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Coevolution

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https://www.readbyqxmd.com/read/29054926/biomolecular-coevolution-and-its-applications-going-from-structure-prediction-toward-signaling-epistasis-and-function
#1
REVIEW
Mehari B Zerihun, Alexander Schug
Evolution leads to considerable changes in the sequence of biomolecules, while their overall structure and function remain quite conserved. The wealth of genomic sequences, the 'Biological Big Data', modern sequencing techniques provide allows us to investigate biomolecular evolution with unprecedented detail. Sophisticated statistical models can infer residue pair mutations resulting from spatial proximity. The introduction of predicted spatial adjacencies as constraints in biomolecular structure prediction workflows has transformed the field of protein and RNA structure prediction toward accuracies approaching the experimental resolution limit...
October 20, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29053356/the-evolution-of-clutch-size-in-hosts-of-avian-brood-parasites
#2
Iliana Medina, Naomi E Langmore, Robert Lanfear, Hanna Kokko
Coevolution with avian brood parasites shapes a range of traits in their hosts, including morphology, behavior, and breeding systems. Here we explore whether brood parasitism is also associated with the evolution of host clutch size. Several studies have proposed that hosts of highly virulent parasites could decrease the costs of parasitism by evolving a smaller clutch size, because hosts with smaller clutches will lose fewer progeny when their clutch is parasitized. We describe a model of the evolution of clutch size, which challenges this logic and shows instead that an increase in clutch size (or no change) should evolve in hosts...
November 2017: American Naturalist
https://www.readbyqxmd.com/read/29047157/protein-contact-prediction-by-integrating-deep-multiple-sequence-alignments-coevolution-and-machine-learning
#3
Badri Adhikari, Jie Hou, Jianlin Cheng
In this work, we report the evaluation of the residue-residue contacts predicted by our three different methods in the CASP12 experiment, focusing on studying the impact of multiple sequence alignment, residue coevolution and machine learning on contact prediction. The first method (MULTICOM-NOVEL) uses only traditional features (sequence profile, secondary structure and solvent accessibility) with deep learning to predict contacts and serves as a baseline. The second method (MULTICOM-CONSTRUCT) uses our new alignment algorithm to generate deep multiple sequence alignment to derive coevolution-based features, which are integrated by a neural network method to predict contacts...
October 19, 2017: Proteins
https://www.readbyqxmd.com/read/29045396/indirect-effects-drive-coevolution-in-mutualistic-networks
#4
Paulo R Guimarães, Mathias M Pires, Pedro Jordano, Jordi Bascompte, John N Thompson
Ecological interactions have been acknowledged to play a key role in shaping biodiversity. Yet a major challenge for evolutionary biology is to understand the role of ecological interactions in shaping trait evolution when progressing from pairs of interacting species to multispecies interaction networks. Here we introduce an approach that integrates coevolutionary dynamics and network structure. Our results show that non-interacting species can be as important as directly interacting species in shaping coevolution within mutualistic assemblages...
October 18, 2017: Nature
https://www.readbyqxmd.com/read/29042498/capsids-and-genomes-of-jumbo-sized-bacteriophages-reveal-the-evolutionary-reach-of-the-hk97-fold
#5
Jianfei Hua, Alexis Huet, Carlos A Lopez, Katerina Toropova, Welkin H Pope, Robert L Duda, Roger W Hendrix, James F Conway
Large icosahedral viruses that infect bacteria represent an extreme of the coevolution of capsids and the genomes they accommodate. One subset of these large viruses is the jumbophages, tailed phages with double-stranded DNA genomes of at least 200,000 bp. We explored the mechanism leading to increased capsid and genome sizes by characterizing structures of several jumbophage capsids and the DNA packaged within them. Capsid structures determined for six jumbophages were consistent with the canonical phage HK97 fold, and three had capsid geometries with novel triangulation numbers (T=25, T=28, and T=52)...
October 17, 2017: MBio
https://www.readbyqxmd.com/read/29038481/the-social-and-cultural-roots-of-whale-and-dolphin-brains
#6
Kieran C R Fox, Michael Muthukrishna, Susanne Shultz
Encephalization, or brain expansion, underpins humans' sophisticated social cognition, including language, joint attention, shared goals, teaching, consensus decision-making and empathy. These abilities promote and stabilize cooperative social interactions, and have allowed us to create a 'cognitive' or 'cultural' niche and colonize almost every terrestrial ecosystem. Cetaceans (whales and dolphins) also have exceptionally large and anatomically sophisticated brains. Here, by evaluating a comprehensive database of brain size, social structures and cultural behaviours across cetacean species, we ask whether cetacean brains are similarly associated with a marine cultural niche...
October 16, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/29033780/evolutionary-musicology-meets-embodied-cognition-biocultural-coevolution-and-the-enactive-origins-of-human-musicality
#7
REVIEW
Dylan van der Schyff, Andrea Schiavio
Despite evolutionary musicology's interdisciplinary nature, and the diverse methods it employs, the field has nevertheless tended to divide into two main positions. Some argue that music should be understood as a naturally selected adaptation, while others claim that music is a product of culture with little or no relevance for the survival of the species. We review these arguments, suggesting that while interesting and well-reasoned positions have been offered on both sides of the debate, the nature-or-culture (or adaptation vs...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/29031737/the-evolution-of-the-genetic-code-impasses-and-challenges
#8
REVIEW
Ádám Kun, Ádám Radványi
The origin of the genetic code and translation is a "notoriously difficult problem". In this survey we present a list of questions that a full theory of the genetic code needs to answer. We assess the leading hypotheses according to these criteria. The stereochemical, the coding coenzyme handle, the coevolution, the four-column theory, the error minimization and the frozen accident hypotheses are discussed. The integration of these hypotheses can account for the origin of the genetic code. But experiments are badly needed...
October 11, 2017: Bio Systems
https://www.readbyqxmd.com/read/29027331/when-does-it-pay-to-invest-in-a-patch-the-evolution-of-intentional-niche-construction
#9
Kathryn A Mohlenhoff, Brian F Codding
Humans modify their environments in ways that significantly transform the earth's ecosystems. Recent research suggests that such niche-constructing behaviors are not passive human responses to environmental variation, but instead should be seen as active and intentional management of the environment. Although such research is useful in highlighting the interactive dynamics between humans and their natural world, the niche-construction framework, as currently applied, fails to explain why people would decide to modify their environments in the first place...
September 2017: Evolutionary Anthropology
https://www.readbyqxmd.com/read/29021172/genital-interactions-during-simulated-copulation-among-marine-mammals
#10
Dara N Orbach, Diane A Kelly, Mauricio Solano, Patricia L R Brennan
Genitalia are morphologically variable across many taxa and in physical contact during intromission, but little is known about how variation in form correlates with function during copulation. Marine mammals offer important insights into the evolutionary forces that act on genital morphology because they have diverse genitalia and are adapted to aquatic living and mating. Cetaceans have a fibroelastic penis and muscular vaginal folds, while pinnipeds have a baculum and lack vaginal folds. We examined copulatory fit in naturally deceased marine mammals to identify anatomical landmarks in contact during copulation and the potential depth of penile penetration into the vagina...
October 11, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28993499/time-is-honey-circadian-clocks-of-bees-and-flowers-and-how-their-interactions-may-influence-ecological-communities
#11
REVIEW
Guy Bloch, Noam Bar-Shai, Yotam Cytter, Rachel Green
The interactions between flowering plants and insect pollinators shape ecological communities and provide one of the best examples of coevolution. Although these interactions have received much attention in both ecology and evolution, their temporal aspects are little explored. Here we review studies on the circadian organization of pollination-related traits in bees and flowers. Research, mostly with the honeybee, Apis mellifera, has implicated the circadian clock in key aspects of their foraging for flower rewards...
November 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28993150/applications-of-sequence-coevolution-in-membrane-protein-biochemistry
#12
REVIEW
John M Nicoludis, Rachelle Gaudet
Recently, protein sequence coevolution analysis has matured into a predictive powerhouse for protein structure and function. Direct Coupling Analysis, a method that uses a global statistical model of sequence coevolution, has enabled the prediction of membrane and disordered protein structures, protein complex architectures, and the functional effects of mutations in proteins. The field of membrane protein biochemistry and structural biology has embraced these computational techniques, which provide functional and structural information in an otherwise experimentally-challenging field...
October 6, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28992238/anti-adhesive-effects-of-plant-wax-coverage-on-insect-attachment
#13
Elena V Gorb, Stanislav N Gorb
The long period of reciprocal antagonistic coevolution between some insect and plant species has led to the development of plant surface attributes that reduce insect attachment. These features serve as a defence against herbivores, sap-sucking insects and nectar robbers, contribute to a temporary capture of insect pollinators, and prevent the escape of insects from traps of carnivorous plants. This review summarises the literature on attachment-mediated insect-plant interactions. A short introduction to attachment systems of insects is presented and the effect of three-dimensional epicuticular waxes on insect attachment is illustrated by many examples...
August 26, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28989067/phylogenies-based-on-combined-mitochondrial-and-nuclear-sequences-conflict-with-morphologically-defined-genera-in-the-eimeriid-coccidia-apicomplexa
#14
Mosun E Ogedengbe, Shiem El-Sherry, Joseph D Ogedengbe, H David Chapman, John R Barta
Partial mitochondrial (mt) cytochrome c oxidase subunit I (COI) and near-complete nuclear (nu) 18S rDNA sequences were obtained from various eimeriid coccidia infecting vertebrates. New and published sequences were used in phylogenetic reconstructions based on nu 18S rDNA, mt COI and concatenated sequence datasets. Bayesian analyses of nu 18S rDNA sequences used secondary structure-based alignments with a doublet nucleotide substitution model; the codon nucleotide substitution model was applied to COI sequences...
October 6, 2017: International Journal for Parasitology
https://www.readbyqxmd.com/read/28980349/protein-protein-interactions-leave-evolutionary-footprints-high-molecular-coeovolution-at-the-core-of-interfaces
#15
Elin Teppa, Diego Javier Zea, Cristina Marino-Buslje
Protein-protein interactions are essential to all aspects of life. Specific interactions result from evolutionary pressure at the interacting interfaces of partner proteins. However, evolutionary pressure is not homogeneous within the interface: for instance, each residue does not contribute equally to the binding energy of the complex. To understand functional differences between residues within the interface, we analyzed their properties in the core and rim regions. Here, we characterized protein interfaces with two evolutionary measures, conservation and coevolution, using a comprehensive dataset of 896 protein complexes...
October 4, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28977715/evolutionary-emergence-and-maintenance-of-horizontally-transmitted-mutualism-that-do-not-rely-on-the-supply-of-standing-variation-in-symbiont-quality
#16
Yu Uchiumi, Hisashi Ohtsuki, Akira Sasaki
Mutualism based on reciprocal exchange of costly services must avoid exploitation by "free-rides". Accordingly, hosts discriminate against free-riding symbionts in many mutualistic relationships. However, as the selective advantage of discriminators comes from the presence of variability in symbiont quality that they eliminate, discrimination and thus mutualism have been considered to be maintained with exogenous supply of free-riders. In this study, we tried to resolve the "paradoxical" coevolution of discrimination by hosts and cooperation by symbionts, by comparing two different types of discrimination: "one-shot" discrimination, where a host does not reacquire new symbionts after evicting free-riders, and "resampling" discrimination, where a host does from the environment...
October 4, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28977708/the-global-impact-of-wolbachia-on-mitochondrial-diversity-and-evolution
#17
Marie Cariou, Laurent Duret, Sylvain Charlat
The spread of maternally inherited microorganisms, such as Wolbachia bacteria, can induce indirect selective sweeps on host mitochondria, to which they are linked within the cytoplasm. The resulting reduction in effective population size might lead to smaller mitochondrial diversity and reduced efficiency of natural selection. While documented in several host species, it is currently unclear if such a scenario is common enough to globally impact the diversity and evolution of mitochondria in Wolbachia-infected lineages...
October 4, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28973943/rapid-evolution-of-hosts-begets-species-diversity-at-the-cost-of-intraspecific-diversity
#18
Jens Frickel, Loukas Theodosiou, Lutz Becks
Ecosystems are complex food webs in which multiple species interact and ecological and evolutionary processes continuously shape populations and communities. Previous studies on eco-evolutionary dynamics have shown that the presence of intraspecific diversity affects community structure and function, and that eco-evolutionary feedback dynamics can be an important driver for its maintenance. Within communities, feedbacks are, however, often indirect, and they can feed back over many generations. Here, we studied eco-evolutionary feedbacks in evolving communities over many generations and compared two-species systems (virus-host and prey-predator) with a more complex three-species system (virus-host-predator)...
October 2, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28959258/the-value-of-a-comparative-approach-to-understand-the-complex-interplay-between-microbiota-and-host-immunity
#19
Norma M Morella, Britt Koskella
The eukaryote immune system evolved and continues to evolve within a microbial world, and as such is critically shaped by-and in some cases even reliant upon-the presence of host-associated microbial species. There are clear examples of adaptations that allow the host to simultaneously tolerate and/or promote growth of symbiotic microbiota while protecting itself against pathogens, but the relationship between immunity and the microbiome reaches far beyond simple recognition and includes complex cross talk between host and microbe as well as direct microbiome-mediated protection against pathogens...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28951480/a-novel-extremely-elongated-and-endocellular-bacterial-symbiont-supports-cuticle-formation-of-a-grain-pest-beetle
#20
Bin Hirota, Genta Okude, Hisashi Anbutsu, Ryo Futahashi, Minoru Moriyama, Xian-Ying Meng, Naruo Nikoh, Ryuichi Koga, Takema Fukatsu
The saw-toothed grain beetle, Oryzaephilus surinamensis (Silvanidae), is a cosmopolitan stored-product pest. Early studies on O. surinamensis in the 1930s described the presence of peculiar bacteriomes harboring endosymbiotic bacteria in the abdomen. Since then, however, the microbiological nature of the symbiont has been elusive. Here we investigated the endosymbiotic system of O. surinamensis in detail. In the abdomen of adults, pupae, and larvae, four oval bacteriomes were consistently identified, whose cytoplasm was full of extremely elongated tubular bacterial cells several micrometers wide and several hundred micrometers long...
September 26, 2017: MBio
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