to understand organismal evolution, information-asymmetric games at the molecular level promise novel insights into endosymbiosis. Using a previously devised biomolecular signaling games approach, we model a sender-receiver information asymmetric game, in which the informed mitochondrial sender signals and the uninformed nuclear receiver may take actions (involving for example apoptosis, senescence, regeneration and autophagy/mitophagy). The simulation shows that cellularization is a stabilizing mechanism for Pareto efficient sender/receiver strategic interaction. In stark contrast, the extracellular environment struggles to maintain efficient outcomes, as senders are indifferent to the effects of their signals upon the receiver. Our hypothesis has translational implications, such as in cellular therapy, as mitochondrial medicine matures. It also inspires speculative conjectures about how an analogous human-AI endosymbiosis may be engineered.

Helicoverpa armigera , the cotton bollworm moth, is one of the world's most important crop pests, and is spreading throughout the New World from its original range in the Old World. In Brazil, invasive H. armigera has been reported to hybridize with local populations of Helicoverpa zea . The correct identification of H. armigera-H. zea hybrids is important in understanding the origin, spread and future outlook for New World regions that are affected by outbreaks, given that hybridization can potentially facilitate H. zea pesticide resistance and host plant range via introgression of H. armigera genes. Here, we present a genome admixture analysis of high quality genome sequences generated from two H. armigera-H. zea F1 hybrids generated in two different labs. Our admixture pipeline predicts 48.8% and 48.9% H. armigera for the two F1 hybrids, confirming its accuracy. Genome sequences from five H. zea and one H. armigera that were generated as part of the study show no evidence of hybridization. Interestingly, we show that four H. zea genomes generated from a previous study are predicted to possess a proportion of H. armigera genetic material. Using unsupervised clustering to identify non-hybridized H. armigera and H. zea genomes, 8511 ancestry informative markers (AIMs) were identified. Their relative frequencies are consistent with a minor H. armigera component in the four genomes, however its origin remains to be established. We show that the size and quality of genomic reference datasets are critical for accurate hybridization prediction. Consequently, we discuss potential pitfalls in genome admixture analysis of H. armigera-H. zea hybrids, and suggest measures that will improve such analyses., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The reviewer MT declared a shared affiliation with the author JV to the handling editor at the time of review., (Copyright © 2024 Trujillo, Mastrangelo, Estevez de Jensen, Verle Rodrigues, Lawrie and Massey.)

Aedes aegypti transmits major arboviruses of public health importance, including dengue, chikungunya, Zika, and yellow fever. The use of insecticides represents the cornerstone of vector control; however, insecticide resistance in Ae. aegypti has become widespread. Understanding the molecular basis of insecticide resistance in this species is crucial to design effective resistance management strategies. Here, we applied Illumina RNA-Seq to study the gene expression patterns associated with resistance to three widely used insecticides (malathion, alphacypermethrin, and lambda-cyhalothrin) in Ae. aegypti populations from two sites (Manatí and Isabela) in Puerto Rico (PR). Cytochrome P450s were the most overexpressed detoxification genes across all resistant phenotypes. Some detoxification genes (CYP6Z7, CYP28A5, CYP9J2, CYP6Z6, CYP6BB2, CYP6M9, and two CYP9F2 orthologs) were commonly overexpressed in mosquitoes that survived exposure to all three insecticides (independent of geographical origin) while others including CYP6BY1 (malathion), GSTD1 (alpha-cypermethrin), CYP4H29 and GSTE6 (lambda-cyhalothrin) were uniquely overexpressed in mosquitoes that survived exposure to specific insecticides. The gene ontology (GO) terms associated with monooxygenase, iron binding, and passive transmembrane transporter activities were significantly enriched in four out of six resistant vs. susceptible comparisons while serine protease activity was elevated in all insecticide-resistant groups relative to the susceptible strain. Interestingly, cuticular-related protein genes (chinase and chitin) were predominantly downregulated, which was also confirmed in the functional enrichment analysis. This RNA-Seq analysis presents a detailed picture of the candidate detoxification genes and other pathways that are potentially associated with pyrethroid and organophosphate resistance in Ae. aegypti populations from PR. These results could inform development of novel molecular tools for detection of resistance-associated gene expression in this important arbovirus vector and guide the design and implementation of resistance management strategies.

HKU4-related coronaviruses are a group of betacoronaviruses belonging to the same merbecovirus subgenus as Middle Eastern Respiratory Syndrome coronavirus (MERS-CoV), which causes severe respiratory illness in humans with a mortality rate of over 30%. The high genetic similarity between HKU4-related coronaviruses and MERS-CoV makes them an attractive subject of research for modeling potential zoonotic spillover scenarios. In this study, we identify a novel coronavirus contaminating agricultural rice RNA sequencing datasets from Wuhan, China. The datasets were generated by the Huazhong Agricultural University in early 2020. We were able to assemble the complete viral genome sequence, which revealed that it is a novel HKU4-related merbecovirus. The assembled genome is 98.38% identical to the closest known full genome sequence, Tylonycteris pachypus bat isolate BtTp-GX2012. Using in silico modeling, we identified that the novel HKU4-related coronavirus spike protein likely binds to human dipeptidyl peptidase 4 (DPP4), the receptor used by MERS-CoV. We further identified that the novel HKU4-related coronavirus genome has been inserted into a bacterial artificial chromosome in a format consistent with previously published coronavirus infectious clones. Additionally, we have found a near complete read coverage of the spike gene of the MERS-CoV reference strain HCoV-EMC/2012, and identify the likely presence of a HKU4-related-MERS chimera in the datasets. Our findings contribute to the knowledge of HKU4-related coronaviruses and document the use of a previously unpublished HKU4 reverse genetics system in apparent MERS-CoV related gain-of-function research. Our study also emphasizes the importance of improved biosafety protocols in sequencing centers and coronavirus research facilities.

Viruses are the simplest of pathogens, but possess sophisticated molecular mechanisms to manipulate host behavior, frequently utilizing molecular mimicry. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been shown to bind to the host receptor neuropilin-1 in order to gain entry into the cell. To do this, the virus utilizes its spike protein polybasic cleavage site (PCS), which mimics the CendR motif of neuropilin-1's endogenous ligands. In addition to facilitating cell entry, binding to neuropilin-1 has analgesic effects. We discuss the potential impact of neuropilin-1 binding by SARS-CoV-2 in ameliorating sickness behavior of the host, and identify a convergent evolutionary strategy of PCS cleavage and subsequent neuropilin binding in other human viruses. In addition, we discuss the evolutionary leap of the ancestor of SARS-COV-2, which involved acquisition of the PCS thus faciliting binding to the neuropilin-1 receptor. Acquisition of the PCS by the ancestor of SARS-CoV-2 appears to have led to pleiotropic beneficial effects including enhancement of cell entry via binding to ACE2, facilitation of cell entry via binding to neuropilin-1, promotion of analgesia, and potentially the formation of decoy epitopes via enhanced shedding of the S1 subunit. Lastly, other potential neuromanipulation strategies employed by SARS-CoV-2 are discussed, including interferon suppression and the resulting reduction in sickness behavior, enhanced transmission through neurally mediated cough induction, and reduction in sense of smell., (© 2021. Springer Nature B.V.)

Mimicry is exhibited in multiple scales, ranging from molecular, to organismal, and then to human society. 'Batesian'-type mimicry entails a conflict of interest between sender and receiver, reflected in a deceptive mimic signal. 'Müllerian'-type mimicry occurs when there is perfect common interest between sender and receiver in a particular type of encounter, manifested by an honest co-mimic signal. Using a signalling games approach, simulations show that invasion by Batesian mimics will make Müllerian mimicry unstable, in a coevolutionary chase. We use these results to better understand the deceptive strategies of SARS-CoV-2 and their key role in the COVID-19 pandemic. At the biomolecular level, we explain how cellularization promotes Müllerian molecular mimicry, and discourages Batesian molecular mimicry. A wide range of processes analogous to cellularization are presented; these might represent a manner of reducing oscillatory instabilities. Lastly, we identify examples of mimicry in human society that might be addressed using a signalling game approach.

Apicomplexans are alveolate parasites which include Plasmodium falciparum, the main cause of malaria, one of the world's biggest killers from infectious disease. Apicomplexans are characterized by a reduction in proteome size, which appears to result from metabolic and functional simplification, commensurate with their parasitic lifestyle. However, other factors may also help to explain gene loss such as population bottlenecks experienced during transmission, and the effect of reducing the overall genomic information content. The latter constitutes an 'informational constraint', which is proposed to exert a selective pressure to evolve and maintain genes involved in informational fidelity and error correction, proportional to the quantity of information in the genome (which approximates to proteome size). The dynamics of gene loss was examined in 41 Apicomplexan genomes using orthogroup analysis. We show that loss of genes involved in amino acid metabolism and steroid biosynthesis can be explained by metabolic redundancy with the host. We also show that there is a marked tendency to lose DNA repair genes as proteome size is reduced. This may be explained by a reduction in size of the informational constraint and can help to explain elevated mutation rates in pathogens with reduced genome size. Multiple Sequentially Markovian Coalescent (MSMC) analysis indicates a recent bottleneck, consistent with predictions generated using allele-based population genetics approaches, implying that relaxed selection pressure due to reduced population size might have contributed to gene loss. However, the non-randomness of pathways that are lost challenges this scenario. Lastly, we identify unique orthogroups in malaria-causing Plasmodium species that infect humans, with a high proportion of membrane associated proteins. Thus, orthogroup analysis appears useful for identifying novel candidate pathogenic factors in parasites, when there is a wide sample of genomes available., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Mimicry is exhibited in multiple scales, ranging from molecular, to organismal, and then to human society. 'Batesian' type mimicry entails a conflict of interest between sender and receiver, reflected in a deceptive mimic signal. 'Mullerian' type mimicry occurs when there is perfect common interest between sender and receiver, manifested by an honest co-mimic signal. Using a signaling games approach, simulations show that invasion by Batesian mimics will make Mullerian mimicry unstable, in a coevolutionary chase. We use these results to better understand the deceptive strategies of SARS-CoV-2 and their key role in the COVID-19 pandemic. At the biomolecular level, we explain how cellularization promotes Mullerian molecular mimicry, and discourages Batesian molecular mimicry. A wide range of processes analogous to cellularization are presented; these might represent a manner of reducing oscillatory instabilities. Lastly, we identify examples of mimicry in human society, that might be addressed using a signaling game approach.

The photosynthetic picoeukaryotes (PPEs) comprise a rare example of free-living eukaryotes that have undergone genome reduction. Here, we examine a duality in the process; the proposed driver of genome reduction (the Black Queen hypothesis, BQH), and the resultant impact of genome information loss (the Proteomic Constraint hypothesis, PCH). The BQH predicts that some metabolites may be shared in the open ocean, thus driving loss of redundant metabolic pathways in individual genomes. In contrast, the PCH predicts that as the information content of a genome is reduced, the total mutation load is also reduced, leading to loss of DNA repair genes due to the resulting reduction in selective constraint. Consistent with the BQH, we observe that biosynthetic pathways involved with soluble metabolites such as amino acids and carotenoids are preferentially lost from the PPEs, in contrast to biosynthetic pathways involved with insoluble metabolites, such as lipids, which are retained. Consistent with the PCH, a correlation between proteome size and the number of DNA repair genes, and numerous other informational categories, is observed. While elevated mutation rates resulting from the loss of DNA repair genes have been linked to reduced effective population sizes in intracellular bacteria, this remains to be established. This study shows that in microbial species with large population sizes, an underlying factor in modulating their DNA repair capacity appears to be information content.

Despite some previous examples of successful application to the field of pharmacogenomics, the utility of machine learning (ML) techniques for warfarin dose predictions in Caribbean Hispanic patients has yet to be fully evaluated. This study compares seven ML methods to predict warfarin dosing in Caribbean Hispanics. This is a secondary analysis of genetic and non-genetic clinical data from 190 cardiovascular Hispanic patients. Seven ML algorithms were applied to the data. Data was divided into 80 and 20% to be used as training and test sets. ML algorithms were trained with the training set to obtain the models. Model performance was determined by computing the corresponding mean absolute error (MAE) and % patients whose predicted optimal dose were within ±20% of the actual stabilization dose, and then compared between groups of patients with "normal" (i.e., > 21 but <49 mg/week), low (i.e., ≤21 mg/week, "sensitive"), and high (i.e., ≥49 mg/week, "resistant") dose requirements. Random forest regression (RFR) significantly outperform all other methods, with a MAE of 4.73 mg/week and 80.56% of cases within ±20% of the actual stabilization dose. Among those with "normal" dose requirements, RFR performance is also better than the rest of models (MAE = 2.91 mg/week). In the "sensitive" group, support vector regression (SVR) shows superiority over the others with lower MAE of 4.79 mg/week. Finally, multivariate adaptive splines (MARS) shows the best performance in the resistant group (MAE = 7.22 mg/week) and 66.7% of predictions within ±20%. Models generated by using RFR, MARS, and SVR algorithms showed significantly better predictions of weekly warfarin dosing in the studied cohorts than other algorithms. Better performance of the ML models for patients with "normal," "sensitive," and "resistant" to warfarin were obtained when compared to other populations and previous statistical models., (Copyright © 2020 Roche-Lima, Roman-Santiago, Feliu-Maldonado, Rodriguez-Maldonado, Nieves-Rodriguez, Carrasquillo-Carrion, Ramos, da Luz Sant’Ana, Massey and Duconge.)

Biomolecular networks have already found great utility in characterizing complex biological systems arising from pairwise interactions amongst biomolecules. Here, we explore the important and hitherto neglected role of information asymmetry in the genesis and evolution of such pairwise biomolecular interactions. Information asymmetry between sender and receiver genes is identified as a key feature distinguishing early biochemical reactions from abiotic chemistry, and a driver of network topology as biomolecular systems become more complex. In this context, we review how graph theoretical approaches can be applied not only for a better understanding of various proximate (mechanistic) relations, but also, ultimate (evolutionary) structures encoded in such networks from among all types of variations they induce. Among many possible variations, we emphasize particularly the essential role of gene duplication in terms of signaling game theory , whereby sender and receiver gene players accrue benefit from gene duplication, leading to a preferential attachment mode of network growth. The study of the resulting dynamics suggests many mathematical/computational problems, the majority of which are intractable yet yield to efficient approximation algorithms, when studied through an algebraic graph theoretic lens. We relegate for future work the role of other possible generalizations, additionally involving horizontal gene transfer, sexual recombination, endo-symbiosis, etc., which enrich the underlying graph theory even further.

Biological macromolecules encode information: some of it to endow the molecule with structural flexibility, some of it to enable molecular actions as a catalyst or a substrate, but a residual part can be used to communicate with other macromolecules. Thus, macromolecules do not need to possess information only to survive in an environment, but also to strategically interact with others by sending signals to a receiving macromolecule that can properly interpret the signal and act suitably. These sender-receiver signalling games are sustained by the information asymmetry that exists among the macromolecules. In both biochemistry and molecular evolution, the important role of information asymmetry remains largely unaddressed. Here, we provide a new unifying perspective on the impact of information symmetry between macromolecules on molecular evolutionary processes, while focusing on molecular deception. Biomolecular games arise from the ability of biological macromolecules to exert precise recognition, and their role as units of selection, meaning that they are subject to competition and cooperation with other macromolecules. Thus, signalling game theory can be used to better understand fundamental features of living systems such as molecular recognition, molecular mimicry, selfish elements and 'junk' DNA. We show how deceptive behaviour at the molecular level indicates a conflict of interest, and so provides evidence of genetic conflict. This model proposes that molecular deception is diagnostic of selfish behaviour, helping to explain the evasive behaviour of transposable elements in 'junk' DNA, for example. Additionally, in this broad review, a range of major evolutionary transitions are shown to be associated with the establishment of signalling conventions, many of which are susceptible to molecular deception. These perspectives allow us to assign rudimentary behaviour to macromolecules, and show how participation in signalling games differentiates biochemistry from abiotic chemistry., (© 2018 The Author(s).)

Stop codon reassignments are widely distributed in prokaryotic, eukaryotic and organellar genomes, but are remarkably convergent in terms of the stop codons and amino acids reassigned. Strikingly, the identities of stop codon reassignments are closely matched to the properties of naturally occurring nonsense suppressor (NONS) tRNAs, suggesting that pre-existing nonsense suppression in an ancestral tRNA facilitated the occurrence of stop codon reassignments. Here this idea is expanded, by exploring the mechanism by which the gene duplication of tRNAs has occurred, leading to the reassignment of stop codons. Two types of stop codon reassignment are identified: those that necessitate a tRNA gene duplication, and those that do not because a single tRNA can recognize the reassigned stop codon and the canonical codon(s) for the cognate amino acid. Where tRNA gene duplication has occurred, this implies a multi-functional ancestral NONS tRNA, followed by adaptive mutation in the anticodon of one of the gene duplicates to become complementary to the stop codon, constituting a clear example of escape from adaptive conflict. The best exemplar is the UAA+UAG →gln reassignment, which has occurred 9 times independently in a diverse range of genomes, and appears to reflect the widespread occurrence of naturally occurring nonsense suppression of the UAA+UAG stop codons by glutamine tRNAs. Consideration of pre-existing tRNA functionality and the mechanism of gene duplication provide new insights into the process of stop codon reassignment., (Copyright © 2017 Elsevier B.V. All rights reserved.)

A large discrepancy between the Amerindian contribution to the mitochondrial and nuclear genetic components of 55 Puerto Rican (PR) genomes from the 1000 Genomes Project is identified, with Amerindian mitochondrial haplotypes being highly represented (67.3%), in strong contrast to the Amerindian autosomal contribution (12.9%). I examine the potential causes behind this strong mitonuclear discordance. The Amerindian contribution to the X chromosome is 19.8%, implying assortative mating with Amerindian females during the establishment of the PR population. However, this scenario does not account for the extraordinarily high Amerindian mitochondrial contribution. Demographic simulation of simple assortative mating scenarios during establishment of the PR population indicates that the observed Amerindian mitochondrial contribution is higher than expected. The simulations show that expansion from a small founding population does not produce the observed frequencies, instead producing the frequencies expected under neutrality, with the Amerindian mitochondrial frequencies approximately twice the Amerindian autosomal proportion. In addition, multiple replicated simulations show that drift is an unlikely explanation for the elevated Amerindian mitochondrial frequency, as these are unable to produce the elevated Amerindian mitochondrial frequency observed in the PR genomic dataset, under a range of different starting conditions. I conclude that the mitonuclear discordance appears most consistent with adaptive mitochondrial benefit; however, the molecular mechanism(s) remain to be characterized before this can be confirmed and warrant further investigation. Lastly, I show potential evidence of selection on autosomes and allosomes, using admixture proportions. Interestingly, the major histocompatibility complex locus on chromosome 6 shows greatly elevated single nucleotide polymorphism density but is unaccompanied by strong admixture variance. The observations on mitonuclear discordance may affect the interpretation of apparent assortative mating in recent human admixture events, which should be treated with caution when relying only on mitochondrial haplotype frequencies., (© 2017 John Wiley & Sons Ltd/University College London.)

Tenuipalpidae comprises mites that transmit viruses to agriculturally important plants. Several tenuipalpid species present parthenogenesis, and in Brevipalpus yothersi , the endosymbiont Cardinium has been associated with female-only colonies. It is unclear what the bacterial composition of B. yothersi is, and how common Cardinium is in those microbiomes. We performed a comparative analysis of the bacteriomes in three populations of B. yothersi and three additional Tetranychoidea species using sequences from V4-fragment of 16S DNA. The bacteriomes were dominated by Bacteroidetes (especially Cardinium ) and Proteobacteria, showing a remarkably low alpha diversity. Cardinium was present in about 22% of all sequences; however, it was not present in R. indica and T. evansi . In B. yothersi , the proportion of Cardinium was higher in adults than eggs, suggesting that proliferation of the bacteria could be the result of selective pressures from the host. This hypothesis was further supported because colonies of B. yothersi from different populations showed different bacterial assemblages, and bacteriomes from different mite species showed similar abundances of Cardinium . A phylogenetic analysis of Cardinium revealed that not only specialization but horizontal transmission has been important for this symbiosis. Together, these results represent a glimpse into the evolution of the Tetranychoidea and Cardinium ., Competing Interests: The authors declare no conflict of interest.

An endogenous retrovirus that is present in the sea slug Elysia chlorotica is expressed in all individuals at the end of the annual life cycle. But the precise role of the virus, if any, in slug senescence or death is unknown. We have determined the genomic sequence of the virus and performed a phylogenetic analysis of the data. The 6060-base pair genome of the virus possesses a reverse transcriptase-domain-containing protein that shows similarity to retrotransposon sequences found in Aplysia californica and Strongylocentrotus purpuratus. However, nucleotide BLAST analysis of the whole genome resulted in hits to only a few portions of the genome, indicating that the Elysia chlorotica retrovirus is novel, has not been previously sequenced, and does not have great genetic similarity to other known viral species. When more invertebrate retroviral genomes are examined, a more precise phylogenetic placement of the Elysia chlorotica retrovirus can be determined.

The standard genetic code (SGC) assigns amino acids to codons in such a way that the impact of point mutations is reduced, this is termed 'error minimization' (EM). The occurrence of EM has been attributed to the direct action of selection, however it is difficult to explain how the searching of alternative codes for an error minimized code can occur via codon reassignments, given that these are likely to be disruptive to the proteome. An alternative scenario is that EM has arisen via the process of genetic code expansion, facilitated by the duplication of genes encoding charging enzymes and adaptor molecules. This is likely to have led to similar amino acids being assigned to similar codons. Strikingly, we show that if during code expansion the most similar amino acid to the parent amino acid, out of the set of unassigned amino acids, is assigned to codons related to those of the parent amino acid, then genetic codes with EM superior to the SGC easily arise. This scheme mimics code expansion via the gene duplication of charging enzymes and adaptors. The result is obtained for a variety of different schemes of genetic code expansion and provides a mechanistically realistic manner in which EM has arisen in the SGC. These observations might be taken as evidence for self-organization in the earliest stages of life., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Forensic science concerns the application of scientific techniques to questions of a legal nature and may also be used to address questions of historical importance. Forensic techniques are often used in legal cases that involve crimes against persons or property, and they increasingly may involve cases of bioterrorism, crimes against nature, medical negligence, or tracing the origin of food- and crop-borne disease. Given the rapid advance of genome sequencing and comparative genomics techniques, we ask how these might be used to address cases of a forensic nature, focusing on the use of microbial genome sequence analysis. Such analyses rely on the increasingly large numbers of microbial genomes present in public databases, the ability of individual investigators to rapidly sequence whole microbial genomes, and an increasing depth of understanding of their evolution and function. Suggestions are made as to how comparative microbial genomics might be applied forensically and may represent possibilities for the future development of forensic techniques. A particular emphasis is on the nascent field of genomic epidemiology, which utilizes rapid whole-genome sequencing to identify the source and spread of infectious outbreaks. Also discussed is the application of comparative microbial genomics to the study of historical epidemics and deaths and how the approaches developed may also be applicable to more recent and actionable cases.

Here, social network analysis approaches are used to characterize the figure of the biblical Moses, and his relationship with characters from the books of the Pentateuch; Genesis, Exodus, Leviticus, Numbers and Deuteronomy. The potential value of using such quantitative approaches is explored in relation to other forms of textual exegesis. Using a maximum likelihood approach, the degree distributions of the social networks are shown to approximate to a power law with exponential cutoff. The node representing Moses is very highly connected and falls outside the best fit line, as does the node representing Yahweh, which may indicate authorial emphasis. Only the social network from Genesis is assortative, a property typical of many real world social networks. A substantial proportion of disassortativity in the social network based around Moses disappears when the node is removed, potentially indicating some artificiality in its orientation within the network. The approximation of the degree distributions to a power law with exponential cutoff represents an emergent property resulting from the combinatorial and collaborative manner of composition, and indicates a bounding constraint on more highly connected nodes. Unusually highly connected nodes representing the deity and prophet may be characteristic of social networks derived from religious texts.

The concept of a "proteomic constraint" proposes that DNA repair capacity is positively correlated with the information content of a genome, which can be approximated to the size of the proteome (P). This in turn implies that DNA repair genes are more likely to be present in genomes with larger values of P. This stands in contrast to the common assumption that informational genes have a core function and so are evenly distributed across organisms. We examined the presence/absence of 18 DNA repair genes in bacterial genomes. A positive relationship between gene presence and P was observed for 17 genes in the total dataset, and 16 genes when only nonintracellular bacteria were examined. A marked reduction of DNA repair genes was observed in intracellular bacteria, consistent with their reduced value of P. We also examined archaeal and DNA virus genomes, and show that the presence of DNA repair genes is likewise related to a larger value of P. In addition, the products of the bacterial genes mutY, vsr, and ndk, involved in the correction of GC/AT mutations, are strongly associated with reduced genome GC content. We therefore propose that a reduction in information content leads to a loss of DNA repair genes and indirectly to a reduction in genome GC content in bacteria by exposure to the underlying AT mutation bias. The reduction in P may also indirectly lead to the increase in substitution rates observed in intracellular bacteria via loss of DNA repair genes., (© The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Nanopore DNA sequencing via transverse current has emerged as a promising candidate for third-generation sequencing technology. It produces long read lengths which could alleviate problems with assembly errors inherent in current technologies. However, the high error rates of nanopore sequencing have to be addressed. A very important source of the error is the intrinsic noise in the current arising from carrier dispersion along the chain of the molecule, i.e., from the influence of neighboring bases. In this work we perform calculations of the transverse current within an effective multi-orbital tight-binding model derived from first-principles calculations of the DNA/RNA molecules, to study the effect of this structural noise on the error rates in DNA/RNA sequencing via transverse current in nanopores. We demonstrate that a statistical technique, utilizing not only the currents through the nucleotides but also the correlations in the currents, can in principle reduce the error rate below any desired precision.

The standard genetic code (SGC) is central to molecular biology and its origin and evolution is a fundamental problem in evolutionary biology, the elucidation of which promises to reveal much about the origins of life. In addition, we propose that study of its origin can also reveal some fundamental and generalizable insights into mechanisms of molecular evolution, utilizing concepts from complexity theory. The first is that beneficial traits may arise by non-adaptive processes, via a process of "neutral emergence". The structure of the SGC is optimized for the property of error minimization, which reduces the deleterious impact of point mutations. Via simulation, it can be shown that genetic codes with error minimization superior to the SGC can emerge in a neutral fashion simply by a process of genetic code expansion via tRNA and aminoacyl-tRNA synthetase duplication, whereby similar amino acids are added to codons related to that of the parent amino acid. This process of neutral emergence has implications beyond that of the genetic code, as it suggests that not all beneficial traits have arisen by the direct action of natural selection; we term these "pseudaptations", and discuss a range of potential examples. Secondly, consideration of genetic code deviations (codon reassignments) reveals that these are mostly associated with a reduction in proteome size. This code malleability implies the existence of a proteomic constraint on the genetic code, proportional to the size of the proteome (P), and that its reduction in size leads to an "unfreezing" of the codon - amino acid mapping that defines the genetic code, consistent with Crick's Frozen Accident theory. The concept of a proteomic constraint may be extended to propose a general informational constraint on genetic fidelity, which may be used to explain variously, differences in mutation rates in genomes with differing proteome sizes, differences in DNA repair capacity and genome GC content between organisms, a selective pressure in the evolution of sexual reproduction, and differences in translational fidelity. Lastly, the utility of the concept of an informational constraint to other diverse fields of research is explored.

Helicobacter pylori is a bacterium that lives in the human stomach and is a major risk factor for gastric cancer and ulcers. H.pylori is host dependent and has been carried with human populations around the world after their departure from Africa. We wished to investigate how H.pylori has coevolved with its host during that time, focusing on strains from Japanese and European populations, given that gastric cancer incidence is high in Japanese populations, while low in European. A positive selection analysis of eight H.pylori genomes was conducted, using maximum likelihood based pairwise comparisons in order to maximize the number of strain-specific genes included in the study. Using the genic Ka/Ks ratio, comparisons of four Japanese H.pylori genomes suggests 25-34 genes under positive selection, while four European H.pylori genomes suggests 16-21 genes; few of the genes identified were in common between lineages. Of the identified genes which were annotated, 38% possessed homologs associated with pathogenicity and / or host adaptation, consistent with their involvement in a coevolutionary 'arms race' with the host. Given the efficacy of identifying host interaction factors de novo, in the absence of functionally annotated homologs our evolutionary approach may have value in identifying novel genes which H.pylori employs to interact with the human gut environment. In addition, the larger number of genes inferred as being under positive selection in Japanese strains compared to European implies a stronger overall adaptive pressure, potentially resulting from an elevated immune response which may be linked to increased inflammation, an initial stage in the development of gastric cancer., (© The Author(s) 2015. Published by Oxford University Press on behalf of the Foundation for Evolution, Medicine, and Public Health.)

Background: Adaptive alleles may rise in frequency as a consequence of positive selection, creating a pattern of decreased variation in the neighboring loci, known as a selective sweep. When the region containing this pattern is compared to another population with no history of selection, a rise in variance of allele frequencies between populations is observed. One challenge presented by large genome-wide datasets is the ability to differentiate between patterns that are remnants of natural selection from those expected to arise at random and/or as a consequence of selectively neutral demographic forces acting in the population., Findings: SmileFinder is a simple program that looks for diversity and divergence patterns consistent with selection sweeps by evaluating allele frequencies in windows, including neighboring loci from two or more populations of a diploid species against the genome-wide neutral expectation. The program calculates the mean of heterozygosity and FST in a set of sliding windows of incrementally increasing sizes, and then builds a resampled distribution (the baseline) of random multi-locus sets matched to the sizes of sliding windows, using an unrestricted sampling. Percentiles of the values in the sliding windows are derived from the superimposed resampled distribution. The resampling can easily be scaled from 1 K to 100 M; the higher the number, the more precise the percentiles ascribed to the extreme observed values., Conclusions: The output from SmileFinder can be used to plot percentile values to look for population diversity and divergence patterns that may suggest past actions of positive selection along chromosome maps, and to compare lists of suspected candidate genes under random gene sets to test for the overrepresentation of these patterns among gene categories. Both applications of the algorithm have already been used in published studies. Here we present a publicly available, open source program that will serve as a useful tool for preliminary scans of selection using worldwide databases of human genetic variation, as well as population datasets for many non-human species, from which such data is rapidly emerging with the advent of new genotyping and sequencing technologies.

Objective: HIV-1 variants with different tropisms are associated with various neuropathologies. This study intends to determine if this correlation is determined by unique viral env sequences. We hypothesize that HIV-1 envelope gene sequence changes are associated with cognition status., Methods: Viral RNA was extracted from peripheral blood mononuclear cells (PBMCs) co-cultures derived from HIV-1 infected Hispanic women that had been characterized for HIV associated neurocognitive disorders (HAND)., Results: Analyses of the C2V4 region of HIV gp120 demonstrated that increased sequence diversity correlates with cognition status as sequences derived from subjects with normal cognition exhibited less diversity than sequences derived from subjects with cognitive impairment. In addition, differences in V3 and V4 loop charges were also noted as well as differences in the N-glycosylation of the V4 region., Conclusions: Our data suggest that the genetic signature within the C2V4 region may contribute to the pathogenesis of HAND. HIV env sequence characteristics for the isolates grouped in milder forms of HAND can provide insightful information of prognostic value to assess neurocognitive status in HIV + subjects, particularly during the era of highly prevalent milder forms of HAND.

Coprolites are fossilized feces that can be used to provide information on the composition of the intestinal microbiota and, as we show, possibly on diet. We analyzed human coprolites from the Huecoid and Saladoid cultures from a settlement on Vieques Island, Puerto Rico. While more is known about the Saladoid culture, it is believed that both societies co-existed on this island approximately from 5 to 1170 AD. By extracting DNA from the coprolites, followed by metagenomic characterization, we show that both cultures can be distinguished from each other on the basis of their bacterial and fungal gut microbiomes. In addition, we show that parasite loads were heavy and also culturally distinct. Huecoid coprolites were characterized by maize and Basidiomycetes sequences, suggesting that these were important components of their diet. Saladoid coprolite samples harbored sequences associated with fish parasites, suggesting that raw fish was a substantial component of their diet. The present study shows that ancient DNA is not entirely degraded in humid, tropical environments, and that dietary and/or host genetic differences in ancient populations may be reflected in the composition of their gut microbiome. This further supports the hypothesis that the two ancient cultures studied were distinct, and that they retained distinct technological/cultural differences during an extended period of close proximity and peaceful co-existence. The two populations seemed to form the later-day Taínos, the Amerindians present at the point of Columbian contact. Importantly, our data suggest that paleomicrobiomics can be a powerful tool to assess cultural differences between ancient populations.

Circadian rhythms in social insects are highly plastic and are modulated by multiple factors. In addition, complex behaviors such as sun-compass orientation and time learning are clearly regulated by the circadian system in these organisms. Despite these unique features of social insect clocks, the mechanisms as well as the functional and evolutionary relevance of these traits remain largely unknown. Here we show a modification of the Drosophila activity monitoring (DAM) system that allowed us to measure locomotor rhythms of the honey bee, Apis mellifera (three variants; gAHB, carnica and caucasica), and two paper wasps (Polistes crinitus and Mischocyttarus phthisicus). A side-by-side comparison of the endogenous period under constant darkness (free-running period) led us to the realization that these social insects exhibit significant deviations from the Earth's 24 h rotational period as well as a large degree of inter-individual variation compared with Drosophila. Experiments at different temperatures, using honey bees as a model, revealed that testing the endogenous rhythm at 35°C, which is the hive's core temperature, results in average periods closer to 24 h compared with 25°C (23.8 h at 35°C versus 22.7 h at 25°C). This finding suggests that the degree of tuning of circadian temperature compensation varies among different organisms. We expect that the commercial availability, cost-effectiveness and integrated nature of this monitoring system will facilitate the growth of the circadian field in these social insects and catalyze our understanding of the mechanisms as well as the functional and evolutionary relevance of circadian rhythms.

Proteins are regarded as being robust to the deleterious effects of mutations. Here, the neutral emergence of mutational robustness in a population of single domain proteins is explored using computer simulations. A pairwise contact model was used to calculate the ΔG of folding (ΔG folding) using the three dimensional protein structure of leech eglin C. A random amino acid sequence with low mutational robustness, defined as the average ΔΔG resulting from a point mutation (ΔΔG average), was threaded onto the structure. A population of 1,000 threaded sequences was evolved under selection for stability, using an upper and lower energy threshold. Under these conditions, mutational robustness increased over time in the most common sequence in the population. In contrast, when the wild type sequence was used it did not show an increase in robustness. This implies that the emergence of mutational robustness is sequence specific and that wild type sequences may be close to maximal robustness. In addition, an inverse relationship between ∆∆G average and protein stability is shown, resulting partly from a larger average effect of point mutations in more stable proteins. The emergence of mutational robustness was also observed in the Escherichia coli colE1 Rop and human CD59 proteins, implying that the property may be common in single domain proteins under certain simulation conditions. The results indicate that at least a portion of mutational robustness in small globular proteins might have arisen by a process of neutral emergence, and could be an example of a beneficial trait that has not been directly selected for, termed a "pseudaptation."

The concept of a 'proteomic constraint' proposes that the information content of the proteome exerts a selective pressure to reduce mutation rates, implying that larger proteomes produce a greater selective pressure to evolve or maintain DNA repair, resulting in a decrease in mutational load. Here, the distribution of 21 recombination repair genes was characterized across 900 bacterial genomes. Consistent with prediction, the presence of 17 genes correlated with proteome size. Intracellular bacteria were marked by a pervasive absence of recombination repair genes, consistent with their small proteome sizes, but also consistent with alternative explanations that reduced effective population size or lack of recombination may decrease selection pressure. However, when only non-intracellular bacteria were examined, the relationship between proteome size and gene presence was maintained. In addition, the more widely distributed (i.e. conserved) a gene, the smaller the average size of the proteomes from which it was absent. Together, these observations are consistent with the operation of a proteomic constraint on DNA repair. Lastly, a correlation between gene absence and genome AT content was shown, indicating a link between absence of DNA repair and elevated genome AT content., (Copyright © 2013 Elsevier B.V. All rights reserved.)

Given that microbial interactions in nature are very complex, we propose that quorum-sensing, as well as quorum-quenching, phenazine and secondary metabolite production, resistance and toxin-antitoxin systems within a microbial community should all comprise the battery of processes involving the study of what we would define as the "sociomicrobiome". In the present study the genes/molecules, subsystems and taxonomic breakup of the mentioned processes were identified in decaying tropical wood from the El Yunque rainforest in Puerto Rico, and soil using a shotgun metagenomic approach. The rapid decomposition of wood and litter in tropical regions suggests that processes in these settings are governed by unexplored microbes with the potential of being further studied and exploited for various purposes. Both ecosystems were characterized by the presence of specific genes/molecules, subsystems and microbes associated with the mentioned processes, although the average abundances for specific processes differed. Of the sociomicrobiomes studied, that from El Yunque was found to be the most complex. The approach considered in the present study could also be applied to study the sociomicrobiome of other ecosystems.

This paper describes a novel application of information-asymmetric (signalling) games to molecular biology in which utility is determined by the message complexity (rate) in addition to the error in information transfer (distortion). We show using a computational model how it is possible for the agents in one such game to evolve a signalling convention (separating equilibrium) that is suboptimal in terms of information transfer, but is nonetheless stable. In the context of an RNA world merging with a nascent amino acid one, such a game's equilibrium is alluded to by the genetic code, which is nearly optimal in terms of information transfer, but is also near-universal and nearly immutable. Such a framework suggests that cellularity may have emerged to encourage coordination between RNA species and sheds light on other aspects of RNA world biochemistry yet to be fully understood.

DNA repair is expected to be a modulator of underlying mutation rates, however the major factors affecting the distribution of DNA repair pathways have not been determined. The Proteomic Constraint theory proposes that mutation rates are inversely proportional to the amount of heredity information contained in a genome, which is effectively the proteome. Thus, organisms with larger proteomes are expected to possess more efficient DNA repair. We show that an important factor influencing the presence or absence of four DNA repair genes mutM, mutY, mutL, and mutS is indeed the size of the bacterial proteome. This is true both of intracellular and other bacteria. In addition, the relationship of DNA repair to genome GC content was examined. In principle, if a DNA repair pathway is biased in the types of mutations it corrects, this may alter the genome GC content. The presence of the mismatch repair genes mutL and mutS was not correlated with genome GC content, consistent with their involvement in an unbiased DNA repair pathway. In contrast, the presence of the base excision repair genes mutM and mutY, whose products both correct GC → AT mutations, was positively correlated with genome GC content, consistent with their biased repair mechanism. Phylogenetic analysis however indicates that the relationship between the presence of mutM and mutY genes and genome GC content is not a simple one.

Background: Helicobacter pylori is a vertically inherited gut commensal that is carcinogenic if it possesses the cag pathogenicity island (cag PaI); infection with H.pylori is the major risk factor for gastric cancer, the second leading cause of death from cancer worldwide (WHO). The cag PaI locus encodes the cagA gene, whose protein product is injected into stomach epithelial cells via a Type IV secretion system, also encoded by the cag PaI. Once there, the cagA protein binds to various cellular proteins, resulting in dysregulation of cell division and carcinogenesis. For this reason, cagA may be described as an oncoprotein. A clear understanding of the mechanism of action of cagA and its benefit to the bacteria is lacking., Results: Here, we reveal that the cagA gene displays strong signatures of positive selection in bacteria isolated from amerindian populations, using the Ka/Ks ratio. Weaker signatures are also detected in the gene from bacteria isolated from asian populations, using the Ka/Ks ratio and the more sensitive branches-sites model of the PAML package. When the cagA gene isolated from amerindian populations was examined in more detail it was found that the region under positive selection contains the EPIYA domains, which are known to modulate the carcinogenicity of the gene. This means that the carcinogenicity modulating region of the gene is undergoing adaptation. The results are discussed in relation to the high incidences of stomach cancer in some latin american and asian populations., Conclusion: Positive selection on cagA indicates antagonistic coevolution between host and bacteria, which appears paradoxical given that cagA is detrimental to the human host upon which the bacteria depends. This suggests several non-exclusive possibilities; that gastric cancer has not been a major selective pressure on human populations, that cagA has an undetermined benefit to the human host, or that horizontal transmission of H.pylori between hosts has been more important in the evolution of H.pylori than previously recognized, reducing the selective pressure to lower the pathogenicity of the bacteria. The different patterns of adaptation of the gene in different human populations indicates that there are population specific differences in the human gut environment - due either to differences in host genetics or diet and other lifestyle features.

In Darwinian evolution, mutations occur approximately at random in a gene, turned into amino acid mutations by the genetic code. Some mutations are fixed to become substitutions and some are eliminated from the population. Partitioning pairs of closely related species with complete genome sequences by average population size of each pair, we looked at the substitution matrices generated for these partitions and compared the substitution patterns between species. We estimated a population genetic model that relates the relative fixation probabilities of different types of mutations to the selective pressure and population size. Parameterizations of the average and distribution of selective pressures for different amino acid substitution types in different population size comparisons were generated with a Bayesian framework. We found that partitions in population size as well as in substitution type are required to explain the substitution data. Selection coefficients were found to decrease with increasingly radical amino acid substitution and with increasing effective population size. To further explore the role of underlying processes in amino acid substitution, we analyzed embryophyte (plant) gene families from TAED (The Adaptive Evolution Database), where solved structures for at least one member exist in the Protein Data Bank. Using PAML, we assigned branches to three categories: strong negative selection, moderate negative selection/neutrality, and positive diversifying selection. Focusing on the first and third categories, we identified sites changing along gene family lineages and observed the spatial patterns of substitution. Selective sweeps were expected to create primary sequence clustering under positive diversifying selection. Co-evolution through direct physical interaction was expected to cause tertiary structural clustering. Under both positive and negative selection, the substitution patterns were found to be nonrandom. Under positive diversifying selection, significant independent signals were found for primary and tertiary sequence clustering, suggesting roles for both selective sweeps and direct physical interaction. Under strong negative selection, the signals were not found to be independent. All together, a complex interplay of population genetic and protein thermodynamics forces is suggested., (Copyright (c) 2009 Elsevier Ltd. All rights reserved.)

The standard genetic code (SGC) has a fundamental error-minimizing property which has been widely attributed to the action of selection. However, a clear mechanism for how selection can give rise to error minimization (EM) is lacking. A search through a space of alternate codes (code space) via codon reassignments would be required, to select a code optimized for EM. There are two commonly discussed mechanisms of codon reassignment; the Codon Capture mechanism, which proposes a loss of the codon during reassignment, and the Ambiguous Intermediate mechanism, which proposes that the codon underwent an ambiguous phase during reassignment. When searching of code space via the Codon Capture mechanism is simulated, an optimized genetic code can rarely be achieved (0-3.2% of the time) with most searches ending in failure. When code space is searched via the Ambiguous Intermediate mechanism, under constraints derived from empirical observations of codon reassignments from extant genomes, the searches also often end in failure. When a local minimum is avoided and optimization is achieved, 20-41 sequential improving codon reassignments are required. Furthermore, the structures of the optimized codes produced by these simulations differ from the structure of the SGC. These data are challenges for the Adaptive Code hypothesis to address, which proposes that the EM property was directly selected for, and suggests that EM is simply a byproduct of the addition of amino acids to the expanding code, as described by the alternative 'Emergence' hypothesis.

Unlabelled: ScanMoment is a webserver designed to identify the presence of the basic faced alpha-helix (BFAH) motif in the nucleic acid binding sites of proteins. The program calculates the 'Basic Moment', a parameter that quantitizes the distribution of basic residues on the surface of an alpha-helix. A sliding window is used to generate a plot displaying regions of the protein sequence that possesses a high Basic Moment and hus likely to possess a BFAH motif. The user may vary the periodicity from that of an alpha-helix (100 degrees ), to those of other secondary structures such as beta sheets and 3(10) helices. The program can also plot the periodicity of basic residues in a protein sequence using a Fourier transformation. The procedure has been used to characterize the presence of BFAHs in the N-terminal extensions of the eukaryotic aminoacyl-tRNA synthetases and to indicate the presence of a BFAH in the tRNA binding site of alanyl-tRNA synthetase., Availability: www.scanmoment.org.

The blood feeding vampire bats emerged from New World leaf-nosed bats that fed on fruit and insects. Plasminogen activator, a serine protease that regulates blood coagulation, is known to be expressed in the saliva of Desmodus rotundus (common vampire bat) and is thought to be a key enzyme for the emergence of blood feeding in vampire bats. To better understand the evolution of this biological function, we studied the plasminogen activator (PA) genes from all vampire bat species in light of their feeding transition to bird and subsequently mammalian blood. We include the rare species Diphylla ecaudata and Diaemus youngi, where plasminogen activator had not previously been studied and demonstrate that PA gene duplication observed in Desmodus is not essential to the vampire phenotype, but relates to the emergence of predominant mammalian blood feeding in this species. Plasminogen activator has evolved through gene duplication, domain loss, and sequence evolution leading to change in fibrin-specificity and susceptibility to plasminogen activator inhibitor-1. Before undertaking this study, only the four plasminogen activator isoforms from Desmodus were known. The evolution of vampire bat plasminogen activators can now be linked phylogenetically to the transition in feeding behavior among vampire bat species from bird to mammalian blood.

Recently, the concept of a "Proteomic Constraint" was introduced to explain the frequency of genetic code deviations in mitochondrial genomes. The Proteomic Constraint was proposed to be proportional to the size of the mitochondrially encoded proteome, hence small proteomes are expected to experience smaller total numbers of errors resulting from genetic code deviations, leading to less likelihood of causing lethality. The concept is now extended to encompass several other aspects of the genetic information system. When the Proteomic Constraint is small, it is proposed that there is little selective pressure to evolve or maintain error correction mechanisms, as a result of the smaller total number of errors that accumulate. Conversely, a large Proteomic Constraint is proposed to result in a correspondingly large selective pressure to evolve or maintain error correction mechanisms. Differences in the size of the Proteomic Constraint can help to explain differences in replicational, transcriptional, and translational fidelities between genomes. A key piece of evidence is the existence of negative power law relationships between proteome size and error rates; these are demonstrated to be diagnostic of the action of the Proteomic Constraint. The Proteomic Constraint is argued to be a major factor determining mutation rates in a diverse range of DNA genomes, implying that mutation rates are clock like. A small Proteomic Constraint partly explains why RNA viruses possess high mutation rates. A reduced Proteomic Constraint in intracellular pathogenic bacteria predicts a drift upwards in mutation rates. Differences in the Proteomic Constraint also appear to be linked to differences in recombination rates between eukaryotes. In addition, a reduced Proteomic Constraint may explain features of resident genomes, such as loss of DNA repair pathways, increased substitution rates, and AT biases, in addition to the occurrence of genetic code deviations. Thus, it is argued that the Proteomic Constraint is a universal factor that influences a wide range of properties of the genetic information system.

The genetic code has the remarkable property of error minimization, whereby the arrangement of amino acids to codons is highly efficient at reducing the deleterious effects of random point mutations and transcriptional and translational errors. Whether this property has been explicitly selected for is unclear. Here, three scenarios of genetic code evolution are examined, and their effects on error minimization assessed. First, a simple model of random stepwise addition of physicochemically similar amino acids to the code is demonstrated to result in substantial error minimization. Second, a model of random addition of physicochemically similar amino acids in a codon expansion scheme derived from the Ambiguity Reduction Model results in improved error minimization over the first model. Finally, a recently introduced 213 Model of genetic code evolution is examined by the random addition of physicochemically similar amino acids to a primordial core of four amino acids. Under certain conditions, 22% of the resulting codes produced according to the latter model possess equivalent or superior error minimization to the standard genetic code. These analyses demonstrate that a substantial proportion of error minimization is likely to have arisen neutrally, simply as a consequence of code expansion, facilitated by duplication of the genes encoding adaptor molecules and charging enzymes. This implies that selection is at best only partly responsible for the property of error minimization. These results caution against assuming that selection is responsible for every beneficial trait observed in living organisms.

Total evidence and the use of large datasets to overcome uncertainty are the state of the art in systematic analysis. This assumes that the only true phylogenetic signal is ancestry and that functional, structural, and other factors will not add an alternative signal. Using gene families, where individual codon positions were sorted into bins based upon average-pairwise dN/dS ratio, we show that standard, common phylogenetic methods that were designed for stochastic, neutral, site-independent processes, generate less robust phylogenetic signal for bins with strong negative or positive selection. This was true for phylogenetic reconstruction with parsimony, distance, and likelihood methods. Further, we present a case for the potential existence of systematic functional or structural signal that competes with ancestral signal. For the example of positive selection, we simulate the evolution of sequences through three dimensional lattice constructs with folding constraint and changing binding functionality and show that total evidence for these lattice genes presents trees with functional signal, but that the neutral synonymous sites in these genes show the true ancestral signal. In this case, sequence convergence is promoted by functional convergence.

Using a comparative genomics approach we demonstrate a negative correlation between the number of codon reassignments undergone by 222 mitochondrial genomes and the mitochondrial genome size, the number of mitochondrial ORFs, and the sizes of the large and small subunit mitochondrial rRNAs. In addition, we show that the TGA-to-tryptophan codon reassignment, which has occurred 11 times in mitochondrial genomes, is found in mitochondrial genomes smaller than those which have not undergone the reassignment. We therefore propose that mitochondrial codon reassignments occur in a wide range of phyla, particularly in Metazoa, due to a reduced "proteomic constraint" on the mitochondrial genetic code, compared to the nuclear genetic code. The reduced proteomic constraint reflects the small size of the mitochondrial-encoded proteome and allows codon reassignments to occur with less likelihood of lethality. In addition, we demonstrate a striking link between nonsense codon reassignments and the decoding properties of naturally occurring nonsense suppressor tRNAs. This suggests that natural preexisting nonsense suppression facilitated nonsense codon reassignments and constitutes a novel mechanism of genetic code change. These findings explain for the first time the identity of the stop codons and amino acids reassigned in mitochondrial and nuclear genomes. Nonsense suppressor tRNAs provided the raw material for nonsense codon reassignments, implying that the properties of the tRNA anticodon have dictated the identity of nonsense codon reassignments.

Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. A relative abundance of coding sequences (CDSs) encoding regulatory proteins likely control the expression of genes encoding carboxysomes, multiple dissolved inorganic nitrogen and phosphate transporters, as well as a phosphonate operon, which provide this species with a variety of options for acquiring these substrates from the environment. Thiom. crunogena XCL-2 is unusual among obligate sulfur-oxidizing bacteria in relying on the Sox system for the oxidation of reduced sulfur compounds. The genome has characteristics consistent with an obligately chemolithoautotrophic lifestyle, including few transporters predicted to have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered throughout the genome., Competing Interests: Competing interests. The authors have declared that no competing interests exist.

Three aminoacyl-tRNA synthetases from yeast, one from plants and one from mammals possess unusual structures at their N termini, namely alpha helices with basic residues distributed asymmetrically, on a single face of the helix. It is unknown if these 'basic faced' alpha helices (BFAHs) are unique to the aminoacyl-tRNA synthetases. Analysis of the amino acid sequences of these five aminoacyl-tRNA synthetases using the hydrophobic moment algorithm failed to accurately identify the BFAHs. A new algorithm was therefore developed, called the 'basic moment'. This is a Fourier analysis procedure that predicts the distribution of basic residues within protein secondary structure. The basic moment identifies with a high degree of accuracy the five known BFAHs and also identifies further potential BFAHs at evolutionarily conserved positions in the peptide extensions of aspartyl-, lysyl- and valyl- tRNA synthetases from a range of eukaryotic species. In addition, the algorithm identifies the two-helix pair tRNA binding domain of alanyl-tRNA synthetase, implying that the domain includes a BFAH. The functional and evolutionary aspects of these structural features are discussed.

We have employed electron microscopic, biochemical, and molecular techniques to clarify the species of origin of the "Chilean Blob," the remains of a large sea creature that beached on the Chilean coast in July 2003. Electron microscopy revealed that the remains are largely composed of an acellular, fibrous network reminiscent of the collagen fiber network in whale blubber. Amino acid analyses of an acid hydrolysate indicated that the fibers are composed of 31% glycine residues and also contain hydroxyproline and hydroxylysine, all diagnostic of collagen. Using primers designed to the mitochondrial gene nad2, an 800-bp product of the polymerase chain reaction (PCR) was amplified from DNA that had been purified from the carcass. The DNA sequence of the PCR product was 100% identical to nad2 of sperm whale (Physeter catadon). These results unequivocally demonstrate that the Chilean Blob is the almost completely decomposed remains of the blubber layer of a sperm whale. This identification is the same as those we have obtained before from other relics such as the so-called giant octopus of St. Augustine (Florida), the Tasmanian West Coast Monster, two Bermuda Blobs, and the Nantucket Blob. It is clear now that all of these blobs of popular and cryptozoological interest are, in fact, the decomposed remains of large cetaceans.

Pioneering studies in the 1960s that elucidated the genetic code suggested that all extant forms of life use the same genetic code. This early presumption has subsequently been challenged by the discovery of deviations of the universal genetic code in prokaryotes, eukaryotic nuclear genomes and mitochondrial genomes. These studies have revealed that the genetic code is still evolving despite strong negative forces working against the fixation of mutations that result in codon reassignment. Recent data from in vitro, in vivo and in silico comparative genomics studies are revealing significant, previously overlooked links between modified nucleosides in tRNAs, genetic code ambiguity, genome base composition, codon usage and codon reassignment.