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Coevolution

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https://www.readbyqxmd.com/read/28827684/whole-genome-based-phylogeny-of-reptile-associated-helicobacter-indicates-independent-niche-adaptation-followed-by-diversification-in-a-poikilothermic-host
#1
Maarten J Gilbert, Birgitta Duim, Arjen J Timmerman, Aldert L Zomer, Jaap A Wagenaar
Reptiles have been shown to host a significant Helicobacter diversity. In order to survive, reptile-associated Helicobacter lineages need to be adapted to the thermally dynamic environment encountered in a poikilothermic host. The whole genomes of reptile-associated Helicobacter lineages can provide insights in Helicobacter host adaptation and coevolution. These aspects were explored by comparing the genomes of reptile-, bird-, and mammal-associated Helicobacter lineages. Based on average nucleotide identity, all reptile-associated Helicobacter lineages in this study could be considered distinct species...
August 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28827317/coevolutionary-arms-race-versus-host-defense-chase-in-a-tropical-herbivore-plant-system
#2
María-José Endara, Phyllis D Coley, Gabrielle Ghabash, James A Nicholls, Kyle G Dexter, David A Donoso, Graham N Stone, R Toby Pennington, Thomas A Kursar
Coevolutionary models suggest that herbivores drive diversification and community composition in plants. For herbivores, many questions remain regarding how plant defenses shape host choice and community structure. We addressed these questions using the tree genus Inga and its lepidopteran herbivores in the Amazon. We constructed phylogenies for both plants and insects and quantified host associations and plant defenses. We found that similarity in herbivore assemblages between Inga species was correlated with similarity in defenses...
August 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28821238/genome-wide-analysis-of-ltr-retrotransposon-diversity-and-its-impact-on-the-evolution-of-the-genus-helianthus-l
#3
Flavia Mascagni, Tommaso Giordani, Marilena Ceccarelli, Andrea Cavallini, Lucia Natali
BACKGROUND: Genome divergence by mobile elements activity and recombination is a continuous process that plays a key role in the evolution of species. Nevertheless, knowledge on retrotransposon-related variability among species belonging to the same genus is still limited. Considering the importance of the genus Helianthus, a model system for studying the ecological genetics of speciation and adaptation, we performed a comparative analysis of the repetitive genome fraction across ten species and one subspecies of sunflower, focusing on long terminal repeat retrotransposons at superfamily, lineage and sublineage levels...
August 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28817954/dissecting-amyloid-beta-deposition-using-distinct-strains-of-the-neurotropic-parasite-toxoplasma-gondii-as-a-novel-tool
#4
Carla M Cabral, Kathryn E McGovern, Wes R MacDonald, Jenna Franco, Anita A Koshy
Genetic and pathologic data suggest that amyloid beta (Aβ), produced by processing of the amyloid precursor protein, is a major initiator of Alzheimer's disease (AD). To gain new insights into Aβ modulation, we sought to harness the power of the coevolution between the neurotropic parasite Toxoplasma gondii and the mammalian brain. Two prior studies attributed Toxoplasma-associated protection against Aβ to increases in anti-inflammatory cytokines (TGF-β and IL-10) and infiltrating phagocytic monocytes. These studies only used one Toxoplasma strain making it difficult to determine if the noted changes were associated with Aβ protection or simply infection...
July 2017: ASN Neuro
https://www.readbyqxmd.com/read/28809135/detecting-signatures-of-past-pathogen-selection-on-human-hla-loci-are-there-needles-in-the-haystack
#5
Bridget S Penman, Sunetra Gupta
Human leucocyte antigens (HLAs) are responsible for the display of peptide fragments for recognition by T-cell receptors. The gene family encoding them is thus integral to human adaptive immunity, and likely to be under strong pathogen selection. Despite this, it has proved difficult to demonstrate specific examples of pathogen-HLA coevolution. Selection from multiple pathogens simultaneously could explain why the evolutionary signatures of particular pathogens on HLAs have proved elusive. Here, we present an individual-based model of HLA evolution in the presence of two mortality-causing pathogens...
August 15, 2017: Parasitology
https://www.readbyqxmd.com/read/28808019/next-step-in-the-ongoing-arms-race-between-myxoma-virus-and-wild-rabbits-in-australia-is-a-novel-disease-phenotype
#6
Peter J Kerr, Isabella M Cattadori, June Liu, Derek G Sim, Jeff W Dodds, Jason W Brooks, Mary J Kennett, Edward C Holmes, Andrew F Read
In host-pathogen arms races, increases in host resistance prompt counteradaptation by pathogens, but the nature of that counteradaptation is seldom directly observed outside of laboratory models. The best-documented field example is the coevolution of myxoma virus (MYXV) in European rabbits. To understand how MYXV in Australia has continued to evolve in wild rabbits under intense selection for genetic resistance to myxomatosis, we compared the phenotypes of the progenitor MYXV and viral isolates from the 1950s and the 1990s in laboratory rabbits with no resistance...
August 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28801221/the-aminoacyl-trna-synthetases-had-only-a-marginal-role-in-the-origin-of-the-organization-of-the-genetic-code-evidence-in-favor-of-the-coevolution-theory
#7
Massimo Di Giulio
The coevolution theory of the origin of the genetic code suggests that the organization of the genetic code coevolved with the biosynthetic relationships between amino acids. The mechanism that allowed this coevolution was based on tRNA-like molecules on which-this theory-would postulate the biosynthetic transformations between amino acids to have occurred. This mechanism makes a prediction on how the role conducted by the aminoacyl-tRNA synthetases (ARSs), in the origin of the genetic code, should have been...
August 9, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28800915/transposable-elements-direct-the-coevolution-between-plants-and-microbes
#8
REVIEW
Michael F Seidl, Bart P H J Thomma
Transposable elements are powerful drivers of genome evolution in many eukaryotes. Although they are mostly considered as 'selfish' genetic elements, increasing evidence suggests that they contribute to genetic variability; particularly under stress conditions. Over the past few years, the role of transposable elements during host-microbe interactions has been recognised. It has been proposed that many pathogenic microbes have evolved a 'two-speed' genome with regions that show increased variability and that are enriched in transposable elements and pathogenicity-related genes...
August 8, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28798399/sexual-conflict-and-the-evolution-of-genitalia-male-damselflies-remove-more-sperm-when-mating-with-a-heterospecific-female
#9
Adolfo Cordero-Rivera
In Calopteryx damselflies, males remove rivals' sperm stored by the female, thereby reducing sperm competition. This behaviour may create a sexual conflict, because females could lose the sperm stored in the spermatheca, used for long-term storage. Comparative evidence suggested antagonistic coevolution between sexes, which might prompt the evolution of narrow spermathecal ducts, or longer spermathecae, hindering sperm removal. Calopteryx haemorrhoidalis and C. splendens coexist and sometimes hybridize. Therefore, here I predicted that if females coevolve with conspecific males, heterospecific males should have an advantage when interspecific matings occur because females will show less resistance to them than to conspecific males...
August 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28797912/genome-wide-identification-functional-and-evolutionary-analysis-of-terpene-synthases-in-pineapple
#10
Xiaoe Chen, Wei Yang, Liqin Zhang, Xianmiao Wu, Tian Cheng, Guanglin Li
Terpene synthases (TPSs) are vital for the biosynthesis of active terpenoids, which have important physiological, ecological and medicinal value. Although terpenoids have been reported in pineapple (Ananas comosus), genome-wide investigations of the TPS genes responsible for pineapple terpenoid synthesis are still lacking. By integrating pineapple genome and proteome data, twenty-one putative terpene synthase genes were found in pineapple and divided into five subfamilies. Tandem duplication is the cause of TPS gene family duplication...
July 6, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28796233/intracellular-directed-evolution-of-proteins-from-combinatorial-libraries-based-on-conditional-phage-replication
#11
Andreas K Brödel, Alfonso Jaramillo, Mark Isalan
Directed evolution is a powerful tool to improve the characteristics of biomolecules. Here we present a protocol for the intracellular evolution of proteins with distinct differences and advantages in comparison with established techniques. These include the ability to select for a particular function from a library of protein variants inside cells, minimizing undesired coevolution and propagation of nonfunctional library members, as well as allowing positive and negative selection logics using basally active promoters...
September 2017: Nature Protocols
https://www.readbyqxmd.com/read/28790313/evolution-of-new-regulatory-functions-on-biophysically-realistic-fitness-landscapes
#12
Tamar Friedlander, Roshan Prizak, Nicholas H Barton, Gašper Tkačik
Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge...
August 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28783683/class-i-hla-haplotypes-form-two-schools-that-educate-nk-cells-in-different-ways
#13
Amir Horowitz, Zakia Djaoud, Neda Nemat-Gorgani, Jeroen Blokhuis, Hugo G Hilton, Vivien Béziat, Karl-Johan Malmberg, Paul J Norman, Lisbeth A Guethlein, Peter Parham
Natural killer (NK) cells are lymphocytes that have vital functions in innate and adaptive immunity, as well as placental reproduction. Polymorphic human leukocyte antigen (HLA) class I educates NK cells through interactions with killer cell immunoglobulin-like receptors (KIRs) and by supplying peptides that bind HLA-E to form ligands for CD94/NKG2A receptors on NK cells. HLA-B dimorphism in the leader peptide modulates this latter function: -21methionine (-21M) delivers functional peptides, but -21threonine (-21T) does not...
September 9, 2016: Science Immunology
https://www.readbyqxmd.com/read/28768866/reverse-engineering-field-isolates-of-myxoma-virus-demonstrates-that-some-gene-disruptions-or-loss-of-function-do-not-explain-virulence-changes-observed-in-the-field
#14
June Liu, Isabella M Cattadori, Derek G Sim, John-Sebastian Eden, Edward C Holmes, Andrew F Read, Peter J Kerr
The coevolution of myxoma virus (MYXV) and wild European rabbits in Australia and Europe is a paradigm for the evolution of a pathogen in a new host species. Genomic analyses have identified the mutations that have characterized this evolutionary process, but defining causal mutations in the pathways from virulence to attenuation and back to virulence has not been possible. Using reverse genetics we examined the role of six selected mutations found in Australian field isolates of MYXV that fall in known or potential virulence genes...
August 2, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28757073/chaotic-provinces-in-the-kingdom-of-the-red-queen
#15
Hanna Schenk, Arne Traulsen, Chaitanya S Gokhale
The interplay between parasites and their hosts is found in all kinds of species and plays an important role in understanding the principles of evolution and coevolution. Usually, the different genotypes of hosts and parasites oscillate in their abundances. The well-established theory of oscillatory Red Queen dynamics proposes an ongoing change in frequencies of the different types within each species. So far, it is unclear under what conditions Red Queen dynamics persists, especially when the number of types per species increases...
July 27, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28751967/protein-sites-with-more-coevolutionary-connections-tend-to-evolve-slower-while-more-variable-protein-families-acquire-higher-coevolutionary-connections
#16
Sapan Mandloi, Saikat Chakrabarti
Background: Amino acid exchanges within proteins sometimes compensate for one another and could therefore be co-evolved. It is essential to investigate the intricate relationship between the extent of coevolution and the evolutionary variability exerted at individual protein sites, as well as the whole protein. Methods: In this study, we have used a reliable set of coevolutionary connections (sites within 10Å spatial distance) and investigated their correlation with the evolutionary diversity within the respective protein sites...
2017: F1000Research
https://www.readbyqxmd.com/read/28750604/inferring-methionine-sulfoxidation-and-serine-phosphorylation-crosstalk-from-phylogenetic-analyses
#17
Juan Carlos Aledo
BACKGROUND: The sulfoxidation of methionine residues within the phosphorylation motif of protein kinase substrates, may provide a mechanism to couple oxidative signals to changes in protein phosphorylation. Herein, we hypothesize that if the residues within a pair of phosphorylatable-sulfoxidable sites are functionally linked, then they might have been coevolving. To test this hypothesis a number of site pairs previously detected on human stress-related proteins has been subjected to analysis using eukaryote ortholog sequences and a phylogenetic approach...
July 27, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28747532/negative-phenotypic-and-genetic-correlation-between-natal-dispersal-propensity-and-nest-defence-behaviour-in-a-wild-bird
#18
Pierre Bize, Grégory Daniel, Vincent A Viblanc, Julien G A Martin, Blandine Doligez
Natural selection is expected to favour the integration of dispersal and phenotypic traits allowing individuals to reduce dispersal costs. Accordingly, associations have been found between dispersal and personality traits such as aggressiveness and exploration, which may facilitate settlement in a novel environment. However, the determinism of these associations has only rarely been explored. Here, we highlight the functional integration of individual personality in nest-defence behaviour and natal dispersal propensity in a long-lived colonial bird, the Alpine swift (Apus melba), providing insights into genetic constraints shaping the coevolution of these two traits...
July 2017: Biology Letters
https://www.readbyqxmd.com/read/28740072/long-term-genomic-coevolution-of-host-parasite-interaction-in-the-natural-environment
#19
Elina Laanto, Ville Hoikkala, Janne Ravantti, Lotta-Riina Sundberg
Antagonistic coevolution of parasite infectivity and host resistance may alter the biological functionality of species, yet these dynamics in nature are still poorly understood. Here we show the molecular details of a long-term phage-bacterium arms race in the environment. Bacteria (Flavobacterium columnare) are generally resistant to phages from the past and susceptible to phages isolated in years after bacterial isolation. Bacterial resistance selects for increased phage infectivity and host range, which is also associated with expansion of phage genome size...
July 24, 2017: Nature Communications
https://www.readbyqxmd.com/read/28739950/coevolution-of-cultural-intelligence-extended-life-history-sociality-and-brain-size-in-primates
#20
Sally E Street, Ana F Navarrete, Simon M Reader, Kevin N Laland
Explanations for primate brain expansion and the evolution of human cognition and culture remain contentious despite extensive research. While multiple comparative analyses have investigated variation in brain size across primate species, very few have addressed why primates vary in how much they use social learning. Here, we evaluate the hypothesis that the enhanced reliance on socially transmitted behavior observed in some primates has coevolved with enlarged brains, complex sociality, and extended lifespans...
July 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
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