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"Evolutionary history"

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https://www.readbyqxmd.com/read/27932931/new-distribution-records-of-the-savanna-specialist-fungus-farming-ant-cyatta-sosa-calvo-et-al-hymenoptera-formicidae-myrmicinae
#1
Aline Machado Oliveira, Rodrigo Machado Feitosa, Heraldo Luis Vasconcelos, Jonas Maravalhas
BACKGROUND: The fungus-farming ant genus Cyatta (Formicidae: Myrmicinae) is represented by a single species, C. abscondita Sosa-Calvo et al., known from a few localities in Brazil (in the states of Ceará, Minas Gerais, São Paulo and the Distrito Federal), and a single locality in the Misiones province, Argentina. Cyatta is known to occur predominantly in savanna habitats and occasionally in the transition zones between the Atlantic Forest and Cerrado. NEW INFORMATION: The new records reported here significantly expand the previously known distribution of Cyatta abscondita and provide further support for the intimate relation between this species and the savannas of South America...
2016: Biodiversity Data Journal
https://www.readbyqxmd.com/read/27931748/lentil-lens-culinaris-medik-nodulates-with-genotypically-and-phenotypically-diverse-rhizobia-in-ethiopian-soils
#2
Wondwosen Tena, Endalkachew Wolde-Meskel, Tulu Degefu, Fran Walley
Forty-eight lentil-nodulating rhizobia were isolated from soil samples collected from diverse agro-ecological locations in Ethiopia, and characterized based on 76 phenotypic traits. Furthermore, 26 representative strains were selected and characterized using multilocus sequence analyses (MLSA) of core (16S rRNA, recA, atpD, glnII and gyrB) and symbiotic (nodA and nifH) genes. Numerical analysis of phenotypic characteristics showed that the 48 test strains fell into three major distinct clusters. The phylogenetic trees based on 16S rRNA genes showed that they belong to the Rhizobium genus...
November 24, 2016: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/27930320/unexpected-central-role-of-the-androgen-receptor-in-the-spontaneous-regeneration-of-myelin
#3
Bartosz Bielecki, Claudia Mattern, Abdel M Ghoumari, Sumaira Javaid, Kaja Smietanka, Charly Abi Ghanem, Sakina Mhaouty-Kodja, M Said Ghandour, Etienne-Emile Baulieu, Robin J M Franklin, Michael Schumacher, Elisabeth Traiffort
Lost myelin can be replaced after injury or during demyelinating diseases in a regenerative process called remyelination. In the central nervous system (CNS), the myelin sheaths, which protect axons and allow the fast propagation of electrical impulses, are produced by oligodendrocytes. The abundance and widespread distribution of oligodendrocyte progenitors (OPs) within the adult CNS account for this remarkable regenerative potential. Here, we report a key role for the male gonad, testosterone, and androgen receptor (AR) in CNS remyelination...
December 7, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27930288/experimental-evolution-reveals-hyperparasitic-interactions-among-transposable-elements
#4
Émilie Robillard, Arnaud Le Rouzic, Zheng Zhang, Pierre Capy, Aurélie Hua-Van
Transposable elements (TEs) are repeated DNA sequences that can constitute a substantial part of genomes. Studying TEs' activity, interactions, and accumulation dynamics is thus of major interest to understand genome evolution. Here, we describe the transposition dynamics of cut-and-paste mariner elements during experimental (short- and longer-term) evolution in Drosophila melanogaster Flies with autonomous and nonautonomous mariner copies were introduced in populations containing no active mariner, and TE accumulation was tracked by quantitative PCR for up to 100 generations...
December 5, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27929068/evolution-of-the-net-noca-nlz-elbow-tlp-1-protein-family-in-metazoans-insights-from-expression-data-and-phylogenetic-analysis
#5
Filipe Pereira, Sara Duarte-Pereira, Raquel M Silva, Luís Teixeira da Costa, Isabel Pereira-Castro
The NET (for NocA, Nlz, Elbow, TLP-1) protein family is a group of conserved zinc finger proteins linked to embryonic development and recently associated with breast cancer. The members of this family act as transcriptional repressors interacting with both class I histone deacetylases and Groucho/TLE co-repressors. In Drosophila, the NET family members Elbow and NocA are vital for the development of tracheae, eyes, wings and legs, whereas in vertebrates ZNF703 and ZNF503 are important for the development of the nervous system, eyes and limbs...
December 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27927166/range-wide-genetic-structure-and-demographic-history-in-the-bat-ectoparasite-cimex-adjunctus
#6
Benoit Talbot, Maarten J Vonhof, Hugh G Broders, Brock Fenton, Nusha Keyghobadi
BACKGROUND: Evolutionary histories of parasite and host populations are intimately linked such that their spatial genetic structures may be correlated. While these processes have been relatively well studied in specialist parasites and their hosts, less is known about the ecological and evolutionary consequences of relationships between generalist ectoparasites and their hosts. The aim of this study was to investigate the genetic structure and demographic history of a bat ectoparasite, Cimex adjunctus, whose host affinity is weak but the biology of the potential hosts have been well studied...
December 7, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27926907/mammalian-meiotic-recombination-a-toolbox-for-genome-evolution
#7
Laia Capilla, Montserrat Garcia Caldés, Aurora Ruiz-Herrera
Meiotic recombination is a process that increases genetic diversity and is fundamental for sexual reproduction. Determining by which mechanisms genetic variation is generated and maintained across different phylogenetic groups provides the basis for our understanding of biodiversity and evolution. In this review, we go through different aspects of this essential phenomenon, paying special attention to mammals. We provide a comprehensive view on the organization of meiotic chromosomes and the mechanisms involved in the formation and genomic distribution of recombination hotspots, focusing on the factors influencing the formation and repair of the massive amount of self-induced DNA breaks in early stages of meiosis...
December 8, 2016: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/27924551/mycotoxins-a-fungal-genomics-perspective
#8
Daren W Brown, Scott E Baker
The chemical and enzymatic diversity in the fungal kingdom is staggering. Large-scale fungal genome sequencing projects are generating a massive catalog of secondary metabolite biosynthetic genes and pathways. Fungal natural products are a boon and bane to man as valuable pharmaceuticals and harmful toxins. Understanding how these chemicals are synthesized will aid the development of new strategies to limit mycotoxin contamination of food and feeds as well as expand drug discovery programs. A survey of work focused on the fumonisin family of mycotoxins highlights technological advances and provides a blueprint for future studies of other fungal natural products...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27923409/geographical-landscape-and-host-associations-of-trypanosoma-cruzi-dtus-and-lineages
#9
Amaia Izeta-Alberdi, Carlos N Ibarra-Cerdeña, David A Moo-Llanes, Janine M Ramsey
BACKGROUND: The evolutionary history and ecological associations of Trypanosoma cruzi, the need to identify genetic markers that can distinguish parasite subpopulations, and understanding the parasite's evolutionary and selective processes have been the subject of a significant number of publications since 1998, the year when the first DNA sequence analysis for the species was published. METHODS: The current analysis systematizes and re-analyzes this original research, focusing on critical methodological and analytical variables and results that have given rise to interpretations of putative patterns of genetic diversity and diversification of T...
December 7, 2016: Parasites & Vectors
https://www.readbyqxmd.com/read/27922098/comparison-of-432-pseudomonas-strains-through-integration-of-genomic-functional-metabolic-and-expression-data
#10
Jasper J Koehorst, Jesse C J van Dam, Ruben G A van Heck, Edoardo Saccenti, Vitor A P Martins Dos Santos, Maria Suarez-Diez, Peter J Schaap
Pseudomonas is a highly versatile genus containing species that can be harmful to humans and plants while others are widely used for bioengineering and bioremediation. We analysed 432 sequenced Pseudomonas strains by integrating results from a large scale functional comparison using protein domains with data from six metabolic models, nearly a thousand transcriptome measurements and four large scale transposon mutagenesis experiments. Through heterogeneous data integration we linked gene essentiality, persistence and expression variability...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27912243/vomeronasal-receptors-in-vertebrates-and-the-evolution-of-pheromone-detection
#11
Liliana Silva, Agostinho Antunes
Pheromones were identified as chemical signals used for intraspecific communication in insects (e.g., sexual attraction) in the 1950s. However, only almost 40 years later the vomeronasal receptors type-1 (V1R) and type-2 (V2R) were identified, usually associated with the presence of a vomeronasal organ (VNO). VRs are widespread in amphibians, reptiles, and mammals, but birds lost the VNO. Similarly, fishes lack VRs and a VNO but can still detect pheromones, instead using the olfactory receptors related to class A and class C G protein-coupled receptors...
November 28, 2016: Annual Review of Animal Biosciences
https://www.readbyqxmd.com/read/27908741/resolving-interspecific-relationships-within-evolutionarily-young-lineages-using-rna-seq-data-an-example-from-pedicularis-section-cyathophora-orobanchaceae
#12
Hong-Juan Wang, Wei-Tao Li, Ya-Nan Liu, Fu-Sheng Yang, Xiao-Quan Wang
Phylogenomics has shown great potential in resolving evolutionary relationships at different taxonomical levels. However, it remains controversial whether all orthologous genes under different selective pressures can be concatenated for phylogenomic reconstruction. Here we used sect. Cyathophora of Pedicularis, one of the most species-rich genera of angiosperms in the alpine and arctic regions of the Northern Hemisphere, as a model to investigate the efficiency of RNA-seq in resolving relationships of closely related congeneric species...
November 28, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27907107/a-time-calibrated-mitogenome-phylogeny-of-catfish-teleostei-siluriformes
#13
Ilias Kappas, Spiros Vittas, Chrysoula N Pantzartzi, Elena Drosopoulou, Zacharias G Scouras
A very significant part of the world's freshwater ichthyofauna is represented by ancient, exceptionally diverse and cosmopolitan ray-finned teleosts of the order Siluriformes. Over the years, catfish have been established as an exemplary model for probing historical biogeography at various scales. Yet, several tantalizing gaps still exist in their phylogenetic history, timeline and mode of diversification. Here, we re-examine the phylogeny of catfish by assembling and analyzing almost all publicly available mitogenome data...
2016: PloS One
https://www.readbyqxmd.com/read/27906638/gene-duplications-and-losses-among-vertebrate-deoxyribonucleoside-kinases-of-the-non-tk1-family
#14
Zeeshan Mutahir, Louise Slot Christiansen, Anders R Clausen, Martin W Berchtold, Zoran Gojkovic, Birgitte Munch-Petersen, Wolfgang Knecht, Jure Piškur
Deoxyribonucleoside kinases (dNKs) salvage deoxyribonucleosides (dNs) and catalyze the rate limiting step of this salvage pathway by converting dNs into corresponding monophosphate forms. These enzymes serve as an excellent model to study duplicated genes and their evolutionary history. So far, among vertebrates only four mammalian dNKs have been studied for their substrate specificity and kinetic properties. However, some vertebrates, such as fish, frogs, and birds, apparently possess a duplicated homolog of deoxycytidine kinase (dCK)...
December 2016: Nucleosides, Nucleotides & Nucleic Acids
https://www.readbyqxmd.com/read/27903912/the-complex-evolutionary-history-of-aminoacyl-trna-synthetases
#15
Anargyros Chaliotis, Panayotis Vlastaridis, Dimitris Mossialos, Michael Ibba, Hubert D Becker, Constantinos Stathopoulos, Grigorios D Amoutzias
Aminoacyl-tRNA synthetases (AARSs) are a superfamily of enzymes responsible for the faithful translation of the genetic code and have lately become a prominent target for synthetic biologists. Our large-scale analysis of >2500 prokaryotic genomes reveals the complex evolutionary history of these enzymes and their paralogs, in which horizontal gene transfer played an important role. These results show that a widespread belief in the evolutionary stability of this superfamily is misconceived. Although AlaRS, GlyRS, LeuRS, IleRS, ValRS are the most stable members of the family, GluRS, LysRS and CysRS often have paralogs, whereas AsnRS, GlnRS, PylRS and SepRS are often absent from many genomes...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27900808/genetic-and-developmental-basis-for-fin-shape-variation-in-african-cichlid-fishes
#16
Dina Navon, Nathan Olearczyk, R Craig Albertson
Adaptive radiations are often characterized by the rapid evolution of traits associated with divergent feeding modes. For example, the evolutionary history of African cichlids is marked by repeated and coordinated shifts in skull, trophic, fin and body shape. Here, we seek to explore the molecular basis for fin shape variation in Lake Malawi cichlids. We first described variation within an F2 mapping population derived by crossing two cichlid species with divergent morphologies including fin shape. We then used this population to genetically map loci that influence variation in this trait...
November 4, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27896958/when-should-we-not-transfer-functional-annotation-between-sequence-paralogs
#17
Mengfei Cao, Lenore J Cowen
Current automated computational methods to assign functional labels to unstudied genes often involve transferring annotation from orthologous or paralogous genes, however such genes can evolve divergent functions, making such transfer inappropriate. We consider the problem of determining when it is correct to make such an assignment between paralogs. We construct a benchmark dataset of two types of similar paralogous pairs of genes in the well-studied model organism S. cerevisiae: one set of pairs where single deletion mutants have very similar phenotypes (implying similar functions), and another set of pairs where single deletion mutants have very divergent phenotypes (implying different functions)...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896731/detecting-and-analyzing-genetic-recombination-using-rdp4
#18
Darren P Martin, Ben Murrell, Arjun Khoosal, Brejnev Muhire
Recombination between nucleotide sequences is a major process influencing the evolution of most species on Earth. The evolutionary value of recombination has been widely debated and so too has its influence on evolutionary analysis methods that assume nucleotide sequences replicate without recombining. When nucleic acids recombine, the evolution of the daughter or recombinant molecule cannot be accurately described by a single phylogeny. This simple fact can seriously undermine the accuracy of any phylogenetics-based analytical approach which assumes that the evolutionary history of a set of recombining sequences can be adequately described by a single phylogenetic tree...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27895050/social-signals-and-aversive-learning-in-honey-bee-drones-and-workers
#19
Arian Avalos, Eddie Pérez, Lianna Vallejo, María E Pérez, Charles I Abramson, Tugrul Giray
The dissemination of information is a basic element of group cohesion. In honey bees (Apis mellifera Linnaeus 1758), like in other social insects, the principal method for colony-wide information exchange is communication via pheromones. This medium of communication allows multiple individuals to conduct tasks critical to colony survival. Social signaling also establishes conflict at the level of the individual who must tradeoff between attending to the immediate environment or the social demand. In this study we examined this conflict by challenging highly social worker honey bees, and less social male drone honey bees undergoing aversive training by presenting them with a social stress signal (isopentyl acetate, IPA)...
November 28, 2016: Biology Open
https://www.readbyqxmd.com/read/27893284/biomarkers-and-metabolic-patterns-in-the-sediments-of-evolving-glacial-lakes-as-a-proxy-for-planetary-lake-exploration
#20
Víctor Parro, Yolanda Blanco, Fernando Puente-Sánchez, Luis A Rivas, Mercedes Moreno-Paz, Alex Echeverría, Guillermo Chong-Díaz, Cecilia Demergasso, Nathalie A Cabrol
Oligotrophic glacial lakes in the Andes Mountains serve as models to study the effects of climate change on natural biological systems. The persistent high UV regime and evolution of the lake biota due to deglaciation make Andean lake ecosystems potential analogues in the search for life on other planetary bodies. Our objective was to identify microbial biomarkers and metabolic patterns that represent time points in the evolutionary history of Andean glacial lakes, as these may be used in long-term studies as microscale indicators of climate change processes...
November 28, 2016: Astrobiology
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