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Phylogenetics

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https://www.readbyqxmd.com/read/28813005/identification-and-functional-divergence-analysis-of-wox-gene-family-in-paper-mulberry
#1
Feng Tang, Naizhi Chen, Meiling Zhao, Yucheng Wang, Ruiping He, Xianjun Peng, Shihua Shen
The WOX (WUSCHEL-related homeobox) is a plant-specific transcription factor involved in plant development and stress response. However, few studies have been reported on the WOX gene in woody plants. In this study, 10 BpWOX genes were isolated from paper mulberry by RACE-PCR and categorized into three clades through phylogenetic analysis, ancient, intermediate and WUS clade. Among them, five members had the transcriptional activity detected by yeast one-hybrid and seven were uniquely localized to the nucleus through green fluorescent protein (GFP) observation...
August 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28812950/expression-of-cytochrome-p450-regulators-in-cynomolgus-macaque
#2
Yasuhiro Uno, Hiroshi Yamazaki
1. Cytochrome P450 (P450) regulators including nuclear receptors and transcription factors have not been fully investigated in cynomolgus macaques, an important species used in drug metabolism studies. In this study, we analyzed seventeen P450 regulators by sequence and phylogenetic analysis, and tissue expression. 2. Gene and genome structures of seventeen P450 regulators were similar to the human orthologs, and the deduced amino acid sequences showed high sequence identities (92-95%) and more closely clustered, with the human orthologs...
August 16, 2017: Xenobiotica; the Fate of Foreign Compounds in Biological Systems
https://www.readbyqxmd.com/read/28812731/cooperation-facilitates-the-colonization-of-harsh-environments
#3
Charlie K Cornwallis, Carlos A Botero, Dustin R Rubenstein, Philip A Downing, Stuart A West, Ashleigh S Griffin
Animals living in harsh environments, where temperatures are hot and rainfall is unpredictable, are more likely to breed in cooperative groups. As a result, harsh environmental conditions have been accepted as a key factor explaining the evolution of cooperation. However, this is based on evidence that has not investigated the order of evolutionary events, so the inferred causality could be incorrect. We resolved this problem using phylogenetic analyses of 4,707 bird species and found that causation was in the opposite direction to that previously assumed...
February 17, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812725/phylogenetics-tertiary-protein-structures-needed
#4
David Penny
No abstract text is available yet for this article.
February 13, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812709/adaptation-to-deep-sea-chemosynthetic-environments-as-revealed-by-mussel-genomes
#5
Jin Sun, Yu Zhang, Ting Xu, Yang Zhang, Huawei Mu, Yanjie Zhang, Yi Lan, Christopher J Fields, Jerome Ho Lam Hui, Weipeng Zhang, Runsheng Li, Wenyan Nong, Fiona Ka Man Cheung, Jian-Wen Qiu, Pei-Yuan Qian
Hydrothermal vents and methane seeps are extreme deep-sea ecosystems that support dense populations of specialized macro-benthos such as mussels. But the lack of genome information hinders the understanding of the adaptation of these animals to such inhospitable environments. Here we report the genomes of a deep-sea vent/seep mussel (Bathymodiolus platifrons) and a shallow-water mussel (Modiolus philippinarum). Phylogenetic analysis shows that these mussel species diverged approximately 110.4 million years ago...
April 3, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812701/contentious-relationships-in-phylogenomic-studies-can-be-driven-by-a-handful-of-genes
#6
Xing-Xing Shen, Chris Todd Hittinger, Antonis Rokas
Phylogenomic studies have resolved countless branches of the tree of life, but remain strongly contradictory on certain, contentious relationships. Here, we use a maximum likelihood framework to quantify the distribution of phylogenetic signal among genes and sites for 17 contentious branches and 6 well-established control branches in plant, animal and fungal phylogenomic data matrices. We find that resolution in some of these 17 branches rests on a single gene or a few sites, and that removal of a single gene in concatenation analyses or a single site from every gene in coalescence-based analyses diminishes support and can alter the inferred topology...
April 10, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812693/direct-benefits-and-evolutionary-transitions-to-complex-societies
#7
Cody J Dey, Constance M O'Connor, Holly Wilkinson, Susanne Shultz, Sigal Balshine, John L Fitzpatrick
The selective forces that drive the evolution of cooperation have been intensely debated. Evolutionary transitions to cooperative breeding, a complex form of cooperation, have been hypothesized to be linked to low degrees of promiscuity, which increases intragroup relatedness and the indirect (that is, kin selected) benefits of helping. However, ecological factors also promote cooperative breeding, and may be more important than relatedness in some contexts. Identifying the key evolutionary drivers of cooperative breeding therefore requires an integrated assessment of these hypotheses...
April 18, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812637/spatial-conservation-prioritization-of-biodiversity-spanning-the-evolutionary-continuum
#8
Silvia B Carvalho, Guillermo Velo-Antón, Pedro Tarroso, Ana Paula Portela, Mafalda Barata, Salvador Carranza, Craig Moritz, Hugh P Possingham
Accounting for evolutionary relationships between and within species is important for biodiversity conservation planning, but is rarely considered in practice. Here we introduce a novel framework to identify priority conservation areas accounting for phylogenetic and intraspecific diversity, integrating concepts from phylogeny, phylogeography, spatial statistics and spatial conservation prioritization. The framework allows planners to incorporate and combine different levels of evolutionary diversity and can be applied to any taxonomic group and to any region in the world...
April 28, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812633/diversity-begets-diversity-in-competition-for-space
#9
Daniel S Maynard, Mark A Bradford, Daniel L Lindner, Linda T A van Diepen, Serita D Frey, Jessie A Glaeser, Thomas W Crowther
Competition can profoundly affect biodiversity patterns by determining whether similar species are likely to coexist. When species compete directly for space, competitive ability differences should theoretically promote trait and phylogenetic clustering, provided that niche differences are otherwise minimal. Yet many sessile communities exhibit high biodiversity despite minimal reliance on niche differentiation. A potential explanation is that intransitive competition ('rock-paper-scissors' competition) not only promotes species richness but also fosters coexistence among highly dissimilar species with different competitive strategies...
May 15, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812611/divergent-demographic-strategies-of-plants-in-variable-environments
#10
Jenni L McDonald, Miguel Franco, Stuart Townley, Thomas H G Ezard, Kim Jelbert, Dave J Hodgson
One of the best-supported patterns in life history evolution is that organisms cope with environmental fluctuations by buffering their most important vital rates against them. This demographic buffering hypothesis is evidenced by a tendency for temporal variation in rates of survival and reproduction to correlate negatively with their contribution to fitness. Here, we show that widespread evidence for demographic buffering can be artefactual, resulting from natural relationships between the mean and variance of vital rates...
January 13, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812610/genome-wide-interrogation-advances-resolution-of-recalcitrant-groups-in-the-tree-of-life
#11
Dahiana Arcila, Guillermo Ortí, Richard Vari, Jonathan W Armbruster, Melanie L J Stiassny, Kyung D Ko, Mark H Sabaj, John Lundberg, Liam J Revell, Ricardo Betancur-R
Much progress has been achieved in disentangling evolutionary relationships among species in the tree of life, but some taxonomic groups remain difficult to resolve despite increasing availability of genome-scale data sets. Here we present a practical approach to studying ancient divergences in the face of high levels of conflict, based on explicit gene genealogy interrogation (GGI). We show its efficacy in resolving the controversial relationships within the largest freshwater fish radiation (Otophysi) based on newly generated DNA sequences for 1,051 loci from 225 species...
January 13, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812601/recent-extinctions-disturb-path-to-equilibrium-diversity-in-caribbean-bats
#12
Luis Valente, Rampal S Etienne, Liliana M Dávalos
Islands are ideal systems to model temporal changes in biodiversity and reveal the influence of humans on natural communities. Although theory predicts biodiversity on islands tends towards an equilibrium value, the recent extinction of large proportions of island biotas complicates testing this model. The well-preserved subfossil record of Caribbean bats-involving multiple insular radiations-provides a rare opportunity to model diversity dynamics in an insular community. Here, we reconstruct the diversity trajectory in noctilionoid bats of the Greater Antilles by applying a dynamic model of colonization, extinction and speciation to phylogenetic and palaeontological data including all known extinct and extant species...
January 9, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812570/independent-evolution-of-shape-and-motility-allows-evolutionary-flexibility-in-firmicutes-bacteria
#13
Fouad El Baidouri, Chris Venditti, Stuart Humphries
Functional morphological adaptation is an implicit assumption across many ecological studies. However, despite a few pioneering attempts to link bacterial form and function, functional morphology is largely unstudied in prokaryotes. One intriguing candidate for analysis is bacterial shape, as multiple lines of theory indicate that cell shape and motility should be strongly correlated. Here we present a large-scale use of modern phylogenetic comparative methods to explore this relationship across 325 species of the phylum Firmicutes...
November 21, 2016: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812555/phylogenetic-and-environmental-context-of-a-tournaisian-tetrapod-fauna
#14
Jennifer A Clack, Carys E Bennett, David K Carpenter, Sarah J Davies, Nicholas C Fraser, Timothy I Kearsey, John E A Marshall, David Millward, Benjamin K A Otoo, Emma J Reeves, Andrew J Ross, Marcello Ruta, Keturah Z Smithson, Timothy R Smithson, Stig A Walsh
The end-Devonian to mid-Mississippian time interval has long been known for its depauperate palaeontological record, especially for tetrapods. This interval encapsulates the time of increasing terrestriality among tetrapods, but only two Tournaisian localities previously produced tetrapod fossils. Here we describe five new Tournaisian tetrapods (Perittodus apsconditus, Koilops herma, Ossirarus kierani, Diploradus austiumensis and Aytonerpeton microps) from two localities in their environmental context...
December 5, 2016: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812171/complete-genome-sequence-of-a-novel-virulent-ahjdlikevirus-bacteriophage-that-infects-enterococcus-faecium
#15
Shaozhen Xing, Xianglilan Zhang, Qiang Sun, Jian Wang, Zhiqiang Mi, Guangqian Pei, Yong Huang, Xiaoping An, Kaifei Fu, Lijun Zhou, Baohua Zhao, Yigang Tong
A novel virulent bacteriophage named vB_EfaP_IME199 that specifically infects Enterococcus faecium was isolated and characterized. Its optimal multiplicity of infection was 0.01, and it had a 30 minute outbreak period. High-throughput sequencing revealed that the phage has a dsDNA genome of 18,838 bp with 22 open reading frames. The genome has very low homology to all other bacteriophage sequences in the GenBank database. Run-off sequencing experiments confirmed that vB_EfaP_IME199 has short inverted terminal repeats...
August 16, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28811909/a-fourth-subtype-of-retinoic-acid-receptor-related-orphan-receptors-is-activated-by-oxidized-all-trans-retinoic-acid-in-medaka-oryzias-latipes
#16
Kotowa Sakai, Haruka Fukushima, Yuya Yamamoto, Toshitaka Ikeuchi
BACKGROUND: The three known subtypes of the retinoic acid receptor-related orphan receptor (ROR) have been implicated in the control of immunity, brain function, and circadian rhythm in mammals. Here, we demonstrate by phylogenetic analysis that there were originally four subtypes of RORs in vertebrates. One of the novel ror paralogs, rord1 (rorca in the Ensembl database), is conserved among teleosts, but absent in mammals. Using medaka (Oryzias latipes) as a model teleost, we evaluated the expression pattern of this gene, its transactivational properties for endogenic chemicals, and its ability to activate the promoters of putative target genes...
2017: Zoological Letters
https://www.readbyqxmd.com/read/28811889/genome-size-in-arthropods-different-roles-of-phylogeny-habitat-and-life-history-in-insects-and-crustaceans
#17
Kristian Alfsnes, Hans Petter Leinaas, Dag Olav Hessen
Despite the major role of genome size for physiology, ecology, and evolution, there is still mixed evidence with regard to proximate and ultimate drivers. The main causes of large genome size are proliferation of noncoding elements and/or duplication events. The relative role and interplay between these proximate causes and the evolutionary patterns shaped by phylogeny, life history traits or environment are largely unknown for the arthropods. Genome size shows a tremendous variability in this group, and it has a major impact on a range of fitness-related parameters such as growth, metabolism, life history traits, and for many species also body size...
August 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28811884/factors-contributing-to-the-accumulation-of-reproductive-isolation-a-mixed-model-approach
#18
Dean M Castillo
The analysis of large datasets describing reproductive isolation between species has been extremely influential in the study of speciation. However, the statistical methods currently used for these data limit the ability to make direct inferences about the factors predicting the evolution of reproductive isolation. As a result, our understanding of iconic patterns and rules of speciation rely on indirect analyses that have clear statistical limitations. Phylogenetic mixed models are commonly used in ecology and evolution, but have not been applied to studies of reproductive isolation...
August 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28811799/diversity-physiochemical-and-phylogenetic-analyses-of-bacteria-isolated-from-various-drinking-water-sources
#19
Neveen H Eid, Huda A Al Doghaither, Taha A Kumosani, Munazza Gull
OBJECTIVE: To evaluate the indigenous bacterial strains of drinking water from the most commercial water types including bottled and filtered water that are currently used in Saudi Arabia. METHODS: Thirty randomly selected commercial brands of bottled water were purchased from Saudi local markets. Moreover, samples from tap water and filtered water were collected in sterilized glass bottles and stored at 4°C. Biochemical analyses including pH, temperature, lactose fermentation test (LAC), indole test (IND), methyl red test (MR), Voges-Proskauer test (VP), urease test (URE), catalase test (CAT), aerobic and anaerobic test (Ae/An) were measured...
May 2017: Pakistan Journal of Medical Sciences Quarterly
https://www.readbyqxmd.com/read/28811755/a-novel-recombined-potato-virus-y-isolate-in-china
#20
Shuxin Han, Yanling Gao, Guoquan Fan, Wei Zhang, Cailing Qiu, Shu Zhang, Yanju Bai, Junhua Zhang, Carl Spetz
This study reports the findings of a distinct Potato virus Y (PVY) isolate found in Northeast China. One hundred and ten samples (leaves and tubers) were collected from potato plants showing mosaic symptoms around the city of Harbin in Heilongjiang province of China. The collected tubers were planted and let to grow in a greenhouse. New potato plants generated from these tubers showed similar symptoms, except for one plant. Subsequent serological analyses revealed PVY as the causing agent of the disease. A novel PVY isolate (referred to as HLJ-C-44 in this study) was isolated from this sample showing unique mild mosaic and crisped leaf margin symptoms...
August 2017: Plant Pathology Journal
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