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https://www.readbyqxmd.com/read/28545149/persistence-of-lineage-iv-peste-des-petits-ruminants-virus-within-israel-since-1993-an-evolutionary-perspective
#1
Brian Clarke, Mana Mahapatra, Orly Friedgut, Velizar Bumbarov, Satya Parida
Peste-des-petits ruminants (PPR) is one of the most important infectious diseases of domesticated small ruminants. From the initial identification in 1942 in West Africa, PPR virus (PPRV) has spread throughout much of the developing world. PPRV is now considered endemic throughout Africa, with the notable exception of South Africa, the Middle-East and Israel, as well as South-, East-, and Central Asia. Despite this widespread dispersal, the evolution and transmission of PPRV in endemic populations is not well understood...
2017: PloS One
https://www.readbyqxmd.com/read/28545148/mitochondrial-genome-evolution-in-alismatales-size-reduction-and-extensive-loss-of-ribosomal-protein-genes
#2
Gitte Petersen, Argelia Cuenca, Athanasios Zervas, Gregory T Ross, Sean W Graham, Craig F Barrett, Jerrold I Davis, Ole Seberg
The order Alismatales is a hotspot for evolution of plant mitochondrial genomes characterized by remarkable differences in genome size, substitution rates, RNA editing, retrotranscription, gene loss and intron loss. Here we have sequenced the complete mitogenomes of Zostera marina and Stratiotes aloides, which together with previously sequenced mitogenomes from Butomus and Spirodela, provide new evolutionary evidence of genome size reduction, gene loss and transfer to the nucleus. The Zostera mitogenome includes a large portion of DNA transferred from the plastome, yet it is the smallest known mitogenome from a non-parasitic plant...
2017: PloS One
https://www.readbyqxmd.com/read/28545003/adaptation-specialization-and-coevolution-within-phytobiomes
#3
REVIEW
David A Baltrus
Growth patterns of individual plants and evolutionary trajectories of plant communities are intimately linked with and are critically affected by host-associated microbiomes. Research across systems has begun to shed light on how these phytobiomes are established under laboratory and natural conditions, and have cultivated hope that a better understanding of the governing principles for host-microbe interactions can guide attempts to engineer microbiomes to boost agricultural yields. One important, yet relatively understudied, parameter in regards to phytobiome membership is the degree to which specialization and coevolution between plant species and microbes provides structure to these communities...
May 22, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28544890/hybrid-neuro-heuristic-methodology-for-simulation-and-control-of-dynamic-systems-over-time-interval
#4
Marcin Woźniak, Dawid Połap
Simulation and positioning are very important aspects of computer aided engineering. To process these two, we can apply traditional methods or intelligent techniques. The difference between them is in the way they process information. In the first case, to simulate an object in a particular state of action, we need to perform an entire process to read values of parameters. It is not very convenient for objects for which simulation takes a long time, i.e. when mathematical calculations are complicated. In the second case, an intelligent solution can efficiently help on devoted way of simulation, which enables us to simulate the object only in a situation that is necessary for a development process...
May 5, 2017: Neural Networks: the Official Journal of the International Neural Network Society
https://www.readbyqxmd.com/read/28544882/inference-and-evolutionary-analysis-of-genome-scale-regulatory-networks-in-large-phylogenies
#5
Christopher Koch, Jay Konieczka, Toni Delorey, Ana Lyons, Amanda Socha, Kathleen Davis, Sara A Knaack, Dawn Thompson, Erin K O'Shea, Aviv Regev, Sushmita Roy
Changes in transcriptional regulatory networks can significantly contribute to species evolution and adaptation. However, identification of genome-scale regulatory networks is an open challenge, especially in non-model organisms. Here, we introduce multi-species regulatory network learning (MRTLE), a computational approach that uses phylogenetic structure, sequence-specific motifs, and transcriptomic data, to infer the regulatory networks in different species. Using simulated data from known networks and transcriptomic data from six divergent yeasts, we demonstrate that MRTLE predicts networks with greater accuracy than existing methods because it incorporates phylogenetic information...
May 24, 2017: Cell Systems
https://www.readbyqxmd.com/read/28544878/evolutionary-context-improves-regulatory-network-predictions
#6
Jonathan L Gordon, Brigida Gallone, Steven Maere, Kevin J Verstrepen
A novel algorithm harnesses phylogenetic information and facilitates a better understanding of the evolutionary divergence of gene regulation between species.
May 24, 2017: Cell Systems
https://www.readbyqxmd.com/read/28544874/the-relative-safety-of-paternal-maternal-and-traditional-foster-care-placements
#7
Jesse J Helton, Brian B Boutwell, Michael DiBernardo
When children are placed into foster care the caseworker must give preference to an adult relative, many of whom are grandparents, over an unrelated caregiver. This kinship preference is based in evolutionary biology, which suggests that the imperative to care for a child should be greater for kin versus non-kin. However, not all kin are related to a child in the same way, and level of paternity uncertainty may influence level of care provided. For instance, maternal grandparents can be assured that they share genetic material with their grandchild, while paternal grandparents may not have the same level of certainty...
May 22, 2017: Child Abuse & Neglect
https://www.readbyqxmd.com/read/28544760/a-novel-pattern-of-yolk-processing-in-developing-snake-eggs-colubridae-lampropeltini-and-its-functional-and-evolutionary-implications
#8
Kathryn G Powers, Daniel G Blackburn
Early amniotic vertebrates evolved large-yolked eggs that permitted production of well-developed, terrestrial hatchlings. This reproductive pattern required new mechanisms for cellularizing the yolk and mobilizing it for embryonic use. In birds, cells that line the yolk sac cavity phagocytose and digest the yolk material, a pattern that is commonly assumed to be universal among oviparous amniotes. However, recent evidence challenges the assumption that all squamate reptiles conform to the avian developmental pattern...
May 24, 2017: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/28544658/the-evolution-of-stories-from-mimesis-to-language-from-fact-to-fiction
#9
REVIEW
Brian Boyd
Why a species as successful as Homo sapiens should spend so much time in fiction, in telling one another stories that neither side believes, at first seems an evolutionary riddle. Because of the advantages of tracking and recombining true information, capacities for event comprehension, memory, imagination, and communication evolved in a range of animal species-yet even chimpanzees cannot communicate beyond the here and now. By Homo erectus, our forebears had reached an increasing dependence on one another, not least in sharing information in mimetic, prelinguistic ways...
May 24, 2017: Wiley Interdisciplinary Reviews. Cognitive Science
https://www.readbyqxmd.com/read/28544594/diversity-of-aromatic-hydroxylating-dioxygenase-genes-in-mangrove-microbiome-and-their-biogeographic-patterns-across-global-sites
#10
Sanderson T P de Sousa, Lucélia Cabral, Gileno Vieira Lacerda Júnior, Valéria M Oliveira
Aromatic hydrocarbons (AH), such as polycyclic aromatic hydrocarbons, are compounds largely found in nature. Aromatic-ring-hydroxylating dioxygenases (ARHD) are proteins involved in AH degradation pathways. We used ARHD functional genes from an oil-impacted mangrove area and compared their diversity with other sites around the world to understand the ARHD biogeographic distribution patterns. For this, a comprehensive database was established with 166 operational protein families (OPFs) from 1,758 gene sequences obtained from 15 different sites worldwide, of which twelve are already published studies and three are unpublished...
May 23, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28544285/salmonella-typhi-genomics-envisaging-the-future-of-typhoid-eradication
#11
REVIEW
Kien-Pong Yap, Kwai Lin Thong
Next-generation whole genome sequencing has revolutionized the study of infectious diseases in recent years. The availability of genome sequences and its understanding have transformed the field of molecular microbiology, epidemiology, infection treatments and vaccine developments. We review the key findings of the publicly accessible genomes of Salmonella enterica serovar Typhi since the first complete genome to the most recent release of thousands of S. typhi genomes, which remarkably shape the genomic research of S...
May 24, 2017: Tropical Medicine & International Health: TM & IH
https://www.readbyqxmd.com/read/28544213/bac-recombineering-of-the-agouti-loci-from-spotted-gar-and-zebrafish-reveals-the-evolutionary-ancestry-of-dorsal-ventral-pigment-asymmetry-in-fish
#12
Laura Cal, Manuel MegÍas, José Miguel Cerdá-Reverter, John H Postlethwait, Ingo Braasch, Josep Rotllant
Dorsoventral pigment patterning, characterized by a light ventrum and a dark dorsum, is one of the most widespread chromatic adaptations in vertebrate body coloration. In mammals, this countershading depends on differential expression of agouti-signaling protein (ASIP), which drives a switch of synthesis of one type of melanin to another within melanocytes. Teleost fish share countershading, but the pattern results from a differential distribution of multiple types of chromatophores, with black-brown melanophores most abundant in the dorsal body and reflective iridophores most abundant in the ventral body...
May 24, 2017: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/28544184/did-some-red-alga-derived-plastids-evolve-via-kleptoplastidy-a-hypothesis
#13
Andrzej Bodył
The evolution of plastids has a complex and still unresolved history. These organelles originated from a cyanobacterium via primary endosymbiosis, resulting in three eukaryotic lineages: glaucophytes, red algae, and green plants. The red and green algal plastids then spread via eukaryote-eukaryote endosymbioses, known as secondary and tertiary symbioses, to numerous heterotrophic protist lineages. The number of these horizontal plastid transfers, especially in the case of red alga-derived plastids, remains controversial...
May 23, 2017: Biological Reviews of the Cambridge Philosophical Society
https://www.readbyqxmd.com/read/28544154/floral-nectar-of-the-obligate-outcrossing-canavalia-gladiata-jacq-dc-fabaceae-contains-only-one-predominant-protein-a-class-iii-acidic-chitinase
#14
Xue-Long Ma, Richard I Milne, Hong-Xia Zhou, Jiang-Yu Fang, Hong-Guang Zha
Floral nectar can affect the fitness of insect-pollinated plants, through both attraction and manipulation of pollinators. Self-incompatible insect-pollinated plants receive more insect visits than their self-compatible relatives, and the nectar of such species might face more risk to be infested by the pathogens carried by pollinators than self-compatible plants. Proteins in nectar (nectarins) play an important role in the protection of nectar, but little is known regarding nectarins in self-incompatible species...
May 20, 2017: Plant Biology
https://www.readbyqxmd.com/read/28544059/objective-assessment-of-the-evolutionary-action-equation-for-the-fitness-effect-of-missense-mutations-across-cagi-blinded-contests
#15
Panagiotis Katsonis, Olivier Lichtarge
A major challenge in genome interpretation is to estimate the fitness effect of coding variants of unknown significance (VUS). Labor, limited understanding of protein functions, and lack of assays generally limit direct experimental assessment of VUS, and make robust and accurate computational approaches a necessity. Often, however, algorithms that predict mutational effect disagree amongst themselves and with experimental data, slowing their adoption for clinical diagnostics. To objectively assess such methods, the Critical Assessment of Genome Interpretation (CAGI) community organizes contests to predict unpublished experimental data, available only to CAGI assessors...
May 23, 2017: Human Mutation
https://www.readbyqxmd.com/read/28543995/the-effects-of-restoring-logged-tropical-forests-on-avian-phylogenetic-and-functional-diversity
#16
Cindy C P Cosset, David P Edwards
Selective logging is the most prevalent land-use change in the tropics. Despite the resulting degradation of forest structure, selectively logged forests still harbour a substantial amount of biodiversity leading to suggestions that their protection is the next best alternative to conserving primary, old-growth forests. Restoring carbon stocks under Reducing Emissions from Deforestation and Forest Degradation (REDD+) schemes is a potential method for obtaining funding to protect logged forests, via enrichment planting and liberation cutting of vines...
May 24, 2017: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/28543388/environmental-constraints-on-the-compositional-and-phylogenetic-beta-diversity-of-tropical-forest-snake-assemblages
#17
Mario R Moura, Henrique C Costa, Antônio J S Argôlo, Walter Jetz
The ongoing biodiversity crisis increases the importance and urgency of studies addressing the role of environmental variation on the composition and evolutionary history of species assemblages, but especially the tropics and ectotherms remain understudied. In regions with rainy summers, coexistence of ectothermic species may be determined by the partitioning of the climatic niche, since ectotherms can rely on water availability and thermoregulatory behaviour to buffer constraints along their climatic niche...
May 22, 2017: Journal of Animal Ecology
https://www.readbyqxmd.com/read/28543308/exocytic-trafficking-pathways-in-plants-why-and-how-they-are-redirected
#18
REVIEW
Takehiko Kanazawa, Takashi Ueda
The membrane trafficking system is responsible for precise transportation and localization of proteins, lipids, and polysaccharides among single membrane-bound organelles, the plasma membrane, and the extracellular space. While the exocytic trafficking pathway is considered to be a default transport pathway in many organisms, including land plants, research has shown that evolutionary processes led to an increase in the number of machinery components involved in the plant exocytic pathway. This study provides an overview of the diversification of exocytic trafficking pathways in plants, which mediate the formation and maintenance of cell polarity, interaction with symbiotic and pathogenic microbes, and cytokinesis...
May 25, 2017: New Phytologist
https://www.readbyqxmd.com/read/28543226/interactions-within-and-between-clades-shaped-the-diversification-of-terrestrial-carnivores
#19
Mathias M Pires, Daniele Silvestro, Tiago B Quental
A longstanding debate in evolutionary biology and paleontology is whether ecological interactions such as competition impose diversity dependence on speciation and extinction rates. Here we analyze the fossil record of terrestrial mammalian carnivores in North America and Eurasia using a Bayesian framework to assess whether their diversity dynamics were affected by diversity dependence within and between families (12 in Eurasia, 10 in North America). We found eight instances of within-clade diversity dependence suppressing speciation rates and detected between-clade effects increasing extinction rates in six instances...
May 22, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28543051/multilevel-and-sex-specific-selection-on-competitive-traits-in-north-american-red-squirrels
#20
David N Fisher, Stan Boutin, Ben Dantzer, Murray M Humphries, Jeffrey E Lane, Andrew G McAdam
Individuals often interact more closely with some members of the population (e.g. offspring, siblings or group members) than they do with other individuals. This structuring of interactions can lead to multilevel natural selection, where traits expressed at the group-level influence fitness alongside individual-level traits. Such multilevel selection can alter evolutionary trajectories, yet is rarely quantified in the wild, especially for species that do not interact in clearly demarcated groups. We quantified multilevel natural selection on two traits, postnatal growth rate and birth date, in a population of North American red squirrels (Tamiasciurus hudsonicus)...
May 23, 2017: Evolution; International Journal of Organic Evolution
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