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"Evolutionary history"

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https://www.readbyqxmd.com/read/28324048/demonstration-of-a-functional-kiss-kissr-system-in-amphioxus-with-implications-for-origin-of-neuroendocrine-regulation
#1
Peng Wang, Meng Wang, Guangdong Ji, Shuangshuang Yang, Shicui Zhang, Zhenhui Liu
Amphioxus belongs to the Cephalochordata, which is the most basal subphylum of the chordates. Despite many studies on the endocrine system of amphioxus, key information about its regulation remains ambiguous. Here we clearly demonstrated the presence of a functional kisspeptin/kisspeptin receptor (Kiss-Kissr) system, which is involved in the regulation of reproduction in amphioxus. Evolutionary analyses revealed large expansion of Kiss and Kissr (gpr54) genes in amphioxus and they might represent the ancestral type of the Kiss/gpr54 genes in chordates...
January 24, 2017: Endocrinology
https://www.readbyqxmd.com/read/28303527/chemical-ecology-of-cave-dwelling-millipedes-defensive-secretions-of-the-typhloiulini-diplopoda-julida-julidae
#2
Slobodan E Makarov, Michaela Bodner, Doris Reineke, Ljubodrag V Vujisić, Marina M Todosijević, Dragan Ž Antić, Boyan Vagalinski, Luka R Lučić, Bojan M Mitić, Plamen Mitov, Boban D Anđelković, Sofija Pavković Lucić, Vlatka Vajs, Vladimir T Tomić, Günther Raspotnig
Cave animals live under highly constant ecological conditions and in permanent darkness, and many evolutionary adaptations of cave-dwellers have been triggered by their specific environment. A similar "cave effect" leading to pronounced chemical interactions under such conditions may be assumed, but the chemoecology of troglobionts is mostly unknown. We investigated the defensive chemistry of a largely cave-dwelling julid group, the controversial tribe "Typhloiulini", and we included some cave-dwelling and some endogean representatives...
March 16, 2017: Journal of Chemical Ecology
https://www.readbyqxmd.com/read/28302556/genomics-research-for-a-new-age-examining-how-our-shared-evolutionary-history-shapes-future-disease-outcomes
#3
REVIEW
Fasil Tekola-Ayele, Emmanuel Peprah
Cardiometabolic diseases are major contributors to mortality and morbidity, and their burden displays global and regional disparities. Gene-environment interactions contribute to the pathogenesis of cardiometabolic diseases. Population differences in genetic structure, ancient environmental pressures that shape the human genome, and early life environmental adversities (e.g., in utero conditions) all contribute to observed disparities in global cardiometabolic diseases. The genetic and sociocultural diversity of global populations presents opportunities for discovering genomic loci that influence cardiometabolic diseases as illustrated by a few genetic, epigenetic, and population-genetic discoveries leading to notable understanding of disease mechanisms...
March 13, 2017: Global Heart
https://www.readbyqxmd.com/read/28301472/independent-introductions-and-admixtures-have-contributed-to-adaptation-of-european-maize-and-its-american-counterparts
#4
Jean-Tristan Brandenburg, Tristan Mary-Huard, Guillem Rigaill, Sarah J Hearne, Hélène Corti, Johann Joets, Clémentine Vitte, Alain Charcosset, Stéphane D Nicolas, Maud I Tenaillon
Through the local selection of landraces, humans have guided the adaptation of crops to a vast range of climatic and ecological conditions. This is particularly true of maize, which was domesticated in a restricted area of Mexico but now displays one of the broadest cultivated ranges worldwide. Here, we sequenced 67 genomes with an average sequencing depth of 18x to document routes of introduction, admixture and selective history of European maize and its American counterparts. To avoid the confounding effects of recent breeding, we targeted germplasm (lines) directly derived from landraces...
March 16, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28301464/investigating-the-case-of-human-nose-shape-and-climate-adaptation
#5
Arslan A Zaidi, Brooke C Mattern, Peter Claes, Brian McEcoy, Cris Hughes, Mark D Shriver
The evolutionary reasons for variation in nose shape across human populations have been subject to continuing debate. An import function of the nose and nasal cavity is to condition inspired air before it reaches the lower respiratory tract. For this reason, it is thought the observed differences in nose shape among populations are not simply the result of genetic drift, but may be adaptations to climate. To address the question of whether local adaptation to climate is responsible for nose shape divergence across populations, we use Qst-Fst comparisons to show that nares width and alar base width are more differentiated across populations than expected under genetic drift alone...
March 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28300533/membranes-energetics-and-evolution-across-the-prokaryote-eukaryote-divide
#6
Michael Lynch, Georgi K Marinov
The evolution of the eukaryotic cell marked a profound moment in Earth's history, with most of the visible biota coming to rely on intracellular membrane-bound organelles. It has been suggested that this evolutionary transition was critically dependent on the movement of ATP synthesis from the cell surface to mitochondrial membranes and the resultant boost to the energetic capacity of eukaryotic cells. However, contrary to this hypothesis, numerous lines of evidence suggest that eukaryotes are no more bioenergetically efficient than prokaryotes...
March 16, 2017: ELife
https://www.readbyqxmd.com/read/28300291/are-rare-variants-really-independent
#7
Asuman Turkmen, Shili Lin
Recent advances in genotyping with high-density markers allow researchers access to genomic variants including rare ones. Linkage disequilibrium (LD) is widely used to provide insight into evolutionary history. It is also the basis for association mapping in humans and other species. Better understanding of the genomic LD structure may lead to better-informed statistical tests that can improve the power of association studies. Although rare variant associations with common diseases (RVCD) have been extensively studied recently, there is very limited understanding, and even controversial view of LD structures among rare variants and between rare and common variants...
March 16, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28298902/global-distribution-and-evolutionary-history-of-enterovirus-d68-with-emphasis-on-the-2014-outbreak-in-ontario-canada
#8
Alireza Eshaghi, Venkata R Duvvuri, Sandra Isabel, Philip Banh, Aimin Li, Adriana Peci, Samir N Patel, Jonathan B Gubbay
Despite its first appearance in 1962, human enterovirus D68 (EV-D68) has been recognized as an emerging respiratory pathogen in the last decade when it caused outbreaks and clusters in several countries including Japan, the Philippines, and the Netherlands. The most recent and largest outbreak of EV-D68 associated with severe respiratory illness took place in North America between August 2014 and January 2015. Between September 1 and October 31 2014, EV-D68 infection was laboratory confirmed among 153/907 (16...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28298350/the-acacia-ants-revisited-convergent-evolution-and-biogeographic-context-in-an-iconic-ant-plant-mutualism
#9
Philip S Ward, Michael G Branstetter
Phylogenetic and biogeographic analyses can enhance our understanding of multispecies interactions by placing the origin and evolution of such interactions in a temporal and geographical context. We use a phylogenomic approach-ultraconserved element sequence capture-to investigate the evolutionary history of an iconic multispecies mutualism: Neotropical acacia ants (Pseudomyrmex ferrugineus group) and their associated Vachellia hostplants. In this system, the ants receive shelter and food from the host plant, and they aggressively defend the plant against herbivores and competing plants...
March 15, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28298348/a-phylogenetic-perspective-on-the-association-between-ants-hymenoptera-formicidae-and-black-yeasts-ascomycota-chaetothyriales
#10
Marie Vasse, Hermann Voglmayr, Veronika Mayer, Cécile Gueidan, Maximilian Nepel, Leandro Moreno, Sybren de Hoog, Marc-André Selosse, Doyle McKey, Rumsaïs Blatrix
The frequency and the geographical extent of symbiotic associations between ants and fungi of the order Chaetothyriales have been highlighted only recently. Using a phylogenetic approach based on seven molecular markers, we showed that ant-associated Chaetothyriales are scattered through the phylogeny of this order. There was no clustering according to geographical origin or to the taxonomy of the ant host. However, strains tended to be clustered according to the type of association with ants: strains from ant-made carton and strains from plant cavities occupied by ants ('domatia') rarely clustered together...
March 15, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28297717/the-true-tempo-of-evolutionary-radiation-and-decline-revealed-on-the-hawaiian-archipelago
#11
Jun Y Lim, Charles R Marshall
Establishing the relationship between rates of change in species richness and biotic and abiotic environmental change is a major goal of evolutionary biology. Although exquisite fossil and geological records provide insight in rare cases, most groups lack high-quality fossil records. Consequently, biologists typically rely on molecular phylogenies to study the diversity dynamics of clades, usually by correlating changes in diversification rate with environmental or trait shifts. However, inferences drawn from molecular phylogenies can be limited owing to the challenge of accounting for extinct species, making it difficult to accurately determine the underlying diversity dynamics that produce them...
March 15, 2017: Nature
https://www.readbyqxmd.com/read/28294981/the-complete-chloroplast-genome-sequences-of-six-rehmannia-species
#12
Shuyun Zeng, Tao Zhou, Kai Han, Yanci Yang, Jianhua Zhao, Zhan-Lin Liu
Rehmannia is a non-parasitic genus in Orobanchaceae including six species mainly distributed in central and north China. Its phylogenetic position and infrageneric relationships remain uncertain due to potential hybridization and polyploidization. In this study, we sequenced and compared the complete chloroplast genomes of six Rehmannia species using Illumina sequencing technology to elucidate the interspecific variations. Rehmannia plastomes exhibited typical quadripartite and circular structures with good synteny of gene order...
March 15, 2017: Genes
https://www.readbyqxmd.com/read/28293305/convergence-of-retrotransposons-in-oomycetes-and-plants
#13
Kirill Ustyantsev, Alexandr Blinov, Georgy Smyshlyaev
BACKGROUND: Retrotransposons comprise a ubiquitous and abundant class of eukaryotic transposable elements. All members of this class rely on reverse transcriptase activity to produce a DNA copy of the element from the RNA template. However, other activities of the retrotransposon-encoded polyprotein may differ between diverse retrotransposons. The polyprotein domains corresponding to each of these activities may have their own evolutionary history independent from that of the reverse transcriptase, thus underlying the modular view on the evolution of retrotransposons...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28291834/the-isolation-and-characterization-of-stenotrophomonas-maltophilia-t4-like-bacteriophage-dlp6
#14
Danielle L Peters, Paul Stothard, Jonathan J Dennis
Increasing isolation of the extremely antibiotic resistant bacterium Stenotrophomonas maltophilia has caused alarm worldwide due to the limited treatment options available. A potential treatment option for fighting this bacterium is 'phage therapy', the clinical application of bacteriophages to selectively kill bacteria. Bacteriophage DLP6 (vB_SmoM-DLP6) was isolated from a soil sample using clinical isolate S. maltophilia strain D1571 as host. Host range analysis of phage DLP6 against 27 clinical S. maltophilia isolates shows successful infection and lysis in 13 of the 27 isolates tested...
2017: PloS One
https://www.readbyqxmd.com/read/28291231/targeted-deep-sequencing-of-flowering-regulators-in-brassica-napus-reveals-extensive-copy-number-variation
#15
Sarah Schiessl, Bruno Huettel, Diana Kuehn, Richard Reinhardt, Rod J Snowdon
Gene copy number variation (CNV) is increasingly implicated in control of complex trait networks, particularly in polyploid plants like rapeseed (Brassica napus L.) with an evolutionary history of genome restructuring. Here we performed sequence capture to assay nucleotide variation and CNV in a panel of central flowering time regulatory genes across a species-wide diversity set of 280 B. napus accessions. The genes were chosen based on prior knowledge from Arabidopsis thaliana and related Brassica species...
March 14, 2017: Scientific Data
https://www.readbyqxmd.com/read/28289558/phylogenetic-factorization-of-compositional-data-yields-lineage-level-associations-in-microbiome-datasets
#16
Alex D Washburne, Justin D Silverman, Jonathan W Leff, Dominic J Bennett, John L Darcy, Sayan Mukherjee, Noah Fierer, Lawrence A David
Marker gene sequencing of microbial communities has generated big datasets of microbial relative abundances varying across environmental conditions, sample sites and treatments. These data often come with putative phylogenies, providing unique opportunities to investigate how shared evolutionary history affects microbial abundance patterns. Here, we present a method to identify the phylogenetic factors driving patterns in microbial community composition. We use the method, "phylofactorization," to re-analyze datasets from the human body and soil microbial communities, demonstrating how phylofactorization is a dimensionality-reducing tool, an ordination-visualization tool, and an inferential tool for identifying edges in the phylogeny along which putative functional ecological traits may have arisen...
2017: PeerJ
https://www.readbyqxmd.com/read/28288942/endemic-palm-species-shed-light-on-habitat-shifts-and-the-assembly-of-the-cerrado-and-restinga-floras
#17
Christine D Bacon, Monica Moraes R, Carlos Jaramillo, Alexandre Antonelli
Species expansions into new habitats are often associated with physiological adaptations, for instance when rain forest lineages colonize dry habitats. Although such shifts have been documented for the Brazilian savanna (Cerrado), little is known about the biogeographic origin of species occupying an extreme South American habitat type, the coastal dunes (Restinga). We examined the formation of this poorly known, endangered habitat by reconstructing the evolutionary history of two endemic species. Due to the proposed recency and uniqueness of this habitat, we hypothesized that Restinga species of the palm genus Allagoptera to be recently evolved and to present derived morphological characters...
March 10, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28286101/the-biogeographic-and-evolutionary-history-of-an-endemic-clade-of-middle-american-sparrows-melozone-and-aimophila-aves-passerellidae
#18
Luis Sandoval, Kevin L Epperly, John Klicka, Daniel J Mennill
The large number of endemic species in Middle America is frequently attributed to the interplay of geographical barriers and historical climatic changes in the region. This process promotes genetic divergence between populations, and given enough time, may yield new species. Animals that inhabit mid-elevation or highland habitats may be disproportionately affected in this way. Genetic analyses of animals in this region allow us to better understand how historical patterns of isolation have influenced the generation of new species in this biodiversity hotspot...
March 7, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28282941/conservation-of-the-keap1-nrf2-system-an-evolutionary-journey-through-stressful-space-and-time
#19
REVIEW
Yuji Fuse, Makoto Kobayashi
The Keap1-Nrf2 system is an evolutionarily conserved defense mechanism against oxidative and xenobiotic stress. Its regulatory mechanisms, e.g., stress-sensing mechanism, proteasome-based regulation of Nrf2 activity and selection of target genes, have been elucidated mainly in mammals. In addition, emerging model animals, such as zebrafish, fruit fly and Caenorhabditis elegans, have been shown to have similar anti-stress systems to mammals, suggesting that analogous defense systems are widely conserved throughout the animal kingdom...
March 9, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28282382/population-genetic-analysis-of-the-darc-locus-duffy-reveals-adaptation-from-standing-variation-associated-with-malaria-resistance-in-humans
#20
Kimberly F McManus, Angela M Taravella, Brenna M Henn, Carlos D Bustamante, Martin Sikora, Omar E Cornejo
The human DARC (Duffy antigen receptor for chemokines) gene encodes a membrane-bound chemokine receptor crucial for the infection of red blood cells by Plasmodium vivax, a major causative agent of malaria. Of the three major allelic classes segregating in human populations, the FY*O allele has been shown to protect against P. vivax infection and is at near fixation in sub-Saharan Africa, while FY*B and FY*A are common in Europe and Asia, respectively. Due to the combination of strong geographic differentiation and association with malaria resistance, DARC is considered a canonical example of positive selection in humans...
March 10, 2017: PLoS Genetics
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