In clear, non-technical language, Ruse offers a full and fair assessment of the status of the argument from design in light of both the advances of modern evolutionary biology and the thinking of ...today's philosophers--with special attention given to the supporters and critics of "intelligent design.".
Gene expression noise is an evolvable property of biological systems that describes differences in expression among genetically identical cells in the same environment. Prior work has shown that ...expression noise is heritable and can be shaped by selection, but the impact of variation in expression noise on organismal fitness has proven difficult to measure. Here, we quantify the fitness effects of altering expression noise for the
gene in
. We show that increases in expression noise can be deleterious or beneficial depending on the difference between the average expression level of a genotype and the expression level maximizing fitness. We also show that a simple model relating single-cell expression levels to population growth produces patterns consistent with our empirical data. We use this model to explore a broad range of average expression levels and expression noise, providing additional insight into the fitness effects of variation in expression noise.
Neurobiologists recently found the brain can use sudden emerged channels to process information. Based on this finding, we put forward a question whether we can build a computation model that is able ...to integrate a sudden emerged new type of perceptual channel into itself in an online way. If such a computation model can be established, it will introduce a channel-free property to the computation model and meanwhile deepen our understanding about the extendibility of the brain. In this article, a biologically inspired neural network named artificial evolution (AE) network is proposed to handle the problem. When a new perceptual channel emerges, the neurons in the network can grow new connections to connect the emerged channel according to the Hebb rule. In this article, we design a sensory channel expansion experiment to test the AE network. The experimental results demonstrate that the AE network can handle the sudden emerged perceptual channels effectively.
Noble pen shell or fan mussel, Pinna nobilis Linnaeus (1758), protected since 1992, was incorporated into the Spanish Catalogue of Threatened Species (Category: Vulnerable, Royal Decree 139/2011). ...The status is presently in the process of being catalogued as critically endangered, pending approval by Spanish Government (https://www.mapama.gob.es/es/biodiversidad/participacion-publica/Borrador_OM_situacion_critica.aspx). The International Union for the Conservation of Nature (IUCN) alerted the countries of the Mediterranean basin to the "emergent situation" due to serious mortality events suffered by the fan mussel, putting it in serious risk of extinction. Thus, emergency actions have been implemented by Spanish authorities in which several research institutes from all over the country are involved. The parasite, Haplosporidium pinnae, was recently characterized by histology, TEM, SEM and molecular biology techniques and it was considered responsible for the mass mortality of P. nobilis in the Mediterranean Sea. In this context, the aim of this study has been to develop species-specific quantitative PCR (qPCR) protocol carrying out a fast, specific and effective molecular diagnose of H. pinnae. In this sense, the detection limit for qPCR was equal to 30 copies of SSU rDNA / ng of DNA using plasmid alone and when 100ng DNA of non-infected oyster were added. The qPCR assay revealed that 94% of the 32 analysed mantle tissues of fan mussel were infected by H. pinnae, showing a high sensitivity and specificity for its detection (100% if we don't consider negative and too much degraded samples). This technique will allow us to make quicker follow-ups of the disease, allowing us to get a better understanding of its evolution in order to help in the rescue of P. nobilis populations.
Rhipicephalus australis Fuller, the Australian cattle tick, is reinstated and the adults and larvae redescribed from material collected in Australia. This long ignored boophilid was previously known ...as R. microplus Canestrini for specimens reported in Australia and New Caledonia. The adults of R. australis are easily recognized by a combination of characters, such as the ventro-medial spurs in the palpal segments of the male, and the abundant, plumose, pale white setae on the dorsum of the female. Other details, such as coxal and adanal shields are more variable among different populations and may lead to incorrect determinations. Larvae of R. australis are clearly smaller than those of R. microplus. The use of principal components analysis on body measurements leads to a clear separation of larvae of both taxa. A phylogenetic analysis based on 12S- and 16S-rDNA gene sequences supports the conspecificity of the neotype material on which the reinstatement of the species is proposed, and of the specimens used for previous interspecific crosses. R. australis is now known to be present in Australia, New Caledonia, the island of Borneo, Philippines, Sumatra, Java, New Guinea, Cambodia, and Tahiti. Both R. microplus and R. australis coexist in some countries in southeastern Asia. Given the extreme importance of these ticks for the cattle industry, field data on their distribution in the region are required to know the actual range of these species and to understand the evolution of the group. Keywords: Rhipicephalus (Boophilus) australis, Australian cattle tick, reinstatement, redescription
Genome sequence data are of great value in describing evolutionary processes in viral populations. However, in such studies, the extent to which data accurately describes the viral population is a ...matter of importance. Multiple factors may influence the accuracy of a dataset, including the quantity and nature of the sample collected, and the subsequent steps in viral processing. To investigate this phenomenon, we sequenced replica datasets spanning a range of viruses, and in which the point at which samples were split was different in each case, from a dataset in which independent samples were collected from a single patient to another in which all processing steps up to sequencing were applied to a single sample before splitting the sample and sequencing each replicate. We conclude that neither a high read depth nor a high template number in a sample guarantee the precision of a dataset. Measures of consistency calculated from within a single biological sample may also be insufficient; distortion of the composition of a population by the experimental procedure or genuine within-host diversity between samples may each affect the results. Where it is possible, data from replicate samples should be collected to validate the consistency of short-read sequence data.
Abstract
Background
Comparative genomics studies are growing in number partly because of their unique ability to provide insight into shared and divergent biology between species. Of particular ...interest is the use of phylogenetic methods to infer the evolutionary history of cis-regulatory sequence features, which contribute strongly to phenotypic divergence and are frequently gained and lost in eutherian genomes. Understanding the mechanisms by which cis-regulatory element turnover generate emergent phenotypes is crucial to our understanding of adaptive evolution. Ancestral reconstruction methods can place species-specific cis-regulatory features in their evolutionary context, thus increasing our understanding of the process of regulatory sequence turnover. However, applying these methods to gain and loss of cis-regulatory features historically required complex workflows, preventing widespread adoption by the broad scientific community.
Results
MapGL simplifies phylogenetic inference of the evolutionary history of short genomic sequence features by combining the necessary steps into a single piece of software with a simple set of inputs and outputs. We show that MapGL can reliably disambiguate the mechanisms underlying differential regulatory sequence content across a broad range of phylogenetic topologies and evolutionary distances. Thus, MapGL provides the necessary context to evaluate how genomic sequence gain and loss contribute to species-specific divergence.
Conclusions
MapGL makes phylogenetic inference of species-specific sequence gain and loss easy for both expert and non-expert users, making it a powerful tool for gaining novel insights into genome evolution.
Enteroviruses, members of the family of picornaviruses, are the most common viral infectious agents in humans causing a broad spectrum of diseases ranging from mild respiratory illnesses to ...life-threatening infections. To efficiently replicate within the host cell, enteroviruses hijack several host factors, such as ACBD3. ACBD3 facilitates replication of various enterovirus species, however, structural determinants of ACBD3 recruitment to the viral replication sites are poorly understood. Here, we present a structural characterization of the interaction between ACBD3 and the non-structural 3A proteins of four representative enteroviruses (poliovirus, enterovirus A71, enterovirus D68, and rhinovirus B14). In addition, we describe the details of the 3A-3A interaction causing the assembly of the ACBD3-3A heterotetramers and the interaction between the ACBD3-3A complex and the lipid bilayer. Using structure-guided identification of the point mutations disrupting these interactions, we demonstrate their roles in the intracellular localization of these proteins, recruitment of downstream effectors of ACBD3, and facilitation of enterovirus replication. These structures uncovered a striking convergence in the mechanisms of how enteroviruses and kobuviruses, members of a distinct group of picornaviruses that also rely on ACBD3, recruit ACBD3 and its downstream effectors to the sites of viral replication.
Our intestine is a melting pot of interactions between microbial and human cells. This gene-rich ecosystem modulates our health, but questions remain unanswered regarding its genetic structure, such ...as, "How rapid is evolutionary change in the human gut microbiome? How can its function be maintained?" Much research on the microbiome has characterized the species it contains. Yet the high growth rate and large population sizes of many species, and the mutation rate of most microbes (approximately 10-3 per genome per generation), could imply that evolution might be happening in our gut along our lifetime. In support of this view, Garud and colleagues present an analysis that begins to unravel the pattern of short- and long-term evolution of dozens of gut species. Even with limited longitudinal short-read sequence data, significant evolutionary dynamics-shaped by both positive and negative selection-can be detected on human microbiomes. This may only be the tip of the iceberg, as recent work on mice suggests, and its full extent should be revealed with dense time series long-read sequence data and new eco-evolutionary theory.
Salmonella enterica subsp. enterica serovar Kentucky is frequently isolated from healthy poultry and dairy cows and is occasionally isolated from people with clinical disease. A genomic analysis of ...119 isolates collected in the United States from dairy cows, ground beef, poultry and poultry products, and human clinical cases was conducted. Results of the analysis demonstrated that the majority of poultry and bovine-associated S. Kentucky were sequence type (ST) 152. Several bovine-associated (n = 3) and food product isolates (n = 3) collected from the United States and the majority of human clinical isolates were ST198, a sequence type that is frequently isolated from poultry and occasionally from human clinical cases in Northern Africa, Europe and Southeast Asia. A phylogenetic analysis indicated that both STs are more closely related to other Salmonella serovars than they are to each other. Additionally, there was strong evidence of an evolutionary divergence between the poultry-associated and bovine-associated ST152 isolates that was due to polymorphisms in four core genome genes. The ST198 isolates recovered from dairy farms in the United States were phylogenetically distinct from those collected from human clinical cases with 66 core genome SNPs differentiating the two groups, but more isolates are needed to determine the significance of this distinction. Identification of S. Kentucky ST198 from dairy animals in the United States suggests that the presence of this pathogen should be monitored in food-producing animals.
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